Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009.Cataloged from PDF version of thesis.Includes bibliographical references.In title on title page, the word "Mitochondrial" is spelled "Mitochondial."Mitochondria are cellular compartments that perform essential roles in energy metabolism, ion homeostasis, and apoptosis. Mitochondrial dysfunction causes disease in 1 in 5,000 live births and also has been associated with aging, neurodegeneration, cancer, and diabetes. To systematically explore the function of mitochondria in health and in disease, it is necessary to identify all of the proteins resident in this organelle and to understand how they integrate into pathways. However, traditional molecular and biochemistry methods have identified only half of the estimated 1200 mitochondrial proteins, including the 13 encoded by the tiny mitochondrial genome. Now, newly available genomic technologies make it possible to identify the remainder and explore their roles in cellular pathways and disease. Toward this goal, we performed mass spectrometry, GFP tagging, and machine learning on multiple genomic datasets to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. We linked poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. We additionally used our matched mRNA and protein measurements to demonstrate a widespread role of upstream open reading frames (uORFs) in blunting translation of mitochondrial and other cellular proteins. Next we used the mitochondrial protein inventory to identify genes underlying inherited diseases of mitochondrial dysfunction. In collaboration with clinicians, we identified causal mutations in five genes underlying diseases including hepatocerebral mtDNA depletion syndrome, autosomal dominant mitochondrial myopathy, and several forms of inherited complex I deficiency. These discoveries have enabled the development of diagnostic tests now widely available. More broadly, the mitochondrial compendium provides a foundation for systematically exploring the organelle's contribution to both basic cellular biology and human disease.by Sarah E. Calvo.Ph.D
