An integrated protein localization and interaction map for Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus

Virology

Volumn 402, Issue 1, 2010, Pages 61-71

  Bandyopadhyay, Anindya ^a   Kopperud, Kristin ^a   Anderson, Gavin ^a   Martin, Kathleen ^a   Goodin, Michael ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

BiFC; Confocal; FRAP; GFP; Interactome; Localization; Nicotiana benthamiana; Nuclear localization; Rhabdovirus; TagRFP

Indexed keywords

M PROTEIN; RNA DIRECTED RNA POLYMERASE; VIRUS PROTEIN; VIRUS RNA; SPACER DNA;

3' UNTRANSLATED REGION; ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; FLUORESCENCE ANALYSIS; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; GENOME ANALYSIS; NICOTIANA BENTHAMIANA; NONHUMAN; NUCLEORHABDOVIRUS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POTATO YELLOW DWARF VIRUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; RHABDOVIRUS; SEQUENCE ANALYSIS; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS NUCLEOCAPSID; VIRUS TRANSMISSION; 5' UNTRANSLATED REGION; CELL NUCLEUS; CELL NUCLEUS MEMBRANE; CHEMISTRY; CLUSTER ANALYSIS; CONFOCAL MICROSCOPY; CYTOPLASM; DNA SEQUENCE; GENE ORDER; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; POTATO; PROTEIN BINDING; SEQUENCE HOMOLOGY; TOBACCO; TWO HYBRID SYSTEM; VIROLOGY;

NICOTIANA BENTHAMIANA; NUCLEORHABDOVIRUS; RHABDOVIRIDAE; SOLANUM TUBEROSUM;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; CELL NUCLEUS; CLUSTER ANALYSIS; CYTOPLASM; DNA, INTERGENIC; GENE ORDER; GENOME, VIRAL; MICROSCOPY, CONFOCAL; MOLECULAR SEQUENCE DATA; NUCLEAR ENVELOPE; OPEN READING FRAMES; PHYLOGENY; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; RHABDOVIRIDAE; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SOLANUM TUBEROSUM; TOBACCO; TWO-HYBRID SYSTEM TECHNIQUES; VIRAL PROTEINS;

EID: 77952569645     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2010.03.013     Document Type: Article

References (56)

1. Adam G., Gaedigk K. Inhibition of Potato Yellow Dwarf Virus infection in vector cell monolayers by lysosomotropic agents. J. Gen. Virol. 1986, 67:2775-2780.
2. Adam G., Hsu H.T. Comparison of structural proteins from two Potato yellow dwarf viruses. J. Gen. Virol. 1984, 65:991-994.
3. Ammar el-D., Tsai C.W., Whitfield A.E., Redinbaugh M.G., Hogenhout S.A. Cellular and molecular aspects of rhabdovirus interactions with insect and plant hosts. Annu. Rev. Entomol. 2009, 54:447-468.
4. Barr J.N., Whelan S.P., Wertz G.W. Transcriptional control of the RNA-dependent RNA polymerase of Vesicular stomatitis virus. Biochem. Biophys. Acta 2002, 1577:337-353.
5. Barrus M.F., Chupp C.C. Yellow dwarf of potatoes. Phytopathology 1922, 12:122-133.
6. Basak S., Polley S., Basu M., Chattopadhyay D., Roy S. Monomer and dimer of Chandipura virus unphosphorylated P-protein binds leader RNA differently: implications for viral RNA synthesis. J. Mol. Biol. 2004, 339(5):1089-1101.
7. Bendtsen J.D., Nielsen H., Heijne G.V., Brunak S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 2004, 340:783-795.
8. Bjellqvist B., Hughes G.J., Pasquali Ch., Paquet N., Ravier F., Sanchez J.-C.h., Frutiger S., Hochstrasser D.F. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14:1023-1031.
9. Blom N., Sicheritz-Ponten T., Gupta R., Gammeltoft S., Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004, 4:1633-1649.
10. Bourhy H., Cowley J.A., Larrous F., Holmes E.C., Walker P.J. Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene. J. Gen. Virol. 2005, 86:2849-2858.
11. Brakke M. Density gradient centrifugation: a new separation technique source. J. Am. Chem. Soc. 1951, 73(4):1847-1848.
12. Brakke M.K., Black L.M., Wyckoff R.W.G. The sedimentation rate of potato yellow-dwarf virus. Am. J. Bot. 1951, 38:332-342.
13. Chakrabarty R., Banerjee R., Chung S.M., Farman M., Citovsky V., Hogenhout S.A., Tzfira T., Goodin M.M. Vector for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interaction. Mol. Plant Microbe Interact. 2007, 20:740-750.
14. Chen B.J., Lamb R.A. Mechanisms for enveloped virus budding: can some viruses do without an ESCRT?. Virology 2008, 372(2):221-232.
15. Chenik M., Schnell M., Conzelmann K.K., Blondel D. Mapping the interacting domains between the rabies virus polymerase and phosphoprotein. J. Virol. 1998, 72(3):1925-1930.
16. Chiu R.J., Liu H.Y., MacLeod R., Black L.M. Potato yellow dwarf virus in leafhopper cell culture. Virology 1970, 40:387-396.
17. Citovsky V., Lee L.Y., Vyas S., Glick E., Chen M.H., Vainstein A., Gafni Y., Gelvin S.B., Tzfira T.J. Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. Mol. Biol. 2006, 362:1120-1131.
18. Dietzgen R.G., Callaghan B., Wetzel T., Dale J.L. Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus. Virus Res. 2006, 118:16-22.
19. Falk B.W., Weathers L.G. Comparison of potato yellow dwarf virus serotypes. Phytopathology 1983, 73:81-85.
20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39(4):783-791.
21. Gaedigk K., Adam G., Mundry K.-W. The spike protein of potato yellow dwarf virus and its functional role in the infection of insect vector cells. J. Gen. Virol. 1986, 67:2763-2773.
22. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 31:3784-3788.
23. Ghosh D., Brooks R.E., Wang R., Lesnaw J., Goodin M.M. Cloning and subcellular localization of phosphoprotein and nucleocapsid proteins of potato yellow dwarf virus, type species of the genus Nucleorhabdovirus. Virus Res. 2008, 135:26-35.
24. Goodin M.M., Austin J., Tobias R., Fujita M., Morales C., Jackson A.O. Interactions and nuclear import of the N and P proteins of sonchus yellow net virus, a plant nucleorhabdovirus. J. Virol. 2001, 75(19):9393-9406.
25. Goodin M., Yelton S., Ghosh D., Mathews S., Lesnaw J. Live-cell imaging of rhabdovirus induced morphological changes in plant nuclear membranes. Mol. Plant Microbe Interact. 2005, 18:703-709.
26. Goodin M.M., Chakrabarty R., Banerjee R., Yelton S., DeBolt S. Membrane and protein dynamics in live plant nuclei infected with sonchus yellow net virus, a plant adapted rhabdovirus. J. Gen. Virol. 2007, 88:1810-1820.
27. Hsu H.T., Black L.M. Inoculation of vector cell monolayers with potato yellow dwarf virus. Virology 1973, 52:187-198.
28. Huang Y.W., Geng Y.F., Ying X.B., Chen X.Y., Fang R.X. Identification of a movement protein of rice yellow stunt rhabdovirus. J. Virol. 2005, 79(4):2108-2114.
29. Irie T., Nagata N., Yoshida T., Sakaguchi T. Recruitment of Alix/AIP1 to the plasma membrane by Sendai virus C protein facilitates budding of virus-like particles. Virology 2008, 371(1):108-120.
30. Irons S.L., Evans D.E., Brandizzi F. The first 238 amino acids of the human lamin B receptor are targeted to the nuclear envelope in plants. J. Ex. Bot. 2003, 54:943-950.
31. Jackson A.O., Dietzgen R.G., Goodin M.M., Bragg J.N., Deng M. Biology of plant rhabdoviruses. Annu. Rev. Phytopathol. 2005, 43:623-660.
32. Knudson D.L., MacLeod R. The proteins of potato yellow dwarf virus. Virology 1972, 47:285-295.
33. Kuzmin I.V., Novella I.S., Dietzgen R.G., Padhi A., Rupprecht C.E. The rhabdoviruses: biodiversity, phylogenetics, and evolution. Infect. Genet. Evol. 2009, 9:541-553.
34. MacLeod R., Black L.M., Moyer F.H. The fine structure and intracellular localization of potato yellow dwarf virus. Virology 1966, 29:540-552.
35. Martin K., Kopperud K., Chakrabarty R., Banerjee R., Brooks R., Goodin M.M. Transient expression in Nicotiana benthamiana fluorescent marker line provides enhanced definition of protein localization, movement and interactions in planta. Plant J. 2009, 59:150-162.
36. Martins C.R., Johnson J.A., Lawrence D.M., Choi T.J., Pisi A.M., Tobin S.L., Lapidus D., Wagner J.D., Ruzin S., McDonald K., Jackson A.O. Sonchus yellow net rhabdovirus nuclear viroplasms contain polymerase-associated proteins. J. Virol. 1998, 72:5669-5679.
37. Masters P.S., Banerjee A.K. Resolution of multiple complexes of phosphoprotein NS with nucleocapsid protein N of vesicular stomatitis virus. J. Virol. 1988, 62(8):2651-2657.
38. Melcher U. The '30K' superfamily of viral movement proteins. J. Gen. Virol. 2000, 81:257-266.
39. Nakai K., Kanehisa M. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 1991, 11:95-110.
40. Nault L.R., Ammar E.D. Leafhopper and planthopper transmission of plant viruses. Annu. Rev. Entomol. 1989, 34:503-529.
41. Reeder G.S., Knudson D.L., Macleod R. The ribonucleic acid of potato yellow dwarf virus. Virology 1972, 50:301-304.
42. Revill P., Trinh X., Dale J., Harding R. Taro vein chlorosis virus: characterization and variability of a new nucleorhabdovirus. J. Gen. Virol. 2005, 86:491-499.
43. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4(4):406-425.
44. Scholthof K.B., Jackson A.O., Van Etten J.L. Myron Kendall Brakke: 1921 to 2007. Phytopathology 2008, 98:1056-1059.
45. Schwartz R.M., Dayhoff M.O. Protein and nucleic acid sequence data and phylogeny. Science 1979, 205(4410):1038-1039.
46. Senthil G., Liu H., Puram G.V., Clark A., Stromberg A., Goodin M.M. Specific and common changes in Nicotiana benthamiana gene expression in response to infection by enveloped viruses. J. Gen. Virol. 2005, 86:2615-2625.
47. Szymkowiak C., Kwan W.-S., Su Q., Toner T.J., Shaw A.R., Youil R. Rapid method for the characterization of 3' and 5' UTRs of influenza viruses. J. Virol. Methods 2003, 107:15-20.
48. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24(8):1596-1599.
49. Tatusov T., Tatusov R. Open reading frame finder. National Center for Biotechnology Information 2007, National Institute of Health, http://www.ncbi.nlm.nih.gov/projects/gorf/.
50. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22(22):4673-4680.
51. Tordo N., Benmansour A., Calisher C., Dietzgen R.G., Fang R.-X., Jackson A.O., Kurath G., Nadin-Davis S., Tesh R.B., Walker P.J. Rhabdoviridae. Virus Taxonomy: Classification and Nomenclature of Viruses. 8th Report of the International Committee on the Taxonomy of Viruses 2005, 623-644. Elsevier Academic Press, London. C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball (Eds.).
52. Tsai C.-H., Redinbaugh M.G., Willie K.J., Reed S., Goodin M., Hogenhout S. Complete genome sequence and in planta subcellular localization of Maize fine streak virus proteins. J. Virol. 2005, 9:5304-5314.
53. van Beek N.A.M., Lohuis D., Dijkstra J., Peters D. Morphogenesis of Sonchus yellow net virus in cowpea protoplasts. J. Ultrastruct. Res. 1985, 90:294-303.
54. Wagner R.R., Prevec L., Brown F., Summers D.F., Sokol F., MacLeod R. Classification of rhabdovirus proteins: a proposal. J. Virol. 1972, 10:1228-1230.
55. Xu X.M., Meulia T., Meier I. Anchorage of plant RanGAP to the nuclear envelope involves novel nuclear-pore-associated hproteins. Curr. Biol. 2007, 17:1157-1163.
56. Zaltsman A., Yi B.Y., Krichevsky A., Gafni Y., Citovsky V. Yeast-plant coupled vector system for identification of nuclear proteins. Plant Physiol. 2007, 145(4):1264-1271.