A RecA Protein Surface Required for Activation of DNA Polymerase V

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DNA polymerase V from the bacterium Escherichia coli is one of a class of DNA polymerases that replicate DNA inaccurately. They thus generate mutations at elevated levels. Whereas this might seem incongruous with the goal of accurate transmission of genetic information from one generation to the next, it is actually part of a specialized bacterial DNA repair process that comes into play principally when cells are severely stressed by high loads of DNA damage. Polymerase V is normally inactive. The transfer of one subunit from the bacterial recombinase RecA, and the addition of ATP, leads to the formation of the active pol V Mutasome (Mut) (UmuD′2C-RecA-ATP). The current study delves deeper into this process, initiating the task of mapping out the molecular details of the interaction between RecA and UmuD′2C. One surface region on the RecA protein required for this activation is defined, the step in the activation process that is affected by this surface is identified, and a direct interaction (or at least very close proximity) between this surface and particular amino acid residues in the UmuC protein is demonstrated. A new RecA variant protein is generated that provides improved separation of function, in that the activation of pol V is abolished while minimally affecting other RecA functions. The study also provides a molecular consummation for a series of incisive genetic studies carried out nearly two decades ago.

Vyšlo v časopise: A RecA Protein Surface Required for Activation of DNA Polymerase V. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005066
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005066

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Zdroje

1. Cox MM (2004) The RecA Protein. In: Higgins NP, editor. The Bacterial Chromosome. Washington, D. C.: American Society of Microbiology. pp. 369–388.

2. Cox MM (2007) 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. pp. 53–94.

3. Lusetti SL, Cox MM (2002) The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu Rev Biochem 71: 71–100. 12045091

4. Arenson TA, Tsodikov OV, Cox MM (1999) Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA. J Mol Biol 288: 391–401. 10329149

5. Bork JM, Cox MM, Inman RB (2001) RecA protein filaments disassemble in the 5' to 3' direction on single-stranded DNA. J Biol Chem 276: 45740–45743. 11574550

6. Cox MM, Lehman IR (1981) Directionality and polarity in RecA protein-promoted branch migration. Proc Natl Acad Sci USA 78: 6018–6022. 6273839

7. Cox JM, Tsodikov OV, Cox MM (2005) Organized unidirectional waves of ATP hydrolysis within a RecA filament. PLoS Biol 3: 231–243.

8. Lindsley JE, Cox MM (1990) Assembly and disassembly of RecA protein filaments occurs at opposite filament ends: relationship to DNA strand exchange. J Biol Chem 265: 9043–9054. 2188972

9. Register JC III, Griffith J (1985) The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange. J Biol Chem 260: 12308–12312. 3900072

10. Bell JC, Plank JL, Dombrowski CC, Kowalczykowski SC (2012) Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature 491: 274–U144. doi: 10.1038/nature11598 23103864

11. Kim B, Little JW (1993) LexA and lambda Cl repressors as enzymes: specific cleavage in an intermolecular reaction. Cell 73: 1165–1173. 8513500

12. Little JW (1991) Mechanism of specific LexA cleavage—autodigestion and the role of RecA coprotease. Biochimie 73: 411–422. 1911941

13. Shinagawa H (1996) SOS response as an adaptive response to DNA damage in prokaryotes. Exs 77: 221–235. 8856977

14. Burckhardt SE, Woodgate R, Scheuermann RH, Echols H (1988) UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci USA 85: 1811–1815. 3279417

15. Nohmi T, Battista JR, Dodson LA, Walker GC (1988) RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci USA 85: 1816–1820. 3279418

16. Shinagawa H, Iwasaki H, Kato T, Nakata A (1988) RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci USA 85: 1806–1810. 3126496

17. Jiang Q, Karata K, Woodgate R, Cox MM, Goodman MF (2009) The active form of DNA polymerase V is UmuD′2C•RecA•ATP. Nature 460: 359–363. doi: 10.1038/nature08178 19606142

18. Janion C (2008) Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli. Int J Biol Sci 4: 338–344. 18825275

19. Bridges BA (2005) Error-prone DNA repair and translesion DNA synthesis. II: The inducible SOS hypothesis. DNA Repair (Amst) 4: 725–726, 739. 15907776

20. McCool JD, Long E, Petrosino JF, Sandler HA, Rosenberg SM, et al. (2004) Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy. Mol Microbiol 53: 1343–1357. 15387814

21. Sutton MD, Smith BT, Godoy VG, Walker GC (2000) The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Annu Rev Genet 34: 479–497. 11092836

22. Walker GC, Smith BT, Sutton MD (2000) The SOS response to DNA damage. In: Storz G, HenggeAronis R, editors. Bacterial Stress Responses. Washington, D.C.: American Society of Microbiology. pp. 131–144.

23. Friedman N, Vardi S, Ronen M, Alon U, Stavans J (2005) Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol 3: 1261–1268.

24. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC (2001) Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics 158: 41–64. 11333217

25. Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, et al. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol 35: 1560–1572. 10760155

26. Bridges BA (1999) DNA repair: Polymerases for passing lesions. Curr Biol 9: R475–477. 10395530

27. Delmas S, Matic I (2006) Interplay between replication and recombination in Escherichia coli: Impact of the alternative DNA polymerases. Proc Natl Acad Sci USA 103: 4564–4569. 16537389

28. Friedberg EC, Fischhaber PL, Kisker C (2001) Error-prone DNA polymerases: novel structures and the benefits of infidelity. Cell 107: 9–12. 11595180

29. Friedberg EC, Wagner R, Radman M (2002) Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science 296: 1627–1630. 12040171

30. Friedberg EC (2005) Suffering in silence: The tolerance of DNA damage. Nature Rev Mol Cell Biol 6: 943–953. 16341080

31. Hubscher U, Nasheuer HP, Syvaoja JE (2000) Eukaryotic DNA polymerases, a growing family. Trends Biochem Sci 25: 143–147. 10694886

32. Livneh Z (2001) DNA damage control by novel DNA polymerases: Translesion replication and mutagenesis. J Biol Chem 276: 25639–25642. 11371576

33. Patel M, Jiang QF, Woodgate R, Cox MM, Goodman MF (2010) A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev Biochem Mol Biol 45: 171–184. doi: 10.3109/10409238.2010.480968 20441441

34. Ramadan K, Shevelev I, Hubscher U (2004) The DNA-polymerase-X family: controllers of DNA quality? Nature Rev Mol Cell Biol 5: 1038–1043. 15573140

35. Schlacher K, Pham P, Cox MM, Goodman MF (2006) Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation. Chem Rev 106: 406–419. 16464012

36. Vaisman A, Lehmann AR, Woodgate R (2004) DNA polymerases eta and iota. DNA Repair Replicat 69: 205–228.

37. Yang W (2003) Damage repair DNA polymerases Y. Curr Opin Struct Biol 13: 23–30. 12581656

38. Maor-Shoshani A, Reuven NB, Tomer G, Livneh Z (2000) Highly mutagenic replication by DNA polymerase V (UmuC) provides a mechanistic basis for SOS untargeted mutagenesis. Proc Natl Acad Sci USA 97: 565–570. 10639119

39. Pham P, Bertram JG, O'Donnell M, Woodgate R, Goodman MF (2001) A model for SOS-lesion-targeted mutations in Escherichia coli involving pol V, RecA, SSB, and β-sliding clamp. Nature 409: 366–370. 11201748

40. Pham P, Rangarajan S, Woodgate R, Goodman MF (2001) Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc Natl Acad Sci USA 98: 8350–8354. 11459974

41. Walker GC (1995) SOS-regulated proteins in translesion DNA synthesis and mutagenesis. Trends Biochem Sci 20: 416–420. 8533155

42. Bruck I, Woodgate R, McEntee K, Goodman MF (1996) Purification of a soluble UmuD'C complex from Escherichia coli—Cooperative binding of UmuD'C to single-stranded DNA. J Biol Chem 271: 10767–10774. 8631887

43. Karata K, Vaisman A, Goodman MF, Woodgate R (2012) Simple and efficient purification of Escherichia coli DNA polymerase V: Cofactor requirements for optimal activity and processivity in vitro. DNA Repair 11: 431–440. doi: 10.1016/j.dnarep.2012.01.012 22341652

44. Tang MJ, Bruck I, Eritja R, Turner J, Frank EG, et al. (1998) Biochemical basis of SOS-induced mutagenesis in Escherichia coli: Reconstitution of in vitro lesion bypass dependent on the UmuD′2C mutagenic complex and RecA protein. Proc Natl Acad Sci USA 95: 9755–9760. 9707548

45. Tang MJ, Shen X, Frank EG, O'Donnell M, Woodgate R, et al. (1999) UmuD′2C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci USA 96: 8919–8924. 10430871

46. Erdem AL, Jaszczur M, Bertram JG, Woodgate R, Cox MM, et al. (2014) DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase. eLife 3: e02384. doi: 10.7554/eLife.02384 24843026

47. Lawrence CW, Borden A, Woodgate R (1996) Analysis of the mutagenic properties of the UmuDC, MucAB and RumAB proteins, using a site-specific abasic lesion. Mol Gen Genet 251: 493–498. 8709953

48. Kulaeva OI, Wootton JC, Levine AS, Woodgate R (1995) Characterization of the Umu-complementing operon from R391. J Bacteriol 177: 2737–2743. 7751283

49. Venderbure C, Chastanet A, Boudsocq F, Sommer S, Bailone A (1999) Inhibition of homologous recombination by the plasmid MucA'B complex. J Bacteriol 181: 1249–1255. 9973352

50. O'Grady PI, Borden A, Vandewiele D, Ozgenc A, Woodgate R, et al. (2000) Intrinsic polymerase activities of UmuD′2C and MucA′2B are responsible for their different mutagenic properties during bypass of a T-T cis-syn cyclobutane dimer. J Bacteriol 182: 2285–2291. 10735873

51. Mead S, Vaisman A, Valjavec-Gratian M, Karata K, Vandewiele D, et al. (2007) Characterization of polV(R391): a Y-family polymerase encoded by rumA'B from the IncJ conjugative transposon, R391. Mol Microbiol 63: 797–810. 17302804

52. Szekeres ES, Woodgate R, Lawrence CW (1996) Substitution of mucAB or rumAB for umuDC alters the relative frequencies of the two classes of mutations induced by a site-specific T-T cyclobutane dimer and the efficiency of translesion DNA synthesis. J Bacteriol 178: 2559–2563. 8626322

53. Bailone A, Sommer S, Knezevic J, Dutreix M, Devoret R (1991) A RecA Protein Mutant Deficient in its Interaction with the UmuDC Complex. Biochimie 73: 479–484. 1911948

54. Bailone A, Devoret R, Sommer S (1995) New RecA Mutants Resistant to UmuD'C Proteins. J Cell Biochem: 346–346.

55. Dutreix M, Moreau PL, Bailone A, Galibert F, Battista JR, et al. (1989) New recA mutations that dissociate the various RecA protein activities in Escherichia coli provide evidence for an additional role for RecA protein in UV mutagenesis. J Bacteriol 171: 2415–2423. 2651400

56. Dutreix M, Burnett B, Bailone A, Radding CM, Devoret R (1992) A partially deficient mutant, recA1730, that fails to form normal nucleoprotein filaments. Mol Gen Genet 232: 489–497. 1534140

57. Sommer S, Boudsocq F, Devoret R, Bailone A (1998) Specific RecA amino acid changes affect RecA-UmuD'C interaction. Mol Microbiol 28: 281–291. 9622353

58. Sommer S, Coste G, Bailone A (2000) Specific amino acid changes enhance the anti-recombination activity of the UmuD'C complex. Mol Microbiol 35: 1443–1453. 10760145

59. Sommer S, Becherel OJ, Coste GV, Bailone A, Fuchs RPP (2003) Altered translesion synthesis in E-coli Pol V mutants selected for increased recombination inhibition. DNA Repair 2: 1361–1369. 14642565

60. Sommer S, Bailone A, Devoret R (1993) The appearance of the UmuD'C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis. Mol Microbiol 10: 963–971. 7934872

61. Rehrauer WM, Bruck I, Woodgate R, Goodman MF, Kowalczykowski SC (1998) Modulation of RecA nucleoprotein function by the mutagenic UmuD'C protein complex. J Biol Chem 273: 32384–32387. 9829966

62. Pham P, Seitz EM, Saveliev S, Shen X, Woodgate R, et al. (2002) Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc Natl Acad Sci USA 99: 11061–11066. 12177433

63. Schlacher K, Leslie K, Wyman C, Woodgate R, Cox MM, et al. (2005) DNA polymerase V and RecA protein, a minimal mutasome. Mol Cell 17: 561–572. 15721259

64. Schlacher K, Cox MM, Woodgate R, Goodman MF (2006) RecA acts in trans to allow replication of damaged DNA by DNA polymerase V. Nature 442: 883–887. 16929290

65. Bakhlanova IV, Dudkina AV, Baitin DM, Knight KL, Cox MM, et al. (2010) Modulating cellular recombination potential through alterations in RecA structure and regulation. Mol Microbiol 78: 1523–1538. doi: 10.1111/j.1365-2958.2010.07424.x 21143322

66. Bates H, Bridges BA (1991) Mutagenic DNA repair in Escherichia coli.19. On the roles of RecA protein in ultraviolet light mutagenesis. Biochimie 73: 485–489. 1911949

67. Chen ZC, Yang HJ, Pavletich NP (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature 453: 489–494. doi: 10.1038/nature06971 18497818

68. Tang M, Pham P, Shen X, Taylor JS, O'Donnell M, et al. (2000) Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404: 1014–1018. 10801133

69. Becherel OJ, Fuchs RPP, Wagner J (2002) Pivotal role of the beta-clamp in translesion DNA synthesis and mutagenesis in E-coli cells. DNA Repair 1: 703–708. 12509274

70. Beuning PJ, Sawicka D, Barsky D, Walker GC (2006) Two processivity clamp interactions differentially alter the dual activities of UmuC. Mol Microbiol 59: 460–474. 16390442

71. Fujii S, Gasser W, Fuchs RP (2004) The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. J Mol Biol 341: 405–417. 15276832

72. Maor-Shoshani A, Livneh Z (2002) Analysis of the stimulation of DNA polymerase V of Escherichia coli by processivity proteins. Biochemistry 41: 14438–14446. 12450411

73. Sutton MD, Farrow MF, Burton BM, Walker GC (2001) Genetic interactions between the Escherichia coli umuDC gene products and the beta processivity clamp of the replicative DNA polymerase. J Bacteriol 183: 2897–2909. 11292811

74. Sutton MD, Narumi I, Walker GC (2002) Posttranslational modification of the umuD-encoded subunit of Escherichia coli DNA polymerase V regulates its interactions with the beta processivity clamp. Proc Natl Acad Sci USA 99: 5307–5312. 11959982

75. Wang JY, Xie JM, Schultz PG (2006) A genetically encoded fluorescent amino acid. J Amer Chem Soc 128: 8738–8739.

76. Wang L, Xie J, Schultz PG (2006) Expanding the genetic code. Annu Rev Biophys Biomol Struct. 35: 225–249. 16689635

77. Chin JW, Martin AB, King DS, Wang L, Schultz PG (2002) Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc Natl Acad Sci USA 99: 11020–11024. 12154230

78. Chin JW, Santoro SW, Martin AB, King DS, Wang L, et al. (2002) Addition of p-azido-L-phenylaianine to the genetic code of Escherichia coli. J Amer Chem Soc 124: 9026–9027.

79. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4: 363–371. doi: 10.1038/nprot.2009.2 19247286

80. Ling H, Boudsocq F, Woodgate R, Yang W (2001) Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication. Cell 107: 91–102. 11595188

81. Boudsocq F, Campbell M, Devoret R, Bailone A (1997) Quantitation of the inhibition of Hfr X F-recombination by the mutagenesis complex UmuD'C. J Mol Biol 270: 201–211. 9236122

82. Boudsocq F, Ling H, Yang W, Woodgate R (2002) Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass. DNA Repair 1: 343–358. 12509239

83. Drees JC, Lusetti SL, Chitteni-Pattu S, Inman RB, Cox MM (2004) A RecA filament capping mechanism for RecX protein. Mol Cell 15: 789–798. 15350222

84. Senecoff JF, Rossmeissl PJ, Cox MM (1988) DNA recognition by the FLP recombinasse of the yeast 2-mμ plasmid—a mutational analysis of the FLP binding-site. J Mol Biol 201: 405–421. 3047402

85. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640–6645. 10829079

86. Lohman TM, Overman LB (1985) Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J Biol Chem 260: 3594–3603. 3882711

87. Craig NL, Roberts JW (1981) Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor. J Biol Chem 256: 8039–8044. 6455420

88. Lohman TM, Green JM, Beyer RS (1986) Large-scale overproduction and rapid purification of the Escherichia coli ssb gene product. Expression of the ssb gene under l PL control. Biochemistry 25: 21–25. 3006753

89. Ryu YH, Schultz PG (2006) Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nature Methods 3: 263–265. 16554830

90. Ma WT, Sandri GV, Sarkar S (1992) Analysis of the Luria-Delbruck Distribution using Discrete Convolution Powers. J Appl Prob 29: 255–267.

91. Sarkar S, Ma WT, Sandri GV (1992) On Fluctuation Analysis—A New, Simple, and Efficient Method for Computing the Expected Number of Mutants. Genetica 85: 173–179. 1624139

92. Hall BM, Ma CX, Liang P, Singh KK (2009) Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. Bioinformatics 25: 1564–1565. doi: 10.1093/bioinformatics/btp253 19369502

93. Foster PL (2006) Methods for determining spontaneous mutation rates. In: Campbell JL, Modrich P, editors. DNA Repair, Pt B. pp. 195–213.

94. Opperman T, Murli S, Walker GC (1996) The genetic requirements for UmuDC-mediated cold sensitivity are distinct from those for SOS mutagenesis. J Bacteriol 178: 4400–4411. 8755866

95. McDonald JP, Maury EE, Levine AS, Woodgate R (1998) Regulation of UmuD cleavage: Role of the amino-terminal tail. J Mol Biol 282: 721–730. 9743621

96. Miller JH (1992) 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.

97. Morrical SW, Lee J, Cox MM (1986) Continuous association of Escherichia coli single-stranded DNA binding protein with stable complexes of RecA protein and single-stranded DNA. Biochemistry 25: 1482–1494. 2939874