Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications

Abstract

Naturally occurring antisense RNAs are small, diffusible, untranslated transcripts that pair to target RNAs at specific regions of complementarity to control their biological function by regulating gene expression at the post-transcriptional level. This review focuses on known cases of antisense RNA control in prokaryotes and provides an overview of some natural RNA-based mechanisms that bacteria use to modulate gene expression, such as mRNA sensors, riboswitches and antisense RNAs. We also highlight recent advances in RNA-based technology. The review shows that studies on both natural and synthetic systems are reciprocally beneficial.

Keywords: Bacteria; Cis-asRNA; Hfq protein; Natural antisense; RNA engineering; RNA silencing; RNA thermosensors; Regulation; Riboswitch; Trans-asRNA.

Fig. 1

Gene silencing by natural antisense RNAs in bacteria. A – Cis-antisense RNAs (cis-asRNAs) are encoded with high degrees of complementarity to the target mRNA. B – Trans-antisense RNAs (trans-asRNAs) are encoded with limited complementarity to the target mRNA. In some species, trans-asRNAs require an RNA chaperone (Hfq) to facilitate binding to the target mRNA. Generally, in either case, once the asRNA is bound to the target mRNA, translation of the target gene is silenced by inhibition of the ribosome binding to the target mRNA (1); by induced RNase degradation of the asRNA–mRNA hybrid (2); or by a combination of the two processes