Transcriptomic changes associated with the depletion of RNA degradosome components PNPase, RNase E and RNase J in Mycobacterium tuberculosis.
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ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis H37Rv
PROVIDER: GSE126286 | GEO | 2019/02/09
REPOSITORIES: GEO
Similar Datasets
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
Project description:Transcriptomic changes associated with the depletion of RNA degradosome components PNPase, RNase E and RNase J in Mycobacterium tuberculosis.
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Project description:Vertebrate mitochondrial genomes show extraordinary GC skew which results in the synthesis of RNAs prone to form G-quadruplexes (G4). Such RNAs, although mostly non-coding, are transcribed at high rate and swiftly degraded by an unknown mechanism. Comprehensive proteomic and transcriptomic approaches revealed that quasi-RRM protein GRSF1 together with the mitochondrial degradosome composed of RNA helicase hSuv3 and PNPase control the levels of G4 containing RNAs in mitochondria. When this machinery is inactivated non-coding mtRNAs are upregulated and novel, previously undescribed transcript, which we named tRNA-like, strongly accumulates. In vitro reconstitution experiments showed that GRSF is responsible for G4 RNA melting essential for degradosome-mediated decay.
2018-06-17 | GSE106368 | GEO
Project description:PNPase, one of the major enzymes with 3ʹ-to-5ʹ single-stranded RNA (ssRNA) degradation and processing activities, can interact with the RNA helicase RhlB independent of RNA degradosome formation in E. coli. Here we report that loss of interaction between RhlB and PNPase impacts cysteine homeostasis in E. coli. By random mutagenesis, we identified a mutant RhlBP238L that loses 75% of its ability to interact with PNPase, but retains normal interaction with RNase E and RNA in addition to exhibiting normal helicase activity. Applying microarray analyses to an E. coli strain with impaired RNA degradosome formation, we investigated the biological consequences of a weakened interaction between RhlB and PNPase.
2015-11-10 | GSE57784 | GEO
Project description:The Bacillus subtilis genome encodes four 3’ exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3’ exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3’ ends within coding sequences was performed in strains that were either deleted for, or had an inactivating point mutation in, the pnpA gene. The pattern of 3’ end accumulation in these strains was highly similar, suggesting that mRNA decay was not occurring in the context of a degradosome, whose structure would be affected by the absence of PNPase. A comparison with mapped 3’ ends in a strain lacking CshA, the major RNA helicase, indicated that different mRNAs may require both PNPase and CshA for efficient decay. RNA-seq analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3’ exoribonucleases. When RNase R was the only 3’ exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet unidentified, 3’ exoribonuclease.
2022-01-03 | GSE192670 | GEO
Project description:Background The RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. Although there are many studies about these exoribonucleases not much is known about their global effect in the transcriptome. Results In order to study the effects of the exoribonucleases on the transcriptome, we sequenced the total RNA (RNA-Seq) from wild-type cells and from mutants for each of the exoribonucleases (∆rnb, ∆rnr and ∆pnp). We compared each of the mutant transcriptome with the wild-type to determine the global effects of the deletion of each exoribonucleases in exponential phase. We determined that the deletion of RNase II significantly affected 187 transcripts, while deletion of RNase R affects 202 transcripts and deletion of PNPase affected 226 transcripts. Surprisingly, many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The results obtained from the transcriptomic analysis pointed to the fact that these enzymes were changing the expression of genes related with flagellum assembly, motility and biofilm formation. The three exoribonucleases affected some stable RNAs, but PNPase was the main exoribonuclease affecting this class of RNAs. We confirmed by qPCR some fold-change values obtained from the RNA-Seq data, we also observed that all the exoribonuclease mutants were significantly less motile than the wild-type cells. Additionally, RNase II and RNase R mutants were shown to produce more biofilm than the wild-type control while the PNPase mutant did not form biofilms. Conclusions In this work we demonstrate how deep sequencing can be used to discover new and relevant functions of the exoribonucleases. We were able to obtain valuable information about the transcripts affected by each of the exoribonucleases and compare the roles of the three enzymes. Our results show that the three exoribonucleases affect cell motility and biofilm formation that are two very important factors for cell survival, especially for pathogenic cells.
2015-03-17 | GSE60107 | GEO
Project description:UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. To identify functionally important sRNA-target RNA interactions we applied crosslinking and sequencing of hybrids (CLASH) to the core degradosome component RNase E in EHEC. RNase E was shown to bind to many classes of RNA, confirming the wide distribution of degradosome targets. These included several hundred sRNA-mRNA duplexes, and the distribution of non-templated oligo(A) tails indicated that the sRNA target RNase E-mediated cleavage at these interaction sites. Functional repression of target mRNAs was confirmed for the core sRNA RyhB, and the pathogenicity-associated sRNA Esr41. In the case of Esr41, three confirmed target mRNAs participate in iron accumulation and the ∆esr41 strain showed increased growth under conditions of iron limitation. We conclude that CLASH can be used to identify functional targets for bacterial sRNAs.
2017-02-14 | GSE77463 | GEO
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
Project description:The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. RNA degradation can be initiated by an endonucleolytic cleavage and then by further promoted by exoribonucleolytic decay. In this study, we analyzed the importance of the Rhodobacter sphaeroides PNPase regarding the physiology and sRNA homeostasis. Moreover, we developed a pipeline to globally identify differential RNA 3’-ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants. The Rhodobacter sphaeroides PNPase mutant exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. Furthermore, the transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, the PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. The RNA 3’-end analysis reveals that 82% of all differential 3’-ends are enriched in the pnp mutant and are mostly located in coding sequences or untranslated regions (UTR). A fair percentage of these ends was also identified as differential RNA 3’-end in RNase E and RNase III mutant strains. The PNPase has a major influence in RNA processing and maturation and thus modulates the transcriptome. This includes regulatory sRNAs, stressing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The 3’-end analysis indicates a sequential processing of UTR- and non-UTR derived sRNAs by several ribonucleases. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5’/3’-ends. It is publicly available on GitHub and is distributed under ICS licence.
2021-02-16 | GSE156818 | GEO
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