RpoS mRNA 5′UTR explained

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

Notes and References

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

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