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

PROVIDER: PRJNA576919 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10259100.fastq.gz	Fastqsanger.gz
	SRR10259101.fastq.gz	Fastqsanger.gz
	SRR10259102.fastq.gz	Fastqsanger.gz
	SRR10259103.fastq.gz	Fastqsanger.gz
	SRR10259082.fastq.gz	Fastqsanger.gz

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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: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

2020-03-20 | GSE145604 | GEO

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

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: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

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

Project description: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.

2020-04-08 | PXD015835 | Pride

Comparison of sRNA populations obtained using HD adapters in A thaliana, with NEB RecJ exonuclease or Superscript II enzymes

Project description:Multiple companies produce RecJ exonuclease and RNA dependent DNA polymerase for making cDNA. Our standard protocol was developed based on the enzymes from Epicenter (epicenter was recently bought by the Illumina company). As an alternative for the enzymes from EPicenter, we tested the RecJ exonuclease from NEB and Superperscript II from Invitrogen in sRNA library construction using HD adapters [Sorefan et al 2012, Xu et al 2015].

2018-12-20 | GSE102509 | 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

Critically ill patients with either gram-positive sepsis or gram-negative sepsis

Project description:Objective: It is unclear whether the host response of gram-positive sepsis differs from gram-negative sepsis at a transcriptome level. Using microarray technology, we compared the gene-expression profiles of gram-positive sepsis and gram-negative sepsis in critically ill patients. Design: A prospective cross-sectional study. Setting: A 20-bed general intensive care unit of a tertiary referral hospital. Patients: Seventy-two patients admitted to the intensive care unit. Interventions: Intravenous blood was collected for leukocyte separation and RNA extraction. Microarray experiements were then performed examing the expression level of 19,232 genes in each sample. Measurements and Main Results: There was no difference in the expression profile between gram-positive and gram-negative sepsis. The finding remained unchanged even when genes with lower expression level were included or after statistical stringency was lowered. There were, however, ninety-four genes differentially expressed between sepsis and control patients. These genes included those involved in immune regulation, inflammation and mitochondrial function. Hierarchical cluster analysis confirmed that the difference in gene expression profile existed between sepsis and control patients, but not between gram-positive and gram-negative patients. Conclusion: Gram-positive and gram-negative sepsis share a common host response at a transcriptome level. These findings support the hypothesis that the septic response is non-specific and is designed to provide a more general response that can be elicited by a wide range of different micro-organisms. Keywords: disease state analysis, gram-positive sepsis, gram-negative sepsis

2007-12-01 | GSE6535 | GEO

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