Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Nature

Volumn 485, Issue 7396, 2012, Pages 95-98

  Martincorena, Iñigo ^a   Seshasayee, Aswin S N ^a,e   Luscombe, Nicholas M ^a,b,c,d  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^e TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

COHORT ANALYSIS; COLIFORM BACTERIUM; EVOLUTIONARY BIOLOGY; EVOLUTIONARY THEORY; GENE EXPRESSION; GENOME; MUTATION; PHYLOGENETICS; POPULATION GENETICS; THEORETICAL STUDY;

ARTICLE; BACTERIAL GENOME; ESCHERICHIA COLI; GENE; GENE EXPRESSION; GENE MUTATION; MUTAGENESIS; MUTATION RATE; NONHUMAN; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; RISK MANAGEMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

BIOLOGICAL EVOLUTION; ESCHERICHIA COLI; GENOME, BACTERIAL; MODELS, GENETIC; MUTAGENESIS; PHYLOGENY; RISK; SELECTION, GENETIC;

ESCHERICHIA COLI;

EID: 84860512528     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature10995     Document Type: Article

References (30)

1. Kimura, M. On the evolutionary adjustment of spontaneousmutation rates. Genet. Res. 9, 23-24 (1967).
2. Levins, R. Theory of fitness in a heterogeneous environment. VI. The adaptive significance of mutation. Genetics 56, 163-178 (1967).
3. Moxon, E. R., Rainey, P. B., Nowak, M. A. & Lenski, R. E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4, 24-33 (1994).
4. Sniegowski, P. D., Gerrish, P. J., Johnson, T. & Shaver, A. The evolution of mutation rates: separating causes from consequences. BioEssays 22, 1057-1066 (2000). (Pubitemid 32010515)
5. Tenaillon, O., Taddei, F., Radman, M. & Matic, I. Second-order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation. Res. Microbiol. 152, 11-16 (2001). (Pubitemid 32168113)
6. Pal, C., Macia, M. D., Oliver, A., Schachar, I. & Buckling, A. Coevolution with viruses drives the evolution of bacterialmutation rates. Nature 450, 1079-1081 (2007). (Pubitemid 350273608)
7. Hodgkinson, A., Ladoukakis, E. & Eyre-Walker, A. Cryptic variation in the human mutation rate. PLoS Biol. 7, e1000027 (2009).
8. McVean, G. T. & Hurst, L. D. Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature 386, 388-392 (1997). (Pubitemid 27154477)
9. Chuang, J. H. & Li, H. Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol. 2, E29 (2004).
10. Braverman, J. M., Hudson, R. R., Kaplan, N. L., Langley, C. H. & Stephan, W. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140, 783-796 (1995).
11. O'Fallon, B. D. A method to correct for the effects of purifying selection on genealogical inference. Mol. Biol. Evol. 27, 2406-2416 (2010).
12. Bustamante, C. D., Nielsen, R. & Hartl, D. L. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Popul. Biol. 63, 91-103 (2003). (Pubitemid 38042772)
13. Drummond, D. A. & Wilke, C. O. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341-352 (2008). (Pubitemid 352010328)
14. McVean, G. A. & Charlesworth, B. A. A population geneticmodel for the evolution of synonymous codon usage: patterns and predictions. Genet. Res. 74, 145-158 (1999). (Pubitemid 29507353)
15. Hartl, D. L., Moriyama, E. N. & Sawyer, S. A. Selection intensity for codon bias. Genetics 138, 227-234 (1994). (Pubitemid 24262194)
16. Eyre-Walker, A.&Bulmer, M. Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res. 21, 4599-4603 (1993). (Pubitemid 23292727)
17. Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255-258 (2009).
18. Andolfatto, P. Adaptive hitchhiking effects on genomevariability. Curr. Opin. Genet. Dev. 11, 635-641 (2001).
19. Touchon, M. et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344 (2009).
20. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Systems Biol. 2, 0008, doi:10.1038/msb4100050 (2006). (Pubitemid 43948152)
21. Eyre-Walker, A. & Bulmer, M. Synonymous substitution rates in enterobacteria. Genetics 140, 1407-1412 (1995).
22. Ochman, H. Neutral mutations and neutral substitutions in bacterial genomes. Mol. Biol. Evol. 20, 2091-2096 (2003). (Pubitemid 38057772)
23. Beletskii, A. & Bhagwat, A. S. 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 (1996). (Pubitemid 26424221)
24. Klapacz, J. & Bhagwat, A. S. Transcription-dependent increase in multiple classes of base substitution mutations in Escherichia coli. J. Bacteriol. 184, 6866-6872 (2002). (Pubitemid 36356122)
25. Francino, M. P., Chao, L., Riley, M. A. & Ochman, H. Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science 272, 107-109 (1996). (Pubitemid 26110761)
26. Wagner, A. Risk management in biological evolution. J. Theor. Biol. 225, 45-57 (2003). (Pubitemid 37237611)
27. Tu, Y., Tornaletti, S. & Pfeifer, G. P. DNA repair domains within a human gene: selective repair of sequences near the transcription initiation site. EMBO J. 15, 675-683 (1996). (Pubitemid 26044581)
28. Hoege, C., Pfander, B., Moldovan, G. L., Pyrowolakis, G. & Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419, 135-141 (2002). (Pubitemid 35025438)
29. Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
30. Lee, W. et al. Themutation spectrumrevealed by paired genomesequences froma lung cancer patient. Nature 465, 473-477 (2010).