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Sinorhizobium meliloti CspA family members mediate stability of structured sRNAs contributing to stress adaptation and effective symbiosis with alfalfa

ABSTRACT: Sinorhizobium meliloti CspA family members mediate stability of structured sRNAs contributing to stress adaptation and effective symbiosis with alfalfa

PROVIDER: PRJNA399112 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5944160.fastq.gz	Fastqsanger.gz
	SRR5944170.fastq.gz	Fastqsanger.gz
	SRR5944180.fastq.gz	Fastqsanger.gz
	SRR5944190.fastq.gz	Fastqsanger.gz
	SRR5944200.fastq.gz	Fastqsanger.gz

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Sinorhizobium meliloti CspA family members mediate stability of structured sRNAs contributing to stress adaptation and effective symbiosis with alfalfa

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Project description:Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. pestis and that Hfq also globally binds noncoding small RNAs (sRNAs) encoded by the intergenic, antisense, and 3′ regions of mRNAs. An Hfq U-rich stretch is highly enriched in sRNAs, while motifs partially complementary to AGAAUAA and GGGGAUUA are enriched in both mRNAs and sRNAs. Hfq-binding motifs are enriched at both terminal sites and in the gene body of mRNAs. Surprisingly, a large fraction of the sRNA and mRNA regions bound by Hfq and those downstream are destabilized, likely via a 5′P-activated RNase E degradation pathway, which is consistent with a model in which Hfq facilitates sRNA-mRNA base pairing and the coupled degradation in Y. pestis. These results together have presented a high-quality Hfq-RNA interaction map in Y. pestis, which should be important for further deciphering the regulatory role of Hfq-sRNAs in Y. pestis.

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