Date on Master's Thesis/Doctoral Dissertation

12-2021

Document Type

Doctoral Dissertation

Degree Name

Ph. D.

Department

Biology

Degree Program

Biology, PhD

Committee Chair

Perlin, Michael

Committee Co-Chair (if applicable)

Schultz, David

Committee Member

Schultz, David

Committee Member

Menze, Michael

Committee Member

Graham, James

Committee Member

Hwangbo, Dae-Sung

Author's Keywords

inheritance; dimorphism; basidiomycete; mitochondria; heteroplasmy; uniparental

Abstract

An important goal in evolutionary biology is to address the origin of Earth’s immense biodiversity through the evolution of complex sexual reproduction mechanisms in eukaryotes. Inheritance of mitochondria during sexual reproduction has received special attention in recent years, as these organelles cannot be synthesized de novo and must be transmitted from parent to offspring. The importance of these organelles far exceeds its common function as the energy-producing “powerhouse” of the cell, as it has been found to also be involved in fundamental processes like apoptosis, aging and metabolic homeostasis. Thus, appropriate inheritance of mitochondria is essential for growth and development of progeny. Sexually reproducing eukaryotes present a variety of mechanisms that allow mitochondria from a single parent to be passed on to the offspring (homoplasmy). However, biparental inheritance of mitochondria has also been described in other systems, in which offspring inherit mitochondrial genomes from both parents (heteroplasmy). Presence of different mitochondrial genomes within the same cytoplasm may result in the dissemination of deleterious mutations arising from the individual nature of each mitochondrial genome (e.g. different DNA replication rates, susceptibility to oxidative damage, etc.). The smut fungus Sporisorium reilianum f. sp. zeae is a pathogen of maize that exhibits a dimorphic lifestyle, being able to switch from budding yeast-like haploid sporidia to pathogenic filamentous dikarya that eventually develop into diploid teliospores. Notably, this smut fungus is equipped with genes for the appropriate segregation of mitochondria during sexual reproduction. Mating in S. reilianum may occur between three parental type strains, a1, a2 and a3, of which only a2 contains genes that promote inheritance of its own mitochondrial genetic material. Accordingly, mitochondrial inheritance in offspring resulting from a cross with the a2 parent is expected to follow a uniparental pattern. However, what happens in a cross between the a1 and a3 partners remains unclear. The present work explores the uniparental inheritance system of mitochondria in S. reilianum through the development of reliable and low-cost diagnostic methodologies to discern between mitogenomes. The study was dependent on the investigation of the genetic diversity of different S. reilianum strains through whole-genome sequencing and gene synteny analysis, which proved to be more reliable, and led to cost-effective methodologies for the detection of polymorphisms. Multiple sequence alignment revealed a slew of mutations throughout the mitochondrial DNA molecule. Mutations that were detected in protein-encoding regions needed further investigation, as they could have detrimental consequences on their predicted polypeptides. Furthermore, unique DNA sequence was detected in the cox1 gene of the Chinese isolate mitogenome, with high percent identity to other species related to S. reilianum. This remarkable finding may hint at a complex evolutionary history of S. reilianum, influenced by potential inter- and intraspecific exchange of mitochondrial genetic material. The distinct polymorphic region detected in Chinese strains of S. reilianum also provided the ideal groundwork for the development of simple diagnostic methods to discern between mitotypes following a mating event in the context of mitochondrial inheritance. Exploration of the mitochondrial inheritance mechanism of S. reilianum was based on previous findings from the closely related species, Ustilago maydis, which involves a degradation-mediated mechanism that renders inheritance uniparental. The diagnostic methods developed were based on Polymerase Chain Reaction (PCR) technology and suggested deviation from predicted inheritance patterns in which the Chinese mitotype was always favored. Additionally, this deviation was not affected in the absence of the Lga2/Rga2 system. Finally, the electron transport chain of S. reilianum was further explored. Bioinformatic analysis and growth inhibition assays using specific respiratory inhibitors revealed the presence of a putative alternative oxidase (AOX), which is associated with alternative respiration in the face of inhibition of one or more of the classical mitochondrial complexes. AOX may play a more prominent role in the pathogenic stage of the fungus, as its absence significantly reduced disease severity. Moreover, expression analysis revealed that alternative oxidase is upregulated in the diploid teliospore stage of the fungus. Compared to haploid sporidia that bud or the dikarya that grow filamentously, such teliospores may benefit from reduced respiratory rates due to their mostly quiescent nature. Combined with the findings regarding mitochondrial inheritance, the characterization of alternative routes facilitated by nuclearly-encoded components like alternative oxidase provide an additional perspective from which to study genomic conflicts during sexual reproduction.

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