Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria

PLoS Biology

Volumn 3, Issue 7, 2005, Pages 1261-1268

  Friedman, Nir ^a,b   Vardi, Shuki ^a   Ronen, Michal ^a,c   Alon, Uri ^a   Stavans, Joel ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b HARVARD UNIVERSITY   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FLUORESCENT DYE; BACTERIAL PROTEIN; DNA DIRECTED DNA POLYMERASE; ESCHERICHIA COLI PROTEIN; RECA PROTEIN; UMUC PROTEIN, E COLI; UMUD PROTEIN, E COLI;

ARTICLE; BACTERIAL CELL; CELL COMMUNICATION; CELL POPULATION; CONTROLLED STUDY; DNA REPAIR; DNA STRAND BREAKAGE; ESCHERICHIA COLI; FLUORESCENCE ANALYSIS; GENE FUNCTION; GENE FUSION; NONHUMAN; OPERON; OSCILLATION; PROMOTER REGION; ULTRAVIOLET IRRADIATION; BIOSYNTHESIS; CELL CYCLE; CYTOLOGY; FLUORESCENCE MICROSCOPY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGY; RADIATION EXPOSURE; RADIATION RESPONSE; ULTRAVIOLET RADIATION;

ESCHERICHIA COLI; MAMMALIA;

BACTERIAL PROTEINS; CELL CYCLE; DNA-DIRECTED DNA POLYMERASE; DOSE-RESPONSE RELATIONSHIP, RADIATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MICROSCOPY, FLUORESCENCE; PROMOTER REGIONS (GENETICS); REC A RECOMBINASES; SOS RESPONSE (GENETICS); ULTRAVIOLET RAYS;

EID: 22744432208     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030238     Document Type: Article

References (41)

1. Little JW (1996) The SOS regulatory system. In: Lin ECC, Simon A, editors. Regulation of gene expression in Escherichia coli. Austin (Texas): Landes. pp. 453-479
2. Friedberg EC, Walker GC, Siede W (1995) DNA repair and mutagenesis. Washington (DC): ASM Press. 698 p.
3. Crowley DJ, Courcelle J (2002) Answering the call: Coping with DNA damage at the most inopportune time. J Biomed Biotechnol 2: 66-74.
4. 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.
5. 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.
6. 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.
7. Lindahl T, Wood RD (1999) Quality control by DNA repair. Science 286: 1897-1905.
8. Aksenov SV (1999) Dynamics of the inducing signal for the SOS regulatory system in Escherichia coli after ultraviolet irradiation. Math Biosci 157: 269-286.
9. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
10. Ronen M, Rosenberg R, Shraiman BI, Alon U (2002) Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A 99: 10555-10560.
11. Ferrell JE, Machleder EM (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280: 895-898.
12. Cluzel P, Surette M, Leibler S (2000) An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science 287: 1652-1655.
13. Nelson DE, Ihekwaba AEC, Elliott M, Johnson JR, Gibney CA, et al. (2004) Oscillations in NF-kappa B signaling control the dynamics of gene expression. Science 306: 704-708.
14. Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green .uorescent protein (GFP). Gene 173: 33-38.
15. Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, et al. (2001) Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292: 2080-2083.
16. Lobner-Olesen A (1999) Distribution of minichromosomes in individual Escherichia coli cells: Implications for replication control. EMBO J 18: 1712-1721.
17. Monod J, Pappenheimer AM, Cohen-Bazire G (1952) [The kinetics of the biosynthesis of beta-galactosidase in Escherichia coli as a function of growth.] Biochim Biophys Acta 9: 648-660.
18. Opperman T, Murli S, Smith BT, Walker GC (1999) A model for a umuDCdependent prokaryotic DNA damage checkpoint. Proc Natl Acad Sci U S A 96: 9218-9223.
19. Tang M, Shen X, Frank EG, O'Donnell M, Woodgate R, et al. (1999) UmuD92C is an error-prone DNA polymerase, Escherichia coli Pol V. Proc Natl Acad Sci U S A 96: 8919-8924.
20. Reuven NB, Arad G, Maor-Shoshani A, Livneh Z (1999) 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.
21. Goodman MF (2000) Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins. Trends Biochem Sci 25: 189-195.
22. Livneh Z (2001) DNA damage control by novel DNA polymerases: Translesion replication and mutagenesis. J Biol Chem 276: 25639-25642.
23. Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, et al. (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet 36: 147-150.
24. Stohl EA, Brockman JP, Burkle KL, Morimatsu K, Kowalczykowski SC, et al. (2003) Escherichia coli RecX inhibits RecA recombinase and coprotease activities in vitro and in vivo. J Biol Chem 278: 2278-2285.
25. Lusetti SL, Drees JC, Stohl EA, Seifert HS, Cox MM (2004) The DinI and RecX proteins are competing modulators of RecA function. J Biol Chem 279: 55073-55079.
26. 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.
27. 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.
28. Rehrauer WM, Lavery PE, Palmer EL, Singh RN, Kowalczykowski SC (1996) Interaction of Escherichia coli RecA protein with LexA repressor .1. LexA repressor cleavage is competitive with binding of a secondary DNA molecule. J Biol Chem 271: 23865-23873.
29. 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.
30. Verma M, Moffat KG, Egan JB (1989) UV irradiation inhibits initiation of DNA-replication from OriC in Escherichia coli. Mol Gen Genet 216: 446-454.
31. Khidhir MA, Casaregola S, Holland IB (1985) Mechanism of transient inhibition of DNA synthesis in ultraviolet-irradiated Escherichia coli-Inhibition is independent of RecA while recovery requires RecA protein itself and an additional, inducible SOS function. Mol Gen Genet 199: 133-140.
32. Witkin EM, Roegner-Maniscalco V, Sweasy JB, McCall JO (1987) Recovery from ultraviolet light-induced inhibition of DNA synthesis requires UmuDC gene-products in RecA718 mutant strains but not in RecA+ strains of Escherichia coli. Proc Natl Acad Sci U S A 84: 6805-6809.
33. Pomerening JR, Sontag ED, Ferrell JE (2003) Building a cell cycle oscillator: Hysteresis and bistability in the activation of Cdc2. Nat Cell Biol 5: 346-351.
34. Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr Op Cell Biol 15: 221-231.
35. McGrew DA, Knight KL (2003) Molecular design and functional organization of the RecA protein. Crit Rev Biochem Mol Biol 38: 385-432.
36. Houchmandzadeh B, Wieschaus E, Leibler S (2002) Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 415: 798-802.
37. Mihalcescu I, Hsing WH, Leibler S (2004) Resilient circadian oscillator revealed in individual cyanobacteria. Nature 430: 81-85.
38. Howard-Flanders P, Theriot L, Simson E (1964) Locus that controls filament formation + sensitivity to radiation in Escherichia coli K-12. Genetics 49: 237-246.
39. Berdichevsky A, Izhar L, Livneh Z (2002) Error-free recombinational repair predominates over mutagenic translesion replication in E coli. Mol Cell 10: 917-924.
40. Yamamoto K, Higashikawa T, Ohta K, Oda Y (1985) A loss of uvrA function decreases the induction of the SOS functions recA and umuC by Mitomycin C in Escherichia coli. Mutat Res 149: 297-302.
41. 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 U S A 85: 1816-1820.