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rpoS mRNA encodes for the rpoS stress factor, sigma S (σS or σ38, 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.


  1. ^ Hengge-Aronis, R. (Sep 2002). "Signal Transduction and Regulatory Mechanisms Involved in Control of the σS (RpoS) Subunit of RNA Polymerase" (Free full text). Microbiology and molecular biology reviews : MMBR. 66 (3): 373–395, table 395 contents. ISSN 1092-2172. PMC 120795Freely accessible. PMID 12208995. doi:10.1128/MMBR.66.3.373-395.2002. 
  2. ^ Merino, J.; Wilkinson, A.; Coughlan, L.; Weeks, M. (Mar 2005). "RNA Structure Analysis at Single Nucleotide Resolution by Selective 2'-Hydroxyl Acylation and Primer Extension (SHAPE)". Journal of the American Chemical Society. 127 (12): 4223–4231. ISSN 0002-7863. PMID 15783204. doi:10.1021/ja043822v. 
  3. ^ Mathews, H.; Disney, D.; Childs, L.; Schroeder, J.; Zuker, M.; Turner, H. (May 2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure" (Free full text). Proceedings of the National Academy of Sciences. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. ISSN 0027-8424. PMC 409911Freely accessible. PMID 15123812. doi:10.1073/pnas.0401799101. 
  4. ^ Soper, J.; Woodson, A. (Sep 2008). "The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA" (Free full text). RNA. 14 (9): 1907–1917. ISSN 1355-8382. PMC 2525945Freely accessible. PMID 18658123. doi:10.1261/rna.1110608.