UV-induced mutagenesis in Escherichia coli SOS response: A quantitative model

PLoS Computational Biology

Volumn 3, Issue 3, 2007, Pages 0451-0462

  Krishna, Sandeep ^a   Maslov, Sergei ^b   Sneppen, Kim ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; ESCHERICHIA COLI; PROTEINS; SYSTEMS ENGINEERING; TOPOLOGY;

ACTIVE PROTEINS; BINDING PROTEINS; DNA DAMAGES; DYNAMICAL MODELING; ESCHERICHIA COLI BACTERIA; PROTEIN DEGRADATION; PROTEIN-PROTEIN BINDING; QUANTITATIVE MODELS; SOS RESPONSE; UV INDUCED;

MUTAGENESIS;

DNA DIRECTED DNA POLYMERASE ALPHA; RECA PROTEIN; BACTERIAL DNA; DNA DIRECTED DNA POLYMERASE;

ARTICLE; CELL DAMAGE; DNA DAMAGE; DNA REPAIR; ENZYME REGULATION; ESCHERICHIA COLI; FEEDBACK SYSTEM; LONG TERM MEMORY; MUTAGENESIS; ULTRAVIOLET RADIATION; BIOLOGICAL MODEL; COMPUTER SIMULATION; DRUG EFFECT; GENETICS; PHYSIOLOGY; RADIATION DOSE; RADIATION EXPOSURE; RADIATION RESPONSE;

ESCHERICHIA COLI;

COMPUTER SIMULATION; DNA DAMAGE; DNA, BACTERIAL; DNA-DIRECTED DNA POLYMERASE; DOSE-RESPONSE RELATIONSHIP, RADIATION; ESCHERICHIA COLI; MODELS, BIOLOGICAL; MUTAGENESIS; RADIATION DOSAGE; SOS RESPONSE (GENETICS); ULTRAVIOLET RAYS;

EID: 34047230771     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030041     Document Type: Article

References (31)

1. Walker GC (1987) The SOS response of Escherichia coli. In: Ingraham J, Low KB, Magasnik B, Niedhart F, Schaecter M, et al., editors. Escherichia coli and Salmonella typhimurium, Vols. I and II. Washington (D.C.): American Society of Microbiology. Chapter 89.
2. Tang M, 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 U S A 96: 8919-8924.
3. Little JW (1983) The SOS regulatory system: Control of its state by the level of RecA protease. J Mol Biol 167: 791-808.
4. Sassanfar M, Roberts JW (1990) Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. J Mol Biol 212: 79-96.
5. Takahashi M, Norden B (1994) Structure of RecA-DNA complex and mechanism of DNA strand exchange reaction in homologous recombination. Adv Biophys 30: 1-35.
6. Little JW, Edmiston SH, Pacelli LZ, Mount DW (1980) Cleavage of the Escherichia coli LexA protein by the RecA protease. Proc Natl Acad Sci U S A 77: 3225-3229.
7. Shinagawa H, Iwasaki H, Kato T, Nakata A (1988) RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci U S A 85: 1806-1810.
8. The NER repair is sometimes referred to as the "dark repair" mechanism. In the presence of light there is an alternative pathway using E. coli DNA photolyase, which can fix cyclobutane pyrimidine dimmers. Brash DE, Franklin WA, Sancar GB, Sancar A, Haseltine WA (1985) Escherichia coli DNA photolyase reverses cyclobutane pyrimidine dimers but not pyrimidine-pyrimidone (6-4) photoproducts. J Biol Chem 260: 11438-11441.
9. Setlow RB, Carrier W (1964) The disappearance of thymine dimers from DNA: An error correcting mechanism. Proc Natl Acad Sci U S A 51: 226-231.
10. 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: e238.
11. Aksenov SV (1999) Dynamics of the inducing signal for the SOS regulatory system in Escherichia coli after ultraviolet irradiation. Math Biosci 157: 269-286.
12. Sutton MD, Opperman T, Walker GC (1999) 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.
13. Cox JM, Tsodikov OV, Cox MM (2005) Organized unidirectional waves of ATP hydrolysis within a RecA filament. PLoS Biol 3: e52.
14. Battista JR, Ohta T, Nohmi T, Sun W, Walker GC (1990) Dominant negative UmuD mutations decreasing RecA-mediated cleavage suggest roles for intact UmuD in modulation of SOS mutagenesis. Proc Natl Acad Sci U S A 87: 7190-7194.
15. Schnarr M, Oertel-Buchheit P, Kazmaier M, Granger-Schnarr M (1991) DNA binding properties of the LexA properties. Biochimie 73: 423-431.
16. McDonald JP, Frank EG, Levine AS, Woodgate R (1998) Intermolecular cleavage by UmuD-like mutagenesis proteins. Proc Natl Acad Sci U S A 95: 1478-1483.
17. Frank EG, Ennis DG, Gonzales M, Levine AS, Woodgate R (1996) Regulation of SOS mutagenesis by proteolysis. Proc Natl Acad Sci U S A 93: 10291-10296.
18. Rangarajan S, Woodgate R, Goodman MF (1999) A phenotype for enigmatic DNA polymerase II: A pivotal role for Pol II in replication restart in UV-irradiated Escherichia coli. Proc Natl Acad Sci U S A 96: 9224-9229.
19. Szekeres ES Jr, 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 dimmer and the efficiency of translesion DNA synthesis. J Bacteriol 178: 2559-2563.
20. Radman M (1999) Enzymes of evolutionary change. Nature 401: 866-869.
21. Opperman T, Murli S, Smith BC, Walker GC (1999) A model for a umuDC-dependent prokaryotic DNA damage checkpoint. Proc Natl Acad Sci U S A 96: 9218-9223.
22. Yasuda T, Morimatsu K, Kato R, Usukura J, Takahashi M, et al. (2001) Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis. EMBO J 20: 1192-1202.
23. Ronen M, Rosenberg R, Shraiman BI, Alon U (2002) Assigning numbers to the arrows: Parametrizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A 99: 10555-10560.
24. Lusetti SL, Voloshin ON, Inman RB, Camerini-Otero RD, Cox MM (2004) The DinI protein stabilizes RecA protein filament. J Biol Chem 279: 30037-30046.
25. Yoshimasu M, Aihara H, Ito Y, Rajesh S, Ishibe S, et al. (2003) An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes. Nucleic Acids Res 31: 1735-1743.
26. Voloshin ON, Ramirez BE, Bax A, Camerini-Otero RD (2001) A model for the abrogation of the SOS response by an SOS protein: A negatively charged helix in DinI mimics DNA in its interaction with RecA. Genes Dev 15: 415-427.
27. Crowley DJ, Hanawalt PC (1998) Induction of the SOS response increases the efficiency of global nucleotide excision repair of cyclobutane pyrimidne dimers but not 6-4 photoproducts in UV-irradiated Escherichia coli. J Bacteriol 180: 3345-3352.
28. Kelman Z, O'Donnell M (1995) DNA polymerase III holoenzyme: Structure and function of a chromosomal replicating machine. Annu Rev Biochem 64: 171-200.
29. Woodgate R, Ennis DG (1991) Levels of chromosomally encoded Umu proteins and requirements for in vivo UmuD cleavage. Mol Gen Genet 229: 10-16.
30. Rupp WD, Howard-Flanders P (1968) Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet radiation. J Mol Biol 31: 291-304.
31. Sommer S, Boudsocq F, Devoret R, Bailone A (1998) Specific RecA amino acid changes affect RecA-UmuD'C interaction. Mol Microbiol 28: 281-291.