title: Compilation and analysis of sigma(54)-dependent promoter sequences.
abstract: Promoters recognized by the RNA-polymerase with the alternative sigma factor sigma(54) (Esigma54) are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site, instead of the typical -35 and -10 boxes. Here we compile 186 -24/-12 promoter sequences reported in the literature and generate an updated and extended consensus sequence. The use of the extended consensus increases the probability of identifying genuine -24/-12 promoters. The effect of several reported mutations at the -24/-12 elements on RNA-polymerase binding and promoter strength is discussed in the light of the updated consensus.
authors.affiliation: Departamento de Reconocimiento Molecular y Bioestructura, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62271, México.
authors.forename: H
authors.initials: H
authors.lastname: Barrios
authors.forename: B
authors.initials: B
authors.lastname: Valderrama
authors.forename: E
authors.initials: E
authors.lastname: Morett
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D016384:Consensus Sequence; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D016208:Databases, Factual; D008969:Molecular Sequence Data; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics* / Q000502:physiology; D051877:RNA Polymerase Sigma 54; D012689:Sequence Homology, Nucleic Acid; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54