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The AAA⁺ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization

¹ Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/Medical Research Council Building, Cambridge CB2 OXY, England, UK
² Cancer Research UK, Cambridge Research Institute, Cambridge CB2 ORE, England, UK
³ Institute of Medical Technology and Tampere University Hospital, University of Tampere, FI-33014 Tampere, Finland

Correspondence to Ian J. Holt: holt{at}mrc-dunn.cam.ac.uk

Many copies of mammalian mitochondrial DNA contain a short triple-stranded region, or displacement loop (D-loop), in the major noncoding region. In the 35 years since their discovery, no function has been assigned to mitochondrial D-loops. We purified mitochondrial nucleoprotein complexes from rat liver and identified a previously uncharacterized protein, ATAD3p. Localization studies suggested that human ATAD3 is a component of many, but not all, mitochondrial nucleoids. Gene silencing of ATAD3 by RNA interference altered the structure of mitochondrial nucleoids and led to the dissociation of mitochondrial DNA fragments held together by protein, specifically, ones containing the D-loop region. In vitro, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-loop, with a marked preference over partially relaxed molecules with a D-loop or supercoiled DNA circles. These results suggest that mitochondrial D-loops serve to recruit ATAD3p for the purpose of forming or segregating mitochondrial nucleoids.

Abbreviations used in this paper: AGE, agarose gel electrophoresis; D-loop, displacement loop; dsRNA, double-stranded RNA; EMSA, electrophoretic mobility shift assay; mtDNA, mitochondrial DNA; NCR, noncoding region.

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