Small RNAs that target G-rich sequences are generated by diverse biogenesis pathways in Epsilonproteobacteria

Bacterial small RNAs (sRNAs) are widespread post-transcriptional regulators controlling bacterial stress responses and virulence. Nevertheless, little is known about how they arise and evolve. Homologues can be difficult to identify beyond the strain level using sequence-based approaches, and similar functionalities can arise by convergent evolution. Here, we found that the virulence-associated CJnc190 sRNA of the foodborne pathogen Campylobacter jejuni resembles the RepG sRNA from the gastric pathogen Helicobacter pylori. However, while both sRNAs bind G-rich sites in their target mRNAs using a C/U-rich loop, they largely differ in their biogenesis. RepG is transcribed from a stand-alone gene and does not require processing, whereas CJnc190 is transcribed from two promoters as precursors that are processed by RNase III and also has a cis-encoded antagonist, CJnc180. By comparing CJnc190 homologues in diverse Campylobacter species, we show that RNase III-dependent processing of CJnc190 appears to be a conserved feature even outside of C. jejuni. We also demonstrate the CJnc180 antisense partner is expressed in C. coli, yet here might be derived from the 3'UTR of the upstream flagella-related gene. Our analysis of G-tract targeting sRNAs in Epsilonproteobacteria demonstrates that similar sRNAs can have markedly different biogenesis pathways.

Features of sRNA biogenesis in rice revealed by genetic dissection of sRNA expression level

We previously conducted a QTL analysis of small RNA (sRNA) abundance in flag leaves of an immortalized rice F₂ (IMF2) population by aligning sRNA reads to the reference genome to quantify the expression levels of sRNAs. However, this approach missed about half of the sRNAs as only 50% of all sRNA reads could be uniquely aligned to the reference genome. Here, we quantified the expression levels of sRNAs and sRNA clusters without the use of a reference genome. QTL analysis of the expression levels of sRNAs and sRNA clusters confirmed the feasibility of this approach. sRNAs and sRNA clusters with identified QTLs were then aligned to the high-quality parental genomes of the IMF2 population to resolve the identified QTLs into local vs. distant regulation mode. We were able to detect new QTL hotspots by considering sRNAs aligned to multiple positions of the parental genomes and sRNAs unaligned to the parental genomes. We found that several local-QTL hotspots were caused by sequence variations in long inverted repeats, which probably function as precursors of sRNAs, between the two parental genomes. The expression levels of these sRNAs were significantly associated with the presence/absence of the long inverted repeats in the IMF2 population. Moreover, we found that the variations in whole-genome sRNA species composition among different IMF2s were attributed to sRNA biogenesis genes including OsDCL2b and OsRDR2. Our results highlight that genetic dissection of sRNA expression is a promising approach to disclose new components functioning in sRNA biogenesis and new mechanisms of sRNA biogenesis.

Prevalence of small base-pairing RNAs derived from diverse genomic loci

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.