Opening and Closing of the Bacterial RNA Polymerase Clamp
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...
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| Published in | Science (American Association for the Advancement of Science) Vol. 337; no. 6094; pp. 591 - 595 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| 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 | |
| Online Access | Get full text |
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| Abstract | 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. |
|---|---|
| AbstractList | Crystal structures of RNA polymerase show that a “clamp” region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open state.
Chakraborty
et al.
(p.
591
) used single-molecule fluorescence energy transfer experiments to detect the clamp's conformational changes in solution during the transcription cycle. The results support a model in which a clamp opening allows DNA to be loaded into the active-center cleft and unwound. Direct interactions with DNA likely trigger clamp closure upon formation of a catalytically competent transcription initiation complex.
Single-molecule fluorescence measurements define the clamp conformation during transcription initiation and elongation.
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. 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. Crystal structures of RNA polymerase show that a "clamp" region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open state. Chakraborty et al. (p. 591) used single-molecule fluorescence energy transfer experiments to detect the clamp's conformational changes in solution during the transcription cycle. The results support a model in which a clamp opening allows DNA to be loaded into the active-center cleft and unwound. Direct interactions with DNA likely trigger clamp closure upon formation of a catalytically competent transcription initiation complex. [PUBLICATION ABSTRACT] 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. [PUBLICATION ABSTRACT] Clamping DownCrystal structures of RNA polymerase show that a "clamp" region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open state. Chakraborty et al. (p. 591) used single-molecule fluorescence energy transfer experiments to detect the clamp's conformational changes in solution during the transcription cycle. The results support a model in which a clamp opening allows DNA to be loaded into the active-center cleft and unwound. Direct interactions with DNA likely trigger clamp closure upon formation of a catalytically competent transcription initiation complex. 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.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. Clamping Down Crystal structures of RNA polymerase show that a “clamp” region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open state. Chakraborty et al. (p. 591) used single-molecule fluorescence energy transfer experiments to detect the clamp's conformational changes in solution during the transcription cycle. The results support a model in which a clamp opening allows DNA to be loaded into the active-center cleft and unwound. Direct interactions with DNA likely trigger clamp closure upon formation of a catalytically competent transcription initiation complex. |
| Author | Jansen, Rolf Chowdhury, Saikat Nixon, B. Tracy Irschik, Herbert Weiss, Shimon Ebright, Richard H. Knight, Jennifer Kortkhonjia, Ekaterine Korlann, You Kim, Taiho Chakraborty, Anirban Wang, Dongye Ebright, Yon W. Wigneshweraraj, Sivaramesh |
| Author_xml | – sequence: 1 givenname: Anirban surname: Chakraborty fullname: Chakraborty, Anirban – sequence: 2 givenname: Dongye surname: Wang fullname: Wang, Dongye – sequence: 3 givenname: Yon W. surname: Ebright fullname: Ebright, Yon W. – sequence: 4 givenname: You surname: Korlann fullname: Korlann, You – sequence: 5 givenname: Ekaterine surname: Kortkhonjia fullname: Kortkhonjia, Ekaterine – sequence: 6 givenname: Taiho surname: Kim fullname: Kim, Taiho – sequence: 7 givenname: Saikat surname: Chowdhury fullname: Chowdhury, Saikat – sequence: 8 givenname: Sivaramesh surname: Wigneshweraraj fullname: Wigneshweraraj, Sivaramesh – sequence: 9 givenname: Herbert surname: Irschik fullname: Irschik, Herbert – sequence: 10 givenname: Rolf surname: Jansen fullname: Jansen, Rolf – sequence: 11 givenname: B. Tracy surname: Nixon fullname: Nixon, B. Tracy – sequence: 12 givenname: Jennifer surname: Knight fullname: Knight, Jennifer – sequence: 13 givenname: Shimon surname: Weiss fullname: Weiss, Shimon – sequence: 14 givenname: Richard H. surname: Ebright fullname: Ebright, Richard H. |
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| Copyright | Copyright © 2012 American Association for the Advancement of Science 2014 INIST-CNRS Copyright © 2012, American Association for the Advancement of Science |
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| DOI | 10.1126/science.1218716 |
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| Keywords | Nucleotidyltransferases Transcription Enzyme Transferases Bacteria DNA-directed RNA polymerase Transcription initiation Elongation Conformation |
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| Snippet | Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription... Crystal structures of RNA polymerase show that a “clamp” region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open... Crystal structures of RNA polymerase show that a "clamp" region which surrounds the DNA binding site can adopt conformations ranging from a closed to an open... Clamping DownCrystal structures of RNA polymerase show that a "clamp" region which surrounds the DNA binding site can adopt conformations ranging from a closed... Clamping Down Crystal structures of RNA polymerase show that a “clamp” region which surrounds the DNA binding site can adopt conformations ranging from a... |
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| SubjectTerms | 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 |
| Title | Opening and Closing of the Bacterial RNA Polymerase Clamp |
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