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Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
Achillefs N. Kapanidis,1,2Emmanuel Margeat,1*Sam On Ho,1Ekaterine Kortkhonjia,1,3Shimon Weiss,1Richard H. Ebright3
Using fluorescence resonance energy transfer to monitor distanceswithin single molecules of abortively initiating transcriptioninitiation complexes, we show that initial transcription proceedsthrough a "scrunching" mechanism, in which RNA polymerase (RNAP)remains fixed on promoter DNA and pulls downstream DNA intoitself and past its active center. We show further that putativealternative mechanisms for RNAP active-center translocationin initial transcription, involving "transient excursions" ofRNAP relative to DNA or "inchworming" of RNAP relative to DNA,do not occur. The results support a model in which a stressedintermediate, with DNA-unwinding stress and DNA-compaction stress,is formed during initial transcription, and in which accumulatedstress is used to drive breakage of interactions between RNAPand promoter DNA and between RNAP and initiation factors duringpromoter escape.
1 Department of Chemistry and Biochemistry and Department of Physiology, University of California, Los Angeles, CA 90095, USA. 2 Clarendon Laboratory, Department of Physics, and IRC in Bionanotechnology, University of Oxford, Oxford OX1 3PU, UK. 3 Howard Hughes Medical Institute, Department of Chemistry, and Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA.
* Present address: Centre de Biochimie Structurale. CNRS UMR 5048.INSERM UMR 554. Université Montpellier I, 29 rue de Navacelles,34090 Montpellier cedex, France.
To whom correspondence should be addressed. E-mail: a.kapanidis1{at}physics.ox.ac.uk, sweiss{at}chem.ucla.edu, ebright{at}waksman.rutgers.edu
Sensor I Threonine of the AAA+ ATPase Transcriptional Activator PspF Is Involved in Coupling Nucleotide Triphosphate Hydrolysis to the Restructuring of {sigma}54-RNA Polymerase.
J. Schumacher, N. Joly, M. Rappas, D. Bradley, S. R. Wigneshweraraj, X. Zhang, and M. Buck (2007)
J. Biol. Chem.
282, 9825-9833
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Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching..
A. Revyakin, C. Liu, R. H. Ebright, and T. R. Strick (2006)
Science
314, 1139-1143
|Abstract »|Full Text »|PDF »