The organization of multiple mitochondrial DNA (mtDNA) molecules in discrete protein-DNA complexes called nucleoids is well studied in Saccharomyces cerevisiae. Similar structures have recently been observed in human cells by the colocalization of a Twinkle-GFP fusion protein with mtDNA. However, nucleoids in mammalian cells are poorly characterized and are often thought of as relatively simple structures, despite the yeast paradigm. In this article we have used immunocytochemistry and biochemical isolation procedures to characterize the composition of human mitochondrial nucleoids. The results show that both the mitochondrial transcription factor TFAM and mitochondrial single-stranded DNA-binding protein colocalize with Twinkle in intramitochondrial foci defined as nucleoids by the specific incorporation of bromodeoxyuridine. Furthermore, mtDNA polymerase POLG and various other as yet unidentified proteins copurify with mtDNA nucleoids using a biochemical isolation procedure, as does TFAM. The results demonstrated that mtDNA in mammalian cells is organized in discrete protein-rich structures within the mitochondrial network. In vivo time-lapse imaging of nucleoids show they are dynamic structures able to divide and redistribute in the mitochondrial network and suggest that nucleoids are the mitochondrial units of inheritance. Nucleoids did not colocalize with dynaminrelated protein 1, Drp1, a protein of the mitochondrial fission machinery.
INTRODUCTIONMammalian mitochondrial DNA (mtDNA) is a 16.5-kb circular double-stranded DNA (Anderson et al., 1981;Bibb et al., 1981) present in one to several thousand of copies per cell (e.g., Takamatsu et al., 2002). All proteins involved in mtDNA maintenance are encoded by the nuclear genome. These are traditional proteins in replication and repair such as the mtDNA polymerase POLG, but also include proteins directly or indirectly involved in e.g., segregation.MtDNA in the yeast Saccharomyces cerevisiae and to a lesser extent in a few other species, appears to be organized in discrete foci within mitochondria called nucleoids (Miyakawa et al., 1984). These have been inferred to be the units of inheritance each containing several copies of yeast mtDNA MacAlpine et al., 2000 and references therein). Biochemical purification and protein analysis have defined several of the constituents of yeast nucleoids (Miyakawa et al., 1995;Newman et al., 1996;Kaufman et al., 2000). One of the core components is the Abf2 protein (Abf2p), an orthologue of the human mitochondrial transcription factor TFAM. The function of Abf2p in yeast is essential for mtDNA maintenance by providing a mtDNApackaging function. It also modestly stimulates yeast transcription in in vitro assays (Parisi et al., 1993). A mouse TFAM knockout shows embryonic lethality with complete loss of mtDNA (Larsson et al., 1998), but this is generally believed to be the result of impairment of transcription initiation that would generate primers for mtDNA replication.Other yeast nucleoid components include Rim1p, the yeast s...