RNA-mediated regulation in bacteria: from natural to artificial systems

RNA folding in living cells

“…These sRNAs are ribo-regulators affecting all steps of gene expression through modulating RNA structure, thereby allowing the cell to adapt to environmental cues and to control bacterial pathogenesis. [102][103][104][105] In general, one has to distinguish between sRNAs acting in trans and those in cis.…”

“…[102][103][104][105] The asRNA regulation typically results in the inhibition of transcription or translation or it induces degradation of target RNAs. These asRNAs can be transcribed from the opposite strand of genes which they regulate.…”

“…These cis-asRNAs usually display extensive base-pairing with a single target mRNA (e.g., the hok-sok pair). [102][103][104][105] Commonly such asRNAs are associated with plasmids, phages and transposons or act as antitoxins. Alternatively, asRNAs are encoded from an autonomous locus in the genome.…”

“…These trans-asRNAs only share short stretches of complementarity with their multiple target mRNAs. [102][103][104][105] The majority of trans-asRNAs depend on an accessory protein for exerting their activity. The best-studied example is the E. coli Sm-like protein Hfq, which, for instance, stabilizes the sRNA DsrA and facilitates its interaction with the rpoS mRNA, thereby altering its structure and in turn activating translation.…”

“…In general, the most common type of regulatory mechanism by trans-asRNAs is translation repression, but a few notable examples for an activating mode of action have been described. [102][103][104][105] In addition, mRNAs, specifically their 5'UTR, can function as a direct sensor for the physical and metabolic state of the cell. One class of cis-regulatory elements, the riboswitches, responds to trans-acting ligands such as the intracellular concentration of metabolites (i.e., nucleobases, coenzymes, sugars, amino acids) and metal ions.…”