Abstract
Trans-encoded bacterial regulatory RNAs (sRNAs) are functional analogues of eukaryotic microRNAs (miRNAs). These RNA classes act by base-pairing complementarity with their RNA targets to modulate gene expression (transcription, half-life and/or translation). Based on base-pairing, algorithms predict binding and the impact of small RNAs on targeted-RNAs expression and fate. However, other actors are involved such as RNA binding proteins and epigenetic modifications of the targeted and small RNAs. Post-transcriptional base modifications are widespread in all living organisms where they lower undesired RNA folds through conformation adjustments and influence RNA pairing and stability, especially if remodeling their ends. In bacteria, sRNAs possess RNA modifications either internally (methylation, pseudouridinylation) or at their ends. Nicotinamide adenine dinucleotide were detected at 5′-ends, and polyadenylation can occur at 3′-ends. Eukaryotic miRNAs possess N6-methyladenosine (m6A), A editing into I, and non-templated addition of uridines at their 3′-ends. Biological functions and enzymes involved in those sRNA and micro RNA epigenetic modifications, when known, are presented and challenged.
Highlights
All living organisms require regulation of gene expression to survive, grow, and spread in their dynamic and precarious environments, e.g., the survival of the fittest
The aim of this review is to focus on the other mechanisms favoring the miRNA diversity including post-transcriptional A-to-I editing mediated by the enzyme adenosine deaminase acting on RNA (ADAR), terminal trimming of nucleotides, or non-templated nucleotide additions (NTA)
Less than 10% of knockout mice for evolutionarily-conserved miRNAs induce developmental or abnormal embryonic phenotypes [78], they probably will be detected in sensitized backgrounds or under stress
Summary
All living organisms require regulation of gene expression to survive, grow, and spread in their dynamic and precarious environments, e.g., the survival of the fittest. A major paradigm for RNA-based regulation in both eukaryotes and prokaryotes are the sRNAs that pair with messenger RNAs (mRNAs), leading to changes in target mRNA stability and/or translation [4]. Downregulation of target RNA expression can occur when a sRNA pairs to, or close to the ribosome binding site (RBS), efficiently preventing translation initiation This interaction often leads to cleavage of the mRNA target through endoribonucleases, to ensure irreversible regulation. More than 160 chemical modifications can be detected on RNAs [6] They can impact RNA structure, conformation dynamics, function and interactions with their macromolecular targets, including mRNAs for the sRNAs and miRNAs. The main purpose of this review is to provide parallels and differences between the bacterial/archaeal sRNA post-transcriptional modifications, and the eukaryotic miRNA modifications. Co-degradations between sRNAs and their RNA targets can occur, to favor timely and reversible regulations. sRNA function can rely on RNA chaperones to increase their stability and assist them during target regulation [11]
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