Faculty / Research
Miguel Garcia-Diaz, PhDAssistant Professor
Consortium for Inter-Disciplinary Environmental Research
Nucleic acids are constantly subject to endogenous and environmental insults. The resulting DNA damage may be encountered by the protein machinery of several fundamental cellular processing pathways, including replication, transcription and DNA repair. These events can potentially lead to mutagenesis, which underlies the etiology of sporadic diseases such as cancer. In addition, subtle defects in the protein machinery that synthesizes and processes nucleic acids can be inherited and are the cause of a large number of genetic pathologies with a broad spectrum of symptoms, ranging from mental retardation to light sensitivity. Our laboratory utilizes a combination of structural (mainly x-ray crystallography), biochemical and genetic approaches to understand the molecular details of different nucleic acid processing pathways. This information is then used to characterize how these pathways are affected by DNA damage and other environmental exposures, and ultimately to understand how alterations in normal nucleic acid biology can result in human disease.
Transcriptional fidelity and mitochondrial transcription
The human mitochondria contains its own small circular genome, encoding some of the proteins of the respiratory chain as well as mitochondrial tRNAs and rRNAs. Appropriate expression of these RNAs and proteins is essential for normal cellular physiology, as manifested by the numerous mitochondrial diseases that originate as a consequence of defects in the mitochondrial genome. Some of these diseases are a consequence of mutations in the nuclear-encoded proteins responsible for replication and expression of the mitochondrial DNA.
We are interested in understanding how the mitochondrial transcription system is regulated, characterize the protein-protein and protein-nucleic acid interactions that are necessary for transcription, and understand the interactions between the transcription and replication machinery. We are also interested in understanding how the fidelity of the transcription process can determine cellular physiology, in particular in the context of the oxidative environment of the mitochondria.
Nuclear DNA replication - DNA synthesis
The nuclear replication process in humans is extremely complex and only partially understood. The accuracy of this process is essential to avoid deleterious mutagenesis. The proteins mainly responsible for this accuracy are DNA polymerases, the enzymes responsible for DNA synthesis. There are at least 15 different DNA polymerases in human cells, and except for a few their functions are largely unknown. Structural analysis of DNA polymerases has made a significant contribution to our understanding of DNA polymerase fidelity and substrate specificity, and this information is precious to understand their biological function.
We are particularly interested in the proteins that initiate human DNA replication, as well as in DNA polymerases responsible for smaller patches of DNA synthesis that mainly take place during DNA repair. We are studying how these enzymes contribute to genome stability, in particular in response to DNA damage, and how their function can be affected by different environmental exposures.
Garcia-Diaz, M, Bebenek, K, Pedersen, L, Kunkel, T. (2007) Role of the catalytic metals during polymerization by DNA polymerase lambda. DNA Repair 6, 1333-1340
Moon A.F., Garcia-Diaz, M., Bebenek, K., Davis, B.J., Zhong, X., Ramsden, D.A., Kunkel, T.A., Pedersen, L. (2007) Structural insight into the substrate specificity of DNA Polymerase mu. Nat. Struct. Mol. Biol. 14, 45-53.
Garcia-Diaz, M., Kunkel, T.A. (2006) Mechanism of a genetic glissando: structural biology of indel mutations. Trends in Biochem. Sci. 31, 206-214
Garcia-Diaz, M., Benenek, K., Krahn, J.M., Pedersen, L.C. and Kunkel, T.A. (2006) Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase. Cell 124, 331-342
Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Kunkel, T.A., Pedersen, L.C. (2005) A closed conformation for the Pol lambda catalytic cycle. Nat. Struct. Mol. Biol. 12, 97-98
Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Blanco, L., Kunkel, T.A., Pedersen, L.C. (2004) A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology. Mol. Cell 13, 561-572
Bebenek, K., Garcia-Diaz, M., Blanco, L., Kunkel. T.A. (2003) The frameshift infidelity of human DNA polymerase lambda. J. Biol. Chem. 278, 34685-34690
García-Díaz, M., Bebenek, K., Sabariegos, R., Dominguez, O., Rodriguez, J., Kirchhoff, T., Garcia-Palomero, E., Picher, A.J., Juarez, R., Ruiz, J.F., Kunkel, T.A., Blanco, L. (2002) DNA polymerase lambda, a novel DNA repair enzyme in human cells. J. Biol. Chem. 277, (13184-13191)
García-Díaz, M., Bebenek, K., Kunkel, T., Blanco, L. (2001) Identification of an intrinsic dRP lyase activity in human DNA polymerase lambda: a possible role in base excision repair. J Biol Chem 276, (34659-34663)