@Article{IPB-2428, author = {Hussain, H. and Ziegler, J. and Mrestani, Y. and Neubert, R. H. H.}, title = {{Studies of the Corneocytary Pathway Across the Stratum Corneum. Part I: Diffusion of Amino Acids Into the Isolated Corneocytes}}, year = {2019}, pages = {340-344}, journal = {Pharmazie}, doi = {10.1691/ph.2019.8098}, url = {https://dx.doi.org/10.1691/ph.2019.8098}, volume = {74}, abstract = {Amino acids (AAs), important constituents of natural moisturizing factors (NMFs) of the skin are decreased in diseased conditions such as psoriasis and atopic dermatitis. No study so far investigated the uptake of AAs into isolated corneocytes (COR). The present study was performed using 19 AAs, including taurine (TAU), to measure their amount diffused into the COR and binding of these AAs to keratin. Incubation of alanine, aspartic acid, asparagine, glutamine, glutamic acid, histidine, proline, serine and TAU with the isolated COR showed uptake after 24 h of 51.6, 95.4, 98.6, 94.1, 95.6, 90.1, 94.6, 72.9 and 57.8 %, respectively, into the COR but no binding with keratin. Uptake of TAU was validated by time dependent in-vitro diffusion models 'without COR and 'with COR'. The time dependent curve fitting showed that in in-vitro diffusion model 'without COR' there was no change in the total concentration of TAU until 72 hours, while in diffusion model 'with COR' the total conc. decreased to 37.8 % after 72 hours. The Pearson's correlation coefficient 'r' between the conc. curves of both in-vitro diffusion models was -0.54 that was an evidence of significant amount of TAU uptake by the COR. AAs as part of the NMFs have a great potential to be diffused into the COR. This property of the AAs can be employed in further dermatological research on diseased or aged skin conditions with NMFs deficiency.} } @Article{IPB-2427, author = {Schulze, A. and Zimmer, M. and Mielke, S. and Stellmach, H. and Melnyk, C. W. and Hause, B. and Gasperini, D.}, title = {{Wound-induced shoot-to-root relocation of JA-Ile precursors coordinates Arabidopsis growth}}, year = {2019}, journal = {Mol Plant}, doi = {10.1016/j.molp.2019.05.013}, url = {https://dx.doi.org/10.1016/j.molp.2019.05.013}, abstract = {Multicellular organisms rely upon the movement of signaling molecules across cells, tissues and organs to communicate among distal sites. In plants, localized leaf damage activates jasmonate (JA)-dependent transcriptional reprogramming in both harmed and unharmed tissues. Although previous evidence indicated that JA species can translocate from damaged into distal sites, the identity of the mobile compound(s), the tissues through which they translocate and the impact of their relocation remain unknown. Here, we found that following shoot wounding, the relocation of endogenous jasmonates through the phloem is essential to initiate JA signaling and stunt growth in unharmed roots of Arabidopsis thaliana. By coupling grafting experiments to hormone profiling, we uncovered that the hormone precursor OPDA and its derivatives, but not the bioactive JA-Ile conjugate, translocate from wounded shoots into undamaged roots. Upon root relocation, the mobile precursors cooperatively regulated JA responses through their conversion into JA-Ile and JA signaling activation. Collectively, our findings demonstrate the existence of long-distance translocation of endogenous OPDA and its derivatives which serve as communication molecules to coordinate shoot-to-root responses, and highlight the importance of a controlled re-distribution of hormone precursors among organs during plant stress acclimation.} } @Article{IPB-2425, author = {Dallery, J.-F. and Zimmer, M. and Halder, V. and Suliman, M. and Pigné, S. and Le Goff, G. and Gianniou, D. D. and Trougakos, I. P. and Ouazzani, J. and Gasperini, D. and O’Connell, R. J.}, title = {{Inhibition of jasmonate-mediated plant defences by the fungal metabolite higginsianin B}}, year = {2019}, journal = {bioRxiv}, doi = {10.1101/651562}, url = {https://dx.doi.org/10.1101/651562}, abstract = {Infection of Arabidopsis thaliana by the ascomycete fungus Colletotrichum higginsianum is characterised by an early symptomless biotrophic phase followed by a destructive necrotrophic phase. The fungal genome contains 77 secondary metabolism-related biosynthetic gene clusters (BGCs), and their expression during the infection process is tightly regulated. Deleting CclA, a chromatin regulator involved in repression of some BGCs through H3K4 trimethylation, allowed overproduction of 3 families of terpenoids and isolation of 12 different molecules. These natural products were tested in combination with methyl jasmonate (MeJA), an elicitor of jasmonate responses, for their capacity to alter defence gene induction in Arabidopsis. Higginsianin B inhibited MeJA-triggered expression of the defence reporter VSP1p:GUS, suggesting it may block bioactive JA-Ile synthesis or signalling in planta. Using the JA-Ile sensor Jas9-VENUS, we found that higginsianin B, but not three other structurally-related molecules, suppressed JA-Ile signalling by preventing degradation of JAZ proteins, the repressors of JA responses. Higginsianin B likely blocks the 26S proteasome-dependent degradation of JAZ proteins because it inhibited chymotrypsin- and caspase-like protease activities. The inhibition of target degradation by higginsianin B also extended to auxin signalling, as higginsianin B treatment reduced IAA-dependent expression of DR5p:GUS. Overall, our data indicate that specific fungal secondary metabolites can act similarly to protein effectors to subvert plant immune and developmental responses.} } @Article{IPB-2422, author = {Wasternack, C.}, title = {{Determination of sex by jasmonate}}, year = {2019}, journal = {J Integr Plant Biol}, doi = {10.1111/jipb.12840}, url = {https://dx.doi.org/10.1111/jipb.12840}, } @Article{IPB-2421, author = {Bellstaedt, J. and Trenner, J. and Lippmann, R. and Poeschl, Y. and Zhang, X. and Friml, J. and Quint, M. and Delker, C.}, title = {{A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls}}, year = {2019}, pages = {757-766}, journal = {Plant Physiol}, doi = {10.1104/pp.18.01377}, url = {https://dx.doi.org/10.1104/pp.18.01377}, volume = {180}, abstract = {Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls, and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by the generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl, where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.} } @Article{IPB-2420, author = {Ronzan, M. and Piacentini, D. and Fattorini, L. and Federica, D. R. and Caboni, E. and Eiche, E. and Ziegler, J. and Hause, B. and Riemann, M. and Betti, C. and Altamura, M. M. and Falasca, G.}, title = {{Auxin-jasmonate crosstalk in Oryza sativa L. root system formation after cadmium and/or arsenic exposure}}, year = {2019}, pages = {59-69}, journal = {Environ Exp Bot}, doi = {10.1016/j.envexpbot.2019.05.013}, url = {https://dx.doi.org/10.1016/j.envexpbot.2019.05.013}, volume = {165}, abstract = {Soil pollutants may affect root growth through interactions among phytohormones like auxin and jasmonates. Rice is frequently grown in paddy fields contaminated by cadmium and arsenic, but the effects of these pollutants on jasmonates/auxin crosstalk during adventitious and lateral roots formation are widely unknown. Therefore, seedlings of Oryza sativa cv. Nihonmasari and of the jasmonate-biosynthetic mutant coleoptile photomorphogenesis2 were exposed to cadmium and/or arsenic, and/or jasmonic acid methyl ester, and then analysed through morphological, histochemical, biochemical and molecular approaches.In both genotypes, arsenic and cadmium accumulated in roots more than shoots. In the roots, arsenic levels were more than twice higher than cadmium levels, either when arsenic was applied alone, or combined with cadmium. Pollutants reduced lateral root density in the wild -type in every treatment condition, but jasmonic acid methyl ester increased it when combined with each pollutant. Interestingly, exposure to cadmium and/or arsenic did not change lateral root density in the mutant. The transcript levels of OsASA2 and OsYUCCA2, auxin biosynthetic genes, increased in the wild-type and mutant roots when pollutants and jasmonic acid methyl ester were applied alone. Auxin (indole-3-acetic acid) levels transiently increased in the roots with cadmium and/or arsenic in the wild-type more than in the mutant. Arsenic and cadmium, when applied alone, induced fluctuations in bioactive jasmonate contents in wild-type roots, but not in the mutant. Auxin distribution was evaluated in roots of OsDR5::GUS seedlings exposed or not to jasmonic acid methyl ester added or not with cadmium and/or arsenic. The DR5::GUS signal in lateral roots was reduced by arsenic, cadmium, and jasmonic acid methyl ester. Lipid peroxidation, evaluated as malondialdehyde levels, was higher in the mutant than in the wild-type, and increased particularly in As presence, in both genotypes.Altogether, the results show that an auxin/jasmonate interaction affects rice root system development in the presence of cadmium and/or arsenic, even if exogenous jasmonic acid methyl ester only slightly mitigates pollutants toxicity.} } @Article{IPB-2426, author = {Goslin, K. and Eschen-Lippold, L. and Naumann, C. and Linster, E. and Sorel, M. and Klecker, M. and Marchi, R. D. and Kind, A. and Wirtz, M. and Lee, J. and Dissmeyer, N. and Graciet, E.}, title = {{Differential N-end rule degradation of RIN4/NOI fragments generated by the AvrRpt2 effector protease}}, year = {2019}, journal = {bioRxiv}, doi = {10.1101/583054}, url = {https://dx.doi.org/10.1101/583054}, abstract = {The protein RPM1-INTERACTING PROTEIN4 (RIN4) is a central regulator of both layers of plant immunity systems, the so-called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). RIN4 is targeted by several effectors, including the Pseudomonas syringae protease effector AvrRpt2. Cleavage of RIN4 by AvrRpt2 generates unstable RIN4 fragments, whose degradation leads to the activation of the resistance protein RPS2 (RESISTANT TO P. SYRINGAE2). Hence, identifying the determinants of RIN4 degradation is key to understanding RPS2-mediated ETI, as well as virulence functions of AvrRpt2. In addition to RIN4, AvrRpt2 cleaves host proteins from the nitrate-induced (NOI) domain family. Although cleavage of NOI-domain proteins by AvrRpt2 may contribute to PTI regulation, the (in)stability of these proteolytic fragments and the determinants that regulate their stability have not been examined. Notably, a common feature of RIN4 and of many NOI-domain protein fragments generated by AvrRpt2 cleavage is the exposure of a new N-terminal residue that is destabilizing according to the N-end rule. Using antibodies raised against endogenous RIN4, we show that the destabilization of AvrRpt2-cleaved RIN4 fragments is independent of the N-end rule pathway (recently renamed N-degron pathway). By contrast, several NOI-domain protein fragments are bona fide substrates of the N-degron pathway. The discovery of this novel set of substrates considerably expands the number of proteins targeted for degradation by this ubiquitin-dependent pathway, for which very few physiological substrates are known in plants. Our results also open new avenues of research to understand the role of AvrRpt2 in promoting bacterial virulence.} } @Article{IPB-2440, author = {Wasternack, C.}, title = {{Termination in Jasmonate Signaling by MYC2 and MTBs}}, year = {2019}, pages = {667-669}, journal = {Trends Plant Sci}, doi = {10.1016/j.tplants.2019.06.001}, url = {https://dx.doi.org/10.1016/j.tplants.2019.06.001}, volume = {24}, abstract = {Jasmonic acid (JA) signaling can be switched off by metabolism of JA. The master regulator MYC2, interacting with MED25, has been shown to be deactivated by the bHLH transcription factors MTB1, MTB2, and MTB3. An autoregulatory negative feedback loop has been proposed for this termination in JA signaling.} } @Article{IPB-2287, author = {Kölling, M. and Kumari, P. and Bürstenbinder, K.}, title = {{Calcium- and calmodulin-regulated microtubule-associated proteins as signal-integration hubs at the plasma membrane–cytoskeleton nexus}}, year = {2019}, pages = {387-396}, journal = {J Exp Bot}, doi = {10.1093/jxb/ery397}, url = {https://dx.doi.org/10.1093/jxb/ery397}, volume = {70}, abstract = {Plant growth and development are a genetically predetermined series of events but can change dramatically in response to environmental stimuli, involving perpetual pattern formation and reprogramming of development. The rate of growth is determined by cell division and subsequent cell expansion, which are restricted and controlled by the cell wall–plasma membrane–cytoskeleton continuum, and are coordinated by intricate networks that facilitate intra- and intercellular communication. An essential role in cellular signaling is played by calcium ions, which act as universal second messengers that transduce, integrate, and multiply incoming signals during numerous plant growth processes, in part by regulation of the microtubule cytoskeleton. In this review, we highlight recent advances in the understanding of calcium-mediated regulation of microtubule-associated proteins, their function at the microtubule cytoskeleton, and their potential role as hubs in crosstalk with other signaling pathways.} } @Article{IPB-2277, author = {Naumann, C. and Müller, J. and Sakhonwasee, S. and Wieghaus, A. and Hause, G. and Heisters, M. and Bürstenbinder, K. and Abel, S.}, title = {{The Local Phosphate Deficiency Response Activates Endoplasmic Reticulum Stress-Dependent Autophagy}}, year = {2019}, pages = {460-476}, journal = {Plant Physiol}, doi = {10.1104/pp.18.01379}, url = {https://dx.doi.org/10.1104/pp.18.01379}, volume = {179}, abstract = {Inorganic phosphate (Pi) is often a limiting plant nutrient. In members of the Brassicaceae family, such as Arabidopsis (Arabidopsis thaliana), Pi deprivation reshapes root system architecture to favor topsoil foraging. It does so by inhibiting primary root extension and stimulating lateral root formation. Root growth inhibition from phosphate (Pi) deficiency is triggered by iron-stimulated, apoplastic reactive oxygen species generation and cell wall modifications, which impair cell-to-cell communication and meristem maintenance. These processes require LOW PHOSPHATE RESPONSE1 (LPR1), a cell wall-targeted ferroxidase, and PHOSPHATE DEFICIENCY RESPONSE2 (PDR2), the single endoplasmic reticulum (ER)-resident P5-type ATPase (AtP5A), which is thought to control LPR1 secretion or activity. Autophagy is a conserved process involving the vacuolar degradation of cellular components. While the function of autophagy is well established under nutrient starvation (C, N, or S), it remains to be explored under Pi deprivation. Because AtP5A/PDR2 likely functions in the ER stress response, we analyzed the effect of Pi limitation on autophagy. Our comparative study of mutants defective in the local Pi deficiency response, ER stress response, and autophagy demonstrated that ER stress-dependent autophagy is rapidly activated as part of the developmental root response to Pi limitation and requires the genetic PDR2-LPR1 module. We conclude that Pi-dependent activation of autophagy in the root apex is a consequence of local Pi sensing and the associated ER stress response, rather than a means for systemic recycling of the macronutrient.} } @Article{IPB-2275, author = {Wasternack, C.}, title = {{New Light on Local and Systemic Wound Signaling}}, year = {2019}, pages = {102-105}, journal = {Trends Plant Sci}, doi = {10.1016/j.tplants.2018.11.009}, url = {https://dx.doi.org/10.1016/j.tplants.2018.11.009}, volume = {24}, abstract = {Electric signaling and Ca2+ waves were discussed to occur in systemic wound responses. Two new overlapping scenarios were identified: (i) membrane depolarization in two special cell types followed by an increase in systemic cytoplasmic Ca2+ concentration ([Ca2+]cyt), and (ii) glutamate sensed by GLUTAMATE RECEPTOR LIKE proteins and followed by Ca2+-based defense in distal leaves.} } @Article{IPB-2120, author = {Wasternack, C. and Strnad, M. }, title = {{Jasmonates are signals in the biosynthesis of secondary metabolites — Pathways, transcription factors and applied aspects — A brief review.}}, year = {2019}, pages = {1-11}, journal = {New Biotechnol}, doi = {10.1016/j.nbt.2017.09.007}, url = {http://www.sciencedirect.com/science/article/pii/S1871678417304429}, volume = {48}, abstract = {Jasmonates (JAs) are signals in plant stress responses and development. One of the first observed and prominent responses to JAs is the induction of biosynthesis of different groups of secondary compounds. Among them are nicotine, isoquinolines, glucosinolates, anthocyanins, benzophenanthridine alkaloids, artemisinin, and terpenoid indole alkaloids (TIAs), such as vinblastine. This brief review describes modes of action of JAs in the biosynthesis of anthocyanins, nicotine, TIAs, glucosinolates and artemisinin. After introducing JA biosynthesis, the central role of the SCFCOI1-JAZ co-receptor complex in JA perception and MYB-type and MYC-type transcription factors is described. Brief comments are provided on primary metabolites as precursors of secondary compounds. Pathways for the biosynthesis of anthocyanin, nicotine, TIAs, glucosinolates and artemisinin are described with an emphasis on JA-dependent transcription factors, which activate or repress the expression of essential genes encoding enzymes in the biosynthesis of these secondary compounds. Applied aspects are discussed using the biotechnological formation of artemisinin as an example of JA-induced biosynthesis of secondary compounds in plant cell factories.} } @Article{IPB-2441, author = {Mielke, S. and Gasperini, D.}, title = {{Interplay between Plant Cell Walls and Jasmonate Production}}, year = {2019}, journal = {Plant Cell Physiol}, doi = {10.1093/pcp/pcz119}, url = {https://dx.doi.org/10.1093/pcp/pcz119}, abstract = {Plant cell walls are sophisticated carbohydrate-rich structures representing the immediate contact surface with the extracellular environment, often serving as the first barrier against biotic and abiotic stresses. Notably, a variety of perturbations in plant cell walls result in upregulated jasmonate (JA) production, a phytohormone with essential roles in defense and growth responses. Hence, cell wall-derived signals can initiate intracellular JA-mediated responses and the elucidation of the underlying signaling pathways could provide novel insights into cell wall maintenance and remodeling, as well as advance our understanding on how is JA biosynthesis initiated. This Mini Review will describe current knowledge about cell wall-derived damage signals and their effects on JA biosynthesis, as well as provide future perspectives.} } @Article{IPB-2372, author = {Berens, M. L. and Wolinska, K. W. and Spaepen, S. and Ziegler, J. and Nobori, T. and Nair, A. and Krüler, V. and Winkelmüller, T. M. and Wang, Y. and Mine, A. and Becker, D. and Garrido-Oter, R. and Schulze-Lefert, P. and Tsuda, K.}, title = {{Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone cross-talk}}, year = {2019}, pages = {2364-2373}, journal = {Proc Natl Acad Sci USA}, doi = {10.1073/pnas.1817233116}, url = {https://dx.doi.org/10.1073/pnas.1817233116}, volume = {116}, abstract = {In nature, plants must respond to multiple stresses simultaneously, which likely demands cross-talk between stress-response pathways to minimize fitness costs. Here we provide genetic evidence that biotic and abiotic stress responses are differentially prioritized in Arabidopsis thaliana leaves of different ages to maintain growth and reproduction under combined biotic and abiotic stresses. Abiotic stresses, such as high salinity and drought, blunted immune responses in older rosette leaves through the phytohormone abscisic acid signaling, whereas this antagonistic effect was blocked in younger rosette leaves by PBS3, a signaling component of the defense phytohormone salicylic acid. Plants lacking PBS3 exhibited enhanced abiotic stress tolerance at the cost of decreased fitness under combined biotic and abiotic stresses. Together with this role, PBS3 is also indispensable for the establishment of salt stress- and leaf age-dependent phyllosphere bacterial communities. Collectively, our work reveals a mechanism that balances trade-offs upon conflicting stresses at the organism level and identifies a genetic intersection among plant immunity, leaf microbiota, and abiotic stress tolerance.} } @Article{IPB-2325, author = {Schulze, A. and Zimmer, M. and Mielke, S. and Stellmach, H. and Melnyk, C. W. and Hause, B. and Gasperini, D.}, title = {{Shoot-to-root translocation of the jasmonate precursor 12-oxo-phytodienoic acid (OPDA) coordinates plant growth responses following tissue damage}}, year = {2019}, journal = {bioRxiv}, doi = {10.1101/517193}, url = {https://doi.org/10.1101/517193}, abstract = {Multicellular organisms rely upon the movement of signaling molecules across cells, tissues and organs to communicate among distal sites. In plants, herbivorous insects, necrotrophic pathogens and mechanical wounding stimulate the activation of the jasmonate (JA) pathway, which in turn triggers the transcriptional changes necessary to protect plants against those challenges, often at the expense of growth. Although previous evidence indicated that JA species can translocate from damaged into distal sites, the identity of the mobile compound(s), the tissues through which they translocate and the consequences of their relocation remain unknown. Here, we demonstrated that endogenous JA species generated after shoot injury translocate to unharmed roots via the phloem vascular tissue in Arabidopsis thaliana. By wounding wild-type shoots of chimeric plants and by quantifying the relocating compounds from their JA-deficient roots, we uncovered that the JA-Ile precursor 12-oxo-phytodienoic acid (OPDA) is a mobile JA species. Our data also showed that OPDA is a primary mobile compound relocating to roots where, upon conversion to the bioactive hormone, it induces JA-mediated gene expression and root growth inhibition. Collectively, our findings reveal the existence of long-distance transport of endogenous OPDA which serves as a communication molecule to coordinate shoot-to-root responses, and highlight the importance of a controlled distribution of JA species among organs during plant stress acclimation.} } @Article{IPB-2342, author = {Chutia, R. and Abel, S. and Ziegler, J.}, title = {{Iron and Phosphate Deficiency Regulators Concertedly Control Coumarin Profiles in Arabidopsis thaliana Roots During Iron, Phosphate, and Combined Deficiencies}}, year = {2019}, pages = {113}, journal = {Front Plant Sci}, doi = {10.3389/fpls.2019.00113}, url = {https://dx.doi.org/10.3389/fpls.2019.00113}, volume = {10}, abstract = {Plants face varying nutrient conditions, to which they have to adapt to. Adaptive responses are nutrient-specific and strategies to ensure supply and homeostasis for one nutrient might be opposite to another one, as shown for phosphate (Pi) and iron (Fe) deficiency responses, where many genes are regulated in an opposing manner. This was also observed on the metabolite levels. Whereas root and exudate levels of catechol-type coumarins, phenylpropanoid-derived 2-benzopyranones, which facilitate Fe acquisition, are elevated after Fe deficiency, they are decreased after Pi deficiency. Exposing plants to combined Pi and Fe deficiency showed that the generation of coumarin profiles in Arabidopsis thaliana roots by Pi deficiency considerably depends on the availability of Fe. Similarly, the effect of Fe deficiency on coumarin profiles is different at low compared to high Pi availability. These findings suggest a fine-tuning of coumarin profiles, which depends on Fe and Pi availability. T-DNA insertion lines exhibiting aberrant expression of genes involved in the regulation of Pi starvation responses (PHO1, PHR1, bHLH32, PHL1, SPX1) and Fe starvation responses (BRUTUS, PYE, bHLH104, FIT) were used to analyze the regulation of the generation of coumarin profiles in Arabidopsis thaliana roots by Pi, Fe, and combined Pi and Fe deficiency. The analysis revealed a role of several Fe-deficiency response regulators in the regulation of Fe and of Pi deficiency-induced coumarin profiles as well as for Pi deficiency response regulators in the regulation of Pi and of Fe deficiency-induced coumarin profiles. Additionally, the regulation of Fe deficiency-induced coumarin profiles by Fe deficiency response regulators is influenced by Pi availability. Conversely, regulation of Pi deficiency-induced coumarin profiles by Pi deficiency response regulators is modified by Fe availability.} } @Article{IPB-2348, author = {Bochnia, M. and Sander, J. and Ziegler, J. and Terhardt, M. and Sander, S. and Janzen, N. and Cavalleri, J.-M. V. and Zuraw, A. and Wensch-Dorendorf, M. and Zeyner, A.}, title = {{Detection of MCPG metabolites in horses with atypical myopathy}}, year = {2019}, pages = {e0211698}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0211698}, url = {https://dx.doi.org/10.1371/journal.pone.0211698}, volume = {14}, abstract = {Atypical myopathy (AM) in horses is caused by ingestion of seeds of the Acer species (Sapindaceae family). Methylenecyclopropylacetyl-CoA (MCPA-CoA), derived from hypoglycin A (HGA), is currently the only active toxin in Acer pseudoplatanus or Acer negundo seeds related to AM outbreaks. However, seeds or arils of various Sapindaceae (e.g., ackee, lychee, mamoncillo, longan fruit) also contain methylenecyclopropylglycine (MCPG), which is a structural analogue of HGA that can cause hypoglycaemic encephalopathy in humans. The active poison formed from MCPG is methylenecyclopropylformyl-CoA (MCPF-CoA). MCPF-CoA and MCPA-CoA strongly inhibit enzymes that participate in β-oxidation and energy production from fat. The aim of our study was to investigate if MCPG is involved in Acer seed poisoning in horses. MCPG, as well as glycine and carnitine conjugates (MCPF-glycine, MCPF-carnitine), were quantified using high-performance liquid chromatography-tandem mass spectrometry of serum and urine from horses that had ingested Acer pseudoplatanus seeds and developed typical AM symptoms. The results were compared to those of healthy control horses. For comparison, HGA and its glycine and carnitine derivatives were also measured. Additionally, to assess the degree of enzyme inhibition of β-oxidation, several acyl glycines and acyl carnitines were included in the analysis. In addition to HGA and the specific toxic metabolites (MCPA-carnitine and MCPA-glycine), MCPG, MCPF-glycine and MCPF-carnitine were detected in the serum and urine of affected horses. Strong inhibition of β-oxidation was demonstrated by elevated concentrations of all acyl glycines and carnitines, but the highest correlations were observed between MCPF-carnitine and isobutyryl-carnitine (r = 0.93) as well as between MCPA- (and MCPF-) glycine and valeryl-glycine with r = 0.96 (and r = 0.87). As shown here, for biochemical analysis of atypical myopathy of horses, it is necessary to take MCPG and the corresponding metabolites into consideration.} } @Article{IPB-2271, author = {Mitra, D. and Klemm, S. and Kumari, P. and Quegwer, J. and Möller, B. and Poeschl, Y. and Pflug, P. and Stamm, G. and Abel, S. and Bürstenbinder, K.}, title = {{Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana}}, year = {2019}, pages = {529-543}, journal = {J Exp Bot}, doi = {10.1093/jxb/ery395}, url = {https://dx.doi.org/10.1093/jxb/ery395}, volume = {70}, abstract = {Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation and cell morphology. Its organization and dynamics are coordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles of calcium in regulation of PC morphogenesis. Our work thus identifies IQD5 as a novel player in PC shape regulation, and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.} } @INBOOK{IPB-2452, author = {Ziegler, J. and Hussain, H. and Neubert, R. H. H. and Abel, S.}, title = {{Amino Acid Analysis}}, year = {2019}, pages = {365-379}, chapter = {{Sensitive and Selective Amino Acid Profiling of Minute Tissue Amounts by HPLC/Electrospray Negative Tandem Mass Spectrometry Using 9-Fluorenylmethoxycarbonyl (Fmoc-Cl) Derivatization}}, journal = {Methods Mol Biol}, editor = {Alterman, M. A., ed.}, doi = {10.1007/978-1-4939-9639-1_27}, url = {https://dx.doi.org/10.1007/978-1-4939-9639-1_27}, volume = {2030}, abstract = {A method for selective and sensitive quantification of amino acids is described. The combination of established derivatization procedures of secondary and primary amino groups with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) and subsequent detection of derivatized amino acids by LC-ESI-MS/MS using multiple reaction monitoring provides high selectivity. The attachment of an apolar moiety enables purification of derivatized amino acids from matrix by a single solid-phase extraction step, which increases sensitivity by reduced ion suppression during LC-ESI-MS/MS detection. Additionally, chromatography of all amino acids can be performed on reversed-phase HPLC columns using eluents without additives, which are known to cause significant decreases in signal to noise ratios. The method has been routinely applied for amino acid profiling of low amounts of liquids and tissues of various origins with a sample throughput of about 50–100 samples a day. In addition to a detailed description of the method, some representative examples are presented.} } @Article{IPB-2411, author = {Hussain, H. and Ziegler, J. and Hause, G. and Wohlrab, J. and Neubert, R. H. H.}, title = {{Quantitative Analysis of Free Amino Acids and Urea Derived from Isolated Corneocytes of Healthy Young, Healthy Aged, and Diseased Skin}}, year = {2019}, pages = {94-100}, journal = {Skin Pharmacol Physiol}, doi = {10.1159/000495992}, url = {https://dx.doi.org/10.1159/000495992}, volume = {32}, abstract = {Background/Aims: Free amino acids (FAAs) and urea, present inside the corneocytes, can be important indicators of skin condition. However, due to the lack of a standard extraction protocol for FAAs from corneocytes, conflicting research results have been reported. Therefore, the purpose of this study was (1) to standardize the extraction protocol and (2) to investigate FAA profiles in healthy young and healthy old volunteers, as well as in psoriasis and atopic dermatitis patients. Methods: Skin samples were collected from four groups (healthy young, healthy old, and psoriasis and atopic dermatitis patients) with 5 volunteers per group. Corneocytes were isolated and examined microscopically. FAAs and urea were extracted from the isolated corneocytes, and their amounts were quantified using LC-ESI/MS/MS (after derivatization with Fmoc-Cl) and colorimetric methods, respectively. Results: The micrographs of the corneocytes showed no morphological features attributable to age or disease conditions. The highest and lowest concentrations of total FAAs and urea were observed in the healthy old group and the healthy young group, respectively. Unlike the other FAAs and urea, citrulline was found at a higher level in the healthy young group than in the disease groups. Conclusion: This study suggests that the levels of FAAs and urea in the skin are affected by age and skin conditions (healthy/diseased). However, further studies are needed to show the effects of different skin conditions on the levels of FAAs and urea.} } @Article{IPB-2454, author = {Wasternack, C. and Hause, B.}, title = {{The missing link in jasmonic acid biosynthesis}}, year = {2019}, pages = {776-777}, journal = {Nat Plants}, doi = {10.1038/s41477-019-0492-y}, url = {https://dx.doi.org/10.1038/s41477-019-0492-y}, volume = {5}, abstract = {Jasmonic acid biosynthesis starts in chloroplasts and is finalized in peroxisomes. The required export of a crucial intermediate out of the chloroplast is now shown to be mediated by a protein from the outer envelope called JASSY.} } @INBOOK{IPB-2413, author = {Möller, B. and Zergiebel, L. and Bürstenbinder, K.}, title = {{Plant Cell Morphogenesis}}, year = {2019}, pages = {151-171}, chapter = {{Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D}}, journal = {Methods Mol Biol}, editor = {Cvrčková, F. \& Žárský, V., eds.}, doi = {10.1007/978-1-4939-9469-4_10}, url = {https://dx.doi.org/10.1007/978-1-4939-9469-4_10}, volume = {1992}, abstract = {The microtubule cytoskeleton plays important roles in cell morphogenesis. To investigate the mechanisms of cytoskeletal organization, for example, during growth or development, in genetic studies, or in response to environmental stimuli, image analysis tools for quantitative assessment are needed. Here, we present a method for texture measure-based quantification and comparative analysis of global microtubule cytoskeleton patterns and subsequent visualization of output data. In contrast to other approaches that focus on the extraction of individual cytoskeletal fibers and analysis of their orientation relative to the growth axis, CytoskeletonAnalyzer2D quantifies cytoskeletal organization based on the analysis of local binary patterns. CytoskeletonAnalyzer2D thus is particularly well suited to study cytoskeletal organization in cells where individual fibers are difficult to extract or which lack a clearly defined growth axis, such as leaf epidermal pavement cells. The tool is available as ImageJ plugin and can be combined with publicly available software and tools, such as R and Cytoscape, to visualize similarity networks of cytoskeletal patterns.} } @INBOOK{IPB-2412, author = {Möller, B. and Poeschl, Y. and Klemm, S. and Bürstenbinder, K.}, title = {{Plant Cell Morphogenesis}}, year = {2019}, pages = {329-349}, chapter = {{Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant}}, journal = {Methods Mol Biol}, editor = {Cvrčková, F. \& Žárský, V., eds.}, doi = {10.1007/978-1-4939-9469-4_22}, url = {https://dx.doi.org/10.1007/978-1-4939-9469-4_22}, volume = {1992}, abstract = {Morphological analysis of cell shapes requires segmentation of cell contours from input images and subsequent extraction of meaningful shape descriptors that provide the basis for qualitative and quantitative assessment of shape characteristics. Here, we describe the publicly available ImageJ plugin PaCeQuant and its associated R package PaCeQuantAna, which provides a pipeline for fully automatic segmentation, feature extraction, statistical analysis, and graphical visualization of cell shape properties. PaCeQuant is specifically well suited for analysis of jigsaw puzzle-like leaf epidermis pavement cells from 2D input images and supports the quantification of global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.} } @INBOOK{IPB-2417, author = {Möller, B. and Bürstenbinder, K.}, title = {{2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)}}, year = {2019}, pages = {199-203}, chapter = {{Semi-Automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level}}, doi = {10.1109/ISBI.2019.8759145}, url = {https://dx.doi.org/10.1109/ISBI.2019.8759145}, abstract = {The structure of the microtubule cytoskeleton provides valuable information related to morphogenesis of cells. The cytoskeleton organizes into diverse patterns that vary in cells of different types and tissues, but also within a single tissue. To assess differences in cytoskeleton organization methods are needed that quantify cytoskeleton patterns within a complete cell and which are suitable for large data sets. A major bottleneck in most approaches, however, is a lack of techniques for automatic extraction of cell contours. Here, we present a semi-automatic pipeline for cell segmentation and quantification of microtubule organization. Automatic methods are applied to extract major parts of the contours and a handy image editor is provided to manually add missing information efficiently. Experimental results prove that our approach yields high-quality contour data with minimal user intervention and serves a suitable basis for subsequent quantitative studies.} } @Article{IPB-2462, author = {Gago-Zachert, S. and Schuck, J. and Weinholdt, C. and Knoblich, M. and Pantaleo, V. and Grosse, I. and Gursinsky, T. and Behrens, S.-E.}, title = {{Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro}}, year = {2019}, journal = {Nucleic Acids Res}, doi = {10.1093/nar/gkz678}, url = {https://dx.doi.org/10.1093/nar/gkz678}, abstract = {In response to a viral infection, the plant’s RNA silencing machinery processes viral RNAs into a huge number of small interfering RNAs (siRNAs). However, a very few of these siRNAs actually interfere with viral replication. A reliable approach to identify these immunologically effective siRNAs (esiRNAs) and to define the characteristics underlying their activity has not been available so far. Here, we develop a novel screening approach that enables a rapid functional identification of antiviral esiRNAs. Tests on the efficacy of such identified esiRNAs of a model virus achieved a virtual full protection of plants against a massive subsequent infection in transient applications. We find that the functionality of esiRNAs depends crucially on two properties: the binding affinity to Argonaute proteins and the ability to access the target RNA. The ability to rapidly identify functional esiRNAs could be of great benefit for all RNA silencing-based plant protection measures against viruses and other pathogens.} } @Article{IPB-2190, author = {Gantner, J. and Ordon, J. and Ilse, T. and Kretschmer, C. and Gruetzner, R. and Löfke, C. and Dagdas, Y. and Bürstenbinder, K. and Marillonnet, S. and Stuttmann, J.}, title = {{Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system}}, year = {2018}, pages = {e0197185}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0197185}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197185}, volume = {13}, abstract = {Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a “peripheral infrastructure” around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies.} } @Article{IPB-2224, author = {Iglesias, M. J. and Terrile, M. C. and Correa-Aragunde, N. and Colman, S. L. and Izquierdo-Álvarez, A. and Fiol, D. F. and París, R. and Sánchez-López, N. and Marina, A. and Calderón Villalobos, L. I. A. and Estelle, M. and Lamattina, L. and Martínez-Ruiz, A. and Casalongué, C. A.}, title = {{Regulation of SCFTIR1/AFBs E3 ligase assembly by S-nitrosylation of Arabidopsis SKP1-like1 impacts on auxin signaling}}, year = {2018}, pages = {200-210}, journal = {Redox Biol}, doi = {10.1016/j.redox.2018.07.003}, url = {https://dx.doi.org/10.1016/j.redox.2018.07.003}, volume = {18}, abstract = {The F-box proteins (FBPs) TIR1/AFBs are the substrate recognition subunits of SKP1–cullin–F-box (SCF) ubiquitin ligase complexes and together with Aux/IAAs form the auxin co-receptor. Although tremendous knowledge on auxin perception and signaling has been gained in the last years, SCFTIR1/AFBs complex assembly and stabilization are emerging as new layers of regulation. Here, we investigated how nitric oxide (NO), through S-nitrosylation of ASK1 is involved in SCFTIR1/AFBs assembly. We demonstrate that ASK1 is S-nitrosylated and S-glutathionylated in cysteine (Cys) 37 and Cys118 residues in vitro. Both, in vitro and in vivo protein-protein interaction assays show that NO enhances ASK1 binding to CUL1 and TIR1/AFB2, required for SCFTIR1/AFB2 assembly. In addition, we demonstrate that Cys37 and Cys118 are essential residues for proper activation of auxin signaling pathway in planta. Phylogenetic analysis revealed that Cys37 residue is only conserved in SKP proteins in Angiosperms, suggesting that S-nitrosylation on Cys37 could represent an evolutionary adaption for SKP1 function in flowering plants. Collectively, these findings indicate that multiple events of redox modifications might be part of a fine-tuning regulation of SCFTIR1/AFBs for proper auxin signal transduction.} } @Article{IPB-2183, author = {Wasternack, C. and Hause, B.}, title = {{A Bypass in Jasmonate Biosynthesis – the OPR3-independent Formation}}, year = {2018}, pages = {276-279}, journal = {Trends Plant Sci}, doi = {10.1016/j.tplants.2018.02.011}, url = {https://www.sciencedirect.com/science/article/pii/S1360138518300426}, volume = {23}, abstract = {For the first time in 25 years, a new pathway for biosynthesis of jasmonic acid (JA) has been identified. JA production takes place via 12-oxo-phytodienoic acid (OPDA) including reduction by OPDA reductases (OPRs). A loss-of-function allele, opr3-3, revealed an OPR3-independent pathway converting OPDA to JA.} } @Article{IPB-1903, author = {Bochnia, M. and Scheidemann, W. and Ziegler, J. and Sander, J. and Vollstedt, S. and Glatter, M. and Janzen, N. and Terhardt, M. and Zeyner, A.}, title = {{Predictive value of hypoglycin A and methylencyclopropylacetic acid conjugates in a horse with atypical myopathy in comparison to its cograzing partners}}, year = {2018}, pages = {24-28}, journal = {Equine Vet Educ}, doi = {10.1111/eve.12596}, url = {http://onlinelibrary.wiley.com/journal/10.1001/(ISSN)2042-3292}, volume = {30}, abstract = {Hypoglycin A (HGA) was detected in blood and urine of a horse suffering from atypical myopathy (AM; Day 2, serum, 8290 μg/l; urine: Day 1, 574, Day 2, 742 μg/l) and in its cograzing partners with a high variability (46–1570 μg/l serum). Over the period of disease, the level of the toxic metabolites (methylencyclopropylacetic acid [MCPA]-conjugates) increased in body fluids of the AM horse (MCPA-carnitine: Day 2, 0.246, Day 3, 0.581 μmol/l serum; MCPA-carnitine: Day 2, 0.621, Day 3, 0.884 μmol/mmol creatinine in urine) and HGA decreased rapidly (Day 3, 2430 μg/l serum). In cograzing horses MCPA-conjugates were not detected. HGA in seeds ranged from 268 to 367 μg/g. Although HGA was present in body fluids of healthy cograzing horses, MCPA-conjugates were not detectable, in contrast to the AM horse. Therefore, increasing concentrations of MCPA-conjugates are supposed to be linked with the onset of AM and both parameters seem to indicate the clinical stage of disease. However, detection of HGA in body fluids of cograzing horses might be a promising step in preventing the disease.} } @Article{IPB-2141, author = {Krägeloh, T. and Cavalleri, J. M. V. and Ziegler, J. and Sander, J. and Terhardt, M. and Breves, G. and Cehak, A.}, title = {{Identification of hypoglycin A binding adsorbents as potential preventive measures in co-grazers of atypical myopathy affected horses}}, year = {2018}, pages = {220-227}, journal = {Equine Vet J}, doi = {10.1111/evj.12723}, url = {https://dx.doi.org/10.1111/evj.12723}, volume = {50}, abstract = {BackgroundIntestinal absorption of hypoglycin A (HGA) and its metabolism are considered major prerequisites for atypical myopathy (AM). The increasing incidence and the high mortality rate of AM urgently necessitate new therapeutic and/or preventative approaches.ObjectivesTo identify a substance for oral administration capable of binding HGA in the intestinal lumen and effectively reducing the intestinal absorption of the toxin.Study designExperimental in vitro study.MethodsSubstances commonly used in equine practice (activated charcoal composition, di‐tri‐octahedral smectite, mineral oil and activated charcoal) were tested for their binding capacity for HGA using an in vitro incubation method. The substance most effective in binding HGA was subsequently tested for its potential to reduce intestinal HGA absorption. Jejunal tissues of 6 horses were incubated in Ussing chambers to determine mucosal uptake, tissue accumulation, and serosal release of HGA in the presence and absence of the target substance. Potential intestinal metabolism in methylenecyclopropyl acetic acid (MCPA)‐conjugates was investigated by analysing their concentrations in samples from the Ussing chambers.ResultsActivated charcoal composition and activated charcoal were identified as potent HGA binding substances with dose and pH dependent binding capacity. There was no evidence of intestinal HGA metabolism.Main limitationsBinding capacity of adsorbents was tested in vitro using aqueous solutions, and in vivo factors such as transit time and composition of intestinal content, may affect adsorption capacity after oral administration.ConclusionsFor the first time, this study identifies substances capable of reducing HGA intestinal absorption. This might have major implications as a preventive measure in cograzers of AM affected horses but also in horses at an early stage of intoxication.} } @Article{IPB-2160, author = {Ibañez, C. and Delker, C. and Martinez, C. and Bürstenbinder, K. and Janitza, P. and Lippmann, R. and Ludwig, W. and Sun, H. and James, G. V. and Klecker, M. and Grossjohann, A. and Schneeberger, K. and Prat, S. and Quint, M.}, title = {{Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1}}, year = {2018}, pages = {303-310.e3}, journal = {Curr Biol}, doi = {10.1016/j.cub.2017.11.077}, url = {http://www.cell.com/current-biology/abstract/S0960-9822(17)31602-0}, volume = {28}, abstract = {Thermomorphogenesis is defined as the suite of morphological changes that together are likely to contribute to adaptive growth acclimation to usually elevated ambient temperature [ 1, 2 ]. While many details of warmth-induced signal transduction are still elusive, parallels to light signaling recently became obvious (reviewed in [ 3 ]). It involves photoreceptors that can also sense changes in ambient temperature [ 3–5 ] and act, for example, by repressing protein activity of the central integrator of temperature information PHYTOCHROME-INTERACTING FACTOR 4 (PIF4 [ 6 ]). In addition, PIF4 transcript accumulation is tightly controlled by the evening complex member EARLY FLOWERING 3 [ 7, 8 ]. According to the current understanding, PIF4 activates growth-promoting genes directly but also via inducing auxin biosynthesis and signaling, resulting in cell elongation. Based on a mutagenesis screen in the model plant Arabidopsis thaliana for mutants with defects in temperature-induced hypocotyl elongation, we show here that both PIF4 and auxin function depend on brassinosteroids. Genetic and pharmacological analyses place brassinosteroids downstream of PIF4 and auxin. We found that brassinosteroids act via the transcription factor BRASSINAZOLE RESISTANT 1 (BZR1), which accumulates in the nucleus at high temperature, where it induces expression of growth-promoting genes. Furthermore, we show that at elevated temperature BZR1 binds to the promoter of PIF4, inducing its expression. These findings suggest that BZR1 functions in an amplifying feedforward loop involved in PIF4 activation. Although numerous negative regulators of PIF4 have been described, we identify BZR1 here as a true temperature-dependent positive regulator of PIF4, acting as a major growth coordinator.} } @Article{IPB-2158, author = {Bagchi, R. and Melnyk, C. W. and Christ, G. and Winkler, M. and Kirchsteiner, K. and Salehin, M. and Mergner, J. and Niemeyer, M. and Schwechheimer, C. and Calderón Villalobos, L. I. A. and Estelle, M.}, title = {{The Arabidopsis ALF4 protein is a regulator of SCF E3 ligases.}}, year = {2018}, pages = {255-268}, journal = {EMBO J}, doi = {10.15252/embj.201797159}, url = {http://onlinelibrary.wiley.com/doi/10.15252/embj.201797159/full}, volume = {37}, abstract = {The cullin-RING E3 ligases (CRLs) regulate diverse cellular processes in all eukaryotes. CRL activity is controlled by several proteins or protein complexes, including NEDD8, CAND1, and the CSN. Recently, a mammalian protein called Glomulin (GLMN) was shown to inhibit CRLs by binding to the RING BOX (RBX1) subunit and preventing binding to the ubiquitin-conjugating enzyme. Here, we show that Arabidopsis ABERRANT LATERAL ROOT FORMATION4 (ALF4) is an ortholog of GLMN. The alf4 mutant exhibits a phenotype that suggests defects in plant hormone response. We show that ALF4 binds to RBX1 and inhibits the activity of SCFTIR1, an E3 ligase responsible for degradation of the Aux/IAA transcriptional repressors. In vivo, the alf4 mutation destabilizes the CUL1 subunit of the SCF. Reduced CUL1 levels are associated with increased levels of the Aux/IAA proteins as well as the DELLA repressors, substrate of SCFSLY1. We propose that the alf4 phenotype is partly due to increased levels of the Aux/IAA and DELLA proteins.} } @Article{IPB-2127, author = {Wasternack, C. and Feussner, I.}, title = {{The Oxylipin Pathways: Biochemistry and Function}}, year = {2018}, pages = {363-386}, journal = {Annu Rev Plant Biol}, doi = {10.1146/annurev-arplant-042817-040440}, url = {https://www.annualreviews.org/doi/10.1146/annurev-arplant-042817-040440}, volume = {69}, abstract = {Plant oxylipins form a constantly growing group of signaling molecules that comprise oxygenated fatty acids and metabolites derived therefrom. In the last decade, the understanding of biosynthesis, metabolism, and action of oxylipins, especially jasmonates, has dramatically improved. Additional mechanistic insights into the action of enzymes and insights into signaling pathways have been deepened for jasmonates. For other oxylipins, such as the hydroxy fatty acids, individual signaling properties and cross talk between different oxylipins or even with additional phytohormones have recently been described. This review summarizes recent understanding of the biosynthesis, regulation, and function of oxylipins.} } @Article{IPB-2381, author = {García, M. L. and Bó, E. D. and da Graça, J. V. and Gago-Zachert, S. and Hammond, J. and Moreno, P. and Natsuaki, T. and Pallás, V. and Navarro, J. A. and Reyes, C. A. and Luna, G. R. and Sasaya, T. and Tzanetakis, I. E. and Vaira, A. M. and Verbeek, M. and ICTV Report Consortium}, title = {{Corrigendum: ICTV Virus Taxonomy Profile: Ophioviridae}}, year = {2018}, pages = {949-949}, journal = {J Gen Virol}, doi = {10.1099/jgv.0.001093}, url = {https://dx.doi.org/10.1099/jgv.0.001093}, volume = {99}, } @Article{IPB-2192, author = {Nishiyama, T. and Sakayama, H. and de Vries, J. and Buschmann, H. and Saint-Marcoux, D. and Ullrich, K. K. and Haas, F. B. and Vanderstraeten, L. and Becker, D. and Lang, D. and Vosolsobě, S. and Rombauts, S. and Wilhelmsson, P. K. I. and Janitza, P. and Kern, R. and Heyl, A. and Rümpler, F and Calderón Villalobos, L. I. A. and Clay, J. M. and Skokan, R. and Toyoda, A. and Suzuki, Y. and Kagoshima, H. and Schijlen, E. and Tajeshwar, N. and Catarino, B. and Hetherington, A. J. and Saltykova, A. and Bonnot, C. and Breuninger, H. and Symeonidi, A. and Radhakrishnan, G. V. and Van Nieuwerburgh, F. and Deforce, D. and Chang, C. and Karol, K. G. and Hedrich, R. and Ulvskov, P. and Glöckner, G. and Delwiche, C. F. and Petrášek, J. and Van de Peer, Y. and Friml, J. and Beilby, M. and Dolan, L. and Kohara, Y. and Sugano, S. and Fujiyama, A. and Delaux, P.-M. and Quint, M. and Theißen, G. and Hagemann, M. and Harholt, J. and Dunand, C. and Zachgo, S. and Langdale, J. and Maumus, F. and Van Der Straeten, D. and Gould, S. B. and Rensing, S. A.}, title = {{The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization}}, year = {2018}, pages = {448-464.e24}, journal = {Cell}, doi = {10.1016/j.cell.2018.06.033}, url = {https://www.sciencedirect.com/science/article/pii/S0092867418308018}, volume = {174}, abstract = {Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.} } @Article{IPB-2213, author = {Jablonická, V. and Ziegler, J. and Vatehová, Z. and Lišková, D. and Heilmann, I. and Obložinský, M. and Heilmann, M.}, title = {{Inhibition of phospholipases influences the metabolism of wound-induced benzylisoquinoline alkaloids in Papaver somniferum L.}}, year = {2018}, pages = {1-8}, journal = {J Plant Physiol}, doi = {10.1016/j.jplph.2018.01.007}, url = {https://dx.doi.org/10.1016/j.jplph.2018.01.007}, volume = {223}, abstract = {Benzylisoquinoline alkaloids (BIAs) are important secondary plant metabolites and include medicinally relevant drugs, such as morphine or codeine. As the de novo synthesis of BIA backbones is (still) unfeasible, to date the opium poppy plant Papaver somniferum L. represents the main source of BIAs. The formation of BIAs is induced in poppy plants by stress conditions, such as wounding or salt treatment; however, the details about regulatory processes controlling BIA formation in opium poppy are not well studied. Environmental stresses, such as wounding or salinization, are transduced in plants by phospholipid-based signaling pathways, which involve different classes of phospholipases. Here we investigate whether pharmacological inhibition of phospholipase A2 (PLA2, inhibited by aristolochic acid (AA)) or phospholipase D (PLD; inhibited by 5-fluoro-2-indolyl des-chlorohalopemide (FIPI)) in poppy plants influences wound-induced BIA accumulation and the expression of key biosynthetic genes. We show that inhibition of PLA2 results in increased morphinan biosynthesis concomitant with reduced production of BIAs of the papaverine branch, whereas inhibition of PLD results in increased production of BIAs of the noscapine branch. The data suggest that phospholipid-dependent signaling pathways contribute to the activation of morphine biosynthesis at the expense of the production of other BIAs in poppy plants. A better understanding of the effectors and the principles of regulation of alkaloid biosynthesis might be the basis for the future genetic modification of opium poppy to optimize BIA production.} } @Article{IPB-2237, author = {Wasternack, C. and Strnad, M.}, title = {{Jasmonates: News on Occurrence, Biosynthesis, Metabolism and Action of an Ancient Group of Signaling Compounds}}, year = {2018}, pages = {2539}, journal = {Int J Mol Sci}, doi = {10.3390/ijms19092539}, url = {https://dx.doi.org/10.3390/ijms19092539}, volume = {19}, abstract = {Jasmonic acid (JA) and its related derivatives are ubiquitously occurring compounds of land plants acting in numerous stress responses and development. Recent studies on evolution of JA and other oxylipins indicated conserved biosynthesis. JA formation is initiated by oxygenation of α-linolenic acid (α-LeA, 18:3) or 16:3 fatty acid of chloroplast membranes leading to 12-oxo-phytodienoic acid (OPDA) as intermediate compound, but in Marchantiapolymorpha and Physcomitrellapatens, OPDA and some of its derivatives are final products active in a conserved signaling pathway. JA formation and its metabolic conversion take place in chloroplasts, peroxisomes and cytosol, respectively. Metabolites of JA are formed in 12 different pathways leading to active, inactive and partially active compounds. The isoleucine conjugate of JA (JA-Ile) is the ligand of the receptor component COI1 in vascular plants, whereas in the bryophyte M. polymorpha COI1 perceives an OPDA derivative indicating its functionally conserved activity. JA-induced gene expressions in the numerous biotic and abiotic stress responses and development are initiated in a well-studied complex regulation by homeostasis of transcription factors functioning as repressors and activators.} } @Article{IPB-2184, author = {Mitra, D. and Kumari, P. and Quegwer, J. and Klemm, S. and Moeller, B. and Poeschl, Y. and Pflug, P. and Stamm, G. and Abel, S. and Bürstenbinder, K.}, title = {{Microtubule-associated protein IQ67 DOMAIN5 regulates interdigitation of leaf pavement cells in Arabidopsis thaliana}}, year = {2018}, journal = {bioRxiv}, doi = {10.1101/268466}, url = {https://www.biorxiv.org/content/early/2018/02/20/268466}, abstract = {Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation and cell morphology. Its organization and dynamics are coordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis, as indicated by reduced interdigitation of neighboring cells in the leaf epidermis of iqd5 mutants. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced asymmetric expansion. Lastly, we provide evidence for IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays. Our work thus identifies IQD5 as a novel player in PC shape regulation, and, for the first time, links calcium signaling to developmental processes that regulate multi-polar growth in PCs.} } @Article{IPB-2248, author = {Anwer, U. and Davis, A. and Davis, S. J. and Quint, M.}, title = {{Photoperiod sensing of the circadian clock is controlled by ELF3 and GI}}, year = {2018}, journal = {BioRxiv}, doi = {10.1101/321794}, url = {https://doi.org/10.1101/321794}, abstract = {ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth during the night and the day, respectively. We also provide evidence that ELF3, for which so far only a growth inhibitory role has been reported, can also act as a growth promoter under certain conditions. Finally, circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by manipulating the combination of these two key genes.} } @Article{IPB-2151, author = {Abel, S. }, title = {{Phosphate scouting by root tips.}}, year = {2017}, pages = {168-177}, journal = {Curr Opin Plant Biol.}, doi = {10.1016/j.pbi.2017.04.016}, url = {http://www.sciencedirect.com/science/article/pii/S1369526617300390}, volume = {39}, abstract = {Chemistry assigns phosphate (Pi) dominant roles in metabolism; however, it also renders the macronutrient a genuinely limiting factor of plant productivity. Pi bioavailability is restricted by low Pi mobility in soil and antagonized by metallic toxicities, which force roots to actively seek and selectively acquire the vital element. During the past few years, a first conceptual outline has emerged of the sensory mechanisms at root tips, which monitor external Pi and transmit the edaphic cue to inform root development. This review highlights new aspects of the Pi acquisition strategy of Arabidopsis roots, as well as a framework of local Pi sensing in the context of antagonistic interactions between Pi and its major associated metallic cations, Fe3+ and Al3+.} } @Article{IPB-2063, author = {Bürstenbinder, K. and Möller, B. and Plötner and R. and Stamm, G. and Hause, G. and Mitra, D. and Abel, S.}, title = {{The IQD family of calmodulin-binding proteins links calcium signaling to microtubules, membrane subdomains, and the nucleus.}}, year = {2017}, pages = {1692-1708}, journal = {Plant Physiol}, doi = {10.1104/pp.16.01743}, url = {http://www.plantphysiol.org/content/173/3/1692}, volume = {173}, abstract = {Calcium (Ca2+) signaling and dynamic reorganization of the cytoskeleton are essential processes for the coordination and control of plant cell shape and cell growth. Calmodulin (CaM) and closely related CaM-like polypeptides (CML) are principal sensors of Ca2+ signals. CaM/CMLs decode and relay information encrypted by the second messenger via differential interactions with a wide spectrum of targets to modulate their diverse biochemical activities. The plant-specific IQ67-DOMAIN (IQD) family emerged as the possibly largest class of CaM interacting proteins with undefined molecular functions and biological roles. Here, we show that the 33 members of the IQD family in Arabidopsis thaliana differentially localize, using GFP-tagged proteins, to multiple and distinct subcellular sites, including microtubule (MT) arrays, plasma membrane microdomains, and nuclear compartments. Intriguingly, the various IQD-specific localization patterns coincide with the subcellular patterns of IQD-dependent recruitment of CaM, suggesting that the diverse IQD members sequester Ca2+-CaM signaling modules to specific subcellular sites for precise regulation of Ca2+-dependent processes. Because MT localization is a hallmark of most IQD family members, we quantitatively analyzed GFP-labeled MT arrays in tobacco cells transiently expressing GFP-IQD fusions and observed IQD-specific MT patterns, which point to a role of IQDs in MT organization and dynamics. Indeed, stable overexpression of select IQD proteins in Arabidopsis altered cellular MT orientation, cell shape, and organ morphology. Because IQDs share biochemical properties with scaffold proteins, we propose that IQD families provide an assortment of platform proteins for integrating CaM-dependent Ca2+ signaling at multiple cellular sites to regulate cell function, shape, and growth. } } @Article{IPB-2091, author = {Winkler, M. and Niemeyer, M. and Hellmuth, A. and Janitza, P. and Christ, G. and Samodelov, S. L. and Wilde, V. and Majovsky, P. and Trujillo, M. and Zurbriggen, M. D. and Hoehenwarter, W. and Quint, M. and Calderón Villalobos, L. I. A.}, title = {{Variation in auxin sensing guides AUX/IAA transcriptional repressor ubiquitylation and destruction.}}, year = {2017}, pages = {15706}, journal = { Nature Commun.}, doi = {10.1038/ncomms15706}, url = {https://www.nature.com/articles/ncomms15706}, volume = {8}, abstract = {Auxin is a small molecule morphogen that bridges SCFTIR1/AFB-AUX/IAA co-receptor interactions leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. We show that TIR1-IAA19 and TIR1-IAA6 have distinct auxin affinities that correlate with ubiquitylation and turnover dynamics of the AUX/IAA. We establish a system to track AUX/IAA ubiquitylation in IAA6 and IAA19 in vitro and show that it occurs in flexible hotspots in degron-flanking regions adorned with specific Lys residues. We propose that this signature is exploited during auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologues, that discriminates the range of auxin concentrations found in plants. We postulate that the intrinsic flexibility of AUX/IAAs might bias their ubiquitylation and destruction kinetics enabling specific auxin responses.} } @Article{IPB-2087, author = {Balzergue, C. and Dartevelle, T. and Godon, C. and Laugier, E. and Meisrimler, C. and Teulon, J.-M. and Creff, A. and Bissler, M. and Brouchoud, C. and Hagège, A. and Müller, J. and Chiarenza, S. and Javot, H. and Becuwe-Linka, N. and David, P. and Péret, B. and Delannoy, E. and Thibaud, M.-C. and Armengaud, J. and Abel, S. and Pellequer, J.-L. and Nussaume, L. and Desnos, T. }, title = {{Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation}}, year = {2017}, pages = {15300}, journal = {Nat Commun}, doi = {10.1038/ncomms15300}, url = {https://www.nature.com/articles/ncomms15300}, volume = {8}, abstract = {Environmental cues profoundly modulate cell proliferation and cell elongation to inform and direct plant growth and development. External phosphate (Pi) limitation inhibits primary root growth in many plant species. However, the underlying Pi sensory mechanisms are unknown. Here we genetically uncouple two Pi sensing pathways in the root apex of Arabidopsis thaliana. First, the rapid inhibition of cell elongation in the transition zone is controlled by transcription factor STOP1, by its direct target, ALMT1, encoding a malate channel, and by ferroxidase LPR1, which together mediate Fe and peroxidase-dependent cell wall stiffening. Second, during the subsequent slow inhibition of cell proliferation in the apical meristem, which is mediated by LPR1-dependent, but largely STOP1–ALMT1-independent, Fe and callose accumulate in the stem cell niche, leading to meristem reduction. Our work uncovers STOP1 and ALMT1 as a signalling pathway of low Pi availability and exuded malate as an unexpected apoplastic inhibitor of root cell wall expansion.} } @Article{IPB-2016, author = {Wasternack, C. and Song, S.}, title = {{Jasmonates: biosynthesis, metabolism, and signaling by proteins activating and repressing transciption}}, year = {2017}, pages = {1303-1321}, journal = {J Exp Bot}, doi = {10.1093/jxb/erw443}, url = {http://jxb.oxfordjournals.org/content/early/2016/12/10/jxb.erw443.abstract}, volume = {68}, abstract = {The lipid-derived phytohormone jasmonate (JA) regulates plant growth, development, secondary metabolism, defense against insect attack and pathogen infection, and tolerance to abiotic stresses such as wounding, UV light, salt, and drought. JA was first identified in 1962, and since the 1980s many studies have analyzed the physiological functions, biosynthesis, distribution, metabolism, perception, signaling, and crosstalk of JA, greatly expanding our knowledge of the hormone’s action. In response to fluctuating environmental cues and transient endogenous signals, the occurrence of multilayered organization of biosynthesis and inactivation of JA, and activation and repression of the COI1–JAZ-based perception and signaling contributes to the fine-tuning of JA responses. This review describes the JA biosynthetic enzymes in terms of gene families, enzymatic activity, location and regulation, substrate specificity and products, the metabolic pathways in converting JA to activate or inactivate compounds, JA signaling in perception, and the co-existence of signaling activators and repressors} } @Article{IPB-2021, author = {Trenner, J. and Poeschl, Y. and Grau, J. and Gogol-Döring, A. and Quint, M. and Delker, C.}, title = {{Auxin-induced expression divergence between Arabidopsis species may originate within the TIR1/AFB–AUX/IAA–ARF module}}, year = {2017}, pages = {539-552}, journal = {J Exp Bot}, doi = {10.1093/jxb/erw457}, url = {https://academic.oup.com/jxb/article/68/3/539/2733323/Auxin-induced-expression-divergence-between?searchresult=1}, volume = {68}, abstract = {Auxin is an essential regulator of plant growth and development, and auxin signaling components are conserved among land plants. Yet, a remarkable degree of natural variation in physiological and transcriptional auxin responses has been described among Arabidopsis thaliana accessions. As intraspecies comparisons offer only limited genetic variation, we here inspect the variation of auxin responses between A. thaliana and A. lyrata. This approach allowed the identification of conserved auxin response genes including novel genes with potential relevance for auxin biology. Furthermore, promoter divergences were analyzed for putative sources of variation. De novo motif discovery identified novel and variants of known elements with potential relevance for auxin responses, emphasizing the complex, and yet elusive, code of element combinations accounting for the diversity in transcriptional auxin responses. Furthermore, network analysis revealed correlations of interspecies differences in the expression of AUX/IAA gene clusters and classic auxin-related genes. We conclude that variation in general transcriptional and physiological auxin responses may originate substantially from functional or transcriptional variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that respect, AUX/IAA gene expression divergence potentially reflects differences in the manner in which different species transduce identical auxin signals into gene expression responses.} } @Article{IPB-2099, author = {Ziegler, J. and Schmidt, S. and Strehmel, N. and Scheel, D. and Abel, S.}, title = {{Arabidopsis Transporter ABCG37/PDR9 contributes primarily highly oxygenated Coumarins to Root Exudation}}, year = {2017}, pages = {3704}, journal = {Sci Rep}, doi = {10.1038/s41598-017-03250-6}, url = {https://www.nature.com/articles/s41598-017-03250-6}, volume = {7}, abstract = {The chemical composition of root exudates strongly impacts the interactions of plants with microorganisms in the rhizosphere and the efficiency of nutrient acquisition. Exudation of metabolites is in part mediated by ATP-binding cassette (ABC) transporters. In order to assess the contribution of individual ABC transporters to root exudation, we performed an LC-MS based non-targeted metabolite profiling of semi-polar metabolites accumulating in root exudates of Arabidopsis thaliana plants and mutants deficient in the expression of ABCG36 (PDR8/PEN3), ABCG37 (PDR9) or both transporters. Comparison of the metabolite profiles indicated distinct roles for each ABC transporter in root exudation. Thymidine exudation could be attributed to ABCG36 function, whereas coumarin exudation was strongly reduced only in ABCG37 deficient plants. However, coumarin exudation was compromised in abcg37 mutants only with respect to certain metabolites of this substance class. The specificity of ABCG37 for individual coumarins was further verified by a targeted LC-MS based coumarin profiling method. The response to iron deficiency, which is known to strongly induce coumarin exudation, was also investigated. In either treatment, the distribution of individual coumarins between roots and exudates in the investigated genotypes suggested the involvement of ABCG37 in the exudation specifically of highly oxygenated rather than monohydroxylated coumarins.} } @Article{IPB-2195, author = {Ibañez, C. and Poeschl, Y. and Peterson, T. and Bellstädt, J. and Denk, K. and Gogol-Döring, A. and Quint, M. and Delker, C.}, title = {{Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana}}, year = {2017}, pages = {114}, journal = {BMC Plant Biol}, doi = {10.1186/s12870-017-1068-5}, url = {https://dx.doi.org/10.1186/s12870-017-1068-5}, volume = {17}, abstract = {BackgroundGlobal increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best.ResultsHere, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown under long day conditions in four different temperatures ranging from 16 to 28 °C. We used Q10, GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions.ConclusionGenotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.} } @Article{IPB-2103, author = {Wasternack, C.}, title = {{A plant's balance of growth and defense - revisited}}, year = {2017}, pages = {1291-1294}, journal = {New Phytol}, doi = {10.1111/nph.14720}, url = {http://onlinelibrary.wiley.com/doi/10.1111/nph.14720/abstract}, volume = {215}, abstract = {This article is a Commentary on Major et al., 215: 1533–1547.} } @Article{IPB-2245, author = {Ibañez, C. and Poeschl, Y. and Peterson, T. and Bellstädt, J. and Denk, K. and Gogol-Döring, A. and Quint, M. and Delker, C.}, title = {{Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana}}, year = {2017}, journal = {BioRxiv}, doi = {10.1101/017285}, url = {https://doi.org/10.1101/017285}, abstract = {Background: Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. Results: Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown in four different temperatures ranging from 16 to 28 °C. We used Q 10 , GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. Conclusion: Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.} } @Article{IPB-2101, author = {García, M. L. and Bó, E. D. and da Graça, J. V. and Gago-Zachert, S. and Hammond, J. and Moreno, P. and Natsuaki, T. and Pallás, V. and Navarro, J. A. and Reyes, C. A. and Luna, G. R. and Sasaya, T. and Tzanetakis, I. E. and Vaira, A. M. and Verbeek, M. and ICTV Report Consortium}, title = {{ICTV Virus Taxonomy Profile: Ophioviridae}}, year = {2017}, pages = {1161-1162}, journal = {J Gen Virol}, doi = {10.1099/jgv.0.000836}, url = {http://jgv.microbiologyresearch.org/content/journal/jgv/}, volume = {98 }, abstract = {Ophioviridae,The Ophioviridae is a family of filamentous plant viruses, with single-stranded negative, and possibly ambisense, RNA genomes of 11.3–12.5 kb divided into 3–4 segments, each encapsidated separately. Virions are naked filamentous nucleocapsids, forming kinked circles of at least two different contour lengths. The sole genus, Ophiovirus, includes seven species. Four ophioviruses are soil-transmitted and their natural hosts include trees, shrubs, vegetables and bulbous or corm-forming ornamentals, both monocots and dicots. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the which is available at http://www.ictv.global/report/ophioviridae.} } @Article{IPB-2119, author = {López-Carrasco, A. and Ballesteros, C. and Sentandreu, V. and Delgado, S. and Gago-Zachert, S. and Flores, R. and Sanjuán, R.}, title = {{Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing}}, year = {2017}, pages = {e1006547}, journal = {PLOS Pathog}, doi = {10.1371/journal.ppat.1006547}, url = {http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006547}, volume = {13}, abstract = {Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplast-replicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear potato spindle tuber viroid (PSTVd, Pospiviroidae). This revealed higher mutation frequencies in ELVd than in PSTVd, as well as marked differences in the types of mutations produced. Rates of spontaneous mutation, quantified in vivo using the lethal mutation method, ranged from 1/1000 to 1/800 for ELVd and from 1/7000 to 1/3800 for PSTVd depending on sequencing run. These results suggest that extremely high mutability is a common feature of chloroplastic viroids, whereas the mutation rates of PSTVd and potentially other nuclear viroids appear significantly lower and closer to those of some RNA viruses.} } @Article{IPB-2140, author = {Liu, S. and Ziegler, J. and Zeier, J. and Birkenbihl, R. P. and Somssich, I. E.}, title = {{Botrytis cinerea B05.10 promotes disease development in Arabidopsis by suppressing WRKY33-mediated host immunity}}, year = {2017}, pages = {2189-2206}, journal = {Plant Cell Environ}, doi = {10.1111/pce.13022}, url = {http://onlinelibrary.wiley.com/doi/10.1111/pce.13022/full}, volume = {40}, abstract = {The large WRKY transcription factor family is mainly involved in regulating plant immune responses. Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic processes towards Botrytis cinerea strain 2100 infection and is essential for resistance. In contrast to B. cinerea strain 2100, the strain B05.10 is virulent on wild-type (WT) Col-0 Arabidopsis plants highlighting the genetic diversity within this pathogen species. We analysed how early WRKY33-dependent responses are affected upon infection with strain B05.10 and found that most of these responses were strongly dampened during this interaction. Ectopic expression of WRKY33 resulted in complete resistance towards this strain indicating that virulence of B05.10, at least partly, depends on suppressing WRKY33 expression/protein accumulation. As a consequence, the expression levels of direct WRKY33 target genes, including those involved in the biosynthesis of camalexin, were also reduced upon infection. Concomitantly, elevated levels of the phytohormone abscisic acid (ABA) were observed. Molecular and genetic studies revealed that ABA negatively influences defence to B05.10 and effects jasmonic acid/ethylene (JA/ET) and salicylic acid (SA) levels. Susceptibility/resistance was determined by the antagonistic effect of ABA on JA, and this crosstalk required suppressing WRKY33 functions at early infection stages. This indicates that B. cinerea B05.10 promotes disease by suppressing WRKY33-mediated host defences.} } @Article{IPB-2159, author = {Gantner, J. and Ilse, T. and Ordon, J. and Kretschmer, C. and Gruetzner, R. and Loefke, C. and Dagdas, Y. and Buerstenbinder, K. and Marillonnet, S. and Stuttmann, J.}, title = {{Peripheral infrastructure vectors and an extended set of plant parts for the modular cloning system}}, year = {2017}, journal = {bioRxiv}, doi = {10.1101/237768}, url = {https://www.biorxiv.org/content/early/2017/12/21/237768}, abstract = {Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. This combinatorial assembly strategy meets the increasingly complex demands in biotechnology and bioengineering, and also represents a cost-efficient and versatile alternative to previous molecular cloning techniques. For Modular Cloning, a collection of commonly used Plant Parts was previously released together with the Modular Cloning toolkit itself, which largely facilitated the adoption of this cloning system in the research community. Here, a collection of approximately 80 additional phytobricks is provided. These phytobricks comprise e.g. modules for inducible expression systems, different promoters or epitope tags, which will increase the versatility of Modular Cloning-based DNA assemblies. Furthermore, first instances of a "peripheral infrastructure" around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. Additionally, DNA modules and assembly strategies for connecting Modular Cloning with Gateway Cloning are presented, which may serve as an interface between available resources and newly adopted hierarchical assembly strategies. The presented material will be provided as a toolkit to the plant research community and will further enhance the usefulness and versatility of Modular Cloning.} } @INBOOK{IPB-2102, author = {Flores, R. and Gago-Zachert, S. and De la Peña, M. and Navarro, B.}, title = {{Viroids and Satellite. - Academic Press}}, year = {2017}, pages = {331-338}, chapter = {{Chrysanthemum Chlorotic Mottle Viroid}}, editor = {Ed. A. Hadidi, et al.}, doi = {10.1016/B978-0-12-801498-1.00031-0}, url = {https://www.sciencedirect.com/science/article/pii/B9780128014981000310}, } @Article{IPB-2116, author = {Möller, B. and Pöschl, Y. and Plötner, R. and Bürstenbinder, K.}, title = {{PaCeQuant: A tool for high-throughput quantification of pavement cell shape characteristics}}, year = {2017}, pages = {988-1017}, journal = {Plant Physiol}, doi = {10.1104/pp.17.00961}, url = {http://www.plantphysiol.org/content/175/3/998}, volume = {175}, abstract = {Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw puzzle shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images, and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell-junctions and three-cell-junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools, and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets.} } @Article{IPB-2089, author = {Bürstenbinder, K. and Mitra, D. and Quegwer, J.}, title = {{Functions of IQD proteins as hubs in cellular calcium and auxin signaling: a toolbox for shape formation and tissue-specification in plants?}}, year = {2017}, pages = {e1331198}, journal = {Plant Signal Behav}, doi = {10.1080/15592324.2017.1331198}, url = {http://www.tandfonline.com/doi/full/10.1080/15592324.2017.1331198}, volume = {12 }, abstract = {Ca2+ ions play pivotal roles as second messengers in intracellular signal transduction, and coordinate many biological processes. Changes in intracellular Ca2+ levels are perceived by Ca2+ sensors such as CaM/CML proteins, which transduce Ca2+ signals into cellular responses by regulation of diverse target proteins. Insights into molecular functions of CaM targets are thus essential to understand the molecular and cellular basis of Ca2+ signaling. During the last decade, IQD proteins emerged as the largest class of CaM targets in plants with mostly unknown functions. In the March issue of Plant Physiology, we presented the first comprehensive characterization of the 33-membered IQD family in Arabidopsis thaliana. We showed, by analysis of the subcellular localization of translational GFP fusion proteins, that most IQD members label MTs, and additionally often localize to the cell nucleus or to membranes, where the recruit CaM Ca2+ sensors. Important functions at MTs are supported by altered MT organization and plant growth in IQD gain-of-function lines. Because IQD proteins share structural hallmarks of scaffold proteins, we propose roles of IQDs in the assembly of macromolecular complexes to orchestrate Ca2+ CaM signaling from membranes to the nucleus. } } @Article{IPB-2044, author = {Wasternack, C.}, title = {{The Trojan horse coronatine: the COI1–JAZ2–MYC2,3,4–ANAC019,055,072 module in stomata dynamics upon bacterial infection.}}, year = {2017}, pages = {972-975}, journal = {New Phytol}, doi = {10.1111/nph.14417}, url = {http://onlinelibrary.wiley.com/doi/10.1111/nph.2017.213.issue-3/issuetoc}, volume = {213}, abstract = {Coronatine (COR) is a phytotoxin produced by a plasmid-encoded operon of genes in several strains of Pseudomonas syringae (Bender et al., 1999). It is a mimic of the defense-associated phytohormone jasmonic acid isoleucine and delivered by the phytopathogenic bacterium to gain access to host plants through stomatal entry and to repress a specific sector of plant immunity. In this issue of New Phytologist (pp. 1378–1392) Gimenez-Ibanez et al. reveal exciting insights into the transcriptional regulation of COR/jasmonic acid isoleucine-governed transcriptional networks modulating stomatal aperture during bacterial invasion.} } @Article{IPB-1852, author = {Gago-Zachert, S.}, title = {{Viroids, infectious long non-coding RNAs with autonomous replication.}}, year = {2016}, pages = {12–24}, journal = {Virus Res.}, doi = {10.1016/j.virusres.2015.08.018}, url = {http://www.sciencedirect.com/science/journal/01681702}, volume = {212}, abstract = {Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.} } @Article{IPB-2250, author = {Drost, H.-J. and Gabel, A. and Domazet-Lošo, T. and Quint, M. and Grosse, I.}, title = {{Capturing Evolutionary Signatures in Transcriptomes with myTAI}}, year = {2016}, journal = {BioRxiv}, doi = {10.1101/051565}, url = {https://doi.org/10.1101/051565}, abstract = {Combining transcriptome data of biological processes or response to stimuli with evolutionary information such as the phylogenetic conservation of genes or their sequence divergence rates enables the investigation of evolutionary constraints on these processes or responses. Such phylotranscriptomic analyses recently unraveled that mid-developmental transcriptomes of fly, fish, and cress were dominated by evolutionarily conserved genes and genes under negative selection and thus recapitulated the developmental hourglass on the transcriptomic level. Here, we present a protocol for performing phylotranscriptomic analyses on any biological process of interest. When applying this protocol, users are capable of detecting different evolutionary constraints acting on different stages of the biological process of interest in any species. For each step of the protocol, modular and easy-to-use open-source software tools are provided, which enable a broad range of scientists to apply phylotranscriptomic analyses to a wide spectrum of biological questions.} } @Article{IPB-2246, author = {Trenner, J. and Poeschl, Y. and Grau, J. and Gogol-Döring, A. and Quint, M. and Delker, C.}, title = {{Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR1/AFB-AUX/IAA-ARF module}}, year = {2016}, journal = {BioRxiv}, doi = {10.1101/038422}, url = {https://doi.org/10.1101/038422}, abstract = {Auxin is an essential regulator of plant growth and development and auxin signaling components are conserved among land plants. Yet, a remarkable degree of natural variation in physiological and transcriptional auxin responses has been described among Arabidopsis thaliana accessions. As intra-species comparisons offer only limited genetic variation, we here inspect the variation of auxin responses between A. thaliana and A. lyrata. This approach allowed the identification of conserved auxin response genes including novel genes with potential relevance for auxin biology. Furthermore, promoter divergences were analyzed for putative sources of variation. De novo motif discovery identified novel and variants of known elements with potential relevance for auxin responses, emphasizing the complex, and yet elusive, code of element combinations accounting for the diversity in transcriptional auxin responses. Furthermore, network analysis revealed correlations of inter-species differences in the expression of AUX/IAA gene clusters and classic auxin-related genes. We conclude that variation in general transcriptional and physiological auxin responses may originate substantially from functional or transcriptional variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that respect, AUX/IAA gene expression divergence potentially reflects differences in the manner in which different species transduce identical auxin signals into gene expression responses.} } @Article{IPB-1849, author = {Dinesh, D. C. and Calderón Villalobos, L. I. A. and Abel, S.}, title = {{Structural Biology of Nuclear Auxin Action}}, year = {2016}, pages = {302-316}, journal = {Trends Plant Sci.}, doi = {10.1016/j.tplants.2015.10.019}, url = {https://www.sciencedirect.com/science/article/pii/S1360138515002782}, volume = {21}, abstract = {Auxin coordinates plant development largely via hierarchical control of gene expression. During the past decades, the study of early auxin genes paired with the power of Arabidopsis genetics have unraveled key nuclear components and molecular interactions that perceive the hormone and activate primary response genes. Recent research in the realm of structural biology allowed unprecedented insight into: (i) the recognition of auxin-responsive DNA elements by auxin transcription factors; (ii) the inactivation of those auxin response factors by early auxin-inducible repressors; and (iii) the activation of target genes by auxin-triggered repressor degradation. The biophysical studies reviewed here provide an impetus for elucidating the molecular determinants of the intricate interactions between core components of the nuclear auxin response module.} } @Article{IPB-1853, author = {Ziegler, J. and Schmidt, S. and Chutia, R. and Müller, J. and Böttcher, C. and Strehmel, N. and Scheel, D. and Abel, S.}, title = {{Non-targeted profiling of semi-polar metabolites in Arabidopsis root exudates uncovers a role for coumarin secretion and lignification during the local response to phosphate limitation.}}, year = {2016}, pages = {1421-1432}, journal = {J. Exp. Bot.}, doi = {10.1093/jxb/erv539}, url = {https://academic.oup.com/jxb/article/67/5/1421/2885100}, volume = {67}, abstract = {Plants have evolved two major strategies to cope with phosphate (Pi) limitation. The systemic response, mainly comprising increased Pi uptake and metabolic adjustments for more efficient Pi use, and the local response, enabling plants to explore Pi-rich soil patches by reorganization of the root system architecture. Unlike previous reports, this study focused on root exudation controlled by the local response to Pi deficiency. To approach this, a hydroponic system separating the local and systemic responses was developed. Arabidopsis thaliana genotypes exhibiting distinct sensitivities to Pi deficiency could be clearly distinguished by their root exudate composition as determined by non-targeted reversed-phase ultraperformance liquid chromatography electrospray ionization quadrupole-time-of-flight mass spectrometry metabolite profiling. Compared with wild-type plants or insensitive low phosphate root 1 and 2 (lpr1 lpr2) double mutant plants, the hypersensitive phosphate deficiency response 2 (pdr2) mutant exhibited a reduced number of differential features in root exudates after Pi starvation, suggesting the involvement of PDR2-encoded P5-type ATPase in root exudation. Identification and analysis of coumarins revealed common and antagonistic regulatory pathways between Pi and Fe deficiency-induced coumarin secretion. The accumulation of oligolignols in root exudates after Pi deficiency was inversely correlated with Pi starvation-induced lignification at the root tips. The strongest oligolignol accumulation in root exudates was observed for the insensitive lpr1 lpr2 double mutant, which was accompanied by the absence of Pi deficiency-induced lignin deposition, suggesting a role of LPR ferroxidases in lignin polymerization during Pi starvation. } } @Article{IPB-1934, author = {Drost, H.-G. and Bellstädt, J. and Ó'Maoiléidigh, D. S. and Silva, A. T. and Gabel, A. and Weinholdt, C. and Ryan, P. T. and Dekkers, B. J. W. and Bentsink, L. and Hilhorst, H. W. M. and Ligterink, W. and Wellmer, F. and Grosse, I. and Quint, M.}, title = {{Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development}}, year = {2016}, pages = {1158-1163}, journal = {Mol Biol Evol}, doi = {10.1093/molbev/msw039}, url = {https://academic.oup.com/mbe/article/33/5/1158/2580081}, volume = {33}, abstract = {The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found postembryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints. } } @Article{IPB-2012, author = {Wasternack, C. and Hause, B.}, title = {{OPDA-Ile – a new JA-Ile-independent signal?}}, year = {2016}, pages = {e125364600}, journal = {Plant Signaling \& Behavior}, doi = {10.1080/15592324.2016.1253646}, url = {http://www.tandfonline.com/doi/full/10.1080/15592324.2016.1253646}, volume = {11}, abstract = {AbstractExpression takes place for most of the jasmonic acid (JA)-induced genes in a COI1- dependent manner via perception of its conjugate JA-Ile in the SCFCOI1-JAZ co-receptor complex. There are, however, numerous genes and processes, which are preferentially induced COI1-independently by the precursor of JA, 12-oxo-phytodienoic acid (OPDA). After recent identification of the Ile-conjugate of OPDA, OPDA-Ile, biological activity of this compound could be unequivocally proven in terms of gene expression. Any interference of OPDA, JA, or JA-Ile in OPDA-Ile-induced gene expression could be excluded by using different genetic background. The data suggest individual signaling properties of OPDA-Ile. Future studies for analysis of an SCFCOI1-JAZ co-receptor-independent route of signaling are proposed.} } @Article{IPB-2388, author = {Gharsallah, C. and Fakhfakh, H. and Grubb, D. and Gorsane, F.}, title = {{Effect of salt stress on ion concentration, proline content, antioxidant enzyme activities and gene expression in tomato cultivars}}, year = {2016}, pages = {plw055}, journal = {AoB PLANTS}, doi = {10.1093/aobpla/plw055}, url = {https://dx.doi.org/10.1093/aobpla/plw055}, volume = {8}, abstract = {Salinity is a constraint limiting plant growth and productivity of crops throughout the world. Understanding the mechanism underlying plant response to salinity provides new insights into the improvement of salt tolerance-crops of importance. In the present study, we report on the responses of twenty cultivars of tomato. We have clustered genotypes into scale classes according to their response to increased NaCl levels. Three local tomato genotypes, representative of different saline scale classes, were selected for further investigation. During early (0 h, 6 h and 12 h) and later (7 days) stages of the response to salt treatment, ion concentrations (Na + , K +  and Ca 2+ ), proline content, enzyme activities (catalase, ascorbate peroxidase and guiacol peroxidase) were recorded. qPCR analysis of candidate genes WRKY (8, 31and 39), ERF (9, 16 and 80), LeNHX (1, 3 and 4) and HKT (class I) were performed. A high K + , Ca 2 + and proline accumulation as well as a decrease of Na +  concentration-mediated salt tolerance. Concomitant with a pattern of high-antioxidant enzyme activities, tolerant genotypes also displayed differential patterns of gene expression during the response to salt stress.} } @Article{IPB-1961, author = {Gasperini, D. and Acosta, I. F. and Farmer, E. E.}, title = {{Cotyledon Wounding of Arabidopsis Seedlings.}}, year = {2016}, pages = {e1712}, journal = {Bio-protocol}, doi = {10.21769/BioProtoc.1712}, url = {http://www.bio-protocol.org/e1712}, volume = {6 (2)}, } @Article{IPB-2019, author = {Kowalski, A. M. and Gooding, M. and Ferrante, A. and Slafer, G. A. and Orford, S. and Gasperini, D. and Griffiths, S.}, title = {{Agronomic assessment of the wheat semi-dwarfing gene Rht8 in contrasting nitrogen treatments and water regimes}}, year = {2016}, pages = {150-160}, journal = { Field Crop Res}, doi = {10.1016/j.fcr.2016.02.026}, url = {http://www.sciencedirect.com/science/article/pii/S0378429016300521}, volume = {191}, abstract = {Reduced height 8 (Rht8) is the main alternative to the GA-insensitive Rht alleles in hot and dry environments where it reduces plant height without yield penalty. The potential of Rht8 in northern-European wheat breeding remains unclear, since the close linkage with the photoperiod-insensitive allele Ppd-D1a is unfavourable in the relatively cool summers. In the present study, two near-isogenic lines (NILs) contrasting for the Rht8/tall allele from Mara in a UK-adapted and photoperiod-sensitive wheat variety were evaluated in trials with varying nitrogen fertiliser (N) treatments and water regimes across sites in the UK and Spain.The Rht8 introgression was associated with a robust height reduction of 11% regardless of N treatment and water regime and the Rht8 NIL was more resistant to root-lodging at agronomically-relevant N levels than the tall NIL. In the UK with reduced solar radiation over the growing season than the site in Spain, the Rht8 NIL showed a 10% yield penalty at standard agronomic N levels due to concomitant reduction in grain number and spike number whereas grain weight and harvest index were not significantly different to the tall NIL. The yield penalty associated with the Rht8 introgression was overcome at low N and in irrigated conditions in the UK, and in the high-temperature site in Spain. Decreased spike length and constant spikelet number in the Rht8 NIL resulted in spike compaction of 15%, independent of N and water regime. The genetic interval of Rht8 overlaps with the compactum gene on 2DS, raising the possibility of the same causative gene. Further genetic dissection of these loci is required.Abbreviations ANOVA, analysis of variance; Y, yield; HI, harvest index; GN, grain number (m−2); SS, spikelet number (spike−1); SN, spike number (m−2); HD, heading date; AN, anthesis; 12L, length of the second internode from the top; 13L, length of the third internode from the top; PAR, photosynthetically active radiation; R: FR, red: far-red light reflectance ratio; RCBD, randomised complete block design} } @INBOOK{IPB-1935, author = {Hellmuth, A. and Calderón Villalobos, L. I. A.}, title = {{Plant Proteostasis}}, year = {2016}, pages = {23-34}, chapter = {{Radioligand Binding Assays for Determining Dissociation Constants of Phytohormone Receptors}}, journal = {Meth. Mol. Biol}, editor = {Lois, L. M.; Matthiesen, R. }, doi = {10.1007/978-1-4939-3759-2_3}, url = {http://link.springer.com/book/10.1007/978-1-4939-3759-2}, volume = {1450}, abstract = {In receptor–ligand interactions, dissociation constants provide a key parameter for characterizing binding. Here, we describe filter-based radioligand binding assays at equilibrium, either varying ligand concentrations up to receptor saturation or outcompeting ligand from its receptor with increasing concentrations of ligand analogue. Using the auxin coreceptor system, we illustrate how to use a saturation binding assay to determine the apparent dissociation constant (K D ′ ) for the formation of a ternary TIR1–auxin–AUX/IAA complex. Also, we show how to determine the inhibitory constant (K i) for auxin binding by the coreceptor complex via a competition binding assay. These assays can be applied broadly to characterize a one-site binding reaction of a hormone to its receptor.} } @Article{IPB-1902, author = {Strehmel, N. and Mönchgesang,S. and Herklotz, S. and Krüger, S. and Ziegler, J. and Scheel, D.}, title = {{Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana.}}, year = {2016}, pages = {1091}, journal = {Int. J. Mol. Sci.}, doi = {10.3390/ijms17071091}, url = {http://www.mdpi.com/journal/ijms}, volume = {17}, abstract = {Piriformospora indica is a root-colonizing fungus, which interacts with a variety of plants including Arabidopsis thaliana. This interaction has been considered as mutualistic leading to growth promotion of the host. So far, only indolic glucosinolates and phytohormones have been identified as key players. In a comprehensive non-targeted metabolite profiling study, we analyzed Arabidopsis thaliana’s roots, root exudates, and leaves of inoculated and non-inoculated plants by ultra performance liquid chromatography/electrospray ionization quadrupole-time-of-flight mass spectrometry (UPLC/(ESI)-QTOFMS) and gas chromatography/electron ionization quadrupole mass spectrometry (GC/EI-QMS), and identified further biomarkers. Among them, the concentration of nucleosides, dipeptides, oligolignols, and glucosinolate degradation products was affected in the exudates. In the root profiles, nearly all metabolite levels increased upon co-cultivation, like carbohydrates, organic acids, amino acids, glucosinolates, oligolignols, and flavonoids. In the leaf profiles, we detected by far less significant changes. We only observed an increased concentration of organic acids, carbohydrates, ascorbate, glucosinolates and hydroxycinnamic acids, and a decreased concentration of nitrogen-rich amino acids in inoculated plants. These findings contribute to the understanding of symbiotic interactions between plant roots and fungi of the order of Sebacinales and are a valid source for follow-up mechanistic studies, because these symbioses are particular and clearly different from interactions of roots with mycorrhizal fungi or dark septate endophytes } } @Article{IPB-1933, author = {López-Carrasco, A. and Gago-Zachert, S. and Mileti, G. and Minoia, S. and Flores, R. and Delgado, S.}, title = {{The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their in vivo RNA conformations}}, year = {2016}, pages = {83-97}, journal = {RNA Biology}, doi = {10.1080/15476286.2015.1119365}, url = {http://www.tandfonline.com/loi/krnb20}, volume = {13}, abstract = {Eggplant latent viroid (ELVd), like other members of family Avsunviroidae, replicates in plastids through a symmetric rolling-circle mechanism in which elongation of RNA strands is most likely catalyzed by a nuclear-encoded polymerase (NEP) translocated to plastids. Here we have addressed where NEP initiates transcription of viroid strands. Because this step is presumably directed by sequence/structural motifs, we have previously determined the conformation of the monomeric linear (+) and (−) RNAs of ELVd resulting from hammerhead-mediated self-cleavage. In silico predictions with 3 softwares led to similar bifurcated conformations for both ELVd strands. In vitro examination by non-denaturing PAGE showed that they migrate as prominent single bands, with the ELVd (+) RNA displaying a more compact conformation as revealed by its faster electrophoretic mobility. In vitro SHAPE analysis corroborated the ELVd conformations derived from thermodynamics-based predictions in silico. Moreover, sequence analysis of 94 full-length natural ELVd variants disclosed co-variations, and mutations converting canonical into wobble pairs or vice versa, which confirmed in vivo most of the stems predicted in silico and in vitro, and additionally helped to introduce minor structural refinements. Therefore, results from the 3 experimental approaches were essentially consistent among themselves. Application to RNA preparations from ELVd-infected tissue of RNA ligase-mediated rapid amplification of cDNA ends, combined with pretreatments to modify the 5′ ends of viroid strands, mapped the transcription initiation sites of ELVd (+) and (−) strands in vivo at different sequence/structural motifs, in contrast with the situation previously observed in 2 other members of the family Avsunviroidae.} } @Article{IPB-1859, author = {Quint, M. and Delker, C. and Franklin, K. A. and Wigge, P. A. and Halliday, K. J. and van Zanten, M.}, title = {{Molecular and genetic control of plant thermomorphogenesis.}}, year = {2016}, pages = {15190}, journal = {Nat Plants }, doi = {10.1038/nplants.2015.190}, url = {http://www.nature.com/nplants/}, volume = {2}, abstract = {Temperature is a major factor governing the distribution and seasonal behaviour of plants. Being sessile, plants are highly responsive to small differences in temperature and adjust their growth and development accordingly. The suite of morphological and architectural changes induced by high ambient temperatures, below the heat-stress range, is collectively called thermomorphogenesis. Understanding the molecular genetic circuitries underlying thermomorphogenesis is particularly relevant in the context of climate change, as this knowledge will be key to rational breeding for thermo-tolerant crop varieties. Until recently, the fundamental mechanisms of temperature perception and signalling remained unknown. Our understanding of temperature signalling is now progressing, mainly by exploiting the model plant Arabidopsis thaliana. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) has emerged as a critical player in regulating phytohormone levels and their activity. To control thermomorphogenesis, multiple regulatory circuits are in place to modulate PIF4 levels, activity and downstream mechanisms. Thermomorphogenesis is integrally governed by various light signalling pathways, the circadian clock, epigenetic mechanisms and chromatin-level regulation. In this Review, we summarize recent progress in the field and discuss how the emerging knowledge in Arabidopsis may be transferred to relevant crop systems.The year 2015 is on track to surpass 2014 as the warmest year ever recorded since systematic temperature measurements began more than a century ago1. In fact, the 10 warmest years on record all occurred after 1998. The fifth report of the Intergovernmental Panel on Climate Change2 projects an increase of 0.8–4.8 °C in global mean surface temperature within the twenty-first century. Such figures are alarming as it is expected that this will strongly affect plant distribution and survival, and therefore threaten biodiversity3,​4,​5,​6,​7,​8,​9,​10,​11. Some studies already indicate that plant species unable to adjust flowering time in response to temperature are disappearing from certain environments5, and species tend to shift to higher altitudes and latitudes12.Likewise, crop productivity will probably suffer greatly from global warming, while food production is required to increase significantly to sustain a growing and more demanding world population9,13,​14,​15. A meta-analysis summarizing more than 1,700 studies on the effects of climate change and adaptations on crop yields revealed consensus that in the second half of this century, climate warming is likely to have a negative effect on yields of important staple crops13.Breeding for crop-level adaptations to cope with high temperatures could potentially reverse this negative trend9,13,​14,​15. In several plant species, mechanisms have evolved to adapt growth and morphology to stimulate mitigation of warmth through enhanced evaporative cooling, increased convection and direct avoidance of heat flux from the Sun16,​17,​18,​19,​20. If understood, the underlying molecular processes of these so-called thermomorphogenesis responses could be attractive breeding targets for improving crops to withstand climate warming.Although abundant literature is available on how plants tolerate extreme heat stress (reviewed in refs 9,21), we are only beginning to understand the molecular mechanisms underlying thermomorphogenesis in response to moderately increased temperatures. A key breakthrough was the identification of the bHLH (basic helix–loop–helix) transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) as a central regulator of ambient temperature signalling in Arabidopsis22. Recent findings have implicated important roles for light signalling pathways, the circadian clock23,​24,​25,​26,​27,​28, auxin22,29,​30,​31 and other phytohormones31,​32,​33,​34 in PIF4-mediated temperature-induced growth. Furthermore, epigenetic mechanisms appear at the nexus of induction35 and attenuation36 of growth acclimation in response to high ambient temperatures.Here we discuss and integrate recent findings on the molecular networks driving thermomorphogenic adaptations. We will highlight missing links and suggest how the knowledge on Arabidopsis could be transferred to crops. In addition to thermomorphogenesis, adaptation to high ambient temperature also involves physiological processes such as photosynthetic acclimation, respiration and changes in carbon balance. For discussions of these topics as well as on phenological changes including premature flowering, we refer the reader to reviews elsewhere20,37,​38,​39.} } @Article{IPB-1894, author = {Hoehenwarter, W. and Mönchgesang, S. and Neumann, S. and Majovsky, P. and Abel, S. and Müller, J.}, title = {{Comparative expression profiling reveals a role of the root apoplast in local phosphate response}}, year = {2016}, pages = {106}, journal = {BMC Plant Biol.}, doi = {10.1186/s12870-016-0790-8}, url = {http://www.biomedcentral.com/search?query=Hoehenwarter&searchType=publisherSearch}, volume = {16 }, abstract = {Plant adaptation to limited phosphate availability comprises a wide range of responses to conserve and remobilize internal phosphate sources and to enhance phosphate acquisition. Vigorous restructuring of root system architecture provides a developmental strategy for topsoil exploration and phosphate scavenging. Changes in external phosphate availability are locally sensed at root tips and adjust root growth by modulating cell expansion and cell division. The functionally interacting Arabidopsis genes, LOW PHOSPHATE RESPONSE 1 and 2 (LPR1/LPR2) and PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2), are key components of root phosphate sensing. We recently demonstrated that the LOW PHOSPHATE RESPONSE 1 - PHOSPHATE DEFICIENCY RESPONSE 2 (LPR1-PDR2) module mediates apoplastic deposition of ferric iron (Fe3+) in the growing root tip during phosphate limitation. Iron deposition coincides with sites of reactive oxygen species generation and triggers cell wall thickening and callose accumulation, which interfere with cell-to-cell communication and inhibit root growth.} } @Article{IPB-1838, author = {Wasternack, C. and Strnad, M.}, title = {{Jasmonate signaling in plant stress responses and development – active and inactive compounds}}, year = {2016}, pages = {604-613}, journal = {New Biotechnology}, doi = {10.1016/j.nbt.2015.11.001}, url = {http://www.sciencedirect.com/science/journal/18716784}, volume = {33 B}, abstract = {Jasmonates (JAs) are lipid-derived signals mediating plant responses to biotic and abiotic stresses and in plant development. Following the elucidation of each step in their biosynthesis and the important components of perception and signaling, several activators, repressors and co-repressors have been identified which contribute to fine-tuning the regulation of JA-induced gene expression. Many of the metabolic reactions in which JA participates, such as conjugation with amino acids, glucosylation, hydroxylation, carboxylation, sulfation and methylation, lead to numerous compounds with different biological activities. These metabolites may be highly active, partially active in specific processes or inactive. Hydroxylation, carboxylation and sulfation inactivate JA signaling. The precursor of JA biosynthesis, 12-oxo-phytodienoic acid (OPDA), has been identified as a JA-independent signaling compound. An increasing number of OPDA-specific processes is being identified. To conclude, the numerous JA compounds and their different modes of action allow plants to respond specifically and flexibly to alterations in the environment.} } @Article{IPB-1851, author = {Floková, K. and Feussner, K. and Herrfurth, C. and Miersch, O. and Mik, V. and Tarkowská, D. and Strnad, M. and Feussner, I. and Wasternack, C. and Novák, O.}, title = {{A previously undescribed jasmonate compound in flowering Arabidopsis thaliana – The identification of cis-(+)-OPDA-Ile.}}, year = {2016}, pages = {230-237}, journal = {Phytochemistry}, doi = {10.1016/j.phytochem.2015.11.012}, volume = {122}, abstract = {Jasmonates (JAs) are plant hormones that integrate external stress stimuli with physiological responses. (+)-7-iso-JA-L-Ile is the natural JA ligand of COI1, a component of a known JA receptor. The upstream JA biosynthetic precursor cis-(+)-12-oxo-phytodienoic acid (cis-(+)-OPDA) has been reported to act independently of COI1 as an essential signal in several stress-induced and developmental processes. Wound-induced increases in the endogenous levels of JA/JA-Ile are accompanied by two to tenfold increases in the concentration of OPDA, but its means of perception and metabolism are unknown. To screen for putative OPDA metabolites, vegetative tissues of flowering Arabidopsis thaliana were extracted with 25% aqueous methanol (v/v), purified by single-step reversed-phase polymer-based solid-phase extraction, and analyzed by high throughput mass spectrometry. This enabled the detection and quantitation of a low abundant OPDA analog of the biologically active (+)-7-iso-JA-L-Ile in plant tissue samples. Levels of the newly identified compound and the related phytohormones JA, JA-Ile and cis-(+)-OPDA were monitored in wounded leaves of flowering Arabidopsis lines (Col-0 and Ws) and compared to the levels observed in Arabidopsis mutants deficient in the biosynthesis of JA (dde2-2, opr3) and JA-Ile (jar1). The observed cis-(+)-OPDA-Ile levels varied widely, raising questions concerning its role in Arabidopsis stress responses.} } @INBOOK{IPB-1718, author = {Tissier, A. and Ziegler, J. and Vogt, T.}, title = {{Ecological Biochemistry: Environmental and Interspecies Interactions}}, year = {2015}, pages = {14-37}, chapter = {{Specialized Plant Metabolites: Diversity and Biosynthesis}}, editor = {Krauss, G.-J. \& Nies, D. H., eds.}, doi = {10.1002/9783527686063.ch2}, url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527686063.ch2/summary}, abstract = {Plant secondary metabolites, also termed specialized plant metabolites, currently comprise more than 200 000 natural products that are all based on a few biosynthetic pathways and key primary metabolites. Some pathways like flavonoid and terpenoid biosynthesis are universally distributed in the plant kingdom, whereas others like alkaloid or cyanogenic glycoside biosynthesis are restricted to a limited set of taxa. Diversification is achieved by an array of mechanisms at the genetic and enzymatic level including gene duplications, substrate promiscuity of enzymes, cell‐specific regulatory systems, together with modularity and combinatorial aspects. Specialized metabolites reflect adaptations to a specific environment. The observed diversity illustrates the heterogeneity and multitude of ecological habitats and niches that plants have colonized so far and constitutes a reservoir of potential new metabolites that may provide adaptive advantage in the face of environmental changes. The code that connects the observed chemical diversity to this ecological diversity is largely unknown. One way to apprehend this diversity is to realize its tremendous plasticity and evolutionary potential. This chapter presents an overview of the most widespread and popular secondary metabolites, which provide a definite advantage to adapt to or to colonize a particular environment, making the boundary between the “primary” and the “secondary” old fashioned and blurry.} } @Article{IPB-1802, author = {Liu, S. and Kracher, B. and Ziegler, J. and Birkenbihl, R. P. and Somssich, I. E.}, title = {{Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100}}, year = {2015}, pages = {e07295}, chapter = {{eLife}}, journal = {eLife}, doi = {10.7554/eLife.07295}, url = {http://elifesciences.org/content/4/e07295}, volume = {4}, abstract = {The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified \>1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.} } @Article{IPB-1850, author = {Drost, H.-G. and Gabel, A. and Grosse, I. and Quint, M.}, title = {{Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis}}, year = {2015}, pages = {1221-1231}, journal = {Mol Biol Evol}, doi = {10.1093/molbev/msv012}, url = {http://mbe.oxfordjournals.org/content/32/5.toc}, volume = {32}, abstract = {The developmental hourglass model has been used to describe the morphological transitions of related species throughout embryogenesis. Recently, quantifiable approaches combining transcriptomic and evolutionary information provided novel evidence for the presence of a phylotranscriptomic hourglass pattern across kingdoms. As its biological function is unknown it remains speculative whether this pattern is functional or merely represents a nonfunctional evolutionary relic. The latter would seriously hamper future experimental approaches designed to test hypotheses regarding its function. Here, we address this question by generating transcriptome divergence index (TDI) profiles across embryogenesis of Danio rerio, Drosophila melanogaster, and Arabidopsis thaliana. To enable meaningful evaluation of the resulting patterns, we develop a statistical test that specifically assesses potential hourglass patterns. Based on this objective measure we find that two of these profiles follow a statistically significant hourglass pattern with the most conserved transcriptomes in the phylotypic periods. As the TDI considers only recent evolutionary signals, this indicates that the phylotranscriptomic hourglass pattern is not a rudiment but possibly actively maintained, implicating the existence of some linked biological function associated with embryogenesis in extant species.} } @Article{IPB-1804, author = {Wasternack, C.}, title = {{How Jasmonates Earned their Laurels: Past and Present}}, year = {2015}, pages = {761-794}, journal = {Journal of Plant Growth Regulation}, doi = {10.1007/s00344-015-9526-5}, volume = {34 (4)}, abstract = {The histories of research regarding all plant hormones are similar. Identification and structural elucidation have been followed by analyses of their biosynthesis, distributions, signaling cascades, roles in developmental or stress response programs, and crosstalk. Jasmonic acid (JA) and its derivatives comprise a group of plant hormones that were discovered recently, compared to auxin, abscisic acid, cytokinins, gibberellic acid, and ethylene. Nevertheless, there have been tremendous advances in JA research, following the general progression outlined above and parallel efforts focused on several other “new” plant hormones (brassinosteroids, salicylate, and strigolactones). This review focuses on historical aspects of the identification of jasmonates, and characterization of their biosynthesis, distribution, perception, signaling pathways, crosstalk with other hormones and roles in plant stress responses and development. The aim is to illustrate how our present knowledge on jasmonates was generated and how that influences current efforts to extend our knowledge.} } @Article{IPB-1770, author = {Guseman, J. M. and Hellmuth, A. and Lanctot, A. and Feldman, T. P. and Moss, B. L. and Klavins, E. and Calderón Villalobos, L. I. A. and Nemhauser, J. L.}, title = {{Auxin-induced degradation dynamics set the pace for lateral root development}}, year = {2015}, pages = {1-5}, journal = {Development}, doi = {10.1242/dev.117234}, url = {http://dev.biologists.org/content/early/2015/01/29/dev.117234.abstract?sid=44c8748f-9cc2-4f71-93df-bfbc96e0a0c2}, volume = {142}, abstract = {Auxin elicits diverse cell behaviors through a simple nuclear signaling pathway initiated by degradation of Aux/IAA co-repressors. Our previous work revealed that members of the large Arabidopsis Aux/IAA family exhibit a range of degradation rates in synthetic contexts. However, it remained an unresolved issue whether differences in Aux/IAA turnover rates played a significant role in plant responses to auxin. Here, we use the well-established model of lateral root development to directly test the hypothesis that the rate of auxin-induced Aux/IAA turnover sets the pace for auxin-regulated developmental events. We did this by generating transgenic plants expressing degradation rate variants of IAA14, a crucial determinant of lateral root initiation. Progression through the well-established stages of lateral root development was strongly correlated with the engineered rates of IAA14 turnover, leading to the conclusion that Aux/IAAs are auxin-initiated timers that synchronize developmental transitions} } @Article{IPB-1801, author = {Ryan,P. T. and Ó’Maoiléidigh, D. S. and Drost, H.-G. and Kwaśniewska, D. and Gabel, A. and Grosse, I. and Graciet, E. and Quint, M. and Wellmer, F.}, title = {{Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation}}, year = {2015}, pages = {488 }, journal = {BMC Genomics}, doi = {10.1186/s12864-015-1699-6}, url = { http://www.biomedcentral.com/content/pdf/s12864-015-1699-6.pdf}, volume = {16}, abstract = {Background:The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thalianaon a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to closethis information gap and to generate a reference dataset for stage-specific gene expression during flower formation.Results:Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups ofco-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We furtherfound that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.Conclusions:Our results highlight and describe the dynamic expression changes undergone by a large numberof genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.} } @Article{IPB-2249, author = {Raschke, A. and Ibañez, C. and Ullrich, K. K. and Anwer, M. U. and Becker, S. and Glöckner, A. and Trenner, J. and Denk, K. and Saal, B. and Sun, X. and Ni, M. and Davis, S. J. and Delker, C. and Quint, M.}, title = {{Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes}}, year = {2015}, journal = {BioRxiv}, doi = {10.1101/015305}, url = {https://doi.org/10.1101/015305}, abstract = {Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis. We identified GIRAFFE2.1, a major QTL explaining ~18% of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth. In combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod cues to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation.} } @Article{IPB-1818, author = {Raschke, A. and Ibañez, C. and Ullrich, K. K. and Anwer, M. U. and Becker, S. and Glöckner, A. and Trenner, J. and Denk, K. and Saal, B. and Sun, X. and Ni, M. and Davis, S. J. and Delker, C. and Quint, M.}, title = {{Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes}}, year = {2015}, pages = {197}, journal = {BMC Plant Biol.}, doi = {10.1186/s12870-015-0566-6}, url = {https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-015-0566-6}, volume = {15}, abstract = {BackgroundPerception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis.ResultsWe identified GIRAFFE2.1, a major QTL explaining ~18 % of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth.ConclusionsIn combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod information to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation. } } @Article{IPB-2243, author = {Drost, H.-G. and Bellstädt, J. and Ó'Maoiléidigh, D. S. and Silva, A. T. and Gabel, A. and Weinholdt, C. and Ryan, P. T. and Dekkers, B. J. W. and Bentsink, L. and Hilhorst, H. W. M. and Ligterink, W. and Wellmer, F. and Grosse, I. and Quint, M.}, title = {{Post-embryonic hourglass patterns mark ontogenetic transitions in plant development}}, year = {2015}, journal = {BioRxiv}, doi = {10.1101/035527}, url = {https://doi.org/10.1101/035527}, abstract = {The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found post-embryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.} } @Article{IPB-1788, author = {Müller, J. and Toev, T. and Heisters, M. and Teller, J. and Moore, K. L. and Hause, G. and Dinesh, D. C. and Bürstenbinder, K. and Abel, S.}, title = {{Iron-Dependent Callose Deposition Adjusts Root Meristem Maintenance to Phosphate Availability}}, year = {2015}, pages = {216–230}, journal = {Devel Cell}, doi = {10.1016/j.devcel.2015.02.007}, url = {http://www.sciencedirect.com/science/article/pii/S1534580715001094}, volume = {33}, abstract = {Plant root development is informed by numerous edaphic cues. Phosphate (Pi) availability impacts the root system architecture by adjusting meristem activity. However, the sensory mechanisms monitoring external Pi status are elusive. Two functionally interacting Arabidopsis genes, LPR1 (ferroxidase) and PDR2 (P5-type ATPase), are key players in root Pi sensing, which is modified by iron (Fe) availability. We show that the LPR1-PDR2 module facilitates, upon Pi limitation, cell-specific apoplastic Fe and callose deposition in the meristem and elongation zone of primary roots. Expression of cell-wall-targeted LPR1 determines the sites of Fe accumulation as well as callose production, which interferes with symplastic communication in the stem cell niche, as demonstrated by impaired SHORT-ROOT movement. Antagonistic interactions of Pi and Fe availability control primary root growth via meristem-specific callose formation, likely triggered by LPR1-dependent redox signaling. Our results link callose-regulated cell-to-cell signaling in root meristems to the perception of an abiotic cue} } @Article{IPB-1792, author = {Dinesh, D. C. and Kovermann, M. and Gopalswamy, M. and Hellmuth, A. and Calderón Villalobos, L. I. A. and Lilie, H. and Balbach, J. and Abel, S.}, title = {{Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response}}, year = {2015}, pages = {6230-6235}, journal = {PNAS}, doi = {10.1073/pnas.1424077112}, url = {http://www.pnas.org/content/112/19/6230}, volume = {112}, abstract = {The plant hormone auxin activates primary response genes by facilitating proteolytic removal of AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA)-inducible repressors, which directly bind to transcriptional AUXIN RESPONSE FACTORS (ARF). Most AUX/IAA and ARF proteins share highly conserved C-termini mediating homotypic and heterotypic interactions within and between both protein families. The high-resolution NMR structure of C-terminal domains III and IV of the AUX/IAA protein PsIAA4 from pea (Pisum sativum) revealed a globular ubiquitin-like β-grasp fold with homologies to the Phox and Bem1p (PB1) domain. The PB1 domain of wild-type PsIAA4 features two distinct surface patches of oppositely charged amino acid residues, mediating front-to-back multimerization via electrostatic interactions. Mutations of conserved basic or acidic residues on either face suppressed PsIAA4 PB1 homo-oligomerization in vitro and confirmed directional interaction of full-length PsIAA4 in vivo (yeast two-hybrid system). Mixing of oppositely mutated PsIAA4 PB1 monomers enabled NMR mapping of the negatively charged interface of the reconstituted PsIAA4 PB1 homodimer variant, whose stoichiometry (1:1) and equilibrium binding constant (KD ∼6.4 μM) were determined by isothermal titration calorimetry. In silico protein–protein docking studies based on NMR and yeast interaction data derived a model of the PsIAA4 PB1 homodimer, which is comparable with other PB1 domain dimers, but indicated considerable differences between the homodimeric interfaces of AUX/IAA and ARF PB1 domains. Our study provides an impetus for elucidating the molecular determinants that confer specificity to complex protein–protein interaction circuits between members of the two central families of transcription factors important to the regulation of auxin-responsive gene expression.} } @Article{IPB-1827, author = {Bochnia, M. and Ziegler, J. and Sander, J. and Uhlig, A. and Schaefer, S. and Vollstedt, S. and Glatter, M. and Abel, S. and Recknagel, S. and Schusser, G. F. and Wensch-Dorendorf, M. and Zeyner, A.}, title = {{Hypoglycin A Content in Blood and Urine Discriminates Horses with Atypical Myopathy from Clinically Normal Horses Grazing on the Same Pasture}}, year = {2015}, pages = {e0136785}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0136785}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136785}, volume = {10}, abstract = {Hypoglycin A (HGA) in seeds of Acer spp. is suspected to cause seasonal pasture myopathy in North America and equine atypical myopathy (AM) in Europe, fatal diseases in horses on pasture. In previous studies, this suspicion was substantiated by the correlation of seed HGA content with the concentrations of toxic metabolites in urine and serum (MCPA-conjugates) of affected horses. However, seed sampling was conducted after rather than during an outbreak of the disease. The aim of this study was to further confirm the causality between HGA occurrence and disease outbreak by seed sampling during an outbreak and the determination of i) HGA in seeds and of ii) HGA and MCPA-conjugates in urine and serum of diseased horses. Furthermore, cograzing healthy horses, which were present on AM affected pastures, were also investigated. AM-pastures in Germany were visited to identify seeds of Acer pseudoplatanus and serum (n = 8) as well as urine (n = 6) from a total of 16 diseased horses were analyzed for amino acid composition by LC-ESI-MS/MS, with a special focus on the content of HGA. Additionally, the content of its toxic metabolite was measured in its conjugated form in body fluids (UPLC-MS/MS). The seeds contained 1.7–319.8 μg HGA/g seed. The content of HGA in serum of affected horses ranged from 387.8–8493.8 μg/L (controls \< 10 μg/L), and in urine from 143.8–926.4 μg/L (controls \< 10 μg/L), respectively. Healthy cograzing horses on AM-pastures showed higher serum (108.8 ± 83.76 μg/L) and urine concentrations (26.9 ± 7.39 μg/L) compared to control horses, but lower concentrations compared to diseased horses. The range of MCPA-carnitine and creatinine concentrations found in diseased horses in serum and urine were 0.17–0.65 mmol/L (controls \< 0.01), and 0.34–2.05 μmol/mmoL (controls \< 0.001), respectively. MCPA-glycine levels in urine of cograzing horses were higher compared to controls. Thus, the causal link between HGA intoxication and disease outbreak could be further substantiated, and the early detection of HGA in cograzing horses, which are clinically normal, might be a promising step in prophylaxis.} } @Article{IPB-2390, author = {Rekik, I. and Drira, N. and Grubb, C. D. and Elleuch, A.}, title = {{Molecular characterization and evolution studies of a SERK like gene transcriptionally induced during somatic embryogenesis in Phoenix Dactylifera L v Deglet Nour}}, year = {2015}, pages = {323-337}, journal = {Genetika}, doi = {10.2298/GENSR1501323R}, url = {https://dx.doi.org/10.2298/GENSR1501323R}, volume = {47}, abstract = {A somatic embryogenesis receptor kinase like (SERKL) cDNA, designated PhSERKL, was isolated from date palm (Phoenix Dactylifera L) using RACE PCR. PhSERKL protein shared all the characteristic domains of the SERK family, including five leucine-rich repeats, one proline-rich region motif, a transmembrane domain, and kinase domains. Phylogenetic analyses using PHYLIP and Notung 2.7 programs suggest that the SERK proteins of some plant species resulted from relatively ancient duplication events. We predict an ancestor protein of monocots and dicots SERK using FASTML program. Somatic embryogenic cultures of date palm were established following transfer of callus cultures to medium containing 2, 4-dichlorophenoxyacetic acid. The role of PhSERKL gene during establishment of somatic embryogenesis in culture was investigated using quantitative real-time PCR. PhSERKL gene was highly expressed during embryogenic competence acquisition and globular embryo formation in culture. Overall, levels of expression of PhSERKL gene were lower in nonembryogenic tissues and organs than in embryogenic callus.} } @Article{IPB-2389, author = {Rekik, I. and Chaabene, Z. and Grubb, C. D. and Drira, N. and Cheour, F. and Elleuch, A.}, title = {{In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour}}, year = {2015}, pages = {23}, journal = {Theor Biol Med Model}, doi = {10.1186/s12976-015-0013-2}, url = {https://dx.doi.org/10.1186/s12976-015-0013-2}, volume = {12}, abstract = {BackgroundDNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.MethodsThe present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.ResultsThe DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn2+ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.ConclusionsA model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn2+ and dAMP).} } @Article{IPB-2387, author = {Zayneb, C. and Bassem, K. and Zeineb, K. and Grubb, C. D. and Noureddine, D. and Hafedh, M. and Amine, E.}, title = {{Physiological responses of fenugreek seedlings and plants treated with cadmium}}, year = {2015}, pages = {10679-10689}, journal = {Environ Sci Pollut Res}, doi = {10.1007/s11356-015-4270-8}, url = {https://dx.doi.org/10.1007/s11356-015-4270-8}, volume = {22}, abstract = {The bioaccumulation efficiency of cadmium (Cd) by fenugreek (Trigonella foenum-graecum) was examined using different concentrations of CdCl2. The germination rate was similar to control except at 10 mM Cd. However, early seedling growth was quite sensitive to the metal from the lowest Cd level. Accordingly, amylase activity was reduced substantially on treatment of seeds with 0.5, 1, and 10 mM Cd. Cadmium also affected various other plant growth parameters. Its accumulation was markedly lower in shoots as compared to roots, reducing root biomass by almost 50 %. Plants treated with 1 and 5 mM Cd presented chlorosis due to a significant reduction in chlorophyll b especially. Furthermore, at Cd concentrations greater than 0.1 mM, plants showed several signs of oxidative stress; an enhancement in root hydrogen peroxide (H2O2) level and in shoot malondialdehyde (MDA) content was observed. Conversely, antioxidant enzyme activities (superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT)) increased in various plant parts. Likewise, total phenolic and flavonoid contents reached their highest values in the 0.5 mM Cd treatment, consistent with their roles in quenching low concentrations of reactive oxygen species (ROS). Consequently, maintaining oxidant and antioxidant balance may permit fenugreek to hyperaccumulate Cd and allow it to be employed in extremely Cd polluted soils for detoxification purposes.} } @Article{IPB-2386, author = {Hamdi, I. and Elleuch, A. and Bessaies, N. and Grubb, C. D. and Fakhfakh, H.}, title = {{First report of Citrus viroid V in North Africa}}, year = {2015}, pages = {87-91}, journal = {J Gen Plant Pathol}, doi = {10.1007/s10327-014-0556-9}, url = {https://dx.doi.org/10.1007/s10327-014-0556-9}, volume = {81}, abstract = {We tested citrus samples from Tunisia using reverse transcription-polymerase chain reaction (RT-PCR), and for the first time, Citrus viroid V (CVd-V) was reported in North Africa. Fourteen of 38 tested citrus trees were infected by CVd-V including the majority of varieties grown in Tunisia. Some RT-PCR results were also supported by biological indexing. After sequencing the RT-PCR products, three new CVd-V variants were identified, showing 80–91 % nucleotide sequence identity with those reported previously. Based on phylogenetic analysis using all CVd-V sequences in GenBank, two main CVd-V groups were identified. Furthermore, construction of a genetic network of the detected haplotypes using the same sequences shows a clear geographical structuring of Tunisian CVd-V variants.} } @Article{IPB-2373, author = {Zayneb, C. and Lamia, K. and Olfa, E. and Naïma, J. and Grubb, C. D. and Bassem, K. and Hafedh, M. and Amine, E.}, title = {{Morphological, Physiological and Biochemical Impact of Ink Industry Effluent on Germination of Maize (Zea mays), Barley (Hordeum vulgare) and Sorghum (Sorghum bicolor)}}, year = {2015}, pages = {687-693}, journal = {Bull Environ Contam Toxicol}, doi = {10.1007/s00128-015-1600-y}, url = {https://dx.doi.org/10.1007/s00128-015-1600-y}, volume = {95}, abstract = {The present study focuses on effects of untreated and treated ink industry wastewater on germination of maize, barley and sorghum. Wastewater had a high chemical oxygen demand (COD) and metal content compared to treated effluent. Germination decreased with increasing COD concentration. Speed of germination also followed the same trend, except for maize seeds exposed to untreated effluent (E), which germinated slightly faster than controls. These alterations of seedling development were mirrored by changes in soluble protein content. E exerted a positive effect on soluble protein content and maximum levels occurred after 10 days with treated effluent using coagulation/flocculation (TEc/f) process and treated effluent using combined process (coagulation/flocculation/biosorption) (TEc/f/b). Likewise, activity of α-amylase was influenced by effluent composition. Its expression depended on the species, exposure time and applied treatment. Nevertheless, current results indicated TEc/f/b had no observable toxic effects on germination and could be a beneficial alternative resource to irrigation water.} } @Article{IPB-1963, author = {Gasperini, D. and Chételat, A. and Acosta, I.F. and Goossens, J. and Pauwels, L. and Goossens, A. and Dreos, R. and Alonso, E. and Farmer, E.E.}, title = {{Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth}}, year = {2015}, pages = {e1005300}, journal = {PLoS Genet.}, doi = {10.1371/journal.pgen.1005300}, volume = {11 (6)}, abstract = {Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require the activation of jasmonate (JA) signalling. Using a novel assay involving repetitive cotyledon wounding in Arabidopsis seedlings, we uncovered a function of JA in suppressing cell division and elongation in roots. Regulatory JA signalling components were then manipulated to delineate their relative impacts on root growth. The new transcription factor mutant myc2-322B was isolated. In vitro transcription assays and whole-plant approaches revealed that myc2-322B is a dosage-dependent gain-of-function mutant that can amplify JA growth responses. Moreover, myc2-322B displayed extreme hypersensitivity to JA that totally suppressed root elongation. The mutation weakly reduced root growth in undamaged plants but, when the upstream negative regulator NINJA was genetically removed, myc2-322B powerfully repressed root growth through its effects on cell division and cell elongation. Furthermore, in a JA-deficient mutant background, ninja1 myc2-322B still repressed root elongation, indicating that it is possible to generate JA-responses in the absence of JA. We show that NINJA forms a broadly expressed regulatory layer that is required to inhibit JA signalling in the apex of roots grown under basal conditions. By contrast, MYC2, MYC3 and MYC4 displayed cell layer-specific localisations and MYC3 and MYC4 were expressed in mutually exclusive regions. In nature, growing roots are likely subjected to constant mechanical stress during soil penetration that could lead to JA production and subsequent detrimental effects on growth. Our data reveal how distinct negative regulatory layers, including both NINJA-dependent and -independent mechanisms, restrain JA responses to allow normal root growth. Mechanistic insights from this work underline the importance of mapping JA signalling components to specific cell types in order to understand and potentially engineer the growth reduction that follows physical damage.} } @Article{IPB-1962, author = {Gasperini, D. and Chauvin, A. and Acosta, I.F. and Kurenda, A. and Stolz, S. and Chétalat, A. and Wolfender J.-L. and Farmer, E.E.}, title = {{Axial and Radial Oxylipin Transport.}}, year = {2015}, pages = {2244-2254}, journal = {Plant Physiol.}, doi = {10.1104/pp.15.01104}, volume = {169}, } @Article{IPB-1826, author = {Buhtz, A. and Witzel, K. and Strehmel, N. and Ziegler, J. and Abel, S. and Grosch, R.}, title = {{Perturbations in the Primary Metabolism of Tomato and Arabidopsis thaliana Plants Infected with the Soil-Borne Fungus Verticillium dahliae}}, year = {2015}, pages = {e0138242}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0138242}, url = {http://www.plosone.org/}, volume = {10}, abstract = {The hemibiotrophic soil-borne fungus Verticillium dahliae is a major pathogen of a number of economically important crop species. Here, the metabolic response of both tomato and Arabidopsis thaliana to V. dahliae infection was analysed by first using non-targeted GC-MS profiling. The leaf content of both major cell wall components glucuronic acid and xylose was reduced in the presence of the pathogen in tomato but enhanced in A. thaliana. The leaf content of the two tricarboxylic acid cycle intermediates fumaric acid and succinic acid was increased in the leaf of both species, reflecting a likely higher demand for reducing equivalents required for defence responses. A prominent group of affected compounds was amino acids and based on the targeted analysis in the root, it was shown that the level of 12 and four free amino acids was enhanced by the infection in, respectively, tomato and A. thaliana, with leucine and histidine being represented in both host species. The leaf content of six free amino acids was reduced in the leaf tissue of diseased A. thaliana plants, while that of two free amino acids was raised in the tomato plants. This study emphasizes the role of primary plant metabolites in adaptive responses when the fungus has colonized the plant.} } @Article{IPB-1803, author = {Moss, B. L. and Mao, H. and Guseman, J. M. and Hinds, T. R. and Hellmuth, A. and Kovenock, M. and Noorassa, A. and Lanctot, A. and Calderón Villalobos, L. I. A. and Zheng, N. and Nemhauser, J.}, title = {{Rate motifs tune Auxin/Indole-3-Acetic acid degradation dynamics.}}, year = {2015}, pages = {803-813}, journal = {Plant Physiol.}, doi = {10.1104/pp.15.00587}, url = { http://www.plantphysiol.org/content/early/2015/07/06/pp.15.00587.abstract?papetoc}, volume = {169}, abstract = {Ubiquitin-mediated protein degradation is a common feature in diverse plant cell signaling pathways; however, the factors that control the dynamics of regulated protein turnover are largely unknown. One of the best-characterized families of E3 ubiquitin ligases, SCFTIR1/AFBs, facilitates ubiquitination of Aux/IAA repressor proteins in the presence of auxin. Rates of auxin-induced degradation vary widely within the Aux/IAA family, and sequences outside of the characterized degron (the minimum region required for auxin-induced degradation) can accelerate or decelerate degradation. We have used synthetic auxin degradation assays in yeast and in plants to characterize motifs flanking the degron that contribute to tuning the dynamics of Aux/IAA degradation. The presence of these "rate motifs" is conserved in phylogenetically-distant members of the Arabidopsis thaliana Aux/IAA family, as well as in their putative Brassica rapa orthologs. We found that rate motifs can act by enhancing interaction between repressors and the E3, but that this is not the only mechanism of action. Phenotypes of transgenic plants expressing a deletion in a rate motif in IAA28 resembled plants expressing degron mutations, underscoring the functional relevance of Aux/IAA degradation dynamics in regulating auxin responses} } @Article{IPB-1640, author = {Wasternack, C. and Hause, B.}, title = {{Jasmonsäure – ein universelles Pflanzenhormon: Blütenduft, Abwehr, Entwicklung}}, year = {2014}, pages = {164 - 171}, journal = {Biologie in unserer Zeit}, doi = {10.1002/biuz.201410535}, url = {http://onlinelibrary.wiley.com/doi/10.1002/biuz.201410535/pdf}, volume = {44}, abstract = {Jasmonsäure (JA) und ihre Metaboliten kommen in allen niederen und höheren Pflanzen vor. Sie sind universell wirksame, aus Lipiden gebildete Signalstoffe bei der Abwehr von biotischem und abiotischem Stress sowie in der pflanzlichen Entwicklung. Rezeptor und Komponenten von JA–Signalketten wurden identifiziert. In der Entwicklung von Blüten, Früchten, Samen, Trichomen oder in der Abwehr von Insekten und Pathogenen treten ähnliche JA-vermittelte Signalproteine auf, die eine Feinregulation der Prozesse erlauben und eine Verbindung (cross-talk) zu anderenPflanzenhormonen aufweisen.} } @INBOOK{IPB-1618, author = {Wasternack, C.}, title = {{Phytohormones: a window to metabolism, signaling and biotechnological applications.}}, year = {2014}, pages = {221-264}, chapter = {{Jasmonates in plant growth and stress responses.}}, editor = {Tran, L.-S.; Pal, S.}, doi = {10.1007/978-1-4939-0491-4_8}, url = {http://www.springer.com/de/book/9781493904907}, volume = {Springer}, abstract = {Abiotic and biotic stresses adversely affect plant growth and productivity. The phytohormones regulate key physiological events under normal and stressful conditions for plant development. Accumulative research efforts have discovered important roles of phytohormones and their interactions in regulation of plant adaptation to numerous stressors. Intensive molecular studies have elucidated various plant hormonal pathways; each of which consist of many signaling components that link a specific hormone perception to the regulation of downstream genes. Signal transduction pathways of auxin, abscisic acid, cytokinins, gibberellins and ethylene have been thoroughly investigated. More recently, emerging signaling pathways of brassinosteroids, jasmonates, salicylic acid and strigolactones offer an exciting gateway for understanding their multiple roles in plant physiological processes.At the molecular level, phytohormonal crosstalks can be antagonistic or synergistic or additive in actions. Additionally, the signal transduction component(s) of one hormonal pathway may interplay with the signaling component(s) of other hormonal pathway(s). Together these and other research findings have revolutionized the concept of phytohormonal studies in plants. Importantly, genetic engineering now enables plant biologists to manipulate the signaling pathways of plant hormones for development of crop varieties with improved yield and stress tolerance.This book, written by internationally recognized scholars from various countries, represents the state-of-the-art understanding of plant hormones’ biology, signal transduction and implications. Aimed at a wide range of readers, including researchers, students, teachers and many others who have interests in this flourishing research field, every section is concluded with biotechnological strategies to modulate hormone contents or signal transduction pathways and crosstalk that enable us to develop crops in a sustainable manner. Given the important physiological implications of plant hormones in stressful environments, our book is finalized with chapters on phytohormonal crosstalks under abiotic and biotic stresses. } } @Article{IPB-1679, author = {Budiharjo, A. and Chowdhury, S.M. and Dietel, C. and Beator, B. and Dolgova, O. and Fan, B. and Bleiss, W. and Ziegler, J. and Schmid, M. and Hartmann, A. and Borris, R.}, title = {{Transposon Mutagenesis of the Plant-Associated Bacillus amyloliquefaciens ssp. plantarum FZB42 Revealed That the nrfA and RBAM17410 Genes Are Involved in Plant-Microbe-Interactions}}, year = {2014}, pages = {e98267}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0098267}, url = {http://www.plosone.org/search/simple;jsessionid=404D2C0CDA3518860596F06F56BA4175?from=globalSimpleSearch&filterJournals=PLoSONE&query=e98267&x=12&y=1}, volume = {9}, abstract = {Bacillus amyloliquefaciens ssp. plantarum FZB42 represents the prototype of Gram-positive plant growth promoting and biocontrol bacteria. In this study, we applied transposon mutagenesis to generate a transposon library, which was screened for genes involved in multicellular behavior and biofilm formation on roots as a prerequisite of plant growth promoting activity. Transposon insertion sites were determined by rescue-cloning followed by DNA sequencing. As in B. subtilis, the global transcriptional regulator DegU was identified as an activator of genes necessary for swarming and biofilm formation, and the DegU-mutant of FZB42 was found impaired in efficient root colonization. Direct screening of 3,000 transposon insertion mutants for plant-growth-promotion revealed the gene products of nfrA and RBAM\_017140 to be essential for beneficial effects exerted by FZB42 on plants. We analyzed the performance of GFP-labeled wild-type and transposon mutants in the colonization of lettuce roots using confocal laser scanning microscopy. While the wild-type strain heavily colonized root surfaces, the nfrA mutant did not colonize lettuce roots, although it was not impaired in growth in laboratory cultures, biofilm formation and swarming motility on agar plates. The RBAM17410 gene, occurring in only a few members of the B. subtilis species complex, was directly involved in plant growth promotion. None of the mutant strains were affected in producing the plant growth hormone auxin. We hypothesize that the nfrA gene product is essential for overcoming the stress caused by plant response towards bacterial root colonization.} } @Article{IPB-1675, author = {Erickson, J. l. and Ziegler, J. and Guevara, D. and Abel, S. and Klösgen, R. B. and Mathur, J. and Rothstein, S. J. and Schattat, M.H. }, title = {{Agrobacterium-derived cytokinin influences plastid morphology and starch accumulation inNicotiana benthamiana during transient assays}}, year = {2014}, pages = {127}, journal = { BMC Plant Biol.}, doi = {10.1186/1471-2229-14-127}, url = {http://www.biomedcentral.com/1471-2229/14/127}, volume = { 14}, abstract = {Background: Agrobacterium tumefaciens-based transient assays have become a common tool for answering questions related to protein localization and gene expression in a cellular context. The use of these assays assumes that the transiently transformed cells are observed under relatively authentic physiological conditions and maintain ‘normal’ sub-cellular behaviour. Although this premise is widely accepted, the question of whether cellular organization andorganelle morphology is altered in Agrobacterium-infiltrated cells has not been examined in detail. The first indications of an altered sub-cellular environment came from our observation that a common laboratory strain, GV3101(pMP90), caused a drastic increase in stromule frequency. Stromules, or ‘stroma-filled-tubules’ emanate fromthe surface of plastids and are sensitive to a variety of biotic and abiotic stresses. Starting from this observation, the goal of our experiments was to further characterize the changes to the cell resulting from short-term bacterial infestation, and to identify the factor responsible for eliciting these changes.Results: Using a protocol typical of transient assays we evaluated the impact of GV3101(pMP90) infiltration on chloroplast behaviour and morphology in Nicotiana benthamiana. Our experiments confirmed that GV3101(pMP90) consistently induces stromules and alters plastid position relative to the nucleus. These effects were found to be the result of strain-dependant secretion of cytokinin and its accumulation in the plant tissue. Bacterial production of the hormone was found to be dependant on the presence of a trans-zeatin synthase gene (tzs) located on the Ti plasmidof GV3101(pMP90). Bacteria-derived cytokinins were also correlated with changes to both soluble sugar level and starch accumulation.Conclusion: Although we have chosen to focus on how transient Agrobacterium infestation alters plastid based parameters, these changes to the morphology and position of a single organelle, combined with the measured increases in sugar and starch content, suggest global changes to cell physiology. This indicates that cells visualized during transient assays may not be as ‘normal’ as was previously assumed. Our results suggest that the impact of the bacteria can be minimized by choosing Agrobacterium strains devoid of the tzs gene, but that the alterations to sub-cellular organization and cell carbohydrate status cannot be completely avoided using this strategy.Keywords: Agrobacterium tumefaciens, Nicotiana benthamiana, Transient assays, GV3101(pMP90), LBA4404, Plastid,Stromules, Bacteria-derived, Cytokinin, Trans-zeatin synthase} } @Article{IPB-1628, author = {Wasternack, C.}, title = {{Perception, signaling and cross-talk of jasmonates and the seminal contributions of the Daoxin Xie´s lab and the Chuanyou Li´s lab}}, year = {2014}, pages = {707-718}, journal = {Plant Cell Rep}, doi = {10.1007/s00299-014-1608-5}, url = {http://link.springer.com/article/10.1007/s00299-014-1608-5}, volume = {33}, abstract = {Jasmonates (JAs) are lipid-derived signals in plant responses to biotic and abiotic stresses and in development. The most active JA compound is (+)-7-iso-JA-Ile, a JA conjugate with isoleucine. Biosynthesis, metabolism and key components of perception and signal transduction have been identified and numerous JA-induced gene expression data collected. For JA-Ile perception, the SCFCOI1–JAZ co-receptor complex has been identified and crystalized. Activators such as MYC2 and repressors such as JAZs including their targets were found. Involvement of JA-Ile in response to herbivores and pathogens and in root growth inhibition is among the most studied aspects of JA-Ile signaling. There are an increasing number of examples, where JA-Ile shows cross-talk with other plant hormones. Seminal contributions in JA/JA-Ile research were given by Daoxin Xie’s lab and Chuanyou Li’s lab, both in Beijing. Here, characterization was done regarding components of the JA-Ile receptor, such as COI1 (JAI1) and SCF, regarding activators (MYCs, MYBs) and repressors (JAV1, bHLH IIId’s) of JA-regulated gene expression, as well as regarding components of auxin biosynthesis and action, such as the transcription factor PLETHORA active in the root stem cell niche. This overview reflects the work of both labs in the light of our present knowledge on biosynthesis, perception and signal transduction of JA/JA-Ile and its cross-talk to other hormones.} } @Article{IPB-1693, author = {Song, S. and Qi, T. and Wasternack, C. and Xie, D.}, title = {{Jasmonate signaling and crosstalk with gibberellin and ethylene}}, year = {2014}, pages = {112-119}, journal = { Curr Opin Plant Biol.}, doi = {10.1016/j.pbi.2014.07.005}, url = {http://www.sciencedirect.com/science/article/pii/S1369526614001022}, volume = {21 }, abstract = {The phytohormone jasmonate (JA) plays essential roles in plant growth, development and defense. In response to the JA signal, the CORONATINE INSENSITIVE 1 (COI1)-based SCF complexes recruit JASMONATE ZIM-domain (JAZ) repressors for ubiquitination and degradation, and subsequently regulate their downstream signaling components essential for various JA responses. Tremendous progress has been made in understanding the JA signaling pathway and its crosstalk with other phytohormone pathways during the past two decades. Recent studies have revealed that a variety of positive and negative regulators act as targets of JAZs to control distinctive JA responses, and that JAZs and these regulators function as crucial interfaces to mediate synergy and antagonism between JA and other phytohormones. Owing to different regulatory players in JA perception and JA signaling, a fine-tuning of JA-dependent processes in plant growth, development and defense is achieved. In this review, we will summarize the latest progresses in JA signaling and its crosstalk with gibberellin and ethylene.} } @Article{IPB-1643, author = {Maldonado-Bonilla, L.D. and Eschen-Lippold, L. and Gago-Zachert, S. and Tabassum, N. and Bauer, N. and Scheel, D. and Lee, J.}, title = {{The Arabidopsis tandem zinc finger 9 protein binds RNA and mediates pathogen-associated molecular pattern-triggered immune responses}}, year = {2014}, pages = {412-425}, journal = {Plant Cell Physiol.}, doi = {10.1093/pcp/pct175}, url = {http://pcp.oxfordjournals.org/content/55/2/412.full.pdf+html}, volume = {55}, abstract = {Recognition of pathogen-associated molecular patterns (PAMPs) induces multiple defense mechanisms to limit pathogen growth. Here, we show that the Arabidopsis thaliana tandem zinc finger protein 9 (TZF9) is phosphorylated by PAMP-responsive mitogen-activated protein kinases (MAPKs) and is required to trigger a full PAMP-triggered immune response. Analysis of a tzf9 mutant revealed attenuation in specific PAMP-triggered reactions such as reactive oxygen species accumulation, MAPK activation and, partially, the expression of several PAMP-responsive genes. In accordance with these weaker PAMP-triggered responses, tzf9 mutant plants exhibit enhanced susceptibility to virulent Pseudomonas syringae pv. tomato DC3000. Visualization of TZF9 localization by fusion to green fluorescent protein revealed cytoplasmic foci that co-localize with marker proteins of processing bodies (P-bodies). This localization pattern is affected by inhibitor treatments that limit mRNA availability (such as cycloheximide or actinomycin D) or block nuclear export (leptomycin B). Coupled with its ability to bind the ribohomopolymers poly(rU) and poly(rG), these results suggest involvement of TZF9 in post-transcriptional regulation, such as mRNA processing or storage pathways, to regulate plant innate immunity. } } @Article{IPB-1697, author = {Jayaweera, T. and Siriwardana, C. and Dharmasiri, S. and Quint, M. and Gray, W. M. and Dharmasiri, N.}, title = {{Alternative Splicing of Arabidopsis IBR5 Pre-mRNA Generates Two IBR5 Isoforms with Distinct and Overlapping Functions}}, year = {2014}, pages = {e102301}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0102301}, volume = {9}, abstract = {The INDOLE-3-BUTYRIC ACID RESPONSE5 (IBR5) gene encodes a dual specificity phosphatase that regulates plant auxinresponses. IBR5 has been predicted to generate two transcripts through alternative splicing, but alternative splicing of IBR5has not been confirmed experimentally. The previously characterized ibr5-1 null mutant exhibits many auxin related defectssuch as auxin insensitive primary root growth, defective vascular development, short stature and reduced lateral rootdevelopment. However, whether all these defects are caused by the lack of phosphatase activity is not clear. Here wedescribe two new auxin insensitive IBR5 alleles, ibr5-4, a catalytic site mutant, and ibr5-5, a splice site mutant.Characterization of these new mutants indicates that IBR5 is post-transcriptionally regulated to generate two transcripts,AT2G04550.1 and AT2G04550.3, and consequently two IBR5 isoforms, IBR5.1 and IBR5.3. The IBR5.1 isoform exhibitsphosphatase catalytic activity that is required for both proper degradation of Aux/IAA proteins and auxin-induced geneexpression. These two processes are independently regulated by IBR5.1. Comparison of new mutant alleles with ibr5-1indicates that all three mutant alleles share many phenotypes. However, each allele also confers distinct defects implicatingIBR5 isoform specific functions. Some of these functions are independent of IBR5.1 catalytic activity. Additionally, analysis ofthese new mutant alleles suggests that IBR5 may link ABP1 and SCFTIR1/AFBs auxin signaling pathways.} } @Article{IPB-1696, author = {Flores, R. and Gago-Zachert, S. and Serra, P. and Sanjuán, R. and Elena, S. F.}, title = {{Viroids: Survivors from the RNA World?}}, year = {2014}, pages = {395 - 414}, journal = {Annual Rev Microbiol }, doi = {10.1146/annurev-micro-091313-103416}, volume = {68}, abstract = {Because RNA can be a carrier of genetic information and a biocatalyst, there is a consensus that it emerged before DNA and proteins, which eventually assumed these roles and relegated RNA to intermediate functions. If such a scenario—the so-called RNA world—existed, we might hope to find its relics in our present world. The properties of viroids that make them candidates for being survivors of the RNA world include those expected for primitive RNA replicons: (a) small size imposed by error-prone replication, (b) high G+ C content to increase replication fidelity, (c) circular structure for assuring complete replication without genomic tags, (d) structural periodicity for modular assembly into enlarged genomes, (e) lack of protein-coding ability consistent with a ribosome-free habitat, and (f) replication mediated in some by ribozymes, the fingerprint of the RNA world. With the advent of DNA and proteins, those protoviroids lost some abilities and became the plant parasites we now know.} } @Article{IPB-1650, author = {Floková, K. and Tarkowská, D. and Miersch, O. and Strnad, M. and Wasternack, C. and Novak, O.}, title = {{UHPLC-MS/MS based target profiling of stress-induced phytohormones}}, year = {2014}, pages = {147-157}, journal = { Phytochemistry}, doi = {10.1016/j.phytochem.2014.05.015}, url = {http://www.sciencedirect.com/science/journal/00319422}, volume = {105}, abstract = {Stress-induced changes in phytohormone metabolite profiles have rapid effects on plant metabolic activity and growth. The jasmonates (JAs) are a group of fatty acid-derived stress response regulators with roles in numerous developmental processes. To elucidate their dual regulatory effects, which overlap with those of other important defence-signalling plant hormones such as salicylic acid (SA), abscisic acid (ABA) and indole-3-acetic acid (IAA), we have developed a highly efficient single-step clean-up procedure for their enrichment from complex plant matrices that enables their sensitive quantitative analysis using hyphenated mass spectrometry technique. The rapid extraction of minute quantities of plant material (less than 20 mg fresh weight, FW) into cold 10% methanol followed by one-step reversed-phase polymer-based solid phase extraction significantly reduced matrix effects and increased the recovery of labile JA analytes. This extraction and purification protocol was paired with a highly sensitive and validated ultra-high performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) method and used to simultaneously profile sixteen stress-induced phytohormones in minute plant material samples, including endogenous JA, several of its biosynthetic precursors and derivatives, as well as SA, ABA and IAA.} } @Article{IPB-1599, author = {Wasternack, C.}, title = {{Action of jasmonates in plant stress responses and development — Applied aspects}}, year = {2014}, pages = {31-39}, journal = {Biotechnol Adv}, doi = {10.1016/j.biotechadv.2013.09.009}, url = {http://www.sciencedirect.com/science/journal/07349750/32/1}, volume = {32 }, abstract = {Jasmonates (JAs) are lipid-derived compounds acting as key signaling compounds in plant stress responses and development. The JA co-receptor complex and several enzymes of JA biosynthesis have been crystallized, and various JA signal transduction pathways including cross-talk to most of the plant hormones have been intensively studied. Defense to herbivores and necrotrophic pathogens are mediated by JA. Other environmental cues mediated by JA are light, seasonal and circadian rhythms, cold stress, desiccation stress, salt stress and UV stress. During development growth inhibition of roots, shoots and leaves occur by JA, whereas seed germination and flower development are partially affected by its precursor 12-oxo-phytodienoic acid (OPDA). Based on these numerous JA mediated signal transduction pathways active in plant stress responses and development, there is an increasing interest in horticultural and biotechnological applications. Intercropping, the mixed growth of two or more crops, mycorrhization of plants, establishment of induced resistance, priming of plants for enhanced insect resistance as well as pre- and post-harvest application of JA are few examples. Additional sources for horticultural improvement, where JAs might be involved, are defense against nematodes, biocontrol by plant growth promoting rhizobacteria, altered composition of rhizosphere bacterial community, sustained balance between growth and defense, and improved plant immunity in intercropping systems. Finally, biotechnological application for JA-induced production of pharmaceuticals and application of JAs as anti-cancer agents were intensively studied.} } @Article{IPB-1702, author = {Bosch, M. and Wright, L. P. and Gershenzon, J. and Wasternack, C. and Hause, B. and Schaller, A. and Stintzi, A.}, title = {{Jasmonic acid and its precursor 12-oxophytodienoic acid control different aspects of constitutive and induced herbivore defenses in tomato}}, year = {2014}, pages = {396-410}, journal = {Plant Physiology}, doi = {10.1104/pp.114.237388}, url = {http://www.plantphysiol.org/search?author1=&fulltext=&pubdate_year=2014&volume=166&firstpage=396&submit=yes}, volume = {166}, abstract = {The jasmonate family of growth regulators includes the isoleucine conjugate of jasmonic acid (JA-Ile) and its biosynthetic precursor 12-oxophytodienoic acid (OPDA) as signaling molecules. In order to assess the relative contribution of JA/JA-Ile and OPDA to insect resistance in tomato, we silenced the expression of OPDA reductase (OPR3) by RNA interference. Consistent with a block in the biosynthetic pathway downstream of OPDA, OPR3-RNAi plants contained wild-type levels of OPDA but failed to accumulate JA or JA-Ile after wounding. JA/JA-Ile deficiency in OPR3-RNAi plants resulted in reduced trichome formation and impaired monoterpene and sesquiterpene production. The loss of these JA/JA-Ile-dependent defense traits rendered them more attractive to the specialist herbivore Manduca sexta with respect to feeding and oviposition. Oviposition preference resulted from reduced levels of repellant mono- and sesquiterpenes. Feeding preference, on the other hand, was caused by increased production of cis-3-hexenal acting as a feeding stimulant for M. sexta larvae in OPR3-RNAi plants. Despite impaired constitutive defenses and increased palatability of OPR3-RNAi leaves, larval development was indistinguishable on OPR3-RNAi and wild-type plants, and much delayed as compared to development on the JA/JA-Ile insensitive (jai1) mutant. Apparently, signaling through JAI1, the tomato ortholog of COI1 in Arabidopsis, is required for defense while the conversion of OPDA to JA/JA-Ile is not. Comparing the signaling activities of OPDA and JA/JA-Ile, we found that OPDA can substitute for JA/JA-Ile in the local induction of defense gene expression, but the production of JA/JA-Ile is required for a systemic response.} } @Article{IPB-1678, author = {Grubb, C. D. and Zipp, B. J. and Kopycki, J. and Schubert, M. and Quint, M. and Lim, E.-K. and Bowles, D. J. and Pedras, M. S. C. and Abel, S. }, title = {{Comparative analysis of Arabidopsis UGT74 glucosyltransferases reveals a special role of UGT74C1 in glucosinolate biosynthesis}}, year = {2014}, pages = {92–105}, journal = {Plant J. }, doi = {10.1111/tpj.12541}, url = { http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-313X}, volume = {79}, abstract = {The study of glucosinolates and their regulation has provided a powerful framework for the exploration of fundamental questions about the function, evolution, and ecological significance of plant natural products, but uncertainties about their metabolism remain. Previous work has identified one thiohydroximate S-glucosyltransferase, UGT74B1, with an important role in the core pathway, but also made clear that this enzyme functions redundantly and cannot be the sole UDP-glucose dependent glucosyltransferase (UGT) in glucosinolate synthesis. Here, we present the results of a nearly comprehensive in vitro activity screen of recombinant Arabidopsis Family 1 UGTs, which implicate other members of the UGT74 clade as candidate glucosinolate biosynthetic enzymes. Systematic genetic analysis of this clade indicates that UGT74C1 plays a special role in the synthesis of aliphatic glucosinolates, a conclusion strongly supported by phylogenetic and gene expression analyses. Finally, the ability of UGT74C1 to complement phenotypes and chemotypes of the ugt74b1-2 knockout mutant and to express thiohydroximate UGT activity in planta provides conclusive evidence for UGT74C1 being an accessory enzyme in glucosinolate biosynthesis with a potential function during plant adaptation to environmental challenge.} } @Article{IPB-1741, author = {Delker, C. and Sonntag, L. and Geo, V. J. and Janitza, P. and Ibañez, C. and Ziermann, H. and Peterson, T. and Denk, K. and Mull, S. and Ziegler, J. and Davis, S. J. and Schneeberger, K. and Quint, M.}, title = {{The DET1-COP1-HY5 Pathway Constitutes a Multipurpose Signaling Module Regulating Plant Photomorphogenesis and Thermomorphogenesis}}, year = {2014}, pages = {1983–1989}, journal = {Cell Rep}, doi = {10.1016/j.celrep.2014.11.043}, url = {http://www.cell.com/cell-reports/abstract/S2211-1247%2814%2901009-2}, volume = {9}, abstract = {Developmental plasticity enables plants to respond to elevated ambient temperatures by adapting their shoot architecture. On the cellular level, the basic-helix-loop-helix (bHLH) transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) coordinates this response by activating hormonal modules that in turn regulate growth. In addition to an unknown temperature-sensing mechanism, it is currently not understood how temperature regulates PIF4 activity. Using a forward genetic approach in Arabidopsis thaliana, we present extensive genetic evidence demonstrating that the DE-ETIOLATED 1 (DET1)-CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)-ELONGATED HYPOCOTYL 5 (HY5)-dependent photomorphogenesis pathway transcriptionally regulates PIF4 to coordinate seedling growth in response to elevated temperature. Our findings demonstrate that two of the most prevalent environmental cues, light and temperature, share a much larger set of signaling components than previously assumed. Similar to the toolbox concept in animal embryonic patterning, multipurpose signaling modules might have evolved in plants to translate various environmental stimuli into adaptational growth processes} } @Article{IPB-1964, author = {Farmer, E.E. and Gasperini, D. and Acosta, I.F. }, title = {{The squeeze cell hypothesis for the activation of jasmonate synthesis in response to wounding}}, year = {2014}, pages = {282-288}, journal = {New Phytol.}, doi = {10.1111/nph.12897}, volume = {204}, } @Article{IPB-1726, author = {Ziegler, J. and Abel S. }, title = {{Analysis of amino acids by HPLC/electrospray negative ion tandem mass spectrometry using 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) derivatization}}, year = {2014}, pages = {2799-2808}, journal = {Amino Acids}, doi = {10.1007/s00726-014-1837-5}, url = {http://link.springer.com/search?query=Ziegler%2C+J%C3%B6rg&search-within=Journal&facet-journal-id=726}, volume = {46}, abstract = {A new method for the determination of amino acids is presented. It combines established methods for the derivatization of primary and secondary amino groups with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) with the subsequent amino acid specific detection of the derivatives by LC–ESI–MS/MS using multiple reaction monitoring (MRM). The derivatization proceeds within 5 min, and the resulting amino acid derivatives can be rapidly purified from matrix by solid-phase extraction (SPE) on HR-X resin and separated by reversed-phase HPLC. The Fmoc derivatives yield several amino acid specific fragment ions which opened the possibility to select amino acid specific MRM transitions. The method was applied to all 20 proteinogenic amino acids, and the quantification was performedusing l-norvaline as standard. A limit of detection as low as 1 fmol/μl with a linear range of up to 125 pmol/μl could be obtained. Intraday and interday precisions were lower than10 % relative standard deviations for most of the amino acids. Quantification usingl-norvaline as internal standard gave very similar results compared to the quantificationusing deuterated amino acid as internal standards. Using this protocol, it was possible to record the amino acid profiles of only a single root from Arabidopsis thaliana seedlings and to compare it with the amino acid profiles of 20 dissected root meristems (200 μm).} } @Article{IPB-1725, author = {Ziegler, J. and Qwegwer, J. and Schubert, M. and Erickson, J.L. and Schattat, M. and Bürstenbinder, K. and Grubb, C.D. and Abel, S.}, title = {{Simultaneous analysis of apolar phytohormones and 1-aminocyclopropan-1-carboxylic acid by high performance liquid chromatography/electrospray negative ion tandem mass spectrometry via 9-fluorenylmethoxycarbonyl chloride derivatization}}, year = {2014}, pages = {102-109}, journal = {J Chromatogr A}, doi = {10.1016/j.chroma.2014.08.029}, url = {http://www.sciencedirect.com/science/article/pii/S002196731401259X}, volume = {1362}, abstract = {A strategy to detect and quantify the polar ethylene precursor 1-aminocyclopropan-1-carboxylic acid (ACC) along with the more apolar phytohormones abscisic acid (ABA), indole-3-acetic acid (IAA), jasmonic acid (JA), jasmonic acid-isoleucine conjugate (JA-Ile), 12-oxo-phytodienoic acid (OPDA), trans-zeatin, and trans-zeatin 9-riboside using a single extraction is presented. Solid phase resins commonly employed for extraction of phytohormones do not allow the recovery of ACC. We circumvent this problem by attaching an apolar group to ACC via derivatization with the amino group specific reagent 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl). Derivatization in the methanolic crude extract does not modify other phytohormones. The derivatized ACC could be purified and detected together with the more apolar phytohormones using common solid phase extraction resins and reverse phase HPLC/electrospray negative ion tandem mass spectrometry. The limit of detection was in the low nanomolar range for all phytohormones, a sensitivity sufficient to accurately determine the phytohormone levels from less than 50 mg (fresh weight) of Arabidopsis thaliana and Nicotiana benthamiana tissues. Comparison with previously published phytohormone levels and the reported changes in phytohormone levels after stress treatments confirmed the accuracy of the method.} } @INBOOK{IPB-1594, author = {Wasternack, C. \& Hause, B.}, title = {{Benno Parthier und die Jasmonatforschung in Halle}}, year = {2013}, pages = {29-38}, chapter = {{Benno Parthier und die Jasmonatforschung in Halle}}, journal = {Nova Acta Leopoldina, NF Supplementum}, volume = {28}, } @Article{IPB-1596, author = {Navarro-Quezada, A. and Schumann, N. \& Quint, M.}, title = {{Plant F-Box protein evolution is determined by lineage-specific timing of major gene family expansion waves}}, year = {2013}, pages = {e68672}, journal = {PLoS One}, doi = {10.1371/journal.pone.0068672}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068672}, volume = {8}, abstract = {F-box proteins (FBPs) represent one of the largest and fastest evolving gene/protein families in the plant kingdom. The FBP superfamily can be divided in several subfamilies characterized by different C-terminal protein-protein interaction domains that recruit targets for proteasomal degradation. Hence, a clear picture of their phylogeny and molecular evolution is of special interest for the general understanding of evolutionary histories of multi-domain and/or large protein families in plants. In an effort to further understand the molecular evolution of F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana, which carries a C-terminal F-box associated domain (FBA proteins) shares evolutionary patterns and signatures of selection with other FBPs. To address this question, we applied phylogenetic and molecular evolution analyses in combination with the evaluation of transcriptional profiles. Based on the 2219 FBA proteins we de novo identified in 34 completely sequenced plant genomes, we compared their evolutionary patterns to a previously analyzed large subfamily carrying C-terminal kelch repeats. We found that these two large FBP subfamilies generally tend to evolve by massive waves of duplication, followed by sequence conservation of the F-box domain and sequence diversification of the target recruiting domain. We conclude that the earlier in evolutionary time a major wave of expansion occurred, the more pronounced these selection signatures are. As a consequence, when performing cross species comparisons among FBP subfamilies, significant differences will be observed in the selective signatures of protein-protein interaction domains. Depending on the species, the investigated subfamilies comprise up to 45% of the complete superfamily, indicating that other subfamilies possibly follow similar modes of evolution.} } @Article{IPB-1595, author = {Huang, H. and Quint, M. \& Gray, W.M.}, title = {{The \textit{eta7/csn3-3} auxin response mutant of Arabidopsis defines a novel function for the CSN3 subunit of the COP9 signalosome}}, year = {2013}, pages = {e66578}, journal = {PLoS One}, doi = {10.1371/journal.pone.0066578}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0066578}, volume = {8}, abstract = {TIR1/AFBTIR1The COP9 signalosome (CSN) is an eight subunit protein complex conserved in all higher eukaryotes. In Arabidopsis thaliana, the CSN regulates auxin response by removing the ubiquitin-like protein NEDD8/RUB1 from the CUL1 subunit of the SCF ubiquitin-ligase (deneddylation). Previously described null mutations in any CSN subunit result in the pleiotropic cop/det/fus phenotype and cause seedling lethality, hampering the study of CSN functions in plant development. In a genetic screen to identify enhancers of the auxin response defects conferred by the tir1-1 mutation, we identified a viable csn mutant of subunit 3 (CSN3), designated eta7/csn3-3. In addition to enhancing tir1-1 mutant phenotypes, the csn3-3 mutation alone confers several phenotypes indicative of impaired auxin signaling including auxin resistant root growth and diminished auxin responsive gene expression. Unexpectedly however, csn3-3 plants are not defective in either the CSN-mediated deneddylation of CUL1 or in SCF-mediated degradation of Aux/IAA proteins. These findings suggest that csn3-3 is an atypical csn mutant that defines a novel CSN or CSN3-specific function. Consistent with this possibility, we observe dramatic differences in double mutant interactions between csn3-3 and other auxin signaling mutants compared to another weak csn mutant, csn1-10. Lastly, unlike other csn mutants, assembly of the CSN holocomplex is unaffected in csn3-3 plants. However, we detected a small CSN3-containing protein complex that is altered in csn3-3 plants. We hypothesize that in addition to its role in the CSN as a cullin deneddylase, CSN3 functions in a distinct protein complex that is required for proper auxin signaling.} } @Article{IPB-1597, author = {Dekkers, B.J.W. and Pearce, S. and van Bolderen-Veldkamp, R.P. and Marshall, A. and Widera, P. and Gilbert, J. and Drost, H.-G. and Basseli, G.W. and Müller, K. and King, J.R. and Wood, A.T.A. and Grosse, I. and Quint, M. and Krasnogor, N. and Leubner-Metzger, G. and Holdsworth, M.J. \& Bentsink, L.}, title = {{Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed Germination}}, year = {2013}, pages = {205-215}, journal = {Plant Physiol}, doi = {10.1104/pp.113.223511}, volume = {163}, abstract = {Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understandinggermination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa,endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes thatlead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seedswith both temporaland spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this highresolutiondata set for the construction ofmeaningful coexpression networks, which provide insight into the genetic control of germination.The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by largetranscriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptionalphase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start ofthe second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlightthe fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show thatexpression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase.Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.} } @Article{IPB-1601, author = {Poeschl, Y. and Delker, C. and Trenner, J. and Ullrich, K. and Quint, M. \& Grosse, I.}, title = {{Optimized probe masking for comparative transcriptomics of closely related species.}}, year = {2013}, pages = {e78497}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0078497}, volume = {8}, abstract = {Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays arerestricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or morespecies often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to amicroarray of a closely related species. When analyzing these cross-species microarray expression data, differences in thetranscriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes dueto mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts ofnon-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach forcomparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcriptsof orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarraydesigned for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomicDNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resultingexpression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringencyand accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. Asan added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.} } @Article{IPB-1638, author = {Elleuch, A. and Chaâbene, Z. and Grubb, D.C. and Drira, N. and Mejdoub, H. and Khemakhem, B.}, title = {{Morphological and biochemical behavior of fenugreek (Trigonella foenum-graecum) under copper stress}}, year = {2013}, pages = {46-53}, journal = {Ecotoxicol Environ Saf}, doi = {10.1016/j.ecoenv.2013.09.028}, volume = {98}, abstract = {The effects of copper on germination and growth of fenugreek (Trigonella foenum-graecum ) was investigated separately using different concentrations of CuSO4. The germination percentage and radical length had different responses to cupric ions: the root growth increased with increasing copper concentration up to 1 mM Cu+2Cu2+ and was inhibited thereafter. In contrast, the germination percentage was largely unaffected by concentrations of copper below 10 mM.The reduction in root growth may have been due to inhibition of hydrolytic enzymes such as amylase. Indeed, the average total amylolytic activity decreased from the first day of treatment with [Cu+2Cu2+] greater than 1 mM. Furthermore, copper affected various plant growth parameters. Copper accumulation was markedly higher in roots as compared to shoots. While both showed a gradual decrease in growth, this was more pronounced in roots than in leaves and in stems. Excess copper induced an increase in the rate of hydrogen peroxide (H2O2) production and lipid peroxidation in all plant parts, indicating oxidative stress. This redox stress affected leaf chlorophyll and carotenoid content which decreased in response to augmented Cu levels. Additionally, the activities of proteins involved in reactive oxygen species (ROS) detoxification were affected. Cu stress elevated the ascorbate peroxidase (APX) activity more than two times at 10 mM CuSO4. In contrast, superoxide dismutase (SOD) and catalase (CAT) levels showed only minor variations, only at 1 mM Cu+2Cu2+. Likewise, total phenol and flavonoid contents were strongly induced by low concentrations of copper, consistent with the role of these potent antioxidants in scavenging ROS such as H2O2, but returned to control levels or below at high [Cu+2Cu2+]. Taken together, these results indicate a fundamental shift in the plant response to copper toxicity at low versus high concentrations.} } @Article{IPB-1536, author = {Wasternack, C. and Hause, B.}, title = {{Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany}}, year = {2013}, pages = {1021-1058}, journal = { Annals of Botany}, doi = {10.1093/aob/mct067}, volume = {111}, abstract = {Background: Jasmonates are important regulators in plant responses to biotic and abiotic stresses as well as indevelopment. Synthesized from lipid-constituents, the initially formed jasmonic acid is converted to differentmetabolites including the conjugate with isoleucine. Important new components of jasmonate signalling includingits receptor were identified, providing deeper insight into the role of jasmonate signalling pathways in stressresponses and development.Scope: The present review is an update of the review on jasmonates published in this journal in 2007. New dataof the last five years are described with emphasis on metabolites of jasmonates, on jasmonate perception andsignalling, on cross-talk to other plant hormones and on jasmonate signalling in response to herbivores and pathogens,in symbiotic interactions, in flower development, in root growth and in light perception.Conclusions: The last few years have seen breakthroughs in the identification of JASMONATE ZIM DOMAIN(JAZ) proteins and their interactors such as transcription factors and co-repressors, and the crystallization of thejasmonate receptor as well as of the enzyme conjugating jasmonate to amino acids. Now, the complex nature ofnetworks of jasmonate signalling in stress responses and development including hormone cross-talk can beaddressed.} } @Article{IPB-1526, author = {Kopycki, J. and Wieduwild, E. and Kohlschmidt, J. and Brandt, W. and Stepanova, A.N. and Alonso, J.M. and Pedras, M.S. and Abel, S. and Grubb, C.D.}, title = {{Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition}}, year = {2013}, pages = {37-46}, journal = {Biochem J}, doi = {10.1042/BJ20121403}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23150922}, volume = {450}, abstract = {Plant genomes encode numerous small molecule glycosyltransferases which modulate the solubility, activity, immunogenicity and/or reactivity of hormones, xenobiotics and natural products. The products of these enzymes can accumulate to very high concentrations, yet somehow avoid inhibiting their own biosynthesis. Glucosyltransferase UGT74B1 (UDP-glycosyltransferase 74B1) catalyses the penultimate step in the core biosynthetic pathway of glucosinolates, a group of natural products with important functions in plant defence against pests and pathogens. We found that mutation of the highly conserved Ser284 to leucine [wei9-1 (weak ethylene insensitive)] caused only very mild morphological and metabolic phenotypes, in dramatic contrast with knockout mutants, indicating that steady state glucosinolate levels are actively regulated even in unchallenged plants. Analysis of the effects of the mutation via a structural modelling approach indicated that the affected serine interacts directly with UDP-glucose, but also predicted alterations in acceptor substrate affinity and the kcat value, sparking an interest in the kinetic behaviour of the wild-type enzyme. Initial velocity and inhibition studies revealed that UGT74B1 is not inhibited by its glycoside product. Together with the effects of the missense mutation, these findings are most consistent with a partial rapid equilibrium ordered mechanism. This model explains the lack of product inhibition observed both in vitro and in vivo, illustrating a general mechanism whereby enzymes can continue to function even at very high product/precursor ratios.} } @Article{IPB-1965, author = {Acosta, I.F. and Gasperini, D. and Chételat, A. and Stolz, S. and Santuari, L. and Farmer, E.E.}, title = {{Role of NINJA in root jasmonate signaling}}, year = {2013}, pages = {15473-15478}, chapter = {{}}, journal = {PNAS}, doi = {10.1073/pnas.1307910110}, volume = {110 (38)}, } @Article{IPB-1607, author = {Abel, S. and Bürstenbinder, K. \& Müller, J.}, title = {{The emerging function of IQD proteins as scaffolds in cellular signaling and trafficking}}, year = {2013}, pages = {e24369}, journal = {Plant Signal Behav}, doi = {10.4161/psb.24369}, url = {http://www.tandfonline.com/loi/kpsb20}, volume = {8}, abstract = {Calcium (Ca2+) signaling modules are essential for adjusting plant growth and performance to environmental constraints. Differential interactions between sensors of Ca2+ dynamics and their molecular targets are at the center of the transduction process. Calmodulin (CaM) and CaM-like (CML) proteins are principal Ca2+-sensors in plants that govern the activities of numerous downstream proteins with regulatory properties. The families of IQ67-Domain (IQD) proteins are a large class of plant-specific CaM/CML-targets (e.g., 33 members in A. thaliana) which share a unique domain of multiple varied CaM retention motifs in tandem orientation. Genetic studies in Arabidopsis and tomato revealed first roles for IQD proteins related to basal defense response and plant development. Molecular, biochemical and histochemical analysis of Arabidopsis IQD1 demonstrated association with microtubules as well as targeting to the cell nucleus and nucleolus. In vivo binding to CaM and kinesin light chain-related protein-1 (KLCR1) suggests a Ca2+-regulated scaffolding function of IQD1 in kinesin motor-dependent transport of multiprotein complexes. Furthermore, because IQD1 interacts in vitro with single-stranded nucleic acids, the prospect arises that IQD1 and other IQD family members facilitate cellular RNA localization as one mechanism to control and fine-tune gene expression and protein sorting.} } @Article{IPB-1608, author = {Bürstenbinder, K. and Savchenko, T. and Müller, J. and Adamson, A.W. and Stamm, G. and Kwong, R. and Zipp, B.J. and Dhurvas Chandrasekaran, D. \& Abel, S.}, title = {{Arabidopsis calmodulin-binding protein IQ67-domain 1 localizes to microtubules and interacts with kinesin light chain-related protein-1}}, year = {2013}, pages = {1871-1882}, journal = {J Biol Chem}, doi = {10.1074/jbc.M112.396200}, url = {http://www.jbc.org/}, volume = {288}, abstract = {Calcium (Ca2+) is a key second messenger in eukaryotes and regulates diverse cellular processes, most notably via calmodulin (CaM). In Arabidopsis thaliana, IQD1 (IQ67 domain 1) is the founding member of the IQD family of putative CaM targets. The 33 predicted IQD proteins share a conserved domain of 67 amino acids that is characterized by a unique arrangement of multiple CaM recruitment motifs, including so-called IQ motifs. Whereas IQD1 has been implicated in the regulation of defense metabolism, the biochemical functions of IQD proteins remain to be elucidated. In this study we show that IQD1 binds to multiple Arabidopsis CaM and CaM-like (CML) proteins in vitro and in yeast two-hybrid interaction assays. CaM overlay assays revealed moderate affinity of IQD1 to CaM2 (Kd ∼ 0.6 μm). Deletion mapping of IQD1 demonstrated the importance of the IQ67 domain for CaM2 binding in vitro, which is corroborated by interaction of the shortest IQD member, IQD20, with Arabidopsis CaM/CMLs in yeast. A genetic screen of a cDNA library identified Arabidopsis kinesin light chain-related protein-1 (KLCR1) as an IQD1 interactor. The subcellular localization of GFP-tagged IQD1 proteins to microtubules and the cell nucleus in transiently and stably transformed plant tissues (tobacco leaves and Arabidopsis seedlings) suggests direct interaction of IQD1 and KLCR1 in planta that is supported by GFP∼IQD1-dependent recruitment of RFP∼KLCR1 and RFP∼CaM2 to microtubules. Collectively, the prospect arises that IQD1 and related proteins provide Ca2+/CaM-regulated scaffolds for facilitating cellular transport of specific cargo along microtubular tracks via kinesin motor proteins.} } @Article{IPB-1378, author = {Goetz, S. and Hellwege, A. and Stenzel, I. and Kutter, C. and Hauptmann, V. and Forner, S. and Mc Caig, B. and Hause, G. and Miersch, O. and Wasternack, C. and Hause, B.}, title = {{Role of cis-12-oxo-phytodienoic acid in tomato embryo development.}}, year = {2012}, pages = {1715-1727}, journal = {Plant Physiol}, url = {http://www.plantphysiol.org/content/158/4/1715.abstract?sid=15b792ec-f1c9-4754-9157-00e7f5042900}, volume = {158 (4)}, abstract = { Oxylipins including jasmonates are signaling compounds in plant growth, development, and responses to biotic and abiotic stresses. In Arabidopsis (Arabidopsis thaliana) most mutants affected in jasmonic acid (JA) biosynthesis and signaling are male sterile, whereas the JA-insensitive tomato (Solanum lycopersicum) mutant jai1 is female sterile. The diminished seed formation in jai1 together with the ovule-specific accumulation of the JA biosynthesis enzyme allene oxide cyclase (AOC), which correlates with elevated levels of JAs, suggest a role of oxylipins in tomato flower/seed development. Here, we show that 35S::SlAOC-RNAi lines with strongly reduced AOC in ovules exhibited reduced seed set similarly to the jai1 plants. Investigation of embryo development of wild-type tomato plants showed preferential occurrence of AOC promoter activity and AOC protein accumulation in the developing seed coat and the embryo, whereas 12-oxo-phytodienoic acid (OPDA) was the dominant oxylipin occurring nearly exclusively in the seed coat tissues. The OPDA- and JA-deficient mutant spr2 was delayed in embryo development and showed an increased programmed cell death in the developing seed coat and endosperm. In contrast, the mutant acx1a, which accumulates preferentially OPDA and residual amount of JA, developed embryos similar to the wild type, suggesting a role of OPDA in embryo development. Activity of the residual amount of JA in the acx1a mutant is highly improbable since the known reproductive phenotype of the JA-insensitive mutant jai1 could be rescued by wound-induced formation of OPDA. These data suggest a role of OPDA or an OPDA-related compound for proper embryo development possibly by regulating carbohydrate supply and detoxification.} } @Article{IPB-1432, author = {Fellenberg, C. and Ziegler, J. and Handrick, V. and Vogt, T.}, title = {{Polyamine homeostasis in wild type and phenolamide deficient \textit{Arabidopsis thaliana} stamens.}}, year = {2012}, pages = {180}, journal = {Front Plant Sci. doi: 10.3389/fpls.2012.00180}, volume = {3}, abstract = { Polyamines (PAs) like putrescine, spermidine, and spermine are ubiquitous polycationic molecules that occur in all living cells and have a role in a wide variety of biological processes. High amounts of spermidine conjugated to hydroxycinnamic acids are detected in the tryphine of Arabidopsis thaliana pollen grains. Tapetum localized spermidine hydroxycinnamic acid transferase (SHT) is essential for the biosynthesis of these anther specific tris-conjugated spermidine derivatives. Sht knockout lines show a strong reduction of hydroxycinnamic acid amides (HCAAs). The effect of HCAA-deficient anthers on the level of free PAs was measured by a new sensitive and reproducible method using 9-fluorenylmethyl chloroformate (FMOC) and fluorescence detection by HPLC. PA concentrations can be accurately determined even when very limited amounts of plant material, as in the case of A. thaliana stamens, are available. Analysis of free PAs in wild type stamens compared to sht deficient mutants and transcript levels of key PA biosynthetic genes revealed a highly controlled regulation of PA homeostasis in A. thaliana anthers.} } @Article{IPB-1454, author = {Janitza, P. and Ullrich, K.K. and Quint, M.}, title = {{Towards a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom}}, year = {2012}, pages = {1-11}, journal = {Front. Plant Sci}, url = {http://www.frontiersin.org/plant_proteomics/10.3389/fpls.2012.00271/abstract}, volume = {3}, abstract = { The mitogen-activated protein kinase (MAPK) pathway is a three-tier signaling cascade that transmits cellular information from the plasma membrane to the cytoplasm where it triggers downstream responses. The MAPKs represent the last step in this cascade and are activated when both tyrosine and threonine residues in a conserved TxY motif are phosphorylated by MAPK kinases, which in turn are themselves activated by phosphorylation by MAPK kinase kinases. To understand the molecular evolution of MAPKs in the plant kingdom, we systematically conducted a Hidden-Markov-Model based screen to identify MAPKs in 13 completely sequenced plant genomes. In this analysis, we included green algae, bryophytes, lycophytes, and several mono- and dicotyledonous species covering \>800 million years of evolution. The phylogenetic relationships of the 204 identified MAPKs based on Bayesian inference facilitated the retraction of the sequence of emergence of the four major clades that are characterized by the presence of a TDY or TEY-A/TEY-B/TEY-C type kinase activation loop. We present evidence that after the split of TDY- and TEY-type MAPKs, initially the TEY-C clade emerged. This was followed by the TEY-B clade in early land plants until the TEY-A clade finally emerged in flowering plants. In addition to these well characterized clades, we identified another highly conserved clade of 45 MAPK-likes, members of which were previously described as MHKs. In agreement with their essential functions, molecular population genetic analysis of MAPK genes in Arabidopsis thaliana accessions reveal that purifying selection drove the evolution of the MAPK family, implying strong functional constraints on MAPK genes. Closely related MAPKs most likely subfunctionalized, a process in which differential transcriptional regulation of duplicates may be involved.} } @Article{IPB-1364, author = {Stenzel, I. and Ischebeck, T. and Quint, M. and Heilmann, I.}, title = {{Variable regions of PI4P 5-kinases direct PtdIns(4,5)P2 towards alternative regulatory functions in tobacco pollen tubes}}, year = {2012}, pages = {114}, journal = {Front. Plant Sci}, url = {http://www.frontiersin.org/plant_physiology/10.3389/fpls.2011.00114/abstract}, volume = {2}, abstract = { The apical plasma membrane of pollen tubes contains different PI4P 5-kinases that all produce phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2] but exert distinct cellular effects. In the present example, overexpression of Arabidopsis AtPIP5K5 or tobacco NtPIP5K6-1 caused growth defects previously attributed to increased pectin secretion. In contrast, overexpression of Arabidopsis AtPIP5K2 caused apical tip swelling implicated in altering actin fine structure in the pollen tube apex. AtPIP5K5, NtPIP5K6-1, and AtPIP5K2 share identical domain structures. Domains required for correct membrane association of the enzymes were identified by systematic deletion of N-terminal domains and subsequent expression of fluorescence-tagged enzyme truncations in tobacco pollen tubes. A variable linker region (Lin) contained in all PI4P 5-kinase isoforms of subfamily B, but not conserved in sequence, was recognized to be necessary for correct subcellular localization of AtPIP5K5, NtPIP5K6-1, and AtPIP5K2. Deletion of N-terminal domains including the Lin domain did not impair catalytic activity of recombinant AtPIP5K5, NtPIP5K6-1, or AtPIP5K2 in vitro; however, the presence of the Lin domain was necessary for in vivo effects on pollen tube growth upon overexpression of truncated enzymes. Overexpression of catalytically inactive variants of AtPIP5K5, NtPIP5K6-1, or AtPIP5K2 did not influence pollen tube growth, indicating that PtdIns(4,5)P2 production rather than structural properties of PI4P 5-kinases was relevant for the manifestation of growth phenotypes. When Lin domains were swapped between NtPIP5K6-1 and AtPIP5K2 and the chimeric enzymes overexpressed in pollen tubes, the chimeras reciprocally gained the capabilities to invoke tip swelling or secretion phenotypes, respectively. The data indicate that the Lin domain directed the enzymes into different regulatory contexts, possibly contributing to channeling of PtdIns(4,5)P2 at the interface of secretion and actin cytoskeleton.} } @Article{IPB-1387, author = {Terrile, M.C. and París, R. and Calderón Villalobos, L.I. and Iglesias, M.J. and Lamattina, L. and Estelle, M. and Casalongué, C.A.}, title = {{Nitric oxide influences auxin signaling through S-nitrosylation of the Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 auxin receptor.}}, year = {2012}, pages = {492-500}, journal = {Plant J}, doi = {10.1111/j.1365-313X.2011.04885.x.}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04885.x/abstract}, volume = {70}, abstract = { Previous studies have demonstrated that auxin (indole-3-acetic acid) and nitric oxide (NO) are plant growth regulators that coordinate several plant physiological responses determining root architecture. Nonetheless, the way in which these factors interact to affect these growth and developmental processes is not well understood. The Arabidopsis thaliana F-box proteins TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) are auxin receptors that mediate degradation of AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to induce auxin-regulated responses. A broad spectrum of NO-mediated protein modifications are known in eukaryotic cells. Here, we provide evidence that NO donors increase auxin-dependent gene expression while NO depletion blocks Aux/IAA protein degradation. NO also enhances TIR1-Aux/IAA interaction as evidenced by pull-down and two-hybrid assays. In addition, we provide evidence for NO-mediated modulation of auxin signaling through S-nitrosylation of the TIR1 auxin receptor. S-nitrosylation of cysteine is a redox-based post-translational modification that contributes to the complexity of the cellular proteome. We show that TIR1 C140 is a critical residue for TIR1Aux/IAA interaction and TIR1 function. These results suggest that TIR1 S-nitrosylation enhances TIR1Aux/IAA interaction, facilitating Aux/IAA degradation and subsequently promoting activation of gene expression. Our findings underline the importance of NO in phytohormone signaling pathways.} } @Article{IPB-1443, author = {Brandt, R. and Salla-Martret, M. and Bou-Torrent, J. and Musielak, T. and Stahl, M. and Lanz, C. and Ott, F. and Schmid, M. and Greb, T. and Schwarz, M. and Choi, S.B. and Barton, M.K. and Reinhart, B.J. and Liu, T. and Quint, M. and Palauqui, J.C. and Martínez-García, J.F. and Wenkel, S.}, title = {{Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses}}, year = {2012}, pages = {31-42}, journal = {Plant J }, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.05049.x/abstract}, volume = {72}, abstract = { Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.} } @Article{IPB-1435, author = {Wasternack, C. and Goetz, S. and Hellwege, A. and Forner, S. and Strnad, M. and Hause, B.}, title = {{Another JA/COI1-independent role of OPDA detected in tomato embryo development.}}, year = {2012}, pages = {1349-1353}, journal = {Plant Signal Behav}, doi = {10.4161/psb.21551}, url = {http://www.tandfonline.com/loi/kpsb20}, volume = {7}, abstract = { Jasmonates (JAs) are ubiquitously occurring signaling compounds in plants formed in response to biotic and abiotic stress as well as in development. (+)-7-iso-jasmonoyl isoleucine, the bioactive JA, is involved in most JA-dependent processes mediated by the F-box protein COI1 in a proteasome-dependent manner. However, there is an increasing number of examples, where the precursor of JA biosynthesis, cis-(+)-12-oxophytodienoic acid (OPDA) is active in a JA/COI1-independent manner. Here, we discuss those OPDA-dependent processes, thereby giving emphasis on tomato embryo development. Recent data on seed coat-generated OPDA and its role in embryo development is discussed based on biochemical and genetic evidences.} } @Article{IPB-1442, author = {Quint, M. and Drost, H.-G. and Gabel, A. and Ullrich, K. K. and Bönn, M. and Grosse, I.}, title = {{A transcriptomic hourglass in plant embryogenesis}}, year = {2012}, pages = {98-101}, journal = {Nature}, url = {http://www.nature.com/nature/journal/v490/n7418/full/nature11394.html}, volume = {490}, abstract = { Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages1. Comparative anatomy of vertebrate developmentbased on the Meckel-Serrès law2 and von Baers laws of embryology3 from the early nineteenth centuryshows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic hourglass4, 5, and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage6. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes7 and global gene expression profiles were reported to be most conserved8. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.} } @INBOOK{IPB-1576, author = {Carbonell, A. and Flores, R. and Gago, S.}, title = {{From Nucleic Acids Sequences to Molecular Medicine}}, year = {2012}, pages = {411-427}, chapter = {{Hammerhead Ribozymes Against Virus and Viroid RNAs}}, journal = {Springer-Verlag Berlin Heidelberg}, editor = {Erdmann, V. A., Barciszewski, J.}, } @Article{IPB-1966, author = {Gasperini, D. and Greenland, A. and Hedden, P. and Dreos, R. and Harwood, W. and Griffiths, S.}, title = {{Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids.}}, year = {2012}, pages = {4419-4436}, chapter = {{}}, journal = { J. Exp. Bot.}, doi = {10.1093/jxb/ers138}, volume = {63}, } @Article{IPB-1388, author = {Calderón Villalobos, L.I. and Lee, S. and De Oliveira, C. and Ivetac, A. and Brandt, W. and Armitage, L. and Sheard, LB. and Tan, X. and Parry, G. and Mao, H. and Zheng, N. and Napier, R. and Kepinski, S. and Estelle, M.}, title = {{A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin.}}, year = {2012}, pages = {477-485}, journal = {Nat. Chem. Biol}, doi = {10.1038/nchembio.926}, url = {http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.926.html}, volume = {8}, abstract = { The plant hormone auxin regulates virtually every aspect of plant growth and development. Auxin acts by binding the F-box protein transport inhibitor response 1 (TIR1) and promotes the degradation of the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressors. Here we show that efficient auxin binding requires assembly of an auxin co-receptor complex consisting of TIR1 and an Aux/IAA protein. Heterologous experiments in yeast and quantitative IAA binding assays using purified proteins showed that different combinations of TIR1 and Aux/IAA proteins form co-receptor complexes with a wide range of auxin-binding affinities. Auxin affinity seems to be largely determined by the Aux/IAA. As there are 6 TIR1/AUXIN SIGNALING F-BOX proteins (AFBs) and 29 Aux/IAA proteins in Arabidopsis thaliana, combinatorial interactions may result in many co-receptors with distinct auxin-sensing properties. We also demonstrate that the AFB5Aux/IAA co-receptor selectively binds the auxinic herbicide picloram. This co-receptor system broadens the effective concentration range of the hormone and may contribute to the complexity of auxin response.} } @Article{IPB-1276, author = {Schumann, N. and Navarro-Quezada, A.R. and Ullrich, K. and Kuhl, C. and Quint, M.}, title = {{Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats}}, year = {2011}, pages = {835-850}, journal = {Plant Physiol}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21119043}, volume = {155}, abstract = { The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.} } @Article{IPB-1445, author = {Costa, C.T. and Strieder, M.L. and Abel, S. and Delatorre, C.A.}, title = {{Phosphorus and nitrogen interaction: loss of QC identity in response to P or N limitation is anticipated in the \textit{pdr23} mutant}}, year = {2011}, pages = {219-229}, journal = {Braz J Plant Physiol }, url = {http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1677-04202011000300006&lng=en&nrm=iso}, volume = {23(3)}, abstract = {Changes in root architecture are an important adaptive strategy used by plants in response to limited nutrient availability to increase the odds of acquiring them. The quiescent center (QC) plays an important role by altering the meristem activity causing differentiation and therefore, inducing a determinate growth program. The arabidopsis mutant pdr23 presents primary short root in the presence of nitrate and is inefficient in the use of nucleic acids as a source of phosphorus. In this study the effect of the pdr23 mutation on the QC maintenance under low phosphorus (P) and/or nitrogen is evaluated. QC identity is maintained in wild-type in the absence of nitrate and/or phosphate if nucleic acids can be used as an alternative source of these nutrients, but not in pdr23. The mutant is not able to use nucleic acids efficiently for substitute Pi, determinate growth is observed, similar to wild-type in the total absence of P. In the absence of N pdr23 loses the expression of QC identity marker earlier than wild-type, indicating that not only the response to P is altered, but also to N. The data suggest that the mutation affects a gene involved either in the crosstalk between these nutrients or in a pathway shared by both nutrients limitation response. Moreover loss of QC identity is also observed in wild-type in the absence of N at longer limitation. Less drastic symptoms are observed in lateral roots of both genotypes. } } @Article{IPB-1304, author = {Abel, S.}, title = {{Phosphate sensing in root development}}, year = {2011}, pages = {303-309}, journal = {Curr. Opin. Plant Biol.}, url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS4-52VW0YT-1-1&_cdi=6252&_user=4832532&_pii=S1369526611000598&_origin=browse&_zone=rslt_list_item&_coverDate=06%2F30%2F2011&_sk=999859996&wchp=dGLzVlb-zSkWW&md5=5356347088bc931a33600d8a2f4e4f08&ie}, volume = {14 (3)}, abstract = {Phosphate (Pi) and its anhydrides constitute major nodes in metabolism. Thus, plant performance depends directly on Pi nutrition. Inadequate Pi availability in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi usage and acquisition. The sensory mechanisms that monitor environmental Pi and transmit the nutritional signal to adjust root development have increasingly come into focus. Recent transcriptomic analyses and genetic approaches have highlighted complex antagonistic interactions between external Pi and Fe bioavailability and have implicated the stem cell niche as a target of Pi sensing to regulate root meristem activity.} } @Article{IPB-1275, author = {Delker, C. and Quint, M.}, title = {{Expression level polymorphisms: heritable traits shaping natural variation}}, year = {2011}, pages = {481-488}, journal = {Trends Plant Sci}, url = {http://dx.doi.org/10.1016/j.tplants.2011.05.009}, volume = {16}, abstract = { Natural accessions of many species harbor a wealth of genetic variation visible in a large array of phenotypes. Although expression level polymorphisms (ELPs) in several genes have been shown to contribute to variation in diverse traits, their general impact on adaptive variation has likely been underestimated. At present, ELPs have predominantly been correlated to quantitative trait loci (eQTLs) that occupy central hubs in signaling networks, which pleiotropically affect numerous traits. To increase the sensitivity of detecting minor effect eQTLs or those that act in a trait-specific manner, we emphasize the need for more systematic approaches. This requires, but is not limited to, refining experimental designs such as reduction of tissue complexity and combinatorial methods including a priori defined networks.} } @INBOOK{IPB-1575, author = {Vaira, A.M. and Gago-Zachert, S. and Garcia, M.L. and Guerri, J. and Hammond, J. and Milne, R.G. and Moreno, P. and Morikawa, T. and Natsuaki, T. and Navarro, J.A. and Pallas, V. and Torok, V. and Verbeek, M. and Vetten, H.J.}, title = {{Virus Taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses}}, year = {2011}, pages = {743-748}, chapter = {{Family Ophioviridae}}, journal = {Elsevier, Academic Press}, editor = {King, A. M. Q., Adams, M. J., Carstens, E. B., Lefkowitz, E. J.}, } @Article{IPB-1574, author = {Carbonell, A. and Flores, R. and Gago, S. }, title = {{Trans -cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA}}, year = {2011}, pages = {2432-2444}, journal = {Nucleic Acids Research}, doi = {10.1093/nar/gkq1051}, url = {https://doi.org/10.1093/nar/gkq1051}, volume = {39}, abstract = {Trans -cleaving hammerheads with discontinuous or extended stem I and with tertiary stabilizing motifs (TSMs) have been tested previously against short RNA substrates in vitro at low Mg 2+ concentration. However, the potential of these ribozymes for targeting longer and structured RNAs in vitro and in vivo has not been examined. Here, we report the in vitro cleavage of short RNAs and of a 464-nt highly structured RNA from potato spindle tuber viroid (PSTVd) by hammerheads with discontinuous and extended formats at submillimolar Mg 2+ . Under these conditions, hammerheads derived from eggplant latent viroid and peach latent mosaic viroid (PLMVd) with discontinuous and extended formats, respectively, where the most active. Furthermore, a PLMVd-derived hammerhead with natural TSMs showed activity in vivo against the same long substrate and interfered with systemic PSTVd infection, thus reinforcing the idea that this class of ribozymes has potential to control pathogenic RNA replicons.} } @Article{IPB-1446, author = {Flores, R. and Grubb, C.D. and Elleuch, A. and Nohales, M.A and Delgado, S. and Gago, S.}, title = {{Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus}}, year = {2011}, pages = {200-206}, journal = {RNA Biol}, doi = {10.4161/rna.8.2.14238}, url = {https://doi.org/10.4161/rna.8.2.14238}, volume = {8(2)}, abstract = { Viroids and viroid-like satellite RNAs from plants, and the human hepatitis delta virus (HDV) RNA share some properties that include small size, circularity and replication through a rolling-circle mechanism. Replication occurs in different cell compartments (nucleus, chloroplast and membrane-associated cytoplasmatic vesicles) and has three steps: RNA polymerization, cleavage and ligation. The first step generates oligomeric RNAs that result from the reiterative transcription of the circular templates of one or both polarities, and is catalyzed by either the RNA-dependent RNA polymerase of the helper virus on which viroid-like satellite RNAs are functionally dependent, or by host DNA-dependent RNA polymerases that, remarkably, viroids and HDV redirect to transcribe RNA templates. Cleavage is mediated by host enzymes in certain viroids and viroid-like satellite RNAs, while in others and in HDV is mediated by cis-acting ribozymes of three classes. Ligation appears to be catalyzed mainly by host enzymes. Replication most likely also involves many other non-catalytic proteins of host origin and, in HDV, the single virus-encoded protein.} } @Article{IPB-1305, author = {Kopycki, J. and Schmidt, J. and Abel, S. and Grubb, D.}, title = {{Chemoenzymatic synthesis of diverse thiohydroximates from gluconsinolate-utilizing enymes from \textit{ Helix pomatia} and \textit{ Caldicellulosiruptor saccharolyticus}}}, year = {2011}, pages = {1039-1046}, journal = {Biotechnol. Lett}, doi = {10.1007/s10529-011-0530-y}, url = {http://www.springerlink.com/content/p4x00m77787534t6/fulltext.pdf}, volume = {33}, abstract = { Thiohydroximates comprise a diverse class of compounds important in both biological and industrial chemistry. Their syntheses are generally limited to simple alkyl and aryl compounds with few stereocenters and a narrow range of functional groups. We hypothesized that sequential action of two recombinant enzymes, a sulfatase from Helix pomatia and a β-O-glucosidase from Caldicellulosiruptor saccharolyticus, on glucosinolates would allow synthesis of thiohydroximates from a structurally broad array of abundant precursors. We report successful synthesis of thiohydroximates of varied chemical classes, including from homochiral compounds of demonstrated biological activity. The chemoenzymatic synthetic route reported here should allow access to many, if not all, of the thiohydroximate core structures of the ~200 known naturally occurring glucosinolates. The enrichment of this group for compounds with possible pharmacological potential is discussed.} } @Article{IPB-1967, author = {Asquini, E. and Gerdol, M. and Gasperini, D. and Igic, B. and Graziosi, G. and Pallavicini A.}, title = {{S-RNase-like Sequences in Styles of Coffea (Rubiaceae). Evidence for S-RNase Based Gametophytic Self-Incompatibility?}}, year = {2011}, pages = {237-249}, journal = {Tropical Plant Biol.}, doi = {10.1007/s12042-011-9085-2}, volume = {4}, } @INBOOK{IPB-1497, author = {Yamaguchi, I. and Cohen, J.D. and Culler, A.H. and Quint, M. and Slovin, J.P. and Nakajima, M. and Sakakibara, H. and Kuroha, T. and Hirai, N. and Yokota, T. and Ohta, H. and Kabayashi, Y. and Mori, H. and Sakagami, Y.}, title = {{Comprehensive Natural Products II}}, year = {2010}, pages = {9-125}, chapter = {{Plant Hormones}}, journal = {Comprehensive Natural Products II, Elsevier, Oxford}, editor = {Lew Mander and Hung-Wen (Ben) Liu}, abstract = {The definition of a plant hormone has not been clearly established, so the compounds classified as plant hormones often vary depending on which definition is considered. In this chapter, auxins, gibberellins (GAs), cytokinins, abscisic acid, brassinosteroids, jasmonic acid-related compounds, and ethylene are described as established plant hormones, while polyamines and phenolic compounds are not included. On the other hand, several peptides that have been proven to play a clear physiological role(s) in plant growth and development, similar to the established plant hormones, are referred. This chapter will focus primarily on the more recent discoveries of plant hormones and their impact on our current understanding of their biological role. In some cases, however, it is critical to place recent work in a proper historical context.} } @Article{IPB-1215, author = {Leon-Reyes, A. and Van der Does, D. and De Lange, E.S. and Delker, C. and Wasternack, C. and Van Wees, S.C. and Ritsema, T. and Pieterse, C.M.}, title = {{Salicylate-mediated suppression of jasmonate-responsive gene expression in Arabidopsis is targeted downstream of the jasmonate biosynthesis pathway}}, year = {2010}, pages = {1423-1432}, journal = {Planta}, url = {http://link.springer.com/article/10.1007/s00425-010-1265-z}, volume = {232(6)}, abstract = { Jasmonates (JAs) and salicylic acid (SA) are plant hormones that play pivotal roles in the regulation of induced defenses against microbial pathogens and insect herbivores. Their signaling pathways cross-communicate providing the plant with a regulatory potential to finely tune its defense response to the attacker(s) encountered. In Arabidopsis thaliana, SA strongly antagonizes the jasmonic acid (JA) signaling pathway, resulting in the downregulation of a large set of JA-responsive genes, including the marker genes PDF1.2 and VSP2. Induction of JA-responsive marker gene expression by different JA derivatives was equally sensitive to SA-mediated suppression. Activation of genes encoding key enzymes in the JA biosynthesis pathway, such as LOX2, AOS, AOC2, and OPR3 was also repressed by SA, suggesting that the JA biosynthesis pathway may be a target for SA-mediated antagonism. To test this, we made use of the mutant aos/dde2, which is completely blocked in its ability to produce JAs because of a mutation in the ALLENE OXIDE SYNTHASE gene. Mutant aos/dde2 plants did not express the JA-responsive marker genes PDF1.2 or VSP2 in response to infection with the necrotrophic fungus Alternaria brassicicola or the herbivorous insect Pieris rapae. Bypassing JA biosynthesis by exogenous application of methyl jasmonate (MeJA) rescued this JA-responsive phenotype in aos/dde2. Application of SA suppressed MeJA-induced PDF1.2 expression to the same level in the aos/dde2 mutant as in wild-type Col-0 plants, indicating that SA-mediated suppression of JAresponsive gene expression is targeted at a position downstream of the JA biosynthesis pathway.} } @Article{IPB-1277, author = {Calderón Villalobos, L.I. and Tan, X. and Zheng, N. and Estelle, M.}, title = {{Auxin perception - structural insights}}, year = {2010}, journal = {CSH Perspect. Biol}, url = {http://cshperspectives.cshlp.org/content/2/7/a005546.full?sid=084e458a-ebe2-449e-a254-577d24ee0e29}, volume = {2(7)}, abstract = { The identity of the auxin receptor(s) and the mechanism of auxin perception has been a subject of intense interest since the discovery of auxin almost a century ago. The development of genetic approaches to the study of plant hormone signaling led to the discovery that auxin acts by promoting degradation of transcriptional repressors called Aux/IAA proteins. This process requires a ubiquitin protein ligase (E3) called SCFTIR1 and related SCF complexes. Surprisingly, auxin works by directly binding to TIR1, the F-box protein subunit of this SCF. Structural studies demonstrate that auxin acts like a molecular glue, to stabilize the interaction between TIR1 and the Aux/IAA substrate. These exciting results solve an old problem in plant biology and reveal new mechanisms for E3 regulation and hormone perception.} } @Article{IPB-1278, author = {Abel, S. and Theologis, A.}, title = {{Odyssey of Auxin}}, year = {2010}, pages = {1-13}, journal = {Cold Spring Habor Perspectives in Biology}, doi = {10.1101/cshperspect.a004572}, url = {http://cshperspectives.cshlp.org/content/2/10/a004572.full.pdf+html?sid=2dcc6405-a286-4a24-a297-b935835ee65a}, volume = {2(10)}, abstract = {The history of plant biology is inexorably intertwined with the conception and discovery of auxin, followed by the many decades of research to comprehend its action during growth and development. Growth responses to auxin are complex and require the coordination of auxin production, transport, and perception. In this overview of past auxin research, we limit our discourse to the mechanism of auxin action. We attempt to trace the almost epic voyage from the birth of the hormonal concept in plants to the recent crystallographic studies that resolved the TIR1-auxin receptor complex, the first structural model of a plant hormone receptor. The century-long endeavor is a beautiful illustration of the power of scientific reasoning and human intuition, but it also brings to light the fact that decisive progress is made when new technologies emerge and disciplines unite.} } @Article{IPB-1219, author = {Sreenivasulu, N. and Radchuk, V. and Alawady, A. and Borisjuk, L. and Weier, D. and Staroske, N. and Fuchs, J. and Miersch, O. and Strickert, M. and Usadel, B. and Wobus, U. and Grimm, B. and Weber, H. and Weschke, W.}, title = {{De-regulation of abscisic acid contents causes abnormal endosperm development in the barley mutant seg8}}, year = {2010}, pages = {589-603}, journal = {The Plant Journal }, doi = {10.1111/j.1365-313X.2010.04350.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04350.x/abstract}, volume = {64(4)}, abstract = {Grain development of the maternal effect shrunken endosperm mutant seg8 was analysed by comprehensive molecular, biochemical and histological methods. The most obvious finding was de-regulation of ABA levels, which were lower compared to wild-type during the pre-storage phase but higher during the transition from cell division/differentiation to accumulation of storage products. Ploidy levels and ABA amounts were inversely correlated in the developing endosperms of both mutant and wild-type, suggesting an influence of ABA on cell-cycle regulation. The low ABA levels found in seg8 grains between anthesis and beginning endosperm cellularization may result from a gene dosage effect in the syncytial endosperm that causes impaired transfer of ABA synthesized in vegetative tissues into filial grain parts. Increased ABA levels during the transition phase are accompanied by higher chlorophyll and carotenoid/xanthophyll contents. The data suggest a disturbed ABA-releasing biosynthetic pathway. This is indicated by up-regulation of expression of the geranylgeranyl reductase (GGR) gene, which may be induced by ABA deficiency during the pre-storage phase. Abnormal cellularization/differentiation of the developing seg8 endosperm and reduced accumulation of starch are phenotypic characteristics that reflect these disturbances. The present study did not reveal the primary gene defect causing the seg8 phenotype, but presents new insights into the maternal/filial relationships regulating barley endosperm development.} } @Article{IPB-1206, author = {Stumpe, M. and Göbel, C. and Faltin, B. and Beike, A.K. and Hause, B. and Himmelsbach, K. and Bode, J. and Kramell, R. and Wasternack, C. and Frank, W. and Reski, R. and Feussner, I.}, title = {{The moss Physcomitrella patens contains cyclopentenones but no jasmonates: mutations in allene oxide cyclase lead to reduced fertility and altered sporophyte morphology}}, year = {2010}, pages = {740-749}, journal = {New Phytologist}, doi = {10.1111/j.1469-8137.2010.03406.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03406.x/abstract}, volume = {188 (3)}, abstract = {Two cDNAs encoding allene oxide cyclases (PpAOC1, PpAOC2), key enzymes in the formation of jasmonic acid (JA) and its precursor (9S,13S)-12-oxo-phytodienoic acid (cis-(+)-OPDA), were isolated from the moss Physcomitrella patens. Recombinant PpAOC1 and PpAOC2 show substrate specificity against the allene oxide derived from 13-hydroperoxy inolenic acid (13-HPOTE); PpAOC2 also shows substrate specificity against the allene oxide derived from 12-hydroperoxy arachidonic acid (12-HPETE). In protonema and gametophores the occurrence of cis-(+)-OPDA, but neither JA nor the isoleucine conjugate of JA nor that of cis-(+)-OPDA was detected. Targeted knockout mutants for PpAOC1 and for PpAOC2 were generated, while double mutants could not be obtained. The DPpAOC1 and DPpAOC2 mutants showed reduced fertility, aberrant sporophyte morphology and interrupted sporogenesis.} } @Article{IPB-1205, author = {Ludwig-Müller, J. and Denk, K. and Cohen, J.D. and Quint, M.}, title = {{An inhibitor of tryptophan-dependent biosynthesis of indole-3-acetic acid alters seedling development in Arabidopsis}}, year = {2010}, pages = {242-248}, journal = {J Plant Growth Regul}, volume = {29}, abstract = {Although polar transport and the TIR1-dependent signaling pathway of the plant hormone auxin/indole-3-acetic acid (IAA) are well characterized, understanding of the biosynthetic pathway(s) leading to the production of IAA is still limited. Genetic dissection of IAA biosynthetic pathways has been complicated by the metabolic redundancy caused by the apparent existence of several parallel biosynthetic routes leading to IAA production. Valuable complementary tools for genetic as well as biochemical analysis of auxin biosynthesis would be molecular inhibitors capable of acting in vivo on specific or general components of the pathway(s), which unfortunately have been lacking. Several indole derivatives have been previously identified to inhibit tryptophan-dependent IAA biosynthesis in an in vitro system from maize endosperm. We examined the effect of one of them, 6-fluoroindole, on seedling development of Arabidopsis thaliana and tested its ability to inhibit IAA biosynthesis in feeding experiments in vivo. We demonstrated a correlation of severe developmental defects or growth retardation caused by 6-fluoroindole with significant downregulation of de novo synthesized IAA levels, derived from the stable isotope-labeled tryptophan pool, upon treatment. Hence, 6-fluoroindole shows important features of an inhibitor of tryptophan-dependent IAA biosynthesis both in vitro and in vivo and thus may find use as a promising molecular tool for the identification of novel components of the auxin biosynthetic pathway(s).} } @Article{IPB-1203, author = {Delker, C. and Pöschl, Y. and Raschke, A. and Ullrich, K. and Ettingshausen, S. and Hauptmann, V. and Grosse, I. and Quint, M.}, title = {{Natural variation of transcriptional auxin response networks in Arabidopsis thaliana}}, year = {2010}, pages = {2184-2200}, journal = {Plant Cell}, url = {http://dx.doi.org/10.1105/tpc.110.073957}, volume = {22}, abstract = {Natural variation has been observed for various traits in Arabidopsis thaliana. Here, we investigated natural variation in the context of physiological and transcriptional responses to the phytohormone auxin, a key regulator of plant development. A survey of the general extent of natural variation to auxin stimuli revealed significant physiological variation among 20 genetically diverse natural accessions. Moreover, we observed dramatic variation on the global transcriptome level after induction of auxin responses in seven accessions. Although we detect isolated cases of major-effect polymorphisms, sequencing of signaling genes revealed sequence conservation, making selective pressures that favor functionally different protein variants among accessions unlikely. However, coexpression analyses of a priori defined auxin signaling networks identified variations in the transcriptional equilibrium of signaling components. In agreement with this, cluster analyses of genome-wide expression profiles followed by analyses of a posteriori defined gene networks revealed accession-specific auxin responses. We hypothesize that quantitative distortions in the ratios of interacting signaling components contribute to the detected transcriptional variation, resulting in physiological variation of auxin responses among accessions.} } @Article{IPB-1189, author = {Robson, F. and Okamoto, H. and Patrick, E. and Harris, S. and Wasternack, C. and Brearley, C. and Turner, J.G.}, title = {{Jasmonate and Phytochrome A Signaling in \textit{Arabidopsis} Wound and Shade Responses Are Integrated through JAZ1 Stability}}, year = {2010}, pages = {1143 - 1160}, journal = {The Plant Cell}, url = {http://www.plantcell.org/search?author1=&fulltext=&pubdate_year=2010&volume=22&firstpage=1143&submit=yes}, volume = {22(4)}, abstract = {Jasmonate (JA) activates plant defense, promotes pollen maturation, and suppresses plant growth. An emerging theme in JA biology is its involvement in light responses; here, we examine the interdependence of the JA- and light-signaling pathways in Arabidopsis thaliana. We demonstrate that mutants deficient in JA biosynthesis and signaling are deficient in a subset of high irradiance responses in far-red (FR) light. These mutants display exaggerated shade responses to low, but not high, R/FR ratio light, suggesting a role for JA in phytochrome A (phyA) signaling. Additionally, we demonstrate that the FR lightinduced expression of transcription factor genes is dependent on CORONATINE INSENSITIVE1 (COI1), a central component of JA signaling, and is suppressed by JA. phyA mutants had reduced JA-regulated growth inhibition and VSP expression and increased content of cis-(+)-12-oxophytodienoic acid, an intermediate in JA biosynthesis. Significantly, COI1-mediated degradation of JASMONATE ZIM DOMAIN1-b-glucuronidase (JAZ1-GUS) in response to mechanical wounding and JA treatment required phyA, and ectopic expression of JAZ1-GUS resulted in exaggerated shade responses.Together, these results indicate that JA and phyA signaling are integrated through degradation of the JAZ1 protein, and both are required for plant responses to light and stress.} } @Article{IPB-1187, author = {Wasternack, C. and Xie, D.}, title = {{The genuine ligand of a jasmonic acid receptor: Improved analysis of jasmonates is now required.}}, year = {2010}, pages = {337 - 340}, journal = {Plant Signal Behav}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958582/}, volume = {5(4)}, abstract = {Jasmonic acid (JA), its metabolites, such as the methyl ester or amino acid conjugates as well as its precursor 12-oxophytodienoic acid (OPDA) are lipid-derived signals. JA, OPDA and JA-amino acid conjugates are known to function as signals in plant stress responses and development. More recently, formation of JA-amino acid conjugates and high biological activity of JA-Isoleucine (JA-Ile) were found to be essential in JA signaling. A breakthrough was the identification of JAZ proteins which interact with the F-box protein COI1 if JA-Ile is bound. This interaction leads to proteasomal degradation of JAZs being negative regulators of JA-induced transcription. Surprisingly, a distinct stereoisomer of JA-Ile, the (+)-7-iso-JA-Ile [(3R,7S) form] is most active. Coronatine, a bacterial phytotoxine with an identical stereochemistry at the cyclopentanone ring, has a similar bioactivity. This was explained by the recent identification of COI1 as the JA receptor and accords well with molecular modeling studies. Whereas over the last two decades JA was quantified to describe any JA dependent process, now we have to take into account a distinct stereoisomer of JA-Ile. Until recently a quantitative analysis of (+)-7-iso-JA-Ile was missing presumable due to its equilibration to (−)-JA-Ile. Now such an analysis was achieved. These aspects will be discussed based on our new knowledge on JA perception and signaling.} } @Article{IPB-1160, author = {Wasternack, C. and Kombrink, E.}, title = {{Jasmonates: Structural Requirements for Lipid-Derived Signals Active in Plant Stress Responses and Development}}, year = {2010}, pages = {63 - 77}, journal = {ACS Chem. Biol doi: 10.1021/cb900269u}, url = {http://pubs.acs.org/doi/abs/10.1021/cb900269u?journalCode=acbcct&quickLinkVolume=5&quickLinkPage=63&selectedTab=citation&volume=5}, volume = {5(1)}, abstract = {Jasmonates are lipid-derived signals that mediate plant stress responses and development processes. Enzymes participating in biosynthesis of jasmonic acid (JA) (1, 2) and components of JA signaling have been extensively characterized by biochemical and molecular-genetic tools. Mutants of Arabidopsis and tomato have helped to define the pathway for synthesis of jasmonoyl-isoleucine (JA-Ile), the active form of JA, and to identify the F-box protein COI1 as central regulatory unit. However, details of the molecular mechanism of JA signaling have only recently been unraveled by the discovery of JAZ proteins that function in transcriptional repression. The emerging picture of JA perception and signaling cascade implies the SCFCOI1 complex operating as E3 ubiquitin ligase that upon binding of JA-Ile targets JAZ repressors for degradation by the 26S-proteasome pathway, thereby allowing the transcription factor MYC2 to activate gene expression. The fact that only one particular stereoisomer, (+)-7-iso-JA-l-Ile (4), shows high biological activity suggests that epimerization between active and inactive diastereomers could be a mechanism for turning JA signaling on or off. The recent demonstration that COI1 directly binds (+)-7-iso-JA-l-Ile (4) and thus functions as JA receptor revealed that formation of the ternary complex COI1-JA-Ile-JAZ is an ordered process. The pronounced differences in biological activity of JA stereoisomers also imply strict stereospecific control of product formation along the JA biosynthetic pathway. The pathway of JA biosynthesis has been unraveled, and most of the participating enzymes are well-characterized. For key enzymes of JA biosynthesis the crystal structures have been established, allowing insight into the mechanisms of catalysis and modes of substrate binding that lead to formation of stereospecific products.} } @Article{IPB-1573, author = {Renovell, A. and Gago, S. and Ruiz-Ruiz, S. and Velázquez, K. and Navarro, L. and Moreno, P. and Vives, M.C. and Guerri, J.}, title = {{Mapping the subgenomic RNA promoter of the Citrus leaf blotch virus coat protein gene by Agrobacterium-mediated inoculation}}, year = {2010}, pages = {360-369}, journal = {Virology}, doi = {10.1016/j.virol.2010.07.034}, url = {https://doi.org/10.1016/j.virol.2010.07.034}, volume = {406}, } @INBOOK{IPB-1158, author = {Wasternack, C.}, title = {{Plant Stress Biology}}, year = {2009}, pages = {91 - 118}, chapter = {{Jasmonates in Stress, Growth, and Development}}, journal = {WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim}, editor = {H. Hirt}, } @INBOOK{IPB-1499, author = {Dorka, R. and Miersch, O. and Hause, B. and Weik, P. and Wasternack, C.}, title = {{Die Mistel in der Tumortherapie 2}}, year = {2009}, pages = {49-56}, chapter = {{Chronobiologische Phänomene und Jasmonatgehalt bei \textit{Viscum album} L.}}, journal = {KVC-Verlag Essen}, editor = {Scheer, R.; Bauer, R.; Bekker, A.; Berg, P. A.; Fintelmann, V.}, } @Article{IPB-1572, author = {Flores, R. and Gas, M.E. and Molina-Serrano, D. and Nohales, M.A. and Carbonell, A. and Gago, S. and de la Peña, M. and Daròs, J.A. }, title = {{Viroid replication: rolling-circles, enzymes and ribozymes}}, year = {2009}, pages = {317-334}, journal = {Viruses}, doi = {10.3390/v1020317}, volume = {1}, } @Article{IPB-1280, author = {Santner, A. and Calderón Villalobos, L.I. and Estelle, M.}, title = {{Plant hormones are versatile chemical regulators of plant growth}}, year = {2009}, pages = {301-307}, journal = {Nat. Chem. Biol}, url = {http://www.nature.com/nchembio/journal/v5/n5/full/nchembio.165.html}, volume = {5(5)}, abstract = { The plant hormones are a structurally unrelated collection of small molecules derived from various essential metabolic pathways. These compounds are important regulators of plant growth and mediate responses to both biotic and abiotic stresses. During the last ten years there have been many exciting advances in our understanding of plant hormone biology, including new discoveries in the areas of hormone biosynthesis, transport, perception and response. Receptors for many of the major hormones have now been identified, providing new opportunities to study the chemical specificity of hormone signaling. These studies also reveal a surprisingly important role for the ubiquitin-proteasome pathway in hormone signaling. In addition, recent work confirms that hormone signaling interacts at multiple levels during plant growth and development. In the future, a major challenge will be to understand how the information conveyed by these simple compounds is integrated during plant growth.} } @Article{IPB-1279, author = {Parry, G. and Calderón Villalobos, L.I. and Prigge, M. and Peret, B. and Dharmasiri, S. and Itoh, H. and Lechner, E. and Gray, W.M. and Bennett, M. and Estelle, M.}, title = {{Complex regulation of the TIR/AFB family of auxin receptors}}, year = {2009}, pages = {22540-22545}, journal = {PNAS USA}, url = {http://www.pnas.org/content/106/52/22528.full}, volume = {106(52)}, abstract = { Auxin regulates most aspects of plant growth and development. The hormone is perceived by the TIR1/AFB family of F-box proteins acting in concert with the Aux/IAA transcriptional repressors. Arabidopsis plants that lack members of the TIR1/AFB family are auxin resistant and display a variety of growth defects. However, little is known about the functional differences between individual members of the family. Phylogenetic studies reveal that the TIR1/AFB proteins are conserved across land plant lineages and fall into four clades. Three of these subgroups emerged before separation of angiosperms and gymnosperms whereas the last emerged before the monocot-eudicot split. This evolutionary history suggests that the members of each clade have distinct functions. To explore this possibility in Arabidopsis, we have analyzed a range of mutant genotypes, generated promoter swap transgenic lines, and performed in vitro binding assays between individual TIR1/AFB and Aux/IAA proteins. Our results indicate that the TIR1/AFB proteins have distinct biochemical activities and that TIR1 and AFB2 are the dominant auxin receptors in the seedling root. Further, we demonstrate that TIR1, AFB2, and AFB3, but not AFB1 exhibit significant posttranscriptional regulation. The microRNA miR393 is expressed in a pattern complementary to that of the auxin receptors and appears to regulate TIR1/AFB expression. However our data suggest that this regulation is complex. Our results suggest that differences between members of the auxin receptor family may contribute to the complexity of auxin response.} } @Article{IPB-1080, author = {Fonseca, S. and Chini, A. and Hamberg, M. and Adie, B. and Porzel, A. and Kramell, R. and Miersch, O. and Wasternack, C. and Solano, R.}, title = {{(+)-7-iso-Jasmonoyl-L-isoleucine is the endogenous bioactive jasmonate}}, year = {2009}, pages = {344-350}, journal = {Nat Chem Biol}, doi = {10.1038/nchembio.161}, url = {http://www.nature.com/nchembio/journal/v5/n5/full/nchembio.161.html}, volume = {5}, abstract = {Hormone-triggered activation of the jasmonate signaling pathway in Arabidopsis thaliana requires SCFCOI1-mediated proteasome degradation of JAZ repressors. (-)-JA-L-Ile is the proposed bioactive hormone, and SCFCOI1 is its likely receptor. We found that the biological activity of (-)-JA-L-Ile is unexpectedly low compared to coronatine and the synthetic isomer (+)-JA-L-Ile, which suggests that the stereochemical orientation of the cyclopentanone-ring side chains greatly affects receptor binding. Detailed GC-MS and HPLC analyses showed that the (-)-JA-L-Ile preparations currently used in ligand binding studies contain small amounts of the C7 epimer (+)-7-iso-JA-L-Ile. Purification of each of these molecules demonstrated that pure (-)-JA-L-Ile is inactive and that the active hormone is (+)-7-iso-JA-L-Ile, which is also structurally more similar to coronatine. In addition, we show that pH changes promote conversion of (+)-7-iso-JA-L-Ile to the inactive (-)-JA-L-Ile form, thus providing a simple mechanism that can regulate hormone activity through epimerization.} } @Article{IPB-1570, author = {Gago, S. and Elena, S.F. and Flores, R. and Sanjuán, R.}, title = {{Extremely high mutation rate of a hammerhead viroid}}, year = {2009}, pages = {1308}, journal = {Science}, volume = {322}, } @Article{IPB-1571, author = {Serra, P. and Hashemian, S.M.B. and Pensabene-Bellavia, G. and Gago, S. and Durán-Vila, N.}, title = {{An artifical chimeric derivative of Citrus viroid V involves the terminal left domain in pathogenicity}}, year = {2009}, pages = {515-522}, journal = {Molecular Plant Pathology}, volume = {10}, } @Article{IPB-1498, author = {Ziegler, J. and Brandt, W. and Geißler, R. and Facchini, P. J.}, title = {{Removal of Substrate Inhibition and Increase in Maximal Velocity in the Short Chain Dehydrogenase/Reductase Salutaridine Reductase Involved in Morphine Biosynthesis}}, year = {2009}, pages = {26758-26767}, journal = {J Biol Chem}, doi = {10.1074/jbc.M109.030957}, url = {http://www.jbc.org/search?fulltext=&author1=&pubdate_year=2009&volume=284&firstpage=26758&submit=yes}, volume = {284}, abstract = {Salutaridine reductase (SalR, EC catalyzes the stereospecific reduction of salutaridine to 7(S)-salutaridinol in the biosynthesis of morphine. It belongs to a new, plant-specific class of short-chain dehydrogenases, which are characterized by their monomeric nature and increased length compared with related enzymes. Homology modeling and substrate docking suggested that additional amino acids form a novel -helical element, which is involved in substrate binding. Site-directed mutagenesis and subsequent studies on enzyme kinetics revealed the importance of three residues in this element for substrate binding. Further replacement of eight additional residues led to the characterization of the entire substrate binding pocket. In addition, a specific role in salutaridine binding by either hydrogen bond formation or hydrophobic interactions was assigned to each amino acid. Substrate docking alsorevealed an alternative mode for salutaridine binding, which could explain the strong substrate inhibition of SalR. An alternate arrangement of salutaridine in the enzyme was corroborated by the effect of various amino acid substitutions on substrate inhibition. In most cases, the complete removal of substrate inhibition was accompanied by a substantial loss in enzyme activity. However, some mutations greatly reduced substrate inhibition while maintaining or even increasing the maximal velocity. Based on these results, a double mutant of SalRwas created that exhibited the complete absence of substrate inhibition and higher activity compared with wild-type SalR.} } @Article{IPB-1131, author = {Ticconi, C.A. and Lucero, R.D. and Sakhonwasee, S. and Adamson, A.W. and Creff, A. and Nussaume, L. and Desnos, T. and Abel, S.}, title = {{ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability}}, year = {2009}, pages = {14174-14179}, journal = {Proc Natl Acad Sci USA (PNAS)}, url = {http://www.pnas.org/content/106/33/14174.full.pdf+html?sid=beb71498-66cd-43f9-8234-b52dc4c60bb0}, volume = {106}, abstract = {Inadequate availability of inorganic phosphate (Pi) in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi acquisition. The sensory mechanisms that monitor environmental Pi status and regulate root growth via altered meristem activity are unknown. Here, we show that phosphate deficiency response 2 (PDR2) encodes the single P5-type ATPase of Arabidopsis thaliana. PDR2 functions in the endoplasmic reticulum (ER) and is required for proper expression of scarecrow (SCR), a key regulator of root patterning, and for stem-cell maintenance in Pi-deprived roots. We further show that the multicopper oxidase encoded by low phosphate root 1 (LPR1) is targeted to the ER and that LPR1 and PDR2 interact genetically. Because the expression domains of both genes overlap in the stem-cell niche and distal root meristem, we propose that PDR2 and LPR1 function together in an ER-resident pathway that adjusts root meristem activity to external Pi. Our data indicate that the Pi-conditional root phenotype of pdr2 is not caused by increased Fe availability in low Pi; however, Fe homeostasis modifies the developmental response of root meristems to Pi availability.} } @Article{IPB-1117, author = {Ziegler, J. and Facchini, P.J. and Geißler, R. and Schmidt, J. and Ammer, C. and Kramell, R. and Voigtländer, S. and Gesell, A. and Pienkny, S. and Brandt, W.}, title = {{Evolution of morphine biosynthesis in opium poppy.}}, year = {2009}, pages = {1696 - 1707}, journal = {Phytochemistry}, doi = {10.1016/j.phytochem.2009.07.006}, url = {http://www.sciencedirect.com/science/article/pii/S0031942209002817}, volume = {70}, abstract = {Benzylisoquinoline alkaloids (BIAs) are a group of nitrogen-containing plant secondary metabolites comprised of an estimated 2500 identified structures. In BIA metabolism, (S)-reticuline is a key branch-point intermediate that can be directed into several alkaloid subtypes with different structural skeleton configurations. The morphinan alkaloids are one subclass of BIAs produced in only a few plant species, most notably and abundantly in the opium poppy (Papaver somniferum). Comparative transcriptome analysis of opium poppy and several other Papaver species that do not accumulate morphinan alkaloids showed that known genes encoding BIA biosynthetic enzymes are expressed at higher levels in P. somniferum. Three unknown cDNAs that are co-ordinately expressed with several BIA biosynthetic genes were identified as enzymes in the pathway. One of these enzymes, salutaridine reductase (SalR), which is specific for the production of morphinan alkaloids, was isolated and heterologously overexpressed in its active form not only from P. somniferum, but also from Papaver species that do not produce morphinan alkaloids.SalR is a member of a class of short chain dehydrogenase/reductases (SDRs) that are active as monomers and possess an extended amino acid sequence compared with classical SDRs. Homology modelling and substrate docking revealed the substrate binding site for SalR. The amino acids residues conferring salutaridine binding were compared to several members of the SDR family from different plant species, which non-specifically reduce ( )-menthone to (+)-neomenthol. Previously, it was shown that some of these proteins are involved in plant defence. The recruitment of specific monomeric SDRs from monomeric SDRs involved in plant defence is discussed.} } @Article{IPB-1114, author = {Pienkny, S. and Brandt, W. and Schmidt, J. and Kramell, R. and Ziegler, J.}, title = {{Functional characterization of a novel benzylisoquinoline O-methyltransferase suggests its involvement in papaverine biosynthesis in opium poppy (Papaver somniferum L.)}}, year = {2009}, pages = {56 - 67}, journal = {The Plant Journal}, volume = {60}, abstract = {The benzylisoquinoline alkaloids are a highly diverse group of about 2500 compounds which accumulate in a species-specific manner. Despite the numerous compounds which could be identified, the biosynthetic pathways and the participating enzymes or cDNAs could be characterized only for a few selected members, whereas the biosynthesis of the majority of the compounds is still largely unknown. In an attempt to characterize additional biosynthetic steps at the molecular level, integration of alkaloid and transcript profiling across Papaver species was performed. This analysis showed high expression of an expressed sequence tag (EST) of unknown function only in Papaver somniferum varieties. After full-length cloning of the open reading frame and sequence analysis, this EST could be classified as a member of the class II type O-methyltransferase protein family. It was related to O-methyltransferases from benzylisoquinoline biosynthesis, and the amino acid sequence showed 68% identical residues to norcoclaurine 6-O-methyltransferase. However, rather than methylating norcoclaurine, the recombinant protein methylated norreticuline at position seven with a Km of 44 lM using S-adenosyl-L-methionine as a cofactor. Of all substrates tested, only norreticuline was converted.Even minor changes in the benzylisoquinoline backbone were not tolerated by the enzyme. Accordingly, the enzyme was named norreticuline 7–O-methyltransferase (N7OMT). This enzyme represents a novel Omethyltransferase in benzylisoquinoline metabolism. Expression analysis showed slightly increased expression of N7OMT in P. somniferum varieties containing papaverine, suggesting its involvement in the partially unknown biosynthesis of this pharmaceutically important compound.} } @Article{IPB-1113, author = {Quint, M. and Barkawi, L.S. and Fan, K.T. and Cohen, J.D. and Gray, W.M.}, title = {{Arabidopsis IAR4 modulates auxin response by regulating auxin homeostasis}}, year = {2009}, pages = {748-758}, journal = {Plant Physiol}, volume = {150}, abstract = {In a screen for enhancers of tir1-1 auxin resistance, we identified two novel alleles of the putative mitochondrial pyruvate dehydrogenase E1α-subunit, IAA-Alanine Resistant4 (IAR4). In addition to enhancing the auxin response defects of tir1-1, iar4 single mutants exhibit numerous auxin-related phenotypes including auxin-resistant root growth and reduced lateral root development, as well as defects in primary root growth, root hair initiation, and root hair elongation. Remarkably, all of these iar4 mutant phenotypes were rescued when endogenous indole-3-acetic acid (IAA) levels were increased by growth at high temperature or overexpression of the YUCCA1 IAA biosynthetic enzyme, suggesting that iar4 mutations may alter IAA homeostasis rather than auxin response. Consistent with this possibility, iar4 mutants exhibit increased Aux/IAA stability compared to wild type under basal conditions, but not in response to an auxin treatment. Measurements of free IAA levels detected no significant difference between iar4-3 and wild-type controls. However, we consistently observed significantly higher levels of IAA-amino acid conjugates in the iar4-3 mutant. Furthermore, using stable isotope-labeled IAA precursors, we observed a significant increase in the relative utilization of the Trp-independent IAA biosynthetic pathway in iar4-3. We therefore suggest that the auxin phenotypes of iar4 mutants are the result of altered IAA homeostasis.} } @Article{IPB-1087, author = {Vandenborre, G. and Miersch, O. and Hause, B. and Smagghe, G. and Wasternack, C. and Van Damme, E.J.M.}, title = {{Spodoptera Littoralis Induced Lectin Expression in Tobacco}}, year = {2009}, pages = {1142-1155}, journal = {Plant Cell Physiol}, doi = {10.1093/pcp/pcp065}, url = {10.1093/pcp/pcp065}, volume = {50}, abstract = {The induced defense response in plants towards herbivores is mainly regulated by jasmonates and leads to the accumulation of so-called jasmonate-induced proteins. Recently, a jasmonate (JA) inducible lectin called Nicotiana tabacum agglutinin or NICTABA was discovered in tobacco( N. tabacum cv Samsun) leaves. Tobacco plants also accumulate the lectin after insect attack by caterpillars. To study the functional role of NICTABA, the accumulation of the JA precursor 12-oxophytodienoic acid (OPDA), JA as well as different JA metabolites were analyzed in tobacco leaves after herbivory by larvae of the cotton leafworm ( Spodoptera littoralis ) and correlated with NICTABA accumulation. It was shown that OPDA, JA as well as its methyl ester can trigger NICTABA accumulation. However, hydroxylation of JA and its subsequent sulfation and glucosylation results in inactive compounds that have lost the capacity to induce NICTABA gene expression. The expression profi le of NICTABA after caterpillar feeding was recorded in local as well as in systemic leaves, and compared to the expression of several genes encodingdefense proteins, and genes encoding a tobacco systemin and the allene oxide cyclase, an enzyme in JA biosynthesis. Furthermore, the accumulation of NICTABA was quantified after S. littoralis herbivory and immunofl uorescence microscopy was used to study the localization of NICTABA in the tobacco leaf.} } @Article{IPB-1079, author = {Mugford, S.G. and Yoshimoto, N. and Reichelt, M. and Wirtz, M. and Hill, L. and Mugford, S.T. and Nakazato, Y. and Noji, M. and Takahashi, H. and Kramell, R. and Gigolashvili, T. and Flügge, U.-I. and Wasternack, C. and Gershenzon, J. and Hell, R. and Saito, K. and Kopriva, S.}, title = {{Disruption of Adenosine-5'-Phosphosulfate Kinase in Arabidopsis Reduces Levels of Sulfated Secondary Metabolites}}, year = {2009}, pages = {910-927}, journal = {Plant Cell}, volume = {21}, abstract = {Plants can metabolize sulfate by two pathways, which branch at the level of adenosine 59-phosphosulfate (APS). APS can be reduced to sulfide and incorporated into Cys in the primary sulfate assimilation pathway or phosphorylated by APS kinase to 39-phosphoadenosine 59-phosphosulfate, which is the activated sulfate form for sulfation reactions. To assess to what extent APS kinase regulates accumulation of sulfated compounds, we analyzed the corresponding gene family in Arabidopsis thaliana. Analysis of T-DNA insertion knockout lines for each of the four isoforms did not reveal any phenotypical alterations. However, when all six combinations of double mutants were compared, the apk1 apk2 plants were significantly smaller than wild-type plants. The levels of glucosinolates, a major class of sulfated secondary metabolites, and the sulfated 12-hydroxyjasmonate were reduced approximately fivefold in apk1 apk2 plants. Although auxin levels were increased in the apk1 apk2 mutants, as is the case for most plants with compromised glucosinolate synthesis, typical high auxin phenotypes were not observed. The reduction in glucosinolates resulted in increased transcript levels for genes involved in glucosinolate biosynthesis and accumulation of desulfated precursors. It also led to great alterations in sulfur metabolism: the levels of sulfate and thiols increased in the apk1 apk2 plants. The data indicate that the APK1 and APK2 isoforms of APS kinase play a major role in the synthesis of secondary sulfated metabolites and are required for normalgrowth rates.} } @Article{IPB-1043, author = {Clarke, S.M. and Cristescu, S.M. and Miersch, O. and Harren, F.J.M. and Wasternack, C. and Mur, L.A.J.}, title = {{Jasmonates act with salicylic acid to confer basal thermotolerance in \textit{Arabidopsis thaliana}}}, year = {2009}, pages = {175-187}, journal = {New Phytol}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02735.x/abstract}, volume = {182}, abstract = {The cpr5-1 Arabidopsis thaliana mutant exhibits constitutive activation of salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) signalling pathways and displays enhanced tolerance of heat stress (HS). cpr5-1 crossed with jar1-1 (a JA-amino acid synthetase) was compromised in basal thermotolerance, as were the mutants opr3 (mutated in OPDA reductase3) and coi1-1 (affected in an E3 ubiquitin ligase F-box; a key JA-signalling component). In addition, heating wild-type Arabidopsis led to the accumulation of a range of jasmonates: JA, 12-oxophytodienoic acid (OPDA) and a JA-isoleucine (JA-Ile) conjugate. Exogenous application of methyl jasmonate protected wild-type Arabidopsis from HS. Ethylene was rapidly produced during HS, with levels being modulated by both JA and SA. By contrast, the ethylene mutant ein2-1 conferred greater thermotolerance. These data suggest that JA acts with SA, conferring basal thermotolerance while ET may act to promote cell death.} } @Article{IPB-1042, author = {Weigelt, K. and Küster, H. and Rutten, T. and Fait, A. and Fernie, A.R. and Miersch, O. and Wasternack, C. and Emery, R.J.N. and Desel, C. and Hosein, F. and Müller, M. and Saalbach, I. and Weber, H.}, title = {{ADP-glucose pyrophosphorylase-deficient pea embryos reveal specific transcriptional and metabolic changes of carbon-nitrogen metabolism and stress responses}}, year = {2009}, pages = {395-411}, journal = {Plant Physiol}, volume = {149}, abstract = {We present a comprehensive analysis of ADP-glucose pyrophosphorylase (AGP)-repressed pea (Pisum sativum) seeds using transcript and metabolite profiling to monitor the effects that reduced carbon flow into starch has on carbon-nitrogen metabolism and related pathways. Changed patterns of transcripts and metabolites suggest that AGP repression causes sugar accumulation and stimulates carbohydrate oxidation via glycolysis, tricarboxylic acid cycle, and mitochondrial respiration. Enhanced provision of precursors such as acetyl-coenzyme A and organic acids apparently support other pathways and activate amino acid and storage protein biosynthesis as well as pathways fed by cytosolic acetyl-coenzyme A, such as cysteine biosynthesis and fatty acid elongation/metabolism. As a consequence, the resulting higher nitrogen (N) demand depletes transient N storage pools, specifically asparagine and arginine, and leads to N limitation. Moreover, increased sugar accumulation appears to stimulate cytokinin-mediated cell proliferation pathways. In addition, the deregulation of starch biosynthesis resulted in indirect changes, such as increased mitochondrial metabolism and osmotic stress. The combined effect of these changes is an enhanced generation of reactive oxygen species coupled with an up-regulation of energy-dissipating, reactive oxygen species protection, and defense genes. Transcriptional activation of mitogen-activated protein kinase pathways and oxylipin synthesis indicates an additional activation of stress signaling pathways. AGP-repressed embryos contain higher levels of jasmonate derivatives; however, this increase is preferentially in nonactive forms. The results suggest that, although metabolic/osmotic alterations in iAGP pea seeds result in multiple stress responses, pea seeds have effective mechanisms to circumvent stress signaling under conditions in which excessive stress responses and/or cellular damage could prematurely initiate senescence or apoptosis.} } @Article{IPB-1039, author = {Halim, V.A. and Altmann, S. and Ellinger, D. and Eschen-Lippold, L. and Miersch, O. and Scheel, D. and Rosahl, S.}, title = {{PAMP-induced defense responses in potato require both salicylic acid and jasmonic acid}}, year = {2009}, pages = {230 - 242}, journal = {Plant Journal}, doi = {10.1111/j.1365-313X.2008.03688.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2008.03688.x/abstract}, volume = {57}, abstract = {To elucidate the molecular mechanisms underlying pathogen-associated molecular pattern (PAMP)-induced defense responses in potato (Solanum tuberosum), the role of the signaling compounds salicylic acid (SA) and jasmonic acid (JA) was analyzed. Pep-13, a PAMP from Phytophthora, induces the accumulation of SA, JA and hydrogen peroxide, as well as the activation of defense genes and hypersensitive-like cell death. We have previously shown that SA is required for Pep-13-induced defense responses. To assess the importance of JA, RNA interference constructs targeted at the JA biosynthetic genes, allene oxide cyclase and 12- oxophytodienoic acid reductase, were expressed in transgenic potato plants. In addition, expression of the F-box protein COI1 was reduced by RNA interference. Plants expressing the RNA interference constructs failed to accumulate the respective transcripts in response to wounding or Pep-13 treatment, neither did they contain significant amounts of JA after elicitation. In response to infiltration of Pep-13, the transgenic plants exhibited a highly reduced accumulation of reactive oxygen species as well as reduced hypersensitive cell death. The ability of the JA-deficient plants to accumulate SA suggests that SA accumulation is independent or upstream of JA accumulation. These data show that PAMP responses in potato require both SA and JA and that, in contrast to Arabidopsis, these compounds act in the same signal transduction pathway. Despite their inability to fully respond to PAMP treatment, the transgenic RNA interference plants are not altered in their basal defense against Phytophthora infestans.} } @Article{IPB-1569, author = {Dufour, D. and de la Peña, M. and Gago, S. and Flores, R. and Gallego, J.}, title = {{Structure-function analyses of the ribozyme of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads}}, year = {2009}, pages = {368-381}, journal = {Nucleic Acids Research}, doi = {10.1093/nar/gkn918}, url = {https://doi.org/10.1093/nar/gkn918}, volume = {37}, } @Article{IPB-1125, author = {Lee, C-W. and Efetova, M. and Engelmann, J.C. and Kramell, R. and Wasternack, C. and Ludwig- Müller, J. and Hedrich, R. and Deeken, R.}, title = {{Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in \textit{Arabidopsis thaliana}.}}, year = {2009}, pages = {2948 - 2962}, journal = {The Plant Cell}, doi = {10.1105/tpc.108.064576}, url = {http://www.plantcell.org/}, volume = {21}, abstract = {Agrobacterium tumefaciens causes crown gall disease by transferring and integrating bacterial DNA (T-DNA) into the plant genome. To examine the physiological changes and adaptations during Agrobacterium-induced tumor development, we compared the profiles of salicylic acid (SA), ethylene (ET), jasmonic acid (JA), and auxin (indole-3-acetic acid [IAA]) with changes in the Arabidopsis thaliana transcriptome. Our data indicate that host responses were much stronger toward the oncogenic strain C58 than to the disarmed strain GV3101 and that auxin acts as a key modulator of the Arabidopsis–Agrobacterium interaction. At initiation of infection, elevated levels of IAA and ET were associated with the induction of host genes involved in IAA, but not ET signaling. After T-DNA integration, SA as well as IAA and ET accumulated, but JA did not.This did not correlate with SA-controlled pathogenesis-related gene expression in the host, although high SA levels in mutant plants prevented tumor development, while low levels promoted it. Our data are consistent with a scenario in which ET and later on SA control virulence of agrobacteria, whereas ET and auxin stimulate neovascularization during tumor formation. We suggest that crosstalk among IAA, ET, and SA balances pathogen defense launched by the host and tumorgrowth initiated by agrobacteria.} } @INBOOK{IPB-855, author = {Quint, M. and Lübberstedt, T.}, year = {2008}, pages = {267-287}, chapter = {{Application of resistance gene analogs in breeding for virus resistance}}, journal = {Techniques in Diagnosis of Plant Viruses. Studium Press LLC, USA}, editor = {Rao, GP, Valverde, RA, Christomas, D.}, } @Article{IPB-983, author = {Brüx, A. and Liu, T-Y. and Krebs, M. and Stierhof, Y.-D. and Lohmann, J.U. and Miersch, O. and Wasternack, C. and Schumacher, K.}, title = {{Reduced V-ATPase activity in the \textit{trans}-Golgi network causes oxylipin-dependent hypocotyl growth inhibition in \textit{Arabidopsis}}}, year = {2008}, pages = {1088-1100}, journal = {The Plant Cell}, volume = {20}, } @Article{IPB-1027, author = {Wasternack, C. and Feussner, I.}, title = {{Multifunctional enzymes in oxylipin metabolism}}, year = {2008}, pages = {2373-2375}, journal = {Chembiochem.}, volume = {9}, } @Article{IPB-980, author = {Kienow, L. and Schneider, K. and Bartsch, M. and Stuible, H.-P. and Weng, H. and Miersch, O. and Wasternack, C. and Kombrink, E.}, title = {{Jasmonates meet fatty acids: functional analysis of a new acyl-coenzyme A synthetase family from \textit{Arabidopsis thaliana}}}, year = {2008}, pages = {403-419}, journal = {J. Exp. Bot.}, volume = {59 (2)}, } @Article{IPB-1018, author = {Schilling, S. and Wasternack, C. and Demuth, H.U.}, title = {{Glutaminyl cyclases from animals and plants: a case of functionally convergent protein evolution}}, year = {2008}, pages = {983-991}, journal = {Biol. Chem }, volume = {389}, } @Article{IPB-1014, author = {Zhang, W. and Ito, H. and Quint, M. and Huang, H. and Noël, L.D. and Gray, W.M.}, title = {{Genetic analysis of CAND1-CUL1 interactions in Arabidopsis supports a role for CAND1-mediated cycling of the SCFTIR1 complex}}, year = {2008}, pages = {8470-8475}, journal = {Proc Natl Acad Sci}, url = {http://www.pnas.org/content/105/24/8470.full.pdf+html}, volume = {105}, abstract = { SKP1-Cullin1-F-box protein (SCF) ubiquitin-ligases regulate numerous aspects of eukaryotic growth and development. Cullin-Associated and Neddylation-Dissociated (CAND1) modulates SCF function through its interactions with the CUL1 subunit. Although biochemical studies with human CAND1 suggested that CAND1 plays a negative regulatory role by sequestering CUL1 and preventing SCF complex assembly, genetic studies in Arabidopsis have shown that cand1 mutants exhibit reduced SCF activity, demonstrating that CAND1 is required for optimal SCF function in vivo. Together, these genetic and biochemical studies have suggested a model of CAND1-mediated cycles of SCF complex assembly and disassembly. Here, using the SCFTIR1 complex of the Arabidopsis auxin response pathway, we test the SCF cycling model with Arabidopsis mutant derivatives of CAND1 and CUL1 that have opposing effects on the CAND1CUL1 interaction. We find that the disruption of the CAND1CUL1 interaction results in an increased abundance of assembled SCFTIR1 complex. In contrast, stabilization of the CAND1CUL1 interaction diminishes SCFTIR1 complex abundance. The fact that both decreased and increased CAND1CUL1 interactions result in reduced SCFTIR1 activity in vivo strongly supports the hypothesis that CAND1-mediated cycling is required for optimal SCF function.} } @Article{IPB-948, author = {Lange, P.R. and Geserick, C. and Tischendorf, G. and Zrenner, R.}, title = {{Functions of chloroplastic adenylate kinases in \textit{Arabidopsis thaliana}}}, year = {2008}, pages = {492-504}, journal = {Plant Physiol.}, volume = {146}, } @Article{IPB-943, author = {Miersch, O. and Neumerkel, J. and Dippe, M. and Stenzel, I. and Wasternack, C.}, title = {{Hydroxylated jasmonates are commonly occurring metabolites of jasmonic acid and contribute to a partial switch-off in jasmonate signaling}}, year = {2008}, pages = {114-127}, journal = {New Phytologist}, volume = {177}, } @Article{IPB-984, author = {Stenzel, I. and Hause, B. and Proels, R. and Miersch, O. and Oka, M. and Roitsch, T. and Wasternack, C.}, title = {{The AOC promoter of tomato is regulated by developmental and environmental stimuli}}, year = {2008}, pages = {1859-1869}, journal = {Phytochemistry}, volume = {69}, } @Article{IPB-1566, author = {Iglesias, N.G. and Gago, S. and Robledo, G. and Costa, N. and Plata, M.I. and Vera, O. and Grau, O. and Semorile, L.C.}, title = {{Population structure of Citrus tristeza virus from field Argentinean isolates}}, year = {2008}, pages = {199-207}, journal = {Virus Genes}, volume = {36}, } @Article{IPB-1568, author = {Serra, P. and Gago, S. and Durán-Vila, N.}, title = {{A single nucleotide change in Hop stunt viroid modulates citrus cachexia symptoms}}, year = {2008}, pages = {130-134}, journal = {Virus Research}, volume = {138}, } @INBOOK{IPB-1567, author = {Flores, R. and Carbonell, A. and Gago, S. and Martínez de Alba, A.E. and Delgado, S. and Rodio, M.E. and di Serio, F.}, title = {{Biology of Plant-Microbe Interactions}}, year = {2008}, pages = {1-9}, chapter = {{Viroid-host interactions: A molecular dialogue between two uneven partners}}, editor = {Lorito, M., Woo, S. L., Scala, F.}, volume = {6 (chap. 58)}, } @Article{IPB-1565, author = {Carbonell, A. and Martínez de Alba, A.E. and Flores, R. and Gago, S.}, title = {{Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families}}, year = {2008}, pages = {44-53}, journal = {Virology}, doi = {10.1016/j.virol.2007.09.031}, url = {https://doi.org/10.1016/j.virol.2007.09.031}, volume = {371}, } @Article{IPB-981, author = {Raffaele, S. and Vailleau, F. and Léger, A. and Joubès, J. and Miersch, O. and Huard, C. and Blée, E. and Mongrand, S. and Domergue, F. and Roby, D.}, title = {{A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in \textit{Arabidopsis}}}, year = {2008}, pages = {752-767}, journal = {The Plant Cell}, volume = {20}, } @Article{IPB-946, author = {Gao, X. and Stumpe, M. and Feussner, I. and Kolomiets, M.}, title = {{A novel plastidial lipoxygenase of maize (\textit{Zea mays}) \textit{ZmLOX6} encodes for a fatty acid hydroperoxide lyase and is uniquely regulated by phytohormones and pathogen infection}}, year = {2008}, pages = {491-503}, journal = {Planta }, volume = {227}, } @Article{IPB-1015, author = {Delker, C. and Raschke, A. and Quint, M.}, title = {{Auxin dynamics: the dazzling complexity of a small molecule's message}}, year = {2008}, pages = {929-941 }, journal = {Planta}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18299888}, volume = {227}, abstract = { The phytohormone auxin is a potent regulator of plant development. Since its discovery in the beginning of the twentieth century many aspects of auxin biology have been extensively studied, ranging from biosynthesis and metabolism to the elucidation of molecular components of downstream signaling. With the identification of the F-box protein TIR1 as an auxin receptor a major breakthrough in understanding auxin signaling has been achieved and recent modeling approaches have shed light on the putative mechanisms underlying the establishment of auxin gradients and maxima essential for many auxin-regulated processes. Here, we review these and other recent advances in unraveling the entanglement of biosynthesis, polar transport and cellular signaling events that allow small auxinic molecules to facilitate their complex regulatory action.} } @Article{IPB-1282, author = {Calderón Villalobos, L.I. and Nill, C. and Marrocco, K. and Kretsch, T. and Schwechheimer, C.}, title = {{The evolutionarily conserved Arabidopsis thaliana F-box protein AtFBP7 is required for efficient translation during temperature stress}}, year = {2007}, pages = {106-116}, journal = {Gene}, volume = {392(1-2)}, abstract = {In eukaryotes, E3 ubiquitin ligases (E3s) mediate the ubiquitylation of proteins that are destined for degradation by the ubiquitin-proteasome system. In SKP1/CDC53/F-box protein (SCF)-type E3 complexes, the interchangeable F-box protein confers specificity to the E3 ligase through direct physical interactions with the degradation substrate. The vast majority of the approximately 700 F-box proteins from the plant model organism Arabidopsis thaliana remain to be characterized. Here, we investigate the previously uncharacterized and evolutionarily conserved Arabidopsis F-box protein 7 (AtFBP7), which is encoded by a unique gene in Arabidopsis (At1g21760). Several apparent fbp7 loss-of-function alleles do not have an obvious phenotype. AtFBP7 is ubiquitously expressed and its expression is induced after cold and heat stress. When following up on a reported co-purification of the eukaryotic elongation factor-2 (eEF-2) with YLR097c, the apparent budding yeast orthologue of AtFBP7, we discovered a general defect in protein biosynthesis after cold and heat stress in fbp7 mutants. Thus, our findings suggest that AtFBP7 is required for protein synthesis during temperature stress.} } @Article{IPB-891, author = {Lannoo, N. and Vandenborre, G. and Miersch, O. and Smagghe, G. and Wasternack, C. and Peumans, W.J. and Van Damme, E.J.M.}, title = {{The jasmonate-induced expression of the \textit{Nicotiana tabacum} leaf lectin}}, year = {2007}, pages = {1207-1218}, journal = {Plant and Cell Physiol.}, volume = {48}, } @Article{IPB-845, author = {Guranowski, A. and Miersch, O. and Staswick, P.E. and Suza, W. and Wasternack, C.}, title = {{Substrate specificity and products of side-reactions catalyzed by jasmonate:amino acid synthetase (JAR1)}}, year = {2007}, pages = {815-820}, journal = {FEBS Letters}, volume = {581}, } @Article{IPB-944, author = {Wasternack, C.}, title = {{Obituary - Clarence A. Bud Ryan (29.09.1931-07.10.2007)}}, year = {2007}, pages = {709}, journal = {Plant Mol. Biol. }, volume = {65}, } @Article{IPB-1281, author = {Tan, X. and Calderón Villalobos, L.I. and Sharon, M. and Zheng, C. and Robinson, C.V. and Estelle, M. and Zheng, N.}, title = {{Mechanism of auxin perception by the TIR1 ubiquitin ligase}}, year = {2007}, pages = {640-645}, journal = {Nature}, volume = {446(7136)}, abstract = {ArabidopsisAuxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the TIR1–ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1–substrate interactions by acting as a ‘molecular glue’. Our results establish the first structural model of a plant hormone receptor.} } @Article{IPB-878, author = {Wasternack, C.}, title = {{Jasmonates: An update on biosynthesis, signal transduction and action in plant stress response, growth and development}}, year = {2007}, pages = {681-697}, journal = {Annals of Botany}, volume = {100}, } @Article{IPB-877, author = {Delker, C. and Zolman, B.K. and Miersch, O. and Wasternack, C.}, title = {{Jasmonate biosynthesis in \textit{Arabidopsis thaliana} requires peroxisomal beta-oxidation enzymes Additional proof by properties of \textit{pex6} and \textit{aim1}}}, year = {2007}, pages = {1642-1650}, journal = {Phytochemistry }, volume = {68}, } @Article{IPB-831, author = {Schilling, S. and Stenzel, I. and von Bohlen, A. and Wermann, M. and Schulz, K. and Demuth, H.-U. and Wasternack, C.}, title = {{Isolation and characterization of the glutaminyl cyclases from \textit{Solanum tuberosum} and \textit{Arabidopsis thaliana}: implications for physiological functions}}, year = {2007}, pages = {145-153}, journal = {Biol. Chem}, volume = {388}, } @Article{IPB-1564, author = {Flores, R. and Navarro, B. and Gago, S. and de la Peña, M.}, title = {{Chrysanthemum Chlorotic Mottle Viroid: a System for Reverse Genetics in the Family Avsunviroidae (Hammerhead Viroids)}}, year = {2007}, pages = {27-32}, journal = {Plant Viruses}, volume = {1}, } @Article{IPB-1283, author = {Schwager, K.M. and Calderón Villalobos, L.I. and Dohmann, E.M. and Willige, B.C. and Knierer, S. and Nill, C. and Schwechheimer, C.}, title = {{Characterization of the VIER F-BOX PROTEINE genes from Arabidopsis reveals their importance for plant growth and development}}, year = {2007}, pages = {1163-1178}, journal = {Plant Cell}, url = {http://www.plantcell.org/content/19/4/1163.full}, volume = {19(4)}, abstract = { E3 ubiquitin ligases (E3s) target proteins for degradation by the 26S proteasome. In SKP1/CDC53/F-box proteintype E3s, substrate specificity is conferred by the interchangeable F-box protein subunit. The vast majority of the 694 F-box proteins encoded by the Arabidopsis thaliana genome remain to be understood. We characterize the VIER F-BOX PROTEINE (VFB; German for FOUR F-BOX PROTEINS) genes from Arabidopsis that belong to subfamily C of the Arabidopsis F-box protein superfamily. This subfamily also includes the F-box proteins TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) proteins and EIN3 BINDING F-BOX proteins, which regulate auxin and ethylene responses, respectively. We show that loss of VFB function causes delayed plant growth and reduced lateral root formation. We find that the expression of a number of auxin-responsive genes and the activity of DR5:ß-glucuronidase, a reporter for auxin reponse, are reduced in the vfb mutants. This finding correlates with an increase in the abundance of an AUXIN/INDOLE-3-ACETIC ACID repressor. However, we also find that auxin responses are not affected in the vfb mutants and that a representative VFB family member, VFB2, cannot functionally complement the tir1-1 mutant. We therefore exclude the possibility that VFBs are functional orthologs of TIR1/AFB proteins.} } @Article{IPB-916, author = {Vigliocco, A. and Alemano, S. and Miersch, O. and Alvarez, D. and Abdala, G.}, title = {{Endogenous jasmonates in dry and imbibed sunflower seeds from plants grown at different soil moisture contents}}, year = {2007}, pages = {91-98}, journal = {Seed Sci. Res. }, volume = {17}, } @Article{IPB-1149, author = {Abel, S.}, title = {{Auxin is surfacing}}, year = {2007}, pages = {380 - 384}, journal = {ACS Chemical Biology}, url = {http://pubs.acs.org/doi/full/10.1021/cb7001158}, volume = {2}, abstract = { Indole-3-acetic acid (IAA or auxin) is essential throughout the life cycle of a plant. It controls diverse cellular processes, including gene expression. The hormone is perceived by a ubiquitin protein ligase (E3) and triggers the rapid destruction of repressors, called Aux/IAA proteins. The first structural model of a plant hormone receptor illustrates how auxin promotes Aux/IAA substrate recruitment by extending the hydrophobic protein-interaction surface. This work establishes a novel mechanism of E3 regulation by small molecules and promises a novel strategy for the treatment of human disorders associated with defective ubiquitin-dependent proteolysis.} } @Article{IPB-1563, author = {Biondi, E. and Branciamore, S. and Fusi, L. and Gago, S. and Gallori, E.}, title = {{Catalytic activity of hammerhead ribozymes in a clay mineral environment: Implications for the RNA world.}}, year = {2007}, pages = {10-18}, journal = {Gene}, volume = {389}, } @INBOOK{IPB-1562, author = {Flores, R. and Carbonell, A. and de la Peña, M. and Gago, S.}, title = {{Herramientas Biotecnológicas en Fitopatología}}, year = {2007}, pages = {407-420}, chapter = {{RNAs autocatalíticos: ribozimas de cabeza de martillo}}, journal = {Spanish Society of Phytopathology}, editor = {Fenoll, C., Marcos, J., Pallás, V., Rodriguez Palenzuela, P.}, } @Article{IPB-942, author = {Dorka, R. and Miersch, O. and Wasternack, C. and Weik, P.}, title = {{11. Chronobiological phenomena and seasonal changes in jasmonate levels during the course of the year and under constant conditions in mistletoe (Viscum album L.)}}, year = {2007}, pages = {DOI:10.1016/j.phymed.2007.07.014 }, journal = {Phytomedicine}, volume = {14}, } @Article{IPB-908, author = {Pedranzani, H. and Sierro-de-Grado, R. and Vigliocco, A. and Miersch, O. and Abdala, G.}, title = {{Cold and water stresses produce changes in endogenous jasmonates in two populations of \textit{Pinus pinaster} Ait}}, year = {2007}, pages = {111-116}, journal = {Plant Growth Regul.}, volume = {52}, } @INBOOK{IPB-780, author = {Wasternack, C.}, title = {{Plant Hormone Signaling}}, year = {2006}, pages = {185-228}, chapter = {{Oxilipins: biosynthesis, signal transduction and action}}, journal = {Ann. Plant Reviews, Blackwell, Oxford, UK}, editor = {Hedden, P., Thomas, S.}, } @Article{IPB-696, author = {Mur, L.A.J. and Kenton, P. and Atzorn, R. and Miersch, O. and Wasternack, C.}, title = {{The outcomes of concentration specific interactions between salicylate and jasmonate signaling include synergy, antagonism and the activation of cell death}}, year = {2006}, pages = {249-262}, journal = {Plant Physiol.}, volume = {140}, } @Article{IPB-1284, author = {Calderón Villalobos, L.I. and Kuhnle, C. and Li, H. and Rosso, M. and Weisshaar, B. and Schwechheimer, C.}, title = {{LucTrap vectors are tools to generate luciferase fusions for the quantification of transcript and protein abundance in vivo}}, year = {2006}, pages = {3-14}, journal = {Plant Physiol}, url = {http://www.plantphysiol.org/content/141/1/3.full}, volume = {141(1)}, abstract = { Proper plant growth and development strongly rely on the plant's ability to respond dynamically to signals and cues from the intra- and extracellular environment. Whereas many of these responses require specific changes at the level of gene expression, in recent years it has become increasingly clear that many plant responses are at least in part also controlled at the level of protein turnover. It is a challenge for signal transduction research to understand how distinct incoming signals are integrated to generate specific changes at the transcript or protein level. The activity of luciferase (LUC) reporters can be detected in nondestructive qualitative and quantitative assays in vivo. Therefore,z LUC reporters are particularly well suited for the detection of changes at the transcript and protein level. To the best of our knowledge, the number of plant transformation vectors for LUC fusions is very limited. In this article, we describe the LucTrap plant transformation vectors that allow generation of targeted and random transcriptional and translational fusions with the modified firefly LUC reporter LUC+. We demonstrate that LucTrap-based fusions can be used to monitor rapid changes in gene expression and protein abundance in vivo.} } @Article{IPB-792, author = {Ederli, L. and Morettini, R. and Borgogni, A. and Wasternack, C. and Miersch, O. and Reale, L. and Ferranti, F. and Tosit, N. and Pasqualini, S.}, title = {{Interaction between nitric oxide and ethylene in the induction of alternative oxidase in ozone-treated tobacco plants}}, year = {2006}, pages = {595-608}, journal = {Plant Physiol.}, volume = {142}, } @Article{IPB-786, author = {Sreenivasulu, N. and Radchuk, V. and Strickert, M. and Miersch, O. and Weschke, W. and Wobus, U.}, title = {{Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA-regulated maturation in developing barley seeds}}, year = {2006}, pages = {310-327}, journal = {The Plant J.}, volume = {47}, } @Article{IPB-700, author = {Sharma, V.K. and Monostori, T. and Göbel, C. and Hänsch, R. and Bittner, F. and Wasternack, C. and Feussner, I. and Mendel, R.R. and Hause, B. and Schulze, J.}, title = {{Transgenic barley plants overexpressing a 13-lipoxygenase to modify oxylipin signature}}, year = {2006}, pages = {264-276 }, journal = {Phytochemistry }, volume = {67}, } @Article{IPB-701, author = {Wasternack, C. and Stenzel, I. and Hause, B. and Hause, G. and Kutter, C. and Maucher, H. and Neumerkel, J. and Feussner, I. and Miersch, O.}, title = {{The wound response in tomato - Role of jasmonic acid}}, year = {2006}, pages = {297-306 }, journal = {J. Plant Physiol}, volume = {163}, } @Article{IPB-1960, author = {De Nardi, B. and Dreos, R. and Del Terra, L. and Martellossi, C. and Asquini, E. and Tornincasa, P. and Gasperini, D. and Pacchioni, B. and Rathinavelu, R. and Pallavicini, A. and Graziosi, G.}, title = {{Differential responses of Coffea arabica L. leaves and roots to chemically induced systemic acquired resistance}}, year = {2006}, pages = {1594-1605}, chapter = {{-->}}, journal = {Genome}, doi = {10.1139/g06-125}, volume = {49}, } @Article{IPB-1561, author = {Carbonell, A. and de la Peña, M. and Flores, R. and Gago, S.}, title = {{Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: difference in co- and post-transcriptional self-cleavage may explain the lack trinucleotide AUC in most natural hammerheads}}, year = {2006}, pages = {5613-5622}, journal = {Nucleic Acids Research}, doi = {10.1093/nar/gkl717}, url = {https://doi.org/10.1093/nar/gkl717}, volume = {34}, } @Article{IPB-1139, author = {Grubb, C.D. and Abel, S.}, title = {{Glucosinolate metabolism and its control}}, year = {2006}, pages = {89 - 100}, journal = {Trends in Plant Science}, doi = {10.1016/j.tplants.2005.12.006}, url = {http://www.sciencedirect.com/science/article/pii/S1360138505003043}, volume = {11}, abstract = { Glucosinolates and their associated degradation products have long been recognized for their distinctive benefits to human nutrition and plant defense. Because most of the structural genes of glucosinolate metabolism have been identified and functionally characterized in Arabidopsis thaliana, current research increasingly focuses on questions related to the regulation of glucosinolate synthesis, distribution and degradation as well as to the feasibility of engineering customized glucosinolate profiles. Here, we highlight recent progress in glucosinolate research, with particular emphasis on the biosynthetic pathway and its metabolic relationships to auxin homeostasis. We further discuss emerging insight into the signaling networks and regulatory proteins that control glucosinolate accumulation during plant development and in response to environmental challenge.} } @Article{IPB-854, author = {Quint, M. and Gray, W.M.}, title = {{Auxin signaling}}, year = {2006}, pages = {448-453}, journal = {Curr Opin Plant Biol}, url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS4-4KHC3HX-2-3&_cdi=6252&_user=4832532&_pii=S1369526606001129&_origin=search&_zone=rslt_list_item&_coverDate=10%2F31%2F2006&_sk=999909994&wchp=dGLbVlz-zSkWB&md5=23a724d38dce3cd047912344f36ea1fe&ie}, volume = {9}, abstract = { Auxin regulates a host of plant developmental and physiological processes, including embryogenesis, vascular differentiation, organogenesis, tropic growth, and root and shoot architecture. Genetic and biochemical studies carried out over the past decade have revealed that much of this regulation involves the SCFTIR1/AFB-mediated proteolysis of the Aux/IAA family of transcriptional regulators. With the recent finding that the TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) proteins also function as auxin receptors, a potentially complete, and surprisingly simple, signaling pathway from perception to transcriptional response is now before us. However, understanding how this seemingly simple pathway controls the myriad of specific auxin responses remains a daunting challenge, and compelling evidence exists for SCFTIR1/AFB-independent auxin signaling pathways.} } @Article{IPB-1141, author = {Levy, M. and Rachmilevitch, S. and Abel, S.}, title = {{Transient Agrobacterium-mediated gene expression in the Arabidopsis hydroponics root system for subcellular localization studies}}, year = {2005}, pages = {179 - 184}, journal = {Plant Mol. Biol. Rep.}, volume = {23}, abstract = { To a great extent, the cellular compartmentalization and molecular interactions are indicative of the function of a protein. The development of simple and efficient tools for testing the subcellular location of proteins is indispensable to elucidate the function of genes in plants. In this report, we assessed the feasibility ofAgrobacterium-mediated transformation of hydroponically grown roots to follow intracellular targeting of proteins fused to green fluorescent protein (GFP). We developed a simple in planta assay for subcellular localization of proteins inArabidopsis roots via transient transformation and tested this method by expressing a GFP fusion of a known nuclear protein, IQD1. Visualization of transiently expressed GFP fusion proteins in roots by means of confocal microscopy is superior to the analysis of green tissues because the roots are virtually transparent and free of chlorophyll autofluorescence.} } @Article{IPB-1285, author = {Calderón Villalobos, L.I. and Kuhnle, C. and Dohmann, E.M. and Li, H. and Bevan, M. and Schwechheimer, C.}, title = {{The evolutionarily conserved TOUGH protein is required for proper development of Arabidopsis thaliana}}, year = {2005}, pages = {24873-2485}, journal = {Plant Cell}, url = {http://www.plantcell.org/content/17/9/2473.full}, volume = {17,9}, abstract = { In this study, we characterize the evolutionarily conserved TOUGH (TGH) protein as a novel regulator required for Arabidopsis thaliana development. We initially identified TGH as a yeast two-hybrid system interactor of the transcription initiation factor TATA-box binding protein 2. TGH has apparent orthologs in all eukaryotic model organisms with the exception of the budding yeast Saccharomyces cerevisiae. TGH contains domains with strong similarity to G-patch and SWAP domains, protein domains that are characteristic of RNA binding and processing proteins. Furthermore, TGH colocalizes with the splicing regulator SRp34 to subnuclear particles. We therefore propose that TGH plays a role in RNA binding or processing. Arabidopsis tgh mutants display developmental defects, including reduced plant height, polycotyly, and reduced vascularization. We found TGH expression to be increased in the amp1-1 mutant, which is similar to tgh mutants with respect to polycotyly and defects in vascular development. Interestingly, we observed a strong genetic interaction between TGH and AMP1 in that tgh-1 amp1-1 double mutants are extremely dwarfed and severely affected in plant development in general and vascular development in particular when compared with the single mutants.} } @Article{IPB-690, author = {Durgbanshi, A. and Arbona, V. and Pozo, O. and Miersch, O. and Sancho, J.V. and Gómez-Cadenas, A.}, title = {{Simultaneous determination of multiple phytohormones in plant extracts by liquid chromatography-electrospray tandem mass spectrometry}}, year = {2005}, pages = {8437-8442}, journal = {J. Agric. Food Chem.}, volume = {53}, } @Article{IPB-787, author = {Denzano, A.M. and Vigliocco, A. and Miersch, O. and Abdala, G.}, title = {{Octadecanoid levels during stolon to tuber transition in potato.}}, year = {2005}, pages = {107-115}, chapter = {{48}}, journal = {Potato Res.}, } @Article{IPB-693, author = {Meixner, C. and Ludwig-Müller, J. and Miersch, O. and Gresshoff, P. and Staehlin, C. and Vierheilig, H.}, title = {{Lack of mycorrhizal autoregulation and phytohormonal changes in the supernodulating soybean mutant nts1007}}, year = {2005}, pages = {709-715}, journal = {Planta }, volume = {222}, } @Article{IPB-432, author = {Gerhard, B. and Fischer, K. and Balkenhohl, T.J. and Pohnert, G. and Kühn, H. and Wasternack, C. and Feussner, I.}, title = {{Lipoxygenase-mediated metabolism of storage lipids in germinating sunflower cotyledons and b-oxidation of (9Z,11E,13S)-13-hydroxy-octadeca-9,11-dienoic acid by the cotyledonary glyoxysomes}}, year = {2005}, pages = {919-930}, journal = {Planta}, volume = {220}, } @Article{IPB-856, author = {Quint, M. and Ito, H. and Zhang, W. and Gray, W.M.}, title = {{Characterization of a novel temperature-sensitive allele of the CUL1/AXR6 subunit of SCF ubiquitin-ligases}}, year = {2005}, pages = {371-383}, journal = {Plant J}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02449.x/full}, volume = {43}, abstract = { Selective protein degradation by the ubiquitin-proteasome pathway has emerged as a key regulatory mechanism in a wide variety of cellular processes. The selective components of this pathway are the E3 ubiquitin-ligases which act downstream of the ubiquitin-activating and -conjugating enzymes to identify specific substrates for ubiquitinylation. SCF-type ubiquitin-ligases are the most abundant class of E3 enzymes in Arabidopsis. In a genetic screen for enhancers of the tir1-1 auxin response defect, we identified eta1/axr6-3, a recessive and temperature-sensitive mutation in the CUL1 core component of the SCFTIR1 complex. The axr6-3 mutation interferes with Skp1 binding, thus preventing SCF complex assembly. axr6-3 displays a pleiotropic phenotype with defects in numerous SCF-regulated pathways including auxin signaling, jasmonate signaling, flower development, and photomorphogenesis. We used axr6-3 as a tool for identifying pathways likely to be regulated by SCF-mediated proteolysis and propose new roles for SCF regulation of the far-red light/phyA and sugar signaling pathways. The recessive inheritance and the temperature-sensitive nature of the pleiotropically acting axr6-3 mutation opens promising possibilities for the identification and investigation of SCF-regulated pathways in Arabidopsis.} } @Article{IPB-694, author = {Rudus, I. and Kepczynska, E. and Kepczynski, J. and Wasternack, C. and Miersch, O.}, title = {{Changes in jasmonates and 12-oxophytodienoic acid contents of Medicago sativa L. during somatic embryogenesis}}, year = {2005}, pages = {497-504}, journal = {Acta Physiol. Plantar.}, volume = {27}, } @Article{IPB-542, author = {Ludwig, A.A. and Saitoh, H. and Felix, G. and Freymark, G. and Miersch, O. and Wasternack, C. and Boller, T. and Jones, J.D.G. and Romeis, T.}, title = {{Ethylene-mediated cross-talk between calcium-dependent protein kinase and MAPK signaling controls stress responses in plants}}, year = {2005}, pages = {10736-10741}, journal = {PNAS }, volume = {102}, } @Article{IPB-689, author = {Andrade, A. and Vigliocco, A. and Alemano, S. and Miersch, O. and Botella, M.A.}, title = {{Endogenous jasmonates and octadecanoids during germination and seedling development: their relation with hypersensitive tomato mutants to abiotic stress}}, year = {2005}, pages = {309-318}, journal = {Seed Sci. Res.}, volume = {15}, } @Article{IPB-435, author = {Danon, A. and Miersch, O. and Felix, G. and op den Camp, R.G.L. and Apel, K.}, title = {{Concurrent activation of cell death-regulating signaling pathways by singlet oxygen in Arabidopsis thaliana}}, year = {2005}, pages = {68-80}, journal = {Plant J.}, volume = {41}, } @Article{IPB-691, author = {Fortes, A.M. and Miersch, O. and Lange, P.R. and Malho, R. and Testillano, P.S. and del Risueno, M.C. and Wasternack, C. and Pais, M.S.}, title = {{Expression of allene oxide cyclase and accumulation of jasmonates during organogenic nodule formation from hop (Humulus lupulus var. Nugget) internodes}}, year = {2005}, pages = {1713-23}, journal = {Plant Cell Physiol.}, volume = {46}, } @Article{IPB-699, author = {Sharma, V.K. and Monostori, T. and Hause, B. and Maucher, H. and Göbel, C. and Hornung, E. and Hänsch, R. and Bittner, F. and Wasternack, C. and Feussner, I. and Mendel, R.R. and Schulze, J.}, title = {{Genetic transformation of barley to modify expression of a 13-lipoxygenase}}, year = {2005}, pages = {33-34 }, journal = {Acta Biol. Szeged }, url = {http://www2.sci.u-szeged.hu/ABS/2005/Acta%20HP/4933.pdf}, volume = {49}, abstract = {Immature scutella of barley were transformed with cDNA coding for a 13-li-poxygenase of barley (LOX-100) via particle bombardment. Regenerated plants were tested by PAT-assay, Western-analysis and PCR-screening. Immunocytochemical assay of T0 plants showed expression of the LOX cDNA both in the chloroplasts and in the cytosol, depending on the presence of the chloroplast signal peptide sequences in the cDNA. A few transgenic plants containing higher amounts of LOX-derived products have been found. These are the candidates for further analysis concerning pathogen resistance.} } @Article{IPB-698, author = {Isayenkov, S. and Mrosk, C. and Stenzel, I. and Strack, D. and Hause, B.}, title = {{Suppression of allene oxide cyclase in hairy roots of Medicago truncatula reduces jasmonate levels and the degree of mycorrhization with Glomus intraradices}}, year = {2005}, pages = {1401-1410}, journal = {Plant Physiol}, volume = {139}, } @INBOOK{IPB-1560, author = {Vaira, A.M. and Acotto, G.P. and Gago-Zachert, S. and García, M.L. and Grau, O. and Milne, R.G. and Morikawa, T. and Natsuaki, T. and Torov, V. and Verbeek, M. and Vetten, H.J.}, title = {{Virus Taxonomy. VIIIth Report of the International Committee on Taxonomy of Viruses. Part II the negative sense single stranded RNA viruses}}, year = {2005}, pages = {673-679}, chapter = {{Genus Ophiovirus}}, journal = {Elsevier, Academic Press}, editor = {Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U., Ball, L. A.}, url = {https://www.elsevier.com/books/virus-taxonomy/fauquet/978-0-12-249951-7}, abstract = {Virus Taxonomy is a standard and comprehensive source for the classification of viruses, created by the International Committee of the Taxonomy of Viruses. The book includes eight taxonomic reports of the ICTV and provides comprehensive information on 3 taxonomic orders of viruses, 73 families, 9 subfamilies, 287 genera, and 1938 virus species. The book also features about 429 colored pictures and diagrams for more efficient learning. The text is divided into four parts, comprised of 16 chapters and presenting the following features: • Compiled data from numerous international experts about virus taxonomy and nomenclature • Organized information on over 6000 recognized viruses, illustrated with diagrams of genome organization and virus replication cycle • Data on the phylogenetic relationships among viruses of the same and different taxa • Discussion of the qualitative and quantitative relationships of virus sequences The book is a definitive reference for microbiologists, molecular biologists, research-level virologists, infectious disease specialists, and pharmaceutical researchers working on antiviral agents. Students and novices in taxonomy and nomenclature will also find this text useful. } } @Article{IPB-1559, author = {Gago, S. and de la Peña, M. and Flores, R.}, title = {{A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability}}, year = {2005}, pages = {1073-1083}, journal = {RNA}, volume = {11}, } @Article{IPB-1142, author = {Levy, M. and Wang, Q. and Kaspi, R. and Parrella, M.P. and Abel, S.}, title = {{Arabidopsis IQD1, a novel calmodulin-binding nuclear protein, stimulates glucosinolate accumulation and plant defense}}, year = {2005}, pages = {79 - 96}, journal = {Plant Journal}, doi = {10.1111/j.1365-313X.2005.02435.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02435.x/full}, volume = {43}, abstract = { Glucosinolates are a class of secondary metabolites with important roles in plant defense and human nutrition. To uncover regulatory mechanisms of glucosinolate production, we screened Arabidopsis thaliana T-DNA activation-tagged lines and identified a high-glucosinolate mutant caused by overexpression of IQD1 (At3g09710). A series of gain- and loss-of-function IQD1 alleles in different accessions correlates with increased and decreased glucosinolate levels, respectively. IQD1 encodes a novel protein that contains putative nuclear localization signals and several motifs known to mediate calmodulin binding, which are arranged in a plant-specific segment of 67 amino acids, called the IQ67 domain. We demonstrate that an IQD1-GFP fusion protein is targeted to the cell nucleus and that recombinant IQD1 binds to calmodulin in a Ca2+-dependent fashion. Analysis of steady-state messenger RNA levels of glucosinolate pathway genes indicates that IQD1 affects expression of multiple genes with roles in glucosinolate metabolism. Histochemical analysis of tissue-specific IQD1::GUS expression reveals IQD1 promoter activity mainly in vascular tissues of all organs, consistent with the expression patterns of several glucosinolate-related genes. Interestingly, overexpression of IQD1 reduces insect herbivory, which we demonstrated in dual-choice assays with the generalist phloem-feeding green peach aphid (Myzus persicae), and in weight-gain assays with the cabbage looper (Trichoplusia ni), a generalist-chewing lepidopteran. As IQD1 is induced by mechanical stimuli, we propose IQD1 to be novel nuclear factor that integrates intracellular Ca2+ signals to fine-tune glucosinolate accumulation in response to biotic challenge.} } @Article{IPB-1140, author = {Abel, S. and Savchenko, T. and Levy, M.}, title = {{Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa}}, year = {2005}, pages = {72 (1-25)}, journal = {BMC Evolutionary Biology}, url = {http://www.biomedcentral.com/1471-2148/5/72}, volume = {5}, abstract = { We identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (~10.3) and frequency of serine residues (~11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants. Comparative phylogenetic analyses indicate that the major IQD gene lineages originated before the monocot-eudicot divergence. The extant IQD loci in Arabidopsis primarily resulted from segmental duplication and reflect preferential retention of paralogous genes, which is characteristic for proteins with regulatory functions. Interaction of IQD1 and IQD20 with calmodulin and the presence of predicted calmodulin binding sites in all IQD family members suggest that IQD proteins are a new class of calmodulin targets. The basic isoelectric point of IQD proteins and their frequently predicted nuclear localization suggest that IQD proteins link calcium signaling pathways to the regulation of gene expression. Our comparative genomics analysis of IQD genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of putative calmodulin targets.} } @Article{IPB-1143, author = {Ebeler, S.E. and Dingley, K.H. and Ubick, E. and Abel, S. and Mitchell, A.E. and Burns, S.A. and Steinberg, F.M. and Clifford, A.J.}, title = {{Animal models and analytical approaches for understanding the relationships between wine and cancer}}, year = {2005}, pages = {19 - 27}, journal = {Drugs Exptl Clin Res}, volume = {31}, } @Article{IPB-433, author = {Schneider, K. and Kienow, L. and Schmelzer, E. and Colby, T. and Bartsch, M. and Miersch, O. and Wasternack, C. and Kombrink, E. and Stuible, H.-P.}, title = {{A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity of activate biosynthetic precursors of jasmonic acid}}, year = {2005}, pages = {13962-13972}, journal = {J. Biol. Chem.}, volume = {280}, } @Article{IPB-369, author = {Groß, N. and Wasternack, C. and Köck, M.}, title = {{Wound induced RNaseLE expression is jasmonate and systemin independent and occurs only locally in tomato (Lycopersicon esculentum cv. Lukullus)}}, year = {2004}, pages = {1343-1350}, journal = {Phytochemistry}, volume = {65}, } @INBOOK{IPB-431, author = {Wasternack, C.}, title = {{Programmed Cell Death and Related Processes in Plants}}, year = {2004}, pages = {143-154}, chapter = {{Jasmonates - Biosynthesis and role in stress responses and developmental processes}}, journal = {Academic Press, New York}, editor = {Nooden, L.D.}, } @Article{IPB-370, author = {Köck, M. and Groß, N. and Stenzel, I. and Hause, G.}, title = {{Phloem-specific expression of the wound-inducible ribonuclease LE from tomato (Lycopersicon esculentum cv. Lukullus)}}, year = {2004}, pages = {233-242}, journal = {Planta}, volume = {219}, } @Article{IPB-1132, author = {Ticconi, C.A. and Abel, S.}, title = {{Short on phosphate: plant surveillance and countermeasures}}, year = {2004}, pages = {548-555}, journal = {Trends Plant Sci}, volume = {9}, } @Article{IPB-430, author = {Wasternack, C.}, title = {{Jasmonates - Introductory remarks on biosynthesis and diversity in action}}, year = {2004}, pages = {167-169}, journal = {J. Plant Growth Reg.}, volume = {23}, } @Article{IPB-857, author = {Frisch, M. and Quint, M. and Lübberstedt, T. and Melchinger, A.E.}, title = {{Duplicate marker loci can result in incorrect locus orders on linkage maps}}, year = {2004}, pages = {305-316}, journal = {Theor Appl Genet}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14968304}, volume = {109}, } @Article{IPB-1133, author = {Ticconi, C.A. and Delatorre, C.A. and Lahner, B. and Salt, D.E. and Abel, S.}, title = {{Arabidopsis pdr2 reveals a phosphate-sensitive checkpoint in root development}}, year = {2004}, pages = {801 - 814}, journal = {Plant Journal}, volume = {37}, } @Article{IPB-371, author = {Maucher, H. and Stenzel, I. and Miersch, O. and Stein, N. and Prasad, M. and Zierold, U. and Schweizer, P. and Dorer, C. and Hause, B. and Wasternack, C.}, title = {{The allene oxide cyclase of barley (Hordeum vulgare L.) - cloning and organ-specific expression}}, year = {2004}, pages = {801-811}, journal = {Phytochemistry}, volume = {65}, } @Article{IPB-253, author = {Schüler, G. and Mithöfer, A. and Baldwin, I.T. and Berger, S. and Ebel, S. and Santos, J.G. and Herrmann, G. and Hölscher, D. and Kramell, R. and Kutchan, T.M. and Maucher, H. and Schneider, B. and Stenzel, I. and Wasternack, C. and Boland, W.}, title = {{Coronalon: a powerful tool in plant stress physiology}}, year = {2004}, pages = {17-22}, journal = {FEBS Lett.}, doi = {10.1016/S0014-5793(04)00239-X}, url = {http://febs.onlinelibrary.wiley.com/hub/journal/10.1002/(ISSN)1873-3468/issues/}, volume = {563}, abstract = {Coronalon, a synthetic 6-ethyl indanoyl isoleucine conjugate, has been designed as a highly active mimic of octadecanoid phytohormones that are involved in insect and disease resistance. The spectrum of biological activities that is affected by coronalon was investigated in nine different plant systems specifically responding to jasmonates and/or 12-oxo-phytodienoic acid. In all bioassays analyzed, coronalon demonstrated a general strong activity at low micromolar concentrations. The results obtained showed the induction of (i) defense-related secondary metabolite accumulation in both cell cultures and plant tissues, (ii) specific abiotic and biotic stress-related gene expression, and (iii) root growth retardation. The general activity of coronalon in the induction of plant stress responses together with its simple and efficient synthesis suggests that this compound might serve as a valuable tool in the examination of various aspects in plant stress physiology. Moreover, coronalon might become employed in agriculture to elicit plant resistance against various aggressors.} } @Article{IPB-1525, author = {Grubb, C.D. and Zipp, J.P. and Ludwig-Müller, J. and Masuno, M.N. and Molinski, T.F. and Abel, S.}, title = {{Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis}}, year = {2004}, pages = {893-908}, journal = {Plant J}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2004.02261.x/abstract}, volume = {40}, } @Article{IPB-1558, author = {Flores, R. and Delgado, S. and Gas, M.E. and Carbonell, A. and Molina, D. and Gago, S. and de la Peña, M.}, title = {{Viroids: the minimal non-coding RNA's with autonomous replication}}, year = {2004}, pages = {42-48}, journal = {FEBS Letters}, volume = {567}, } @INBOOK{IPB-428, author = {Weichert, H. and Maucher, H. and Hornung, E. and Wasternack, C. and Feussner, I.}, title = {{Advanced Research on Plant Lipids}}, year = {2003}, pages = {275-278}, chapter = {{Shift in fatty acid and oxylipin pattern of tomato leaves following overexpression of the allene oxide cyclase}}, journal = {Kluwer Academic Publishers}, editor = {Murata, N., Yamada, M., Nishida, I., Okuyama, H., Sekijar, J., Hajme, W.}, } @Article{IPB-359, author = {Färber, K. and Schumann, B. and Miersch, O. and Roos, W.}, title = {{Selective desensitization of jasmonate- and pH-dependent signaling in the induction of benzophenanthridine biosynthesis in cells of Eschscholzia californica}}, year = {2003}, pages = {491-500}, journal = {Phytochemistry}, volume = {62}, } @Article{IPB-424, author = {Schilling, S. and Manhart, S. and Hoffmann, T. and Ludwig, H.-H. and Wasternack, C. and Demuth, H.-U.}, title = {{Substrate specificity of glutaminyl cyclases from plants and animals}}, year = {2003}, pages = {1583-1592}, journal = {Biol. Chem.}, volume = {384}, } @Article{IPB-859, author = {Dussle, C.M. and Quint, M. and Xu, M.L. and Melchinger, A.E. and Lübberstedt, T.}, title = {{Saturation of two chromosome regions conferring resistance to SCMV with SSR and AFLP markers by targeted BSA}}, year = {2003}, pages = {485-493}, journal = {Theor Appl Genet}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12589549}, volume = {106}, } @Article{IPB-367, author = {O'Donnell, P.J. and Schmelz, E. and Block, A. and Miersch, O. and Wasternack, C. and Jones, J.B. and Klee, H.J.}, title = {{Multiple hormones cooperatively control a susceptible tomato pathogen defense response}}, year = {2003}, pages = {1181-1189}, journal = {Plant Physiol.}, volume = {133}, } @Article{IPB-425, author = {Schilling, S. and Niestroj, A.J. and Rahfeld, J.-U. and Hoffmann, T. and Wermann, M. and Zunkel, K. and Wasternack, C. and Demuth, H.-U.}, title = {{Identification of human glutaminyl cyclase as a metalloenzyme - Potent inhibition by imidazole derivatives and heterocyclic chelators}}, year = {2003}, pages = {49773-49779}, journal = {J. Biol. Chem.}, volume = {278}, } @Article{IPB-358, author = {Abdala, G. and Miersch, O. and Kramell, R. and Vigliocco, A. and Agostini, E. and Forchetti, G. and Alemano, S.}, title = {{Jasmonate and octadecanoid occurrence in tomato hairy roots. Endogenous level changes in response to NaCl}}, year = {2003}, pages = {21-27}, journal = {Plant Growth Regul.}, volume = {40}, } @Article{IPB-858, author = {Quint, M. and Dussle, C.M. and Melchinger, A.E. and Lübberstedt, T.}, title = {{Identification of genetically linked RGAs by BAC screening in maize and implication for gene cloning, mapping, and MAS}}, year = {2003}, pages = {1171-1177}, journal = {Theor Appl Genet}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12748766}, volume = {106}, } @Article{IPB-1144, author = {Dingley, K.H. and Ubick, E.A. and Chiarappa-Zucca, M.L. and Nowell, S. and Abel, S. and Ebeler, S.E. and Mitchell, A.E. and Burns, S.A. and Steinberg, F.M. and Clifford, A.J.}, title = {{Effect of dietary constituents with chemopreventive potential on adduct formation of a low dose of the heterocyclic amines PhIP and IQ and Phase II hepatic enzymes}}, year = {2003}, pages = {212 - 221}, journal = {Nutr \& Cancer}, volume = {46}, } @Article{IPB-365, author = {Stenzel, I. and Ziehte, K. and Schurath, J. and Hertel, S.C. and Bosse, D. and Köck, M.}, title = {{Differential expression of PSI14, a phosphatase gene family, in response to phosphate availability, plant infection and pathogen infection}}, year = {2003}, pages = {138-146}, journal = {Physiol. Plant}, volume = {118}, } @INBOOK{IPB-427, author = {Stumpe, M. and Stenzel, I. and Weichert, H. and Hause, B. and Feussner, I.}, title = {{Advanced Research on Plant Lipids}}, year = {2003}, pages = {287-290}, chapter = {{The lipoxygenase pathway in mycorrhizal roots of Medicago truncatula}}, journal = {Kluwer Academic Publishers, Dordrecht}, editor = {Murata, N., Yamada, M., Nishida, I., Okuyama, H., Sekijar, J., Hajme, W.}, } @INBOOK{IPB-426, author = {Stenzel, I. and Hause, B. and Feussner, I. and Wasternack, C.}, title = {{Advanced Research on Plant Lipids}}, year = {2003}, pages = {267-270}, chapter = {{Transcriptional activation of jasmonate biosynthesis enzymes is not reflected at protein level}}, journal = {Kluwer Academic Publishers}, editor = {Murata, N., Yamada, M., Nishida, I., Okuyama, H., Sekijar, J., Hajme, W.}, } @Article{IPB-360, author = {Gidda, K.S. and Miersch, O. and Schmidt, J. and Wasternack, C. and Varin, L.}, title = {{Biochemical and molecular characterization of a hydroxy-jasmonate sulfotransferase from Arabidopsis thaliana}}, year = {2003}, pages = {17895-17900}, journal = {J. Biol. Chem.}, doi = {10.1074/jbc.M211943200}, url = {http://www.jbc.org/content/by/year}, volume = {278}, abstract = { 12-Hydroxyjasmonate, also known as tuberonic acid, was first isolated from Solanum tuberosum and was shown to have tuber-inducing properties. It is derived from the ubiquitously occurring jasmonic acid, an important signaling molecule mediating diverse developmental processes and plant defense responses. We report here that the gene AtST2a from Arabidopsis thaliana encodes a hydroxyjasmonate sulfotransferase. The recombinant AtST2a protein was found to exhibit strict specificity for 11- and 12-hydroxyjasmonate with Km values of 50 and 10 µM, respectively. Furthermore, 12-hydroxyjasmonate and its sulfonated derivative are shown to be naturally occurring in A. thaliana. The exogenous application of methyljasmonate to A. thaliana plants led to increased levels of both metabolites, whereas treatment with 12-hydroxyjasmonate led to increased level of 12-hydroxyjasmonate sulfate without affecting the endogenous level of jasmonic acid. AtST2a expression was found to be induced following treatment with methyljasmonate and 12-hydroxyjasmonate. In contrast, the expression of the methyljasmonate-responsive gene Thi2.1, a marker gene in plant defense responses, is not induced upon treatment with 12-hydroxyjasmonate indicating the existence of independent signaling pathways responding to jasmonic acid and 12-hydroxyjasmonic acid. Taken together, the results suggest that the hydroxylation and sulfonation reactions might be components of a pathway that inactivates excess jasmonic acid in plants. Alternatively, the function of AtST2a might be to control the biological activity of 12-hydroxyjasmonic acid.} } @Article{IPB-1959, author = {Naum-Onganı́a, G. and Gago-Zachert, S. and Peña, E. and Grau, O. and Garcia, M. L.}, title = {{Citrus psorosis virus RNA 1 is of negative polarity and potentially encodes in its complementary strand a 24K protein of unknown function and 280K putative RNA dependent RNA polymerase}}, year = {2003}, pages = { 49–61}, journal = {Virus Res}, doi = {10.1016/S0168-1702(03)00172-2}, url = {http://www.sciencedirect.com/science/journal/01681702}, volume = { 96}, abstract = {Citrus psorosis virus (CPsV), the type member of genus Ophiovirus, has three genomic RNAs. Complete sequencing of CPsV RNA 1 revealed a size of 8184 nucleotides and Northern blot hybridization with chain specific probes showed that its non-coding strand is preferentially encapsidated. The complementary strand of RNA 1 contains two open reading frames (ORFs) separated by a 109-nt intergenic region, one located near the 5′-end potentially encoding a 24K protein of unknown function, and another of 280K containing the core polymerase motifs characteristic of viral RNA-dependent RNA polymerases (RdRp). Comparison of the core RdRp motifs of negative-stranded RNA viruses, supports grouping CPsV, Ranunculus white mottle virus (RWMV) and Mirafiori lettuce virus (MiLV) within the same genus (Ophiovirus), constituting a monophyletic group separated from all other negative-stranded RNA viruses. Furthermore, RNAs 1 of MiLV, CPsV and RWMV are similar in size and those of MiLV and CPsV also in genomic organization and sequence.} } @Article{IPB-1557, author = {de la Peña, M. and Gago, S. and Flores, R.}, title = {{Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity}}, year = {2003}, pages = {5561-5570}, journal = {The EMBO Journal}, volume = {22}, } @Article{IPB-1134, author = {Abel, S. and Ticconi, C.A. and Delatorre, C.A.}, title = {{Phosphate sensing in higher plants}}, year = {2002}, pages = {1 - 8}, journal = {Plant Physiology}, volume = {115}, } @Article{IPB-350, author = {Feussner, I. and Wasternack, C.}, title = {{The lipoxygenase pathway}}, year = {2002}, pages = {275-297}, journal = {Annu. Rev. Plant Biol.}, volume = {53}, abstract = {Lipid peroxidation is common to all biological systems, both appearing in developmentally and environmentally regulated processes of plants. The hydroperoxy polyunsaturated fatty acids, synthesized by the action of various highly specialized forms of lipoxygenases, are substrates of at least seven different enzyme families. Signaling compounds such as jasmonates, antimicrobial and antifungal compounds such as leaf aldehydes or divinyl ethers, and a plant-specific blend of volatiles including leaf alcohols are among the numerous products. Cloning of many lipoxygenases and other key enzymes within the lipoxygenase pathway, as well as analyses by reverse genetic and metabolic profiling, revealed new reactions and the first hints of enzyme mechanisms, multiple functions, and regulation. These aspects are reviewed with respect to activation of this pathway as an initial step in the interaction of plants with pathogens, insects, or abiotic stress and at distinct stages of development.} } @Article{IPB-349, author = {Ellis, C. and Karafyllidis, I. and Wasternack, C. and Turner, J.G.}, title = {{The Arabidopsis mutant cev1 links cell wall signaling to jasmonate and ethylene responses}}, year = {2002}, pages = {1557-1566}, journal = {The Plant Cell}, volume = {14}, } @Article{IPB-353, author = {Schilling, S. and Hoffmann, T. and Rosche, F. and Manhart, S. and Wasternack, C. and Demuth, H.-U.}, title = {{Heterologous expression and characterization of human glutaminyl cyclase: evidence for a disulfide bond with importance for catalytic activity}}, year = {2002}, pages = {10849-10857}, journal = {Biochemistry}, volume = {41}, } @Article{IPB-1294, author = {Laskowski, M.J. and Dreher, K.A. and Gehring, M. and Abel, S. and Gensler, A. and Sussex, I.M.}, title = {{FQR1, a novel primary auxin-response gene, encodes an FMN-binding quinone reductase.}}, year = {2002}, pages = {578-686}, journal = {Plant Physiology}, url = {http://www.plantphysiol.org/content/128/2/578.abstract?sid=3f1f8a7a-ed15-40f3-9d7f-723ae31566f1}, volume = {128}, abstract = { FQR1 is a novel primary auxin-response gene that codes for a flavin mononucleotide-binding flavodoxin-like quinone reductase. Accumulation of FQR1 mRNA begins within 10 min of indole-3-acetic acid application and reaches a maximum of approximately 10-fold induction 30 min after treatment. This increase in FQR1 mRNA abundance is not diminished by the protein synthesis inhibitor cycloheximide, demonstrating thatFQR1 is a primary auxin-response gene. Sequence analysis reveals that FQR1 belongs to a family of flavin mononucleotide-binding quinone reductases. Partially purified His-tagged FQR1 isolated fromEscherichia coli catalyzes the transfer of electrons from NADH and NADPH to several substrates and exhibits in vitro quinone reductase activity. Overexpression of FQR1 in plants leads to increased levels of FQR1 protein and quinone reductase activity, indicating that FQR1 functions as a quinone reductase in vivo. In mammalian systems, glutathione S-transferases and quinone reductases are classified as phase II detoxification enzymes. We hypothesize that the auxin-inducible glutathioneS-transferases and quinone reductases found in plants also act as detoxification enzymes, possibly to protect against auxin-induced oxidative stress.} } @Article{IPB-357, author = {Weichert, H. and Kolbe, A. and Kraus, A. and Wasternack, C. and Feussner, I.}, title = {{Metabolic profiling of oxylipins in germinating cucumber seedlings - lipoxygenase-dependent degradation of triacylglycerols and biosynthesis of volatile aldehydes}}, year = {2002}, pages = {612-619}, journal = {Planta}, volume = {215}, } @Article{IPB-1293, author = {Schwechheimer, C. and Calderón Villalobos, L.I.}, title = {{Cullin-containing E3 ubiquitin ligases in plant development}}, year = {2002}, pages = {677-686}, journal = {Curr. Opin. Plant Biol.}, url = {http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236252%232004%23999929993%23523857%23FLA%23&_cdi=6252&_pubType=J&_auth=y&_acct=C000065317&_version=1&_urlVersion=0&_userid=4832532&md5=c784aeed2f5d5cdf916aeca40dee0117}, volume = {7(6)}, abstract = { In eukaryotes, the ubiquitinproteasome system participates in the control of signal transduction events by selectively eliminating regulatory proteins. E3 ubiquitin ligases specifically bind degradation substrates and mediate their poly-ubiquitylation, a prerequisite for their degradation by the 26S proteasome. On the basis of the analysis of the Arabidopsis genome sequence, it is predicted that there are more than 1000 E3 ubiquitin ligases in plants. Several types of E3 ubiquitin ligases have already been characterized in eukaryotes. Recently, some of these E3 enzymes have been implicated in specific plant signaling pathways.} } @Article{IPB-352, author = {Nibbe, M. and Hilpert, B. and Wasternack, C. and Miersch, O. and Apel, K.}, title = {{Cell death and salicylate- and jasmonate-dependent stress responses in Arabidopsis are controlled by single cet genes}}, year = {2002}, pages = {120-128}, journal = {Planta}, volume = {216}, } @Article{IPB-347, author = {Abdala, G. and Castro, G. and Miersch, O. and Pierce, D.}, title = {{Changes in jasmonate and gibberellin levels during development of potato plants (Solanum tuberosum)}}, year = {2002}, pages = {121-126}, journal = {Plant Growth Reg.}, volume = {36}, } @Article{IPB-861, author = {Quint, M. and Mihaljevic, R. and Dussle, C.M. and Xu, M.L. and Melchinger, A.E. and Lübberstedt, T.}, title = {{Development of RGA-CAPS markers and genetic mapping of candidate genes for SCMV resistance in maize}}, year = {2002}, pages = {355-366}, journal = {Theor Appl Genet}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12582538}, volume = {105}, } @Article{IPB-354, author = {Schilling, S. and Hoffmann, T. and Wermann, M. and Heiser, U. and Wasternack, C. and Demuth, H.-U.}, title = {{Continuous spectrometric assays for glutaminyl cyclase activity}}, year = {2002}, pages = {49-56}, journal = {Analytical Biochemistry}, volume = {303}, } @INBOOK{IPB-423, author = {Scheel, D. and Wasternack, C.}, title = {{Plant Signal Transduction}}, year = {2002}, pages = {1-5}, chapter = {{Signal transduction in plants: Cross-talk with the environment}}, journal = {University Press, Oxford, UK}, editor = {Scheel, D., Wasternack, C.}, } @INBOOK{IPB-457, author = {Wasternack, C. and Hause, B.}, title = {{Progress in Nucleic Acid Research and Molecular Biology}}, year = {2002}, pages = {165-221}, chapter = {{Jasmonates and octadecanoids: Signals in plant stress responses and development}}, editor = {Moldave, K.}, doi = {10.1016/S0079-6603(02)72070-9}, volume = {72}, } @Article{IPB-452, author = {Hause, B. and Maier, W. and Miersch, O. and Kramell, R. and Strack, D.}, title = {{Induction of jasmonate biosynthesis in arbuscular mycorrhizal barley roots}}, year = {2002}, pages = {1213-1220}, journal = {Plant Physiol.}, doi = {10.1104/pp.006007}, url = {http://www.ncbi.nlm.nih.gov/pmc/journals/69/}, volume = {130}, abstract = { Colonization of barley (Hordeum vulgare cv Salome) roots by an arbuscular mycorrhizal fungus, Glomus intraradices Schenck \& Smith, leads to elevated levels of endogenous jasmonic acid (JA) and its amino acid conjugate JA-isoleucine, whereas the level of the JA precursor, oxophytodienoic acid, remains constant. The rise in jasmonates is accompanied by the expression of genes coding for an enzyme of JA biosynthesis (allene oxide synthase) and of a jasmonate-induced protein (JIP23). In situ hybridization and immunocytochemical analysis revealed that expression of these genes occurred cell specifically within arbuscule-containing root cortex cells. The concomitant gene expression indicates that jasmonates are generated and act within arbuscule-containing cells. By use of a near-synchronous mycorrhization, analysis of temporal expression patterns showed the occurrence of transcript accumulation 4 to 6 d after the appearance of the first arbuscules. This suggests that the endogenous rise in jasmonates might be related to the fully established symbiosis rather than to the recognition of interacting partners or to the onset of interaction. Because the plant supplies the fungus with carbohydrates, a model is proposed in which the induction of JA biosynthesis in colonized roots is linked to the stronger sink function of mycorrhizal roots compared with nonmycorrhizal roots.} } @Article{IPB-1145, author = {Wang, Q. and Grubb, C.D. and Abel, S.}, title = {{Direct analysis of single leaf disks for chemopreventive glucosinolates}}, year = {2002}, pages = {152 - 157}, journal = {Phytochem Anal}, doi = {10.1002/pca.636}, url = {http://onlinelibrary.wiley.com/doi/10.1002/pca.636/abstract}, volume = {13}, abstract = {Natural isothiocyanates, produced during plant tissue damage from methionine-derived glucosinolates, are potent inducers of mammalian phase 2 detoxification enzymes such as quinone reductase (QR). A greatly simplified bioassay for glucosinolates based on induction and colorimetric detection of QR activity in murine hepatoma cells is described. It is demonstrated that excised leaf disks of Arabidopsis thaliana (ecotype Columbia) can directly and reproducibly substitute for cell-free leaf extracts as inducers of murine QR, which reduces sample preparation to a minimum and maximizes throughput. A comparison of 1 and 3 mm diameter leaf disks indicated that QR inducer potency was proportional to disk circumference (extent of tissue damage) rather than to area. When compared to the QR inducer potency of the corresponding amount of extract, 1 mm leaf disks were equally effective, whereas 3 mm disks were 70% as potent. The QR inducer potency of leaf disks correlated positively with the content of methionine-derived glucosinolates, as shown by the analysis of wild-type plants and mutant lines with lower or higher glucosinolate content. Thus, the microtitre plate-based assay of single leaf disks provides a robust and inexpensive visual method for rapidly screening large numbers of plants in mapping populations or mutant collections and may be applicable to other glucosinolate-producing species.} } @Article{IPB-1146, author = {Grubb, C.D. and Gross, H.B. and Chen, D.L. and Abel, S.}, title = {{Identification of Arabidopsis mutants with altered glucosinolate profiles based on isothiocyanate bioactivity}}, year = {2002}, pages = {143 - 152}, journal = {Plant Sci}, doi = {10.1016/S0168-9452(01)00550-7}, url = {http://www.sciencedirect.com/science/article/pii/S0168945201005507}, volume = {162}, abstract = {Glucosinolates are a diverse class of nitrogen- and sulfur-containing secondary metabolites. They are rapidly hydrolyzed on tissue disruption to a number of biologically active compounds that are increasingly attracting interest as anticarcinogenic phytochemicals and crop protectants. Several glucosinolate-derived isothiocyanates are potent chemopreventive agents that favorably modulate carcinogen metabolism in mammals. Methylsulfinylalkyl isothiocyanates, in particular the 4-methylsulfinylbutyl derivative, are selective and potent inducers of mammalian detoxification enzymes such as quinone reductase (QR). Cruciferous plants including Arabidopsis thaliana (L.) Heyhn, synthesize methylsulfinylalkyl glucosinolates, which are derived from methionine. Using a colorimetric assay for QR activity in murine hepatoma cells and high performance liquid chromatography (HPLC) analysis of desulfoglucosinolates, we have demonstrated a strong positive correlation between leaf QR inducer potency and leaf content of methionine-derived glucosinolates in various A. thaliana ecotypes and available glucosinolate mutants. In a molecular genetic approach to glucosinolate biosynthesis, we screened 3000 chemically mutagenized M2 plants of the Columbia ecotype for altered leaf QR inducer potency. Subsequent HPLC analysis of progeny of putative mutants identified six lines with significant and heritable changes in leaf glucosinolate content and composition.} } @Article{IPB-355, author = {Vigliocco, A. and Bonamico, M.B. and Alemano, S. and Miersch, O. and Abdala, G.}, title = {{Activation of jasmonic acid production in Zea mays L. infected by the maize rough dwarf virus-Río Cuarto. Reversion of symptoms by salicylic acid}}, year = {2002}, pages = {369-374}, journal = {Biocell}, volume = {26(3)}, } @Article{IPB-860, author = {Dussle, C.M. and Quint, M. and Xu, M.L. and Melchinger, A.E. and Lübberstedt, T.}, title = {{Conversion of AFLP fragments tightly linked to Scmv1 and Scmv2 into simple PCR-based markers}}, year = {2002}, pages = {1190-1195}, journal = {Theor Appl Genet}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12582898}, volume = {105}, } @Article{IPB-1136, author = {Abel, S. and Köck, M.}, title = {{Secretory ribonucleases from tomato (Lycopersicon esculentum cv. Mill.)}}, year = {2001}, pages = {351 - 368}, journal = {Meth Enzymol}, volume = {341}, } @Article{IPB-343, author = {Feussner, I. and Kühn, H. and Wasternack, C.}, title = {{The lipoxygenase dependent degradation of storage lipids}}, year = {2001}, pages = {268-273}, journal = {Trends Plant Sci.}, volume = {6}, } @Article{IPB-1147, author = {Li, G. and Goyal, G.S. and Abel, S. and Quiros, C.F.}, title = {{Inheritance of three major genes involved in the synthesis of aliphatic glucosinolates in Brassica oleracea}}, year = {2001}, pages = {427 - 431}, journal = {J Amer Soc Hort Sci}, volume = {126}, } @Article{IPB-344, author = {Hilpert, B. and Bohlmann, H. and Den Camp, R.O. and Przybyla, D. and Miersch, O. and Buchala, A. and Apel, K.}, title = {{Isolation and characterization of signal transduction mutants of Arabidopsis thaliana that constitutively activate the octadecanoid pathway and form necrotic microlesions}}, year = {2001}, pages = {435-446}, journal = {Plant J.}, volume = {26}, } @Article{IPB-345, author = {Weichert, H. and Kohlmann, M. and Wasternack, C. and Feussner, I.}, title = {{Lipids and signalling: oxylipins 3 - functional aspects}}, year = {2001}, pages = {861-862}, journal = {Biochem. Soc. Trans.}, volume = {28}, } @Article{IPB-346, author = {Weichert, H. and Kolbe, A. and Wasternack, C. and Feussner, I.}, title = {{Formation of 4-hydroxy-1-alkenals in barley leaves}}, year = {2001}, pages = {850-851}, journal = {Biochem. Soc. Trans.}, volume = {28}, } @Article{IPB-342, author = {Berger, S. and Weichert, H. and Porzel, A. and Wasternack, C. and Kühn, H. and Feussner, I.}, title = {{Enzymatic and non-enzymatic lipid peroxidation in leaf development}}, year = {2001}, pages = {266-276}, journal = {Biochim. Biophys. Acta}, volume = {1533}, } @Article{IPB-1135, author = {Ticconi, C.A. and Delatorre, C.A. and Abel, S.}, title = {{Attenuation of phosphate starvation responses by phosphate in Arabidopsis thaliana}}, year = {2001}, pages = {963 - 972}, journal = {Plant Physiol}, volume = {127}, } @Article{IPB-339, author = {Miersch, O. and Wasternack, C.}, title = {{Octadecanoid and jasmonate signaling in tomato leaves (Lycopersicon esculentum Mill.): Endogenous jasmonates do not induce jasmonate biosynthesis}}, year = {2000}, pages = {715-722}, journal = {Biol. Chem.}, volume = {381}, abstract = {Jasmonates and their precursors, the octadecanoids, are signals in stress-induced alteration of gene expression. Several mRNAs coding for enzymes of jasmonic acid (JA) biosynthesis are up-regulated upon JA treatment or endogenous rise of JA level. Here we inspected the positive feed back of endogenous JA on JA formation as well as its beta-oxidation steps. JA responsive gene expression was recorded in terms of proteinase inhibitor2 (pin2) mRNA accumulation. JA formed upon treatment of tomato (Lycopersicon esculentum cv. Moneymaker) leaves with JA derivatives carrying different length of the carboxylic acid side chain was quantified by gas chromatography-mass spectrometry (GC-MS). The data reveal that beta-oxidation of the side chain occurs up to a butyric acid moiety. The amount of JA formed from side-chain modified JA derivatives, correlated with pin2-mRNA accumulation. JA derivatives with a carboxylic side chain of 3, 5 or 7 carbon atoms were unable to form JA and to express on pin2, whereas even numbered derivatives were active. After treatment of tomato leaves with (10-2H)-(-)-12-oxophytoenoic acid, (4-2H)-(-)-JA and its methyl ester were formed and could be quantified separately from the endogenously unlabeled JA pool by GC-MS analysis via isotopic discrimination. The level of 8 nmol per g f.w. JA and its methyl ester originated exclusively from labeled 12-oxophytoenic acid. This and further data indicate that endogenous synthesis of the JA precursor 12-oxophytodienoic acid as well as of JA and its methyl ester are not induced in tomato leaves, suggesting that positive feedback in JA biosynthesis does not function in vivo.} } @Article{IPB-337, author = {Kramell, R. and Miersch, O. and Atzorn, R. and Parthier, B. and Wasternack, C.}, title = {{Octadecanoid-derived alteration of gene expression and the 'oxylipin signature' in stressed barley leaves - implications for different signalling pathways}}, year = {2000}, pages = {177-186}, journal = {Plant Physiol.}, volume = {123}, abstract = {Stress-induced gene expression in barley (Hordeum vulgare cv. Salome) leaves has been correlated with temporally changing levels of octadecanoids and jasmonates, quantified by means of gas chromatography/mass spectrometry-single ion monitoring. Application of sorbitol-induced stress led to a low and transient rise of jasmonic acid (JA), its precursor 12-oxophytodienoic acid (OPDA) and the methyl esters JAME and OPDAME, respectively, followed by a large increase in their levels. JA and JAME peaked between 12 and 16 h, about 4 hours before OPDA and OPDAME. However, OPDA accumulated up to a 2.5-fold higher level than the other compounds. Dihomo-jasmonic acid and 9,13-didehydro-12- oxophytoenoic acid were identified as minor components. Kinetic analyses revealed that a transient threshold of jasmonates or octadecanoids is necessary and sufficient to initiate JA responsive gene expression. Although OPDA and OPDAME applied exogenously were metabolized to JA in considerable amounts, both of them can induce gene expression per se as evidenced by those genes which do not respond to endogenously formed JA. Also, coronatine induces JA-responsive genes independently from endogenous JA. As evidenced by application of deuterated JA, endogenous synthesis of JA is not induced by JA treatment. The data are discussed in terms of distinct signalling pathways.} } @Article{IPB-1138, author = {Abel, S. and Nürnberger, T. and Ahnert, V. and Krauss, G.J. and Glund, K.}, title = {{Induction of an extracellular cyclic nucleotide phosphodiesterase as an accessory ribonucleolytic activity during phosphate starvation of cultured tomato cells}}, year = {2000}, pages = {543 - 532}, journal = {Plant Physiology}, volume = {122}, } @Article{IPB-340, author = {Wasternack, C. and Hause, B.}, title = {{Jasmonate - Signale zur Stressabwehr und Entwicklung in Pflanzen}}, year = {2000}, pages = {312-319}, journal = {Biologie in unserer Zeit}, volume = {30}, } @Article{IPB-1137, author = {Chen, D.L. and Delatorre,.C.A. and Bakker, A. and Abel, S.}, title = {{Conditional identification of phosphate starvation-response mutants in Arabidopsis thaliana}}, year = {2000}, pages = {13 - 22}, journal = {Planta}, volume = {211}, } @Article{IPB-862, author = {Quint, M. and Melchinger, A.E. and Dussle, C.M. and Lübberstedt, T.}, title = {{Breeding for virus resistance in maize}}, year = {2000}, pages = {283-291}, journal = {Genetika}, volume = {32}, } @Article{IPB-1295, author = {Colon-Carmona, A. and Chen, D.L. and Yeh, K.C. and Abel, S.}, title = {{Aux/IAA proteins are phosphorylated by phytochrome in vitro}}, year = {2000}, pages = {1728-1738}, journal = {Plant Physiology}, url = {http://www.plantphysiol.org/content/124/4/1728.abstract?sid=0f984af4-c856-4351-babb-929b34461f87}, volume = {124}, abstract = { Auxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived transcription factors that are induced as a primary response to the plant growth hormone IAA or auxin. Gain-of-function mutations in Arabidopsis genes,SHY2/IAA3, AXR3/IAA17, andAXR2/IAA7 cause pleiotropic phenotypes consistent with enhanced auxin responses, possibly by increasing Aux/IAA protein stability. Semidominant mutations shy2-1D,shy2-2, axr3-1, and axr2-1induce ectopic light responses in dark-grown seedlings. Because genetic studies suggest that the shy2-1D andshy2-2 mutations bypass phytochrome requirement for certain aspects of photomorphogenesis, we tested whether SHY2/IAA3 and related Aux/IAA proteins interact directly with phytochrome and whether they are substrates for its protein kinase activity. Here we show that recombinant Aux/IAA proteins from Arabidopsis and pea (Pisum sativum) interact in vitro with recombinant phytochrome A from oat (Avena sativa). We further show that recombinant SHY2/IAA3, AXR3/IAA17, IAA1, IAA9, and Ps-IAA4 are phosphorylated by recombinant oat phytochrome A in vitro. Deletion analysis of Ps-IAA4 indicates that phytochrome A phosphorylation occurs on the N-terminal half of the protein. Metabolic labeling and immunoprecipitation studies with affinity-purified antibodies to IAA3 demonstrate increased in vivo steady-state levels of mutant IAA3 in shy2-2 plants and phosphorylation of the SHY2-2 protein in vivo. Phytochrome-dependent phosphorylation of Aux/IAA proteins is proposed to provide one molecular mechanism for integrating auxin and light signaling in plant development.} } @Article{IPB-97, author = {Ziegler, J. and Stenzel, I. and Hause, B. and Maucher, H. and Miersch, O. and Hamberg, M. and Grimm, M. and Ganal, M. and Wasternack, C.}, title = {{Molecular cloning of allene oxide cyclase: The enzyme establishing the stereochemistry of octadecanoids and jasmonates}}, year = {2000}, pages = {19132-19138}, journal = {J. Biol. Chem.}, doi = {10.1074/jbc.M002133200}, url = {http://www.jbc.org/content/275/25/19132.abstract?sid=04f09be3-5f6e-4d78-aa97-a7b681940e00}, volume = {275}, abstract = { Allene oxide cyclase (AOC) catalyses the stereospecific cyclisation of an unstable allene oxide to 9(S),13(S)-12-oxo-10,15(Z)-phytodienoic acid, the ultimate precursor of jasmonic acid. This enzyme has previously been purified, and two identical N-terminal peptides were found suggesting AOC to be a homodimeric protein. Furthermore, the native protein was N-terminal processed. Using degenerate primers, a PCR fragment could be generated from tomato, which was further used to isolate a full length cDNA clone of 1kb coding for a protein with 245 amino acids with a molecular mass of 26 kDa. Whereas expression of the whole coding region failed to detect AOC activity, a 5-'truncated protein showed high activity, suggesting that additional amino acids impair the enzymatic function. Steric analysis of the 12-oxo-phytodienoic acid formed by the recombinant AOC revealed exclusive (\>99%) formation of the 9(S),13(S) enantiomer. Exclusive formation of this enantiomer was also found in wounded tomato leaves. Southern analysis and genetic mapping revealed the existence of a single gene for AOC located on chromosome 2 of tomato. Inspection of the N-terminus revealed the presence of a chloroplastic transit peptide, and the location of AOC protein in that compartment could be shown by immunohistochemical methods. Concomitant with the jasmonate levels, the accumulation of AOC mRNA was transiently induced after wounding of tomato leaves.} } @Article{IPB-1148, author = {Gross, H.B. and Dalebout, T. and Grubb, C.D. and Abel, S.}, title = {{Functional detection of chemopreventive glucosinolates in Arabidopsis thaliana}}, year = {2000}, pages = {265 - 272}, journal = {Plant Science}, volume = {159}, } @Article{IPB-331, author = {Miersch, O. and Kramell, R. and Parthier, B. and Wasternack, C.}, title = {{Structure-activity relations of substituted, deleted or stereospecifically altered jasmonic acid in gene expression of barley leaves}}, year = {1999}, pages = {353-361}, journal = {Phytochemistry}, volume = {50}, } @Article{IPB-422, author = {Miersch, O. and Bohlmann, H. and Wasternack, C.}, title = {{Jasmonates and related compounds form Fusarium oxysporum}}, year = {1999}, pages = {517-523}, journal = {Phytochemistry}, volume = {50}, } @Article{IPB-421, author = {Kramell, R. and Miersch, O. and Schneider, G. and Wasternack, C.}, title = {{Liquid chromatography of jasmonic acid amine conjugates}}, year = {1999}, pages = {42-46}, journal = {Chromatographia}, volume = {49}, } @Article{IPB-419, author = {Herde, O. and Peña-Cortés, H. and Wasternack, C. and Willmitzer, L. and Fisahn, J.}, title = {{Electric signaling and PIN2 gene expression on different abiotic stimuli depend on a distinct threshold level of endogenous ABA in several ABA-deficient tomato mutants}}, year = {1999}, pages = {213-218}, journal = {Plant Physiol.}, volume = {119}, } @Article{IPB-1296, author = {Morgan, K.E. and Zarembinski, T.I. and Theologis, A. and Abel, S.}, title = {{Biochemical characterization of recombinant polypeptides corresponding to the predicted ßαα-fold in Aux/IAA proteins}}, year = {1999}, pages = {283-287}, journal = {FEBS Letters}, url = {http://www.febsletters.org/article/S0014-5793%2899%2900819-4/abstract}, volume = {454}, abstract = { The plant hormone indoleacetic acid (IAA or auxin) transcriptionally activates a select set of early genes. The Auxl IAA class of early auxin-responsive genes encodes a large family of short-lived, nuclear proteins. Aux/IAA polypeptides homo-and heterodimerize, and interact with auxin-response transcription factors (ARFs) via C-terminal regions conserved in both protein families. This shared region contains a predicted βαα motif similar to the prokaryotic β-Ribbon DNA binding domain, which mediates both protein dimerization and DNA recognition. Here, we show by circular dichroism spectroscopy and by chemical cross-linking experiments that recombinant peptides corresponding to the predicted βαα region of three Aux/IAA proteins from Arabidopsis thaliana contain substantial α-helical secondary structure and undergo homo- and heterotypic interactions in vitro. Our results indicate a similar biochemical function of the plant βαα domain and suggest that the βαα fold plays an important role in mediating combinatorial interactions of Aux/IAA and ARF proteins to specifically regulate secondary gene expression in response to auxin.} } @Article{IPB-420, author = {Kenton, P. and Mur, L.A.J. and Atzorn, R. and Wasternack, C. and Draper, J.}, title = {{(—)-Jasmonic Acid Accumulation in Tobacco Hypersensitive Response Lesions}}, year = {1999}, pages = {74-78}, journal = {Mol. Plant Microbiol. Interactions}, doi = {10.1094/MPMI.1999.12.1.74}, url = {http://apsjournals.apsnet.org/loi/mpmi?open=1999}, volume = {12}, abstract = {Tobacco infected with Pseudomonas syringae pv. phaseolicola undergoes a hypersensitive response (HR). Jasmonic acid (JA) accumulated within the developing lesion 3 to 9 h after infection and this accumulation preceded protein loss, cell death, and malondialdehyde accumulation. Accumulating JA consisted largely of the (—)-JA stereoisomer and was essentially restricted to the HR lesion} } @Article{IPB-1555, author = {Gago, S. and Costa, N. and Semorile, L. and Grau, O.}, title = {{Sequence variability in p27 gene of Citrus tristeza virus (CTV) revealed by SSCP analysis}}, year = {1999}, pages = {41-50}, journal = {Electronic Journal of Biotechnology}, volume = {2}, } @Article{IPB-404, author = {Bohlmann, H. and Vignutelli, A. and Hilpert, B. and Miersch, O. and Wasternack, C. and Apel, K.}, title = {{Wounding and chemicals induce expression of the Arabidopsis gene Thi2.1, encoding a fungal defense thionin, via the octadecanoid pathway}}, year = {1998}, pages = {281-286}, journal = {FEBS Letters}, volume = {437}, } @INBOOK{IPB-414, author = {Feussner, I. and Blée, E. and Weichert, H. and Rousset, C. and Wasternack, C.}, title = {{Advances in Plant Lipid Research}}, year = {1998}, pages = {311-313}, chapter = {{Fatty acid catabolism at the lipid body membrane of germinating cucumber cotyledons}}, journal = {Secretariado de Publicaciones de la Universidad de Sevilla}, editor = {Sánchez, J., Cerdá-Olmedo, E., Martínez-Force, E.}, } @INBOOK{IPB-416, author = {Kohlmann, M. and Kuntzsch, A. and Wasternack, C. and Feussner, I.}, title = {{Natural Product Analysis}}, year = {1998}, pages = {339-340}, chapter = {{Effect of jasmonic acid methyl ester on enzymes of the lipoxygenase pathway in barley leaves}}, journal = {P. Vieweg, Wiesbaden}, editor = {Schreier, P., Herderich, M., Humpf, H.-U., Schwab, W.}, } @INBOOK{IPB-417, author = {Kramell, R. and Porzel, A. and Miersch, O. and Schneider, G.}, title = {{Natural Product Analysis}}, year = {1998}, pages = {77}, chapter = {{Characterization of isoleucine conjugates of cucurbic acid isomers by reversed-phase and chiral high-performance liquid chromatography}}, journal = {P. Vieweg, Wiesbaden}, editor = {Schreier, P., Herderich, M., Humpf, H.-U., Schwab, W.}, } @INBOOK{IPB-413, author = {Balkenhohl, T. and Kühn, H. and Wasternack, C. and Feussner, I.}, title = {{Advances in Plant Lipid Research}}, year = {1998}, pages = {320-322}, chapter = {{A lipase specific for esterified oxygenated polyenoic fatty acids in lipid bodies of cucumber cotyledons}}, journal = {Secretariado de Publicaciones de la Universidad de Sevilla}, editor = {Sánchez, J., Cerdá-Olmedo, E., Martínez-Force, E.}, } @INBOOK{IPB-415, author = {Feussner, I. and Balkenhohl, T. and Porzel, A. and Kühn, H. and Wasternack, C.}, title = {{Natural Product Analysis}}, year = {1998}, pages = {57-58}, chapter = {{Structural elucidation of oxygenated triacylglycerols in cucumber and sunflower cotyledons}}, journal = {P. Vieweg, Wiesbaden}, editor = {Schreier, P., Herderich, M., Humpf, H.-U., Schwab, W.}, } @INBOOK{IPB-412, author = {Bachmann, A. and Kohlmann, M. and Wasternack, C. and Feussner, I.}, title = {{Advances in Plant Lipid Research}}, year = {1998}, pages = {288-290}, chapter = {{Oxylipins in sorbitol-stressed barley leaf segments}}, journal = {Secretariado de Publicaciones de la Universidad de Sevilla}, editor = {Sánchez, J., Cerdá-Olmedo, E., Martínez-Force, E.}, } @Article{IPB-409, author = {Vignutelli, A. and Wasternack, C. and Apel, K. and Bohlmann, H.}, title = {{Systemic and local induction of an Arabidopsis thionin gene by wounding and pathogens}}, year = {1998}, pages = {285-295}, journal = {The Plant J.}, volume = {14}, } @Article{IPB-406, author = {Feussner, I. and Wasternack, C.}, title = {{Lipoxygenase catalyzed oxygenation of lipids}}, year = {1998}, pages = {146-152}, journal = {Fett/Lipid}, volume = {100}, } @Article{IPB-332, author = {Vörös, K. and Feussner, I. and Kühn, H. and Lee, J. and Graner, A. and Löbler, M. and Parthier, B. and Wasternack, C.}, title = {{Characterization of methyljasmonate-inducible lipoxygenase from barley (Hordeum vulgare cv. Salome) leaves}}, year = {1998}, pages = {36-44}, journal = {Eur. J. Biochem.}, volume = {251}, } @Article{IPB-471, author = {Binarová, P. and Hause, B. and Dolezel, J. and Dráber, P.}, title = {{Association of g-tubulin with kinetochore/centromeric region of plant chromosomes}}, year = {1998}, pages = {751-757}, journal = {Plant J.}, doi = {10.1046/j.1365-313x.1998.00166.x}, url = {http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-313X}, volume = {14}, abstract = { Monoclonal antibodies raised against a phylogenetically conserved peptide from the C-terminal domain of g-tubulin molecule were used for immunofluorescence detection of g-tubulin in acentriolar mitotic spindles of plant cells. The antibodies stained kinetochore fibres along their whole length, including the close vicinity of kinetochores. After microtubule disassembly by the anti-microtubular drugs aminoprophos-methyl (APM), oryzalin, and colchicine, g -tubulin was found on remnants of kinetochore fibres attached to chromosomes. In cells recovering from the amiprophosmethyl treatment, g-tubulin was localized with the re-growing kinetochore microtubule fibres nucleated or captured by kinetochore/centromeric regions. On isolated chromosomes, g-tubulin co-localized with g-tubulin in the kinetochore/centromeric region. The presented data suggest that in acentriolar higher plant cells g -tubulin might be directly or indirectly involved in modulation and/or stabilization of kinetochore-microtubule interactions.} } @Article{IPB-407, author = {Miersch, O. and Knöfel, H.-D. and Schmidt, J. and Kramell, R. and Parthier, B.}, title = {{A jasmonic acid conjugate, N-[()-jasmonoyl]-tyramine, from Petunia pollen}}, year = {1998}, pages = {327-329}, journal = {Phytochemistry}, volume = {47}, } @INBOOK{IPB-389, author = {Feussner, I. and Kühn, H. and Wasternack, C.}, title = {{Physiology, Biochemistry and Molecular Biology of Plant Lipids}}, year = {1997}, pages = {250-252}, chapter = {{Do Lipoxygenases initiate ß-oxidation?}}, journal = {Kluwer Academic Publishers, Dordrecht}, editor = {Williams, J.P., Mobashsher, U., Khan, M.U. \& Lem, N.W.}, } @Article{IPB-400, author = {Ziegler, J. and Hamberg, M. and Miersch, O. and Parthier, B.}, title = {{Purification and characterization of allene oxide cyclase from dry corn seeds}}, year = {1997}, pages = {565-573}, journal = {Plant Physiol.}, volume = {114}, } @Article{IPB-396, author = {Hertel, S. and Knöfel, H.-D. and Kramell, R. and Miersch, O.}, title = {{Partial purification and characterization of a jasmonic acid conjugate cleaving amidohydrolase from the fungus Botryodiplodia theobromae}}, year = {1997}, pages = {105-110}, journal = {FEBS Letters}, volume = {407}, } @Article{IPB-393, author = {Görschen, E. and Dunaeva, M. and Reeh, I. and Wasternack, C.}, title = {{Overexpression of the jasmonate inducible 23 kDa protein (JIP 23) from barley in transgenic tobacco leads to the repression of leaf proteins}}, year = {1997}, pages = {58-62}, journal = {FEBS Letters}, volume = {419}, } @Article{IPB-390, author = {Feussner, I. and Kühn, H. and Wasternack, C.}, title = {{Hypothesis. Do specific linoleate 13-lipoxygenases initiate b-oxidation?}}, year = {1997}, pages = {1-5}, journal = {FEBS Letters}, volume = {406}, } @Article{IPB-391, author = {Feussner, K. and Feussner, I. and Leopold, I. and Wasternack, C.}, title = {{Isolation of a cDNA coding for an ubiquitin-conjugating enzyme UBCI of tomato - the first stress-induced UBC of higher plants}}, year = {1997}, pages = {211-215}, journal = {FEBS Letters}, volume = {409}, } @Article{IPB-334, author = {Wasternack, C. and Parthier, B.}, title = {{Jasmonate-signalled gene expression}}, year = {1997}, pages = {302-307}, journal = {Trends in Plant Sci.}, volume = {2}, } @Article{IPB-399, author = {Ward, J. and Gaskin, P. and Sessions, R. and Koda, Y. and Wasternack, C. and Beale, M.}, title = {{Molecular modelling, synthesis and biological activity of methyl 3-methyljasmonate and related derivatives}}, year = {1997}, pages = {8181-8194}, journal = {Tetrahedron}, volume = {53}, } @Article{IPB-397, author = {Kramell, R. and Schneider, G. and Miersch, O.}, title = {{Chiral separation of amide conjugates of jasmonic acid by liquid chromatography}}, year = {1997}, pages = {104-108}, journal = {Chromatographia}, volume = {45}, } @Article{IPB-395, author = {Hause, B. and Kogel, K.-H. and Parthier, B. and Wasternack, C.}, title = {{In barley leaf cells, jasmonates do not act as a signal during compatible or incompatible interactions with the powdery mildew fungus (\textit{Erysiphe graminis} f. sp. \textit{hordei})}}, year = {1997}, pages = {127-132}, journal = {J. Plant Physiol.}, doi = {10.1016/S0176-1617(97)80191-5}, volume = {150}, abstract = {We have studied a possible function of jasmonates as mediators in the host-pathogen interaction of barley (Hordeum vulgare L.) with the powdery mildew fungus Egh (Erysiphe graminis f. sp. hordei). Previous findings from whole-leaf extracts demonstrated that (i) extracts from infected barley leaves did not contain enhanced levels of jasmonates, (ii) transcripts of jasmonate-inducible genes were not expressed upon infection, and (iii) exogenous application of jasmonates did not induce resistance to Egh (Kogel et al., 1995). Nevertheless, the question arises whether or not jasmonates are involved in the interaction of barley with the powdery mildew fungus at the local site of infection. Using an immunocytological approach the analysis of leaf cross-sections from a susceptible barley cultivar and its near-isogenic mlo5-resistant line revealed no accumulation of JIP-23, the most abundant jasmonate inducible protein, neither in epidermal cells attacked by the pathogen nor in adjacent mesophyll cells. As a positive control, cross-sections from methyl jasmonate-treated leaf segments showed a strong signal for JIP-23 accumulation. Because the presence of the jasmonate-inducible protein is highly indicative for an already low threshold level of endogenous jasmonate (Lehmann et al., 1995), the lack of JIP-23 accumulation at the sites of attempted fungal infection clearly demonstrates the absence of enhanced levels of jasmonates. This excludes even a local rise of jasmonate confined to those single cells penetrated (Mlo genotype) or attacked (mlo5 genotype) by the fungus.} } @Article{IPB-487, author = {Görschen, E. and Dunaeva, M. and Hause, B. and Reeh, I. and Wasternack, C. and Parthier, B.}, title = {{Expression of the ribosome-inactivating protein JIP60 from barley in transgenic tobacco leads to an abnormal phenotype and alterations on the level of translation}}, year = {1997}, pages = {470-478}, journal = {Planta}, volume = {202}, } @Article{IPB-388, author = {Feussner, I. and Fritz, I.G. and Hause, B. and Ullrich, W.R. and Wasternack, C.}, title = {{Induction of a new lipoxygenase form in cucumber leaves by salicylic acid or 2,6-dichloroisonicotinic acid}}, year = {1997}, pages = {101-108}, journal = {Bot. Acta}, doi = {10.1111/j.1438-8677.1997.tb00616.x}, url = {http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1438-8677/issues}, volume = {110}, abstract = {Changes in lipoxygenase (LOX) protein pattern and/or activity were investigated in relation to acquired resistance of cucumber (Cucumis sativus L.) leaves against two powdery mildews, Sphaerotheca fuliginea (Schlecht) Salmon and Erysiphe cichoracearum DC et Merat. Acquired resistance was established by spraying leaves with salicylic acid (SA) or 2,6-dichloroisonicotinic acid (INA) and estimated in whole plants by infested leaf area compared to control plants. SA was more effective than INA. According to Western blots, untreated cucumber leaves contained a 97 kDa LOX form, which remained unchanged for up to 48 h after pathogen inoculation. Upon treatment with SA alone for 24 h or with INA plus pathogen, an additional 95 kDa LOX form appeared which had an isoelectric point in the alkaline range. For the induction of this form, a threshold concentration of 1 mM SA was required, higher SA concentrations did not change LOX-95 expression which remained similar between 24 h and 96 h but further increased upon mildew inoculation. Phloem exudates contained only the LOX-97 form, in intercellular washing fluid no LOX was detected. dichloroisonicotinic localization revealed LOX protein in the cytosol of the mesophyll cells without differences between the forms.} } @Article{IPB-333, author = {Feussner, I. and Balkenhohl, T.J. and Porzel, A. and Kühn, H. and Wasternack, C.}, title = {{Structural elucidation of oxygenated storage lipids in cucumber cotyledons. Implication of lipid body lipoxygenase in lipid mobilization during germination}}, year = {1997}, pages = {21635-21641}, journal = {J. Biol. Chem.}, volume = {272}, } @Article{IPB-118, author = {Feussner, I. and Porzel, A. and Wasternack, C. and Kühn, H.}, title = {{Quantitative Analyse von Lipoxygenase-Metaboliten in Lipiden durch NMR-Spektroskopie}}, year = {1997}, pages = {54-58}, journal = {Biospektrum}, volume = {3}, } @Article{IPB-522, author = {Ziegler, J. and Vogt, T. and Miersch, O. and Strack, D.}, title = {{Concentration of dilute protein solutions prior to sodium dodecylsulfate polyacrylamide gel electrophoresis}}, year = {1997}, pages = {257-260}, journal = {Anal. Biochem}, doi = {10.1006/abio.1997.2248}, url = { http://www.sciencedirect.com/science/article/pii/S000326979792248X}, volume = {250}, } @INBOOK{IPB-401, author = {Ziegler, J. and Hamberg, M. and Miersch, O.}, title = {{Physiology, Biochemistry and Molecular Biology of Plant Lipids}}, year = {1997}, pages = {99-101}, chapter = {{Allene oxide cyclase from corn: Partial purification and characterization}}, journal = {Kluwer Academic Publishers, Dordrecht}, editor = {Williams, J.P., Mobashsher, U., Khan, M.U., Lem, N.W.}, } @Article{IPB-385, author = {Peña-Cortés, H. and Prat, S. and Atzorn, R. and Wasternack, C. and Willmitzer, L.}, title = {{Pin2 gene expression in potato and tomato detached leaves from ABA-deficient potato and tomato plants upon systemin treatment}}, year = {1996}, pages = {447-451}, journal = {Planta}, volume = {198}, } @Article{IPB-379, author = {Abdala, G. and Castro, G. and Guinazu, M. and Tizio, R. and Miersch, O.}, title = {{Occurrence of jasmonic acid in organs of Solanum tuberosum L. c.v. Spunta and its effect on tuberization}}, year = {1996}, pages = {139-143}, journal = {Plant Growth Reg.}, volume = {19}, } @Article{IPB-383, author = {Herde, O. and Atzorn, R. and Fisahn, J. and Wasternack, C. and Willmitzer, L. and Peña-Cortés, H.}, title = {{Localized wounding by heat initiates the accumulation of proteinase inhibitor II in abscisic acid-deficient plants by triggering jasmonic acid biosynthesis}}, year = {1996}, pages = {853-860}, journal = {Plant Physiol.}, volume = {112}, } @Article{IPB-335, author = {O'Donnell, P.J. and Calvert, C. and Atzorn, R. and Wasternack, C. and Leyser, H.M.O. and Bowles, D.J.}, title = {{Ethylene as a signal mediating the wound response of tomato plants}}, year = {1996}, pages = {1914-1917}, journal = {Science}, volume = {274}, } @Article{IPB-1299, author = {Wong, L.M. and Abel, S. and Shen, N. and de la Foata, M. and Mal, Y. and Theologis, A.}, title = {{Differential activation of the primary auxin response genes, PS-IAA4/5 and PS-IAA6, during early plant development.}}, year = {1996}, pages = {587-599}, journal = {Plant Journal}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313X.1996.9050587.x/abstract}, volume = {9}, abstract = { The plant growth hormone auxin typified by indoleacetic acid (IAA) transcriptionally activates early genes in pea, PS-IAA4/5 and PS-IAA6, that are members of a multigene family encoding short-lived nuclear proteins. To gain first insight into the biological role of PS-IAA4/5 and PSIAA6, promoter-β-glucuronidase (GUS) gene fusions were constructed and their expression during early development of transgenic tobacco seedlings was examined. The comparative analysis reveals spatial and temporal expression patterns of both genes that correlate with cells, tissues, and developmental processes known to be affected by auxin. GUS activity in seedlings of both transgenic lines is located in the root meristem, sites of lateral root initiation and in hypocotyls undergoing rapid elongation. In addition, mutually exclusive cell-specific expression is evident. For instance, PS-IAA4/5GUS but not PS-IAA6GUS is expressed in root vascular tissue and in guard cells, whereas only PS-IAA6GUS activity is detectable in glandular trichomes and redistributes to the elongating side of the hypocotyl upon gravitropic stimulation. Expression of PS-IAA4/5 and PS-IAA6 in elongating, dividing, and differentiating cell types indicates multiple functions during development. The common and yet distinct activity patterns of both genes suggest a combinatorial code of spatio-temporal co-expression of the various PS-IAA4/ 5-like gene family members in plant development that may mediate cell-specific responses to auxin.} } @Article{IPB-1298, author = {Abel, S. and Ballas, N. and Wong, L-M. and Theologis, A.}, title = {{DNA elements responsive to auxin}}, year = {1996}, pages = {647-654}, journal = {Bio Essays}, url = {http://onlinelibrary.wiley.com/doi/10.1002/bies.950180808/abstract}, volume = {18(8)}, abstract = { Genes induced by the plant hormone auxin are probably involved in the execution of vital cellular functions and developmental processes. Experimental approaches designed to elucidate the molecular mechanisms of auxin action have focused on auxin perception, genetic dissection of the signaling apparatus and specific gene activation. Auxin-responsive promoter elements of early genes provide molecular tools for probing auxin signaling in reverse. Functional analysis of several auxin-specific promoters of unrelated early genes suggests combinatorial utilization of both conserved and variable elements. These elements are arranged into autonomous domains and the combination of such modules generates uniquely composed promoters. Modular promoters allow for auxin-mediated transcriptional responses to be revealed in a tissue- and development-specific manner.} } @Article{IPB-1297, author = {Abel, S. and Theologis, A.}, title = {{Early genes and auxin action}}, year = {1996}, pages = {9-17}, journal = {Plant Physiology}, url = {http://www.plantphysiol.org/content/111/1/9.full.pdf+html}, volume = {111}, } @Article{IPB-380, author = {Feussner, K. and Guranowski, A. and Kostka, S. and Wasternack, C.}, title = {{Diadenosine 5'5'''-P1,P4-tetraphosphate (Ap4A) hydrolase from tomato (Lycopersicon esculentum cv. Lukullus) - Purification, Biochemical properties and behaviour during stress}}, year = {1996}, pages = {477-486}, journal = {Z. Naturforsch.}, volume = {51c}, } @Article{IPB-381, author = {Feussner, I. and Hause, B. and Nellen, A. and Wasternack, C. and Kindl, H.}, title = {{Lipid-body lipoxygenase is expressed in cotyledons during germination prior to other lipoxygenase forms}}, year = {1996}, pages = {288-293}, journal = {Planta}, doi = {10.1007/BF00206255}, url = {http://link.springer.com/journal/425}, volume = {198}, abstract = {Lipid bodies are degraded during germination. Whereas some proteins, e.g. oleosins, are synthesized during the formation of lipid bodies of maturating seeds, a new set of proteins, including a specific form of lipoxygenase (LOX; EC, is detectable in lipid bodies during the stage of fat degradation in seed germination. In cotyledons of cucumber (Cucumis sativus L.) seedlings at day 4 of germination, the most conspicuous staining with anti-LOX antibodies was observed in the cytosol. At very early stages of germination, however, the LOX form present in large amounts and synthesized preferentially was the lipid-body LOX. This was demonstrated by immunocytochemical staining of cotyledons from 1-h and 24-h-old seedlings: the immunodecoration of sections of 24-h-old seedlings with anti-LOX antiserum showed label exclusively correlated with lipid bodies of around 3 μm in diameter. In accordance, the profile of LOX protein isolated from lipid bodies during various stages of germination showed a maximum at day 1. By measuring biosynthesis of the protein in vivo we demonstrated that the highest rates of synthesis of lipid-body LOX occurred at day 1 of germination. The early and selective appearance of a LOX form associated with lipid bodies at this stage of development is discussed.} } @Article{IPB-386, author = {Wasternack, C. and Atzorn, R. and Pena-Cortes, H. and Parthier, B.}, title = {{Alteration of gene expression by jasmonate and ABA in tobacco and tomato}}, year = {1996}, pages = {503-510}, journal = {J. Plant Physiol.}, volume = {147}, } @Article{IPB-1301, author = {Abel, S. and Nguyen, M.D. and Theologis, A.}, title = {{The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana}}, year = {1995}, pages = {19093-19099}, journal = {Journal of Biological Chemistry}, url = {http://www.jbc.org/content/270/32/19093.abstract?sid=c17d6e17-db5e-4424-8236-1c3dccb9ded2}, volume = {270}, abstract = { 1-Aminocyclopropane-1-carboxylic acid (ACC) synthase is the key regulatory enzyme in the biosynthetic pathway of the plant hormone ethylene. The enzyme is encoded by a divergent multigene family in Arabidopsis thaliana, comprising at least five genes, ACS1-5 (Liang, X., Abel, S., Keller, J. A., Shen, N. F., and Theologis, A.(1992) Proc. Natl. Acad. Sci. U. S. A. 89, 11046-11050). In etiolated seedlings, ACS4 is specifically induced by indoleacetic acid (IAA). The response to IAA is rapid (within 25 min) and insensitive to protein synthesis inhibition, suggesting that the ACS4 gene expression is a primary response to IAA. The ACS4 mRNA accumulation displays a biphasic dose-response curve which is optimal at 10 μM of IAA. However, IAA concentrations as low as 100 nM are sufficient to enhance the basal level of ACS4 mRNA. The expression of ACS4 is defective in the Arabidopsis auxin-resistant mutant lines axr1-12, axr2-1, and aux1-7. ACS4 mRNA levels are severely reduced in axr1-12 and axr2-1 but are only 1.5-fold lower in aux1-7. IAA inducibility is abolished in axr2-1. The ACS4 gene was isolated and structurally characterized. The promoter contains four sequence motifs reminiscent of functionally defined auxin-responsive cis-elements in the early auxin-inducible genes PS-IAA4/5 from pea and GH3 from soybean. Conceptual translation of the coding region predicts a protein with a molecular mass of 53,795 Da and a theoretical isoelectric point of 8.2. The ACS4 polypeptide contains the 11 invariant amino acid residues conserved between aminotransferases and ACC synthases from various plant species. An ACS4 cDNA was generated by reverse transcriptase-polymerase chain reaction, and the authenticity was confirmed by expression of ACC synthase activity in Escherichia coli.} } @Article{IPB-375, author = {Kogel, K.-H. and Ortel, B. and Jarosch, B. and Atzorn, R. and Schiffer, R. and Wasternack, C.}, title = {{Resistance in barley against the powdery mildew fungus (Erysiphe graminis f. sp. hordei) is not associated with enhanced levels of endogenous jasmonates}}, year = {1995}, pages = {319-332}, journal = {Eur. J. Plant Pathol.}, volume = {101}, } @Article{IPB-378, author = {Wasternack, C. and Atzorn, R. and Leopold, J. and Feussner, I. and Rademacher, W. and Parthier, B.}, title = {{Synthesis of jasmonate-induced proteins in barley (Hordeum vulgare) is inhibited by the growth retardant tetcyclacis}}, year = {1995}, pages = {335-341}, journal = {Physiol. Plantarum}, volume = {94}, } @Article{IPB-376, author = {Kramell, R. and Atzorn, R. and Schneider, G. and Miersch, O. and Brückner, C. and Schmidt, J. and Sembdner, G. and Parthier, B.}, title = {{Occurrence and identification of jasmonic acid and its amino acid conjugates induced by osmotic stress in barley leaf tissue}}, year = {1995}, pages = {29-36}, journal = {J. Plant Growth Reg.}, volume = {14}, } @Article{IPB-374, author = {Harms, K. and Atzorn, R. and Brash, A. and Kühn, H. and Wasternack, C. and Willmitzer, L. and Peña-Cortés, H.}, title = {{Expression of a flax allene oxide synthase cDNA leads to an increase in the endogenous jasmonic acid level in transgenic potato plants but not to a corresponding activation of jasmonic acid-responding genes}}, year = {1995}, pages = {1645-1654}, journal = {The Plant Cell}, volume = {7}, } @Article{IPB-1300, author = {Abel, S. and Theologis, A.}, title = {{A polymorphic bipartite motif signals nuclear targeting of early auxin- inducible proteins related to PS-IAA4 from pea (Pisum sativum)}}, year = {1995}, pages = {87-96}, journal = {Plant Journal}, url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313X.1995.08010087.x/abstract}, volume = {8}, abstract = { The plant hormone, indoleacetic acid (IAA), transcriptionally activates two early genes in pea, PS-IAA4/5 and PS-IAA6, that encode short-lived nuclear proteins. The identification of the nuclear localization signals (NLS) in PS-IAA4 and PS-IAA6 using progressive deletion analysis and site-directed mutagenesis is reported. A C-terminal SV40-type NLS is sufficient to direct the β-glucuronidase reporter to the nucleus of transiently transformed tobacco protoplasts, but is dispensible for nuclear localization of both proteins. The dominant and essential NLS in PS-IAA4 and PS-IAA6 overlap with a bipartite basic motif which is polymorphic and conserved in related proteins from other plant species, having the consensus sequence (KKNEK)KR-X(2471)-(RSXRK)/(RK/RK). Both basic elements of this motif in PS-IAA4, (KR-X41-RSYRK), function interdependently as a bipartite NLS. However, in PS-IAA6 (KKNEKKR-X36-RKK) the upstream element of the corresponding motif contains additional basic residues which allow its autonomous function as an SV40-type monopartite NLS. The spacer-length polymorphism, X(2470), in respective bipartite NLS peptides of several PS-IAA4-like proteins from Arabidopsis thaliana does not affect nuclear targeting function. The structural and functional variation of the bipartite basic motif in PS-IAA4-like proteins supports the proposed integrated consensus of NLS.} } @Article{IPB-377, author = {Lehmann, J. and Atzorn, R. and Brückner, C. and Reinbothe, S. and Leopold, J. and Wasternack, C. and Parthier, B.}, title = {{Accumulation of jasmonate, abscisic acid, specific transcripts and proteins in osmotically stressed barley leaf segments}}, year = {1995}, pages = {156-162}, journal = {Planta}, volume = {197}, } @Article{IPB-1302, author = {Abel, S. and Theologis, A.}, title = {{Transient transformation of Arabidopsis leaf protoplasts: a versatile experimental system to study gene expression}}, year = {1994}, pages = {421-427}, journal = {Plant Journal}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.1994.00421.x/abstract}, volume = {5}, abstract = { An improved protocol is reported to isolate and transiently transform mesophyll protoplasts of Arabidopsis thaliana. Transfected leaf protoplasts support high levels of expression of the bacterial reporter gene coding for β-glucuronidase (GUS), under the control of the cauliflower mosaic virus (CaMV) 35S promoter. Transient expression of GUS activity was monitored spectrophotometrically and reached a maximum between 18 and 48 h after polyethylene glycol (PEG)-mediated DNA uptake. Histochemical staining for GUS activity revealed reproducible transformation frequencies between 40 and 60%, based on the number of protoplasts survived. To demonstrate the applicability of the transient expression system, the subcellular localization of GUS proteins tagged with different nuclear polypeptides was studied in transfected mesophyll protoplasts, revealing nuclear compartmentalization of the chimeric GUS enzymes. Furthermore, Arabidopsis mesophyll protoplasts support auxin-mediated induction of chloramphenicol acetyl-transferase (CAT) activity when transfected with a transcriptional fusion between the CAT reporter gene and the early auxin-inducible PS-IAA4/5 promoter. Hence, the method allows in vivo analysis of promoter activity and subcellular localization of fusion proteins in a homologous transformation system.} } @Article{IPB-1303, author = {Abel, S. and Oeller, P.W. and Theologis, A.}, title = {{Early auxin-induced genes encode short-lived nuclear proteins}}, year = {1994}, pages = {326-330}, journal = {PNAS USA}, url = {http://www.pnas.org/content/91/1/326.abstract?sid=0275c798-0364-443d-b538-9a6e50ab9d68}, volume = {91}, abstract = { The plant growth hormone indoleacetic acid (IAA) transcriptionally activates gene expression in plants. Some of the genes whose expression is induced by IAA encode a family of proteins in pea (PS-IAA4 and PS-IAA6) and Arabidopsis (IAA1 and IAA2) that contain putative nuclear localization signals that direct a beta-glucuronidase reporter protein into the nucleus. Pulse-chase and immunoprecipitation experiments have defined the t1/2 of the PS-IAA4 and PS-IAA6 proteins to be 8 and 6 min, respectively. Their most prominent feature is the presence of a beta alpha alpha motif similar to the beta-sheet DNA-binding domain found in prokaryotic repressors of the Arc family. Based on these data, we suggest that plant tissues express short-lived nuclear proteins as a primary response to IAA. We propose that these proteins act as activators or repressors of genes responsible for mediating the various auxin responses.} }