@Article{IPB-2540, author = {Trenner, J. and Poeschl, Y. and Grau, J. and Gogol-Döring, A. and Quint, M. and Delker, C. and}, 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}, 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-2538, author = {Drost, H.-G. and Gabel, A. and Domazet-Lošo, T. and Quint, M. and Grosse, I. and}, title = {{Capturing Evolutionary Signatures in Transcriptomes with myTAI}}, year = {2016}, journal = {bioRxiv}, doi = {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-1032, author = {Quint, M. and Delker, C. and Franklin, K. A. and Wigge, P. A. and Halliday, K. J. and van Zanten, M. and}, title = {{Molecular and genetic control of plant thermomorphogenesis}}, year = {2016}, pages = {15190}, journal = {Nat. Plants}, doi = {10.1038/nplants.2015.190}, 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.} } @Article{IPB-1021, author = {Otto, M. and Naumann, C. and Brandt, W. and Wasternack, C. and Hause, B. and}, title = {{Activity Regulation by Heteromerization of Arabidopsis Allene Oxide Cyclase Family Members}}, year = {2016}, pages = {3}, journal = {Plants}, doi = {10.3390/plants5010003}, volume = {5}, abstract = {Jasmonates (JAs) are lipid-derived signals in plant stress responses and development. A crucial step in JA biosynthesis is catalyzed by allene oxide cyclase (AOC). Four genes encoding functional AOCs (AOC1, AOC2, AOC3 and AOC4) have been characterized for Arabidopsis thaliana in terms of organ- and tissue-specific expression, mutant phenotypes, promoter activities and initial in vivo protein interaction studies suggesting functional redundancy and diversification, including first hints at enzyme activity control by protein-protein interaction. Here, these analyses were extended by detailed analysis of recombinant proteins produced in Escherichia coli. Treatment of purified AOC2 with SDS at different temperatures, chemical cross-linking experiments and protein structure analysis by molecular modelling approaches were performed. Several salt bridges between monomers and a hydrophobic core within the AOC2 trimer were identified and functionally proven by site-directed mutagenesis. The data obtained showed that AOC2 acts as a trimer. Finally, AOC activity was determined in heteromers formed by pairwise combinations of the four AOC isoforms. The highest activities were found for heteromers containing AOC4 \+ AOC1 and AOC4 \+ AOC2, respectively. All data are in line with an enzyme activity control of all four AOCs by heteromerization, thereby supporting a putative fine-tuning in JA formation by various regulatory principles.} } @Article{IPB-1011, author = {López-Carrasco, A. and Gago-Zachert, S. and Mileti, G. and Minoia, S. and Flores, R. and Delgado, S. and}, 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 Biol.}, doi = {10.1080/15476286.2015.1119365}, 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-1005, author = {Kowalski, A. M. and Gooding, M. and Ferrante, A. and Slafer, G. A. and Orford, S. and Gasperini, D. and Griffiths, S. and}, title = {{Agronomic assessment of the wheat semi-dwarfing gene Rht8 in contrasting nitrogen treatments and water regimes}}, year = {2016}, pages = {150-160}, journal = {Field Crops Res.}, doi = {10.1016/j.fcr.2016.02.026}, 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.} } @Article{IPB-998, author = {Hoehenwarter, W. and Mönchgesang, S. and Neumann, S. and Majovsky, P. and Abel, S. and Müller, J. and}, 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}, volume = {16}, abstract = {BackgroundPlant 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.ResultsWe took advantage of the opposite phosphate-conditional root phenotype of the phosphate deficiency response 2 mutant (hypersensitive) and low phosphate response 1 and 2 double mutant (insensitive) to investigate the phosphate dependent regulation of gene and protein expression in roots using genome-wide transcriptome and proteome analysis. We observed an overrepresentation of genes and proteins that are involved in the regulation of iron homeostasis, cell wall remodeling and reactive oxygen species formation, and we highlight a number of candidate genes with a potential function in root adaptation to limited phosphate availability. Our experiments reveal that FERRIC REDUCTASE DEFECTIVE 3 mediated, apoplastic iron redistribution, but not intracellular iron uptake and iron storage, triggers phosphate-dependent root growth modulation. We further highlight expressional changes of several cell wall-modifying enzymes and provide evidence for adjustment of the pectin network at sites of iron accumulation in the root.ConclusionOur study reveals new aspects of the elaborate interplay between phosphate starvation responses and changes in iron homeostasis. The results emphasize the importance of apoplastic iron redistribution to mediate phosphate-dependent root growth adjustment and suggest an important role for citrate in phosphate-dependent apoplastic iron transport. We further demonstrate that root growth modulation correlates with an altered expression of cell wall modifying enzymes and changes in the pectin network of the phosphate-deprived root tip, supporting the hypothesis that pectins are involved in iron binding and/or phosphate mobilization.} } @Article{IPB-991, author = {Gharsallah, C. and Fakhfakh, H. and Grubb, D. and Gorsane, F. and}, 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}, 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-989, author = {Gasperini, D. and Acosta, I. F. and Farmer, E. E. and}, title = {{Cotyledon Wounding of Arabidopsis Seedlings}}, year = {2016}, pages = {e1712}, journal = {Bio Protoc.}, doi = {10.21769/BioProtoc.1712}, volume = {6}, abstract = {Damage to plant organs through both biotic and abiotic injury is very common in nature. Arabidopsis thaliana 5-day-old (5-do) seedlings represent an excellent system in which to study plant responses to mechanical wounding, both at the site of the damage and in distal unharmed tissues. Seedlings of wild type, transgenic or mutant lines subjected to single or repetitive cotyledon wounding can be used to quantify morphological alterations (e.g., root length, Gasperini et al., 2015), analyze the dynamics of reporter genes in vivo (Larrieu et al., 2015; Gasperini et al., 2015), follow transcriptional changes by quantitative RT-PCR (Acosta et al., 2013; Gasperini et al., 2015) or examine additional aspects of the wound response with a plethora of downstream procedures. Here we illustrate how to rapidly and reliably wound cotyledons of young seedlings, and show the behavior of two promoters driving the expression of β-glucuronidase (GUS) in entire seedlings and in the primary root meristem, following single or repetitive cotyledon wounding respectively. We describe two procedures that can be easily adapted to specific experimental needs.} } @Article{IPB-988, author = {Gago-Zachert, S. and}, 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}, 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-984, 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. and}, 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.} } @Article{IPB-1063, author = {Ziegler, J. and Schmidt, S. and Chutia, R. and Müller, J. and Böttcher, C. and Strehmel, N. and Scheel, D. and Abel, S. and}, 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}, 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-1056, author = {Wasternack, C. and Hause, B. and}, title = {{OPDA-Ile – a new JA-Ile-independent signal?}}, year = {2016}, pages = {e1253646}, journal = {Plant Signal Behav.}, doi = {10.1080/15592324.2016.1253646}, volume = {11}, abstract = {Expression 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-1055, author = {Wasternack, C. and Strnad, M. and}, title = {{Jasmonate signaling in plant stress responses and development – active and inactive compounds}}, year = {2016}, pages = {604-613}, journal = {New Biotechnol.}, doi = {10.1016/j.nbt.2015.11.001}, volume = {33}, 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-1045, author = {Strehmel, N. and Mönchgesang, S. and Herklotz, S. and Krüger, S. and Ziegler, J. and Scheel, D. and}, title = {{Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana}}, year = {2016}, pages = {1091}, journal = {Int. J. Mol. Sci.}, doi = {10.3390/ijms17071091}, 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-961, author = {Arnold, M. D. and Gruber, C. and Floková, K. and Miersch, O. and Strnad, M. and Novák, O. and Wasternack, C. and Hause, B. and}, title = {{The Recently Identified Isoleucine Conjugate of cis-12-Oxo-Phytodienoic Acid Is Partially Active in cis-12-Oxo-Phytodienoic Acid-Specific Gene Expression of Arabidopsis thaliana}}, year = {2016}, pages = {e0162829}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0162829}, volume = {11}, abstract = {Oxylipins of the jasmonate family are active as signals in plant responses to biotic and abiotic stresses as well as in development. Jasmonic acid (JA), its precursor cis-12-oxo-phytodienoic acid (OPDA) and the isoleucine conjugate of JA (JA-Ile) are the most prominent members. OPDA and JA-Ile have individual signalling properties in several processes and differ in their pattern of gene expression. JA-Ile, but not OPDA, is perceived by the SCFCOI1-JAZ co-receptor complex. There are, however, numerous processes and genes specifically induced by OPDA. The recently identified OPDA-Ile suggests that OPDA specific responses might be mediated upon formation of OPDA-Ile. Here, we tested OPDA-Ile-induced gene expression in wild type and JA-deficient, JA-insensitive and JA-Ile-deficient mutant background. Tests on putative conversion of OPDA-Ile during treatments revealed only negligible conversion. Expression of two OPDA-inducible genes, GRX480 and ZAT10, by OPDA-Ile could be detected in a JA-independent manner in Arabidopsis seedlings but less in flowering plants. The data suggest a bioactivity in planta of OPDA-Ile.} } @Article{IPB-976, 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. and}, 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}, 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-973, author = {Dinesh, D. C. and Calderón Villalobos, L. I. A. and Abel, S. and}, title = {{Structural Biology of Nuclear Auxin Action}}, year = {2016}, pages = {302-316}, journal = {Trends Plant Sci.}, doi = {10.1016/j.tplants.2015.10.019}, 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.} } @INBOOK{IPB-57, author = {Wasternack, C. and}, title = {{eLS}}, year = {2016}, chapter = {{Jasmonates: Synthesis, Metabolism, Signal Transduction and Action}}, doi = {10.1002/9780470015902.a0020138.pub2}, abstract = {Jasmonic acid and other fatty‐acid‐derived compounds called oxylipins are signals in stress responses and development of plants. The receptor complex, signal transduction components as well as repressors and activators in jasmonate‐induced gene expression have been elucidated. Different regulatory levels and cross‐talk with other hormones are responsible for the multiplicity of plant responses to environmental and developmental cues.} } @INBOOK{IPB-52, author = {Parniske, M. and Ried, M. K. and}, title = {{Die Sprache der Moleküle – Chemische Kommunikation in der Natur}}, year = {2016}, pages = {105-116}, chapter = {{Wahrnehmung und Interpretation symbiontischer Signale durch Pflanzen und ihre bakteriellen Partner}}, editor = {Deigele, C., ed.}, abstract = {Mutualistic symbioses between plant roots and microorganisms can reduce the demand for chemical fertilizers in agriculture. Most crops are able to establish arbuscular mycorrhiza (AM) symbiosis with fungi to take up phosphate more efficiently. A second symbiosis, nitrogen-fixing root nodule symbiosis, supersedes energy-intensive nitrogen fertilization: Legumes such as peas, clover and soybeans take up rhizobia – special bacteria that are capable of converting atmospheric nitrogen into ammonium – into their root cells. Plant root cells perceive rhizobia and AM fungi via very similar signaling molecules (N-acetylglucosamine tetra- or pentamers), even though the resultant developmental processes differ strongly. Interestingly, N-acetylglucosamine containing signals including fungal chitin- and bacterial peptidoglycan-fragments from their cell walls, also play a role in the recognition of pathogenic microorganisms.Despite the intrinsic sustainability potential of the nitrogen-fixing root nodule symbiosis, too much of a good thing, however, has led to global problems: The massive increase in global meat production is largely based on soybean. Large scale soybean monoculture destroyed ecosystems in South America. Large scale animal production results in excessive methane and nitrogen release into the environment, which causes climate change and death zones in marine ecosystems, respectively. This calls for a considerable reduction in meat consumption.} } @INBOOK{IPB-48, author = {Hellmuth, A. and Calderón Villalobos, L. I. A. and}, title = {{Plant Proteostasis}}, year = {2016}, pages = {23-34}, chapter = {{Radioligand Binding Assays for Determining Dissociation Constants of Phytohormone Receptors}}, journal = {Methods Mol. Biol.}, editor = {Lois, L. M. \& Matthiesen, R., eds.}, doi = {10.1007/978-1-4939-3759-2_3}, 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 (Ki) 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.} }