Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination
The genetic recombination systems of bacteria have not evolved for optimal enzymatic function. As recombination and recombination systems can have deleterious effects, these systems have evolved sufficient function to repair a level of DNA double strand breaks typically encountered during replication and cell division. However, maintenance of genome stability requires a proper balance between all aspects of DNA metabolism. A substantial increase in recombinase function is possible, but it comes with a cellular cost. Here, we use a kind of directed evolution to generate variants of the Escherichia coli RecA protein with an enhanced capacity to promote conjugational recombination. The mutations all occur within a targeted 59 amino acid segment of the protein, encompassing a significant part of the subunit-subunit interface. The RecA variants exhibit a range of altered activities. In general, the mutations appear to increase RecA protein persistence as filaments formed on DNA creating barriers to DNA replication and/or transcription. The barriers can be eliminated via expression of more robust forms of a RecA regulator, the RecX protein. The results elucidate an evolutionary compromise between the beneficial and deleterious effects of recombination.
Vyšlo v časopise:
Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination. PLoS Genet 11(6): e32767. doi:10.1371/journal.pgen.1005278
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005278
Souhrn
The genetic recombination systems of bacteria have not evolved for optimal enzymatic function. As recombination and recombination systems can have deleterious effects, these systems have evolved sufficient function to repair a level of DNA double strand breaks typically encountered during replication and cell division. However, maintenance of genome stability requires a proper balance between all aspects of DNA metabolism. A substantial increase in recombinase function is possible, but it comes with a cellular cost. Here, we use a kind of directed evolution to generate variants of the Escherichia coli RecA protein with an enhanced capacity to promote conjugational recombination. The mutations all occur within a targeted 59 amino acid segment of the protein, encompassing a significant part of the subunit-subunit interface. The RecA variants exhibit a range of altered activities. In general, the mutations appear to increase RecA protein persistence as filaments formed on DNA creating barriers to DNA replication and/or transcription. The barriers can be eliminated via expression of more robust forms of a RecA regulator, the RecX protein. The results elucidate an evolutionary compromise between the beneficial and deleterious effects of recombination.
Zdroje
1. Aguilera A, Gomez-Gonzalez B. Genome instability: a mechanistic view of its causes and consequences. Nat Rev Genet. 2008;9(3):204–17. Epub 2008/01/30. doi: 10.1038/nrg2268 18227811.
2. Kim N, Jinks-Robertson S. Transcription as a source of genome instability. Nature Rev Genet. 2012;13(3):204–14. doi: 10.1038/nrg3152 WOS:000300609900005.
3. Rudolph CJ, Upton AL, Stockum A, Nieduszynski CA, Lloyd RG. Avoiding chromosome pathology when replication forks collide. Nature. 2013;500(7464):608–611. doi: 10.1038/nature12312 WOS:000323625900041.
4. Wimberly H, Shee C, Thornton PC, Sivaramakrishnan P, Rosenberg SM, Hastings PJ. R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nature Commun. 2013;4. doi: 10.1038/ncomms3115 WOS:000323715700010.
5. Dewar JM, Walter JC. Chromosome biology: conflict management for replication and transcription. Curr Biol. 2013;23(5):R200–R2. doi: 10.1016/j.cub.2013.01.054 WOS:000315764000011.
6. Helmrich A, Ballarino M, Nudler E, Tora L. Transcription-replication encounters, consequences and genomic instability. Nature Struct Mol Biol. 2013;20(4):412–8. doi: 10.1038/nsmb.2543 WOS:000317044400005.
7. Merrikh H, Zhang Y, Grossman AD, Wang JD. Replication-transcription conflicts in bacteria. Nature Rev Microbiol. 2012;10(7):449–58. doi: 10.1038/nrmicro2800 WOS:000305471800010.
8. Michel B, Boubakri H, Baharoglu Z, LeMasson M, Lestini R. Recombination proteins and rescue of arrested replication forks. DNA Repair. 2007;6(7):967–80. ISI:000248092000010.
9. Michel B, Ehrlich SD, Uzest M. DNA double-strand breaks caused by replication arrest. EMBO J. 1997;16(2):430–8. 9029161
10. Michel B, Grompone G, Flores MJ, Bidnenko V. Multiple pathways process stalled replication forks. Proc Natl Acad Sci USA. 2004;101(35):12783–8. 15328417
11. Cox MM. Recombinational DNA repair of damaged replication forks in Escherichia coli: questions. Ann Rev Genet. 2001;35:53–82. 11700277
12. Cox MM. Historical overview: Searching for replication help in all of the rec places. Proc Natl Acad Sci USA. 2001;98(15):8173–80. 11459950
13. Cox MM, Goodman MF, Kreuzer KN, Sherratt DJ, Sandler SJ, Marians KJ. The importance of repairing stalled replication forks. Nature. 2000;404(6773):37–41. 10716434
14. Kowalczykowski SC. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem Sci. 2000;25:156–65. 10754547
15. Kuzminov A. Single-strand interruptions in replicating chromosomes cause double-strand breaks. Proc Natl Acad Sci USA. 2001;98(15):8241–6. 11459959
16. Kuzminov A. DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination. Proc Natl Acad Sci USA. 2001;98(15):8461–8. 11459990
17. Cox MM. The bacterial RecA protein as a motor protein. Ann Rev Microbiol. 2003;57:551–77. 14527291
18. Lusetti SL, Cox MM. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Ann Rev Biochem. 2002;71:71–100. 12045091
19. Cox MM. The bacterial RecA protein: structure, function, and regulation. In: Rothstein R, Aguilera A, editors. Topics in Current Genetics: Molecular Genetics of Recombination. Heidelberg: Springer-Verlag; 2007. p. 53–94.
20. Cox MM. Motoring along with the bacterial RecA protein. Nature Rev Mol Cell Biol. 2007;8(2):127–38. ISI:000247564900002.
21. Clark AJ, Margulies AD. Isolation and characterization of recombination-deficient mutants of Escherichia coli K12. Proc Natl Acad Sci USA. 1965;53:451–9. 14294081
22. Howard-Flanders P, Theriot L. Mutants of Escherichia coli K-12 defective in DNA repair and in genetic recombination. Genetics. 1966;53:1137–50. 5335129
23. Rupp WD, Wilde CEd, Reno DL, Howard-Flanders P. Exchanges between DNA strands in ultraviolet-irradiated Escherichia coli. J Mol Biol. 1971;61(1):25–44. 4947693
24. Cox MM. Recombinational DNA repair in bacteria and the RecA protein. Prog Nuc Acids Res Mol Biol. 2000;63:311–66.
25. Cox MM. Regulation of bacterial RecA function. Crit Rev Biochem Mol Biol. 2007;42:41–63. 17364684
26. Kolodner RD, Putnam CD, Myung K. Maintenance of genome stability in Saccharomyces cerevisiae. Science. 2002;297(5581):552–7. 12142524
27. Myung K, Kolodner RD. Suppression of genome instability by redundant S-phase checkpoint pathways in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2002;99(7):4500–7. 11917116
28. Myung KJ, Datta A, Kolodner RD. Suppression of spontaneous chromosomal rearrangements by S phase checkpoint functions in Saccharomyces cerevisiae. Cell. 2001;104(3):397–408. 11239397
29. Thompson LH, Schild D. Recombinational DNA repair and human disease. Mutat Res-Fund Mol Mech Mutagen. 2002;509(1–2):49–78.
30. Shibata T, Das Gupta C, Cunningham RP, Radding CM. Purified Escherichia coli RecA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci USA. 1979;76(4):1638–42. 156361
31. Cunningham RP, Das Gupta C, Shibata T, Radding CM. Homologous pairing in genetic recombination: RecA protein makes joint molecules of gapped circular DNA and closed circular DNA. Cell. 1980;20(1):223–35. 7388943
32. Cunningham RP, Wu AM, Shibata T, Das Gupta C, Radding CM. Homologous pairing and topological linkage of DNA molecules by combined action of E. coli RecA protein and topoisomerase I. Cell. 1981;24(1):213–23. 6263487
33. Das Gupta C, Radding CM. Polar branch migration promoted by RecA protein: effect of mismatched base pairs. Proc Natl Acad Sci USA. 1982;79(3):762–6. 6950427
34. Cox MM, Lehman IR. Directionality and polarity in RecA protein-promoted branch migration. Proc Natl Acad Sci USA. 1981;78(10):6018–22. 6273839
35. McEntee K, Weinstock GM, Lehman IR. Initiation of general recombination catalyzed in vitro by the RecA protein of Escherichia coli. Proc Natl Acad Sci USA. 1979;76(6):2615–9. 379861
36. Cox MM, Lehman IR. RecA protein of Escherichia coli promotes branch migration, a kinetically distinct phase of DNA strand exchange. Proc Natl Acad Sci USA. 1981;78(6):3433–7. doi: 10.1073/pnas.78.6.3433 WOS:A1981LW77700025.
37. McEntee K, Weinstock GM, Lehman IR. Binding of the recA protein of Escherichia coli to single- and double-stranded DNA. J Biol Chem. 1981;256(16):8835–44. 7021553
38. Dunn K, Chrysogelos S, Griffith J. Electron microscopic visualization of RecA-DNA filaments: evidence for a cyclic extension of duplex DNA. Cell. 1982;28(4):757–65. 7046950
39. Stasiak A, Di Capua E. The helicity of DNA in complexes with RecA protein. Nature (London). 1982;299:185–6. 7050731
40. Griffith JD, Harris LD, Register Jd. Visualization of SSB-ssDNA complexes active in the assembly of stable RecA-DNA filaments. Cold Spring Harbor Symp Quant Biol. 1984;49(553):553–9. 6397310
41. Egner C, Azhderian E, Tsang SS, Radding CM, Chase JW. Effects of various single-stranded-DNA-binding proteins on reactions promoted by RecA protein. J Bacteriol. 1987;169(8):3422–8. 3301800
42. Shan Q, Cox MM. RecA filament dynamics during DNA strand exchange reactions. J Biol Chem. 1997;272(17):11063–73. 9111000
43. Haruta N, Yu XN, Yang SX, Egelman EH, Cox MM. A DNA pairing-enhanced conformation of bacterial RecA proteins. J Biol Chem. 2003;278(52):52710–23. 14530291
44. Witkin EM. Thermal enhancement of ultraviolet mutability in a tif-1 uvrA derivative of Escherichia coli B/r: evidence that ultraviolet mutagenesis depends upon an inducible function. Proc Natl Acad Sci USA. 1974;71(5):1930–4. 4600265
45. Witkin EM. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol Rev. 1976;40(4):869–907. 795416
46. Linn LL, Little JW. Autodigestion and RecA-dependent cleavage of Ind- mutant LexA proteins. J Mol Biol. 1989;210(3):473-. 2693735
47. Little JW. Mechanism of specific LexA cleavage—autodigestion and the role of RecA coprotease. Biochimie. 1991;73(4):411–22. 1911941
48. Little JW, Edmiston SH, Pacelli LZ, Mount DW. Cleavage of the Escherichia coli LexA protein by the RecA protease. Proc Natl Acad Sci USA. 1980;77(6):3225–9. 6447873
49. Devoret R. Les fonctions SOS ou comment les bactéries survivent aux lésions de leur ADN. Annales de l'Inst Pasteur Actualités. 1992;1:11–20.
50. Ennis DG, Fisher B, Edmiston S, Mount DW. Dual role for Escherichia coli RecA protein in SOS mutagenesis. Proc Natl Acad Sci USA. 1985;82(10):3325–9. 3159017
51. Lu C, Echols H. RecA protein and SOS. Correlation of mutagenesis phenotype with binding of mutant RecA proteins to duplex DNA and LexA cleavage. J Mol Biol. 1987;196(3):497–504. 2960817
52. Radman M. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. In: Hanawalt P, Setlow RB, editors. Molecular mechanisms for repair of DNA, Part A. New York: Plenum Publishing Corp.; 1975. p. 355–67.
53. Walker GC, Smith BT, Sutton MD. The SOS response to DNA damage. In: Storz G, HenggeAronis R, editors. Bacterial Stress Responses. Washington, D.C.: American Society of Microbiology; 2000. p. 131–44.
54. Witkin EM. RecA protein in the SOS response: milestones and mysteries. Biochimie. 1991;73(2–3):133–41.
55. Bridges BA. Error-prone DNA repair and translesion DNA synthesis. II: The inducible SOS hypothesis. DNA Repair (Amst). 2005;4(6):725–6, 39. 15907776.
56. Sweasy JB, Witkin EM, Sinha N, Roegner-Maniscalco V. RecA protein of Escherichia coli has a third essential role in SOS mutator activity. J Bacteriol. 1990;172(6):3030–6. 2188949
57. Witkin EM, Kogoma T. Involvement of the activated form of RecA protein in SOS mutagenesis and stable DNA replication in Escherichia coli. Proc Natl Acad Sci USA. 1984;81(23):7539–43. 6390441
58. Tang MJ, Shen X, Frank EG, O'Donnell M, Woodgate R, Goodman MF. UmuD'C-2 is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci USA. 1999;96(16):8919–24. doi: 10.1073/pnas.96.16.8919 WOS:000081835500029.
59. Napolitano RL, Lambert IB, Fuchs RP. SOS factors involved in translesion synthesis. Proc Natl Acad Sci USA. 1997;94(11):5733–8. 9159142
60. Burckhardt SE, Woodgate R, Scheuermann RH, Echols H. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci USA. 1988;85(6):1811–5. 3279417
61. Nohmi T, Battista JR, Dodson LA, Walker GC. RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci USA. 1988;85(6):1816–20. 3279418
62. Shinagawa H, Iwasaki H, Kato T, Nakata A. RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci USA. 1988;85(6):1806–10. 3126496
63. Erdem AL, Jaszczur M, Bertram JG, Woodgate R, Cox MM, Goodman MF. DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase. eLife. 2014;3:e02384. doi: 107554/eLife.02384 WOS:000334923200008.
64. Gruber AJ, Erdem AL, Sabat G, Karata K, Jaszczur MM, Vo DD, et al. A RecA protein surface required for activation of DNA polymerase V. PLoS Genet. 2015;11(3):e1005066. doi: 10.1371/journal.pgen.1005066 25811184
65. Jiang Q, Karata K, Woodgate R, Cox MM, Goodman MF. The active form of DNA polymerase V is UmuD'2C•RecA•ATP. Nature. 2009;460:359–63. doi: 10.1038/nature08178 19606142
66. Patel M, Jiang QF, Woodgate R, Cox MM, Goodman MF. A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol. 2010;45(3):171–84. doi: 10.3109/10409238.2010.480968 ISI:000279107800001.
67. Schlacher K, Leslie K, Wyman C, Woodgate R, Cox MM, Goodman MF. DNA polymerase V and RecA protein, a minimal mutasome. Mol Cell. 2005;17(4):561–72. 15721259
68. Ogawa T, Wabiko H, Tsurimoto T, Horii T, Masukata H, Ogawa H. Characteristics of purified RecA protein and the regulation of its synthesis in vivo. Cold Spring Harbor Symp Quant Biol. 1979;2(909):909–15.
69. Roberts JW, Roberts CW, Craig NL, Phizicky EM. Activity of the Escherichia coli recA-gene product. Cold Spring Harbor Symp Quant Biol. 1979;43:917–20. 158477
70. Das Gupta C, Shibata T, Cunningham RP, Radding CM. The topology of homologous pairing promoted by RecA protein. Cell. 1980;22(2 Pt 2):437–46. 7004644
71. Brenner SL, Mitchell RS, Morrical SW, Neuendorf SK, Schutte BC, Cox MM. RecA protein-promoted ATP hydrolysis occurs throughout RecA nucleoprotein filaments. J Biol Chem. 1987;262(9):4011–6. 2951381
72. Shan Q, Bork JM, Webb BL, Inman RB, Cox MM. RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins. J Mol Biol. 1997;265(5):519–40. 9048946
73. Schutte BC, Cox MM. Homology-dependent changes in adenosine 5'-triphosphate hydrolysis during RecA protein promoted DNA strand exchange: evidence for long paranemic complexes. Biochemistry. 1987;26(18):5616–25. 3314992
74. Galletto R, Amitani I, Baskin RJ, Kowalczykowski SC. Direct observation of individual RecA filaments assembling on single DNA molecules. Nature. 2006;443(7113):875–8. ISI:000241362700056.
75. Handa N, Amitani I, Gumlaw N, Sandler SJ, Kowalczykowski SC. Single molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions. J Biol Chem. 2009;284(28):18664–73. doi: 10.1074/jbc.M109.004895 WOS:000267711500015.
76. Shibata T, Cunningham RP, Das Gupta C, Radding CM. Homologous pairing in genetic recombination: complexes of RecA protein and DNA. Proc Natl Acad Sci USA. 1979;76(10):5100–4. 159453
77. Das Gupta C, Wu AM, Kahn R, Cunningham RP, Radding CM. Concerted strand exchange and formation of Holliday structures by E. coli RecA protein. Cell. 1981;25(2):507–16. 7026047
78. Kahn R, Cunningham RP, Das Gupta C, Radding CM. Polarity of heteroduplex formation promoted by Escherichia coli RecA protein. Proc Natl Acad Sci USA. 1981;78(8):4786–90. 6272272
79. West SC, Cassuto E, Howard-Flanders P. Heteroduplex formation by RecA protein: polarity of strand exchanges. Proc Natl Acad Sci USA. 1981;78(10):6149–53. 6273854
80. Massoni SC, Leeson MC, Long JE, Gemme K, Mui A, Sandler SJ. Factors limiting SOS expression in log-phase cells of Escherichia coli. J Bacteriol. 2012;194(19):5325–33. doi: 10.1128/jb.00674-12 WOS:000308749700018.
81. Massoni SC, Sandler SJ. Specificity in suppression of SOS expression by recA4162 and uvrD303. DNA Repair. 2013;12(12):1072–80. doi: 10.1016/j.dnarep.2013.09.003 WOS:000328595000008.
82. Lusetti SL, Hobbs MD, Stohl EA, Chitteni-Pattu S, Inman RB, Seifert HS, et al. The RecF protein antagonizes RecX function via direct interaction. Mol Cell. 2006;21(1):41–50. 16387652
83. Umezu K, Kolodner RD. Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J Biol Chem. 1994;269(47):30005–13. 7962001
84. Bentchikou E, Servant P, Coste G, Sommer S. A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genet. 2009;6:e1000774. doi: 10.1371/journal.pgen.1000774 20090937
85. Morimatsu K, Kowalczykowski SC. RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: A universal step of recombinational repair. Mol Cell. 2003;11(5):1337–47. 12769856
86. Morimatsu K, Wu Y, Kowalczykowski SC. RecFOR proteins target RecA protein to a DNA gap with either DNA or RNA at the 5 ' terminus: implication for repair of stalled replication forks. J Biol Chem. 2012;287(42):35621–30. doi: 10.1074/jbc.M112.397034 WOS:000309968000074.
87. Sakai A, Cox MM. RecFOR and RecOR as distinct RecA loading pathways. J Biol Chem. 2009;284(5):3264–72. doi: 10.1074/jbc.M807220200 ISI:000262700900069.
88. Drees JC, Lusetti SL, Chitteni-Pattu S, Inman RB, Cox MM. A RecA filament capping mechanism for RecX protein. Mol Cell. 2004;15(5):789–98. 15350222
89. Drees JC, Lusetti SL, Cox MM. Inhibition of RecA protein by the Escherichia coli RecX protein—Modulation by the RecA C terminus and filament functional state. J Biol Chem. 2004;279(51):52991–7. 15466870
90. Gruenig MC, Stohl EA, Chitteni-Pattu S, Seifert HS, Cox MM. Less Is More: Neisseria gonorrhoeae RecX protein stimulates recombination by inhibiting RecA. J Biol Chem. 2010;285(48):37188–97. doi: 10.1074/jbc.M110.171967 WOS:000284424000012.
91. Lusetti SL, Drees JC, Stohl EA, Seifert HS, Cox MM. The DinI and RecX proteins are competing modulators of RecA function. J Biol Chem. 2004;279(53):55073–9. 15489505
92. Venkatesh R, Ganesh N, Guhan N, Reddy MS, Chandrasekhar T, Muniyappa K. RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: Insights into negative regulation of homolgous recombination. Proc Natl Acad Sci USA. 2002;99(19):12091–6. 12218174
93. Lusetti SL, Voloshin ON, Inman RB, Camerini-Otero RD, Cox MM. The DinI protein stabilizes RecA protein filaments. J Biol Chem. 2004;279(29):30037–46. 15138263
94. Yoshimasu M, Aihara H, Ito Y, Rajesh S, Ishibe S, Mikawa T, et al. An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes. Nuc Acids Res. 2003;31(6):1735–43. 12626715
95. Drees JC, Chitteni-Pattu S, McCaslin DR, Inman RB, Cox MM. Inhibition of RecA protein function by the RdgC protein from Escherichia coli. J Biol Chem. 2006;281(8):4708–17. 16377615
96. Petrova V, Satyshur KA, George NP, McCaslin D, Cox MM, Keck JL. X-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of RecA. J Biol Chem. 2010;285(40):30615–21. doi: 10.1074/jbc.M110.152298 ISI:000282135500030.
97. Uranga LA, Balise VD, Benally CV, Grey A, Lusetti SL. The Escherichia coli DinD protein modulates RecA activity by Iinhibiting postsynaptic RecA filaments. J Biol Chem. 2011;286(34):29480–91. doi: 10.1074/jbc.M111.245373 WOS:000294046600005.
98. Flores MJ, Sanchez N, Michel B. A fork-clearing role for UvrD. Mol Microbiol. 2005;57(6):1664–75. 16135232
99. Veaute X, Delmas P, Selva M, Jeusset J, Le Cam E, Matic I, et al. UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. EMBO J. 2005;24(1):180–9. 15565170
100. Petrova V, Chen SH, Molzberger ET, Tomko EJ, Chitteni-Pattu S, Jia HF, et al. Active displacement of RecA filaments by UvrD translocase activity. Nuc Acids Res. 2015;43.
101. Papavinasasundaram KG, Colston MJ, Davis EO. Construction and complementation of a recA deletion mutant of Mycobacterium smegmatis reveals that the intein in Mycobacterium tuberculosis recA does not affect RecA function. Mol Microbiol. 1998;30(3):525–34. 9822818
102. Sano Y. Role of the recA-related gene adjacent to the recA gene in Pseudomonas aeruginosa. J Bacteriol. 1993;175(8):2451–4. 8468303
103. Sukchawalit R, Vattanaviboon P, Utamapongchai S, Vaughn G, Mongkolsuk S. Characterization of Xanthomonas oryzae pv. oryzae recX, a gene that is required for high-level expression of recA. FEMS Microbiol Lett. 2001;205(1):83–9. 11728720
104. Vierling S, Weber T, Wohlleben W, Muth G. Transcriptional and mutational analyses of the Streptomyces lividans recX gene and its interference with RecA activity. J Bacteriol. 2000;182(14):4005–11. 10869079
105. Pages V, Koffel-Schwartz N, Fuchs RP. recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli. DNA Repair. 2003;2(3):273–84. 12547390
106. Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski SC, Siefert HS. Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo. J Biol Chem. 2003;278(4):2278–85. 12427742
107. VanLoock MS, Yu X, Yang S, Galkin VE, Huang H, Rajan SS, et al. Complexes of RecA with LexA and RecX differentiate between active and Inactive RecA nucleoprotein filaments. J Mol Biol. 2003;333(2):345–54. 14529621
108. Smith GR. Conjugational recombination in E. coli: myths and mechanisms. Cell. 1991;64(1):19–27. 1986865
109. Lloyd RG, Buckman C. Conjugational recombination in Escherichia coli: genetic analysis of recombinant formation in Hfr x F- crosses. Genetics. 1995;139(3):1123–48. 7768428
110. Battista JR, Earl AM, Park MJ. Why is Deinococcus radiodurans so resistant to ionizing radiation? Trends Microbiol. 1999;7(9):362–5. 10470044
111. Blasius M, Hubscher U, Sommer S. Deinococcus radiodurans: What belongs to the survival kit? Crit Rev Biochem Mol Biol. 2008;43(3):221–38. doi: 10.1080/10409230802122274 ISI:000256840600003.
112. Cox MM, Battista JR. Deinococcus radiodurans—The consummate survivor. Nature Rev Microbiol. 2005;3(11):882–92. 16261171
113. Kim J-I, Cox MM. The RecA proteins of Deinococcus radiodurans and Escherichia coli promote DNA strand exchange via inverse pathways. Proc Natl Acad Sci USA. 2002;99:7917–21. 12048253
114. Ngo KV, Molzberger ET, Chitteni-Pattu S, Cox MM. Regulation of Deinococcus radiodurans RecA protein function via modulation of active and inactive nucleoprotein filament states. J Biol Chem. 2013;288(July 19):21351–66.
115. Slade D, Lindner AB, Paul G, Radman M. Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans. Cell. 2009;136(6):1044–55. doi: 10.1016/j.cell.2009.01.018 ISI:000264403900011.
116. Byrne RT, Klingele AJ, Cabot EL, Schackwitz WS, Martin JA, Martin J, et al. Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair eLife. 2014;3:e01322. doi: 10.7554/eLife.01322 24596148
117. Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, et al. Directed evolution of radiation resistance in Escherichia coli. J Bacteriol. 2009;191:5240–52. doi: 10.1128/JB.00502-09 19502398
118. Bakhlanova IV, Dudkina AV, Baitin DM, Knight KL, Cox MM, Lanzov VA. Modulating cellular recombination potential through alterations in RecA structure and regulation. Mol Microbiol. 2010;78(6):1523–38. doi: 10.1111/j.1365-2958.2010.07424.x WOS:000285156600016.
119. McGrew DA, Knight KL. Molecular design and functional organization of the RecA protein. Crit Rev Biochem Mol Biol. 2003;38(5):385–432. doi: 10.1080/10409230390242489 WOS:000188164100001.
120. Firnberg E, Ostermeier M. The genetic code constrains yet facilitates Darwinian evolution. Nuc Acids Res. 2013;41(15):7420–8. doi: 10.1093/nar/gkt536 WOS:000323970700027.
121. Vetsigian K, Woese C, Goldenfeld N. Collective evolution and the genetic code. Proc Natl Acad Sci USA. 2006;103(28):10696–701. doi: 10.1073/pnas.0603780103 WOS:000239047400029.
122. Irvine D, Tuerk C, Gold L. SELEXION—Systematic evolution of ligands by exponential enrichment with integrated optimization by nonlinear analysis. J Mol Biol. 1991;222(3):739–61. doi: 10.1016/0022-2836(91)90509-5 WOS:A1991GV58300027.
123. Schneider D, Gold L, Platt T. Selective enrichment of RNA species for tight binding to Escherichia coli Rho factor. FASEB J. 1993;7(1):201–7. WOS:A1993KH88000031.
124. Schneider D, Tuerk C, Gold L. Selection of high-affinity RNA ligands to the bacteriophage-R17 coat protein. J Mol Biol. 1992;228(3):862–9. doi: 10.1016/0022-2836(92)90870-p WOS:A1992KD72100014.
125. Tuerk C, Macdougal S, Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type-1 reverse transcriptase. Proc Natl Acad Sci USA. 1992;89(15):6988–92. doi: 10.1073/pnas.89.15.6988 WOS:A1992JF85600068.
126. Cox JM, Li H, Wood EA, Chitteni-Pattu S, Inman RB, Cox MM. Defective dissociation of a "Slow" RecA mutant protein imparts an Escherichia coli growth defect. J Biol Chem. 2008;283(36):24909–21. doi: 10.1074/jbc.M803934200 ISI:000258820000054.
127. Hoeijmakers JHJ. Molecular origins of cancer: DNA Damage, Aging, and Cancer. New Eng J Med. 2009;361(15):1475–85. doi: 10.1056/NEJMra0804615 WOS:000270540000009.
128. Bedale WA, Cox M. Evidence for the coupling of ATP hydrolysis to the final (extension) phase of RecA protein-mediated DNA strand exchange. J Biol Chem. 1996;271(10):5725–32. 8621438
129. Kim JI, Cox MM, Inman RB. On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. II. Four-strand exchanges. J Biol Chem. 1992;267(23):16444–9. 1644828
130. Kim JI, Cox MM, Inman RB. 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. 1992;267(23):16438–43. 1644827
131. Lee JW, Cox MM. Inhibition of RecA protein-promoted ATP hydrolysis. I. ATPγS and ADP are antagonistic inhibitors. Biochemistry. 1990;29(33):7666–76. 2148682
132. Lee JW, Cox MM. Inhibition of RecA protein-promoted ATP hydrolysis. II. Longitudinal assembly and disassembly of RecA protein filaments mediated by ATP and ADP. Biochemistry. 1990;29(33):7677–83. 2271526
133. Lusetti SL, Wood EA, Fleming CD, Modica MJ, Korth J, Abbott L, et al. C-terminal deletions of the Escherichia coli RecA protein—Characterization of in vivo and in vitro effects. J Biol Chem. 2003;278(18):16372–80. 12598539
134. Arenson TA, Tsodikov OV, Cox MM. Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA. J Mol Biol. 1999;288(3):391–401. 10329149
135. Baitin DM, Bakhlanova IV, Chervyakova DV, Kil YV, Lanzov VA, Cox MM. Two RecA protein types that mediate different modes of hyperrecombination. J Bacteriol. 2008;190:3036–45. doi: 10.1128/JB.01006-07 18296520
136. Cox JM, Abbott SN, Chitteni-Pattu S, Inman RB, Cox MM. Complementation of one RecA protein point mutation by another—Evidence for trans catalysis of ATP hydrolysis. J Biol Chem. 2006;281(18):12968–75. 16527806
137. Cox JM, Tsodikov OV, Cox MM. Organized unidirectional waves of ATP hydrolysis within a RecA filament. PLoS Biol. 2005;3(2):231–43.
138. Kowalczykowski SC, Clow J, Krupp RA. Properties of the duplex DNA-dependent ATPase activity of Escherichia coli RecA protein and its role in branch migration. Proc Natl Acad Sci USA. 1987;84(10):3127–31. 3033635
139. Eggler AL, Lusetti SL, Cox MM. The C terminus of the Escherichia coli RecA protein modulates the DNA binding competition with single-stranded DNA-binding protein. J Biol Chem. 2003;278(18):16389–96. 12598538
140. Shan Q, Cox MM. RecA protein dynamics in the interior of RecA nucleoprotein filaments. J Mol Biol. 1996;257:756–74. 8636980
141. Nayak S, Bryant FR. Differential rates of NTP hydrolysis by the mutant [S69G]RecA protein—Evidence for a coupling of NTP turnover to DNA strand exchange. J Biol Chem. 1999;274(37):25979–82. 10473540
142. Shan Q, Cox MM. On the mechanism of RecA-mediated repair of double-strand breaks: no role for four-strand DNA pairing intermediates. Mol Cell. 1998;1:309–17. 9659927
143. Caillet FP, Maenhaut MG,. Nature of the SOS mutator activity: genetic characterization of untargeted mutagenesis in Escherichia coli. Mol Gen Genet. 1988;213(2–3):491–8. 3185512
144. Cazaux C, Mazard AM, Defais M. Inducibility of the SOS response in a recA730 or recA441 strain is restored by transformation with a new recA allele. Mol Gen Genet. 1993;240(2):296–301. 8355662
145. Gruenig MC, Renzette N, Long E, Chitteni-Pattu S, Inman RB, Cox MM, et al. RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis. Mol Microbiol. 2008;69(5):1165–79. ISI:000258222700007. doi: 10.1111/j.1365-2958.2008.06341.x
146. Lieberman HB, Witkin EM. DNA degradation, UV sensitivity and SOS-mediated mutagenesis in strains of Escherichia coli deficient in single-strand DNA binding protein: effects of mutations and treatments that alter levels of exonuclease V or RecA protein. Mol Gen Genet. 1983;190(1):92–100. 6343804
147. Lenski RE, Rose MR, Simpson SC, Tadler SC. Long-term experimental evolution in Escherichia-coli.1. Adaptation and divergence during 2,000 generations. American Naturalist. 1991;138(6):1315–41. doi: 10.1086/285289 WOS:A1991HB55000001.
148. Centore RC, Sandler SJ. UvrD limits the number and intensities of RecA-Green fluorescent protein structures in Escherichia coli K-12. J Bacteriol. 2007;189(7):2915–20. ISI:000245842000037.
149. Lestini R, Michel B. UvrD controls the access of recombination proteins to blocked replication forks. EMBO J. 2007;26(16):3804–14. Epub 2007/07/21. 7601804 [pii] doi: 10.1038/sj.emboj.7601804 17641684; PubMed Central PMCID: PMC1952219.
150. Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev. 1999;63(4):751–813. 263KC-0002.
151. Rehrauer WM, Kowalczykowski SC. Alteration of the nucleoside triphosphate (NTP) catalytic domain within Escherichia coli recA protein attenuates NTP hydrolysis but not joint molecule formation. J Biol Chem. 1993;268(2):1292–7. 8419331
152. Shan Q, Cox MM, Inman RB. DNA strand exchange promoted by RecA K72R. Two reaction phases with different Mg2+ requirements. J Biol Chem. 1996;271(10):5712–24. 8621437
153. Neuendorf SK, Cox MM. Exchange of RecA protein between adjacent RecA protein-single-stranded DNA complexes. J Biol Chem. 1986;261(18):8276–82. 3755133
154. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA. 2000;97(12):6640–5. 10829079
155. Britt RL, Haruta N, Lusetti SL, Chitteni-Pattu S, Inman RB, Cox MM. Disassembly of Escherichia coli RecA E38K/ΔC17 nucleoprotein filaments is required to complete DNA strand exchange. J Biol Chem. 2010;285(5):3211–26. doi: 10.1074/jbc.M109.028951 19910465
156. Petrova V, Chitteni-Pattu S, Drees JC, Inman RB, Cox MM. An SOS inhibitor that binds to free RecA protein: the PsiB protein. Mol Cell. 2009;36:121–30. doi: 10.1016/j.molcel.2009.07.026 19818715
157. Lohman TM, Overman LB. Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J Biol Chem. 1985;260(6):3594–603. 3882711
158. Craig NL, Roberts JW. Function of nucleoside triphosphate and polynucleotide in Escherichia coli RecA protein-directed cleavage of phage lambda repressor. J Biol Chem. 1981;256(15):8039–44. 6455420
159. Hill DE, Oliphant AR, Struhl K. Mutagenesis with degenerate oligonucleotides—an efficient method for saturating a defined DNA region with base pair substitutions. Meth Enzymol. 1987;155:558–68. WOS:A1987M168800034.
160. Reidhaar-Olson JF, Bowie JU, Breyer RM, Hu JC, Knight KL, Lim WA, et al. Random mutagenesis of protein sequences using oligonucleotide cassettes. Meth Enzymol. 1991;208:564–86. WOS:A1991MC42800028.
161. Miller JH. A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1992.
162. Lindsley JE, Cox MM. Assembly and disassembly of RecA protein filaments occurs at opposite filament ends: relationship to DNA strand exchange. J Biol Chem. 1990;265(16):9043–54. 2188972
163. Morrical SW, Cox MM. Stabilization of RecA protein-ssDNA complexes by the single-stranded DNA binding protein of Escherichia coli. Biochemistry. 1990;29(3):837–43. 2186808
164. Breed RS, Dotterrer WD. The number of colonies allowable on satisfactory agar plates. J Bacteriol. 1916;1:321–31. 16558698
165. Chen ZC, Yang HJ, Pavletich NP. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature. 2008;453(7194):489–94. ISI:000256023700035. doi: 10.1038/nature06971
166. Shibata T, Ohtani T, Iwabuchi M, Ando T. D-loop cycle. A circular reaction sequence which comprises formation and dissociation of D-loops and inactivation and reactivation of superhelical closed circular DNA promoted by RecA protein of Escherichia coli. J Biol Chem. 1982;257(23):13981–6. 6754721
167. Wu AM, Kahn R, Das Gupta C, Radding CM. Formation of nascent heteroduplex structures by RecA protein and DNA. Cell. 1982;30(1):37–44. 6751562
168. Pugh BF, Cox MM. Stable binding of RecA protein to duplex DNA. Unraveling a paradox. J Biol Chem. 1987;262(3):1326–36. 3543002
169. Pugh BF, Cox MM. General mechanism for RecA protein binding to duplex DNA. J Mol Biol. 1988;203(2):479–93. 3058986
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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