Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria

The SOS genetic network is responsible for the repair/bypass of DNA damage in bacterial cells. While the initial stages of the response have been well characterized, less is known about the dynamics of the response after induction and its shutoff. To address this, we followed the response of the SOS network in living individual Escherichia coli cells. The promoter activity (PA) of SOS genes was monitored using fluorescent protein-promoter fusions, with high temporal resolution, after ultraviolet irradiation activation. We find a temporal pattern of discrete activity peaks masked in studies of cell populations. The number of peaks increases, while their amplitude reaches saturation, as the damage level is increased. Peak timing is highly precise from cell to cell and is independent of the stage in the cell cycle at the time of damage. Evidence is presented for the involvement of the umuDC operon in maintaining the pattern of PA and its temporal precision, providing further evidence for the role UmuD cleavage plays in effecting a timed pause during the SOS response, as previously proposed. The modulations in PA we observe share many features in common with the oscillatory behavior recently observed in a mammalian DNA damage response. Our results, which reveal a hitherto unknown modulation of the SOS response, underscore the importance of carrying out dynamic measurements at the level of individual living cells in order to unravel how a natural genetic network operates at the systems level.

[1]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[2]  J. Sweasy,et al.  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. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Z. Livneh.  DNA Damage Control by Novel DNA Polymerases: Translesion Replication and Mutagenesis* , 2001, The Journal of Biological Chemistry.

[4]  Eduardo Sontag,et al.  Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2 , 2003, Nature Cell Biology.

[5]  E. G. Frank,et al.  UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Battista,et al.  RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[7]  J. Collins,et al.  Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling , 2003, Science.

[8]  A. Bax,et al.  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. , 2001, Genes & development.

[9]  M. Goodman,et al.  Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins. , 2000, Trends in biochemical sciences.

[10]  Joel P. Brockman,et al.  Escherichia coli RecX Inhibits RecA Recombinase and Coprotease Activities in Vitro and in Vivo * , 2003, The Journal of Biological Chemistry.

[11]  U. Alon,et al.  Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  J E Ferrell,et al.  The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. , 1998, Science.

[13]  Z. Livneh,et al.  Error-free recombinational repair predominates over mutagenic translesion replication in E. coli. , 2002, Molecular cell.

[14]  S. V. Aksenov,et al.  Dynamics of the inducing signal for the SOS regulatory system in Escherichia coli after ultraviolet irradiation. , 1999, Mathematical biosciences.

[15]  G. Walker,et al.  The SOS response: recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. , 2000, Annual review of genetics.

[16]  J. W. Little.  The SOS Regulatory System , 1996 .

[17]  M. Cox,et al.  The DinI and RecX Proteins Are Competing Modulators of RecA Function* , 2004, Journal of Biological Chemistry.

[18]  E. Friedberg,et al.  DNA Repair and Mutagenesis , 2006 .

[19]  Kendall L Knight,et al.  Molecular Design and Functional Organization of the RecA Protein , 2003, Critical reviews in biochemistry and molecular biology.

[20]  J. Monod,et al.  [The kinetics of the biosynthesis of beta-galactosidase in Escherichia coli as a function of growth]. , 1952, Biochimica et biophysica acta.

[21]  D B Kell,et al.  Oscillations in NF-kappaB signaling control the dynamics of gene expression. , 2004, Science.

[22]  S Falkow,et al.  FACS-optimized mutants of the green fluorescent protein (GFP). , 1996, Gene.

[23]  S. Leibler,et al.  Establishment of developmental precision and proportions in the early Drosophila embryo , 2002, Nature.

[24]  S. Casaregola,et al.  Mechanism of transient inhibition of DNA synthesis in ultraviolet-irradiated E. coli: Inhibition is independent of recA whilst recovery requires RecA protein itself and an additional, inducible SOS function , 2004, Molecular and General Genetics MGG.

[25]  A. Løbner-Olesen,et al.  Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control , 1999, The EMBO journal.

[26]  J. Egan,et al.  UV irradiation inhibits initiation of DNA replication from oriC in Escherichia coli , 1989, Molecular and General Genetics MGG.

[27]  S. Leibler,et al.  An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. , 2000, Science.

[28]  Stanislas Leibler,et al.  Resilient circadian oscillator revealed in individual cyanobacteria , 2004, Nature.

[29]  T. Lindahl,et al.  Quality control by DNA repair. , 1999, Science.

[30]  L. Theriot,et al.  A LOCUS THAT CONTROLS FILAMENT FORMATION AND SENSITIVITY TO RADIATION IN ESCHERICHIA COLI K-12. , 1964, Genetics.

[31]  J. Courcelle,et al.  Answering the Call: Coping with DNA Damage at the Most Inopportune Time , 2002, Journal of biomedicine & biotechnology.

[32]  R. Woodgate,et al.  Identification of additional genes belonging to the LexA regulon in Escherichia coli , 2000, Molecular microbiology.

[33]  S. Kowalczykowski,et al.  Interaction of Escherichia coli RecA Protein with LexA Repressor , 1996, The Journal of Biological Chemistry.

[34]  K. Yamamoto,et al.  A loss of uvrA function decreases the induction of the SOS functions recA and umuC by mitomycin C in Escherichia coli. , 1985, Mutation research.

[35]  Uri Alon,et al.  Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.

[36]  J. Courcelle,et al.  Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. , 2001, Genetics.

[37]  Z. Livneh,et al.  The Mutagenesis Protein UmuC Is a DNA Polymerase Activated by UmuD′, RecA, and SSB and Is Specialized for Translesion Replication* , 1999, The Journal of Biological Chemistry.

[38]  G. Walker,et al.  A model for a umuDC-dependent prokaryotic DNA damage checkpoint. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[39]  A. S. Lynch,et al.  Regulation of Gene Expression in Escherichia coli , 1996, Springer US.

[40]  F. Harmon,et al.  Interaction of Escherichia coli RecA Protein with LexA Repressor , 1996, The Journal of Biological Chemistry.

[41]  R. Kato,et al.  Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis , 2001, The EMBO journal.

[42]  U. Alon,et al.  Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria , 2001, Science.

[43]  James R. Johnson,et al.  Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression , 2004, Science.

[44]  Jeffrey W. Roberts,et al.  Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. , 1990, Journal of molecular biology.