User:Michelle Meyer BC/L4

The S10 operon in E. coli consists of 11 genes (rpsJ, rplC, rplD, rplW, rplB, rpsS, rplV, rpsC, rplP, rpmD, rpsQ) and is negatively regulated by L4, encoded by rplD through interactions with an mRNA structure in the 5’-UTR. This RNA structure acts via two mechanisms, translation inhibition and transcription termination, which can decrease gene expression by 30-fold when excess L4 is present. The L4 regulatory RNA consists of five hairpins, the first three (HA-HC) of which are highly variable both in sequence and length. However, experimentation has shown that these helices are not necessary for regulation. The last three helices (HD-HG) are required for transcription termination and show greater sequence conservation. L4 most likely interacts with the loop of helix HD. Helix HE is always present and portions of it are required for transcription termination. The helix is often followed by the string of uridines typical of rho-independent intrinsic transcription termination. Deletion of HA-HD or HE has been shown to have little effect on translation efficiency, while point mutations to HE have significant effects on translation efficiency. The proposed mechanism involves alternative pairing between bases within both HG and HE, though this stem is not stable in the E. coli sequence and there is no evidence for this alternative pairing using larger sequence alignments.