User:Michelle Meyer BC/EC S4

The alpha operon in E. coli (rpsM, rpsK, rpsD, rpoA, and rplQ) is autogenously regulated through interactions with ribosomal protein S4 with an RNA structure within the 5’-UTR of rpsM. The RNA structure interacting with ribosomal protein S4 is a complex double-pseudoknot that partially overlaps rpsM, and translationally represses only the ribosomal proteins, apparently not affecting expression of the intervening rpoA. Helix H1 shows little to no sequence conservation, but has great co-variation, indicating that the structure, rather than the sequence, is important. No co-variation is present in the psuedoknots, which is likely due to overlap with the rpsM coding region. Additionally, mutagenesis studies have shown that compensatory mutations to H2 do not restore S4 binding, even when the stem is maintained. A distinct mRNA structure is known to interact with S4 to regulate rpsD in B. subtilis, but it bears no resemblance to the RNA structure in E. coli.