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Hfq Globally Binds and Destabilizes the bound sRNAs and mRNAs in Yersinia pestis

By Yanping Han, Dong Chen, Yanfeng Yan, Hongduo Wang, Zizhong Liu, Yaqiang Xue, Ruifu Yang, Yi Zhang

Posted 05 Dec 2018
bioRxiv DOI: 10.1101/487769

Hfq is a ubiquitous Sm-like RNA binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding natures still remain elusive. Here we reported the first study of the Hfq-bound RNAs map in Yersinia pestis, the causative agent of a kind of plague, by using Cross-Linking Immunoprecipitation coupled with deep sequencing (CLIP-Seq) approach. We show that Hfq binds over 80% mRNAs of Y. pestis, and also globally binds non-coding sRNAs encoded by the intergenic, antisense, and the 3' regions of mRNAs. 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 and consistent with Hfq-facilitated 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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