Proteomics,Multiomics

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Biochemical partitioning of RNA collectives reveals ProQ as a global RNA chaperone in bacteria

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: GSE62988PRJNA266346PRJNA266347

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Sl1344

SUBMITTER: Andreas Otto  

LAB HEAD: Andreas Otto

PROVIDER: PXD003360 | Pride | 2017-07-21

REPOSITORIES: Pride

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Dataset's files

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110923_O2_P1_SG__JV_Spur20_1.RAW Raw
110923_O2_P1_SG__JV_Spur20_10.RAW Raw
110923_O2_P1_SG__JV_Spur20_2.RAW Raw
110923_O2_P1_SG__JV_Spur20_3.RAW Raw
110923_O2_P1_SG__JV_Spur20_4.RAW Raw
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Publications

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.

Smirnov Alexandre A   Förstner Konrad U KU   Holmqvist Erik E   Otto Andreas A   Günster Regina R   Becher Dörte D   Reinhardt Richard R   Vogel Jörg J  

Proceedings of the National Academy of Sciences of the United States of America 20160926 41

The functional annotation of transcriptomes and identification of noncoding RNA (ncRNA) classes has been greatly facilitated by the advent of next-generation RNA sequencing which, by reading the nucleotide order of transcripts, theoretically allows the rapid profiling of all transcripts in a cell. However, primary sequence per se is a poor predictor of function, as ncRNAs dramatically vary in length and structure and often lack identifiable motifs. Therefore, to visualize an informative RNA land  ...[more]

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