title: Visualizing the activity of Escherichia coli divergent promoters and probing their dependence on superhelical density using dual-colour fluorescent reporter vector.
abstract: Mosaic pattern of transcription in alternating directions is a common feature of prokaryotic and eukaryotic genomes which rationality and origin remain enigmatic. In Escherichia coli approximately 25% of genes comprise pairs of topologically linked divergently transcribed units. Given that transcriptional complex formation at each promoter in the pair induces topological changes and is itself sensitive to DNA structural perturbations, study of the functional anatomy in such areas requires special approaches. Here we suggested the dual-colour promoter probe vector which may become an ideal tool for divergent transcription profiling. The vector was used to characterize the specific genomic region nearby appY with multiple bidirectional promoters predicted in silico. Only three promoters of this region were shown to be engaged in the transcription initiation resulting in the expression of reporter genes. RNA product transcribed in antisense direction is suggested as a novel RNA. Nalidixin-induced topological modulation differentially affected transcription in sense and antisense directions thus exemplifying anticooperative mode in the response to topological alterations.
authors.affiliation: Laboratory of functional genomics and cellular stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russian Federation.
authors.forename: Irina S
authors.initials: IS
authors.lastname: Masulis
authors.affiliation: Laboratory of functional genomics and cellular stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russian Federation.
authors.forename: Zaira Sh
authors.initials: ZSh
authors.lastname: Babaeva
authors.affiliation: Group of molecular biotechnology, Branch of Shemyakin &Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russian Federation.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Chernyshov
authors.affiliation: Laboratory of functional genomics and cellular stress, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russian Federation.
authors.forename: Olga N
authors.initials: ON
authors.lastname: Ozoline
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004278:DNA, Superhelical; D004926:Escherichia coli / Q000235:genetics*; D015870:Gene Expression; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D005822:Genetic Vectors / Q000235:genetics*; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D004278:DNA, Superhelical