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Mitochondrial DNA (mtDNA)-protein complexes were released from the organelles by sodium dodecyl sulfate-lysis and purified by PhenyI-Sepharose CL-4B chromatography. The mitochondrial DNA-binding protein P16 was the only detectable protein in the complex. Treatment of the complex with proteinase K, or subtilisin, revealed the presence of a proteaseinsensitive, submolecular domain (M, ~ 6,000) that retained the capacity to bind tenaciously to the DNA. Analysis of chemically fixed complexes by CsCI isopycnic gradient centrifugation showed that P16 was bound to a large subpopulation of mtDNA enriched in displacement loops (D-loops). Based upon the effective buoyant density of the complex in CsCl gradients and the molecular weights of P16 and mtDNA, it was estimated that a mean of 49 P16 molecules were bound per mtDNA. For this measurement, the variation in hydration of protein and DNA at different CsCI concentrations was ignored. Analysis of restriction endonucleasedigested complexes by glass fiber filters that bind only protein-associated DNA resulted in the retention of a single fragment regardless of the enzyme, or enzymes, used. In each case, the retained fragment was the D-loop-containing fragment. With direct electron microscopy, the protein was readily visualized on the displaced single strand portions of D-loops and expanding D-loops. The nucleoprotein fibers were ~12 nm in diameter without correcting for the thickness of tungsten coating and roughly 1/3 the length of the double strand segment of the corresponding D-loop structure. In addition, occasional molecules with the characteristics of gapped circles were seen exhibiting a nucleoprotein fibril, presumably containing the single strand gap segment, linking the ends of double strand DNA. P16 was not seen on the double strand portions in any of the complexes.Evidence from a number of laboratories suggests that the region of the origin of replication of animal mtDNA is associated with a proteinaceous component. For example, an mtDNA-protein complex was isolated from Triton X-100-lysates of HeLa cell mitochondria (1). Electron microscopic examination of restriction endonuclease fragments containing this structure revealed the presence of a membrane-like patch in the vicinity of the displacement loop (D-loop)L A fraction of these complexes retained a smaller proteinaceous structure Abbreviations used in this paper: D-loop, displacement loop; H-and L-strand, heavy and light strand of mtDNA, respectively; mtDNA, mitochondrial DNA; TE, l0 mM Tris-HCI, 1 mM disodium EDTA, pH 7.4.(5-10 nm) after treatment with SDS. In Drosophila melanogaster (2) the mtDNA was shown to have several regions near the replication origin that were precluded from cross-linking with photoactivated trimethylpsoralen. The protection against cross-linking was interpreted to result from the association of proteins at the non-cross-linked sites. In studies with Xenopus laevis mitochondria (3), a polymeric protein with a subunit molecular weight of 12,500 was isolated by DNA-cellulos...

The mitochondrial DNA-binding protein P16 was isolated from rat liver mitochondrial lysates by affinity chromatography on single strand DNA agarose and separated from DNA in the preparation by alkaline CsCI isopycnic gradients. The top fraction of the gradients contained a single polypeptide species (Mr ~ 15,200) based upon SDS PAGE. Digestion of single strand DNA-bound P16 with proteinase K produced a protease-insensitive, DNAbinding fragment (Mr ~ 6,000) that has been purified by essentially the same procedures used for intact P16. The partial amino acid compositions for P16 and the DNA-binding fragment were obtained by conventional methods. Analysis of subcellular fractions revealed that nearly all of the cellular P16 was located in the mitochondria and that only trace amounts of protein of comparable electrophoretic mobility could be isolated from the nuclear or cytoplasmic fractions. The labeling of P16 with [35S]methionine in primary rat hepatocyte cultures was inhibited by more than 90% by the cytoplasmic translation inhibitor cycloheximide, but unaffected by the mitochondrial-specific agent chloramphenicol. These results indicate that P16 is synthesized on cytoplasmic ribosomes and imported into the mitochondria. The addition of purified P16 to deproteinized mitochondrial DNA resulted in the complete protection of the labeled nascent strands of displacement loops against branch migrational loss during cleavage of parental DNA with SstI, thus providing strong evidence that P16 is the single entity required for this in vitro function. Incubation of P16 with single strand ~X174 DNA, double strand (RF) ~Xl 74 DNA, or Escherichia coil ribosomal RNA and subsequent analysis of the nucleic acid species for bound protein indicated a strong preference of P16 for single strand DNA and no detectable affinity for RNA or double strand DNA. Examination of P16-single strand ¢X174 DNA complexes by direct electron microscopy revealed thickened, irregular fibers characteristic of protein-associated single strand DNA.A previous study from our laboratory (1) identified P I6 (Mr ----16,000) as the single detectable polypeptide present in native mtDNA-protein complexes isolated from rat liver mitochondria. One function of the bound protein component was to stabilize the displacement loop (D-loop) structure by protecting the nascent strand of the D-loop from branch migration upon parental strand cleavage in vitro. In the accompanying paper (2), PI6 was found to bind exclusively to the displaced single strand of normal and expanded Dloops and to the single strand gap segment of molecules with the characteristics of/3-gapped circles. Thus, in addition to stabilization of the D-loop structure, P 16 probably functions at all stages of the asymmetrical replication cycle of mtDNA. Further evidence from that study indicated that there were an average of ~49 P16 molecules per mtDNA in the bound population composed predominantly of D-loop DNA.The work presented here describes the isolation of Pl 6 and a protease resistant, DNA...

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