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J. Biol. Chem., Vol. 280, Issue 35, 31200-31207, September 2, 2005

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Preponderance of Free Mediator in the Yeast Saccharomyces cerevisiae^*

Yuichiro Takagi¶, James Z. Chadick||¶, Joshua A. Davis||, and Francisco J. Asturias||**

From the ^||Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037 and the Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94035

Biochemical evidence suggesting that the predominant form of Mediator in the yeast Saccharomyces cerevisiae might be one in which the complex is associated with RNA polymerase II to form a holoenzyme has led to the proposition of a holoenzyme-based model for transcription initiation. We report that polymerase-free Mediator, isolated early on during a whole-cell extract fractionation protocol, is in fact the most abundant form of the Mediator complex. The existence of free Mediator would make possible independent recruitment of Mediator and RNA polymerase II to the preinitiation complex. This is in agreement with reports from in vivo studies of time and spatial independence of Mediator and RNA polymerase II promoter interaction, with current models of preinitiation complex structure in which promoter DNA upstream of the transcription start site is positioned between Mediator and polymerase, and with the proposed role of Mediator as the major component of the Scaffold complex involved in transcription reinitiation.

Received for publication, April 1, 2005 , and in revised form, June 21, 2005.

^* This work was funded by National Institutes of Health Grant R01 GM67167 (to F. J. A.). 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.

Supported by National Institutes of Health Grant R01 GM36659 to Roger D. Kornberg.

^¶ These two authors contributed equally to the work described in this manuscript.

^** A Scholar of the Leukemia and Lymphoma Society of America. To whom correspondence should be addressed: Dept. of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. E-mail: asturias{at}scripps.edu.

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