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A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

ABSTRACT: 22 total proteome samples from S. pneumoniae wild type resolved on a glycerol gradient resulting in 20 fractions and a pellet fraction. A lysate sample is given as input control.

INSTRUMENT(S): LTQ Orbitrap Velos, Orbitrap Fusion

ORGANISM(S): Streptococcus Pneumoniae Tigr4

SUBMITTER: Jens Hör

LAB HEAD: Jörg Vogel

PROVIDER: PXD015835 | Pride | 2020-04-08

REPOSITORIES: Pride

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			Action	DRS
	2017-05-22_Fusion_11148.raw	Raw
	2017-05-22_Fusion_11149.raw	Raw
	2017-05-22_Fusion_11150.raw	Raw
	2017-05-22_Fusion_11151.raw	Raw
	2017-05-22_Fusion_11152.raw	Raw

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Publications

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control.

Hör Jens J Garriss Geneviève G Di Giorgio Silvia S Hack Lisa-Marie LM Vanselow Jens T JT Förstner Konrad U KU Schlosser Andreas A Henriques-Normark Birgitta B Vogel Jörg J

The EMBO journal 20200330 9

RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% o ...[more]

PMID: 32227509

Similar Datasets

A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

Project description:Affinity purification samples performed with different sRNAs as the bait. Single lanes were cut from a gel and submitted for MS.

2020-04-08 | PXD015842 | Pride

Exonuclease-mediated sRNA activation in competence regulation in a Gram-positive bacterium

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-20 | GSE145605 | GEO

A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

Project description:RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1 (a.k.a. YhaM) with sRNAs that control bacterial competence. Contrary to expectation, the nucleolytic activity of Cbf1 stabilized these sRNAs, thereby promoting their function as repressors of competence. These results illustrate how this first RNA/protein complexome resource for a Gram-positive species can be utilized to identify new molecular factors in RNA-based regulation of pathways with relevance to bacterial virulence.

2021-01-27 | GSE138732 | GEO

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control.

Project description:RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1/YhaM with sRNAs that control bacterial competence for DNA uptake. Unexpectedly, the nucleolytic activity of Cbf1 stabilizes these sRNAs, thereby promoting their function as repressors of competence. Overall, these results provide the first RNA/protein complexome resource of a Gram-positive species and illustrate how this can be utilized to identify new molecular factors with functions in RNA-based regulation of virulence-relevant pathways.

| S-EPMC7196914 | biostudies-literature

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

2020-03-20 | GSE145604 | GEO

Exonuclease-mediated sRNA activation in competence regulation in a Gram-positive bacterium

Project description:Exonuclease-mediated sRNA activation in competence regulation in a Gram-positive bacterium

| PRJNA607724 | ENA

A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

Project description:A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

| PRJNA576919 | ENA

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

Project description:22 total proteome samples from E. coli wild type resolved on a glycerol gradient resulting in 20 fractions and a pellet fraction. A lysate sample is given as input control. Further, 2 affinity purification samples comparing YggL-3xFLAG pulldown vs. the wild type is given. In this case, each sample was run on a gel and the lanes cut into 15 gel pieces each.

2020-08-10 | PXD019900 | Pride

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

Project description:Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

| PRJNA607729 | ENA

An in vivo reporter assay for sRNA-directed gene control in Gram-positive bacteria: identifying a novel sRNA target in Staphylococcus aureus.

Project description:Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, for the most part, are unknown. This is mainly due to difficulties in identifying their targets. To aid in the identification of sRNA targets in Gram-positive bacteria, we set up an in vivo method for fast analysis of sRNA-mediated post-transcriptional control at the 5? regions of target mRNAs. The technology is based on the co-expression of an sRNA and a 5? sequence of an mRNA target fused to a green fluorescent protein (GFP) reporter. The system was challenged on Staphylococcus aureus, an opportunistic Gram-positive pathogen. We analyzed several established sRNA-mRNA interactions, and in addition, we identified the ecb mRNA as a novel target for SprX2 sRNA. Using our in vivo system in combination with in vitro experiments, we demonstrated that SprX2 uses an antisense mechanism to prevent ecb mRNA translation initiation. Furthermore, we used our reporter assay to validate sRNA regulations in other Gram-positive organisms, Bacillus subtilis and Listeria monocytogenes. Overall, our method is broadly applicable to challenge the predicted sRNA-mRNA interactions in Gram-positive bacteria.

| S-EPMC5416835 | biostudies-other

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