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A conserved seed-pairing domain affords small RNA-mediated stress resistance in enterobacteria

ABSTRACT: A conserved seed-pairing domain affords small RNA-mediated stress resistance in enterobacteria

PROVIDER: PRJNA515599 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8447500.fastq.gz	Fastqsanger.gz
	SRR8447510.fastq.gz	Fastqsanger.gz
	SRR8447501.fastq.gz	Fastqsanger.gz
	SRR8447511.fastq.gz	Fastqsanger.gz
	SRR8447502.fastq.gz	Fastqsanger.gz

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A conserved seed-pairing domain affords small RNA-mediated stress resistance in enterobacteria

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-22 | GSE125224 | GEO

A conserved RNA seed-pairing domain directs small RNA-mediated stress resistance in enterobacteria.

Project description:Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram-negative bacteria is a paradigm for sRNA-mediated stress management and involves, among other factors, the alternative sigma factor E (σE ) and one or more sRNAs. In this study, we identified the MicV sRNA as a new member of the σE regulon in Vibrio cholerae. We show that MicV acts redundantly with another sRNA, VrrA, and that both sRNAs share a conserved seed-pairing domain allowing them to regulate multiple target mRNAs. V. cholerae lacking σE displayed increased sensitivity toward antimicrobials, and over-expression of either of the sRNAs suppressed this phenotype. Laboratory selection experiments using a library of synthetic sRNA regulators revealed that the seed-pairing domain of σE -dependent sRNAs is strongly enriched among sRNAs identified under membrane-damaging conditions and that repression of OmpA is crucial for sRNA-mediated stress relief. Together, our work shows that MicV and VrrA act as global regulators in the ESR of V. cholerae and provides evidence that bacterial sRNAs can be functionally annotated by their seed-pairing sequences.

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A conserved RNA seed-pairing domain directs small RNA-mediated stress resistance in enterobacteria

Project description:Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram-negative bacteria is a paradigm for sRNA-mediated stress management and involves, among other factors, the alternative sigma factor E (?E) and one or more sRNAs. In this study, we identified the MicV sRNA as a new member of the ?E regulon in Vibrio cholerae. We show that MicV acts redundantly with another sRNA, VrrA, and that both sRNAs share a conserved seed-pairing domain allowing them to regulate multiple target mRNAs. V. cholerae lacking ?E displayed increased sensitivity towards antimicrobials and overexpression of either of the sRNAs suppressed this phenotype. Laboratory selection experiments using a library of synthetic sRNA regulators revealed that the seed-pairing domain of ?E-dependent sRNAs is strongly enriched among sRNAs identified under membrane-damaging conditions and that repression of OmpA is crucial for sRNA-mediated stress relief. Together, our work shows that MicV and VrrA act as global regulators in the ESR of V. cholerae and provides evidence that bacterial sRNAs can be functionally annotated by their seed-pairing sequences.

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Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA

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Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA [Ribo-seq]

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Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA [RNA-seq]

Project description:The C.elegans transcriptomes of single-nt let-7a 3' non-seed mutants (U13A / U18A). In order to identified gene perturbance and determine the post-transcriptional regulation mechanism caused by disrupting 3' non-seed pairing of let-7a, we examined the global gene expression by RNAseq in addition to ribosome profiling of L4 whole animals. To include the deadenylated but temperally stable mRNA in the enrichment, we used a RNase H based ribosomal RNA depletion with antisense oligos specifically designed for C.elegans to enrich mRNA (PMID: 33005886). lin-41(ma480) was used in the background to filter out downstream regulation related to the lin-41 pathway.

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