Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission

References

1. Anisimova M., Nielsen R., Yang Z. 2003; Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229–1236
   [Google Scholar]
2. Atreya P. L., Atreya C. D., Pirone T. P. 1991; Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proc Natl Acad Sci U S A 88:7887–7891 [CrossRef]
   [Google Scholar]
3. Atreya P. L., Lopez-Moya J.-J., Chu M., Atreya C. D., Pirone T. P. 1995; Mutational analysis of the coat protein N-terminal amino acids involved in potyvirus transmission by aphids. J Gen Virol 76:265–270 [CrossRef]
   [Google Scholar]
4. Bandla M. D., Campbell L. R., Ullman D. E., Sherwood J. L. 1998; Interaction of tomato spotted wilt virus (TSWV) glycoproteins with a thrips midgut protein, a potential cellular receptor for TSWV. Phytopathology 88:98–104 [CrossRef]
   [Google Scholar]
5. Blanc S., Lopez-Moya J.-J., Wang R., Garcia-Lampasona S., Thornbury D. W., Pirone T. P. 1997; A specific interaction between coat protein and helper component correlates with aphid transmission of a Potyvirus . Virology 231:141–147 [CrossRef]
   [Google Scholar]
6. Brault V., van den Heuvel J. F., Verbeek M. 7 other authors 1995; Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74. EMBO J 14:650–659
   [Google Scholar]
7. Brault V., Bergdoll M., Mutterer J., Prasad V., Pfeffer S., Erdinger M., Richards K. E., Ziegler-Graff V. 2003; Effects of point mutations in the major capsid protein of beet western yellows virus on capsid formation, virus accumulation and aphid transmission. J Virol 77:3247–3256 [CrossRef]
   [Google Scholar]
8. Callaway A., Giesman-Cookmeyer D., Gillock E. T., Sit T. L., Lommel S. A. 2001; The multifunctional capsid proteins of plant RNA viruses. Annu Rev Phytopathol 39:419–460 [CrossRef]
   [Google Scholar]
9. Demler S. A., Rucker-Feeney D. G., Skaf J. S., de Zoeten G. A. 1997; Expression and suppression of circulative aphid transmission in pea enation mosaic virus. J Gen Virol 78:511–523
   [Google Scholar]
10. Domingo E., Holland J. J. 1997; RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151–178 [CrossRef]
    [Google Scholar]
11. Eigen M. 1987; New concepts for dealing with the evolution of nucleic acids. Cold Spring Harb Symp Quant Biol 52:307–319 [CrossRef]
    [Google Scholar]
12. Elena S. F. 2002; Restrictions to RNA virus adaptation: an experimental approach. Antonie Van Leeuwenhoek 81:135–142 [CrossRef]
    [Google Scholar]
13. Gal-On A., Antignus Y., Rosner A., Raccah B. 1992; A zucchini yellow mosaic virus coat protein gene mutation restores aphid transmissibility but has no effect on multiplication. J Gen Virol 73:2183–2187 [CrossRef]
    [Google Scholar]
14. García-Arenal F., Fraile A., Malpica J. M. 2001; Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39:157–186 [CrossRef]
    [Google Scholar]
15. Gaunt M. W., Sall A. A., de Lamballerie X., Falconar A. K., Dzhivanian T. I., Gould E. A. 2001; Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography. J Gen Virol 82:1867–1876
    [Google Scholar]
16. Gray S. M., Banerjee N. 1999; Mechanisms of arthropod transmission of plant and animal viruses. Microbiol Mol Biol Rev 63:128–148
    [Google Scholar]
17. Harvey P. H., Pagel M. D. 1993 The Comparative Method in Evolutionary Biology Oxford: Oxford University Press;
    [Google Scholar]
18. Holmes E. C. 2003a; Error thresholds and the constraints to RNA virus evolution. Trends Microbiol 11:543–546 [CrossRef]
    [Google Scholar]
19. Holmes E. C. 2003b; Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol 77:11296–11298 [CrossRef]
    [Google Scholar]
20. Jenkins G. M., Rambaut A., Pybus O. G., Holmes E. C. 2002; Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54:156–165 [CrossRef]
    [Google Scholar]
21. Jones C. T., Ma L., Burgner J. W., Groesch T. D., Post C. B., Kuhn R. J. 2003; Flavivirus capsid is a dimeric alpha-helical protein. J Virol 77:7143–7149 [CrossRef]
    [Google Scholar]
22. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; mega2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245 [CrossRef]
    [Google Scholar]
23. Langevin C., Jaaro H., Bressanelli S., Fainzilber M., Tuffereau C. 2002; Rabies virus glycoprotein (RVG) is a trimeric ligand for the N-terminal cysteine-rich domain of the mammalian p75 neurotrophin receptor. J Biol Chem 277:37655–37662 [CrossRef]
    [Google Scholar]
24. Lazarowitz S. G. 2001; Plant viruses. In Fundamental Virology . , 4th edn. pp  377–442 Edited by Knipe D. M., Howley P. M. Philadelphia: Lippincott, Williams & Wilkins;
25. Liu S., He X., Park G., Josefsson C., Perry K. L. 2002; A conserved capsid protein surface domain of cucumber mosaic virus is essential for efficient aphid vector transmission. J Virol 76:9756–9762 [CrossRef]
    [Google Scholar]
26. Medeiros R. B., Ullman D. E., Sherwood J. L., German T. L. 2000; Immunoprecipitation of a 50-kDa protein: a candidate receptor component for tomato spotted wilt tospovirus ( Bunyaviridae ) in its main vector, Frankliniella occidentalis . Virus Res 67:109–118 [CrossRef]
    [Google Scholar]
27. Moya A., Holmes E. C., González-Candelas F. 2004; The population genetics and evolutionary epidemiology of RNA viruses. Nat Rev Microbiol 2:279–288 [CrossRef]
    [Google Scholar]
28. Novella I. S., Hershey C. L., Escarmis C., Domingo E., Holland J. J. 1999; Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells. J Mol Biol 287:459–465 [CrossRef]
    [Google Scholar]
29. Perry K. L., Zhang L., Shintaku M. H., Palukaitis P. 1994; Mapping determinants in cucumber mosaic virus for transmission by Aphis gossypii . Virology 205:591–595 [CrossRef]
    [Google Scholar]
30. Perry K. L., Zhang L., Palukaitis P. 1998; Amino acid changes in the coat protein of cucumber mosaic virus differentially affect transmission by the aphids Myzus persicae and Aphis gossypii . Virology 242:204–210 [CrossRef]
    [Google Scholar]
31. Posada D. 2002; Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol 19:708–717 [CrossRef]
    [Google Scholar]
32. Power A. G. 2000; Insect transmission of plant viruses: a constraint on virus variability. Curr Opin Plant Biol 3:336–340 [CrossRef]
    [Google Scholar]
33. Power A. G., Flecker A. S. 2003; Virus specificity in disease systems: Are species redundant?. In The Importance of Species pp  330–346 Edited by Levin S. A., Kareiva P. Princeton: Princeton University Press;
    [Google Scholar]
34. Sanz M. A., Rejas M. T., Carrasco L. 2003; Individual expression of sindbis virus glycoproteins. E1 alone promotes cell fusion. Virology 305:463–472 [CrossRef]
    [Google Scholar]
35. Sawyer S. 1989; Statistical tests for detecting gene conversion. Mol Biol Evol 6:526–538
    [Google Scholar]
36. Scott T. W., Weaver S. C., Mallampalli V. L. 1994; Evolution of mosquito-borne viruses. In Evolutionary Biology of Viruses pp  293–324 Edited by Morse S. S. NY: Raven Press;
    [Google Scholar]
37. Shintaku M. H., Zhang L., Palukaitis P. 1992; A single amino acid substitution in the coat protein of cucumber mosaic virus induces chlorosis in tobacco. Plant Cell 4:751–757 [CrossRef]
    [Google Scholar]
38. Swofford D. L. 2002; paup*. Phylogenetics Analysis Using Parsimony (*and other methods). Version 4: Sunderland, MA: Sinauer Associates;
    [Google Scholar]
39. Syller J. 2002; Umbraviruses – the unique plant viruses that do not encode a capsid protein. Acta Microbiol Pol 51:99–113
    [Google Scholar]
40. Tamada T., Schmitt C., Saito M., Guilley H., Richards K., Jonard G. 1996; High resolution analysis of the readthrough domain of beet necrotic yellow vein virus readthrough protein: a KTER motif is important for efficient transmission of the virus by Polymyxa betae . J Gen Virol 77:1359–1367 [CrossRef]
    [Google Scholar]
41. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
    [Google Scholar]
42. Turner P. E., Elena S. F. 2000; Cost of host radiation in an RNA virus. Genetics 156:1465–1470
    [Google Scholar]
43. Weaver S. C., Brault A. C., Kang W., Holland J. J. 1999; Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cells. J Virol 73:4316–4326
    [Google Scholar]
44. Woelk C. H., Holmes E. C. 2002; Reduced positive selection in vector-borne RNA viruses. Mol Biol Evol 19:2333–2336 [CrossRef]
    [Google Scholar]
45. Yang Z. 1997; paml: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556
    [Google Scholar]
46. Yang Z., Nielsen R., Goldman N., Pedersen A.-M. K. 2000; Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449
    [Google Scholar]