title: Genome wide interactions of wild-type and activator bypass forms of σ54.
abstract: Enhancer-dependent transcription involving the promoter specificity factor σ(54) is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ(54)-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since activators can be bypassed in vitro, bypass transcription in vivo could be a source of emergent gene expression along evolutionary pathways yielding new control networks and transcription patterns. At a single test promoter in vivo bypass transcription was not observed. We now use genome-wide transcription profiling, genome-wide mutagenesis and gene over-expression strategies in Escherichia coli, to (i) scope the range of bypass transcription in vivo and (ii) identify genes which might alter bypass transcription in vivo. We find little evidence for pervasive bypass transcription in vivo with only a small subset of σ(54) promoters functioning without activators. Results also suggest no one gene limits bypass transcription in vivo, arguing bypass transcription is strongly kept in check. Promoter sequences subject to repression by σ(54) were evident, indicating loss of rpoN (encoding σ(54)) rather than creating rpoN bypass alleles would be one evolutionary route for new gene expression patterns. Finally, cold-shock promoters showed unusual σ(54)-dependence in vivo not readily correlated with conventional σ(54) binding-sites.
authors.affiliation: Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK.
authors.forename: Jorrit
authors.initials: J
authors.lastname: Schaefer
authors.affiliation: Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5BN, UK c.engl@imperial.ac.uk.
authors.forename: Christoph
authors.initials: C
authors.lastname: Engl
authors.affiliation: Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK.
authors.forename: Edward
authors.initials: E
authors.lastname: Lawton
authors.affiliation: Faculty of Natural Sciences, Division of Cell & Molecular Biology, Imperial College London, London SW7 2AZ, UK m.buck@imperial.ac.uk.
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
mesh_terms: D000483:Alleles; D001665:Binding Sites; D003080:Cold Temperature; D004926:Escherichia coli / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics; D016296:Mutagenesis; D011401:Promoter Regions, Genetic; D051877:RNA Polymerase Sigma 54 / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012097:Repressor Proteins; D015534:Trans-Activators; D051877:RNA Polymerase Sigma 54