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

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. Overall design: To study the temporal regulation of the SOS response in E. coli, we used a sub-lethal dose of ciprofloxacin to induce DNA damage in E. coli grown in batch culitvation in biorectors. Samples for RNA-sequencing were collected 1 min before treatment and 1, 10, 25, 50, 75, and 120 min after treatment. All samples were taken during exponential growth phase. The growth rate of the untreated control and ciprofloxacin treated cultures were nearly identical due to the sub-lethal dose of ciprofloxacin. The experiments were conducted in 3 biological replicas. RNA-sequencing samples were supplemented with signalomics and metabolomics samples. Comparative gene expression profiling analysis between the ciprofloxacin treated and untreated control was conducted.