Skip to main content

Functional Analysis of Mutant Mitochondrial DNA Polymerase Proteins Involved in Human Disease

  • Protocol
Mitochondrial DNA

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 554))

Abstract

DNA polymerase γ (pol γ) is the only DNA polymerase within the mitochondrion and is thus essential for replication and repair of mtDNA. POLG, the gene encoding the catalytic subunit of pol γ, is a major locus for a wide spectrum of mitochondrial diseases with more than 100 known disease mutations. Thus, we need to understand how and why pol γ defects lead to disease. By using an extensive array of methods, we are developing a clearer understanding of how defects in pol γ contribute to disease. Furthermore, crucial knowledge concerning the role of pol γ in mtDNA replication and repair can be acquired. Here we present the protocols to characterize mutant DNA pol γ proteins, namely, assays for processive DNA synthesis, exonuclease activity, DNA binding, subunit interaction, and protein stability.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Naviaux, R. K. (2004). Developing a systematic approach to the diagnosis and classification of mitochondrial disease. Mitochondrion 4, 351–361.

    Article  CAS  PubMed  Google Scholar 

  2. Dimauro, S. and Davidzon, G. (2005). Mitochondrial DNA and disease. Ann Med 37, 222–32.

    Article  CAS  PubMed  Google Scholar 

  3. Yakubovshaya, E., Chen, Z., Carrodeguas, J. A., Kisker, C. and Bogenhagen, D. F. (2006). Functional human mitochondrial DNA polymerase γ forms a heterotrimer. J Biol Chem 281, 374–382.

    Article  Google Scholar 

  4. Graziewicz, M. A., Longley, M. J. and Copeland, W. C. (2006). DNA polymerase gamma in Mitochondrial DNA Replication and Repair. Chem Rev 106, 383–405.

    Article  CAS  PubMed  Google Scholar 

  5. Longley, M. J., Clark, S., Yu Wai Man, C., Hudson, G., Durham, S. E., Taylor, R. W., Nightingale, S., Turnbull, D. M., Copeland, W. C. and Chinnery, P. F. (2006). Mutant POLG2 Disrupts DNA Polymerase γ Subunits and Causes Progressive External Ophthalmoplegia. Am J Hum Genet 78, 1026–34.

    Article  CAS  PubMed  Google Scholar 

  6. Longley, M. J., Ropp, P. A., Lim, S. E. and Copeland, W. C. (1998). Characterization of the native and recombinant catalytic subunit of human DNA polymerase γ: identification of residues critical for exonuclease activity and dideoxynucleotide sensitivity. Biochemistry 37, 10529–39.

    Article  CAS  PubMed  Google Scholar 

  7. Ponamarev, M. V., Longley, M. J., Nguyen, D., Kunkel, T. A. and Copeland, W. C. (2002). Active Site Mutation in DNA Polymerase γ Associated with Progressive External Ophthalmoplegia Causes Error-prone DNA Synthesis. J Biol Chem 277, 15225–8.

    Article  CAS  PubMed  Google Scholar 

  8. Graziewicz, M. A., Longley, M. J., Bienstock, R. J., Zeviani, M. and Copeland, W. C. (2004). Structure-function defects of human mitochondrial DNA polymerase in autosomal dominant progressive external ophthalmoplegia. Nat Struct Mol Biol 11, 770–6.

    Article  CAS  PubMed  Google Scholar 

  9. Chan, S. S. L., Longley, M. J., Naviaux, R. K. and Copeland, W. C. (2005). Mono-allelic POLG expression resulting from nonsense-mediated decay and alternative splicing in a patient with Alpers syndrome. DNA Repair 4, 1381–9.

    Article  CAS  PubMed  Google Scholar 

  10. Luoma, P. T., Luo, N., Loscher, W. N., Farr, C. L., Horvath, R., Wanschitz, J., Kiechl, S., Kaguni, L. S. and Suomalainen, A. (2005). Functional defects due to spacer-region mutations of human mitochondrial DNA polymerase in a family with an ataxia-myopathy syndrome. Hum Mol Genet 14, 1907–20.

    Article  CAS  PubMed  Google Scholar 

  11. Chan, S. S. L., Longley, M. J. and Copeland, W. C. (2005). The common A467T mutation in the human mitochondrial DNA polymerase (POLG) compromises catalytic efficiency and interaction with the accessory subunit. J Biol Chem 280, 31341–6.

    Article  CAS  PubMed  Google Scholar 

  12. Chan, S. S. L., Longley, M. J. and Copeland, W. C. (2006). Modulation of the W748S mutation in DNA polymerase γ by the E1143G polymorphism in mitochondrial disorders. Hum Mol Genet 15, 3473–83.

    Article  CAS  PubMed  Google Scholar 

  13. Yamanaka, H., Gatanaga, H., Kosalaraksa, P., Matsuoka-Aizawa, S., Takahashi, T., Kimura, S. and Oka, S. (2007). Novel Mutation of Human DNA Polymerase γ Associated with Mitochondrial Toxicity Induced by Anti-HIV Treatment. J Infect Dis 195, 1419–25.

    Article  CAS  PubMed  Google Scholar 

  14. Lim, S. E. and Copeland, W. C. (2001). Differential incorporation and removal of antiviral deoxynucleotides by human DNA polymerase γ. J Biol Chem 276, 23616–23.

    Article  CAS  PubMed  Google Scholar 

  15. Longley, M. J. and Copeland, W. C. (2002). Purification, separation and identification of the catalytic and accessory subunits of the human mitochondrial DNA polymerase. In Mitochondrial DNA: Methods and Protocols (Copeland, W. C., ed.), Vol. 197, pp. 245–258. Humana Press, Totowa, New Jersey.

    Google Scholar 

  16. Lim, S. E., Longley, M. J. and Copeland, W. C. (1999). The mitochondrial p55 accessory subunit of human DNA polymerase γ enhances DNA binding, promotes processive DNA synthesis, and confers N-ethylmaleimide resistance. J Biol Chem 274, 38197–203.

    Article  CAS  PubMed  Google Scholar 

  17. Lim, S. E., Ponamarev, M. V., Longley, M. J. and Copeland, W. C. (2003). Structural Determinants in Human DNA Polymerase γ Account for Mitochondrial Toxicity from Nucleoside Analogs. J Mol Biol 329, 45–57.

    Article  CAS  PubMed  Google Scholar 

  18. DeRose, E. F., Kirby, T. W., Mueller, G. A., Bebenek, K., Garcia-Diaz, M., Blanco, L., Kunkel, T. A. and London, R. E. (2003). Solution structure of the lyase domain of human DNA polymerase λ. Biochemistry 42, 9564–74.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Chan, S.S.L., Copeland, W.C. (2009). Functional Analysis of Mutant Mitochondrial DNA Polymerase Proteins Involved in Human Disease. In: Stuart, J.A. (eds) Mitochondrial DNA. Methods in Molecular Biology™, vol 554. Humana Press. https://doi.org/10.1007/978-1-59745-521-3_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-521-3_4

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-934115-60-2

  • Online ISBN: 978-1-59745-521-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics