The rate and spectrum of spontaneous mutations in a plant RNA virus

Genetics

Volumn 185, Issue 3, 2010, Pages 983-989

  Tromas, Nicolas ^a   Elena, Santiago F ^a,b  

^a Ciudad Politécnica de la Innovación   (Spain)

^b SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA; RNA DIRECTED RNA POLYMERASE; VIRUS RNA;

ANIMAL EXPERIMENT; ARTICLE; CODON; CONTROLLED STUDY; GENE DELETION; GENETIC SELECTION; NONHUMAN; PLANT VIRUS; POTYVIRUS; PRIORITY JOURNAL; RNA VIRUS; SITE DIRECTED MUTAGENESIS; SPONTANEOUS MUTATION; TOBACCO ETCH POTYVIRUS; TRANSGENE; VIRUS LOAD; VIRUS REPLICATION; VIRUS STRAIN; GENETICS; MUTATION; POLYMERASE CHAIN REACTION; TOBACCO; VIROLOGY; VIRUS GENOME;

ANIMALIA; RNA VIRUSES; TOBACCO ETCH VIRUS;

GENOME, VIRAL; MUTATION; POLYMERASE CHAIN REACTION; POTYVIRUS; RNA, VIRAL; TOBACCO;

EID: 77956850103     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.115915     Document Type: Article

References (40)

1. AGRESTI, A., and B. A. COULL, 1998 Approximate is better than "exact" for interval estimation of binomial proportions. Am. Stat. 52: 119-126.
2. ALI, A., H. LI, W. L. SCHNEIDER, D. J. SHERMAN, S. GRAY et al., 2006 Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus. J. Virol. 80: 8345-8350.
3. AREZI, B., and H. H. HOGREFE, 2007 Escherichia coli DNA polymerase III epsilon subunit increases Moloney murine leukemia virus reverse transcriptase fidelity and accuracy of RT-PCR procedures. Anal. Biochem. 360: 84-91.
4. BEACHY, R. N., and M. HEINLEIN, 2000 Role of P30 in replication and spread of TMV. Traffic 1: 540-544.
5. BETANCOURT, M., A. FERERES, A. FRAILE and F. GARCÍA-ARENAL, 2008 Estimation of the effective number of founders that initiate an infection after aphid transmission of a multipartite plant virus. J. Virol. 82: 12416-12421.
6. BONHOEFFER, S., C. CHAPPEY, N. T. PARKIN, J. M. WHITCOMB and C. J. PETROPOULOS, 2004 Evidence for positive epistasis in HIV-1. Science 306: 1547-1550.
7. BRACHO, M. A., A. MOYA and E. BARRIO, 1998 Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J. Gen. Virol. 79: 2921-2928.
8. CAMPBELL, C. L., and L. V. MADDEN, 1990 Introduction to Plant Disease Epidemiology. John Wiley & Sons, New York.
9. CARRASCO, P., J. A. DARÒS, P. AGUDELO-ROMERO and S. F. ELENA, 2007 A real-time RT-PCR assay for quantifying the fitness of Tobacco etch virus in competition experiments. J. Virol. Meth. 139: 181-188.
10. CHAO, L., C. U. RANG and L. E. WONG, 2002 Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage φ6. J. Virol. 76: 3276-3281.
11. CLINE, J., J. C. BRAMAN and H. H. HOGREFE, 1996 PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 24: 3546-3551.
12. CLUNE, J., D. MISEVIC, C. OFRIA, R. E. LENSKI, S. F. ELENA et al., 2008 Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Comp. Biol. 4: e1000187.
13. CROW, J. F., and M. KIMURA, 1970 An Introduction to Population Genetics Theory. Harper & Row, New York.
14. CUEVAS, J. M., F. GONZÁLEZ-CANDELAS, A. MOYA and R. SANJUÁN, 2009 Effect of ribavirin on the mutation rate and spectrum of Hepatitis C virus in vivo. J. Virol. 83: 5760-5764.
15. DOLJA, V. V., H. J. MCBRIDE, J. C. CARRINGTON, 1992 Tagging of plant potyvirus replication and movement by insertion of beta-glucuronidase into the viral polyprotein. Proc. Natl. Acad. Sci. USA 89: 10208-10212.
16. DRAKE, J. W., and J. J. HOLLAND, 1999 Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. USA 96: 13910-13913.
17. DRAKE, J. W., B. CHARLESWORTH, D. CHARLESWORTH and J. F. CROW, 1998 Rates of spontaneous mutation. Genetics 148: 1667-1686.
18. ELENA, S. F., and R. SANJUÁN, 2005 Adaptive value of high mutation rates of RNA viruses: separating causes from consequences. J. Virol. 79: 11555-11558.
19. FARGETTE, D., A. PINEL, M. RAKOTOMALALA, E. SANGU, O. TRAORÉ et al., 2008 Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses. J. Virol. 82: 3584-3589.
20. FRAILE, A., F. ESCRIU, M. A. ARANDA, J. M. MALPICA, A. J. GIBBS et al., 1997 A century of tobamovirus evolution in an Australian population of Nicotiana glauca. J. Virol. 71: 8316-8320.
21. FRENCH, R., and D. C. STENGER, 2003 Evolution of Wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation. Annu. Rev. Phytopathol. 41: 199-214.
22. GARCÍA-ARENAL, F., A. FRAILE, and J. M. MALPICA, 2001 Variability and genetic structure of plant virus populations. Annu. Rev. Phytopathol. 39: 157-186.
23. GIBBS, A. J., K. OHSHIMA, M. J. PHILLIPS and M. J. GIBBS, 2008 The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One 3: e2523.
24. HALL, J. S., R. FRENCH, G. L. HEIN, J. MORRIS and D. C. STENGER, 2001 Three distinct mechanisms facilitate genetic isolation of sympatric Wheat streak mosaic virus lineages. Virology 282: 230-236.
25. HERRÁNZ, M. C., M. AL RWAHNIH, J. A. SÁNCHEZ-NAVARRO, S. F. ELENA, E. CHOUEIRI et al., 2008 Low genetic variability in the coat and movement proteins of American plum line pattern virus isolates from different geographic origins. Arch. Virol. 153: 367-373.
26. KAMP, C., C. O. WILKE, C. ADAMI and S. BORNHOLDT, 2003 Viral evolution under the pressure of an adaptive immune system: optimal mutation rates for viral escape. Complexity 8: 28-33.
27. LI, H., and M. J. ROOSSINCK, 2004 Genetic bottlenecks reduce population variation in an experimental RNA virus population. J. Virol. 78: 10582-10587.
28. LI, X. H., and J. C. CARRINGTON, 1995 Complementation of Tobacco etch potyvirus mutants by active RNA polymerase expressed in transgenic cells. Proc. Natl. Acad. Sci. USA 92: 457-461.
29. MALPICA, J. M., A. FRAILE, A., I. MORENO, C. I. OBIES, J. W. DRAKE, et al., 2002 The rate and character of spontaneous mutation in an RNA virus. Genetics 162: 1505-1511.
30. MARCO, C. F., and M. A. ARANDA, 2005 Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus. J. Gen. Virol. 86: 815-822.
31. MOURY, B., F. FABRE and R. SENOUSSI, 2007 Estimation of the number of virus particles transmitted by an insect vector. Proc. Natl. Acad. Sci. USA 104: 17891-17896.
32. PUGACHEV, K. V., F. GUIRAKHOO, S. W. OCRAN, F. MITCHELL, M. PARSONS et al., 2004 High fidelity of Yellow fever virus RNA polymerase. J. Virol. 78: 1032-1038.
33. RODRÍGUEZ-CEREZO, E., S. F. ELENA, A. MOYA and F. GARCÍA-ARENAL, 1991 High genetic stability in natural populations of the plant RNA virus Tobacco mild green mosaic virus. J. Mol. Evol. 32: 328-332.
34. SACRISTÁN, S., J. M. MALPICA, A. FRAILE and F. GARCÍA-ARENAL, 2003 Estimation of population bottleneck during systemic movement of Tobacco mosaic virus in tobacco plants. J. Virol. 77: 9906-9911.
35. SANJUÁN, R., A. MOYA and S. F. ELENA, 2004 The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. USA 101: 8396-8401.
36. SANJUÁN, R., P. AGUDELO-ROMERO and S. F. ELENA, 2009 Upper limit mutation rate estimation for a plant RNA virus. Biol. Lett. 5: 394-396.
37. SARDANYÉS, J., R. V. SOLÉ and S. F. ELENA, 2009 Replication mode and landscape topology differentially affect RNA virus mutational load and robustness. J. Virol. 83: 12579-12589.
38. STEINHAUER, D. A., E. DOMINGO and J. J. HOLLAND, 1992 Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 122: 281-288.
39. TAMURA, K., J. DUDLEY, M. NEI and S. KUMAR, 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
40. URCUQUI-INCHIMA, S., A. L. HAENNI and F. BERNARDI, 2001 Potyvirus proteins: a wealth of functions. Virus Res. 74: 157-175.