PXD003360

PXD003360 is an original dataset announced via ProteomeXchange.

Title	Biochemical partitioning of RNA collectives reveals ProQ as a global RNA chaperone in bacteria
Description	The vast number of noncoding RNAs in bacteria suggests that major post-transcriptional circuits beyond those controlled by the global RNA-binding proteins Hfq and CsrA may exist. To identify additional globally acting RNPs we have developed a method (gradient profiling by sequencing; Grad-seq) to partition the full ensemble of cellular RNAs based on their biochemical behavior. Consequently, we discovered transcripts that commonly interact with the osmoregulatory protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant RNA-binding protein with a wide range of targets, including a new class of ProQ-associated small RNAs that are highly structured and function to regulate mRNAs in trans. Based on its ability to chart the functional landscape of all cellular transcripts irrespective of their length and sequence diversity, Grad-seq promises to aid the discovery of major functional RNA classes and RNA-binding proteins in many organisms.
HostingRepository	PRIDE
AnnounceDate	2017-07-21
AnnouncementXML	Submission_2017-07-21_00:35:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Otto
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-16 05:31:52	ID requested
⏵ 1	2017-07-21 00:35:44	announced

Smirnov A, F, ö, rstner KU, Holmqvist E, Otto A, G, ü, nster R, Becher D, Reinhardt R, Vogel J, Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proc Natl Acad Sci U S A, 113(41):11591-11596(2016) [pubmed]

curator keyword: Biological

submitter keyword: Salmonella enterica, ncRNA

Andreas Otto
contact affiliation	Andreas Otto, Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, F.-L. Jahnstrasse 15, 17489 Greifswald, Germany
contact email	andreas.otto@uni-greifswald.de
lab head
Andreas Otto
contact affiliation	Institute for Microbiology
contact email	andreas.otto@uni-greifswald.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/2017/07/PXD003360

PRIDE project URI

• PRIDE
  1. PXD003360
     1. Label: PRIDE project
     2. Name: Biochemical partitioning of RNA collectives reveals ProQ as a global RNA chaperone in bacteria