Variable epistatic effects between mutations at host recognition sites in φX174 bacteriophage

Evolution

Volumn 61, Issue 7, 2007, Pages 1710-1724

  Pepin, Kim M ^a,b   Wichman, Holly A ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b NEW MEXICO STATE UNIVERSITY   (United States)

Author keywords

X174; Epistasis; Fitness; Mutation; Reaction norm

Indexed keywords

BACTERIOPHAGE; EPISTASIS; EVOLUTION; FITNESS; MUTATION; RECOGNITION;

ARTICLE; BACTERIOPHAGE PHI X 174; GENETIC EPISTASIS; GENETICS; MUTATION; VIRUS GENE;

BACTERIOPHAGE PHI X 174; EPISTASIS, GENETIC; GENES, VIRAL; MUTATION;

EID: 34347332282     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2007.00143.x     Document Type: Article

References (70)

1. Barton, N. H., and B. Charlesworth. 1998. Why sex and recombination? Science 281 : 1986 1990.
2. Bohannan, B. J. M., M. Travisano, and R. E. Lenski. 1999. Epistatic interactions can lower the cost of resistance to multiple consumers. Evolution 53 : 292 295.
3. 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.
4. Bull, J. J., M. R. Badgett, H. A. Wichman, J. P. Huelsenbeck, D. M. Hillis, A. Gulati, C. Ho, and I. J. Molineux. 1997. Exceptional convergent evolution in a virus. Genetics 147 : 1497 1507.
5. Bull, J. J., M. R. Badgett, and H. A. Wichman. 2000. Big-benefit mutations in a bacteriophage inhibited with heat. Mol. Biol. Evol. 17 : 942 950.
6. Burch, C. L., and L. Chao. 2004. Epistasis and its relationship to canalization in the RNA virus f6. Genetics 167 : 559 567.
7. Burch, C. L., P. E. Turner, and K. A. Hanley. 2003. Patterns of epistasis in RNA viruses: a review of the evidence from vaccine design. J. Evol. Biol. 16 : 1223 1235.
8. Butcher, D. 1995. Muller's ratchet, epistasis and mutation effects. Genetics 141 : 431 437.
9. Charlesworth, D., M. T. Morgan, and B. Charlesworth. 1993. Mutation accumulation in finite outbreeding and inbreeding populations. Genet. Res. 61 : 39 56.
10. Clark, A. G., and L. Wang. 1997. Epistasis in measured genotypes: Drosophila P-element insertions. Genetics 147 : 157 163.
11. Crill, W. D., H. A. Wichman, and J. J. Bull. 2000. Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154 : 27 37.
12. Crow, J. F. 1993. Mutation, mean fitness, and genetic load. Oxf. Surv. Evol. Biol. 9 : 3 42.
13. de Visser, J. A. G. M., R. F. Hoekstra, and H. van den Ende. 1997. Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51 : 1499 1505.
14. Dias, P. C. 1996. Sources and sinks in population biology. Trends Ecol. Evol. 11 : 326 330.
15. Elena, S. F. 1999. Little evidence for synergism among deleterious mutations in a nonsegmented RNA virus. J. Mol. Evol. 49 : 703 707.
16. Elena, S. F., and R. E. Lenski. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390 : 395 8.
17. Elena, S. F., and R. E. Lenski. 2001. Epistasis between new mutations and genetic background and a test of genetic canalization. Evolution 55 : 1746 1752.
18. Fisher, R. A. 1958. The genetical theory of natural selection. Dover Publications, New York.
19. Gamian, A., and E. Romanowska. 1982. The core structure of Shigella sonnei lipopolysaccharide and the linkage between O-specific polysaccharide and the core region. Eur. J. Biochem. 129 : 105 109.
20. Gavrilets, S. 2004. Fitness landscapes and the origin of species. Princeton Univ. Press, Princeton, NJ.
21. Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38 : 1116 1129.
22. Hanley, K. A., L. R. Manlucu, L. E. Gilmore, J. E. Blaney, Jr., C. T. Hanson, B. R. Murphy, and S. S. Whitehead. 2003. A trade-off in replication in mosquito versus mammalian systems conferred by a point mutation in the NS4B protein of dengue virus type 4. Virology 312 : 222 232.
23. Hayashi, M., A. Aoyama, D. L. Richardson, Jr., and M. N. Hayashi. 1988. Biology of the bacteriophage φX174. Pp. 1 71 in R. Calendar, ed. The bacteriophages. Plenum Press, New York.
24. Heinrichs, D. E., M. A. Monteiro, M. B. Perry, and C. Whitfield. 1998. The assembly system for the lipopolysaccharide R2 core-type of Escherichia coli is a hybrid of those found in Escherichia coli K-12 and Salmonella enterica. Structure and function of the R2 WaaK and WaaL homologs. J. Biol. Chem. 273 : 8849 8859.
25. Holder, K. K., and J. J. Bull. 2001. Profiles of adaptation in two similar viruses. Genetics 159 : 1393 1404.
26. Holmes, E. C., and A. Rambaut. 2004. Viral evolution and the emergence of SARS coronavirus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359 : 1059 1065.
27. Holt, R. D., M. Barfield, and R. Gomulkiewicz. 2004. Temporal variation can facilitate niche evolution in harsh sink environments. Am. Nat. 164 : 187 200.
28. Inagaki, M., A. Tanaka, R. Suzuki, H. Wakashima, T. Kawaura, S. Karita, S. Nishikawa, and N. Kashimura. 2000. Characterization of the binding of spike H protein of bacteriophage φX174 with receptor lipopolysaccharides. J. Biochem. 127 : 577 583.
29. Inagaki, M., H. Wakashima, M. Kato, K. Kaitani, and S. Nishikawa. 2005. Crucial role of the lipid part of lipopolysaccharide for conformational change of minor spike H protein of bacteriophage φX174. FEMS Microbiol. Lett. 251 : 305 311.
30. Kauffman, S. A. 1993. The origins of order. Oxford Univ. Press, New York.
31. Kondrashov, A. S. 1982. Selection against harmful mutations in large sexual and asexual populations. Genet. Res. 40 : 325 332.
32. Kondrashov, A. S. 1984. Deleterious mutations as an evolutionary factor. I. The advantage of recombination. Genet. Res. 44 : 199 218.
33. Kondrashov, A. S. 1994. Muller's rachet under epistatic selection. Genetics 136 : 1469 1473.
34. Kondrashov, A. S. 1995. Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? J. Theor. Biol. 175 : 583 594.
35. Llamas-Saiz, A. L., M. Agbandje-McKenna, J. S. Parker, A. T. Wahid, C. R. Parrish, and M. G. Rossmann. 1996. Structural analysis of a mutation in canine parvovirus which controls antigenicity and host range. Virology 225 : 65 71.
36. Lunzer, M., S. P. Miller, R. Felsheim, and A. M. Dean. 2005. The biochemical architecture of an ancient adaptive landscape. Science 310 : 499 501.
37. Malmberg, R. L., S. Held, A. Waits, and R. Mauricio. 2005. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse. Genetics 171 : 2013 2027.
38. Michalakis, Y., and D. Roze. 2004. Evolution. Epistasis in RNA viruses. Science 306 : 1492 1493.
39. Michalakis, Y., and M. Slatkin. 1996. Interaction of selection and recombination in the fixation of negative-epistatic genes. Genet. Res. 67 : 257 269.
40. Muller, H. J. 1964. The relation of recombination to mutational advance. Mut. Res. 1 : 2 9.
41. Nikaido, H., M. Levinthal, K. Nikaido, and K. Nakane. 1967. Extended deletions in the histidine-rough-B region of the Salmonella chromosome. Proc. Natl. Acad. Sci. USA 57 : 1825 1832.
42. Ohta, T. 1998. Evolution by nearly-neutral mutations. Genetica 102/103 83 90.
43. Orr, H. A. 1995. The population genetics of speciation: the evolution of hybrid incompatibilities. Genetics 139 : 1805 1813.
44. Orr, H. A. 2001. The genetics of species differences. Trends Ecol. Evol. 16 : 343 350.
45. Otto, S. P., and M. W. Feldman. 1997. Deleterious mutations, variable epistatic interactions, and the evolution of recombination. Theor. Popul. Biol. 51 : 134 147.
46. Otto, S. P., and Y. Michalakis. 1998. The evolution of recombination in changing environments. Trends Ecol. Evol. 13 : 145 151.
47. Pepin, K. M., M. A. Samuel, and H. A. Wichman. 2006. Variable pleiotropic effects from mutations at the same locus hamper prediction of fitness from a fitness component. Genetics 172 : 2047 2056.
48. Peters, A. D., and C. M. Lively. 2000. Epistasis and the maintenance of sex. Pp. 99 112 in J. B. Wolf, E. D. I. Brodie, and M. J. Wade, eds. Epistasis and the evolutionary process. Oxford Univ. Press, New York.
49. Phillips, P. C. 1996. Waiting for a compensatory mutation: phase zero of the shifting-balance process. Genet. Res. 67 : 271 283.
50. Phillips, P. C., S. P. Otto, and M. C. Whitlock. 2000. Beyond the average: the evolutionary importance of epistatic effects of gene interactions and variability Pp. 20 38 in J. B. Wolf, E. D. I. Brodie, and M. J. Wade, eds. Epistasis and the Evolutionary Process. Oxford Univ. Press, New York.
51. Poon, A., and L. Chao. 2005. The rate of compensatory mutation in the DNA bacteriophage φX174. Genetics 170 : 989 999.
52. Provine, W. B. 1971. The origins of theoretical population genetics. Univ. of Chicago Press, Chicago.
53. Rainey, G. J., A. Natonson, L. F. Maxfield, and J. M. Coffin. 2003. Mechanisms of avian retroviral host range extension. J. Virol. 77 : 6709 6719.
54. Remold, S. K., and R. E. Lenski. 2004. Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nat. Genet. 36 : 423 426.
55. Rokyta, D. R., C. L. Burch, S. B. Caudle, and H. A. Wichman. 2006. Horizontal gene transfer and the evolution of microvirid coliphage genomes. J. Bacteriol. 188 : 1134 1142.
56. Sanger, F., G. M. Air, B. G. Barrell, N. L. Brown, A. R. Coulson, C. A. Fiddes, C. A. Hutchison, P. M. Slocombe, and M. Smith. 1977. Nucleotide sequence of bacteriophage φX174 DNA. Nature 265 : 687 695.
57. Sanjuan, R., A. Moya, and S. F. Elena. 2004. The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl. Acad. Sci. USA 101 : 15376 15379.
58. Sanjuan, R., J. M. Cuevas, A. Moya, and S. F. Elena. 2005. Epistasis and the adaptability of an RNA virus. Genetics 170 : 1001 1008.
59. Schultz, S. T., and M. Lynch. 1997. Mutation and extinction: the role of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution 51 : 1363 1371.
60. Truyen, U., J. F. Evermann, E. Vieler, and C. R. Parrish. 1996. Evolution of canine parvovirus involved loss and gain of feline host range. Virology 215 : 186 189.
61. Wade, M. J., and C. J. Goodnight. 1998. Perspective: the theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments. Evolution 52 : 1537 1553.
62. Wagner, A., G. P. Wagner, and P. Similion. 1994. Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model. Genetics 138 : 533 545.
63. Welch, J. J., and D. Waxman. 2005. The nk model and population genetics. J. Theor. Biol. 234 : 329 340.
64. Whitlock, M. C., P. C. Phillips, B.-G. Moore, and S. J. Tonsor. 1995. Multiple fitness peaks and epistasis. Annu. Rev. Ecol. Syst. 26 : 601 629.
65. Wichman, H. A., L. A. Scott, C. D. Yarber, and J. J. Bull. 2000. Experimental evolution recapitulates natural evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355 : 1677 1684.
66. Wilke, C. O., and C. Adami. 2003. Evolution of mutational robustness. Mut. Res. 522 : 3 11.
67. Wilke, C. O., R. E. Lenski, and C. Adami. 2003. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evol. Biol. 3 : 3.
68. Wolf, J. B., E. D. I. Brodie, and M. J. Wade. 2000. Epistasis and the evolutionary process. Oxford Univ. Press, New York.
69. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Pp. 356 66 in D. F. Jones, ed. Proceedings of the Sixth International Congress of Genetics, Electronic Scholarly Publishing.
70. You, L., and J. Yin. 2002. Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage T7. Genetics 160 : 1273 1281.