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

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 foodborne pathogen Campylobacter jejuni. While CJnc180 processing by RNase III requires CJnc190, In contrast, 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 antagonize bacterial sRNAs.

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogenCampylobacter jejuni

“…MNase: micrococcal nuclease, Cm: chloramphenicol, Onc: oncocin, Ret: retapamulin, Api: apidaecin. (B) Ribo-seq and paired RNA-seq distinguish the coding gene Cj1650 from the non-coding sRNA CJnc180 (Svensson and Sharma, 2021). Y-axis: rpm (reads per million).…”

“…In general, our “standard” C. jejuni Ribo-seq dataset successfully differentiated between known coding and non-coding regions. For example, cDNA reads for the sRNA CJnc180 (Dugar et al, 2013; Svensson and Sharma, 2022, 2021) were mainly restricted to the RNA-seq (transcriptome) library prepared in parallel, while the adjacent ORF Cj1650 had both RNA-seq and Ribo-seq coverage ( Fig. 1B ).…”

“…C. jejuni strains show high genotypic and phenotypic diversity and RNA-seq has provided insights into its transcriptome structure and revealed several sRNAs (Dugar et al, 2013; Porcelli et al, 2013; Taveirne et al, 2013). For example, we previously generated primary transcriptome maps for four C. jejuni strains (Dugar et al, 2013), which revealed conserved and infection-relevant sRNAs, strain-specific promoter usage, and potential variation in ORF lengths (Alzheimer et al, 2020; Svensson and Sharma, 2021). In contrast, the C. jejuni translatome and small proteome have not yet been refined.…”

Interplay of two small RNAs fine-tunes hierarchical flagellar gene expression in the foodborne pathogenCampylobacter jejuni

“…Our in-depth 5'-end mapping and cotranscriptional analyses indicate that a minor fraction is transcribed from its own RpoDdependent promoter, while most of FlmE expression seems to be generated by processing from the same RpoN-dependent transcript as flgE, encoding the flagellar hook protein. FlmE adds to an expanding number of bacterial sRNAs that are processed by RNase III (Faubladier et al, 1990;Lalaouna et al, 2019;Melamed et al, 2020;Svensson and Sharma, 2021). So far, examples are mainly restricted to bacteria that lack RNase E, such as Gram-positive Staphylococcus aureus (RsaC, via cleavage of the mntABC mRNA 3'UTR (Lalaouna et al, 2019;Lioliou et al, 2012)) and C. jejuni (processing of the antisense sRNA pair CJnc180/190 (Svensson and Sharma, 2021)).…”

RNase III coding genes modulate the cross-kingdom biofilm of Streptococcus mutans and Candida albicans

“…Ribonuclease III (RNase III) is the endonuclease in bacteria and eukaryotes that participates in RNA biogenesis to control gene expression (Svensson and Sharma, 2021). Our previous studies have illuminated that the gene encoding S. mutans RNase III, rnc, enhances the EPS synthesis and cariogenicity of bacterial biofilms through non-coding RNAs that target vicR, the gene encoding a response regulator of EPS metabolism (Lei et al, 2018(Lei et al, , 2020.…”