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PXD059580

PXD059580 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons
DescriptionBacterial genomes are shaped by cryptic prophages, which are viral genomes integrated into the bacterial chromosome. Escherichia coli genomes have 10 prophages on average. Though usually inactive, prophage genes can profoundly impact host cell physiology. Among the phage genes in the E. coli chromosome, there are several putative transcription factors (TFs). These prophage TFs are predicted to control only phage promoters, however their regulatory functions are not well characterized. The co-habitation of prophages and bacteria has led to conditions under which the majority of prophage genes are unexpressed, at least under normal growth conditions. We characterized a Rac prophage TF, YdaT, expression of which is normally inhibited by Rac TFs and, surprisingly, by the host global regulator OxyR. YdaT, when expressed, leads to a toxic phenotype manifested by drastic cell filamentation and cell death. We determined the binding sites and regulatory action for YdaT, finding two sites within the Rac locus, and one upstream of the host rcsA gene, which codes for the global regulator RcsA. The resulting increase in RcsA strongly impacts the bacterial RcsA/B regulon, which includes operons related to motility, capsule biosynthesis, colanic acid production, biofilm formation and cell division. Our results provide novel insights into the host’s genetic network, which appears to integrate YdaT in a complex manner, favoring its maintenance in the silenced state. The fact that the potentially-toxic YdaT locus remains unmutated suggests its importance and potential benefits for the host, which may appear under stress conditions that are not yet known.
HostingRepositoryPRIDE
AnnounceDate2025-05-07
AnnouncementXMLSubmission_2025-05-07_06:43:02.634.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterInez Mruk
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListiodoacetamide derivatized residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-01-09 04:29:22ID requested
12025-05-07 06:43:03announced
Publication List
10.1093/nar/gkaf113;
Wons E, Gucwa K, Lewandowska N, Wisniewska A, Kozlowski LP, Mruk I, A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons. Nucleic Acids Res, 53(5):(2025) [pubmed]
Keyword List
submitter keyword: proteomics,Escherichia coli, Rac prophage TF,ydaT locus, DDA, putative transcription factors
Contact List
Paulina Czaplewska
contact affiliationIntercollegiate Faculty of BIotechnology, University of Gdansk and Medical University of Gdansk, Mass Spectrometry Laboratory, Abrahama 58, 80-307 Gdansk, Poland
contact emailpaulina.czaplewska@ug.edu.pl
lab head
Inez Mruk
contact affiliationIntercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk
contact emailinez.mruk@phdstud.ug.edu.pl
dataset submitter
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Dataset FTP location
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