PXD032939

PXD032939 is an original dataset announced via ProteomeXchange.

Title	RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins
Description	RNA-binding proteins (RPBs) are deeply involved in many fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to globally identifying bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down mRNA-protein complexes. By overexpressing the poly(A) polymerase I, we drastically increase the frequency of polyadenylated RNA in E. coli, allowing us to pull down RNA-protein complexes using immobilized oligo-d(T) as bait. With this approach, we identified 167 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of several proteins previously unknown to interact with RNA, including the uncharacterized protein YhgF. YhgF is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF in vivo RNA targets using CLIP-seq, two of which were verified using electromobility shift assays. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lays the foundation for further studies of the strongly conserved RBP Yhg
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:55:21.552.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032939
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Erik Jansson
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-02 13:52:39	ID requested
⏵ 1	2023-11-14 08:55:22	announced

10.6019/PXD032939;

submitter keyword: LC-MS,RNA interactome capture, Escherichia coli

Erik Jansson
contact affiliation	Uppsala University, Department of Pharmaceutical Biosciences
contact email	erik.jansson@farmbio.uu.se
lab head
Erik Jansson
contact affiliation	Uppsala University
contact email	erik.jansson@farmbio.uu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD032939
     1. Label: PRIDE project
     2. Name: RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins