Opening and Closing of the Bacterial RNA Polymerase Clamp

• Published in: Science (American Association for the Advancement of Science) Vol. 337; no. 6094; pp. 591 - 595
• Main Authors: Chakraborty, Anirban, Wang, Dongye, Ebright, Yon W., Korlann, You, Kortkhonjia, Ekaterine, Kim, Taiho, Chowdhury, Saikat, Wigneshweraraj, Sivaramesh, Irschik, Herbert, Jansen, Rolf, Nixon, B. Tracy, Knight, Jennifer, Weiss, Shimon, Ebright, Richard H.
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 03.08.2012; The American Association for the Advancement of Science
• Subjects: Bacteria; Binding sites; Biochemistry; Biological and medical sciences; Clamps; Collapsed states; Crystal structure; Deoxyribonucleic acid; DNA; DNA Polymerase III - chemistry; DNA Polymerase III - drug effects; DNA probes; DNA-directed RNA polymerase; Energy transfer; Fluorescence; Fluorescence Resonance Energy Transfer - methods; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Bacterial; Isomerization; Ligation; Microbiology; Molecular biophysics; Molecular probes; Molecules; Polymerase; Protein Conformation; Ribonucleic acids; RNA; RNA polymerase; Structure in molecular biology; Transcription, Genetic; Tridimensional structure; Nucleotidyltransferases; Transcription; Enzyme; Transferases; Bacteria; DNA-directed RNA polymerase; Transcription initiation; Elongation; Conformation
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.1218716

Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription initiation and elongation. We find that the clamp predominantly is open in free RNAP and early intermediates in transcription initiation but closes upon formation of a catalytically competent transcription initiation complex and remains closed during initial transcription and transcription elongation. We show that four RNAP inhibitors interfere with clamp opening. We propose that clamp opening allows DNA to be loaded into and unwound in the RNAP active-center cleft, that DNA loading and unwinding trigger clamp closure, and that clamp closure accounts for the high stability of initiation complexes and the high stability and processivity of elongation complexes.