User:Michelle Meyer BC/S4

The Bacillus subtilis S4-interacting RNA regulates only rpsD, the gene encoding S4. S4 in B. subtilis is autoregulated after transcription initiation, though the mechanism of action is unknown. This family of autoregulators is found in Firmicutes (Bacilli only), Tenericutes, and Thermotogae.

S4 is known to interact with 16S rRNA, and parts of the S4 5’ leader have sequence and structural similarity to the 16S rRNA. Specifically, there is a conserved ‘GUAA’ bulge in the S4-leader binding structure that has sequence identity to a bulge on the 16S rRNA. Also, there is the possibility of a secondary, non-binding structure, first proposed by Yao (2007), but as there is little sequence conservation or covariation in this alternative structure, it is not included in the alignment at this time.

In Gammaproteobacteria rpsD is part of the alpha operon of ribosomal protein genes. S4 is also the regulator for this operon in E. coli, interacting with an unrelated RNA structure [RF00140].