title: Identification of conserved regulatory RNA structures in prokaryotic metabolic pathway genes.
abstract: A combination of algorithms to search RNA sequence for the potential for secondary structure formation, and search large numbers of sequences for structural similarity, were used to search the 5'UTRs of annotated genes in the Escherichia coli genome for regulatory RNA structures. Using this approach, similar RNA structures that regulate genes in the thiamin metabolic pathway were identified. In addition, several putative regulatory structures were discovered upstream of genes involved in other metabolic pathways including glycerol metabolism and ethanol fermentation. The results demonstrate that this computational approach is a powerful tool for discovery of important RNA structures within prokaryotic organisms.
authors.affiliation: Ibis Therapeutics, Carlsbad, CA 92008, USA.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Lesnik
authors.forename: Gary B
authors.initials: GB
authors.lastname: Fogel
authors.forename: Dana
authors.initials: D
authors.lastname: Weekes
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Henderson
authors.forename: Harold B
authors.initials: HB
authors.lastname: Levene
authors.forename: Rangarajan
authors.initials: R
authors.lastname: Sampath
authors.forename: David J
authors.initials: DJ
authors.lastname: Ecker
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D004926:Escherichia coli / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions