A path for coevolution of recombinational DNA repair, transposition, and the common nucleotides

Mutation Research - DNA Repair

Volumn 384, Issue 1, 1997, Pages 15-22

  Cox, Michael M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Evolution; Isocytosine; Isoguanosine; RecA; Recombination; Repair; Transposition; Triplex

Indexed keywords

CYTOSINE; GUANOSINE; NUCLEOTIDE; RECOMBINANT DNA;

DNA REPAIR; DNA TRANSPOSITION; GENETIC RECOMBINATION; PRIORITY JOURNAL; REVIEW;

DEOXYRIBONUCLEOTIDES; DNA; DNA REPAIR; DNA TRANSPOSABLE ELEMENTS; EVOLUTION; HYDROGEN BONDING; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION;

EID: 0031001221     PISSN: 09218777     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0921-8777(97)00010-4     Document Type: Review

References (49)

1. Adzuma K. Stable synapsis of homologous DNA molecules mediated by the Escherichia coli RecA protein involves local exchange of DNA strands. Genes Dev. 6:1992;1679-1694.
2. Baliga R., Singleton J.W., Dervan P.B. RecA. oligonucleotide filaments bind in the minor groove of double-stranded DNA. Proc. Natl. Acad. Sci. USA. 92:1995;10393-10397.
3. Benner S.A., Allemann R.K., Ellington L., Ge L., Glasfeld A., Leanz G.F., Krauch T., MacPherson L.J., Moroney S., Piccirilli J.A., Weinhold E. Natural selection, protein engineering, and the last riboorganism: rational model building in Biochemistry. Cold Spring Harbor Symp. Quant. Biol. 52:1987;53-63.
4. Bernstein H., Byerly H.C., Hopf F.A., Michod R.E. Genetic damage, mutation, and the evolution of sex. Science. 229:1985;1277-1281.
5. Bernstein, H., F.A. Hopf and R.E. Michod (1988) Is meiotic recombination an adaptation for repairing DNA, producing genetic variation, or both?, in: R.E. Michod and B.R. Levin (Eds.), The Evolution of Sex: an Examination of Current Ideas, Sinauer Associates, Sunderland, MA, pp. 139-160.
6. Clark A.J., Sandler S.J. Homologous genetic recombination: the pieces begin to fall into place. Crit. Rev. Microbiol. 20:1994;125-142.
7. Cox M.M. The RecA protein as a recombinational repair system. Mol. Microbiol. 5:1991;1295-1299.
8. Cox M.M. Relating Biochemistry to Biology: how the recombinational repair function of the recA system is manifested in its molecular properties. BioEssays. 15:1993;617-623.
9. Cox M.M. Why does RecA protein hydrolyze ATP. Trends Biochem. Sci. 19:1994;217-222.
10. Cox M.M. Alignment of three (but not four) DNA strands in a RecA protein filament. J. Biol. Chem. 270:1995;26021-26024.
11. Crow, J.F. (1988) The importance of recombination, in: R.E. Michod and B.R. Levin (Eds.), The evolution of sex: an examination of current ideas, Sinauer Associates, Sunderland, MA, pp. 56-73.
12. Daly M.J., Ouyang L., Fuchs P., Minton K.W. In vivo damage and recA-dependent repair of plasmid and chromosomal DNA in the radiation-resistant bacterium Deinococcus radiodurans. J. Bacteriol. 176:1994;3508-3517.
13. Dougherty, E.C. (1955) Comparative evolution and the origin of sexuality, Syst. Zool., 4, 145-169, 190.
14. Frank-Kamenetskii M.D., Mirkin S.M. Triplex DNA structures. Annu. Rev. Biochem. 64:1995;65-95.
15. Ghiselin, M.T. (1988) The evolution of sex: a history of competing points of view, in: R.E. Michod and B.R. Levin (Eds.), The Evolution of Sex: an Examination of Current Ideas, Sinauer Associates, Sunderland, MA, pp. 7-23.
16. Horlacher J., Hottiger M., Podust V.N., Hubscher U., Benner S.A. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc. Natl. Acad. Sci. USA. 92:1995;6329-6333.
17. Kowalczykowski S.C., Dixon D.A., Eggleston A.K., Lauder S.D., Rehrauer W.M. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:1994;401-465.
18. Kuzminov, A. (1996) Recombinational Repair of DNA Damage, R.G. Landes, Georgetown, TX.
19. Lacks S. Integration efficiency and genetic recombination in pneumococcal transformation. Genetics. 53:1966;207-235.
20. Lazcano A., Miller S.L. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell. 85:1996;793-798.
21. Leach A.R., Kollman P.A. Theoretical investigations of novel nucleic acid bases. J. Am. Chem. Soc. 114:1992;3675-3683.
22. Levin, B.R. (1988) The evolution of sex in bacteria, in: R.B. Michod and B.R. Levin (Eds.), The Evolution of Sex: an Examination of Current Ideas, Sinauer Associates, Sunderland, MA, pp. 194-211.
23. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 362:1993;709-715.
24. Maynard Smith, J. (1978) The Evolution of Sex, Cambridge University Press, Cambridge, UK.
25. Maynard Smith, J. (1988) The evolution of recombination, in: R.E. Michod and B.R. Levin (Eds.), The Evolution of Sex: an Examination of Current Ideas, Sinauer Associates, Sunderland, MA, pp. 106-125.
26. Menetski J.P., Bear D.G., Kowalczykowski S.C. Stable DNA heteroduplex formation catalyzed by the Escherichia coli RecA protein in the absence of ATP hydrolysis. Proc. Natl. Acad. Sci. USA. 87:1990;21-25.
27. Michod, R.E. (1995) Eros and Evolution: a Natural Philosophy of Sex, Addison Wesley, Menlo Park, CA.
28. Miller S.L. Which organic compounds could have occurred on the prebiotic earth? Cold Spring Harbor Symp. Quant. Biol. 52:1987;17-27.
29. Minton K.W. DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans. Mol. Microbiol. 13:1994;9-15.
30. Minton K.W., Daly M.J. A model for repair of radiation-induced DNA double-strand breaks in the extreme radiophile Deinococcus radiodurans. Bioessays. 17:1995;457-464.
31. Mizuuchi K. Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61:1992;1011-1052.
32. Nielsen P.E. DNA analogues with nonphosphodiester backbones. Annu. Rev. Biophys. Biomol. Struct. 24:1995;167-183.
33. Orgel L.E. The origin of life on the earth. Sci. Am. 271:1994;76-83.
34. Podyminogin M.A., Meyer R.B., Gamper H.B. Sequence-specific covalent modification of DNA by cross-linking oligonucleotides. Catalysis by RecA and implication for the mechanism of synaptic joint formation. Biochemistry. 34:1995;13098-13108.
35. Podyminogin M.A., Meyer R.B., Gamper H.B. RecA-catalyzed, sequence-specific alkylation of DNA by crosslinking oligonucleotides. Effects of length and nonhomologous base substitution. Biochemistry. 35:1996;7267-7274.
36. Potter, H. and D. Dressler (1988) Genetic recombination: molecular biology, biochemistry, and evolution, in: K.B. Low (Ed.), The Recombination of Genetic Material, Academic Press, San Diego, CA, pp. 217-282.
37. Rao B.J., Chiu S.K., Bazemore L.R., Reddy G., Radding C.M. How specific is the first recognition step of homologous recombination? Trends Biochem. Sci. 20:1995;109-113.
38. Rich, A. (1962), in: M. Kasha and B. Pullman (Eds.), Horizons in Biochemistry, Academic Press, New York, pp. 103-126.
39. Roca, A.I. and M.M. Cox (1997) RecA protein: structure, function, and role in recombinational DNA repair, Prog. Nucl. Acids Res. Mol. Biol., 56, 129-223.
40. Selander R.K., Levin B.R. Genetic diversity and structure in Escherichia coli populations. Science. 210:1980;545-547.
41. Shchyolkina A.K., Timofeev E.N., Borisova O.F., Il'icheva I.A., Minyat E.E., Khomyakova E.B., Florentiev V.L. The R-form of DNA does exist. FEBS Lett. 339:1994;113-118.
42. Smith G.R. Conjugational recombination in E. coli: myths and mechanisms. Cell. 64:1991;19-27.
43. Smith J.M. The role of sex in bacterial evolution. J. Heredity. 84:1993;326-327.
44. Stasiak A. Three-stranded DNA structure; is this the secret of DNA homologous recognition? Mol. Microbiol. 6:1992;3267-3276.
45. Switzer C.Y., Moroney S.E., Benner S.A. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Biochemistry. 32:1993;10489-10496.
46. Tor Y., Dervan P.B. Site-specific enzymatic incorporation of and unnatural base, N6-(6-Aminohexyl)isoguanosine, into RNA. J. Am. Chem. Soc. 115:1993;4461-4467.
47. West S.C. The processing of recombination intermediates: Mechanistic insights from studies of bacterial proteins. Cell. 76:1994;9-15.
48. West S.C., Cassuto E., Howard-Flanders P. Mechanism of E. coli RecA protein directed strand exchanges in post-replication repair of DNA. Nature (Lond.). 294:1981;659-662.
49. Zhurkin V.B., Raghunathan G., Ulyanov N.B., Camerini O.R., Jernigan R.L. A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol. 239:1994;181-200.