PXD047394-1

PXD047394 is an original dataset announced via ProteomeXchange.

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
Description	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, and a low dose of ciprofloxacin was used to activate the SOS response while avoiding 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 increasing 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.
HostingRepository	PRIDE
AnnounceDate	2024-03-26
AnnouncementXML	Submission_2024-03-26_10:47:48.337.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amanda Singleton
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-30 01:18:51	ID requested
⏵ 1	2024-03-26 10:47:48	announced
2	2024-10-22 06:34:39	announced	2024-10-22: Updated project metadata.

10.3389/FMICB.2024.1373344;

submitter keyword: signalomics,Escherichia coli, ciprofloxacin, SOS response

Marit Otterlei
contact affiliation	Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
contact email	marit.otterlei@ntnu.no
lab head
Amanda Singleton
contact affiliation	NTNU
contact email	amanda.singleton@ntnu.no
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047394
     1. Label: PRIDE project
     2. Name: 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