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RpoS mRNA 5′UTR

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rpoS mRNA encodes for the rpoS stress factor, sigma S (σ or σ) 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. 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. 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. Comparative genomics has shown that this regulatory secondary structure is conserved across several gram-negative bacteria species.

References

  1. Hengge-Aronis, R. (Sep 2002). "Signal Transduction and Regulatory Mechanisms Involved in Control of the σS (RpoS) Subunit of RNA Polymerase". Microbiology and Molecular Biology Reviews. 66 (3): 373–395, table 395 contents. doi:10.1128/MMBR.66.3.373-395.2002. ISSN 1092-2172. PMC 120795. PMID 12208995.
  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. doi:10.1021/ja043822v. ISSN 0002-7863. PMID 15783204.
  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". Proceedings of the National Academy of Sciences. 101 (19): 7287–7292. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. ISSN 0027-8424. PMC 409911. PMID 15123812.
  4. Soper, J.; Woodson, A. (Sep 2008). "The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA". RNA. 14 (9): 1907–1917. doi:10.1261/rna.1110608. ISSN 1355-8382. PMC 2525945. PMID 18658123.
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