Koc

Emine C. Koc, PhD
Associate Professor
koce@marshall.edu

Research Interests

Protein synthesis in mammalian mitochondria

The role of mitochondria in aging, heart disease, diabetes, neurodegenerative disorders, obesity, and cancer is becoming more apparent due to their central role in energy metabolism. In mammals, mitochondria are responsible for providing over 90% of the energy in the form of ATP, which is generated by the process of oxidative phosphorylation (Figure). Mitochondria have their own 16.5 kb circular genome and translation machinery/ribosomes essential for the synthesis of 13 essential proteins of the oxidative phosphorylation (OXPHOS) complexes (Figure). Mammalian mitochondrial ribosome (55S) is composed of ~80 mitochondrial ribosomal proteins (MRPs), about half of which have homologs in bacterial ribosomes. Although many of the maternally-inherited mitochondrial disorders result from mutations in mitochondrial DNA, alterations in expression levels and mutations of MRPs also affect mitochondrial protein synthesis and cell growth. Indeed, there is growing evidence suggesting the involvement of MRPs in various disease states, apoptosis and cancer. Clearly, changes in the expression of MRPs influence mitochondrial metabolism and alter the balance between apoptosis and tumor formation due to the changes in energy production.

Our laboratory has paved the way to study mitochondrial translation by identifying all the protein components of the ribosome and translation initiation factor 3 (mtIF3) in mammalian mitochondria. Recently, we revealed the modification of MRPs by phosphorylation and acetylation at steady-state levels using mass spectrometry-based proteomics. Based on these observations, we postulated that the mitochondrial translation machinery is regulated by post-translational modifications (PTMs) as NAD+ and ATP levels regulate the activities of many other mitochondrial enzymes involved in oxidative phosphorylation (Figure). The location of the phosphorylated ribosomal proteins mainly at the functional regions such as the mRNA- and tRNA-binding paths and L7/L12 stalk of the ribosome is particularly exciting and suggest important functional roles for these modifications in the regulation of translation. Kinase(s) responsible for phosphorylation of the MRPs is currently under investigation in our laboratory. Another novel regulatory mechanism we discovered is the regulation of mitochondrial protein synthesis by reversible acetylation of a ribosomal protein, MRPL10. We have also shown the deacetylation of MRPL10 by a ribosome associated deacetylase, SIRT3, in an NAD+-dependent manner. A member of the sirtuin family of NAD+-dependent deacetylases, SIRT3, is located in mammalian mitochondria and is important for the regulation of mitochondrial metabolism, cell survival and longevity. Thus, specific deacetylation of MRPL10 by SIRT3 may play a pivotal role in coordinating the activity of the mitochondrial protein synthesis machinery with the [NADH]/[NAD+] ratio and regulate oxidative phosphorylation in mammalian mitochondria (Figure). Our current research interests are all integrative and aimed at determining how components of mitochondrial translation/ribosomes affect the oxidative phosphorylation and apoptosis in normal and disease conditions. As we learn more about the regulatory roles of MRPs and their PTMs, new strategies will be devised to manipulate mitochondrial function/dysfunction in metabolic diseases, cancer, and aging. Our multidisciplinary research takes advantage of biochemical, molecular and cell biological, and mass spectrometry-based proteomics technologies in a “systems biology” approach.

Selected Publications

Surovtseva, Y.V., T.E. Shutt, J. Cotney, H. Cimen, S.Y. Chen, E.C. Koc, and G.S, Shadel (2011). Mitochondrial Ribosomal Protein L12 selectively associates with human mitochondrial RNA polymerase to activate transcription. Proc. Natl. Acad. Sci. USA (epub ahead of print).

Han, M-J., H. Cimen, J.L. Miller-Lee, H. Koc, and E.C. Koc (2011). Purification of human mitochondrial ribosomal L7/L12 stalk proteins and reconstitution of functional hybrid ribosomes in Escherichia coli. Protein Expr. Purif. 78(1), 48-54.

Haque, M.E., K.B. Elmore, A. Tripathy, H. Koc, E.C. Koc, and L.L. Spremulli (2010). Properties of the C-terminal tail of human mitochondrial inner membrane protein Oxa1L and its interaction with mammalian mitochondrial ribosomes. J. Biol. Chem. 285(36), 28353-28362.

Koc, E.C., M.E. Haque, and L.L. Spremulli (2010). Current views of the structure of the mammalian mitochondrial ribosome. Isr. J. Chem. 50(1), 45-59.

Han, M-J., D. Chiu, and E.C. Koc (2010). Regulation of mitochondrial ribosomal protein S29 (MRPS29) expression by a 5′-upstream open reading frame. Mitochondrion 10(3), 274-283.

Cimen, H., M-J. Han, Y. Yang, Q. Tong, H. Koc, and E.C. Koc (2010). Regulation of succinate dehydrogenase activity by SIRT3 in mammalian mitochondria. Biochemistry 49(2), 304-311.

Yang, Y., H. Cimen, M-J. Han, T. Shi, J-H Deng, H. Koc, O.M. Palacios, L. Montier, Y. Bai, Q. Tong, and E.C. Koc (2009). NAD+-dependent deacetylase SIRT3 regulates mitochondrial protein synthesis by deacetylation of the ribosomal protein MRPL10. J. Biol. Chem. 285(10), 7417-7429.

Miller, J.L., H. Cimen, H. Koc, and E.C. Koc (2009). Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis. J. Proteome Res. 8(10), 4789-4798.

Soung, G.Y., J.L. Miller, H. Koc, and E.C. Koc (2009). Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes. J. Proteome Res. 8(7), 3390-3402.

Miller, J.L., H. Koc, and E.C. Koc (2008). Identification of phosphorylation sites in mammalian mitochondrial ribosomal protein DAP3. Prot. Science 17, 251-260.

Levin, I., N. Kessler, N. Moor, L. Klipcan, E. Koc, P. Templeton, L. Spremulli, and M. Safro (2007). Purification, crystallization and preliminary X-ray characterization of a human mitochondrial phenylalanyl-tRNA synthetase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63, 761-764.

Sharma, M.R., E.C. Koc, P.P. Datta, T.M. Booth, L.L. Spremulli, and R.K. Agrawal (2003). Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell 115, 97-108.

Koc, E.C. and L.L. Spremulli (2003). RNA-binding proteins of mammalian mitochondria. Mitochondrion 2, 277-291.

Koc, E.C. and L.L. Spremulli (2002). Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs. J. Biol. Chem. 277, 35541-35549.

Koc, E.C., W. Burkhart, K. Blackburn, M.B. Moyer, D.M. Schlatzer, A. Moseley, and L.L. Spremulli (2001). The large subunit of the mammalian mitochondrial ribosome: Analysis of the complement of ribosomal protein present. J. Biol. Chem. 276, 43958-43969.

Koc, E.C., W. Burkhart, K. Blackburn, A. Moseley, and L.L. Spremulli (2001). The small subunit of the mammalian mitochondrial ribosome: Identification of the full complement of ribosomal proteins present. J. Biol. Chem. 276, 19363-19374.

Koc, E.C., A. Ranasinghe, W. Burkhart, K. Blackburn, H. Koc, A. Moseley, and L.L. Spremulli (2001). A new face on apoptosis: Death-associated protein 3 and PDCD9 are mitochondrial ribosomal proteins. FEBS Lett. 492, 166-170.

Koc, E.C., W. Burkhart, K. Blackburn, H. Koc, A. Moseley, and L.L. Spremulli (2001). Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach. Prot. Science 10, 471-481.

Koc, E.C., W. Burkhart, K. Blackburn, A. Moseley, H. Koc, and L.L. Spremulli (2000). A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J. Biol. Chem. 275, 32585-32591.

Koc, E.C., K. Blackburn, W. Burkhart, and L.L. Spremulli (1999). Identification of a mammalian mitochondrial homolog of ribosomal protein S7. Biochem. Biophys. Res. Comm. 266, 141-146.

Koc, E.C., S. Bagga, D.D. Songsted, S.R. Betz, G.D. Kuehn, and G.C. Phillips (1998). Occurence of uncommon polyamines in cultured tissues of maize. In vitro Cell. and Dev. Biol.-Plant 34, 252-255.

Laboratory Personnel

Caroline Hunter – PhD Student