Sim Minji, Nguyen Jeffers, Škopová Karolína, Yoo Kyungyoon, Tai Chin-Hsien, Knipling Leslie, Chen Qing, Kim David, Nolan Summer, Elaksher Rawan, Majdalani Nadim, Lorenzi Hernan, Stibitz Scott, Moon Kyung, Hinton Deborah M
Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, USA.
bioRxiv. 2024 Nov 19:2024.11.19.624354. doi: 10.1101/2024.11.19.624354.
Bacterial sRNAs together with the RNA chaperone Hfq post-transcriptionally regulate gene expression by affecting ribosome binding or mRNA stability. In the human pathogen , the causative agent of whooping cough, hundreds of sRNAs have been identified, but their roles in biology are mostly unknown. Here we characterize a Hfq-dependent sRNA (S17), whose level is dramatically higher in the virulence (Bvg) mode. We show that transcription from a σ-dependent promoter yields a long form of 190 nucleotides (nts) that is processed by RNase E to generate a shorter, more stable form (S17S) of 67 nts. Using RNA-seq and RT-qPCR, we identify 92 genes whose expression significantly increases in the absence of S17. Of these genes, 70 contain sequences at/near their ribosome binding sites (RBSs) that are complementary to single-stranded (ss) regions (Sites 1 or 2) of S17S. The identified genes include those encoding multiple transporters and 3 transcriptional regulators. Using a translational reporter system, we demonstrate that S17S directly represses one of these genes, , a σ-dependent transcriptional regulator, suggesting the repression of a σ regulon in the Bvg mode. We find that the S17S region containing Sites 1 and 2 is 100% conserved throughout various Betaproteobacteria species, and the S17S target sites are often conserved in the homologs of the target genes. We speculate that S17S regulation represents a highly conserved process that fine-tunes gene expression in the Bvg mode of and perhaps under other conditions in related bacteria.
细菌小RNA（sRNA）与RNA伴侣蛋白Hfq一起通过影响核糖体结合或mRNA稳定性在转录后调节基因表达。在人类病原体百日咳的致病因子中，已鉴定出数百种sRNA，但它们在生物学中的作用大多未知。在这里，我们对一种Hfq依赖性sRNA（S17）进行了表征，其水平在毒力（Bvg）模式下显著更高。我们表明，从一个依赖σ因子的启动子转录产生一个190个核苷酸（nt）的长形式，该长形式由核糖核酸酶E加工以产生一个更短、更稳定的67 nt形式（S17S）。使用RNA测序和逆转录定量聚合酶链反应（RT-qPCR），我们鉴定出92个基因，其表达在没有S17的情况下显著增加。在这些基因中，70个在其核糖体结合位点（RBS）处或附近含有与S17S的单链（ss）区域（位点1或2）互补的序列。鉴定出的基因包括那些编码多种转运蛋白和3种转录调节因子的基因。使用翻译报告系统，我们证明S17S直接抑制其中一个基因，一种依赖σ因子的转录调节因子，这表明在Bvg模式下对一个σ调节子的抑制。我们发现，包含位点1和2的S17S区域在各种β-变形杆菌物种中100%保守，并且S17S靶位点在靶基因的同源物中通常也保守。我们推测S17S调节代表了一个高度保守的过程，该过程在百日咳博德特氏菌的Bvg模式下以及可能在相关细菌的其他条件下微调基因表达。
