Origin, Evolution, and Loss of Bacterial Small RNAs

Abstract

Despite the central role of bacterial non-coding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here, we compile what has been studied to date and trace a life cycle of sRNAs-from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from pre-existing genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently-emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss, and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.

A Small Regulatory RNA Controls Cell Wall Biosynthesis and Antibiotic Resistance

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“…In many respects, the relatively simple operating mechanism of sRNAs accounts for their variety and rapid evolution [33,34]. The dynamics around the origin, evolution, and loss of sRNAs have been uncovered by previous studies and reviewed recently [35].…”

Are Antisense Proteins in Prokaryotes Functional?

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