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Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism

ABSTRACT: Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism

PROVIDER: PRJNA627171 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11580630.fastq.gz	Fastqsanger.gz
	SRR11580631.fastq.gz	Fastqsanger.gz
	SRR11580632.fastq.gz	Fastqsanger.gz
	SRR11580633.fastq.gz	Fastqsanger.gz
	SRR11580634.fastq.gz	Fastqsanger.gz

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Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism

Project description:Ribonuclease P (RNase P) is the only ribonuclease responsible for 5'-end maturation of tRNAs in all kingdoms of life. In Escherichia coli, it is also essential for separation of pre-tRNAs from multiple polycistronic transcripts. Using RNA sequencing (RNA-seq), we show here that RNase P affects the abundance of ~44% of the expressed mRNAs demonstrating a much more widespread role in mRNA decay than previously thought. Furthermore, our data also demonstrate for the first time that the polyadenylation of transcripts by PAP I modulates RNase P-mediated mRNA decay as well as tRNA processing.

2021-09-09 | GSE149024 | GEO

Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism.

Project description:Ribonuclease P (RNase P), which is required for the 5'-end maturation of tRNAs in every organism, has been shown to play a limited role in other aspects of RNA metabolism in Escherichia coli. Using RNA-sequencing (RNA-seq), we demonstrate that RNase P inactivation affects the abundances of ~46% of the expressed transcripts in E. coli and provide evidence that its essential function is its ability to generate pre-tRNAs from polycistronic tRNA transcripts. The RNA-seq results agreed with the published data and northern blot analyses of 75/83 transcripts (mRNAs, sRNAs, and tRNAs). Changes in transcript abundances in the RNase P mutant also correlated with changes in their half-lives. Inactivating the stringent response did not alter the rnpA49 phenotype. Most notably, increases in the transcript abundances were observed for all genes in the cysteine regulons, multiple toxin-antitoxin modules, and sigma S-controlled genes. Surprisingly, poly(A) polymerase (PAP I) modulated the abundances of ~10% of the transcripts affected by RNase P. A comparison of the transcriptomes of RNase P, RNase E, and RNase III mutants suggests that they affect distinct substrates. Together, our work strongly indicates that RNase P is a major player in all aspects of post-transcriptional RNA metabolism in E. coli.

| S-EPMC8766891 | biostudies-literature

RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis.

Project description:Bordetella pertussis has been shown to encode regulatory RNAs, yet the post-transcriptional regulatory circuits on which they act remain to be fully elucidated. We generated mutants lacking the endonucleases RNase III and RNase E and assessed their individual impact on the B. pertussis transcriptome. RNA-Seq analysis showed differential expression of ~25% of the B. pertussis transcriptome in each mutant with only 28% overlap between data sets. Both endonucleases exhibited substantial impact on genes involved in amino acid uptake e.g. ABC transporters, and in virulence e.g. the type III secretion system, and the autotransporters vag8, tcfA and brkA. Interestingly, mutations in RNase III and RNase E drove the stability of many transcripts, including those involved in virulence, in opposite directions; a result that was validated by qPCR and immunoblot for tcfA and brkA. Of note, whereas similar mutations to RNase E in E. coli have subtle effects on transcript stability, a striking >20-fold reduction in four gene transcripts, including tcfA and vag8, was observed in B. pertussis. We further compared our data set to the regulon controlled by the RNA chaperone Hfq to identify B. pertussis loci influenced by regulatory RNAs. This analysis identified ~120 genes and 19 operons potentially regulated at the post-transcriptional level. Thus, our findings revealed how changes in RNase III- and RNase E-mediated RNA turnover influence pathways associated with virulence and cellular homeostasis. Moreover, we highlighted loci potentially influenced by regulatory RNAs, providing insights into the post-transcriptional regulatory networks involved in fine tuning B. pertussis gene expression.

2021-08-11 | GSE164312 | GEO

Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq]

Project description:RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA-sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting an interesting connection between RNA metabolism and a regulator that bridges primary and specialized metabolism. We also connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct, but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

2025-05-30 | GSE285999 | GEO

Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq-induced]

Project description:RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA-sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant, this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting an interesting connection between RNA metabolism and a regulator that bridges primary and specialized metabolism. We connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct, but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

2025-05-30 | GSE286000 | GEO

Multiple roles of RNase Y in Streptococcus pyogenes mRNA metabolism

2013-02-01 | GSE40198 | GEO

RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis.

Project description:RNase III and RNase E influence post-transcriptional regulatory networks involved in virulence factor production, metabolism and regulatory RNAs processing in Bordetella pertussis.

| PRJNA689835 | ENA

Multiple roles of RNase Y in Streptococcus pyogenes mRNA metabolism

Project description:Streptococcus pyogenes (Group A streptococcus, GAS) is an important human pathogen that causes a variety of infectious diseases and sequelae. Recent studies showed virulence factor expression was controlled at multiple levels, including the post-transcriptional regulation. In this study, we examined the global half-lives of S. pyogenes mRNAs and explored the role RNase Y played in mRNA metabolism with microarray analysis. key word: genetic modification Streptococcus pyogenes NZ131 wild-type cells and ?rny strains were grown in C-medium until late exponential phase. Rifampicin was added to the cell culture and samples were collected before and after rifampicin addition. The transcriptional profile of the whole genome before and after rifampicin addition was examined with microarray. Please note that mRNA decay assay resulted in considerable variations in the datasets. Samples were taken after rifampicin addition and subsequent incubation for different time intervals. During that time no new RNA is produced and the remaining RNA is degraded to various degrees.

2013-02-01 | E-GEOD-40198 | biostudies-arrayexpress

Genome-wide alterations in yeast strains lacking RNase H1, RNase H2, or both RNase H1 and RNase H2

Project description:Two types of RNA:DNA associations can lead to genome instability: the formation of R-loops during transcription and the incorporation of ribonucleotide monophosphates (rNMPs) into DNA during replication. Both ribonuclease (RNase) H1 and RNase H2 degrade the RNA component of R-loops, whereas only RNase H2 can remove one or a few rNMPs from DNA. We performed high-resolution mapping of mitotic recombination events throughout the yeast genome in diploid strains of Saccharomyces cerevisiae lacking RNase H1 (rnh1Δ), RNase H2 (rnh201Δ), or both RNase H1 and RNase H2 (rnh1Δ rnh201Δ). We found little effect on recombination in the rnh1Δ strain, but elevated recombination in both the rnh201Δ and the double-mutant strains; levels of recombination in the double mutant were about 50% higher than in the rnh201 single-mutant strain. An rnh201Δ mutant that additionally contained a mutation that reduces rNMP incorporation by DNA polymerase ε (pol2-M644L) had a level of instability similar to that observed in the presence of wild-type Polε. This result suggests that the elevated recombination observed in the absence of only RNase H2 is primarily a consequence of R loops rather than misincorporated rNMPs.

2015-09-23 | GSE73334 | GEO

Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq]

Project description:Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq]

| PRJNA1207462 | ENA

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