RprA RNA

{{Infobox rfam

| Name = RprA RNA

| image = RF00034.jpg

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| caption = Predicted secondary structure and sequence conservation of RprA

| Symbol = RprA

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| Rfam = RF00034

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| RNA_type = Gene; sRNA

| Tax_domain = Bacteria

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| SO = {{SO|0000387}}

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The RprA RNA gene encodes a 106 nucleotide regulatory non-coding RNA. Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site.{{cite journal |doi=10.1021/bi800479p |vauthors=Updegrove T, Wilf N, Sun X, Wartell RM |title=Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5′ rpoS mRNA leader region. |journal=Biochemistry |volume=47 |issue=43 |pages=11184–11195 |year=2008 |pmid=18826256}}{{cite journal |doi=10.1128/JB.00206-06 |vauthors=Jones AM, Goodwill A, Elliott T |title=Limited Role for the DsrA and RprA Regulatory RNAs in rpoS Regulation in Salmonella enterica |journal=J Bacteriol |volume=188 |issue=14 |pages=5077–5088 |year=2006 |pmid=16816180 |pmc=1539969}}

Clones carrying rprA (RpoS regulator RNA A) increased the translation of RpoS. As with DsrA, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. RprA also appears to bind to the RpoS leader.{{cite journal | last = Majdalani | first = N |author2=Hernandez D |author3=Gottesman S | year = 2002 | title = Regulation and mode of action of the second small RNA activator of RpoS translation, RprA | journal = Mol Microbiol | volume = 46 | pages = 813–826 | pmid = 12410838 | doi = 10.1046/j.1365-2958.2002.03203.x | issue = 3| doi-access = free }} RprA is non-essential.{{cite journal | last = Majdalani | first = N |author2=Chen S |author3=Murrow J |author4=St John K |author5=Gottesman S | year = 2001 | title = Regulation of RpoS by a novel small RNA: the characterization of RprA | journal = Mol Microbiol | volume = 39 | pages = 1382–1394 | pmid = 11251852 | doi = 10.1111/j.1365-2958.2001.02329.x | issue = 5| s2cid = 90988055 | doi-access = free }} Wasserman et al. demonstrated that this RNA is bound by the Hfq protein.{{cite journal |vauthors=Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S | title = Identification of novel small RNAs using comparative genomics and microarrays | journal = Genes Dev. | volume = 15 | issue = 13 | pages = 1637–1651 | year = 2001 | pmid = 11445539 | doi = 10.1101/gad.901001 | pmc = 312727 }} Binding to Hfq alters the conformation of RprA.{{cite journal|vauthors=Henderson CA, Vincent HA, Casamento A, Stone CM, Phillips JO, Cary PD, Sobott F, Gowers DM, Taylor JE, Callaghan AJ |title=Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS.|journal=RNA|date=August 2013|volume=19|issue=8|pages=1089–1104|pmid=23804244|doi=10.1261/rna.034595.112 |pmc=3708529}} In the presence of Hfq the stability of RprA is influenced by the osmolarity of the cell, this is dependent on the endoribonuclease RNase E.{{cite journal |vauthors=Madhugiri R, Basineni SR, Klug G |title=Turn-over of the small non-coding RNA RprA in E. coli is influenced by osmolarity |journal=Mol Genet Genomics |volume= 284|issue= 4|pages= 307–318|year=2010 |pmid=20717695 |doi=10.1007/s00438-010-0568-x|s2cid=23732166 }}

It has been shown the RprA regulates the protein coding genes, called csgD, this protein encodes a stationary phase-induced biofilm regulator and ydaM, which encodes a diguanylate cyclase involved in activating csgD transcription. These two target genes are repressed by RprA which results in regulation of biofilm formation.{{cite journal |vauthors=Mika F, Busse S, Possling A, Berkholz J, Tschowri N, Sommerfeldt N, Pruteanu M, Hengge R |title=Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli. |journal=Mol Microbiol |volume= 84|issue= 1|pages= 51–65|year=2012 |pmid=22356413 |doi=10.1111/j.1365-2958.2012.08002.x|pmc=3465796}}