Transcriptomic changes associated with the depletion of RNA degradosome components PNPase, RNase E and RNase J in Mycobacterium tuberculosis.
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ABSTRACT:
PROVIDER: PRJNA521480 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8550310_1.fastq.gz | Fastqsanger.gz | |||
| SRR8550310_2.fastq.gz | Fastqsanger.gz | |||
| SRR8550311_1.fastq.gz | Fastqsanger.gz | |||
| SRR8550311_2.fastq.gz | Fastqsanger.gz | |||
| SRR8550302_1.fastq.gz | Fastqsanger.gz |
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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
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:The RNA degradosome, a multi-protein complex regulating mRNA levels in bacteria, assembles in Pseudomonadota (Proteobacteria) on the RNase E C-terminal domain (CTD) via short linear motifs (SLiMs) that bind other RNA degradosome components and RNA. The composition of Pseudomonas aeruginosa RNA degradosome remains unknown, and its RNase E CTD shows limited similarity to those in well-studied Proteobacteria models like Escherichia coli or Caulobacter crescentus. Our study identified and characterized the SLiMs in P. aeruginosa RNase E, revealing a large duplicated sequence termed the 'REER-repeats' region. This region, along with AR1 and AR4 SLiMs, mediates RNase E CTD RNA binding and is necessary for the subcellular localization of the RNA degradosome in foci. Pull-down and bacterial two-hybrid assays identified PNPase and RhlB as RNase E-interacting proteins. We confirmed through protein-protein binding assays that PNPase and RhlB directly interact with RNase E, and additionally show that the interactions are mediated by the NDPR and AR1 SLiMs, respectively. Additionally, we confirm that the RhlE2 RNA helicase interacts with RNase E, but this interaction involves RNase E N-terminal domain. Finally, we show that RNase E CTD truncations are impaired in growth on cold and mutations affecting CTD RNA binding impaired twitching motility and virulence in a Galleria mellonella infection model. This study elucidates and highlights the critical role of RNase E CTD-mediated RNA binding and RNA degradosome assembly in the virulence and adaptability of P. aeruginosa.
2025-02-13 | GSE287326 | GEO
Project description:Many bacteria and archaea use CRISPR-Cas systems, which provide RNA-based, adaptive, and inheritable immune defenses against invading viruses and other foreign genetic elements. The proper processing of CRISPR guide RNAs (crRNAs) is a crucial step in the maturation of the defense complexes and is frequently performed by specialized ribonucleases encoded by cas genes. However, some systems employ enzymes associated with degradosome or housekeeping functions, such as RNase III or the endoribonuclease RNase E. Here, the endo- and 5´-exoribonuclease RNase J was identified as additional enzyme involved in crRNA maturation, acting jointly with RNase E in the crRNA maturation of a type III-Bv CRISPR-Cas system, and possibly together with a further RNase. Co-IP experiments revealed a small set of proteins that were co-enriched with RNase J, among them PNPase. Despite a measured, strong 3’ exonucleolytic activity of the recombinant enzyme, PNPase was not confirmed to contribute to crRNA maturation. However, the co-IP results indicate that PNPase is a component of the cyanobacterial degradosome that can recruit either RNase E or RNase J, together with additional enriched proteins.
2025-10-06 | PXD060866 | Pride
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:To identify mRNA substrates for the human RNase MRP complex, we examined the effects of siRNA-mediated depletion of RNase MRP (and RNase P) on the transcriptome of HEp-2 cells. The expression of two RNase MRP protein components, hPop1 and Rpp40, was knocked-down and after 48 hours mRNA was isolated from these cells as well as from cells transfected with an siRNA targeting the GFP mRNA (siEGFP), which was used as a control. The expression levels of mRNAs were analyzed on a genome-wide scale using 21K microarrays.
2011-04-01 | E-TABM-981 | biostudies-arrayexpress
Project description:mRNA degradation is a fundamentally important process that is regulated in response to stress in the globally important pathogen Mycobacterium tuberculosis. Several mycobacterial ribonucleases (RNases) are hypothesized to function together to coordinate mRNA degradation, but the interactions among them are mostly undefined. One of these enzymes, RNase E, contains intrinsically disordered regions (IDRs) and initiates mRNA degradation. Here, we aimed to define the interactions between major mycobacterial mRNA degradation enzymes and identify the function(s) of the two IDRs of RNase E in the nonpathogenic model Mycolicibacterium smegmatis. We found that the two IDRs differentially impact mRNA degradation rates in vivo but are largely functionally redundant in their impacts on steady-steady transcript abundance. In vitro, the IDRs are uninvolved in catalysis but play major roles in RNA binding and interactions with other mRNA degradation enzymes, namely PNPase, RNase J, and RhlE1. In vivo, these enzymes localize with RNase E, but its IDRs play only a minor role, suggesting substantial redundancy in subcellular localization mechanisms. Collectively, we propose a degradosome-like network model in mycobacteria, held together by dynamic, transient interactions among RNA degradation enzymes and RNA that can be disrupted during physiologically relevant stress to allow for adaptability.
2025-12-31 | GSE313996 | GEO
Project description:RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with different enzymes such as RNA degradosome components in the post-transcriptional regulation. As the regulation as a whole RNA degradosome is complicated and might differ case by case, we would like to seperate the effect of catalytic activity of RNase E per se and the effect of RNA degradosome. On the other hand, the physiology of bacterial growth in liquid culture is different from that on swmming plate culture. In real growing enviromnent, in which E. coli grows in the gut of warm-blooded organism, is a condition more like in soft-agar system instead of liquid culture that commonly adapted in laboratory study. To study the regulatory role of RNase E per se and RNA degradosmoe in gene regualtion of soft-agar culture, we used two different length of N-terminal RNase E which give different catalytic acitvity and compared theire effect of the transcriptome expressional level of strain with full-length RNase E.Here we found different groups of transcript that was regulated by merely RNase E catalytic acitivity, effect of RNA degradosome, or both. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system.
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Project description:RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with other protein components to form a RNA degradosome to regulate gene expression. Here, we aim to study the impact of RNA degradosome formation on E. coli gene expression by comparing the whole transcriptiome isolate from wildtype Rne strain and Rne C-terminal truncated strain that deleting the RNA degradosome binding domain. We choose to study the bacterial growth conditions in soft-agar culture because it is a condition more silimar to that in the gut of warm-blooded organism compared to merely liquid culture condition.Here we found different groups of transcript that was affected by Rne C-termianl truncation mutant. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system.
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