RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist.

Sarah Lauren Svensson,Cynthia Mira Sharma

doi:10.7554/elife.69064

Abstract

Bacterial small RNAs (sRNAs) are important post-transcriptional regulators in stress responses and virulence. They can be derived from an expanding list of genomic contexts, such as processing from parental transcripts by RNase E. The role of RNase III in sRNA biogenesis is less well understood despite its well-known roles in rRNA processing, RNA decay, and cleavage of sRNA-mRNA duplexes. Here, we show that RNase III processes a pair of cis-encoded sRNAs (CJnc190 and CJnc180) of the food-borne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, RNase III processes CJnc190 independent of CJnc180 via cleavage of an intramolecular duplex. We also show that CJnc190 directly represses translation of the colonization factor PtmG by targeting a G-rich ribosome-binding site, and uncover that CJnc180 is a cis-acting antagonist of CJnc190, indirectly affecting ptmG regulation. Our study highlights a role for RNase III in sRNA biogenesis and adds cis-encoded RNAs to the expanding diversity of transcripts that can antagonize bacterial sRNAs.

Highlights

40 Bacterial small, regulatory RNAs are an important class of post-transcriptional41 gene expression regulators that control adaptation to changing environmental conditions42 or stresses (Storz et al, 2011), or can regulate virulence genes in pathogens (Quereda43 and Cossart, 2017; Svensson and Sharma, 2016; Westermann, 2018)
Our comparative dRNA-seq study of multiple C. jejuni isolates revealed a conserved pair of antisense sRNAs, CJnc[180] and CJnc[190] (annotated as 99 and 216 nucleotides, 139 respectively, in strain NCTC11168) (Dugar et al, 2013) (Figure 1A)
We previously observed that deletion of CJnc180/190 affects C. jejuni adherence and 148 internalization in our Caco-2 cell based tissue-engineered model of the human intestine

Summary

39 INTRODUCTION

40 Bacterial small, regulatory RNAs (sRNAs) are an important class of post-transcriptional. Its expropriation for biogenesis of CRISPR RNAs (Deltcheva et al, 2011; Dugar et al, 2018), as well as genome-wide studies of the RNase III targetome that report sRNAs as potential targets in Gram-negative and Gram[77] positive species (Altuvia et al, 2018; Gordon et al, 2017; Le Rhun et al, 2017; Lioliou et al, 2013, 2012; Lybecker et al, 2014; Rath et al, 2017), indicate that RNase III might process sRNAs in diverse bacteria. We have characterized the biogenesis and mode of action of a conserved, 119 processed pair of C. jejuni cis-encoded, antisense RNAs, CJnc180/190. Our characterization of the CJnc[190] biogenesis pathway 132 demonstrates a role for RNase III in sRNA maturation and reveals the potential for cis[133] encoded sRNA-sRNA targeting

135 RESULTS

415 DISCUSSION

553 MATERIALS AND METHODS

926 REFERENCES

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