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BIOLOGICAL SCIENCES / BIOCHEMISTRY
The elongation factor RfaH and the initiation factor bind to the same site on the transcription elongation complex

Anastasiya Sevostyanova^*, Vladimir Svetlov^*, Dmitry G. Vassylyev, and Irina Artsimovitch^*,

*Department of Microbiology, Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210; and Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, 402B Kaul Genetics Building, 720 Twentieth Street South, Birmingham, AL 35294

Edited by Jeffrey W. Roberts, Cornell University, Ithaca, NY, and approved December 6, 2007 (received for review September 5, 2007)

RNA polymerase is a target for numerous regulatory events in all living cells. Recent studies identified a few "hot spots" on the surface of bacterial RNA polymerase that mediate its interactions with diverse accessory proteins. Prominent among these hot spots, the β' subunit clamp helices serve as a major binding site for the initiation factor and for the elongation factor RfaH. Furthermore, the two proteins interact with the nontemplate DNA strand in transcription complexes and thus may interfere with each other's activity. We show that RfaH does not inhibit transcription initiation but, once recruited to RNA polymerase, abolishes -dependent pausing. We argue that this apparent competition is due to a steric exclusion of by RfaH that is stably bound to the nontemplate DNA and clamp helices, both of which are necessary for the recruitment to the transcription complex. Our findings highlight the key regulatory role played by the clamp helices during both initiation and elongation stages of transcription.

clamp helices | RNA polymerase | transcription factor | nontemplate DNA

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0708432105/DC1.

To whom correspondence should be addressed. E-mail: artsimovitch.1{at}osu.edu

© 2008 by The National Academy of Sciences of the USA

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