Mechanism of Bacterial Transcription Initiation: RNA Polymerase - Promoter Binding, Isomerization to Initiation-Competent Open Complexes, and Initiation of RNA Synthesis

• Published in: Journal of molecular biology Vol. 412; no. 5; pp. 754 - 771
• Main Authors: Saecker, Ruth M., Record, M. Thomas, deHaseth, Pieter L.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 07.10.2011
• Subjects: Bacteria; Bacteria - genetics; Bacteria - metabolism; biosynthesis; Catalytic Domain; DNA; DNA, Bacterial; DNA, Bacterial - metabolism; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases; DNA-Directed RNA Polymerases - metabolism; energy; genetics; Intermediate complexes; isomerization; metabolism; Models, Biological; Models, Molecular; Promoter; Promoter Regions, Genetic; Protein Binding; Protein Conformation; RNA; RNA polymerase; RNA, Bacterial; RNA, Bacterial - biosynthesis; RNA, Messenger; RNA, Messenger - biosynthesis; Sigma factor; Transcription initiation; Transcription, Genetic; NT; lpm; Sigma factor; RNA polymerase; αCTD; Intermediate complexes; RNAP; myxo; Promoter; T; SI; FRET; Transcription initiation
• ISSN: 0022-2836; 1089-8638; 1089-8638
• DOI: 10.1016/j.jmb.2011.01.018

Initiation of RNA synthesis from DNA templates by RNA polymerase (RNAP) is a multi-step process, in which initial recognition of promoter DNA by RNAP triggers a series of conformational changes in both RNAP and promoter DNA. The bacterial RNAP functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex DNA in the active site cleft and then separating the nontemplate and template strands in the region surrounding the start site of RNA synthesis. In this initial unstable “open” complex the template strand appears correctly positioned in the active site. Subsequently, the nontemplate strand is repositioned and a clamp is assembled on duplex DNA downstream of the open region to form the highly stable open complex, RP o. The transcription initiation factor, σ 70, plays critical roles in promoter recognition and RP o formation as well as in early steps of RNA synthesis.