title: The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure.
abstract: The leading region of the conjugal bacterial plasmid ColIb-P9 contains three dispersed repeats of a 328 bp sequence homologous to Frpo, a sequence from plasmid F that acts as a promoter in single-stranded DNA. One of these sequences, ssi3, inactive in the double-stranded form, promoted in vitro transcription exclusively from the single strand that is transferred during conjugation. Promoter activity was dependent on the presence of RNA polymerase holoenzyme containing sigma 70. Transcription initiated from the position predicted from folding the single-stranded DNA to form a pseudo double-stranded hairpin structure containing recognizable -35 and -10 promoter elements. Footprinting of RNA polymerase holoenzyme on single-stranded ssi3 DNA was consistent with this suggestion. Mutagenesis of the putative -35 region inactivated the promoter, but random mutations in the -10 region had little effect. The putative -10 region is a poor match to the consensus sequence and contains mismatched bases. Elimination of these mismatches invariably destroyed single-strand promoter activity. These observations reveal the crucial contribution of the unpaired bases in the -10 region in potentiating the formation of the productive open complex with RNA polymerase.
authors.affiliation: Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK.
authors.forename: M T
authors.initials: MT
authors.lastname: Nasim
authors.forename: I C
authors.initials: IC
authors.lastname: Eperon
authors.forename: B M
authors.initials: BM
authors.lastname: Wilkins
authors.forename: W J
authors.initials: WJ
authors.lastname: Brammar
mesh_terms: D003086:Bacteriocin Plasmids / Q000235:genetics*; D020137:Base Pair Mismatch; D003227:Conjugation, Genetic; D016384:Consensus Sequence; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000235:genetics / Q000502:physiology; D004277:DNA, Single-Stranded / Q000235:genetics / Q000502:physiology*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D005144:F Factor / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D009154:Mutation; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D017385:Sequence Homology; D012808:Sigma Factor / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases