Problems and Paradigms: Relating biochemistry to biology: How the recombinational repair function of RecA protein is manifested in its molecular properties
Tóm tắt
The multiple activities of the RecA protein in DNA metabolism have inspired over a decade of research in dozens of laboratories around the world. This effort has nevertheless failed to yield an understanding of the mechanism of several RecA protein‐mediated processes, the DNA strand exchange reactions prominent among them. The major factors impeding progress are the invalid constraints placed upon the problem by attempting to understand RecA protein‐mediated DNA strand exchange within the context of an inappropriate biological paradigm – namely, homologous genetic recombination as a mechanism for generating genetic diversity. In this essay I summarize genetic and biochemical data demonstrating that RecA protein evolved as the central component of a recombinational DNA repair system, with the generation of genetic diversity being a sometimes useful byproduct, and review the major in vitro activities of RecA protein from a repair perspective. While models proposed for both recombination and recombinational repair often make use of DNA strand cleavage and transfer steps that appear to be quite similar, the molecular and thermodynamic requirements of the two processes are very different. The recombinational repair function provides a much more logical and informative framework for thinking about the biochemical properties of RecA and the strand exchange reactions it facilitates.
Từ khóa
Tài liệu tham khảo
Radding C. M., 1991, Helical interactions in homologous pairing and strand exchange driven by RecA protein, J. Biol. Chem., 266, 5355, 10.1016/S0021-9258(19)67599-X
Fishel R. A., 1988, Mechanisms and Consequences of DNA Damage Processing, 23
Howard‐Flanders P., 1975, Repair by genetic recombination in bacteria: overview, Basic Life Sci., 5, 265
Nussbaum A., 1992, Restriction‐stimulated homologous recombination of plasmids by the RecE pathway of Escherichia coli, Genetics, 130, 37, 10.1093/genetics/130.1.37
Capaldo F. N., 1974, Analysis of the growth of recombination‐deficient strains of Escherichai coli K‐12, J. Bacteriol., 118, 242, 10.1128/jb.118.1.242-249.1974
Carlsson J., 1980, The RecA+ gene product is more important than catalase and superoxide dismutase in protecting Escherichia coli against hydrogen peroxide toxicity, J. Bacteriol., 142, 319, 10.1128/jb.142.1.319-321.1980
Thomas B., 1988, Suppression of the UV‐sensitive phenotype of Escherichia coli recF mutants by RecA(Srf) and RecA(Tif) mutations requires recJ+, J. Bacteriol., 170, 3675, 10.1128/jb.170.8.3675-3681.1988
Wang T. C., 1986, RecA (Srf) suppression of recF deficiency in the post‐replication repair of UV‐irradiated Escherichia coli K‐12, J. Bacteriol., 168, 940, 10.1128/jb.168.2.940-946.1986
Weinstock G. M., 1987, Escherichia coli and Salmonella Typhimurium, Cellular and Molecular Biology, 1034
Witkin E. M., 1992, Overproduction of DnaE protein (alpha subunit of DNA polymerase III) restores viability in a conditionally inviable Escherichia coli strain deficient in DNA polymerase I, J. Bacteriol., 174, 4166, 10.1128/jb.174.12.4166-4168.1992
Morimyo M., 1982, Anaerobic incubation enhances the colony formation of a polA recB strain of Escherichia coli K‐12, J. Bacteriol., 152, 208, 10.1128/jb.152.1.208-214.1982
Feng W.‐Y., 1991, Recombinogenic processing of UV‐light photoproducts in nonreplicating phage DNA by the Escherichia coli methyl‐directed mismatch repair system, Genetics, 129, 1007, 10.1093/genetics/129.4.1007
Stamm L. V., 1991, Cloning of the RecA gene from a free‐living Leptospire and distribution of RecA‐like protein among Spirochetes, Appl. Environ. Microbiol., 57, 183, 10.1128/aem.57.1.183-189.1991
Rosenberg M., 1990, Differential recognition of ultraviolet lesions by RecA protein ‐ possible mechanism for preferential targeting of SOS mutagenesis to (6‐4) dipyrimidine sites, J. Biol. Chem., 265, 20641, 10.1016/S0021-9258(17)30551-3
see also theLindsleyandCox(1990b)
andConleyandWest(1990). papers cited in reference 5 above.
Kim J. I., 1992, On the role of ATP hydrolysis in RecA protein‐mediated DNA strand exchange. II. Four‐strand exchanges, J. Biol. Chem., 267, 16444, 10.1016/S0021-9258(18)42023-6
Rehrauer W. M., 1993, Alteration of the nucleoside triphosphate (NTP) catalytic domain withi Escherichia coli recA protein attenuates NTP hydrolysis but not joint molecule formation, J. Biol. Chem., 268, 1292, 10.1016/S0021-9258(18)54073-4
Kim J. I., 1992, On the role of ATP hydrolysis in RecA protein‐mediated DNA strand exchange.I. Bypassing a short heterologous insert in one DNA substrate, J. Biol. Chem., 267, 16438, 10.1016/S0021-9258(18)42022-4