Organization of DNA in Mammalian Mitochondria

Abstract

As with all organisms that must organize and condense their DNA to fit within the limited volume of a cell or a nucleus, mammalian mitochondrial DNA (mtDNA) is packaged into nucleoprotein structures called nucleoids. In this study, we first introduce the general modes of DNA compaction, especially the role of the nucleoid-associated proteins (NAPs) that structure the bacterial chromosome. We then present the mitochondrial nucleoid and the main factors responsible for packaging of mtDNA: ARS- (autonomously replicating sequence-) binding factor 2 protein (Abf2p) in yeast and mitochondrial transcription factor A (TFAM) in mammals. We summarize the single-molecule manipulation experiments on mtDNA compaction and visualization of mitochondrial nucleoids that have led to our current knowledge on mtDNA compaction. Lastly, we discuss the possible regulatory role of DNA packaging by TFAM in DNA transactions such as mtDNA replication and transcription.

Keywords: mitochondrial DNA; mtDNA compaction; mtDNA maintenance; mtDNA replication; mtDNA transcription.

Figure 1

Architectural protein activities from bacterial nucleoids, eukaryotic chromatin, and mitochondrial nucleoids. (A) The bacterial chromosome is organized by several different NAPs that bend (IHF, FIS, HU), wrap (HU), and stiffen (arrows) and bridge (H-NS) DNA (grey duplex). (B) In the eukaryotic nucleus, chromosomal DNA is tightly wrapped around a nucleosome comprised of a histone octamer. (C) In yeast mitochondria, mtDNA is compacted by Abf2, which induces sharp U-turns. (D) In mammalian mitochondria, TFAM compacts mtDNA via U-turns and bridging (two left panels). In addition, TFAM slides along DNA (dashed arrow) and binds cooperatively to a TFAM patch, as well as increases DNA flexibility via local denaturation (DNA bubble, right panel).

Figure 2

Comparison of yeast Abf2 and human TFAM. Left panels: Protein architecture of Abf2 (yellow) and TFAM (green) showing the mitochondrial targeting sequence (MTS), HMG boxes A and B, linker, and C-terminus. Middle panels: Abf2 and TFAM bind to DNA (grey duplex) non-specifically and induce compaction. Right panels: Abf2 has no promoter-specific binding activity and does not function as a transcription factor. Mammalian mitochondrial promoters have TFAM binding sites (blue duplex) to which TFAM can bind specifically and activate transcription. TSS- transcription start site.

Figure 3

Regulatory role of TFAM in DNA transactions. Model of how TFAM levels and DNA compaction (upper panel) regulate replication and transcription in mitochondria (lower panel). Increases in TFAM levels (green) result in more DNA (grey duplex ring) compaction, which ultimately results in a fully compacted nucleoid. Mitochondria with low TFAM levels and, thus, less compacted mtDNA are permissive environments for replication (black arrow) and transcription (orange line). Increases in mitochondrial TFAM levels lead to more fully-compacted nucleoids that are refractory to replication and transcription, and fewer actively replicating/transcribing mtDNA molecules.

Figure 4

Dynamics of TFAM binding during transcription and replication. Model of how nucleoid decompaction and re-compaction facilitate transcription (upper panel) and replication (lower panel). TFAM (green) unloads from the DNA (grey duplex) ahead of the transcription bubble or replication fork to enable progression (dark arrows) of the transcription and replication machineries. TFAM may then reload directly behind in order to recompact the DNA.