PXD046416

PXD046416 is an original dataset announced via ProteomeXchange.

Title	A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum
Description	The common oral microbe Fusobacterium nucleatum has recently gained attention when it was found to colonize tumors throughout the human body. Fusobacteria are also interesting in regard to bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. Here, to search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that copurified with 19 different sRNAs. Our approach recovered a 6S RNA-RNA polymerase complex in this species and discovered high enrichment of the KH domain proteins KhpA and KhpB with almost any tested sRNA, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the cellular stability of several of their targets. RNA-seq analysis and cell biological assays suggest that KhpA/B have several physiological functions, including a strong requirement for ethanolamine utilization. Our RBP search and discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.
HostingRepository	PRIDE
AnnounceDate	2024-02-08
AnnouncementXML	Submission_2024-02-08_09:17:42.512.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Falk Ponath
SpeciesList	scientific name: Fusobacterium nucleatum subsp. nucleatum ATCC 23726; NCBI TaxID: 525283;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-26 06:31:55	ID requested
⏵ 1	2024-02-08 09:17:43	announced

Zhu Y, Ponath F, Cosi V, Vogel J, A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum. Nucleic Acids Res, 52(7):3950-3970(2024) [pubmed]

10.1093/nar/gkae010;

submitter keyword: RBP

KH-domain

Fusobacterium nucleatum

sRNA

Jörg Vogel
contact affiliation	Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
contact email	joerg.vogel@helmholtz-hiri.de
lab head
Falk Ponath
contact affiliation	Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
contact email	falk.ponath@helmholtz-hiri.de
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/2024/02/PXD046416

PRIDE project URI

• PRIDE
  1. PXD046416
     1. Label: PRIDE project
     2. Name: A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum