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Mitochondrial Molecular Biology
Daniel Bogenhagen, M.D.
Professor, Pharmacological Sciences
M.D., Stanford University
Postdoctoral, Carnegie Institution of Washington
Department of Embryology
Single-base mutations and deletions in mtDNA contribute to a variety of human diseases and have been documented in a large fraction of cancers. A comprehensive understanding of the replication, repair, and expression of mtDNA is required to explain the pathological effects of these mutations. Since the 17-kB mtDNA genome encodes none of the proteins required for its own replication or transcription, mitochondrial DNA and RNA polymerases, along with a set of transcription and replication factors, must be synthesized as products of nuclear genes and imported into mitochondria. A long-term goal of this laboratory is to understand important features of nuclear-mitochondrial interactions. Our laboratory has purified, studied and, in many cases, cloned, mitochondrial regulatory proteins including both subunits of DNA polymerase g, mtRNA polymerase, mitochondrial transcription factors mtTFA and mtTFB, mtDNA ligase, mitochondrial single stranded DNA binding protein, and topoisomerase.
The small subunit of DNA polymerase g functions as a processivity factor for the large subunit. The large subunit contains the catalytic center of the DNA polymerase and is closely related to DNA pol I of E. coli and to HIV reverse transcriptase. Much of the toxicity of nucleoside inhibitors (eg., AZT, ddC) used in treatment of AIDS is due to inhibition of mitochondrial DNA polymerase. DNA pol g is obviously important for the sort of mutagenesis of mtDNA that is observed in some human diseases. In collaboration with the lab of Dr. Caroline Kisker of this Department, we have recently solved the structure of the small subunit. This protein shows a dramatic similarity to prokaryotic tRNA synthetases, qualifying it as a unique example of a polymerase processivity factor distinct from sliding clamps such as PCNA.
We have shown that DNA pol g works with mtDNA ligase in a classical base excision repair mechanism to permit repair of some types of DNA lesions. Interestingly, many of the proteins involved in base excision repair in mitochondrial are differentially-expressed variant products of genes that also supply repair factors to the nucleus. MtDNA ligase is one example of this “mitochondrial moonlighting” since it is a product of the DNA ligase III gene. We are actively studying the control of expression of these dual-function genes, since misregulation of their expression may lead to increased mutagenesis in mtDNA. Other types of lesions in mtDNA are not subject to base excision repair and appear to persist in mtDNA. We are exploring the possibility that mistakes made by the polymerase in copying damaged DNA may contribute to mutagenesis.
Matsumoto, Y., Kim, K., and Bogenhagen D.F. (1994). Proliferating cell nuclear antigen (PCNA)-dependent abasic site repair in Xenopus laevis oocytes: an alternative pathway of base excision repair. Mol. Cell. Biol. 14. 6187-6197
Antoshechkin, I. and Bogenhagen, D.F. (1995). Distinct roles for two purified factors in transcription of Xenopus mtDNA. Mol. Cell. Biol. 15: 7032-7042.
Pinz, K.G. and Bogenhagen, D.F. (1998). Efficient Repair of Abasic Sites in DNA by Mitochondrial Enzymes. Mol. Cell. Biol. 18: 1257-1265.
Carrodeguas, J.A. , Kobayashi, R., Lim, S. E.,. Copeland, W. C and Bogenhagen, D. F. (1999). The accessory subunit of X. laevis mitochondrial DNA polymerase g increases processivity of the catalytic subunit of human DNA polymerase g and is related to class II aminoacyl-tRNA synthetases. Mol. Cell. Biol. 19: 4039-4046.
Bogenhagen, D.F. (1999). Repair of Mitochondrial DNA. Am. J. Hum. Genet. 64:1276-1281.
Carrodeguas, J.A., Theis, K., Bogenhagen, D.F. and Kisker, C. (2001). Crystal Structure and Deletion Analysis Show that the Accessory Subunit of Mammalian DNA Polymerase g, Pol gB, Functions as a Homodimer. Mol. Cell 7: 43-54.
