RpoS mRNA 5′UTR

rpoS mRNA encodes for the rpoS stress factor, sigma S (σ^S or σ³⁸) in Escherichia coli and related bacteria, where DsrA in conjunction with the Sm like RNA binding protein, Hfq promote the translation of this rpoS mRNA.^[1] The 5′ UTR of the rpoS mRNA forms a self-inhibitory stem loop that shields the shine-dalgarno sequence and therefore inhibits translation. The secondary structure of the 5′UTR was predicted by acetylation of ribose 2′-hydroxyls with NMIA and by using a secondary structure prediction program, RNAstructure.^[2][3] DsrA stimulates rpoS translation by binding in the 5′UTR and causes the stem loop to open, exposing the ribosome binding site.

Site-directed mutagenesis and deletion analysis located an AAYAA motif identified upstream of the stem loop structure which is required for Hfq binding.^[4] Comparative genomics has shown that this regulatory secondary structure is conserved across several gram-negative bacteria species.