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Emine KocAssistant Professor of Biochemistry and Molecular Biology 103 Althouse Laboratory, University Park, PA 16802 B.S. in Chemistry & Biochemistry, Ege University, Turkey |
Investigation of Mammalian Mitochondrial Ribosomes
Background
Over 90 % of the energy used by mammalian cells is generated in mitochondria through the process of oxidative phosphorylation. Mitochondria not only play a key role in cellular metabolism but also play a critical part in cell death signaling pathways and numerous disease states (Alzheimer's and Parkinson's diseases, osteoarthritis, type 2 diabetes mellitus, and cancer). Mitochondria contain their own DNA which in mammals is about 16,000 base pairs in length. The formation of the membrane complexes essential for respiration requires the expression of numerous genes. Most of these genes are located in the nucleus. However, 13 proteins of the respiratory complex and the ATP synthase are the products of genes present in the mitochondrial DNA. The synthesis of these proteins is carried out by a specific protein synthesizing system called “mitochondrial translational machinery” within this organelle (see figure).
Our research interests consist of three distinct but complementary approaches to investigate the mitochondrial translation machinery, especially the mitochondrial ribosomes, in protein synthesis, apoptosis and various disease states of the mitochondria.
Structural Studies of Mitochondrial Ribosomes
We have recently identified all the protein components, ~80 proteins, of the mitochondrial ribosome using proteomics approaches. Almost half of these mitochondrial ribosomal proteins have homologs in prokaryotic ribosomes, and these homologous proteins, similar to their counterparts, are important for the protein synthesis in mitochondria. The remaining half of the proteins present in mitochondrial ribosomes fall into new classes of ribosomal proteins whose functions and locations remain to be discovered.
Using a combination of molecular biological and biochemical methods with “state-of -the-art” proteomics techniques, we are investigating post-translational modifications, protein-protein interactions, and protein-RNA interactions focusing on the mammalian mitochondrial ribosomes. These studies will provide a better understanding of the mitochondrial translational machinery and may allow us to design more specific antibiotics against bacterial infections.
Role of Mitochondrial Ribosomes in Apoptosis
Two of the new classes of mitochondrial ribosomal proteins, the death associated protein 3 (DAP3) and the programmed cell death 9 protein (PDCD9), are proapoptotic proteins of unknown function. Their precise role in the induction of cell death is not known. However, these two proapoptotic proteins and/or mitochondrial ribosomes might be one of the major players in cellular apoptotic signaling pathways (See figure. Adapted from: Wallace, DC. Am. J. Med. Genet. 2001;106 (1):71-93). We are interested in examining the possible interaction of mitochondrial ribosomes and/or mitochondrial ribosomal proteins, DAP3 and PDCD9, with inner membrane components in TNF-α and FAS-induced cell death. Furthermore, possible modification of DAP3 and PDCD9 will be examined using proteomics approache in cells undergoing apoptosis.
Mitochondrial Ribosomes in Disease States
Tissues such as brain, muscle and heart have high levels of mitochondria, which results in vulnerability of these tissues to mitochondrial dysfunction. Alterations in mitochondria are observed in more than 100 different human diseases such as Alzheimer's and Parkinson's diseases, various myopathies, ophthalmoplegia, cardiomyopathy, lactic acidosis, diabetes, stroke, and deafness. Many of these pathological conditions are known to be caused by mutations in mitochondrial DNA. It has also been proposed that splice-variants, mutations and aberrant expression of proteins required for mitochondrial RNA processing and protein synthesis may also be involved in mitochondrial diseases. In fact, recent advancements in the characterization of the protein components of the mammalian mitochondrial proteins have begun to reveal involvements of some of these ribosomal proteins in various diseases. We are going to focus our studies on modifications and changes in expression of mitochondrial ribosomes in various disease states and cancer to develop protein biomarkers.
Representative Publications:
- “Cryo-EM Structure of the mitochondrial 55S ribosome.” Sharma, MR, Koc EC, Datta, PP, Booth T, Silasagaram, A,. Spremulli, LL, and Agrawal, RK. In preparation.
- “RNA-Binding Proteins of Mammalian Mitochondria.” Koc, EC and Spremulli, LL. (2003) Mitochondrion 2(4):277-291.
- “Identification of mammalian mitochondrial translational initiation factor 3 and role in initiation complex formation with natural mRNAs.” Koc, EC and Spremulli, LL. (2002) J. Biol. Chem. 277(38):35541-9.
- “The large subunit of the mammalian mitochondrial ribosome: Analysis of the complement of ribosomal proteins present.” Koc EC, Burkhart W, Blackburn K, Moyer MB, Schlatzer DM, Moseley A, Spremulli LL.(2001) J. Biol. Chem. 276(47):43958-69.
- “The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present.” Cavdar Koc E, Burkhart W, Blackburn K, Moseley A, Spremulli LL. (2001) J. Biol. Chem. 276(22):19363-74.
- “A new face on apoptosis: death-associated protein 3 and PDCD9 are mitochondrial ribosomal proteins.” Cavdar Koc E, Ranasinghe A, Burkhart W, Blackburn K, Koc H, Moseley A, Spremulli LL. (2001) FEBS Lett. 492(1-2):166-70.
- “A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins.” Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL. (2000) J. Biol. Chem. 275(42):32585-91.