JUMPstart RNA motif

{{Infobox rfam

| Name = JUMPstart RNA

| image = JUMPstart-RNA.svg

| width = 290

| caption = Consensus secondary structure of JUMPstart RNAs

| Symbol = JUMPstart RNA

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| Rfam = RF01707

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| RNA_type = Cis-regulatory element

| Tax_domain = Bacteria

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The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements.{{cite journal |vauthors=Weinberg Z, Wang JX, Bogue J, etal |title=Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes |journal=Genome Biol |volume=11 |issue=3 |pages=R31 |date=March 2010 |pmid=20230605 |doi=10.1186/gb-2010-11-3-r31 |pmc=2864571 |doi-access=free }} The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis.{{cite journal |vauthors=Hobbs M, Reeves PR |title=The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters |journal=Mol. Microbiol. |volume=12 |issue=5 |pages=855–856 |date=June 1994 |pmid=8052136 |doi= 10.1111/j.1365-2958.1994.tb01071.x|s2cid=19948539 }} The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates.{{cite journal |vauthors=Marolda CL, Valvano MA |title=Promoter region of the Escherichia coli O7-specific lipopolysaccharide gene cluster: structural and functional characterization of an upstream untranslated mRNA sequence |journal=J. Bacteriol. |volume=180 |issue=12 |pages=3070–3079 |date=June 1998 |pmid=9620955 |pmc=107806 |doi= 10.1128/JB.180.12.3070-3079.1998}}

JUMPstart sequences include an ops element, which is an acronym for "operon-polarity suppressor" and has the nucleotide consensus GGCGGUAG.{{cite journal |vauthors=Nieto JM, Bailey MJ, Hughes C, Koronakis V |title=Suppression of transcription polarity in the Escherichia coli haemolysin operon by a short upstream element shared by polysaccharide and DNA transfer determinants |journal=Mol. Microbiol. |volume=19 |issue=4 |pages=705–713 |date=February 1996 |pmid=8820641 |doi= 10.1046/j.1365-2958.1996.446951.x|s2cid=39593320 }} The ops element acts in concert with the RfaH protein to improve transcription of genes downstream of the ops element, especially genes far away within long operons.{{cite journal |vauthors=Leeds JA, Welch RA |title=Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism |journal=J. Bacteriol. |volume=179 |issue=11 |pages=3519–3527 |date=June 1997 |pmid=9171395 |pmc=179143 |doi= 10.1128/jb.179.11.3519-3527.1997}}{{cite journal |vauthors=Wang L, Jensen S, Hallman R, Reeves PR |title=Expression of the O antigen gene cluster is regulated by RfaH through the JUMPstart sequence |journal=FEMS Microbiol. Lett. |volume=165 |issue=1 |pages=201–206 |date=August 1998 |pmid=9711858 |doi= 10.1111/j.1574-6968.1998.tb13147.x|doi-access=free }}