1887

Abstract

The genome sequence of the constricta strain of (CYDV) was determined to be 12 792 nt long and organized into seven ORFs with the gene order 3′-N-X-P-Y-M-G-L-5′, which encodes the nucleocapsid, phospho, movement, matrix, glyco, and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. Cloned ORFs for each gene, except L, were used to construct a protein interaction and localization map (PILM) for this virus, which shares greater than 80 % amino acid similarity in all ORFs except X and P with the sanguinolenta strain of this species (SYDV). Protein localization patterns and interactions unique to each viral strain were identified, resulting in strain-specific PILMs. Localization of CYDV and SYDV proteins in virus-infected cells mapped subcellular loci likely to be sites of replication, morphogenesis and movement.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.000771
2017-06-01
2020-01-26
Loading full text...

Full text loading...

/deliver/fulltext/jgv/98/6/1526.html?itemId=/content/journal/jgv/10.1099/jgv.0.000771&mimeType=html&fmt=ahah

References

  1. Nagy PD. Tombusvirus-host interactions: co-opted evolutionarily conserved host factors take center Court. Annu Rev Virol 2016;3:491–515 [CrossRef][PubMed]
    [Google Scholar]
  2. Min BE, Martin K, Wang R, Tafelmeyer P, Bridges M et al. A host-factor interaction and localization map for a plant-adapted rhabdovirus implicates cytoplasm-tethered transcription activators in cell-to-cell movement. Mol Plant Microbe Interact 2010;23:1420–1432 [CrossRef][PubMed]
    [Google Scholar]
  3. Martínez F, Rodrigo G, Aragonés V, Ruiz M, Lodewijk I et al. Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection. BMC Genomics 2016;17:87 [CrossRef][PubMed]
    [Google Scholar]
  4. Rodrigo G, Daròs JA, Elena SF. Virus-host interactome: putting the accent on how it changes. J Proteomics 2017;156:1–4 [CrossRef][PubMed]
    [Google Scholar]
  5. Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X et al. Viral strain-specific differential alterations in Arabidopsis developmental patterns. Mol Plant Microbe Interact 2015;28:1304–1315 [CrossRef][PubMed]
    [Google Scholar]
  6. Pita JS, Morris V, Roossinck MJ. Mutation and recombination frequencies reveal a biological contrast within strains of Cucumber mosaic virus. J Virol 2015;89:6817–6823 [CrossRef][PubMed]
    [Google Scholar]
  7. Chowda-Reddy RV, Sun H, Hill JH, Poysa V, Wang A. Simultaneous mutations in multi-viral proteins are required for soybean mosaic virus to gain virulence on soybean genotypes carrying different R genes. PLoS One 2011;6:e28342 [CrossRef][PubMed]
    [Google Scholar]
  8. Fargette D, Konaté G, Fauquet C, Muller E, Peterschmitt M et al. Molecular ecology and emergence of tropical plant viruses. Annu Rev Phytopathol 2006;44:235–260 [CrossRef][PubMed]
    [Google Scholar]
  9. Dietzgen RG, Kondo H, Goodin MM, Kurath G, Vasilakis N. The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins. Virus Res 2017;227:158–170 [CrossRef][PubMed]
    [Google Scholar]
  10. Ramalho TO, Figueira AR, Sotero AJ, Wang R, Geraldino Duarte PS et al. Characterization of Coffee ringspot virus-Lavras: a model for an emerging threat to coffee production and quality. Virology 2014;464-465:385–396 [CrossRef][PubMed]
    [Google Scholar]
  11. Martin KM, Dietzgen RG, Wang R, Goodin MM. Lettuce necrotic yellows cytorhabdovirus protein localization and interaction map, and comparison with nucleorhabdoviruses. J Gen Virol 2012;93:906–914 [CrossRef][PubMed]
    [Google Scholar]
  12. Dietzgen RG, Martin KM, Anderson G, Goodin MM. In planta localization and interactions of impatiens necrotic spot Tospovirus proteins. J Gen Virol 2012;93:2490–2495 [CrossRef][PubMed]
    [Google Scholar]
  13. Jackson AO, Dietzgen RG, Goodin MM, Bragg JN, Deng M. Biology of plant rhabdoviruses. Annu Rev Phytopathol 2005;43:623–660 [CrossRef][PubMed]
    [Google Scholar]
  14. Dietzgen RG, Kuhn JH, Clawson AN, Freitas-Astúa J, Goodin MM et al. Dichorhavirus: a proposed new genus for Brevipalpus mite-transmitted, nuclear, bacilliform, bipartite, negative-strand RNA plant viruses. Arch Virol 2014;159:607–619 [CrossRef][PubMed]
    [Google Scholar]
  15. Kormelink R, Garcia ML, Goodin M, Sasaya T, Haenni AL. Negative-strand RNA viruses: the plant-infecting counterparts. Virus Res 2011;162:184–202 [CrossRef][PubMed]
    [Google Scholar]
  16. Dietzgen RG, Callaghan B, Wetzel T, Dale JL. Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus. Virus Res 2006;118:16–22 [CrossRef][PubMed]
    [Google Scholar]
  17. Kondo H, Maeda T, Shirako Y, Tamada T. Orchid fleck virus is a rhabdovirus with an unusual bipartite genome. J Gen Virol 2006;87:2413–2421 [CrossRef][PubMed]
    [Google Scholar]
  18. Bandyopadhyay A, Kopperud K, Anderson G, Martin K, Goodin M. An integrated protein localization and interaction map for Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus. Virology 2010;402:61–71 [CrossRef][PubMed]
    [Google Scholar]
  19. Hsu HT, Black LM. Inoculation of vector cell monolayers with potato yellow dwarf virus. Virology 1973;52:187–198 [CrossRef][PubMed]
    [Google Scholar]
  20. Black LM. Genetic variation in the clover leafhopper's ability to transmit Potato yellow-dwarf virus. Genetics 1943;28:200–209[PubMed]
    [Google Scholar]
  21. Black LM. Strains of Potato yellow-dwarf virus. Am J Bot 1940;27:386–392 [CrossRef]
    [Google Scholar]
  22. Black LM, Smith KM, Hills GJ, Markham R. Ultrastructure of potato yellow-dwarf virus. Virology 1965;27:446–449 [CrossRef][PubMed]
    [Google Scholar]
  23. Macleod R, Black LM, Moyer FH. The fine structure and intracellular localization of potato yellow dwarf virus. Virology 1966;29:540–552 [CrossRef][PubMed]
    [Google Scholar]
  24. Reeder GS, Knudson DL, Macleod R. The ribonucleic acid of potato yellow dwarf virus. Virology 1972;50:301–304 [CrossRef][PubMed]
    [Google Scholar]
  25. Brakke MK, van Pelt N. Linear-log sucrose gradients for estimating sedimentation coefficients of plant viruses and nucleic acids. Anal Biochem 1970;38:56–64 [CrossRef][PubMed]
    [Google Scholar]
  26. Ghosh D, Brooks RE, Wang R, Lesnaw J, Goodin MM. Cloning and subcellular localization of the phosphoprotein and nucleocapsid proteins of Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus. Virus Res 2008;135:26–35 [CrossRef][PubMed]
    [Google Scholar]
  27. Falk BW, Weathers LG. Comparison of potato yellow dwarf virus serotypes. Phytopathology 1983;73:81–85 [CrossRef]
    [Google Scholar]
  28. Pappi PG, Dovas CI, Efthimiou KE, Maliogka VI, Katis NI. A novel strategy for the determination of a rhabdovirus genome and its application to sequencing of Eggplant mottled dwarf virus. Virus Genes 2013;47:105–113 [CrossRef][PubMed]
    [Google Scholar]
  29. Anderson G, Wang R, Bandyopadhyay A, Goodin M. The nucleocapsid protein of Potato Yellow dwarf virus: protein interactions and nuclear import mediated by a non-canonical nuclear localization signal. Front Plant Sci 2012;3:14 [CrossRef][PubMed]
    [Google Scholar]
  30. Goodin MM, Chakrabarty R, Yelton S, Martin K, Clark A et al. 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 [CrossRef][PubMed]
    [Google Scholar]
  31. Kosugi S, Hasebe M, Matsumura N, Takashima H, Miyamoto-Sato E et al. Six classes of nuclear localization signals specific to different binding grooves of importin α. J Biol Chem 2009;284:478–485 [CrossRef][PubMed]
    [Google Scholar]
  32. Boni A, Politi AZ, Strnad P, Xiang W, Hossain MJ et al. Live imaging and modeling of inner nuclear membrane targeting reveals its molecular requirements in mammalian cells. J Cell Biol 2015;209:705–720 [CrossRef][PubMed]
    [Google Scholar]
  33. Pusch S, Dissmeyer N, Schnittger A. Bimolecular-fluorescence complementation assay to monitor kinase-substrate interactions in vivo. Methods Mol Biol 2011;779:245–257 [CrossRef][PubMed]
    [Google Scholar]
  34. Mann KS, Johnson KN, Carroll BJ, Dietzgen RG. Cytorhabdovirus P protein suppresses RISC-mediated cleavage and RNA silencing amplification in planta. Virology 2016;490:27–40 [CrossRef][PubMed]
    [Google Scholar]
  35. Koonin EV, Gorbalenya AE. Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins?. J Mol Evol 1989;28:524–527 [CrossRef][PubMed]
    [Google Scholar]
  36. Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 2008;9:267–276 [CrossRef][PubMed]
    [Google Scholar]
  37. Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF. Temporal dynamics of intrahost molecular evolution for a plant RNA virus. Mol Biol Evol 2015;32:1132–1147 [CrossRef][PubMed]
    [Google Scholar]
  38. Boudreault S, Martenon-Brodeur C, Caron M, Garant JM, Tremblay MP et al. Global profiling of the cellular alternative RNA splicing Landscape during Virus-Host interactions. PLoS One 2016;11:e0161914 [CrossRef][PubMed]
    [Google Scholar]
  39. Scheckel C, Darnell RB. Microexons-tiny but mighty. Embo J 2015;34:273–274 [CrossRef][PubMed]
    [Google Scholar]
  40. Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 2014;159:1511–1523 [CrossRef][PubMed]
    [Google Scholar]
  41. Parrella G, Greco B. Sequence variation of block III segment identifies three distinct lineages within Eggplant mottled dwarf virus isolates from Italy, Spain and Greece. Acta Virol 2016;60:100–105 [CrossRef][PubMed]
    [Google Scholar]
  42. Jackson AO, Li Z. Developments in Plant Negative-Strand RNA virus Reverse Genetics. Annu Rev Phytopathol 2016;54:469–498 [CrossRef][PubMed]
    [Google Scholar]
  43. Wang Q, Ma X, Qian S, Zhou X, Sun K et al. Rescue of a plant negative-strand RNA virus from cloned cDNA: insights into enveloped plant virus movement and morphogenesis. PLoS Pathog 2015;11:e1005223 [CrossRef][PubMed]
    [Google Scholar]
  44. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 2013;8:1494–1512 [CrossRef][PubMed]
    [Google Scholar]
  45. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007;35:D5–D12 [CrossRef][PubMed]
    [Google Scholar]
  46. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003;31:3784–3788 [CrossRef][PubMed]
    [Google Scholar]
  47. Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993;14:1023–1031 [CrossRef][PubMed]
    [Google Scholar]
  48. Nakai K, Kanehisa M. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 1991;11:95–110 [CrossRef][PubMed]
    [Google Scholar]
  49. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: signaIP 3.0. J Mol Biol 2004;340:783–795 [CrossRef][PubMed]
    [Google Scholar]
  50. Blom N, Sicheritz-Pontén 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 [CrossRef][PubMed]
    [Google Scholar]
  51. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008;36:W465–W469 [CrossRef][PubMed]
    [Google Scholar]
  52. Ramalho TO, Figueira AR, Wang R, Jones O, Harris LE et al. Detection and survey of coffee ringspot virus in Brazil. Arch Virol 2016;161:335–343 [CrossRef][PubMed]
    [Google Scholar]
  53. Lamprecht RL, Pietersen G, Kasdorf GGF, Nel LH. Characterisation of a proposed Nucleorhabdovirus new to South Africa. Eur J Plant Pathol 2009;123:105–110 [CrossRef]
    [Google Scholar]
  54. Chakrabarty R, Banerjee R, Chung SM, Farman M, Citovsky V et al. PSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interactions. Mol Plant Microbe Interact 2007;20:740–750 [CrossRef][PubMed]
    [Google Scholar]
  55. Martin K, Kopperud K, Chakrabarty R, Banerjee R, Brooks R et al. Transient expression in Nicotiana benthamiana fluorescent marker lines provides enhanced definition of protein localization, movement and interactions in planta. Plant J 2009;59:150–162 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.000771
Loading
/content/journal/jgv/10.1099/jgv.0.000771
Loading

Data & Media loading...

Most cited articles

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error