I. Understand the selection forces that determine the evolution and spread of mutant mitochondrial genomes in populations
Biology is hierarchically organized. Genomes reside within cells, cells within organisms, and organisms within groups. Cooperation between units at each level is necessary for the proper functioning of collectives at increasing levels of complexity. However, such cooperation is challenged by cheaters, which reap the benefits from the collective without incurring the costs of contribution. Patel lab applies the concepts of cooperation and cheating to mitochondrial genomes, given that they are organized in a hierarchical fashion, and consequently subject to selection at multiple levels. This unique evolutionary approach provides a powerful framework to determine the principles that govern transmission of pathogenic mitochondrial genome mutations from one generation to the next, which is crucial for understanding inheritance of mitochondrial diseases.
Because cells contain multiple non-recombining and independently replicating mitochondrial genomes, wildtype and mutant genomes can coexist together in a state of heteroplasmy. Wildtype genomes can be viewed as cooperators that produce energy for the collective good of the cell, whereas mutant genomes can be considered cheaters that reap the benefit of being replicated without making functional contributions. Viewed from this perspective, the fundamental challenge is to understand 1) how selection operates at multiple levels of the biological hierarchy to shape the evolution and spread of mutant mitochondrial genomes, and 2) how these selection forces are affected by changes in the environment. We employ evolutionary and molecular biology approaches to address these questions.
II. Determine the mechanisms that lead to different levels of mutant mitochondrial genomes between cell types
Although all pathogenic mitochondrial genome mutations ultimately impact the same biochemical process of oxidative phosphorylation, one of the most striking aspects of the mitochondrial genome disorders is their extreme heterogeneity. The cellular principles that underlie this phenotypic heterogeneity are not well understood. While environment and genetic variation likely contribute, a broader biological framework is needed to fully explain this heterogeneity. We hypothesize that this phenotypic diversity is the product of the cellular heterogeneity in mitochondrial genome mutant levels. This heterogeneity can result from differential inheritance of mutant mitochondrial genome levels during embryogenesis. Alternatively, given that mitochondrial genomes replicate independent of the cell cycle, cell type specific differences in the rate of mitochondrial genome turnover can also lead to this cellular heterogeneity. The Patel lab has developed a pipeline to measure cell type specific heterogeneity in mutant mitochondrial genome levels and to decipher the underlying molecular mechanisms.
III. Understand how cells control mitochondrial genome copy number
Appropriate regulation of mitochondrial genome copy number in the female germline is crucial to ensure deposition of sufficient mitochondrial genome levels in the embryo. Control of mitochondrial genome copy number is also likely to play an important role in regulating mutant mitochondrial genome levels. The importance of mitochondrial genome copy number regulation is further highlighted by mitochondrial genome depletion syndromes; a collection of devastating disorders defined by insufficient mitochondrial genome levels. However, the molecular basis of mitochondrial genome copy number control remains elusive. Excitingly, the Patel Lab has discovered the existence of mitochondrial genome copy number control in C. elegans. Furthermore, consistent with the data from skeletal muscles of heteroplasmic patients, our data suggest that heteroplasmic mutant mitochondrial genomes exploit copy number control to hitchhike to high levels. Our discovery provides us with a unique opportunity to determine the molecular basis of mitochondrial genome copy number control, and its role in regulation of mutant mitochondrial genome levels.
IV. Characterize cellular response to defects in mitochondrial RNA processing
Due to its compact organization, the mitochondrial genome is transcribed as a single, contiguous polycistronic transcript. This polycistron is then cleaved and processed into individual transcripts. Failure of mitochondrial RNA processing is a major source of mitochondrial diseases. While many of the nuclear-encoded proteins required for mitochondrial transcription and subsequent RNA processing are known, the mechanisms that maintain mitochondrial RNA homeostasis are poorly understood. The knowledge of how cells maintain mitochondrial RNA homeostasis in the face of perturbations is crucial to gain insights into diseases that are caused by defects in RNA processing. The Patel Lab is characterizing a novel cellular response, which they have discovered is elicited by improper mitochondrial RNA processing.