Evolutionary Genomic Responses to Mitochondrial Dysfunction in Caenorhabditis elegans Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/bv73c322r

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  • Understanding the impact of mitochondrial dysfunction on genome evolution has the potential not only to provide new insights on the basic evolutionary processes influencing mitochondrial and nuclear genomes, but may also reveal novel avenues for evolutionary adaptive recovery from harmful mutations. Aberrant mitochondrial activity is fundamental to the pathology of mitochondrial diseases in addition to neurodegenerative disorders. While the effects of mitochondrial dysfunction have received much attention, less is known about their impact on genome evolution and potential target mechanisms for ameliorating the harmful effects of mitochondrial impairment. Characterizing genome modifications in animal populations predisposed to mitochondrial dysfunction may identify novel genes, mechanisms, and physiological pathways to target for recovery and provides a genome-wide perspective on the impact of aberrant mitochondrial activity. This dissertation research investigates how mitochondrial and nuclear genomes evolve in organisms genetically predisposed to mitochondrial dysfunction and contrasts genomic evolution in large and small population sizes. This work furthers understanding of the impact of evolutionary forces which influence genome evolution in population with reduced fitness, and reveals new insights into genomic responses to mitochondrial dysfunction. Chapters 2 and 3 of this dissertation focus on genome evolution using a set of mitochondrial respiratory chain mutant (gas-1¬ strain) and wild-type (N2 strain) Caenorhabditis elegans mutation-accumulation (MA) lines that experienced single-worm bottlenecking. The N2 MA lines, derived from a previous experiment, were bottlenecked for 250 generations. The gas-1 MA lines were created for this research, and bottlenecked in the laboratory for a maximum of 50 generations. Chapter 2 investigates mitogenomic evolution and heteroplasmic inheritance patterns evolving under extreme drift in gas-1 and N2 MA lines. Chapter 3 analyzes nuclear genome evolution using this same set of gas-1 and N2 MA lines. In contrast, Chapter 4 provides a complementary perspective, analyzing mitochondrial and nuclear genome evolution in twenty-four gas-1 'recovery line' (RC) populations, evolved in large population sizes for sixty generations. Bioinformatic methods and computational simulations were applied to characterize and evaluate genome evolution and provide a comprehensive investigation of the impact of mitochondrial dysfunction within a population genetics framework. In Chapter 2 our results of inherited mitochondrial DNA (mtDNA) heteroplasmy are in alignment with predictions of theories where a small subset of mtDNA molecules from the parental generation repopulates the mitochondrial genome pool for the progeny. Comparisons between Chapter 2 and 4 suggest that in both gas-1 and N2 strains organelle genome copy number is elevated in an environment characterized with extreme genetic drift but is less impacted throughout evolution in large populations when the force of genetic drift is reduced. Investigation of nuclear genome evolution in Chapter 3 revealed putative beneficial nuclear mutations in bottlenecked gas-1 populations. Additionally, compared to the N2 MA lines, the gas-1 MA lines were also observed to have a greater number of mutations located within the gas-1 gene interaction network. These observations reveal new insights into the potential fitness landscape for beneficial mutation and how nuclear genome evolution differs when predisposed to mitochondrial dysfunction in an environment characterized by extreme genetic drift. In Chapter 4, focusing on evolution in large populations, we observed parallel and potentially compensatory mitochondrial mutations indicative of positive selection in the gas-1 RC lines. Identified at heteroplasmy levels near-fixation, these mtDNA mutations were located in genes predicted to physically interact with the gas-1 gene. As signatures of positive selection were not detected in the mitochondrial genomes of gas-1 MA lines analyzed in Chapter 2, this work suggests that the processes by which beneficial mtDNA mutations rise to homoplasmy within the population may be less likely to occur in small populations. Additionally, we determined the evolutionary rate of nuclear genome change in Chapter 4 to be three times slower than published mutations rate values for C. elegans suggesting the influence of purifying selection in RC lines. Given that a quarter of nuclear mutations were located in genes exhibiting interactions within two-degrees of gas-1 it is likely that positive selection also influenced nuclear genome evolution. Overall, this research demonstrates that although adaptation from harmful mutation may occur in small or large populations, the observed paths to evolutionary adaptive recovery involve different mechanisms and suggests that although an environment with pervasive genetic drift may permit the fixation of beneficial nuclear mutations, the processes by which beneficial mtDNA mutations rise to homoplasmy within the population may be less permissive.
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