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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 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.

| S-EPMC6694218 | biostudies-literature

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 (?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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RBPL-1, the C. elegans homolog of RBBP6, promotes meiotic homolog pairing through a conserved DWNN domain

Project description:Accurate chromosome segregation during meiosis depends on precise homolog pairing, a process driven by a series of specialized proteins that link chromosomes to cytoskeletal motors and coordinate chromosome movement for homolog recognition and alignment. Here, we demonstrate that RBPL-1, the C. elegans homolog of RBBP6, is necessary for normal meiotic progression, particularly for proper homolog pairing and associated nuclear reorganization. RBPL-1 is enriched on the autosomes in early and mid- pachytene nuclei. Depletion of RBPL-1 led to reduced levels of ZIM/HIM-8 family proteins and PLK-2 kinase, two critical mediators of homolog pairing. Notably, RBPL-1's role in homolog pairing is independent of the RING finger domain, which mediates ubiquitination, and its Zn knuckle domain, which is implicated in APA/mRNA processing. Instead, we reveal that the evolutionarily conserved yet functionally enigmatic DWNN domain is essential for RBPL-1's function. Our findings uncover a previously unrecognized regulatory mechanism governing homolog pairing during meiosis.

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RBPL-1, the C. elegans homolog of RBBP6, promotes meiotic homolog pairing through a conserved DWNN domain

Project description:RBPL-1, the C. elegans homolog of RBBP6, promotes meiotic homolog pairing through a conserved DWNN domain

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Mapping effective microRNA pairing beyond the seed using abasic modifications

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base-pairing to complementary sites in mRNAs. The primary element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, the structural determinants of effective pairing outside the seed are not fully understood. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this modification compared to wild-type miR-34a on the cellular transcriptome and proteome using RNA-seq and mass spectrometry. We find that a subset of sites with predicted supplementary pairing are affected by miRNA transfection, with up to two-fold decreases in site repression at the mRNA level, although the effect at the protein level is less pronounced. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.

2025-05-07 | PXD059550 | Pride

Mapping effective microRNA pairing beyond the seed using abasic mutations

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base-pairing to complementary sites in mRNAs. The most important element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, it is not clear how large an effect supplementary pairing has on target site efficiency, or which sites are most affected by it. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this mutation compared to wild-type miR-34a on the cellular transcriptome using RNA-seq. We find that a subset of sites with predicted supplementary pairing are affected 24 hours after miRNA overexpression, with up to two-fold decreases in site repression. We show that miR-34a 3'-pairing is sensitive to GU wobble pairs in a position-specific manner and favors bulges in the miRNA over the target. These results were validated with luciferase reporter assays. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.

2025-05-07 | GSE271495 | GEO

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