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Series GSE249682 Query DataSets for GSE249682
Status Public on Mar 26, 2024
Title 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
Organism Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Torheim Bergum OE, Holstad Singleton A, Røst LM, Bodein A, Scott-Boyer M, Beck Rye M, Droit A, Bruheim P, Otterlei M
Citation(s) 38596376
Submission date Dec 08, 2023
Last update date Apr 24, 2024
Contact name Amanda Holstad Singleton
E-mail(s) amanda.singleton@ntnu.no
Organization name Norwegian University of Science and Technology
Department Department of Clinical and Molecular Medicine
Street address Erling Skjalgsons gate 1
City Trondheim
ZIP/Postal code 7491
Country Norway
 
Platforms (1)
GPL21117 Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)
Samples (42)
GSM7957302 Ciprofloxacin (12 ng/mL) 1 min pre-treatment; BR 1
GSM7957303 Ciprofloxacin (12 ng/mL) 1 min post-treatment; BR 1
GSM7957304 Ciprofloxacin (12 ng/mL) 10 min post-treatment; BR 1
Relations
BioProject PRJNA1050180

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE249682_countFile.csv.gz 1.7 Mb (ftp)(http) CSV
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