PXD063711

PXD063711 is an original dataset announced via ProteomeXchange.

Title	Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog of Bordetella pertussis
Description	Bordetella pertussis is a Gram-negative, strictly human re-emerging respiratory pathogen and the causative agent of whooping cough. The requirement of the RNA chaperone Hfq for the virulence of B. pertussis suggests that Hfq-dependent small regulatory RNAs (sRNAs) are involved in the virulence of this pathogen. To identify their potential mRNA targets, we applied a method combining experimental and computational approaches called RIL-seq. Our RIL-seq analysis revealed putative targets of several sRNAs including CT_532. This sRNA can interact with 5´UTR regions of mRNAs encoding the outer membrane proteins BP0840 and BP0943 (OmpA). The CT_532 sRNA shares 60% identity with the E. coli sRNA MicA and its expression is modulated by the heat and cold shocks as well as by osmotic stress. Collectively, these results suggest that CT_532 represents a MicA homolog. Importantly, the mutant lacking the first 22 nucleotides of CT_532 as well as its complemented variant overproducing CT_532 displayed reduced cytotoxicity towards human macrophages and impaired biofilm production compared to the wt strain. In addition, proteomic analysis revealed that CT_532 mutant produces increased amounts of OmpA protein.
HostingRepository	PRIDE
AnnounceDate	2025-07-14
AnnouncementXML	Submission_2025-07-13_16:10:53.892.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jana Jasprova
SpeciesList	scientific name: Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251); NCBI TaxID: 257313;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-07 00:52:56	ID requested
⏵ 1	2025-07-13 16:10:54	announced

10.1093/nar/gkaf614;

Kumar D, Beles M, Saha A, Proch, á, zkov, á I, Dienstbier A, Dr, ž, m, í, š, ek J, Č, apek J, Č, urnov, á I, Hot D, Petr, á, č, kov, á D, Ve, č, erek B, Bordetella pertussis. Nucleic Acids Res, 53(13):(2025) [pubmed]

submitter keyword: omics analysis, sRNA,Bordetella pertussis, RIL-seq, outer membrane, biofilm

Branislav Večerek
contact affiliation	Laboratory of Post-Transcriptional Control of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Czech Republic
contact email	vecerek@biomed.cas.cz
lab head
Jana Jasprova
contact affiliation	Charles University, Faculty of Science
contact email	vanikova@natur.cuni.cz
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/2025/07/PXD063711

PRIDE project URI

• PRIDE
  1. PXD063711
     1. Label: PRIDE project
     2. Name: Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog of Bordetella pertussis