@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-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.} } @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-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-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-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.} } @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.} }