Mitochondrial Genome Variation And Its Influence On Mitochondrial And Nuclear Mutation

Duong Nguyen, Wayne State University






August 2018

Advisor: Dr. Weilong Hao

Major: Biological Sciences

Degree: Master of Science

Mitochondria are responsible to produce ATP for most cellular functions that are necessary survival, growth and replication. Loss of mitochondrial DNA (mtDNA) can impair the stability of the nuclear genome and lead to aging, genetic disorder, and human disease. Genes encoded by mtDNA also have tight interactions with the nuclear genome in order to maintain efficient mitochondrial function and cell survival. Replacement of mtDNA may interfere the coordination between the mitochondrial and nuclear genomes. Despite the important functional consequences of mtDNA depletion and replacement at the cellular level, their genome-wide inheritable mutagenic consequences are still largely unknown. Furthermore, mitochondrial genomes are remarkably diverse in genome size and organization, but the origins of dynamic mitochondrial genomes architectures and variations are still poorly understood. Mutation and recombination are main sources of genetic variation. Spontaneous mutations are caused by DNA replication error, mismatch repair failure, and other factors such as oxidative damage, DNA methylation. Recombination contributes to genetic variation by breaking-down linkage disequilibrium and facilitating selection. To better understand the evolution of genetic variation, it is crucial to comprehensively understand the processes involving mutation accumulation and recombination. Yeast is an advance model organism to study mitochondrial genome size variation, mutation rates and spectra variation as well as the influence of mitochondrial loss and replacement on the cell.

Chapter 2 was a study on the sequence analysis of introns, GC-clusters, tandem repeats, homopolymers of 33 yeast species. The results showed that mitochondrial genomic variation are dependent on the timescale, e.g., intraspecific versus interspecific, perhaps due to a combination of different turnover rates of mobile sequences, variable insertion spaces and functional constraints. There is a positive correlation between mitochondrial genome size and the level of genetic drift, suggesting that mitochondrial genome expansion in yeast is likely driven by multiple types of sequence insertions in a primarily non-adaptive manner. The results support an important role of genetic drift in the evolution of yeast mitochondrial genomes.

The mutation accumulation (MA) data in chapter 3 shows that the mtDNA-lacking strain exhibits an elevated rate of spontaneous substitution mutation with a mutation pattern consistent with increased oxidative damage. The strain containing foreign mtDNA shows significant slower growth on solid media, which could be due to mito-nuclear discordance, but there is no significant elevation in spontaneous substitution mutation. The mito-nuclear discordance between S. paradoxus mtDNA and S. cerevisiae nuclear DNA have a negative impact on colony growth, but do not significantly alter nuDNA or mtDNA mutation.

Chapter 4 demonstrated that there is substantial variation in mutation rates and mutation spectra among four heterozygous diploid yeast species in the Saccharomycodaceae family. High rates of spontaneous mutation in fast-growing species are likely due to increased oxidative damage during fast-growth. Elevated substitution rates are evident at CpG sites in all four species but their mutation spectra are inconsistent with being caused by cytosine methylation. There is also rapid loss of heterozygosity (LOH) via gene conversion. The four yeast species have different spectra of gene conversion to counteract mutation biases. Balance between gene conversion bias and mutation bias in each species ultimately determines the variable genome-wide base composition in yeast species.