protein-binding sRNAs

Question

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on

A bit of background and context: In bacteria, a regulatory protein termed CsrA binds certain structures in the UTR regions of genes and prevents their translation. These structures are short hairpin-like and all have AGGA nucleotides in the exposed part. There are sRNAs that isolate the protein from its targets, a common feature of these sRNAs is that they have several repetitive hairpins that more or less display AGGA nucleotides in the exposed part. So basically, the sRNAs mimic the structures on the targets of the proteins and that makes them potent competitors for protein binding against the genes actually targeted by the protein. By relying on this mimickry the sRNAs bind CsrA, isolate it from its targets and remove its suppression on gene translation.

My question: Are there any other examples that illustrate similar mechanisms of analogy/mimickry of sRNAs to bind protein?

What I tried I've skimmed through a lot of literature to identify other similar systems in bacteria where sRNAs have conserved repetitive structures but to no avail. I hope someone with deeper experience directs me to such examples in any living organism, preferably bacteria but I am open to suggestion. I found CRISPRs but these are DNA based, I have come across few other cis-acting sRNAs which target mRNAs and aren't protein-binding. So could it be the case that sRNA mimickers aren't very pervasive in bacteria after all ?!

Answer 1

The sRNA mediated regulation in bacteria operates via diverse mechanisms. This case of sRNA competing with a mRNA for a protein is a passive kind of regulation. This might be good for finetuning but may not be very efficient. It is much better to actively regulate a mRNA by direct binding. Also, it will work only if the concerned protein is in limiting concentrations.

I haven't come across any examples of what you are interested in. There may be one similar situation in case of a eukaryotic system. miRNAs can be titrated away by long RNAs that bear multiple binding sites for that miRNA, thus making the miRNAs unavailable for binding to the target mRNA. These long RNAs are called ceRNA (competing endogenous RNA) or miRNA-sponges (this term is mostly used if the RNA is exogenous). However this is not really a protein-RNA interaction even though RISC complex contains proteins.