User:Michelle Meyer BC/EC S15

In E. coli, the S15-binding RNA structure allows negative feedback regulation of its own S15 synthesis. The RNA structure is positioned in the 5’-UTR, with sequence of the RNA structure partially overlapping the rpsO (S15) coding sequence and acts via a ribosomal entrapment mechanism. The S15-bound form of the RNA is pseudoknotted, but an alternative structure consisting of two hairpins has also been proposed. The pseudoknotted structure is consistent with mutagenesis and structural probing assays performed , and displays greater covariation and fewer non-canonical pairs and insertions that the double hairpin structure. The ‘C-G’ and ‘UG’ base pairs in the upper portion of H1 and the purine between H1 and H2 are rigorously conserved and are likely involved in recognition. Loop L2 is variable in length consistent with deletion studies showing it can be reduced to 7 nucleotides (including the ‘AUG’). This RNA is narrowly distributed, occurring only in Gammaproteobacteria. Additional mRNA structures known to interact with S15 to regulate rpsO in other organisms are known, but they bear no resemblance to the RNA structure in E. coli and cross-species RNA-protein binding assays indicate distinct binding between the species tested.