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Vol. 18, Issue 9, 3225-3236, September 2007

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The Mitochondrial Transcription Factor TFAM Coordinates the Assembly of Multiple DNA Molecules into Nucleoid-like Structures

Brett A. Kaufman^*,, Nela Durisic^,, Jeffrey M. Mativetsky, Santiago Costantino^*,, Mark A. Hancock, Peter Grutter, and Eric A. Shoubridge^*,||

*Department of Neurology and Neurosurgery and Program in NeuroEngineering, Montreal Neurological Institute, Department of Physics, Sheldon Biotechnology Centre, and ^||Department of Human Genetics, McGill University, Montreal, QC, H3A 2B4, Canada

Submitted May 3, 2007; Revised May 31, 2007; Accepted June 8, 2007
Monitoring Editor: Thomas Fox

Packaging DNA into condensed structures is integral to the transmission of genomes. The mammalian mitochondrial genome (mtDNA) is a high copy, maternally inherited genome in which mutations cause a variety of multisystem disorders. In all eukaryotic cells, multiple mtDNAs are packaged with protein into spheroid bodies called nucleoids, which are the fundamental units of mtDNA segregation. The mechanism of nucleoid formation, however, remains unknown. Here, we show that the mitochondrial transcription factor TFAM, an abundant and highly conserved High Mobility Group box protein, binds DNA cooperatively with nanomolar affinity as a homodimer and that it is capable of coordinating and fully compacting several DNA molecules together to form spheroid structures. We use noncontact atomic force microscopy, which achieves near cryo-electron microscope resolution, to reveal the structural details of protein–DNA compaction intermediates. The formation of these complexes involves the bending of the DNA backbone, and DNA loop formation, followed by the filling in of proximal available DNA sites until the DNA is compacted. These results indicate that TFAM alone is sufficient to organize mitochondrial chromatin and provide a mechanism for nucleoid formation.

The online version of this article contains supplemental material at MBC Online (http://www.molbiolcell.org).

These authors contributed equally to this work.

Address correspondence to: Eric A. Shoubridge (eric{at}ericpc.mni.mcgill.ca).

Abbreviations used: AFM, atomic force microscopy; EMSA, electrophoretic mobility shift assay; mtDNA, mitochondrial DNA; NC-AFM, noncontact atomic force microscopy; SPR, surface plasmon resonance.