TY - JOUR ID - 2582 TI - Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity JO - bioRxiv PY - 2020 SP - AU - Bassal, M. AU - Majovsky, P. AU - Thieme, D. AU - Herr, T. AU - Abukhalaf, M. AU - Ayash, M. AU - Al Shweiki, M. R. AU - Proksch, C. AU - Hmedat, A. AU - Ziegler, J. AU - Neumann, S. AU - Hoehenwarter, W. VL - UR - https://dx.doi.org/10.1101/2020.03.09.978627 DO - 10.1101/2020.03.09.978627 AB - Proteome remodeling is a fundamental adaptive response and proteins in complex and functionally related proteins are often co-expressed. Using a deep sampling strategy we define Arabidopsis thaliana tissue core proteomes at around 10,000 proteins per tissue and absolutely quantify (copy numbers per cell) nearly 16,000 proteins throughout the plant lifecycle. A proteome wide survey of global post translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue and age specific roles of entire signaling modules regulating transcription in photosynthesis, seed development and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like Kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were co-expressed tissue and age specifically indicating functional promiscuity in the assembly of these little described protein complexes in Arabidopsis. Treatment of seedlings with flg22 for 16 hours allowed us to characterize proteome architecture in basal immunity in detail. The results were complemented with parallel reaction monitoring (PRM) targeted proteomics, phytohormone, amino acid and transcript measurements. We obtained strong evidence of suppression of jasmonate (JA) and JA-Ile levels by deconjugation and hydroxylation via IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2) under the control of JASMONATE INSENSITIVE 1 (MYC2). This previously unknown regulatory switch is another part of the puzzle of the as yet understudied role of JA in pattern triggered immunity. The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community. A2 - C1 - Synergy Research Groups; Molecular Signal Processing ER - TY - JOUR ID - 2598 TI - Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies JO - Nat Commun PY - 2020 SP - 2277 AU - Niemeyer, M. AU - Moreno Castillo, E. AU - Ihling, C. H. AU - Iacobucci, C. AU - Wilde, V. AU - Hellmuth, A. AU - Hoehenwarter, W. AU - Samodelov, S. L. AU - Zurbriggen, M. D. AU - Kastritis, P. L. AU - Sinz, A. AU - Calderón Villalobos, L. I. A. VL - 11 UR - https://dx.doi.org/10.1038/s41467-020-16147-2 DO - 10.1038/s41467-020-16147-2 AB - Cullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5 and their AUX/IAA targets perceive the phytohormone auxin. The F-box protein TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, by adopting biochemical, structural proteomics and in vivo approaches we unveil how flexibility in AUX/IAAs and regions in TIR1 affect their conformational ensemble allowing surface accessibility of degrons. We resolve TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. We identify essential residues at the TIR1 N- and C-termini, which provide non-native interaction interfaces with IDRs and the folded PB1 domain of AUX/IAAs. We thereby establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for a multiplicity of functional states. A2 - C1 - Synergy Research Groups; Molecular Signal Processing ER - TY - JOUR ID - 2481 TI - Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin receptor assemblies JO - bioRxiv PY - 2019 SP - AU - Niemeyer, M. AU - Moreno Castillo, E. AU - Ihling, C. H. AU - Iacobucci, C. AU - Wilde, V. AU - Hellmuth, A. AU - Hoehenwarter, W. AU - Samodelov, S. L. AU - Zurbriggen, M. D. AU - Kastritis, P. L. AU - Sinz, A. AU - Calderón Villalobos, L. I. A. VL - UR - https://dx.doi.org/10.1101/787770 DO - 10.1101/787770 AB - Cullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5 and their ubiquitylation targets, AUX/IAAs, sense auxin concentrations in the nucleus. TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, we resolved TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron′s vicinity, cooperatively position AUX/IAAs on TIR1. The AUX/IAA PB1 interaction domain also assists in non-native contacts, affecting AUX/IAA dynamic interaction states. Our results establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation and might provide conformational flexibility for adopting a multiplicity of functional states. We postulate IDRs in distinct members of the AUX/IAA family to be an adaptive signature for protein interaction and initiation region for proteasome recruitment. A2 - C1 - Synergy Research Groups; Molecular Signal Processing ER - TY - JOUR ID - 2381 TI - Corrigendum: ICTV Virus Taxonomy Profile: Ophioviridae JO - J Gen Virol PY - 2018 SP - 949-949 AU - García, M. L. AU - Bó, E. D. AU - da Graça, J. V. AU - Gago-Zachert, S. AU - Hammond, J. AU - Moreno, P. AU - Natsuaki, T. AU - Pallás, V. AU - Navarro, J. A. AU - Reyes, C. A. AU - Luna, G. R. AU - Sasaya, T. AU - Tzanetakis, I. E. AU - Vaira, A. M. AU - Verbeek, M. AU - ICTV Report Consortium VL - 99 UR - https://dx.doi.org/10.1099/jgv.0.001093 DO - 10.1099/jgv.0.001093 AB - A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 2099 TI - Arabidopsis Transporter ABCG37/PDR9 contributes primarily highly oxygenated Coumarins to Root Exudation JO - Sci Rep PY - 2017 SP - 3704 AU - Ziegler, J. AU - Schmidt, S. AU - Strehmel, N. AU - Scheel, D. AU - Abel, S. VL - 7 UR - https://www.nature.com/articles/s41598-017-03250-6 DO - 10.1038/s41598-017-03250-6 AB - 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. A2 - C1 - Molecular Signal Processing; Stress and Developmental Biology ER - TY - JOUR ID - 2101 TI - ICTV Virus Taxonomy Profile: Ophioviridae JO - J Gen Virol PY - 2017 SP - 1161-1162 AU - García, M. L. AU - Bó, E. D. AU - da Graça, J. V. AU - Gago-Zachert, S. AU - Hammond, J. AU - Moreno, P. AU - Natsuaki, T. AU - Pallás, V. AU - Navarro, J. A. AU - Reyes, C. A. AU - Luna, G. R. AU - Sasaya, T. AU - Tzanetakis, I. E. AU - Vaira, A. M. AU - Verbeek, M. AU - ICTV Report Consortium VL - 98 UR - http://jgv.microbiologyresearch.org/content/journal/jgv/ DO - 10.1099/jgv.0.000836 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 2091 TI - Variation in auxin sensing guides AUX/IAA transcriptional repressor ubiquitylation and destruction. JO - Nature Commun. PY - 2017 SP - 15706 AU - Winkler, M. AU - Niemeyer, M. AU - Hellmuth, A. AU - Janitza, P. AU - Christ, G. AU - Samodelov, S. L. AU - Wilde, V. AU - Majovsky, P. AU - Trujillo, M. AU - Zurbriggen, M. D. AU - Hoehenwarter, W. AU - Quint, M. AU - Calderón Villalobos, L. I. A. VL - 8 UR - https://www.nature.com/articles/ncomms15706 DO - 10.1038/ncomms15706 AB - 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. A2 - C1 - Synergy Research Groups; Molecular Signal Processing ER - TY - JOUR ID - 1853 TI - 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 JO - J Exp Bot PY - 2016 SP - 1421-1432 AU - Ziegler, J. AU - Schmidt, S. AU - Chutia, R. AU - Müller, J. AU - Böttcher, C. AU - Strehmel, N. AU - Scheel, D. AU - Abel, S. VL - 67 UR - https://academic.oup.com/jxb/article/67/5/1421/2885100 DO - 10.1093/jxb/erv539 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1902 TI - Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana JO - Int J Mol Sci PY - 2016 SP - 1091 AU - Strehmel, N. AU - Mönchgesang, S. AU - Herklotz, S. AU - Krüger, S. AU - Ziegler, J. AU - Scheel, D. VL - 17 UR - https://dx.doi.org/10.3390/ijms17071091 DO - 10.3390/ijms17071091 AB - 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 A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1894 TI - Comparative expression profiling reveals a role of the root apoplast in local phosphate response JO - BMC Plant Biol PY - 2016 SP - 106 AU - Hoehenwarter, W. AU - Mönchgesang, S. AU - Neumann, S. AU - Majovsky, P. AU - Abel, S. AU - Müller, J. VL - 16 UR - https://dx.doi.org/10.1186/s12870-016-0790-8 DO - 10.1186/s12870-016-0790-8 AB - 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. A2 - C1 - Synergy Research Groups; Molecular Signal Processing ER - TY - JOUR ID - 1826 TI - Perturbations in the Primary Metabolism of Tomato and Arabidopsis thaliana Plants Infected with the Soil-Borne Fungus Verticillium dahliae JO - PLoS ONE PY - 2015 SP - e0138242 AU - Buhtz, A. AU - Witzel, K. AU - Strehmel, N. AU - Ziegler, J. AU - Abel, S. AU - Grosch, R. VL - 10 UR - http://www.plosone.org/ DO - 10.1371/journal.pone.0138242 AB - 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. A2 - C1 - Stress and Developmental Biology; Molecular Signal Processing ER - TY - CHAP ID - 1575 TI - Family - Ophioviridae T2 - Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses PB - PY - 2012 SP - 743-748 AU - Vaira, A. M. AU - Gago-Zachert, S. AU - Garcia, M. L. AU - Guerri, J. AU - Hammond, J. AU - Milne, R. G. AU - Moreno, P. AU - Morikawa, T. AU - Natsuaki, T. AU - Navarro, J. A. AU - Pallas, V. AU - Torok, V. AU - Verbeek, M. AU - Vetten, H. J. VL - UR - https://dx.doi.org/10.1016/B978-0-12-384684-6.00060-4 SN - 978-0-12-384684-6 DO - 10.1016/B978-0-12-384684-6.00060-4 AB - 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. A2 - King, A. M. Q., et al., eds. C1 - Molecular Signal Processing ER - TY - JOUR ID - 1206 TI - The moss Physcomitrella patens contains cyclopentenones but no jasmonates: mutations in allene oxide cyclase lead to reduced fertility and altered sporophyte morphology JO - New Phytol PY - 2010 SP - 740-749 AU - Stumpe, M. AU - Göbel, C. AU - Faltin, B. AU - Beike, A. K. AU - Hause, B. AU - Himmelsbach, K. AU - Bode, J. AU - Kramell, R. AU - Wasternack, C. AU - Frank, W. AU - Reski, R. AU - Feussner, I. VL - 188 (3) UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2010.03406.x/abstract DO - 10.1111/j.1469-8137.2010.03406.x AB - 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 linolenic 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 ΔPpAOC1 and ΔPpAOC2 mutants showed reduced fertility, aberrant sporophyte morphology and interrupted sporogenesis. A2 - C1 - Molecular Signal Processing; Cell and Metabolic Biology ER - TY - JOUR ID - 1279 TI - Complex regulation of the TIR/AFB family of auxin receptors JO - Proc Natl Acad Sci USA PY - 2009 SP - 22540-22545 AU - Parry, G. AU - Calderón Villalobos, L.I. AU - Prigge, M. AU - Peret, B. AU - Dharmasiri, S. AU - Itoh, H. AU - Lechner, E. AU - Gray, W.M. AU - Bennett, M. AU - Estelle, M. VL - 106(52) UR - http://www.pnas.org/content/106/52/22528.full DO - 10.1073/pnas.0911967106 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1113 TI - Arabidopsis IAR4 modulates auxin response by regulating auxin homeostasis JO - Plant Physiol PY - 2009 SP - 748-758 AU - Quint, M. AU - Barkawi, L.S. AU - Fan, K.T. AU - Cohen, J.D. AU - Gray, W.M. VL - 150 UR - DO - 10.1104/pp.109.136671 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1014 TI - Genetic analysis of CAND1-CUL1 interactions in Arabidopsis supports a role for CAND1-mediated cycling of the SCFTIR1 complex JO - Proc Natl Acad Sci PY - 2008 SP - 8470-8475 AU - Zhang, W. AU - Ito, H. AU - Quint, M. AU - Huang, H. AU - Noël, L.D. AU - Gray, W.M. VL - 105 UR - http://www.pnas.org/content/105/24/8470.full.pdf+html DO - 10.1073/pnas.0804144105 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 946 TI - A novel plastidial lipoxygenase of maize (Zea mays) ZmLOX6 encodes for a fatty acid hydroperoxide lyase and is uniquely regulated by phytohormones and pathogen infection JO - Planta PY - 2008 SP - 491-503 AU - Gao, X. AU - Stumpe, M. AU - Feussner, I. AU - Kolomiets, M. VL - 227 UR - DO - 10.1007/s00425-007-0634-8 AB - A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 947 TI - Reduction of divinyl ether-containing polyunsaturated fatty acids in transgenic potato plants JO - Phytochemistry PY - 2007 SP - 797-801 AU - Eschen-Lippold, L. AU - Rothe, G. AU - Stumpe, M. AU - Göbel, C. AU - Feussner, I. AU - Rosahl, S. VL - 68 UR - DO - 10.1016/j.phytochem.2006.12.010 AB - A2 - C1 - Molecular Signal Processing; Biochemistry of Plant Interactions ER - TY - JOUR ID - 854 TI - Auxin signaling JO - Curr Opin Plant Biol PY - 2006 SP - 448-453 AU - Quint, M. AU - Gray, W.M. VL - 9 UR - DO - 10.1016/j.pbi.2006.07.006 AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - CHAP ID - 1560 TI - Genus Ophiovirus T2 - Virus Taxonomy. VIIIth Report of the International Committee on Taxonomy of Viruses. Part II the negative sense single stranded RNA viruses PB - Elsevier, Academic Press PY - 2005 SP - 673-679 AU - Vaira, A.M. AU - Acotto, G.P. AU - Gago-Zachert, S. AU - García, M.L. AU - Grau, O. AU - Milne, R.G. AU - Morikawa, T. AU - Natsuaki, T. AU - Torov, V. AU - Verbeek, M. AU - Vetten, H.J. VL - UR - https://www.elsevier.com/books/virus-taxonomy/fauquet/978-0-12-249951-7 SN - 9780080575483; 9780122499517 AB - 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. A2 - Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U., Ball, L. A. C1 - Molecular Signal Processing ER - TY - JOUR ID - 856 TI - Characterization of a novel temperature-sensitive allele of the CUL1/AXR6 subunit of SCF ubiquitin-ligases JO - Plant J PY - 2005 SP - 371-383 AU - Quint, M. AU - Ito, H. AU - Zhang, W. AU - Gray, W.M. VL - 43 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2005.02449.x/full AB - 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. A2 - C1 - Molecular Signal Processing ER - TY - CHAP ID - 427 TI - The lipoxygenase pathway in mycorrhizal roots of Medicago truncatula T2 - Advanced Research on Plant Lipids PB - Kluwer Academic Publishers, Dordrecht PY - 2003 SP - 287-290 AU - Stumpe, M. AU - Stenzel, I. AU - Weichert, H. AU - Hause, B. AU - Feussner, I. VL - 0 UR - AB - A2 - Murata, N., Yamada, M., Nishida, I., Okuyama, H., Sekijar, J., Hajme, W. C1 - Molecular Signal Processing; Cell and Metabolic Biology ER -