title: The bacterial cell cycle regulator GcrA is a σ70 cofactor that drives gene expression from a subset of methylated promoters.
abstract: Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we found that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active σ(70)-dependent promoters in vivo but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ(70) interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrated that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identified a regulon of ∼ 200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than recruitment exclusively.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Diane L
authors.initials: DL
authors.lastname: Haakonsen
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
authors.forename: Andy H
authors.initials: AH
authors.lastname: Yuan
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
authors.forename: Michael T
authors.initials: MT
authors.lastname: Laub
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D016935:Caulobacter crescentus / Q000166:cytology* / Q000201:enzymology / Q000235:genetics*; D003067:Coenzymes / Q000235:genetics* / Q000378:metabolism*; D048749:Cytokinesis / Q000235:genetics; D019175:DNA Methylation; D004261:DNA Replication; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D012808:Sigma Factor / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D003067:Coenzymes; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases
keywords: Caulobacter crescentus; DNA methylation; bacterial transcription; cell cycle