PXD050404

PXD050404 is an original dataset announced via ProteomeXchange.

Title	A new world of RNA-binding proteins in heterocyst-forming cyanobacteria.
Description	RNA-binding proteins (RBPs) are central components of gene regulatory networks and RNA metabolism. The differentiation of nitrogen-fixing heterocysts in some filamentous cyanobacteria and their cooperation with vegetative cells in the same filament is one of the evolutionarily oldest cases of true multicellularity. Nostoc sp. PCC 7120 (Nostoc) is a model organism for filamentous cyanobacteria that differentiate heterocysts. Although hundreds of noncoding transcripts may be involved in this process, the RBPs that could cooperate with them are poorly characterized. We have used R-DeeP/GradR, a technique based on the differential sedimentation of RNA-protein complexes after RNase treatment in density gradients. All macromolecular complexes in the cell are fractionated by a sucrose gradient followed by high-resolution proteomics. We have compared gradients of RNase-treated with untreated samples in triplicates. If a protein was part of an RNA-protein complex, the complex should be disassembled after the RNase treatment and a shift of the protein position in the gradient should be observed (RNA-dependent proteins). Our approach yielded 333 RNA-dependent proteins. The results were compared to a bioinformatic prediction of RBPs and biochemical validation. We validated in vivo the RNA-binding capacity of 6 new RBPs. Some of these proteins were previously known to be involved in essential biological processes such as photosynthesis or heterocyst differentiation, but their association with RNA was previously unknown. In other cases, the function of the validated candidates was unknown. A knock-out strain of alr1700, a gene encoding a validated RNA-binding protein of unknown function, showed a deregulation of heterocyst differentiation, confirming the role of RBPs in regulating this cell differentiation process.
HostingRepository	PRIDE
AnnounceDate	2024-11-08
AnnouncementXML	Submission_2024-11-08_06:07:27.068.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frank Stein
SpeciesList	scientific name: Nostoc sp. (strain PCC 7120 / UTEX 2576); NCBI TaxID: 103690;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-06 06:19:12	ID requested
⏵ 1	2024-11-08 06:07:27	announced

Dataset with its publication pending

submitter keyword: Nostoc sp. PCC 7120, heterocyst differentiation, R-DeeP, RNA-binding proteins.

Prof. Dr. Wolfgang Hess
contact affiliation	Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
contact email	wolfgang.hess@biologie.uni-freiburg.de
lab head
Frank Stein
contact affiliation	EMBL
contact email	frank.stein@embl.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/2024/11/PXD050404

PRIDE project URI

• PRIDE
  1. PXD050404
     1. Label: PRIDE project
     2. Name: A new world of RNA-binding proteins in heterocyst-forming cyanobacteria.