Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Hillung, Julia ^a   Elena, Santiago F ^a,b   Cuevas, José M ^a,c  

^a CSIC   (Spain)

^b SANTA FE INSTITUTE   (United States)

^c UNIVERSITY OF VALENCIA   (Spain)

Author keywords

Bayesian phylogenetic methods; Host range determinants; Molecular evolution; Potyvirus; Virus evolution; Virus fitness components

Indexed keywords

ALLELE; EVOLUTIONARY BIOLOGY; EXPERIMENTAL STUDY; GENOME; HOST SPECIFICITY; INTRASPECIFIC VARIATION; PHENOTYPE; PROTEIN; SPECIES DIVERSITY; VIRUS;

BRASSICA RAPA SUBSP. RAPA; POTATO VIRUS Y; POTYVIRIDAE; POTYVIRUS; TURNIP MOSAIC VIRUS;

VIRUS PROTEIN;

ARABIDOPSIS; ARTICLE; BRASSICA RAPA; GENE; GENETICS; HOST PATHOGEN INTERACTION; METABOLISM; MOLECULAR EVOLUTION; PHYSIOLOGY; POTYVIRUS; REPRODUCTIVE FITNESS; STOP CODON; TOBACCO; VIROLOGY;

ARABIDOPSIS; BRASSICA RAPA; CODON, TERMINATOR; EVOLUTION, MOLECULAR; GENES; GENETIC FITNESS; HOST-PATHOGEN INTERACTIONS; POTYVIRUS; TOBACCO; VIRAL PROTEINS;

EID: 84887374361     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-249     Document Type: Article

References (44)

1. Highlights and prospects of potyvirus molecular biology. Riechmann JL, Lain S, García JA, J Gen Virol 1992 73 1 16 10.1099/0022-1317-73-1-1 1730931
2. Taxonomy of potyviruses: current problems and some solutions. Ward CW, Shukla DD, Intervirology 1991 32 269 296 1657820
3. Alternative translation initiation site in the DA strain of Theiler's murine encephalomyelitis virus. Kong WP, Roos RP, J Virol 1991 65 3395 3399 2033677
4. Taxonomy of the caliciviruses. Green KY, Ando T, Balayan MS, Berke T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Studdert MJ, et al. J Infect Dis 2000 181 322 S330 10.1086/315591 10804145 (Pubitemid 30395087)
5. Nucleotide sequence and genomic organization of Acyrthosiphon pisum virus. van der Wilk F, Dullemans AM, Verbeek M, van den Heuvel JF, Virology 1997 238 353 362 10.1006/viro.1997.8835 9400608 (Pubitemid 28218153)
6. Potyvirus proteins: a wealth of functions. Urcuqui-Inchima S, Haenni AL, Bernardi F, Virus Res 2001 74 157 175 10.1016/S0168-1702(01)00220-9 11226583 (Pubitemid 32168202)
7. An overlapping essential gene in the Potyviridae. Chung BY, Miller WA, Atkins JF, Firth AE, Proc Natl Acad Sci U S A 2008 105 5897 5902 10.1073/pnas.0800468105 18408156 (Pubitemid 351758469)
8. Formation of complexes at plasmodesmata for potyvirus intercellular movement is mediated by the viral protein P3N-PIPO. Wei T, Zhang C, Hong J, Xiong R, Kasschau KD, Zhou X, Carrington JC, Wang A, PLoS Pathog 2010 6 1000962 10.1371/journal.ppat.1000962 20585568
9. Mutational analysis of the putative PIPO of Soybean mosaic virus suggests disruption of PIPO protein impedes movement. Wen RH, Hajimorad MR, Virology 2010 400 1 7 10.1016/j.virol.2010.01.022 20170935
10. Interaction of the trans-frame Potyvirus protein P3N-PIPO with host protein PCaP1 facilitates potyvirus movement. Vijayapalani P, Maeshima M, Nagasaki-Takekuchi N, Miller WA, PLoS Pathog 2012 8 1002639 10.1371/journal. ppat.1002639 22511869
11. Interaction between potyvirus P3 and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) of host plants. Lin L, Luo Z, Yan F, Lu Y, Zheng H, Chen J, Virus Genes 2011 43 90 92 10.1007/s11262-011-0596-6 21400205
12. Quantitative and qualitative involvement of P3N-PIPO in overcoming recessive resistance against Clover yellow vein virus in pea carrying the cyv1 gene. Choi SH, Hagiwara-Komoda Y, Nakahara KS, Atsumi G, Shimada R, Hisa Y, Naito S, Uyeda I, J Virol 2013 87 7326 7337 10.1128/JVI.00065-13 23616656
13. Phylogeography and molecular evolution of Potato virus Y. Cuevas JM, Delaunay A, Visser JC, Bellstedt DU, Jacquot E, Elena SF, PLoS ONE 2012 7 37853 10.1371/journal.pone.0037853 22655074
14. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
15. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
16. RDP3: a flexible and fast computer program for analyzing recombination. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P, Bioinformatics 2010 26 2462 2463 10.1093/bioinformatics/btq467 20798170
17. Genetically engineered resistance to Plum pox virus infection in herbaceous and stone fruit hosts. Ilardi V, Nicola-Negri ED, GM Crops 2011 2 24 33 10.4161/gmcr.2.1.15096 21844696
18. Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers. Schubert J, Fomitcheva V, Sztangret-Wisniewska J, J Virol Methods 2007 140 66 74 10.1016/j.jviromet.2006.10.017 17182113 (Pubitemid 46201706)
19. Patterns of recombination in Turnip mosaic virus genomic sequences indicate hotspots of recombination. Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ, J Gen Virol 2007 88 298 315 10.1099/vir.0.82335-0 17170463 (Pubitemid 46085141)
20. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ, PLoS Comput Biol 2006 2 62 10.1371/journal.pcbi.0020062 16789820 (Pubitemid 43990669)
21. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Kosakovsky Pond SL, Frost SD, Mol Biol Evol 2005 22 1208 1222 10.1093/molbev/msi105 15703242 (Pubitemid 40577758)
22. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Delport W, Poon AF, Kosakovsky, Pond SL, Bioinformatics 2010 26 2455 2457 10.1093/bioinformatics/btq429 20671151
23. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
24. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Parker J, Rambaut A, Pybus OG, Infect Genet Evol 2008 8 239 246 10.1016/j.meegid.2007.08.001 17921073 (Pubitemid 351597657)
25. A cladistic measure of gene flow inferred from the phylogenies of alleles. Slatkin M, Maddison WP, Genetics 1989 123 603 613 2599370 (Pubitemid 19274683)
26. Identification of shared populations of Human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system. Wang TH, Donaldson YK, Brettle RP, Bell JE, Simmonds P, J Virol 2001 75 11686 11699 10.1128/JVI.75.23.11686-11699.2001 11689650 (Pubitemid 33063260)
27. Identification of Turnip mosaic virus isolates causing yellow stripe and spot on calla lily. Chen CC, Chao CH, Chen CC, Yeh SD, Tsai HT, Chang CA, Plant Dis 2003 87 901 905 10.1094/PDIS.2003.87.8.901 (Pubitemid 36953116)
28. Dynamics of the establishment of systemic Potyvirus infection: independent yet cumulative action of primary infection sites. Lafforgue G, Tromas N, Elena SF, Zwart MP, J Virol 2012 86 12912 12922 10.1128/JVI.02207-12 22993154
29. The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ, PLoS ONE 2008 3 2523 10.1371/journal.pone.0002523 18575612
30. Sequence variability, recombination analysis, and specific detection of the W strain of Plum pox virus. Glasa M, Malinowski T, Predajna L, Pupola N, Dekena D, Michalczuk L, Candresse T, Phytopathology 2011 101 980 985 10.1094/PHYTO-12-10-0334 21425932
31. Phylogenies and the comparative method. Felsenstein J, Am Nat 1985 125 1 15 10.1086/284325 (Pubitemid 16276188)
32. One is enough: In vivo effective population size is dose-dependent for a plant RNA virus. Zwart MP, Daròs JA, Elena SF, PLoS Pathog 2011 7 1002122 10.1371/journal.ppat.1002122 21750676
33. Effect of potyvirus effective population size in inoculated leaves on viral accumulation and the onset of symptoms. Zwart MP, Daròs JA, Elena SF, J Virol 2012 86 9737 9747 10.1128/JVI.00909-12 22740417
34. Virus adaptation by manipulation of host's gene expression. Agudelo-Romero P, Carbonell P, Pérez-Amador MA, Elena SF, PLoS ONE 2008 3 2397 10.1371/journal.pone.0002397 18545680
35. The dual role of the potyvirus P3 protein of Turnip mosaic virus as a symptom and avirulence determinant in brassicas. Jenner CE, Wang X, Tomimura K, Ohshima K, Ponz F, Walsh JA, Mol Plant Microbe Interact 2003 16 777 784 10.1094/MPMI.2003.16.9.777 12971601 (Pubitemid 37065314)
36. An important determinant of the ability of Turnip mosaic virus to infect Brassica spp. and/or Raphanus sativus is in its P3 protein. Suehiro N, Natsuaki T, Watanabe T, Okuda S, J Gen Virol 2004 85 2087 2098 10.1099/vir.0.79825-0 15218194 (Pubitemid 39023288)
37. The P3 protein of Turnip mosaic virus can alone induce hypersensitive response-like cell death in Arabidopsis thaliana carrying TuNI. Kim BM, Suehiro N, Natsuaki T, Inukai T, Masuta C, Mol Plant Microbe Interact 2010 23 144 152 10.1094/MPMI-23-2-0144 20064058
38. Multiple determinants in the coding region of Pea seed-borne mosaic virus P3 are involved in virulence against sbm-2 resistance. Hjulsager CK, Olsen BS, Jensen DM, Cordea MI, Krath BN, Johansen IE, Lund OS, Virology 2006 355 52 61 10.1016/j.virol.2006.07.016 16908044 (Pubitemid 44585056)
39. Increase in Zucchini yellow mosaic virus symptom severity in tolerant zucchini cultivars is related to a point mutation in P3 protein and is associated with a loss of relative fitness on susceptible plants. Desbiez C, Gal-On A, Girard M, Wipf-Scheibel C, Lecoq H, Phytopathology 2003 93 1478 1484 10.1094/PHYTO.2003.93.12.1478 18943611 (Pubitemid 37481663)
40. Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Slovakia and Czech Republic. Glasa M, Svoboda J, Novakova S, Virus Genes 2007 35 415 421 10.1007/s11262-007-0101-4 17497214 (Pubitemid 47087555)
41. Gain of virulence on Rsv1-genotype soybean by an avirulent Soybean mosaic virus requires concurrent mutations in both P3 and HC-Pro. Eggenberger AL, Hajimorad MR, Hill JH, Mol Plant Microbe Interact 2008 21 931 936 10.1094/MPMI-21-7-0931 18533833 (Pubitemid 352008685)
42. Amino acid changes in P3, and not the overlapping PIPO-encoded protein, determine virulence of Soybean mosaic virus on functionally immune Rsv1-genotype soybean. Wen RH, Maroof MA, Hajimorad MR, Mol Plant Pathol 2011 12 799 807 10.1111/j.1364-3703.2011.00714.x 21726381
43. Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. Tan Z, Gibbs AJ, Tomitaka Y, Sánchez F, Ponz F, Ohshima K, J Gen Virol 2005 86 501 510 10.1099/vir.0.80540-0 15659771 (Pubitemid 40227963)
44. An internal RNA element in the P3 cistron of Wheat streak mosaic virus revealed by synonymous mutations that affect both movement and replication. Choi IR, Horken KM, Stenger DC, French R, J Gen Virol 2005 86 2605 2614 10.1099/vir.0.81081-0 16099920 (Pubitemid 41167609)