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.{{Cite journal

| pmid = 12208995

| date=Sep 2002 | last1 = Hengge-Aronis | first1 = R.

| title = Signal Transduction and Regulatory Mechanisms Involved in Control of the σS (RpoS) Subunit of RNA Polymerase

| volume = 66

| issue = 3

| pages = 373–395, table 395 contents

| issn = 1092-2172

| pmc = 120795

| journal = Microbiology and Molecular Biology Reviews

| doi = 10.1128/MMBR.66.3.373-395.2002

}} 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.{{Cite journal

| last3 = Coughlan | first1 = J. | first2 = A.

| last2 = Wilkinson| first3 = L. | first4 = M.

| title = RNA Structure Analysis at Single Nucleotide Resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE)

| last1 = Merino

| journal = Journal of the American Chemical Society

| last4 = Weeks

| volume = 127

| issue = 12

| pages = 4223–4231

| date=Mar 2005 | issn = 0002-7863

| pmid = 15783204

| doi = 10.1021/ja043822v

}}{{Cite journal| first1 = H.

| last2 = Disney

| last3 = Childs

| last5 = Zuker

| last4 = Schroeder | first2 = D. | first3 = L. | first4 = J. | first5 = M.

| title = Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

| last1 = Mathews | first6 = H.

| last6 = Turner

| journal = Proceedings of the National Academy of Sciences

| volume = 101

| issue = 19

| pages = 7287–7292

| date=May 2004 | issn = 0027-8424

| pmid = 15123812

| pmc = 409911

| doi = 10.1073/pnas.0401799101

|bibcode = 2004PNAS..101.7287M | doi-access = free

}} 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.{{Cite journal| first1 = J. | first2 = A.

| title = The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA

| last2 = Woodson

| journal = RNA

| last1 = Soper

| volume = 14

| issue = 9

| pages = 1907–1917

| date=Sep 2008 | issn = 1355-8382

| pmid = 18658123

| pmc = 2525945

| doi = 10.1261/rna.1110608

}} Comparative genomics has shown that this regulatory secondary structure is conserved across several gram-negative bacteria species.