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The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

ABSTRACT: The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

PROVIDER: PRJEB33968 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3477186_1.fastq.gz	Fastqsanger.gz
	ERR3477186_2.fastq.gz	Fastqsanger.gz
	ERR3477187.fastq.gz	Fastqsanger.gz
	ERR3477188_1.fastq.gz	Fastqsanger.gz
	ERR3477188_2.fastq.gz	Fastqsanger.gz

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The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

Project description:In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS ,we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.

2019-08-22 | E-MTAB-8244 | biostudies-arrayexpress

The conserved 3’ UTR-derived small RNA NarS counteracts the risk of toxic nitric oxide accumulation during nitrate respiration

Project description:The conserved 3’ UTR-derived small RNA NarS counteracts the risk of toxic nitric oxide accumulation during nitrate respiration

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The conserved 3' UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration.

Project description:Small noncoding RNAs (sRNAs) from mRNA 3' UTRs seem to present a previously unrecognized layer of bacterial post-transcriptional control whereby mRNAs influence each other's expression, independently of transcriptional control. Studies in Escherichia coli and Salmonella enterica showed that such sRNAs are natural products of RNase E-mediated mRNA decay and associate with major RNA-binding proteins (RBPs) such as Hfq and ProQ. If so, there must be additional sRNAs from mRNAs that accumulate only under specific physiological conditions. We test this prediction by characterizing candidate NarS that represents the 3' UTR of nitrate transporter NarK whose gene is silent during standard aerobic growth. We find that NarS acts by Hfq-dependent base pairing to repress the synthesis of the nitrite transporter, NirC, resulting in mRNA cross-regulation of nitrate and nitrite transporter genes. Interestingly, the NarS-mediated repression selectively targets the nirC cistron of the long nirBDC-cysG operon, an observation that we rationalize as a mechanism to protect the bacterial cytoplasm from excessive nitrite toxicity during anaerobic respiration with abundant nitrate. Our successful functional assignment of a 3' UTR sRNA from a non-standard growth condition supports the notion that mRNA crossregulation is more pervasive than currently appreciated.

| S-EPMC7038943 | biostudies-literature

The conserved 3’ UTR-derived small RNA NarS counteracts the risk of toxic nitric oxide accumulation during nitrate respiration

Project description:In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS, we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.

2019-08-13 | GSE135757 | GEO

MR-1 nitrate sample to fumarate sample

Project description:One of the most striking observations in the S. oneidensis genome regarding nitrate respiration is that napC is missing and nrfBCD is degenerated. To gain insights into candidate genes encoding the protein(s) in place of NapC and NrfBCD function, i.e., delivering electrons to NapA and NrfA, transcriptional profiling was carried out using the S. oneidensis whole-genome cDNA microarray. Cells of MR-1 grown on nitrate or fumarate under anaerobic conditions were sampled at the exponential phase for the analysis. The quality of the array data was statistically assessed using the method reported previously. Keywords: Compararive microarray study Compare transcriptional profiles of MR-1 grown on nitrate and Fumarate aiming at finding the electron transfer proteins to NapA and NrfA.

2010-05-19 | E-GEOD-11198 | biostudies-arrayexpress

MR-1 nitrate sample to fumarate sample

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no treatment / nitrate starvation / nitrate induction-Study of the primary nitrate response (PNR) in nlp2 mutant and WT

Project description:ngs2018_11_nlp2-no treatment / nitrate starvation / nitrate induction-Is NLP2 involved in the PNR Nitrate starvation and nitrate induction effects on wild type and mutant nlp2

2023-02-08 | GSE142628 | GEO

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Project description:The purpose of this study is to determine whether dietary nitrate supplementation improves performance in cardiopulmonary exercise testing (CPET).

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VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation

Project description:N6-methyadenosine (m6A) is enriched in 3`UTR (3` untranslated region) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m6A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3`UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m6A enrichment in 3`UTR. Depletions of VIRMA and METTL3 induce 3`UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3`UTR of over 2,800 mRNAs, 84% of which are modified with m6A. Together our studies provide insights into m6A deposition specificity in 3`UTR and its correlation with alternative polyadenylation.

2018-03-07 | GSE102493 | GEO

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