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J. Biol. Chem., Vol. 281, Issue 29, 20107-20119, July 21, 2006

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Domain Structure and Protein Interactions of the Silent Information Regulator Sir3 Revealed by Screening a Nested Deletion Library of Protein Fragments^*

From the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115

Transcriptional silencing in yeast is mediated by the interactions of silent information regulator (Sir) proteins with chromatin and with one another. The stable association of Sir3 with Sir4 is mediated by a C-terminal region of Sir3 that has additional functions including the dimerization of Sir3. We have developed a simple, robust expression screening methodology that allows for the unbiased identification of functional protein domains expressed from nested-deletion libraries of full-length genes. Using these methodologies, Sir3 dimerization was shown to be mediated by two separate domains. One of these domains also binds cooperatively to the C-terminal coiled-coil motif of Sir4 and dimerization further increases the affinity of Sir3 for Sir4. The resulting Sir3-Sir4 complexes form progressively higher order assemblies with increasing protein concentration, with implications for the mechanism of gene silencing.

Received for publication, November 28, 2005 , and in revised form, May 19, 2006.

^* This work was supported by National Institutes of Health, NCI Research Grant P01 CA92584 and NIGMS Grant R01 GM52504. 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 supplemental Figs. S1–S3.

¹ To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biophysics, WA University School of Medicine, St. Louis, MO 63110. Tel.: 314-747-8893; E-mail: tome{at}biochem.wustl.edu.

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