Neutral Mutations and Neutral Substitutions in Bacterial Genomes

Molecular Biology and Evolution

Volumn 20, Issue 12, 2003, Pages 2091-2096

  Ochman, Howard ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

Bacterial evolution; E. coli; Mutation rates; Nucleotide substitutions; S. enterica

Indexed keywords

ARTICLE; BACTERIAL GENOME; ESCHERICHIA COLI; GENE MUTATION; GENETIC ANALYSIS; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; SALMONELLA ENTERICA; SEQUENCE ANALYSIS; SUBSTITUTION REACTION;

AMINO ACID SUBSTITUTION; CHROMOSOMES, BACTERIAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MUTATION; SALMONELLA ENTERICA; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA; SALMONELLA; SALMONELLA ENTERICA;

EID: 0346726023     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg229     Document Type: Article

References (38)

1. Beletskii, A., and A. S. Bhagwat. 1996. Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc. Natl. Acad. Sci. USA 93:13919-13924.
2. -. 1998. Correlation between transcription and C to T mutations in the non-transcribed DNA strand. J. Biol. Chem. 379:549-551.
3. Berg, O. G., and M. Martelius. 1995. Synonymous substitution-rate constants in Escherichia coli and Salmonella typhimurium and their relationship to gene expression and selection pressure. J. Mol. Evol. 41:449-456.
4. Birky, C. W., Jr., and J. B. Walsh. 1992. Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes. Genetics 130:677-683.
5. Bjedov, I., O. Tenaillon, B. Gerard, V. Souza, E. Denamur, M. Radman, F. Taddei, and I. Matic. 2003. Stress-induced mutagenesis in bacteria. Science 300:1404-1409.
6. Blake, R. D., S. T. Hess, and J. Nicholson-Tuell. 1992. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J. Mol. Evol. 34:189-200.
7. Brown, W. M., E. M. Prager, A. Wang, and A. C. Wilson. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18:225-239.
8. Cupples, C. G., and J. H. Miller, 1989. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc. Natl. Acad. Sci. USA 86:5345-5349.
9. Daubin, V., and G. Perriere. 2003. G + C structuring along the genome: a common feature of prokaryotes. Mol. Biol. Evol. 20:471-483.
10. Doolittle, R. F., D. F. Feng, S. Tsang, G. Cho, and E. Little. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-477.
11. Duret, L., M. Semon, G. Piganeau, D. Mouchiroud, and N. Galtier. 2002. Vanishing GC-rich isochores in mammalian genomes. Genetics 162:1837-1847.
12. Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148:1667-1686.
13. Eyre-Walker, A., and M. Bulmer. 1995. Synonymous substitution rates in enterobacteria. Genetics 140:1407-1412.
14. Fijalkowska, I. J., P. Jonczyk, M. M. Tkaczyk, M. Bialoskorska, and R. M. Schaaper. 1998. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. USA 95:10020-10025.
15. Francino, M. P., L. Chao, M. A. Riley, and H. Ochman. 1996. Patterns of substitutions in enterobacterial genes are generated by transcription-coupled repair. Science 272:107-109.
16. Francino, M. P., and H. Ochman. 2001. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 18:1147-1150.
17. Gojobori, T., K. Ishii, and M. Nei. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18:360-369.
18. Green, P., B. Ewing, W. Miller, P. J. Thomas, and E. D. Green. 2003. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33:514-517.
19. Hall, B. G. 1991. Spectrum of mutations that occur under selective and non-selective conditions in E. coli. Genetica 84:73-76.
20. Hudson, R. E., U. Bergthorsson, J. R. Roth, and H. Ochman. 2002. Effect of chromosome location on bacterial mutation rates. Mol. Biol. Evol. 19:85-92.
21. Hudson, R. E., U. Bergthorsson, and H. Ochman. 2003. Transcription increases a broad spectrum of spontaneous mutations in bacteria. Nucleic Acids Res. 31:4517-4522.
22. Klapacz, J., and A. S. Bhagwat. 2002. Transcription-dependent increase in multiple classes of base substitution mutations in Escherichia coli. J. Bacteriol. 184:6866-6872.
23. Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
24. MacKay, W. J., S. Han, and L. D. Samson. 1994. DNA alkylation repair limits spontaneous base substitution mutations in Escherichia coli. J. Bacteriol. 176:3224-3230.
25. Mira, A., and H. Ochman. 2002, Gene location and bacterial sequence divergence. Mol. Biol. Evol. 19:1350-1358.
26. Moran, N. A., M. A. Munson, P. Baumann, and H. Ishikawa. 1993. A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc. R. Soc. Lond. Ser. B 253:167-171.
27. Muto, A., and S. Osawa. 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84:166-169.
28. Ochman, H., S. Elwyn, and N. A. Moran. 1999. Calibrating bacterial evolution. Proc. Natl. Acad. Sci. USA 96:12638-12643.
29. Ochman, H., and A. C. Wilson. 1988. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:74-86.
30. Schaaper, R. M., and R. L. Dunn. 1991. Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129:317-326.
31. Selby, C.P., and A. Sancar. 1993. Transcription-repair coupling and mutation frequency decline. J. Bacteriol. 175:7509-7514.
32. Sharp, P. M. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J. Mol. Evol. 33:23-33.
33. Sharp, P. M., and W. H. Li. 1987. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4:222-230.
34. Sharp, P. M., D. C. Shields, K. H. Wolfe, and W. H. Li. 1989. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246:808-810.
35. Sueoka, N. 1962. On the genetic basis of variation and heterogeneity in base composition. Proc. Natl. Acad. Sci. USA 48:582-592.
36. -. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85:2653-2657.
37. Wright, B. E., A. Longacre, and J. M. Reimers. 1999. Hypermutation in derepressed operons of Escherichia coli K12. Proc. Natl. Acad. Sci. USA 96:5089-5094.
38. Yoshiyama, K., and H. Maki. 2003. Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli: transcription-dependent mutagenesis involving template-switching mechanisms. J. Mol. Biol. 327:7-18.