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SOS Genes Are Rapidly Induced While Mutagenesis Is Temporally Regulated by Changes in Protein Activation and Nucleotide Pools After a Sub-lethal Dose of Ciprofloxacin in Escherichia coli

ABSTRACT: The DNA damage inducible SOS response in bacteria serves to increase survival of the species. The SOS response first initiates error-free repair which is followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response using transcriptomics, signalomics, and metabolomics. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions. Ciprofloxacin was used to induce the SOS response at a concentration that avoided extensive cell death. Our results show that expression of genes involved in error-free and error-prone repair were both induced shortly after DNA damage, thus, challenging the established perception that the expression of error-prone repair genes is delayed. By combining transcriptomics with signalomics, we found that temporal segregation of error-free and error-prone repair is primarily regulated after transcription. Furthermore, the heterology index was correlated to the maximum increase in gene expression and not to the time of induction of SOS genes. Finally, quantification of metabolites revealed an increase in pyrimidine pools as a late feature of the SOS response. Our results elucidate how the SOS response is coordinated, showing a rapid transcriptional response and temporal regulation of mutagenesis on the protein and metabolite levels.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE249682 | GEO | 2024/03/26

REPOSITORIES: GEO

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Project description:The SOS response is a conserved pathway that is activated under certain stress conditions and is regulated by the repressor LexA and the activator RecA. The food-borne pathogen Listeria monocytogenes contains RecA and LexA homologs, but their roles in Listeria have not been established. In this study, we identified the SOS regulon in L. monocytogenes by comparing the transcription profiles of the wild-type strain and the ÎrecA mutant strain after exposure to the DNA damaging agent mitomycinC (MMC). The SOS response is an inducible pathway involved in DNA repair, restart of stalled replication forks, and in induction of genetic variation in stressed and stationary phase cells. It is regulated by LexA and RecA. LexA is an autoregulatory repressor which binds to a consensus sequence in the promoter region of the SOS response genes, thereby repressing transcription. A consensus LexA binding motif for L. monocytogenes has not been identified thus far. Generally, the SOS response is induced under circumstances in which single stranded DNA accumulates in the cell. This results in activation of RecA, which in turn stimulates cleavage of LexA, and ultimately in the induction of the SOS response. Keywords: stress response, loop design, SOS response, mitomycin c, listeria monocytogenes, RecA, LexA Triple loop design of 3 independent experiments (series A, B, and C) using Wt strain and recA mutant (activator of the SOS response). Sampling was done before (t=0) and 1 hour after (t=60) exposure to mitomycin C (MMC) for both the wild-type strain and the recA mutant strain. One series therefore contains 4 samples and the complete experiments consists of 12 samples. Each of the 3 series was designed in a loop (wt, t=0 =>wt, t=60 => recA, t=60 => recA, t=0 => wt, t=0). These 3 loops were connected using series B as the central loop. Series B was connected to series A as follows: wt, t=0 (B) => recA, t=0 (A) and wt, t=60 (B) => recA, t=60 (A). Series B was connected to series C as follows: recA, t=0 (B) => wt, t=0 (C) and recA, t=60 (B) => wt, t=60 (C).

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SOS Genes Are Rapidly Induced While Mutagenesis Is Temporally Regulated by Changes in Protein Activation and Nucleotide Pools After a Sub-lethal Dose of Ciprofloxacin in Escherichia coli

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