| The human oxidative phosphorylation (OxPhos) system consists of 89 proteins encoded by nuclear and mitochondrial genomes and serves as the primary cellular pathway for ATP biosynthesis. While the core protein machinery for OxPhos is well characterized, many of its assembly, maturation, and regulatory factors remain unknown. In this dissertation I describe the application of computational and genetic methods to predict and validate novel regulators of OxPhos. I first describe a new computational method, Expression Screening, which integrates information from thousands of microarray data sets in a principled manner to identify genes that are consistently co-expressed with the core OxPhos machinery across biological contexts. One novel candidate resulting from this analysis, SLIRP, plays an essential role in maintaining mitochondrial mRNA transcripts that encode OxPhos protein subunits. We next applied similar genome-wide co-expression analyses in conjunction with phylogenetic profiling to identify putative modulators of mitochondrial calcium uptake, a process known to regulate the activity of OxPhos, but whose molecular players have not been identified. From these analyses we identify PRANA, a protein whose biochemical, genetic and pharmacological behavior is consistent with it forming a component of the mitochondrial calcium uniporter. Finally, I present a large-scale mitochondria-wide genetic screen to identify regulators of mitochondrial DNA copy-number, providing the first genetic screen in mammals for this important phenotype. Taken together, our computational and experimental findings provide a catalogue of both potential and validated OxPhos regulators that advance our understanding of cellular respiration. |
