Genomic and proteomic approaches to understanding mitochondrial diversity in eukaryotic microbes

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Mitochondria are eukaryotic subcellular structures that originated from the integration of a bacterial endosymbiont into an archaeal host. Though they retain a relic genome, almost all proteins that function within mitochondria including proteins involved in key processes like energy conversion and programmed cell death are encoded in the nuclear genome. It is therefore necessary to systematically identify nucleus-encoded mitochondrial proteins in order to fully understand mitochondrial function and evolution. Mitochondrial proteome studies have been carried out in animals, plants, and fungi; however, such a narrow phylogenetic focus on multicellular organisms biases evolutionary interpretations. It is therefore imperative to characterize mitochondria from a broad sampling of eukaryotic microbes (protists), because they make up the bulk of genetic diversity within Eukarya. A small number of protist mitochondria have been intensively studied, revealing considerable metabolic variation between different lineages, and many novel, functionally unannotated proteins. As a result, much remains to be learned about: 1) the diversity of mitochondrial metabolism in protists, especially uncultured groups whose genomes are completely unexplored, and 2) the functions of protist mitochondrial proteins whose functions are not understood due to the scarcity of genetic tools necessary to dissect their function. Our research aim is to address these two problems. 1) Mitochondrial diversity: To expand our understanding of mitochondrial functional versatility, we will use single-cell genomics and transcriptomics to predict mitochondrial proteins in Foraminifera, an abundant group of marine heterotrophs that are notoriously difficult to culture. This work will examine how mitochondria from cells living in oxygenated and anoxic sediments differ, providing important clues to how mitochondria evolve to function in low oxygen. This is an important topic given recent global increases in oceanic oxygen minimum zones. 2) Mitochondrial function: My group will also employ the model amoebozoan, Dictyostelium discoideum, as a tool to investigate mitochondrial evolution and function in protists. By taking advantage of Dictyostelium's ease of cultivation, genetic toolkit, and complex life cycle including unicellular and multicellular stages we will use proteomics, along with comparative and functional genomics, to reconstruct mitochondrial ancestral states, elucidate the role that mitochondria play in the transition from unicellularity to multicellularity, and interrogate the functions of novel mitochondrial proteins. This work will be important to evolutionary biologists interested in tracing how genome evolution affects the composition of mitochondria, and to functional biologists interested in establishing putative functions for proteins that are either not present in model systems, or those whose function is obscured by the complex biology of multicellular systems.