title: Thermodynamic analysis of the transcription cycle in E. coli.
abstract: The E. coli RNA transcription cycle can be divided into three major phases, which are generally called initiation, elongation, and termination. In this paper, we review recent biophysical studies of the interactions of the transcriptional regulatory proteins, sigma 70 and NusA, with themselves and with core RNA polymerase in solution, as well as with core polymerase within the transcription complex. The different affinities of sigma 70 and NusA for core RNA polymerase at various stages in the transcription cycle, together with other quantitative data, are then used to construct a partial free energy diagram for the overall transcription process. This thermodynamic framework, which is interrupted by at least two irreversible steps, can be used to rationalize physiological aspects of the transcription cycle and its regulation, as well as to identify crucial points at which our knowledge is still incomplete.
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene 97403.
authors.forename: S C
authors.initials: SC
authors.lastname: Gill
authors.forename: T D
authors.initials: TD
authors.lastname: Yager
authors.forename: P H
authors.initials: PH
authors.lastname: von Hippel
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D007700:Kinetics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000096:biosynthesis*; D012808:Sigma Factor / Q000378:metabolism; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases