Professor of Genetics
Publications | Research | Faculty
Background:
Thomas D. Fox, a Professor of Genetics, is a member of both the Graduate Field of Genetics and Development and the Graduate Field of Biochemistry, Molecular and Cell Biology. He received his B.S. degree from Cornell University in 1971 and his Ph.D. in Biochemistry and Molecular Biology from Harvard University in 1976. He received a Helen Hay Whitney Foundation Fellowship to do postdoctoral research at the Biocenter in Basel, Switzerland. He became a faculty member in the Department of Biochemistry at the Biocenter before moving to Cornell in 1981. He has received a Dupont Young Faculty Award, a Research Career Development Award from the National Institutes of Health, and the State University of New York Chancellor's Award for Excellence in Teaching. Dr. Fox has served as a member of the National Institutes of Health Biochemistry Study Section, and is an Associate Editor of Molecular Biology of the Cell. He is a member of the Genetics Society of America, the American Society for Microbiology, the American Society for Cell Biology, and the Society for the Study of Amphibians and Reptiles. He has been elected a member of the American Academy of Microbiology, and a Fellow of American Association for the Advancement of Science.
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The mitochondrial genetic systems of eukaryotes have evolved mechanisms for synthesis of small numbers of hydrophobic proteins encoded in mtDNA, insertion of those proteins into the inner membrane, and assembly of those proteins with imported nuclearly encoded subunits into active respiratory complexes. Thus, mitochondrial and nucleo-cytoplasmic gene expression must be coordinated for the synthesis and assembly of the oxidative phosphorylation machinery in the organelles. We exploit the budding yeast Saccharomyces cerevisiae to elucidate mechanisms, many conserved in humans, that control expression and assembly of mitochondrially coded proteins, focusing on the assembly of respiratory complex IV, cytochrome c oxidase. In addition to the well known tools of yeast genetics and molecular biology, our work is facilitated by the ability to modify the mitochondrial genome using genetic transformation and homologous recombination.
Yeast cells expressing GFP from a recoded gene inserted into mitochondrial DNA
Yeast mitochondrial gene expression depends upon mRNA-specific translational activators, encoded in the nucleus, that regulate the levels of protein synthesis and help target mitochondrial gene products to their sites of assembly in the inner membrane. These activator proteins, coded by nuclear genes, are present inside mitochondria, associated with the inner membrane. The activator proteins interact with the mitochondrially encoded 5' untranslated leaders of their target mRNAs, and at least one of them interacts with mitochondrial ribosomes, suggesting that their role is to mediate the binding of ribosomes with their target mRNAs. The synthesis of Cox1, the largest subunit of cytochrome c oxidase, from its mitochondrially coded mRNA is controlled by two activator proteins, Pet309 and Mss51. Mss51 is of particular interest since it interacts with both the COX1 mRNA and with newly synthesized Cox1 protein, and is required for both synthesis and assembly of Cox1. Thus, distinct activities of Mss51 couple Cox1 synthesis to assembly of cytochrome c oxidase in a homeostatic fashion.
Multiple activities of Mss51: 1) Mss51 and Pet309 activate COX1 mRNA through the 5'-UTR. 2) Mss51 interacts with newly synthesized Cox1 and allows completed translation through an unknown mechanism. 3) The assembly factor Cox14 enters a complex nucleated by newly synthesized Cox1 that stabilizes the binding of Mss51 to Cox1. 4) Shy1, a protein conserved in humans, associates with the complex shown in (3) and facilitates dissociation of an early assembly intermediate (5) and 'free' Mss51 (6). Released Mss51 is available to activate another round of COX1 mRNA translation.
Insertion of mitochondrial gene products into the inner membrane is closely tied to their translation. We have focused our studies of membrane insertion on the mitochondrially encoded Cox2 subunit of cytochrome oxidase, which is of particular interest because its substantial hydrophilic N-tail and C-tail domains are exported through the inner membrane to the intermembrane space while the two transmembrane (TM) helices between them are inserted into the membrane. Translocation and insertion of Cox2 domains requires Oxa1 and Cox18, distantly related paralogous translocases that are both related to bacterial YidC. Their functions in the mitochondrial inner membrane are conserved at least to the extent that expression in yeast of cDNAs encoding the human proteins partially complements the corresponding yeast mutations. We are studying the activities of Oxa1 and Cox18 in vivo, together with other proteins required for topogenesis and assembly of Cox2 into cytochrome c oxidase.
Export of the Cox2 N-tail requires Oxa1, while export of the C-tail requires Oxa1, Cox18, Mss2 and Cox20.
Click here to view Dr. Fox's PubMed listings.
Mick, D., T.D. Fox and P. Rehling. 2011. Inventory control: cytochrome oxidase assembly regulates mitochondrial translation. Nat. Rev. Mol. Cell Biol. 12: 14-20.
Shingú-Vázquez, M., Y. Camacho-Villasana, L. Sandoval-Romero, C.A. Butler, T.D. Fox, and X. Pérez-Martínez. 2010. The carboxyl-terminal end of Cox1 is required for feedback-assembly regulation of Cox1 synthesis in Saccharomyces cerevisiae mitochondria. J. Biol. Chem. 285: 34382-34389.
Yogev, O., O. Yogev, M. Goldberg, T.D. Fox, and O. Pines. 2010. Fumarase: A mitochondrial metabolic enzyme and a cytosolic/nuclear component of the DNA damage response. PloS Biology 8 (3): e1000328.
Bonnefoy, N., H.L. Fiumera, G. Dujardin and T.D. Fox. 2009. Roles of Oxa1-related inner membrane translocases in assembly of respiratory chain complexes. Biochim. Biophys. Acta 1793(1):60-70.
Fiumera, H.L., M.J. Dunham, S.A. Saracco, C.A. Butler, J.A. Kelly, and T.D. Fox. 2009. Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1, in the absence of Cox18. Genetics 182: 519-528.
Xochitl Perez-Martinez, X., C.A. Butler, M. Shingu-Vazquez and T.D. Fox. 2009. Dual functions of Mss51 couple synthesis of Cox1 to assembly of cytochrome c oxidase in Saccharomyces cerevisiae mitochondria. Mol. Biol. Cell. 20: 4371-4380
Williams, E.H., N. Bsat, N. Bonnefoy, C.A. Butler and T.D. Fox. 2005. Alteration of a novel dispensable mitochondrial ribosomal small subunit protein, Rsm28p, allows translation of defective COX2 mRNAs. Eukaryot. Cell 4: 337-345.
Fiori, A., X. Perez-Martinez and T.D. Fox. 2005. Overexpression of the COX2 translational activator, Pet111p, prevents translation of COX1 mRNA and cytochrome c oxidase assembly in mitochondria of Saccharomyces cerevisiae. Mol. Microbiol. 56: 1689-1704.
Williams, E.H., X. Perez-Martinez and T.D. Fox. 2004. MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria. Genetics 167: 65-75.
Perez-Martinez, X., S.A. Broadley and T.D. Fox. 2003. Mss51p promotes mitochondrial Cox1p synthesis and interacts with newly synthesized Cox1p. EMBO J. 22:5951-5961
Demlow, C.M., and Fox, T.D. (2003). Activity of mitochondrially synthesized reporter proteins is lower than imported proteins, and is increased by lowering cAMP in glucose-grown Saccharomyces cerevisiae cells. Genetics 165, 961-974.
Fiori, A., T.L. Mason and T.D. Fox. 2003. Evidence that synthesis of the Saccharomyces cerevisiae mitochondrially-encoded ribosomal protein Var1p may be membrane localized. Eukaryot. Cell 2: 651-653.
Williams, E.H. and T.D. Fox. 2003. Antagonistic Signals within the COX2 mRNA Coding Sequence Control Its Translation in Saccharomyces cerevisiae Mitochondria. RNA 9: 419-431.
Naithani, S., Saracco, S.A., Butler, C.A. and T.D. Fox. 2003. Interactions among COX1 , COX2 and COX3 mRNA-specific translational activator proteins on the inner surface of the mitochondrial inner membrane of Saccharomyces cerevisiae. Mol. Biol. Cell 14: 324-333.
Saracco, S.A. and T.D. Fox. 2002. Cox18p is required for export of the mitochondrially encoded Saccharomyces cerevisiae Cox2p C-tail, and interacts with Pnt1p and Mss2p in the inner membrane. Mol. Biol. Cell 13: 1122-1131.
Broadley, S.A., C.M. Demlow and T.D. Fox. 2001. A peripheral mitochondrial inner membrane protein, Mss2p, required for export of the mitochondrially coded Cox2p C-tail in Saccharomyces cerevisiae . Mol. Cell. Biol. 21: 7663-7672.
Kolesnikova, O.A., Entelis, N.S., Mireau, H., Fox, T.D., Martin, R.P., and Tarassov, I.A. (2000). Suppression of mutations in mitochondrial DNA by tRNAs imported from the cytoplasm. Science 289, 1931-1933.
Highly diverged homologs of Saccharomyces cerevisiae mitochondrial mRNA-specific translational activators have orthologous functions in other budding yeasts. Genetics 154: 999-1012 (2000). With M.C. Costanzo, N. Bonnefoy, E. H. Williams and G. D. Clark-Walker.
Accumulation of mitochondrially synthesized Saccharomyces cerevisiae Cox2p and Cox3p depends on targeting information in untranslated portions of their mRNAs. EMBO J. 17: 5796-5804 1998). With M.E. Sanchirico and T.L. Mason.