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J. Biol. Chem., Vol. 282, Issue 49, 35482-35490, December 7, 2007

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Transcription Factor E Is a Part of Transcription Elongation Complexes^*

Sebastian Grünberg, Michael S. Bartlett¹, Souad Naji², and Michael Thomm³

From the Lehrstuhl für Mikrobiologie, Universitaet Regensburg, 93053 Regensburg, Germany and the Department of Biology, Portland State University, Portland, Oregon 97207

A homologue of the N-terminal domain of the subunit of the general eukaryotic transcription factor TFE is encoded in the genomes of all sequenced archaea, but the position of archaeal TFE in transcription complexes has not yet been defined. We show here that TFE binds nonspecifically to single-stranded DNA, and photochemical cross-linking revealed TFE binding to a preformed open transcription bubble. In preinitiation complexes, the N-terminal part of TFE containing a winged helix-turn-helix motif is cross-linked specifically to DNA of the nontemplate DNA strand at positions –9 and –11. In complexes stalled at +20, TFE cross-linked specifically to positions +9, +11, and +16 of the non-template strand. Analyses of transcription complexes stalled at position +20 revealed a TFE-dependent increase of the resumption efficiency of stalled RNA polymerase and a TFE-induced enhanced permanganate sensitivity of thymine residues in the transcription bubble. These results demonstrate the presence of TFE in early elongation complexes and suggest a role of TFE in stabilization of the transcription bubble during elongation.

Received for publication, September 4, 2007 , and in revised form, October 4, 2007.

^* This work was supported by grants from the priority program "Genome function and regulation" of the Deutsche Forschungsgemeinschaft (to M. T.) and the American Heart Association Northwest Affiliate to (M. S. B.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains a supplemental figure.

² Present address: The Scripps Research Institute, Dept. of Cell Biology, IMM-10, 10550 North Torrey Pines Rd., La Jolla, CA 92037.

¹ To whom correspondence may be addressed: Dept. of Biology, Portland State University, P.O. Box 751, Portland, OR, 97207. Tel.: 503-725-3858; Fax: 503-725-3888; E-mail: micb{at}pdx.edu. ³ To whom correspondence may be addressed: Lehrstuhl für Mikrobiologie, Universitaet Regensburg, 93053 Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany. Tel.: 49-941-943-3160; Fax: 49-941-943-2403; E-mail: michael.thomm{at}biologie.uni-r.de.

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				M. Micorescu, S. Grunberg, A. Franke, P. Cramer, M. Thomm, and M. Bartlett Archaeal Transcription: Function of an Alternative Transcription Factor B from Pyrococcus furiosus J. Bacteriol., January 1, 2008; 190(1): 157 - 167. [Abstract] [Full Text] [PDF]