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SsDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

ABSTRACT: DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria this coordination is mediated by the SOS response through LexA , which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL-motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated DNA-binding activation. Biochemical and in vivo studies support the structural model. Our data indicate this as a conserved mechanism of signaling for WYL-containing regulators.

ORGANISM(S): Caulobacter vibrioides

PROVIDER: GSE197978 | GEO | 2022/05/15

REPOSITORIES: GEO

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Project description:Shimoni2009 - Escherichia Coli SOS Simple model, involving only the basic components of the circuit, sufficient to explain the peaks in the promoter activities of recA and lexA. This model is described in the article: Stochastic analysis of the SOS response in Escherichia coli. Shimoni Y, Altuvia S, Margalit H, Biham O PloS one. 2009; 4(5):e5363 Abstract: BACKGROUND: DNA damage in Escherichia coli evokes a response mechanism called the SOS response. The genetic circuit of this mechanism includes the genes recA and lexA, which regulate each other via a mixed feedback loop involving transcriptional regulation and protein-protein interaction. Under normal conditions, recA is transcriptionally repressed by LexA, which also functions as an auto-repressor. In presence of DNA damage, RecA proteins recognize stalled replication forks and participate in the DNA repair process. Under these conditions, RecA marks LexA for fast degradation. Generally, such mixed feedback loops are known to exhibit either bi-stability or a single steady state. However, when the dynamics of the SOS system following DNA damage was recently studied in single cells, ordered peaks were observed in the promoter activity of both genes (Friedman et al., 2005, PLoS Biol. 3(7):e238). This surprising phenomenon was masked in previous studies of cell populations. Previous attempts to explain these results harnessed additional genes to the system and deployed complex deterministic mathematical models that were only partially successful in explaining the results. PRINCIPAL FINDINGS: Here we apply stochastic methods, which are better suited for dynamic simulations of single cells. We show that a simple model, involving only the basic components of the circuit, is sufficient to explain the peaks in the promoter activities of recA and lexA. Notably, deterministic simulations of the same model do not produce peaks in the promoter activities. SIGNIFICANCE: We conclude that the double negative mixed feedback loop with auto-repression accounts for the experimentally observed peaks in the promoter activities. In addition to explaining the experimental results, this result shows that including additional regulations in a mixed feedback loop may dramatically change the dynamic functionality of this regulatory module. Furthermore, our results suggests that stochastic fluctuations strongly affect the qualitative behavior of important regulatory modules even under biologically relevant conditions, thus emphasizing the importance of stochastic analysis of regulatory circuits. This model is hosted on BioModels Database and identified by: MODEL2937159804. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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SsDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

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