Small RNAs as a Diverse Toolkit of Bacteria

Bacteria use a diverse set of small regulatory RNAs (sRNAs) to coordinate physiological processes in multiple ways. Although the spectrum of regulatory RNAs differs from that of higher organisms, basic principles are shared. For instance, bacterial CRISPR-cas systems use complexes of guide crRNAs and endonucleases for destroying alien genetic material in a manner similar to short RNA-mediated interference in eukaryotes. Several types of sRNAs originally discovered in eukaryotes, including circular (circRNAs) and extracellular (exRNAs) RNA fragments, were subsequently found in bacteria. Their functionality is now becoming an emerging area of research. Most well characterized sRNAs are encoded by their own genes. However, recently the regulatory role for fragments of tRNAs (tRFs) and 3’-UTRs of some mRNAs was also discovered. Of these, tRFs can act as signaling molecules establishing inter-kingdom communications in microbiomes. Their precursors, therefore, were evolutionarily selected to participate in completely different cellular processes. Another type of dual functionality is evident for intergenic or antisense-encoded sRNAs carrying translated open reading frames. Thus, being multifunctional in their ability to interact with various proteins and partially complementary nucleic acids, some sRNAs can also supply cells with peptides, which complicates the regulation of their own expression.

The goal of this Research Topic is to collect cutting-edge studies in exploring sRNA-mediated regulatory pathways or other sRNA-functionalities operating inside bacterial cells and beyond their boundaries.

We propose to focus on bacteria as biological models whose importance and prevalence now is coming to full appreciation. We welcome Reviews, Mini Reviews and other types of papers setting forth fundamental conclusions on the complexity of the sRNAs toolbox in bacteria for regulatory and other purposes, highlighting problems and formulating new ideas. Topics covered may include, but are not limited to:

• sRNAs regulatory networks: how large and cross-talking are they?
• microRNA-size transcripts in bacteria and bacterial homologs of Ago proteins: are they components of RNA-interference?
• cis-encoded antisense RNAs: have they evolved to regulate a single target RNA?
• sRNAs encoding peptides (dual-functioning RNAs): what is the degree of prevalence and how are the two functions are balanced?
• CRISPR-cas systems: how do bacteria avoid “immunization” against their own genomes?
• Extracellular RNAs: what can they do outside the cells?
• tRFs, fragments of UTRs and circRNAs in bacteria: “Every little piece counts”?
• Other emerging topics on sRNAs research, e.g., chimeric RNAs, novel classes of sRNAs and RNA-binding proteins, etc.