@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-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-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-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-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 = {https://dx.doi.org/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-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-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.} } @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 = {2012}, pages = {743-748}, chapter = {{Family - Ophioviridae}}, editor = {King, A. M. Q., et al., eds.}, doi = {10.1016/B978-0-12-384684-6.00060-4}, url = {https://dx.doi.org/10.1016/B978-0-12-384684-6.00060-4}, abstract = {This chapter focuses on Ophioviridae family whose sole member genus is Ophiovirus. The member species of the genus include Citrus psorosis virus (CPsV), Freesia sneak virus(FreSV), Lettuce ring necrosis virus (LRNV), and Mirafiori lettuce big-vein virus (MiLBVV).The single stranded negative/possibly ambisense RNA genome is divided into 3–4 segments, each of which is encapsidated in a single coat protein (43–50 kDa) forming filamentous virions of about 3 nm in diameter, in shape of kinked or probably internally coiled circles of at least two different contour lengths. Ophioviruses can be mechanically transmitted to a limited range of test plants, inducing local lesions and systemic mottle. The natural hosts of CPsV, ranunculus white mottle virus (RWMV), MiLBVV, and LRNV are dicotyledonous plants of widely differing taxonomy. CPsV has a wide geographical distribution in citrus in the Americas, in the Mediterranean and in New Zealand. FreSV has been reported in two species of the family Ranunculacae from Northern Italy, and in lettuce in France and Germany. Tulip mild mottle mosaic virus (TMMMV) has been reported in tulips in Japan. LRNV is closely associated with lettuce ring necrosis disease in The Netherlands, Belgium, and France, and FreSV has been reported in Europe, Africa, North America and New Zealand.} } @Article{IPB-1305, author = {Kopycki, J. and Schmidt, J. and Abel, S. and Grubb, C. D.}, title = {{Chemoenzymatic synthesis of diverse thiohydroximates from glucosinolate-utilizing enzymes from Helix pomatia and 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-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-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 = {Proc Natl Acad Sci USA}, doi = {10.1073/pnas.0911967106}, 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-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}, doi = {10.1104/pp.109.136671}, 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-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 = {Plant J}, doi = {10.1111/j.1365-313X.2009.03937.x}, 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-1066, author = {Jindaprasert, A. and Springob, K. and Schmidt, J. and De-Eknamkul, W. and Kutchan, T.M.}, title = {{Pyrone polyketides synthesized by a type III polyketide synthase from Drosophyllum lusitanicum}}, year = {2008}, pages = {3043-3053}, journal = {Phytochemistry}, doi = {10.1016/j.phytochem.2008.03.013}, url = {http://www.sciencedirect.com/science/journal/00319422/69/18}, volume = {69}, abstract = {To isolate cDNAs involved in the biosynthesis of acetate-derived naphthoquinones in Drosophyllum lusitanicum, an expressed sequence tag analysis was performed. RNA from callus cultures was used to create a cDNA library from which 2004 expressed sequence tags were generated. One cDNA with similarity to known type III polyketide synthases was isolated as full-length sequence and termed DluHKS. The translated polypeptide sequence of DluHKS showed 51–67% identity with other plant type III PKSs. Recombinant DluHKS expressed in Escherichia coli accepted acetyl-coenzyme A (CoA) as starter and carried out sequential decarboxylative condensations with malonyl-CoA yielding α-pyrones from three to six acetate units. However, naphthalenes, the expected products, were not isolated. Since the main compound produced by DluHKS is a hexaketide α-pyrone, and the naphthoquinones in D. lusitanicum are composed of six acetate units, we propose that the enzyme provides the backbone of these secondary metabolites. An involvement of accessory proteins in this biosynthetic pathway is discussed.} } @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}, doi = {10.1073/pnas.0804144105}, 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-1049, author = {Fellenberg, C. and Milkowski, C. and Hause, B. and Lange, P. and Böttcher, C. and Schmidt, J. and Vogt, T.}, title = {{Tapetum-specific location of a cation-dependent O-methyltransferase in Arabidopsis thaliana}}, year = {2008}, pages = {132-145}, journal = {Plant J}, doi = {10.1111/j.1365-313X.2008.03576.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2008.03576.x/full}, volume = {56}, abstract = {Cation- and S-adenosyl-l-methionine (AdoMet)-dependent plant natural product methyltransferases are referred to as CCoAOMTs because of their preferred substrate, caffeoyl coenzyme A (CCoA). The enzymes are encoded by a small family of genes, some of which with a proven role in lignin monomer biosynthesis. In Arabidopsis thaliana individual members of this gene family are temporally and spatially regulated. The gene At1g67990 is specifically expressed in flower buds, and is not detected in any other organ, such as roots, leaves or stems. Several lines of evidence indicate that the At1g67990 transcript is located in the flower buds, whereas the corresponding CCoAOMT-like protein, termed AtTSM1, is located exclusively in the tapetum of developing stamen. Flowers of At1g67990 RNAi-suppressed plants are characterized by a distinct flower chemotype with severely reduced levels of the N ′,N ′′-bis-(5-hydroxyferuloyl)-N ′′′-sinapoylspermidine compensated for by N1,N5,N10-tris-(5-hydroxyferuloyl)spermidine derivative, which is characterized by the lack of a single methyl group in the sinapoyl moiety. This severe change is consistent with the observed product profile of AtTSM1 for aromatic phenylpropanoids. Heterologous expression of the recombinant protein shows the highest activity towards a series of caffeic acid esters, but 5-hydroxyferuloyl spermidine conjugates are also accepted substrates. The in vitro substrate specificity and the in vivo RNAi-mediated suppression data of the corresponding gene suggest a role of this cation-dependent CCoAOMT-like protein in the stamen/pollen development of A. thaliana.} } @Article{IPB-854, author = {Quint, M. and Gray, W.M.}, title = {{Auxin signaling}}, year = {2006}, pages = {448-453}, journal = {Curr Opin Plant Biol}, doi = {10.1016/j.pbi.2006.07.006}, 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-794, author = {Ziegler, J. and Voigtländer, S. and Schmidt, J. and Kramell, R. and Miersch, O. and Ammer, C. and Gesell, A. and Kutchan, T.M.}, title = {{Comparative transcript and alkaloid profiling in Papaver species identifies a short chain dehydrogenase/reductase involved in morphine biosynthesis}}, year = {2006}, pages = {177-192}, journal = {Plant J}, doi = {10.1111/j.1365-313X.2006.02860.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02860.x/full}, volume = {48}, abstract = {Plants of the order Ranunculales, especially members of the species Papaver, accumulate a large variety of benzylisoquinoline alkaloids with about 2500 structures, but only the opium poppy (Papaver somniferum) and Papaver setigerum are able to produce the analgesic and narcotic morphine and the antitussive codeine. In this study, we investigated the molecular basis for this exceptional biosynthetic capability by comparison of alkaloid profiles with gene expression profiles between 16 different Papaver species. Out of 2000 expressed sequence tags obtained from P. somniferum, 69 show increased expression in morphinan alkaloid-containing species. One of these cDNAs, exhibiting an expression pattern very similar to previously isolated cDNAs coding for enzymes in benzylisoquinoline biosynthesis, showed the highest amino acid identity to reductases in menthol biosynthesis. After overexpression, the protein encoded by this cDNA reduced the keto group of salutaridine yielding salutaridinol, an intermediate in morphine biosynthesis. The stereoisomer 7-epi-salutaridinol was not formed. Based on its similarities to a previously purified protein from P. somniferum with respect to the high substrate specificity, molecular mass and kinetic data, the recombinant protein was identified as salutaridine reductase (SalR; EC 1.1.1.248). Unlike codeinone reductase, an enzyme acting later in the pathway that catalyses the reduction of a keto group and which belongs to the family of the aldo-keto reductases, the cDNA identified in this study as SalR belongs to the family of short chain dehydrogenases/reductases and is related to reductases in monoterpene metabolism.} } @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-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-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-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}, } @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}, }