Escherichia coli Y family DNA polymerases

Frontiers in Bioscience

Volumn 16, Issue 7, 2011, Pages 3164-3182

  Walsh, Jason M ^a   Hawver, Lisa A ^a   Beuning, Penny J ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

DinB; DNA damage; DNA polymerase; Mutation; Pol IV; Pol V; Translesion synthesis; UmuC; UmuD; Y family

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

DINB PROTEIN, E COLI; DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE BETA; DNA POLYMERASE V, E COLI; ESCHERICHIA COLI PROTEIN;

BACTERIAL GENE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; REVIEW;

DNA DAMAGE; DNA POLYMERASE BETA; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENES, BACTERIAL; MODELS, BIOLOGICAL; MODELS, MOLECULAR; SOS RESPONSE (GENETICS);

EID: 79959567810     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3904     Document Type: Article

References (160)

1. Miroslav Radman: SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci 5A, 355-367 (1975)
2. Roger Woodgate, Malini Rajagopalan, Chi Lu and Harrison Echols: UmuC mutagenesis protein of Escherichia coli: purification and interaction with UmuD and UmuD'. Proc Natl Acad Sci U S A 86, 7301-7305 (1989) (Pubitemid 19254448)
3. Wei Yang: Portraits of a Y-family DNA polymerase. FEBS Letters 579, 868-872 (2005) (Pubitemid 40361856)
4. Haruo Ohmori, Errol Friedberg, Robert Fuchs, Myron Goodman, Fumio Hanaoka, David Hinkle, Thomas Kunkel, Christopher Lawrence, Zvi Livneh, Takehiko Nohmi, Louise Prakash, Satya Prakash, Takeshi Todo, Graham Walker, Zhigang Wang and Roger Woodgate: The Y-family of DNA polymerases. Mol Cell 8, 7-8 (2001) (Pubitemid 32772900)
5. Errol Friedberg, Graham Walker, Wolfram Siede, Richard Wood, Roger Schultz and Tom Ellenberger. DNA Repair and Mutagenesis, ASM Press, Washington DC, 2 edition, (2006)
6. Janice Pata: Structural diversity of the Y-family DNA polymerases. Biochem Biophys Acta 1804, 1124-1135 (2010)
7. Wei Yang and Roger Woodgate: What a different a decade makes: Insights into translesion DNA synthesis. Proc Natl Acad Sci U S A 104, 15591-15598 (2007) (Pubitemid 350035345)
8. Francois Boudsocq, Hong Ling, Wei Yang and Roger Woodgate: 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 (2002) (Pubitemid 34603160)
9. Haruo Ohmori, Eriko Hatada, Yun Qiao, Masaharu Tsuji and Ryuji Fukuda: dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues. Mutat Res 347, 1-7 (1995)
10. Hong Ling, Francois Boudsocq, Roger Woodgate and Wei Yang: Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102 (2001) (Pubitemid 32972040)
11. Sushil Chandani, Christopher Jacobs and Edward Loechler: Architecture of Y-Family DNA Polymerases Relevant to Translesion DNA Synthesis as Revealed in Structural and Molecular Modeling Studies. Journal of Nucleic Acids 2010, Article ID 784081 20 pages (2010)
12. William Beard and Samuel Wilson: Structural Insights into the Origins of DNA Polymerase Fidelity. Structure 11, 489-496 (2003) (Pubitemid 36579127)
13. Neerja Kaushik, Virendra Pandey and Mukund Modak: Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket. Biochemistry 35, 7256-66 (1996) (Pubitemid 26182119)
14. Masonori Ogawa, Aki Tosaka, Yasutomo Ito, Shonen Yoshida and Motoshi Suzuki: Enhanced ribonucleotide incorporation by an O-helix mutant of Thermus aquaticus DNA polymerase I. Mutat Res 485, 197-207 (2001) (Pubitemid 32232303)
15. Daniel Jarosz, Penny Beuning, Susan Cohen and Graham Walker: Y-family DNA polymerases in Escherichia coli. Trends Microbiol 15, 70-77 (2007) (Pubitemid 46199189)
16. Hong Ling, Francois Boudsocq, Brian Plosky, Roger Woodgate and Wei Yang: Replication of a cis-syn thymine dimer at atomic resolution. Nature 424, 1083-1087 (2003) (Pubitemid 37064312)
17. Laura Silvian, Eric Toth, Phuong Pham, Myron Goodman and Tom Ellenberger: Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat Struct Biol 8, 984-989 (2001) (Pubitemid 33032369)
18. Bo-Lu Zhou, Janice Pata and Thomas Steitz: Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol Cell 8, 427-37 (2001) (Pubitemid 32831559)
19. Miroslav Radman. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis. In Molecular and environmental aspects of mutagenesis (Louise Prakash, Fred Sherman, Morton W. Miller, Christopher W. Lawrence, Harry Warren Taber and John W. Stewart, eds.), pp. xv, 289 p. Thomas, Springfield, Ill., (1974)
20. Evelyn Witkin: The radiation sensitivity of Escherichia coli B: a hypothesis relating filament formation and prophage induction. Proc Natl Acad Sci U S A 57, 1275-1279 (1967)
21. Toshihiro Horii, Tomoko Ogawa, Tomoyuki Nakatani, Toshiharu Hase, Hiroshi Matsubara and Hideyuki Ogawa: Regulation of SOS functions: purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein. Cell 27, 515-522 (1981) (Pubitemid 12200788)
22. Lyle Simmons, James Foti, Susan Cohen and Graham Walker. Chapter 5.4.3 The SOS Regulatory Network. In EcoSal-Escherichia coli and Salmonella: cellular and molecular biology (A. Bock, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nystrom, J. M. Slauch, C. L. Squires and D. Ussary, eds.). ASM Press, Washington, D.C. (2008)
23. Sabine Burckhardt, Roger Woodgate, Richard Scheuermann and Harrison Echols: UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci U S A 85, 1811-1815 (1988) (Pubitemid 24315772)
24. Takehiko Nohmi, John Battista, Lori Dodson and Graham Walker: RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci U S A 85, 1816-1820 1988) (Pubitemid 24315773)
25. Hideo Shinagawa, Hiroshi Iwasaki, Takesi Kato and Atsuo Nakata: RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci U S A 85, 1806-1810 (1988) (Pubitemid 24315771)
26. Timothy Opperman, Sumati Murli, Bradley Smith and Graham Walker: A model for a umuDC-dependent prokaryotic DNA damage checkpoint. Proc Natl Acad Sci U S A 96, 9218-9223 (1999) (Pubitemid 29374735)
27. Veronica Godoy, Daniel Jarosz, Sharotka Simon, Alexej Abyzov, Valentin Ilyin and Graham Walker: UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB. Molecular Cell 28, 1058-1070 (2007) (Pubitemid 350297024)
28. Lorraine Marsh and Graham Walker: Cold sensitivity induced by overproduction of UmuDC in Escherichia coli. J Bacteriol 162, 155-161 (1985) (Pubitemid 15095847)
29. Nina Reuven, Gali Arad, Ayelet Maor-Shoshani and Zvi Livneh: The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J Biol Chem 274, 31763-31766 (1999)
30. Mark Sutton and Graham Walker: umuDC-mediated cold sensitivity is a manifestation of functions of the UmuD(2)C complex involved in a DNA damage checkpoint control. J Bacteriol 183, 1215-1224 (2001) (Pubitemid 32107717)
31. Mengjia Tang, Xuan Shen, Ekatarine Frank, Michael O'Donnell, Roger Woodgate and Myron Goodman: UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci U S A 96, 8919-8924 (1999)
32. Jaylene Ollivierre, Jing Fang and Penny Beuning: The roles of UmuD in regulating mutagenesis. J Nucleic Acids 2010, 947680 (2010)
33. Jerome Wagner, Petr Gruz, Su-Rang Kim, Masami Yamada, Keiko Matsui, Robert Fuchs and Takehiko Nohmi: The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol Cell 4, 281-286 (1999) (Pubitemid 29456897)
34. Cynthia Kenyon and Graham Walker: DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc Natl Acad Sci U S A 77, 2819-2823 (1980) (Pubitemid 10057928)
35. Su-Ryang Kim, Keiko Matsui, Masami Yamada, Petr Gruz and Takehiko Nohmi: Roles of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli. Mol Genet Genomics 266, 207-215 (2001) (Pubitemid 32938414)
36. Kaori Uchida, Asako Furukohri, Yutaka Shinozaki, Tetsuya Mori, Daichi Ogawara, Shigehiko Kanaya, Takehiko Nohmi, Hisaji Maki and Masahiro Akiyama: Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol 70, 608-622 (2008)
37. Asako Furukohri, Myron Goodman and Hisaji Maki: A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on thesliding clamp. J Biol Chem 283, 11260-11269 (2008)
38. Gregory McKenzie, Peter Lee, Mary-Jane Lombardo, PJ Hastings and Susan Rosenberg: SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol Cell 7, 571-579 (2001) (Pubitemid 32706349)
39. Joshua Tompkins, Jennifer Nelson, Jill Hazel, Stacey Leugers, Jefferey Stumpf and Patricia Foster: Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli. J Bacteriol 185, 3469-3472 (2003) (Pubitemid 36617761)
40. Patricia Foster: Stress-Induced Mutagenesis in Bacteria Crit Rev in Biochem and Molec Biol 42, 373-397 (2007) (Pubitemid 47537271)
41. Jill Layton and Patricia Foster: Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli. Mol Microbiol 50, 549-561 (2003) (Pubitemid 37297134)
42. Mary-Jane Lombardo, Ildiko Aponyi and Susan Rosenberg: General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics 166, 669-680 (2004) (Pubitemid 38391733)
43. Rodrigo Galhardo, Robert Do, Masami Yamada, Errol Friedberg, PJ Hastings, Takehiko Nohmi and Susan Rosenberg: DinB upregulation is the sole role of the SOS response in stress-induced mutagenesis in Escherichia coli. Genetics 182, 55-68 (2009)
44. Gregory McKenzie, Daniel Magner, Peter Lee and Susan Rosenberg: The dinB operon and spontaneous mutagenesis in Escherichia coli. Journal of Bacteriology 185, 3972-3977 (2003) (Pubitemid 36735950)
45. E. Susan Slechta, Kim Bunny, Elisabeth Kugelberg, Eric Kofoid, Dan Andersson and John Roth: Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc Natl Acad Sci U S A 100, 12847-12852 (2003) (Pubitemid 37339988)
46. Megan Hersh, Rebecca Ronder, PJ Hastings and Susan Rosenberg: Adaptive mutation and amplication in Escherichia coli: two pathways of genome amplification under stress. Res Microbiol 155, 352-359 (2004) (Pubitemid 38781178)
47. John R. Roth, Elisabeth Kugelberg, Andrew B. Reams, Eric Kofoid and Dan I. Andersson: Origin of Mutations Under Selection: The Adaptive Mutation Controversy. Annu Rev Microbiol 60, 477-501 (2006) (Pubitemid 44627958)
48. Rodrigo S. Galhardo, Philip J. Hastings and Susan M. Rosenberg: Mutation as a Stress Response and the Regulation of Evolvability. Crit Rev in Biochem and Molec Biol 42, 399-435 (2007) (Pubitemid 47537269)
49. Philip J. Hastings: Adaptive Amplification. Crit Rev in Biochem and Molec Biol 42, 271-283 (2007) (Pubitemid 47237760)
50. Jill Layton and Patricia Foster: Error-prone DNA polymerase IV is regulated by the heat shock chaperone GroE in Escherichia coli. J Bacteriol 187, 449-457 (2005) (Pubitemid 40096233)
51. Tatiana Perez-Capilla, Maria-Rosario Baquero, Jose-Maria Gomez-Gomez, Alina Ionel, Soledad Martin and Jesus Blazquez: SOS-Independent Induction of dinB Transcription by {beta}-Lactam-Mediated Inhibition of Cell Wall Synthesis in Escherichia coli. J. Bacteriol. 187, 1515-1518 (2005) (Pubitemid 40299476)
52. Gregory McKenzie and Susan Rosenberg: Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr Opin Microbiol 4, 586-594 (2001) (Pubitemid 32964109)
53. Peter Smith and Floyd Romesberg: Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nat Chem Biol 3, 549-556 (2007) (Pubitemid 47294401)
54. Ryan Cirz and Floyd Romesberg: Controlling Mutation: Intervention in Evolution as a Therapeutic Strategy Crit Rev in Biochem and Molec Biol 42, 341-354 (2007) (Pubitemid 47537266)
55. Joseph Petrosino, Rodrigo Galhardo, Liza Morales and Susan Rosenberg: Stress-induced beta-lactam antibiotic resistance mutation and sequences of stationary-phase mutations in the Escherichia coli chromosome. J Bacteriol 191, 5881-5889 (2009)
56. Daniel Jarosz, Veronica Godoy, James Delaney, John Essigmann and Graham Walker: A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates. Nature 439, 225-228 (2006) (Pubitemid 43083146)
57. Daniel Jarosz, Susan Cohen, James Delaney, John Essigmann and Graham Walker: A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase. Proc Natl Acad Sci U S A 106, 21137-21142 (2009)
58. Jan Barciszewski, Miroslawa Barciszewska, Gunhild Siboska, Suresh Rattan and Brian Clark: Some unusual nucleic acid bases are products of hydroxyl radical oxidation of DNA and RNA. Mol Biol Reports 26, 231-238 (1999) (Pubitemid 30023371)
59. 2-(1-carboxyethyl)-2′- deoxyguanosine by DinB DNA polymerase in vitro and in vivo. Proc Natl Acad Sci U S A 105, 8679-8684 (2008) (Pubitemid 351987740)
60. 2-dG adduct are bypassed by different lesion-bypass DNA polymerases in E. coli. DNA Repair (Amst) 5, 515-522 (2006)
61. Xuan Shen, Jane Sayer, Heiko Kroth, Ingrid Ponten, Michael O'Donnell, Roger Woodgate, Donald Jerina and Myron Goodman: Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts. J Biol Chem 277, 5265-5274 (2002) (Pubitemid 34968570)
62. Robert Fuchs, Shingo Fujii and Jerome Wagner: Properties and functions of Escherichia coli: Pol IV and Pol V. Adv Protein Chem 69, 229-264 (2004) (Pubitemid 39600962)
63. Nathalie Lenne-Samuel, Regine Janel-Bintz, Aleksandr Kolbanovskiy, Nicholas Geacintov and Robert Fuchs: The processing of a Benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli. Mol Microbiol 38, 299-307 (2000)
64. Irina Minko, Kinrin Yamanaka, Ivan Kozekov, Albena Kozekova, Chiara Indiani, Michael O'Donnell, Qingfei Jiang, Myron Goodman, Carmelo Rizzo and R. Stephen Lloyd: Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family. Chem Res Toxicol 21, 1983-1990 (2008)
65. Anuradha Kumari, Irina Minko, Michael Harbut, Steven Finkel, Myron Goodman and R. Stephen Lloyd: Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV. J Biol Chem 283, 27433-27437 (2008)
66. Naomi Suzuki, Eiji Ohashi, Ken Hayashi, Haruo Ohmori, Arthur Grollman and Shinya Shibutani: Translesional synthesis past acetylaminofluorene-derived DNA adducts catalyzed by human DNA polymerase kappa and Escherichia coli DNA polymerase IV. Biochemistry 40, 15176-15183 (2001) (Pubitemid 33151932)
67. Masaki Hori, Shin-Ichiro Yonekura, Takehiko Nohmi, Petr Gruz, Hiroshi Sugiyama, Shuji Yonei and Qiu-Mei Zhang-Akiyama: Error-prone translesion DNA synthesis by Escherichia coli DNA polymerase IV (DinB) on templates containing 1,2-dihydro-2-oxoadenine. J Nucleic Acids 2010, 807579 (2010)
68. Masami Yamada, Tatsuo Nunoshiba, Masatomi Shimizu, Petr Gruz, Hiroyuki Kamiya, Hideyoshi Harashima and Takehiko Nohmi: Involvement of Y-family DNA polymerases in mutagenesis caused by oxidized nucleotides in Escherichia coli. J Bacteriol 188, 4992-4995 (2006) (Pubitemid 43956097)
69. Sawami Kobayashi, Michael Valentine, Phuong Pham, Mike O'Donnell and Myron Goodman: Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. J Biol Chem 277, 34198-34207 (2002)
70. Ayelet Maor-Shoshani, Ken Hayashi, Haruo Ohmori and Zvi Livneh: Analysis of translesion replication across an abasic site by DNA polymerase IV of Escherichia coli. DNA Repair 2, 1227-1238 (2003) (Pubitemid 37340179)
71. George Streisinger, Yohei Okada, Jaqueline Emrich, J Newton, A. Tsugita, E. Terzaghi and M. Inouye: Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol 31, 77-84 (1966)
72. Brigette Tippin, Sawami Kobayashi, Jeffrey Bertram and Myron Goodman: To slip or to skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases. J Biol Chem 279, 45360-45368 (2004) (Pubitemid 39491519)
73. James Foti, Angela DeLucia, Catherine Joyce and Graham Walker: UmuD(2) inhibits a non-covalent step during DinBmediated template slippage on homopolymeric nucleotide runs. J Biol Chem 285, 23086-23095 (2010)
74. Thomas Kunkel and Aruna Soni: Mutagenesis by transient misalignment. J Biol Chem 263, 14784-14789 (1988)
75. Katarzyna Bebenek and Thomas Kunkel: Frameshift errors initiated by nucleotide misincorporation. Proc Natl Acad Sci U S A 87, 4946-4950 (1990)
76. Angela DeLucia, Nigel Grindley and Catherine Joyce: Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence. Biochemistry 46, 10790-10803 (2007) (Pubitemid 47469673)
77. Kwang Seo, Jun Yin, Prashant Donthamsetti, Sushil Chandani, Chui Lee and Edward Loechler: Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli. J Mol Biol 392, 270-282 (2009)
78. Mekbib Astatke, Kimmie Ng, Nigel Grindley and Catherine Joyce: A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc Natl Acad Sci U S A 95, 3402-3407 (1998) (Pubitemid 28173140)
79. Angela DeLucia, Santanov Chaudhuri, Olga Potapova, Nigel Grindley and Catherine Joyce: The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases. J Biol Chem 281, 27286-27291 (2006) (Pubitemid 44401756)
80. Brenna Shurtleff, Jaylene Ollivierre, Mohammed Tehrani, Graham Walker and Penny Beuning: Steric gate variants of UmuC confer UV hypersensitivity on Escherichia coli. J Bacteriol 191, 4815-4823 (2009)
81. Jerome Wagner, Shingo Fujii, Petr Gruz, Takehiko Nohmi and Robert Fuchs: The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity. EMBO Rep 1, 484-488 (2000)
82. Anne Brotcorne-Lannoye and Genevieve Maenhaut-Michel: Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene. Proc Natl Acad Sci U S A 83, 3904-3908 (1986) (Pubitemid 16062390)
83. Olivier Becherel, Robert Fuchs and Jerome Wagner: Pivotal role of the beta-clamp in translesion DNA synthesis and mutagenesis in E. coli cells. DNA Repair (Amst) 1, 703-708 (2002)
84. Nathalie Lenne-Samuel, Jerome Wagner, Helene Etienne and Robert Fuchs: The processivity factor beta controls DNA polymerase IV traffic during spontaneous and tranlesion synthesis in vivo. EMBO Rep 3, 45-49 (2002) (Pubitemid 34144814)
85. Karen Bunting, S. Mark Roe and Lawrence Pearl: Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J 22, 5883-5892 (2003) (Pubitemid 37408825)
86. Jerome Wagner, Helene Etienne, Robert Fuchs, Agnes Cordonnier and Dominique Burnouf: Distinct beta-clamp interactions govern the activities of the Y family PolIV DNA polymerase. Mol Microbiol 74, 1143-1151 (2009)
87. Peggy Farnham, Jack Greenblatt and Terry Platt: Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. Cell 29, 945-951 (1982) (Pubitemid 12027916)
88. Jack Greenblatt and Joyce Li: Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription. Cell 24, 421-428 (1981) (Pubitemid 11066826)
89. Kebin Liu, Yuying Zhang, Konstantin Severinov, Asis Das and Michelle Hanna: Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor NusA. EMBO J 15, 150-161 (1996) (Pubitemid 26022473)
90. Susan Cohen, Veronica Godoy and Graham Walker: Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli. J Bacteriol 191, 665-672 (2009)
91. Yoshikazu Nakamura, Saeko Mizusawa, Donald Court and Akiko Tsugawa: Regulatory defects of a conditionally lethal nusAts mutant of Escherichia coli. Positive and negative modulator roles of NusA protein in vivo. J Mol Biol 189, 103-111 (1986) (Pubitemid 16063829)
92. Susan Cohen, Cindi Lewis, Rachel Mooney, Michael Kohanski, James Collins, Robert Landick and Graham Walker: Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A 107, 15517-15522 (2010)
93. Susan Cohen and Graham Walker: The transcription elongation factor NusA is required for stress-induced mutagenesis in Escherichia coli. Curr Biol 20, 80-85 (2010)
94. Anne Bagg, Cynthia Kenyon and Graham Walker: Inducibility of a gene product required for UV and chemical mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 78, 5749-5753 (1981)
95. Takesi Kato and Yukiko Shinoura: Isolation and characterization of mutants of Escherichia coli deficient in induction of mutations by ultraviolet light. Mol Gen Genet 156, 121-131 (1977) (Pubitemid 8217165)
96. Gerhard Steinborn: Uvm mutants of Escherichia coli K12 deficient in UV mutagenesis. I. Isolation of uvm mutants and their phenotypical characterization in DNA repair and mutagenesis. Mol Gen Genet 165, 87-93 (1978) (Pubitemid 9021075)
97. Bryn Bridges and Roger Woodgate: Mutagenic repair in Escherichia coli: products of the recA gene and of the umuD and umuC genes act at different steps in UVinduced mutagenesis. Proc Natl Acad Sci U S A 82, 4193-4197 (1985) (Pubitemid 15053608)
98. Malini Rajagopalan, Chi Lu, Roger Woodgate, Mike O'Donnell, Myron Goodman and Harrison Echols: Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III. Proc Natl Acad Sci U S A 89, 10777-10781 (1992)
99. Graham Walker: Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev 48, 60-93 (1984) (Pubitemid 14150426)
100. Bryn Bridges and Roger Woodgate: The two-step model of bacterial UV mutagenesis. Mutat Res 150, 133-139 (1985) (Pubitemid 15226341)
101. Shingo Fujii and Robert Fuchs: Defining the position of the switches between replicative and bypass DNA polymerases. EMBO J 23, 4342-4352 (2004) (Pubitemid 39546171)
102. Mengjia Tang, Irina Bruck, Ramon Eritja, Jennifer Turner, Ekatarine Frank, Roger Woodgate, Mike O'Donnell and Myron Goodman: 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 U S A 95, 9755-9760 (1998)
103. Irina Bruck, Roger Woodgate, Kevin McEntee and Myron Goodman: 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 (1996) (Pubitemid 26145813)
104. William Rehrauer, Irina Bruck, Roger Woodgate, Myron Goodman and Stephen Kowalczykowski: Modulation of RecA nucleoprotein function by the mutagenic UmuD'C protein complex. J Biol Chem 273, 32384-32387 (1998) (Pubitemid 28557608)
105. Suzanne Sommer, Adriana Bailone and Raymond Devoret: The appearance of the UmuD'C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis. Mol Microbiol 10, 963-971 (1993) (Pubitemid 24040874)
106. Hanna Szpilewska, Pascale Bertrand, Adriana Bailone and Marie Dutreix: In vitro inhibition of RecA-mediated homologous pairing by UmuD'C proteins. Biochimie 77, 848-853 (1995)
107. Justin Courcelle, Janet Donaldson, Kin-Hoe Chow and Charmain Courcelle: DNA damage-induced replication fork regression and processing in Escherichia coli. Science 299, 1064-1067 (2003) (Pubitemid 36222932)
108. Justin Courcelle and Philip Hanawalt: RecA-dependent recovery of arrested DNA replication forks. Annu Rev Genet 37, 611-646 (2003) (Pubitemid 38041439)
109. Justin Courcelle and Philip Hanawalt: Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination. Proc Natl Acad Sci U S A 98, 8196-8202 (2001) (Pubitemid 32678013)
110. Charmain Courcelle, Jerilyn Belle and Justin Courcelle: Nucleotide excision repair or polymerase Vmediated lesion bypass can act to restore UV-arrested replication forks in Escherichia coli. J Bacteriol 187, 6953-6961 (2005) (Pubitemid 41428871)
111. Justin Courcelle: Shifting replication between IInd, IIIrd, and IVth gears. Proc Natl Acad Sci U S A 106, 6027-6028 (2009)
112. Charmain Courcelle, Kin-Hoe Chow, Andrew Casey and Justin Courcelle: Nascent DNA processing by RecJ favors lesion repair over translesion synthesis at arrested replication forks in Escherichia coli. Proc Natl Acad Sci U S A 103, 9154-9159 (2006) (Pubitemid 43902548)
113. Mark Sutton, Timothy Opperman and Graham Walker: The Escherichia coli SOS mutagenesis proteins UmuD and UmuD' interact physically with the replicative DNA polymerase. Proc Natl Acad Sci U S A 96, 12373-12378 (1999) (Pubitemid 29513509)
114. Mark Sutton, Issay Narumi and Graham Walker: 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 U S A 99, 5307-5312 (2002) (Pubitemid 34411544)
115. Mark Sutton. Damage signals triggering the Escherichia coli SOS response. In DNA Damage and Recognition (Wolfram Seide, Yoke Kow and Paul Doetsch, eds.), pp. 781-802. New York : Taylor & Francis (2006)
116. Olivier Becherel and Robert Fuchs: SOS mutagenesis results from up-regulation of translesion synthesis. J Mol Biol 294, 299-306 (1999)
117. Shingo Fujii, Veronique Gasser and Robert Fuchs: The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. J Mol Biol 341, 405-417 (2004) (Pubitemid 38987778)
118. Mengjia Tang, Phuong Pham, Xuan Shen, John-Stephen Taylor, Michael O'Donnell, Roger Woodgate and Myron Goodman: Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404, 1014-1018 (2000) (Pubitemid 30243598)
119. Phuong Pham, Jeffrey Bertram, Mike O'Donnell, Roger Woodgate and Myron Goodman: A model for SOS-lesion-targeted mutations in Escherichia coli. Nature 409, 366-370 (2001) (Pubitemid 32151244)
120. William Neeley, Sarah Delaney, Yuriy Alekseyev, Daniel Jarosz, James Delaney, Graham Walker and John Essigmann: DNA polymerase V allows bylass of toxic guanine oxidation products in vivo. J Biol Chem 282, 12741-12748 (2007) (Pubitemid 47100576)
121. Penny Beuning, Dorota Sawicka, Daniel Barsky and Graham Walker: Two processivity clamp interactions differentially alter the dual activities of UmuC. Mol Microbiol 59, 460-474 (2006)
122. Chiu Hong Lee, Sushil Chandani and Edward Loechler: Homology modeling of four Y-family lesionbypass DNA polymerases: The case that E. coli Pol IV and human Pol kappa are orthologs, and E. coli Pol V and human Pol eta are orthologs. J Mol Graph Model 25, 87-102 (2005) (Pubitemid 44291544)
123. Lorraine Marsh, Takehiko Nohmi, Sean Hinton and Graham Walker: New mutations in cloned Escherichia coli umuDC genes: novel phenotypes of strains carrying a umuC125 plasmid. Mutat Res 250, 183-197 (1991)
124. Sushil Chandani and Edward Loechler: Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications. J Mol Graph Model 27, 759-769 (2009)
125. Penny Beuning, Sarah Chan, Lauren Waters, Haripriya Addepalli, Jaylene Ollivierre and Graham Walker: Characterization of novel alleles of the Escherichia coli umuDC genes identifies additional interaction sites of UmuC with the beta clamp. J Bacteriol 191, 5910-5920 (2009)
126. Walter Koch, Don Ennis, Arthur Levine and Roger Woodgate: Escherichia coli umuDC mutants: DNA sequence alterations and UmuD cleavage. Mol Gen Genet 233, 443-448 (1992)
127. Helen Bates, Bryn Bridges and Roger Woodgate: Mutagenic DNA repair in Escherichia coli, XX. Overproduction of UmuD' protein results in suppression of the umuC36 mutation in excision defective bacteria. Mutat Res 250, 199-204 (1991)
128. Brian Dalrymple, Kritaya Kongsuwan, Gene Wijffels, Nicholas Dixon and Philip Jennings: A universal proteinprotein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci U S A 98, 11627-11632 (2001) (Pubitemid 32928779)
129. Suzanne Sommer, Jelena Knezevic, Adriana Bailone and Raymond Devoret: Induction of only one SOS operon, umuDC, is required for SOS mutagenesis in Escherichia coli. Mol Gen Genet 239, 137-144 (1993) (Pubitemid 23167492)
130. Gail Arad, Ayal Hendel, Claus Urbanke, Ute Curth and Zvi Livneh: Single-stranded DNA-binding protein recruits DNA polymerase V to primer termini on RecA-coated DNA. J Biol Chem 283, 8274-8282 (2008)
131. Ayelet Maor-Shoshani and Zvi Livneh: Analysis of the stimulation of DNA polymerase V of Escherichia coli by processivity proteins. Biochemistry 41, 14438-14446 (2002) (Pubitemid 35403365)
132. Nina Reuven, Gali Arad, Alicja Stasiak, Andrzej Stasiak and Zvi Livneh: Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament. J Biol Chem 276, 5511-5517 (2001)
133. Qingfei Jiang, Kiyonobu Karata, Roger Woodgate, Michael Cox and Myron Goodman: The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP. Nature 460, 359-363 (2009)
134. Phuong Pham, Erica Seitz, Sergel Saveliev, Xuan Shen, Roger Woodgate, Michael Cox and Myron Goodman: Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc Natl Acad Sci U S A 99, 11061-11066 (2002) (Pubitemid 34920879)
135. Katharina Schlacher, Michael Cox, Roger Woodgate and Myron Goodman: RecA acts in trans to allow replication of damaged DNA by DNA polymerase V. Nature 442, 883-887 (2006) (Pubitemid 44285938)
136. Katharina Schlacher, Kris Leslie, Claire Wyman, Roger Woodgate, Michael Cox and Myron Goodman: DNA polymerase V and RecA protein, a minimal mutasome. Mol Cell 17, 561-572 (2005) (Pubitemid 40269120)
137. Shingo Fujii and Robert Fuchs: Biochemical basis for the essential genetic requirements of RecA and the betaclamp in Pol V activation. Proc Natl Acad Sci U S A 106, 14825-14830 (2009)
138. Alvin Clark and Ann Margulies: Isolation and Characterization of Recombination-Deficient Mutants of Escherichia Coli K12. Proc Natl Acad Sci U S A 53, 451-459 (1965)
139. Katharina Schlacher, Phuong Pham, Michael Cox and Myron Goodman: Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation. Chem Rev 106, 406-419 (2006)
140. Meghna Patel, Qingfei Jiang, Roger Woodgate, Michael Cox and Myron Goodman: A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev in Biochem and Molec Biol 45, 171-184 (2010)
141. Joann Sweasy: RecA kicks Pol V into gear. Nat Struct Mol Biol 12, 215-216 (2005) (Pubitemid 43079360)
142. Arthur Kornberg and Tania Baker. DNA Replication, W.H. Freeman & Company, New York, Second edition, (1992)
143. Michael Cox, Daniel Soltis, Zvi Livneh and I. R. Lehman: On the role of single-stranded DNA binding protein in recA protein-promoted DNA strand exchange. J Biol Chem 258, 2577-2585 (1983) (Pubitemid 13118459)
144. John Flory and Charles Radding: Visualization of recA protein and its association with DNA: a priming effect of single-strand-binding protein. Cell 28, 747-756 (1982)
145. Dominique Burnouf, Vincent Olieric, Jerome Wagner, Shingo Fujii, J. Reinbolt, Robert Fuchs and Philippe Dumas: Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. J Mol Biol 335, 1187-1197 (2004) (Pubitemid 38077239)
146. Jingsong Yang, Zhizao Zhuang, Rosa Maria Roccasecca, Michael Trakselis and Stephen Benkovic: The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci U S A 101, 8289-8294 (2004) (Pubitemid 38736568)
147. Vincent Pages and Robert Fuchs: How DNA lesions are turned into mutations within cells? Oncogene 21, 8957-8966 (2002) (Pubitemid 36110825)
148. Justin Heltzel, Robert Maul, Sarah Scouten Ponticelli and Mark Sutton: A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp. Proc Natl Acad Sci U S A 106, 12664-9 (2009)
149. Ryan Heller and Kenneth Marians: Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439, 557-562 (2006) (Pubitemid 43185374)
150. Alan Lehmann and Robert Fuchs: Gaps and forks in DNA replication: Rediscovering old models. DNA Repair (Amst) 5, 1495-1498 (2006) (Pubitemid 44739451)
151. Massimo Lopes, Marco Foiani and Jose Sogo: Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol Cell 21, 15-27 (2006) (Pubitemid 43017845)
152. Vincent Pages and Robert Fuchs: Uncoupling of leading-and lagging-strand DNA replication during lesion bypass in vivo. Science 300, 1300-1303 (2003) (Pubitemid 36618243)
153. Justin Heltzel, Sarah Scouten Ponticelli, Laurie Sanders, Jill Duzen, Vivian Cody, James Pace, Edward Snell and Mark Sutton: Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli. J Mol Biol 387, 74-91 (2009)
154. Elena Curti, John McDonald, Samantha Mead and Roger Woodgate: DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli. Mol Microbiol 71, 315-331 (2009)
155. Robert Fuchs and Shingo Fujii: Translesion synthesis in Escherichia coli: Lessons from the NarI mutation hot spot. DNA Repair 6, 1032-1041 (2007) (Pubitemid 46880482)
156. Stéphane Delmas and Ivan Matic: Interplay between replication and recombination in Escherichia coli: impact of the alternative DNA polymerases. Proc Natl Acad Sci U S A 103, 4564-4569 (2006)
157. Rita Napolitano, Regine Janel-Bintz, Jerome Wagner and Robert Fuchs: All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J 19, 6259-6265 (2000)
158. Mark Sutton and Jill Duzen: Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli. DNA Repair (Amst) 5, 312-23 (2006) (Pubitemid 43247598)
159. Samer Lone, Sharon Townson, Sacha Uljon, Robert Johnson, Amrita Brahma, Deepak Nair, Satya Prakash, Louise Prakash and Aneel Aggarwal: Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Mol Cell 25, 601-614 (2007)
160. Katharina Schlacher, Qingfei Jiang, Roger Woodgate and Myron Goodman: Purification and characterization of Escherichia coli DNA polymerase V. Methods Enzymol 408, 378-390 (2006)