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

TLDR

Packaging DNA into condensed structures is essential for genome transmission, and in mammals the high‑copy mitochondrial genome is organized into nucleoids, yet the mechanism of nucleoid assembly remains unknown. The study aims to demonstrate that TFAM can cooperatively bind DNA and compact multiple DNA molecules into spheroid structures. Using noncontact atomic force microscopy, the authors show that TFAM induces DNA bending and looping, sequentially filling nearby sites to compact multiple DNA molecules into spheroid structures. TFAM alone is sufficient to organize mitochondrial chromatin, providing a mechanism for nucleoid formation.

Abstract

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.