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RNA-bound proteome of Mycobacterium bovis

ABSTRACT: The dataset accompanying a publication describing the RNA degradosome components in Mycobacterium tuberculosis (Mtb). The RNA-bound proteome was determined by affinity purification of protein-RNA complexes from Mycobacterium bovis cells fed with 4-thiouridine and crosslinked via photoactivation at 365nm. Affinity purified RNA-protein complexes were subjected to LC-MS analysis

OTHER RELATED OMICS DATASETS IN: GSE126286

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mycobacterium Bovis

SUBMITTER: Przemyslaw Plocinski

LAB HEAD: Andrzej Dziembowski

PROVIDER: PXD012661 | Pride | 2019-04-01

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	3012570lau_RNAplus.raw	Raw
	3012571lau_RNAminus.raw	Raw
	306251645lau_U-.raw	Raw
	306251646lau_U.raw	Raw
	307171830lau_U2-.raw	Raw

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1 - 5 of 17

Publications

Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis.

Płociński Przemysław P Macios Maria M Houghton Joanna J Niemiec Emilia E Płocińska Renata R Brzostek Anna A Słomka Marcin M Dziadek Jarosław J Young Douglas D Dziembowski Andrzej A

Nucleic acids research 20190601 11

The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-l ...[more]

PMID: 30957850

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RNA degradosome components purified from Mycobacterium tuberculosis

Project description:The dataset accompanying a publication describing the RNA degradosome components in Mycobacterium tuberculosis (Mtb). Individual RNA degradosome components from Mtb (PNPase, RNase E, RNase J, RhlE and Enolase) were tagged with eGFP and used as baits to pull-down their interaction partners. The protein-complexes were purified by affinity chromatography, using previously published protocols, and submitted to LC-MS analysis.

2019-04-01 | PXD012662 | Pride

Mass spectrometry approach to identify mitochondrial poly(A) RNA interacting proteins

Project description:To identify mitochondrial RNA-interacting proteins, we developed three related mass spectrometry based methods. In the first method, called mitochondrial crosslinking (MXL), mitochondria of 4-thiouridine labelled cells were isolated, exposed to UV-light and poly(A) RNA was isolated. In the second method, called whole cell crosslinking (WCXL), 4-thiouridine labelled cells were first exposed to UV-light, subsequently mitochondria were isolated followed by a poly(A) RNA extraction. The third method, called ethidium bromide whole cell crosslinking (WCXL_EtBr), is exactly the same as the WCXL method, but the cells are cultured with ethidium bromide to reduce the amount of mitochondrial RNA. In all methods poly(A) RNA was degraded and proteins in the sample were digested and identified using mass spectrometry.

2019-10-15 | PXD014957 | Pride

Structural elucidation of a novel mechanism for bacteriophage-based inhibition of the RNA degradosome

Project description:In all domains of life, the catalysed degradation of RNA facilitates rapid adaption to changing environmental conditions. We identified a virus-encoded protein that directly binds and inhibits the RNA degradation machinery of its bacterial host, allowing efficient accumulation of viral RNA in the infected cell. Encoded by the giant phage фKZ, KZ37/Dip associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome. Thereby, KZ37/Dip competes with the binding of RNA substrates, resulting in effective inhibition of RNA degradation. The crystal structure of KZ37/Dip (2.2 Å) reveals an unprecedented fold for which there are no identified structural homologues. The protein forms a homo-dimer that resembles a partially opened scroll and binds RNase E through exposed acidic patches on its convex outer surface. Through the activity of KZ37/Dip, фKZ has evolved a unique mechanism to down regulate a key process of its host.

2016-07-27 | PXD003285 | Pride

mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains

Project description:mRNA decay in E. Coli degradosome mutants and their parental strains following transcriptional arrest with rifampicin. Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design

2006-01-06 | GSE3978 | GEO

mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains

2006-01-05 | E-GEOD-3978 | biostudies-arrayexpress

Global analysis of Escherichia coli RNA degradosome function

Project description:This SuperSeries is composed of the following subset Series: GSE3977: Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains GSE3978: mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes Refer to individual Series

2006-03-07 | E-GEOD-4394 | biostudies-arrayexpress

Global analysis of Escherichia coli RNA degradosome function

Project description:Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes This SuperSeries is composed of the SubSeries listed below.

2006-03-08 | GSE4394 | GEO

Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

Project description:Comparative transcript abundance in E. Coli degradosome mutants and their parental strains. Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. Keywords: genetic_modification_design

2006-01-06 | GSE3977 | GEO

Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

2006-01-05 | E-GEOD-3977 | biostudies-arrayexpress

Transcriptomic changes associated with the depletion of RNA degradosome components PNPase, RNase E and RNase J in Mycobacterium tuberculosis.

Project description:RNA-Seq results accompanying submission of a manuscript describing roles of RNA degradosome components PNPase, RNase E and RNase J in shaping the transcriptome of the H37Rv Mycobacterium tuberculosis. Next generation sequenicing results are provided for three independent biological replicates for the wild type control, genetic knockout of RNase J and CRISPR/Cas9 (DNA cleavage defiecient) regulated knockdowns of PNPase and RNase E along with a control strain expressing solely the Cas9 enzyme, not the target sgRNA. We have found that removal of RNase J had little effect on the transcriptional profile of investigated strain, while depletion of PNPase or RNase E altered about a quarter of the entire transcriptome, including changes to non-coding RNA.

2019-02-09 | GSE126286 | GEO

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