JUMPstart RNA motif

The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements.[1] The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis.[2] The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates.[3]

JUMPstart RNA
Consensus secondary structure of JUMPstart RNAs
Identifiers
SymbolJUMPstart RNA
RfamRF01707
Other data
RNA typeCis-regulatory element
Domain(s)Bacteria
PDB structuresPDBe

JUMPstart sequences include an ops element, which is an acronym for "operon-polarity suppressor" and has the nucleotide consensus GGCGGUAG.[4] 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.[3][4][5][6]

References
  1. Weinberg Z, Wang JX, Bogue J, et al. (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605.
  2. Hobbs M, Reeves PR (June 1994). "The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters". Mol. Microbiol. 12 (5): 855–856. doi:10.1111/j.1365-2958.1994.tb01071.x. PMID 8052136.
  3. Marolda CL, Valvano MA (June 1998). "Promoter region of the Escherichia coli O7-specific lipopolysaccharide gene cluster: structural and functional characterization of an upstream untranslated mRNA sequence". J. Bacteriol. 180 (12): 3070–3079. PMC 107806. PMID 9620955.
  4. Nieto JM, Bailey MJ, Hughes C, Koronakis V (February 1996). "Suppression of transcription polarity in the Escherichia coli haemolysin operon by a short upstream element shared by polysaccharide and DNA transfer determinants". Mol. Microbiol. 19 (4): 705–713. doi:10.1046/j.1365-2958.1996.446951.x. PMID 8820641.
  5. Leeds JA, Welch RA (June 1997). "Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism". J. Bacteriol. 179 (11): 3519–3527. doi:10.1128/jb.179.11.3519-3527.1997. PMC 179143. PMID 9171395.
  6. Wang L, Jensen S, Hallman R, Reeves PR (August 1998). "Expression of the O antigen gene cluster is regulated by RfaH through the JUMPstart sequence". FEMS Microbiol. Lett. 165 (1): 201–206. doi:10.1111/j.1574-6968.1998.tb13147.x. PMID 9711858.
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