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J. Biol. Chem., Vol. 281, Issue 43, 32898-32908, October 27, 2006

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Double-stranded DNA Binding, an Unusual Property of DNA Polymerase , Promotes Epigenetic Silencing in Saccharomyces cerevisiae^*

Toshiaki Tsubota¹², Rie Tajima¹, Kunitomo Ode, Hajime Kubota, Naoshi Fukuhara, Takeshi Kawabata, Satoko Maki³, and Hisaji Maki

From the Department of Molecular Biology, Graduate School of Biological Sciences and Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan

We have previously shown that DNA polymerase (Pol )of Saccharomyces cerevisiae binds stably to double-stranded DNA (dsDNA), a property not generally associated with DNA polymerases. Here, by reconstituting Pol activity from Pol2p-Dpb2p and Dpb3p-Dpb4p, its two component subassemblies, we report that Dpb3p-Dpb4p, a heterodimer of histone-fold motif-containing subunits, is responsible for the dsDNA binding. Substitution of specific lysine residues in Dpb3p, highlighted by homology modeling of Dpb3p-Dpb4p based on the structure of the histone H2A-H2B dimer, indicated that they play roles in binding of dsDNA by Dpb3p-Dpb4p, in a manner similar to the histone-DNA interaction. The lysine-substituted dpb3 mutants also displayed reduced telomeric silencing, whose degree paralleled that of the dsDNA-binding activity of Pol in the corresponding dpb3 mutants. Furthermore, additional amino acid substitutions to lysines in Dpb4p, to compensate for the loss of positive charges in the Dpb3p mutants, resulted in simultaneous restoration of dsDNA-binding activity by Pol and telomeric silencing. We conclude that the dsDNA-binding property of Pol is required for epigenetic silencing at telomeres.

Received for publication, July 12, 2006 , and in revised form, August 16, 2006.

^* This work was supported in part by a Grant-in-aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (11241203 to S. M.) and the 21st Century COE Program (to S. M.). 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.

This article was selected as Paper of the Week.

¹ These authors contributed equally to this work.

² Supported by a postdoctoral fellowship from the BIO-COE Fund of the Nara Institute of Science and Technology. Present address: University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605-2324.

³ To whom correspondence should be addressed: Dept. of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan. Tel.: 81-743-72-5493; Fax: 81-743-72-5499; E-mail: smaki{at}bs.naist.jp.

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