Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation

PLoS Computational Biology

Volumn 8, Issue 8, 2012, Pages

  Wylie, C Scott ^a,b   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; GENOME; MUTAGENESIS; POPULATION STATISTICS; PROTEINS; STOCHASTIC SYSTEMS;

COEFFICIENTS OF VARIATIONS; FINITE POPULATION; GENETIC DRIFTS; GENOMICS; HIGH MUTATION RATE; INFINITE POPULATION SIZES; LETHAL MUTAGENESIS; MUTATION RATES; STOCHASTIC POPULATION; THEORETICAL MODELING;

VIRUSES;

ARTICLE; BIOPHYSICS; GENETIC DRIFT; GENETIC EPISTASIS; LETHAL ISOLATION; MUTAGENESIS; MUTATION; MUTATION RATE; PHASE TRANSITION; POPULATION GENETICS; POPULATION SIZE; PROTEIN FOLDING; SIMULATION; SPECIES EXTINCTION; SURVIVAL; VIRUS;

EID: 84866126396     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002609     Document Type: Article

References (56)

1. Loeb LA, Essigmann JM, Kazazi F, Zhang J, Rose KD, et al. (1999) Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc Natl Acad Sci U S A 96: 1492-1497.
2. Wilke CO, Bull JJ, Sanjuan R, (2007) Theory of lethal mutagenesis for viruses. J Virol 81: 2930-2939.
3. Zeldovich KB, Chen P, Shakhnovich EI, (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A 104: 16152.
4. Wilke CO, Bull JJ, (2008) Lethal Mutagenesis of Bacteria. Genetics 180: 1061-1070.
5. Chen P, Shakhnovich EI, (2009) Lethal mutagenesis in viruses and bacteria. Genetics 183: 639-650.
6. O'dea EB, Keller TE, Wilke CO, (2010) Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations? PLoS Comput Biol 6: e1000811.
7. Martin G, Gandon S, (2010) Lethal mutagenesis and evolutionary epidemiology. Philos Trans R Soc B Biol Sci 365: 1953-1963.
8. Domingo E, Sierra S, Davila M, Lowenstein PR, (2000) Response of foot-and-mouth disease virus to increased mutagenesis: Influence of viral load and fitness in loss of infectivity. J Virol 74: 8316-8323.
9. Domingo E, Pariente N, Sierra S, Lowenstein PR, (2001) Efficient virus extinction by combinations of a mutagen and antiviral inhibitors. J Virol 75: 9723-9730.
10. Lowenstein PR, Grande-Perez A, Sierra S, Castro MG, Domingo E, (2002) Molecular indetermination in the transition to error catastrophe: Systematic elimination of lymphocytic choriomeningitis virus through mutagenesis does not correlate linearly with large increases in mutant spectrum complexity. Proc Natl Acad Sci U S A 99: 12938-12943.
11. Anderson JP, Daifuku R, Loeb LA, (2004) Viral error catastrophe by mutagenic nucleosides. Annu Rev Microbiol 58: 183-205.
12. Freistadt MS, Meades GD, Cameron CE, (2004) Lethal mutagens: broad-spectrum antivirals with limited potential for development of resistance? Drug Resist Updat 7: 19-24.
13. Cameron CE, Graci JD, Harki DA, Korneeva VS, Edathil JP, et al. (2007) Lethal mutagenesis of poliovirus mediated by a mutagenic pyrimidine analogue. J Virol 81: 11256-11266.
14. Cameron CE, Graci JD, Too K, Smidansky ED, Edathil JP, et al. (2008) Lethal mutagenesis of picornaviruses with n-6-modified purine nucleoside analogues. Antimicrob Agents Chemother 52: 971-979.
15. Lynch M, (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 104: 8597-8604.
16. Kimura M (1985) The neutral theory of molecular evolution. Cambridge University Press.
17. Felsenstein J, (1974) The evolutionary advantage of recombination. Genetics 78: 737-756.
18. Haigh J, (1978) The accumulation of deleterious genes in a population-Muller's Ratchet. Theor Popul Biol 14: 251-267.
19. Lynch M, Gabriel W, (1990) Mutation load and the survival of small populations. Evolution 44: 1725-1737.
20. Lynch M, Burger R, Butcher D, Gabriel W, (1993) The mutational meltdown in asexual populations. J Hered 84: 339-44.
21. Lande R, (1994) Risk of Population Extinction from Fixation of New Deleterious Mutations. Evolution 48: 1460-1469.
22. Schultz ST, Lynch M, (1997) Mutation and extinction: the role of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution pp. 1363-1371.
23. Whitlock MC, (2000) Fixation of new alleles and the extinction of small populations: Drift load, beneficial alleles, and sexual selection. Evolution 54: 1855-1861.
24. Gordo I, Charlesworth B, (2000) The degeneration of asexual haploid populations and the speed of Muller's ratchet. Genetics 154: 1379-1387.
25. Halligan DL, Keightley PD, (2009) Spontaneous mutation accumulation studies in evolutionary genetics. Annu Rev Ecol Evol Syst 40: 151-172.
26. Tannenbaum E, Deeds EJ, Shakhnovich EI, (2004) Semiconservative replication in the quasispecies model. Phys Rev E Stat Nonlin Soft Matter Phys 69: 061916.
27. Wylie CS, Shakhnovich EI, (2011) A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci U S A 108: 9916-9921.
28. Ewens WJ (2004) Mathematical Population Genetics. Springer.
29. Grande-Perez A, Lazaro E, Lowenstein P, Domingo E, Manrubia SC, (2005) Suppression of viral infectivity through lethal defection. Proc Natl Acad Sci U S A 102: 4448-4452.
30. Elena SF, Carrasco P, Daros JA, Sanjuan R, (2006) Mechanisms of genetic robustness in RNA viruses. EMBO Rep 7: 168-173.
31. Perelson AS, (2002) Modelling viral and immune system dynamics. Nat Rev Immunol 2: 28-36.
32. Drake JW, Charlesworth B, Charlesworth D, Crow JF, (1998) Rates of spontaneous mutation. Genetics 148: 1667-1686.
33. Sanjuan R, Nebot MR, Chirico N, Mansky LM, Belshaw R, (2010) Viral mutation rates. J Virol 84: 9733-9748.
34. Gabriel W, Lynch M, Burger R, (1993) Mullers Ratchet and Mutational Meltdowns. Evolution 47: 1744-1757.
35. Markowitz M, Louie M, Hurley A, Sun E, Di Mascio M, (2003) A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-Cell decay in vivo. J Virol 77: 5037-5038.
36. Charlesworth B, (2009) Fundamental Concepts in Genetics: Effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10: 195-205.
37. Crow JFaK M (1970) An introduction to population genetics theory. Harper and Row Publishers.
38. Poon A, Otto SP (2000) Compensating for our load of mutations: freezing the meltdown of small populations. Evolution: 1467-1479.
39. Hill W, Robertson A, (1966) The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
40. Wang Z, Zhang J, (2011) Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci U S A 108: E67-76.
41. Kondrashov A, (1994) Muller's ratchet under epistatic selection. Genetics 136: 1469.
42. Eigen M, (1971) Self organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
43. Nowak M, Schuster P, (1989) Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet. J Theor Biol 137: 375-395.
44. Crotty S, Cameron CE, Andino R, (2001) RNA virus error catastrophe: direct molecular test by using ribavirin. Proc Natl Acad Sci U S A 98: 6895-6900.
45. Crotty S, Andino R, (2002) Implications of high RNA virus mutation rates: lethal mutagenesis and the antiviral drug ribavirin. Microbes Infect 4: 1301-1307.
46. Crotty S, Maag D, Arnold JJ, Zhong W, Lau JY, et al. (2000) The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen. Nat Med 6: 1375-1379.
47. Severson WE, Schmaljohn CS, Javadian A, Jonsson CB, (2003) Ribavirin causes error catastrophe during Hantaan virus replication. J Virol 77: 481-488.
48. Fares MA, Ruiz-González MX, Moya A, Elena SF, Barrio E, (2002) Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417: 398.
49. Maisnier-Patin S, Roth JR, Fredriksson A, Nystrom T, Berg OG, et al. (2005) Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet 37: 1376-1379.
50. Fernandez A, Lynch M, (2011) Non-adaptive origins of interactome complexity. Nature 474: 502-505.
51. van Ham RCHJ, Kamerbeek J, Palacios C, Rausell C, Abascal F, et al. (2003) Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A 100: 581-586.
52. Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN, Tawfik DS, (2009) Do viral proteins possess unique biophysical features? Trends Biochem Sci 34: 53-59.
53. Privalov P, (1979) Stability of proteins: small globular proteins. Adv Protein Chem 33: 167.
54. Serrano L, Day AG, Fersht AR, (1993) A Procedure for Engineering Increased Stability of Proteins and an Experimental Analysis of the Evolution of Protein Stability. J Mol Biol 233: 305-312.
55. Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS, (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369: 1318-1332.
56. Kumar M, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, et al. (2006) ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res 34: 204-206.