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Originally published In Press as doi:10.1074/jbc.M206658200 on August 16, 2002

J. Biol. Chem., Vol. 277, Issue 45, 43206-43215, November 8, 2002
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Major Conformational Changes Occur during the Transition from an Initiation Complex to an Elongation Complex by T7 RNA Polymerase*

Kaiyu MaDagger , Dmitri TemiakovDagger , Manli Jiang, Michael Anikin, and William T. McAllister§

From the Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, New York 11203-2098

To examine changes that occur during the transition from an initiation complex (IC) to an elongation complex (EC) in T7 RNA polymerase (RNAP), we used nucleic acid-protein cross-linking methods to probe interactions of the RNAP with RNA and DNA in a halted EC. As the RNA is displaced from the RNA-DNA hybrid ~9 bp upstream from the active site (at -9) it interacts with a region within the specificity loop (residues 744-750) and is directed toward a positively charged surface that surrounds residues Lys-302 and Lys-303. Surprisingly, the template and non-template strands of the DNA at the upstream edge of the hybrid (near the site where the RNA is displaced) interact with a region in the N-terminal domain of the RNAP (residues 172-191) that is far away from the specificity loop before isomerization (in the IC). To bring these two regions of the RNAP into proximity, major conformational changes must occur during the transition from an IC to an EC. The observed nucleic acid-protein interactions help to explain the behavior of a number of mutant RNAPs that are affected at various stages in the initiation process and in termination.

* This work was supported by National Institutes of Health Grant GM38147 (to W. T. M.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Dagger These authors contributed equally to this work.

§ To whom correspondence should be addressed: Dept. of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Ave., Brooklyn, New York 11203-2098. Tel.: 718-270-1238; Fax: 718-270-2656; E-mail: pogo51@aol.com.

Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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