What makes a small RNA work?

Abstract

Bacterial small RNAs (sRNAs) are key regulators of gene expression, interacting with target messenger RNAs (mRNAs) through imperfect base pairing. Unlike other non-coding RNAs such as microRNAs and PIWI-interacting RNAs, bacterial sRNAs exhibit significant sequence and structural diversity, complicating functional predictions. Recent high-throughput profiling of the sRNA interactome has accentuated this problem by revealing a highly complex network of sRNA interactions. It is clear that there is an incredible diversity of sRNA interactions with different RNA classes in vivo, including different interaction modes with mRNAs. In this review, we attempt to summarize the known sequence and structural features that contribute to sRNA function in bacteria. As many of these features drive recruitment of protein partners, we necessarily focus on interactions with chaperones and ribonucleases, the best studied being Hfq and RNase E. Where possible, we have included examples outside this well-studied system as diversity and rule breaking appear to be central themes of sRNA biology. Understanding the sequences and structures that drive sRNA function will enhance our ability to predict regulatory outcomes, and this may inform the development of effective RNA therapeutics that are inspired by bacterial sRNA mechanisms.

Graphical Abstract

Figure 1.

Schematic representation of how sRNA can bind Hfq. (Left panel) Class I sRNA encodes for a poly(U) tail that binds to the Hfq proximal face (red sticks) and UA-rich motif that binds to the lateral rim (green sticks). (Central panel) Class II sRNAs also contain a poly(U) tail but instead of a UA-rich motif they contain an ARN motif that binds to Hfq distal face (blue sticks). (Right panel) RNA sponges act similarly to Class II sRNAs but regulate other sRNAs rather than mRNA targets. The Hfq structure (PDB: 1HK9) [128] is represented in a yellow mesh format.

Figure 2

Sequences and structural elements that drive sRNA function. sRNAs encode for specific sequences and structural motifs that enable their interaction with RNA-binding proteins (e.g. Hfq and ProQ) and ribonucleases (e.g. RNase E). The Hfq structure (PDB: 1HK9) [128] is represented in a yellow mesh format.

Figure 3

RNase E architecture and interaction with sRNAs. (A) The structural features that allow RNase E (PDB: 6G63) to bind sRNA. RNase E forms a tetramer that can bind sRNAs via a 5′ phosphate sensor pocket (orange) and an internal/direct entry site (blue). (B) The unstructured C-terminal domain of RNase E contains multiple sites that allow sRNA binding, i.e. AR2 and RBD domains. (C) Illustration of how sRNA can guide RNase E to process mRNA targets in E. coli.