PXD047655

PXD047655 is an original dataset announced via ProteomeXchange.

Title	Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σE-dependent small RNA with unusual mRNA activation activity
Description	The oral commensal Fusobacterium nucleatum can spread to extra-oral sites where it is associated with diverse pathologies including pre-term birth and cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of RNA regulatory networks that allow this bacterium to adapt to its various niches. As a first step in that direction, we recently showed that F. nucleatum harbors a global stress response governed by the extracytoplasmic function sigma factor σE, which displays a striking functional conservation with Proteobacteria and includes a noncoding arm in the form of a regulatory small RNA (sRNA), FoxI. To search for putative additional σE-dependent sRNAs, we comprehensively mapped 5’- and 3’-ends of transcripts in the model strain ATCC 23726. This enabled the discovery of FoxJ, a ~156 nucleotide sRNA previously misannotated as the 5’ UTR of ylmH. FoxJ is tightly controlled by σE and activated by the same stress conditions as FoxI. Both sRNAs act as mRNA repressors of the abundant porin FomA, but FoxJ also regulates genes that are distinct from the target suite of FoxI. Moreover, FoxJ differs from most other σE-dependent sRNAs in that it also positively regulates genes at the post-transcriptional level. We provide preliminary evidence for a new mode of sRNA-mediated mRNA activation, which involves the targeting of intra-operonic terminators. Overall, our study provides an important resource through the comprehensive annotation of 5’- and 3’ UTRs in F. nucleatum and expands our understanding of the σE-response in this evolutionarily distant bacterium.
HostingRepository	PRIDE
AnnounceDate	2024-02-08
AnnouncementXML	Submission_2024-02-08_09:22:32.441.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	2023-12-08 07:58:57	ID requested
⏵ 1	2024-02-08 09:22:32	announced

10.1128/MBIO.03536-23;

submitter keyword: Fusobacterium

sRNA

sigma E;post-transcriptional regulation

Jörg Vogel
contact affiliation	Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 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/PXD047655

PRIDE project URI

• PRIDE
  1. PXD047655
     1. Label: PRIDE project
     2. Name: Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σE-dependent small RNA with unusual mRNA activation activity