The rate of compensatory mutation in the DNA bacteriophage φX174

Genetics

Volumn 170, Issue 3, 2005, Pages 989-999

  Poon, Art ^a,b   Chao, Lin ^a  

^a University of California at San Diego   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL MUTATION; BACTERIOPHAGE PHI X 174; COMPENSATORY MUTATION; GENETIC EPISTASIS; GENOME; GENOTYPE; MISSENSE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING; SITE DIRECTED MUTAGENESIS;

ADAPTATION, BIOLOGICAL; BACTERIOPHAGE PHI X 174; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; MUTATION; PLAQUE ASSAY; SEQUENCE ANALYSIS, DNA;

EID: 21044438202     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.039438     Document Type: Article

References (33)

1. BERMAN, H. M., J. WESTBROOK, Z. FENG, G. GILLILAND, T. N. BHAT et al., 2000 The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
2. BURCH, A. D., and B. A. FANE, 2000 Foreign and chimeric scaffolding proteins as inhibitors of Microviridae morphogenesis. J. Virol. 74: 9347-9352.
3. BURCH, C. L., and L. CHAO, 1999 Evolution by small steps and rugged landscapes in the RNA virus φ6. Genetics 151: 921-927.
4. BURCH, C. L., and L. CHAO, 2004 Epistasis and its relationship to canalization in the RNA virus φ6. Genetics 167: 559-567.
5. CHAO, L., T. T. TRAN and T. T. TRAN, 1997 The advantage of sex in the RNA virus φ6. Genetics 147: 953-959.
6. CRILL, W. D., H. A. WICHMAN and J. J. BULL, 2000 Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154: 27-37.
7. DOKLAND, T., R. MCKENNA, L. L. ILAG, B. R. BOWMAN, N. L. INCARDONA et al., 1997 Structure of a viral procapsid with molecular scaffolding. Nature 389: 308-313.
8. FANE, B. A., and M. HAYASHI, 1991 Second-site suppressors of a cold-sensitive prohead accessory protein of bacteriophage φX174. Genetics 128: 663-671.
9. FANE, B. A., and P. E. PREVELIGE, JR., 2003 Mechanism of scaffolding-assisted viral assembly. Adv. Protein Chem. 64: 259-299.
10. FANE, B. A., S. SHIEN and M. HAYASHI, 1993 Second-site suppressors of a cold- sensitive external scaffolding protein of bacteriophage φX174. Genetics 134: 1003-1011.
11. FISHER, R. A., 1930 The Genetical Theory of Natural Selection, Ed 2. Dover Publications, New York.
12. GERRISH, P. J., and R. E. LENSKI, 1998 The fate of competing beneficial mutations in an asexual population. Genetica 102/103: 127-144.
13. HAFENSTEIN, S. L., M. CHEN and B. A. FANE, 2004 Genetic and functional analysis of the φX174 DNA binding protein: the effects of substitutions for amino acid residues that spatially organize the two DNA binding domains. Virology 318: 204-213.
14. HAYASHI, M., A. AOYAMA, D. L. RICHARDSON, JR. and M. N. HAYASHI, 1988 Biology of the bacteriophage φX174, pp. 1-71 in The Bacteriophages, edited by R. CALENDAR. Plenum Press, New York.
15. JENNINGS, B., and B. A. FANE, 1997 Genetic analysis of the φX174 DNA binding protein. Virology 227: 370-377.
16. KIMURA, M., 1985 The role of compensatory neutral mutations in molecular evolution. J. Genet. 64: 7-19.
17. KONDRASHOV, A. S., 1994 Muller's ratchet under epistatic selection. Genetics 136: 1469-1473.
18. 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.
19. LEVIN, B. R., V. PERROT and N. WALKER, 2000 Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics 154: 985-997.
20. MAISNIER-PATIN, S., and D. I. ANDERSSON, 2004 Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res. Microbiol. 155: 360-369.
21. MCKENNA, R., D. XIA, P. WILLINGMANN, L. L. ILAG, S. KRISHNASWAMY et al., 1992 Atomic structure of single-stranded DNA bacteriophage φX174 and its functional implications. Nature 355: 137-143.
22. NOVAK, C. R., and B. A. FANE, 2004 The functions of the N terminus of the φX174 internal scaffolding protein, a protein encoded in an overlapping reading frame in a two scaffolding protein system. J. Mol. Biol. 335: 383-390.
23. ORR, H. A., 2003 The distribution of fitness effects among beneficial mutations. Genetics 163: 1519-1526.
24. ORR, H. A., and J. A. COYNE, 1992 The genetics of adaptation: a reassessment. Am. Nat. 140: 725-742.
25. PETTERSEN, E. F., T. D. GODDARD, C. C. HUANG, G. S. COUCH, D. M. GREENBLATT et al., 2004 UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25:1605-1612.
26. POON, A., B. H. DAVIS and L. CHAO, 2005 The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood. Genetics 170: 1323-1332.
27. PORTER, M. L., and K. A. CRANDALL, 2003 Lost along the way: the significance of evolution in reverse. Trends Ecol. Evol. 18: 541-547.
28. READ, K. L. Q., 1998 A lognormal approximation for the collector's problem. Am. Stat. 52: 175-180.
29. ROKYTA, D. R., P. JOYCE, S. B. CAUDLE and H. A. WICHMAN, 2005 An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat. Genet. 37: 441-444.
30. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. SANGER, F., A. R. COULSON, T. FRIEDMANN, G. M. AIR, B. G. BARRELL et al., 1978 The nucleotide sequence of bacteriophage φX174. J. Mol. Biol. 125: 225-246.
32. SUJATHA, S., and D. CHATTERJI, 2000 Understanding protein-protein interactions by genetic suppression. J. Genet. 79: 125-129.
33. WHITLOCK, M. C., and S. P. OTTO, 1999 The panda and the phage: compensatory mutations and the persistence of small populations. Trends Ecol. Evol. 14: 295-296.