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J. Biol. Chem., Vol. 283, Issue 6, 3665-3675, February 8, 2008

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The Layered Structure of Human Mitochondrial DNA Nucleoids^*

Daniel F. Bogenhagen¹, Denis Rousseau, and Stephanie Burke

From the Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York 11794-8651 and the Laboratoire Biochimie et Biophysique des Systèmes Intégrés p438B, Institut de Recherches en Technologies et Sciences pour le Vivant, UMR5092 CNRS-UJF-CEA-Grenoble, 17 Rue des Martyrs, 38054 Grenoble Cedex 09, France

Mitochondrial DNA (mtDNA) occurs in cells in nucleoids containing several copies of the genome. Previous studies have identified proteins associated with these large DNA structures when they are biochemically purified by sedimentation and immunoaffinity chromatography. In this study, formaldehyde cross-linking was performed to determine which nucleoid proteins are in close contact with the mtDNA. A set of core nucleoid proteins is found in both native and cross-linked nucleoids, including 13 proteins with known roles in mtDNA transactions. Several other metabolic proteins and chaperones identified in native nucleoids, including ATAD3, were not observed to cross-link to mtDNA. Additional immunofluorescence and protease susceptibility studies showed that an N-terminal domain of ATAD3 previously proposed to bind to the mtDNA D-loop is directed away from the mitochondrial matrix, so it is unlikely to interact with mtDNA in vivo. These results are discussed in relation to a model for a layered structure of mtDNA nucleoids in which replication and transcription occur in the central core, whereas translation and complex assembly may occur in the peripheral region.

Received for publication, October 11, 2007 , and in revised form, December 5, 2007.

^* This work was supported by National Institutes of Health Grant R01-ES12039. 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 Tables 1 and 2.

¹ To whom correspondence should be addressed. Fax: 631-444-3218; E-mail: dan{at}pharm.sunysb.edu.

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