PXD059580

PXD059580 is an original dataset announced via ProteomeXchange.

Title	A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons
Description	Bacterial 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.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_06:43:02.634.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Inez Mruk
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-09 04:29:22	ID requested
⏵ 1	2025-05-07 06:43:03	announced

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]

submitter keyword: proteomics,Escherichia coli, Rac prophage TF,ydaT locus, DDA, putative transcription factors

Paulina Czaplewska
contact affiliation	Intercollegiate Faculty of BIotechnology, University of Gdansk and Medical University of Gdansk, Mass Spectrometry Laboratory, Abrahama 58, 80-307 Gdansk, Poland
contact email	paulina.czaplewska@ug.edu.pl
lab head
Inez Mruk
contact affiliation	Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk
contact email	inez.mruk@phdstud.ug.edu.pl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD059580

PRIDE project URI

• PRIDE
  1. PXD059580
     1. Label: PRIDE project
     2. Name: A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons