David J. Pagliarini
Biochemistry and Systems Biology of Mitochondrial Disorders
Mitochondria are complex and dynamic organelles that are essential to the survival of nearly every eukaryotic cell. The approximately ten million billion mitochondria throughout our bodies produce the bulk of our chemical energy in the form of ATP, and are the cellular home to a vast array of metabolic pathways and processes. Dysfunction of these organelles underlies more than 150 inborn errors of metabolism, and strongly contributes to a growing list of common metabolic and neurodegenerative disorders including type II diabetes, Parkinson's disease, Alzheimer's disease, and various forms of cancer.
Despite this central role for mitochondria in human health and disease, much of the basic biology of these organelles remains obscure. By blending classic biochemistry, molecular & cellular biology, and bioenergetics with large-scale proteomics and systems approaches, our lab aims to systematically annotate the functions of uncharacterized mitochondrial proteins (MXPs) and to establish the detailed mechanisms that drive essential mitochondrial pathways.
Orphan mitochondrial proteins
Recently, we led an integrative effort to generate a catalog of the mammalian mitochondrial proteome””termed MitoCarta””that has advanced our understanding of basic mitochondrial biology and has catalyzed the discovery of gene mutations that underlie mitochondrial diseases. However, strikingly, nearly one-quarter of the mammalian mitochondrial proteome has no established biochemical function. As such, elucidation of these functions has become a major bottleneck in understanding mitochondrial function and pathophysiology. To address this, we are now leveraging robust computation- and mass spectrometry-based platforms for systematically characterizing ~100 of these orphan proteins, and are employing rigorous molecular and structural biology methods to establish the specific functions of select proteins at biochemical depth.
Coenzyme Q biosynthesis
Coenzyme Q (CoQ) is a requisite component of the mitochondrial oxidative phosphorylation machinery””discovered at UW-Madison more that 50 years ago””whose deficiency is associated with multiple human diseases. Recent studies have identified nine of the proteins (COQ1-9) that are required for CoQ biosynthesis, most of which catalyze chemical modifications to CoQ precursors. However, two main obstacles have precluded a more comprehensive understanding of this key pathway: 1) COQ4, COQ8 and COQ9 are MXPs with no clear biochemical functions, and 2) at multiple steps in the CoQ pathway are likely fulfilled by yet-to-be-identified proteins. We are integrating various biochemical, genetic and structural biology approaches to further elucidate the steps of this essential pathway.
Our studies have revealed that mitochondria are replete with proteins harboring post-translational modifications (PTMs) whose abundances change significantly under contrasting biological states. These data have led us to hypothesize that these PTMs are widely important in regulating mitochondrial metabolism, and that aberrant levels of these modifications are among the relevant alterations underlying mitochondrial pathophysiology. To further develop these concepts, we are now elucidating how these PTMs affect the activities of select mitochondrial proteins and are characterizing enzymes in mitochondria that regulate PTM abundance.