Cell-selfish modes of evolution and mutations directed after transcriptional bypass

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 510, Issue 1-2, 2002, Pages 141-152

  Holmquist, Gerald P ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

Directed mutations; Disparate segregation; Life cycle; Linkage disequilibrium; Retromutations; Selfish evolution; Sex; Transcriptional mutagenesis

Indexed keywords

5 HYDROXYMETHYLURACIL; 8 HYDROXYGUANINE; ADENINE DERIVATIVE; BASE; DIHYDROURACIL; GUANINE DERIVATIVE; MUTANT PROTEIN; RNA POLYMERASE; URACIL;

ALLELE; DIPLOIDY; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; EUKARYOTIC CELL; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GERM LINE; HUMAN; MOLECULAR CLONING; MOLECULAR EVOLUTION; MUTAGENESIS; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; REPRODUCTION; REVIEW; RNA TRANSLATION;

DARWINIA; EUKARYOTA; METAZOA; PROKARYOTA;

EID: 0037196068     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0027-5107(02)00259-2     Document Type: Article

References (52)

1. Luria S.E., Delbruck M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics. 28:1943;491-511.
2. Cairns J., Overbaugh J., Miller S. The origin of mutants. Nature. 335:1988;142-145.
3. Hall B.G. Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations. Genetica. 102/103:1998;109-125.
4. Foster P.L. Nonadaptive mutations occur on the F′ episome during adaptive mutation conditions in E. coli. J. Bacteriol. 179:1997;1550-1554.
5. Rosenberg S.M., Thulin C., Harris R.S. Transient and heritable mutators in adaptive evolution in the lab and in nature. Genetics. 148:1998;1559-1566.
6. McKenzie G.J., Lee P.L., Lombardo M.J., Hastings P.J., Rosenberg S.M. SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol. Cell. 7:2001;571-579.
7. McKenzie G.J., Rosenberg S.M. Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr. Opin. Microbiol. 4:2001;586-594.
8. Giraud A., Matic I., Tenaillon O., Clara A., Radman M., Fons M., Taddei F. Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut. Science. 291:2001;2606-2608.
9. Hall B.G. Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions. Proc. Natl. Acad. Sci. U.S.A. 88:1991;5882-5886.
10. Sniegowski P.D., Gerrish P.J., Lenski R.E. Evolution of high mutation rates in experimental populations of E. coli. Nature. 387:1997;703-705.
11. Torkelson J., Harris R.S., Lombardo M.J., Nagendran J., Thulin C., Rosenberg S.M. Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation. EMBO J. 16:1997;3303-3311.
12. Bridges B.A. Hypermutation in bacteria and other cellular systems. Philos. Trans. R. Soc. London B Biol. Sci. 356:2001;29-39.
13. Bridges B.A. Starvation-associated mutation in Escherichia coli: a spontaneous lesion hypothesis for "directed" mutation. Mutat. Res. 307:1994;149-156.
14. Bridges B.A. Mutation in resting cells; the role of endogenous DNA damage. Cancer Serv. 28155:1996;167.
15. Bridges B.A. DNA turnover and mutation in resting cells. BioEssays. 19:1997;347-352.
16. Viswanathan A., Liu J., Doetsch P.W. E. coli RNA polymerase bypass of DNA base damage. Mutagenesis at the level of transcription 7. Ann. N.Y. Acad. Sci. 870:1999;386-388.
17. Liu J., Doetsch P.W. Escherichia coli RNA and DNA polymerase bypass of dihydrouracil: mutagenic potential via transcription and replication. Nucleic Acids Res. 26:1998;1707-1712.
18. Liu J., Zhou W., Doetsch P.W. RNA polymerase bypass at sites of dihydrouracil: implications for transcriptional mutagenesis. Mol. Cell Biol. 15:1995;6729-6735.
19. You H.J., Viswanathan A., Doetsch P.W. In vivo technique for determining transcriptional mutagenesis. Methods. 22(1):2000;120-126.
20. Viswanathan A., You H.J., Doetsch P.W. Phenotypic change caused by transcriptional bypass of uracil in nondividing cells. Science. 284(11):1999;159-162. (see comments).
21. P.W. Doetsch, A. Viswanathan, W. Zhou, J. Liu, Bypass of DNA damage by RNA polymerases, in: M. Dizdaroglu, A. Karakaya (Eds.), Advances in DNA Damage and Repair, Plenum Publishers, New York, 1999, pp. 97-110.
22. Blank A., Gallant J.A., Burgess R.R., Loeb L.A. An RNA polymerase mutant with reduced accuracy of chain elongation. Biochemistry. 25:1986;5920-5928.
23. Rosenberger R.F., Hilton J. The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of E. coli. Mol. Gen. Genet. 191:1983;207-212.
24. Ninio J. Transient mutators: a semiquantitative analysis of the influence of translation and transcription errors on mutation rates. Genetics. 129:1991;957-962.
25. Tamames J., Ouzounis C., Sander C., Valencia A. Genomes with distinct function composition. FEBS Lett. 389:1996;96-101.
26. Feil E.J., Spratt B.G. Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55:2001;561-590.
27. Smith J.M., Feil E.J., Smith N.H. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays. 22:2000;1115-1122.
28. Levin B.R. Periodic selection, infections gene exchange, and the genetic structure of E. coli populations. Genetics. 99:1981;1-23.
29. Sonneborn T.M. Sex, sex inheritance and sex determination in Paramecium aurelia. Proc. Natl. Acad. Sci. U.S.A. 23:1937;378-385.
30. Dacks J., Roger A.J. The first sexual lineage and the relevance of facultative sex. J. Mol. E. 48:1999;779-783.
31. S. Wright, Statistical genetics in relation to evolution, in: W.B. Provine (Ed.), Selected Papers of Sewall Wright, University of Chicago Press, Chicago, 1986, p. 326.
32. Snel B., Bork P., Huynen M.A. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. U.S.A. 99:2002;5890-5895.
33. Huynen M.A., Bork P. Measuring genome evolution. Proc. Natl. Acad. Sci. U.S.A. 95:1998;5849-5856.
34. Huynen M.A., Snel B., Bork P. Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17:2001;304-306.
35. McKusick V.M. The anatomy of the human genome. Am. J. Med. 69:1980;267-276.
36. Anderson W.W., Arnold J., Baldwin D.G., Beckenbach A.T., Brown C.J., Bryant S.H., Coyne J.A., Harshman L.G., Heed W.B., Jeffery D.E. Four decades of inversion polymorphism in Drosophila pseudoobscura. Proc. Natl. Acad. Sci. U.S.A. 88:1991;10367-10371.
37. Rice W.R., Chippindale A.K. Sexual recombination and the power of natural selection. Science. 294:2001;555-559.
38. Neher E. How frequent are correlated changes in families of protein sequences. Proc. Natl. Acad. Sci. U.S.A. 91:1994;98-102.
39. Saito S., Sasai M., Yomo T. Evolution of the folding ability of proteins through functional selection. Proc. Natl. Acad. Sci. U.S.A. 94:1997;11324-11328.
40. Kimura M. The role of compensatory neutral mutations in molecular evolution. J. Genet. 64:1985;7-19.
41. Hall B.G. Adaptive evolution that requires multiple spontaneous mutations. I. Mutations involving an insertion sequence. Genetics. 120:1988;887-897.
42. Innan H., Stephan W. Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions. Genetics. 159:2001;389-399.
43. Furusawa M., Doi H. Asymmetrical DNA replication promotes evolution: disparity theory of evolution. Genetica. 102/103:1998;333-347.
44. Wada K.N., Doi H., Tanaka S., Wada Y., Furusawa M. A neo-Darwinian algorithm: asymmetrical mutations due to semiconservative DNA-type replication promote evolution. Proc. Natl. Acad. Sci. U.S.A. 90:1993;11934-11938.
45. V.A. Ratner, A.A. Zharkikh, N.A. Kolchanov, S.N. Rodin, V.V. Solovyov, A.S. Antonov, Molecular Evolution, Springer, Berlin, 1996.
46. Bridges B.A. Dirty transcripts from clean DNA. Science. 284:1999;62-63.
47. Kaiser D. Building a multicellular organism. Annu. Rev. Genet. 35:2001;103-123.
48. Ye N., Bianchi M.S., Bianchi N.O., Holmquist G.P. Adaptive enhancement and kinetics of nucleotide excision repair in humans. Mutat. Res. DNA Repair. 435:1999;43-61.
49. Marnett L.J., Burcham P.C. Endogenous DNA adducts: potential and paradox. Chem. Res. Toxicol. 6:1993;771-785.
50. Remington K.M., Bennett S.E., Harris C.M., Harris T.M., Bebenek K. Highly mutagenic bypass synthesis by T7 RNA polymerase of site-specific benzo[a]pyrene diol epoxide-adducted template DNA. J. Biol. Chem. 273:1998;13170-13176.
51. Lindahl T., Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry. 11:1972;3610-3618.
52. Patel P.H., Loeb L.A. Multiple amino acid substitutions allow DNA polymerases to synthesize RNA. J. Biol. Chem. 275:2000;40266-40272.