Investigating the Role of Paralogous Gene Expansion and Functional Homology of Membrane-Trafficking Machinery in Organellogenesis: Apicomplexan Parasites as a Model Case

• Author / Creator

  Klinger, Christen

• The ease with which large multicellular organisms, such as plants and animals, may be observed belies an unappreciated wealth of diversity; the majority of eukaryotes are unicellular, and display a dazzling array of morphologies and lifestyles. Some eukaryotes are free-living or symbiotic, including heterotrophs that feed on other cells and phototrophs that harness solar energy through biochemical reactions; still others are parasitic, relying on host organisms for nutrients. This biodiversity is underpinned by a concomitant wealth of cellular diversity, and begets questions: 1) how did the diversity of extant eukaryotes arise? 2) What are the underlying mechanisms that give rise to this diversity? 3) Given this diversity, to what extent can eukaryotic features and cellular machinery (genes) be considered conserved?
  One cellular system that is instructive in answering these questions is the membrane-trafficking system (MTS), which encompasses the set of membrane-bound organelles and machinery that mediates movement of material between them. This system is a eukaryotic innovation, absent from prokaryotic and archaeal cells, and is critical in defining cellular ultrastructure, homeostasis, and interaction with the extracellular environment. In an attempt to answer the third question posed above, numerous studies have elucidated the core set of organelles and machinery across eukaryotes, which, by parsimony, are also presumed to have been present in the Last Eukaryotic Common Ancestor (LECA). MTS machinery is well-conserved, and the LECA is inferred to have possessed a complex trafficking system, similar to what is observed in extant eukaryotes. However, all such studies have relied on an implicit assumption of functional homology, that orthologous genes identified through in silico analyses of genomic data from diverse eukaryotes perform the same function; this assumption has never been formally tested. In addition, it is unclear how differences in the MTS across eukaryotes, both in terms of organelles and machinery, could arise based solely on the presence of conserved MTS machinery.
  Hence, the first two questions posed above become key considerations. As the MTS is a eukaryotic innovation and a complex MTS is inferred in LECA, it must have arisen sometime between the advent of eukaryotes (eukaryogenesis) and the radiation of extant eukaryotes from LECA. One hypothesis to explain how a complex system could be generated from primordial components is the Organelle Paralogy Hypothesis (OPH), which posits that gene duplication and divergence would have resulted in a simultaneous increase both in number of distinct endomembrane compartments and trafficking machinery. Although the OPH was originally described to explain the ancient origins of eukaryotic complexity, it represents a viable hypothesis for the emergence of cellular complexity since the LECA, including in parasitic eukaryotes.
  The focus of this thesis is on understanding the relationship between gene duplication, gene function, and organelle complement in extant eukaryotes. Although the OPH presents an attractive hypothesis to explain the continued emergence of novel organelles across eukaryotes, reliable inference of such events relies on the functional constraint of machinery inherited from the LECA (i.e. functional homology). Without this constraint, individual pieces of machinery could perform diverse functions, and the predictive significance of machinery gained in a lineage since the LECA for explaining novel organelles is essentially lost.
  Hence, this thesis investigates in detail an enigmatic group of parasites, the Apicomplexa, which possess unique secretory organelles in addition to a “core set” of eukaryotic organelles and are therefore attractive candidates for studying the OPH. Chapter 2 demonstrates the utility of including high-quality genomes of closely related free-living taxa for mapping evolutionary events during apicomplexan evolution. Chapter 3 presents a pan-eukaryotic literature analysis focussing on the question of functional homology within the MTS. Chapter 4 introduces novel data that systematically demonstrate, for the first time, the presence of additional paralogues within some MTS families in the Apicomplexa; Chapter 5 then investigates three novel paralogues in the model apicomplexan Toxoplasma gondii, providing data to support that one such paralogue is involved in trafficking to additional organelles within the parasite.
  The data presented in this thesis provide an initial basis to explore the questions posed in the first paragraph and suggest that the OPH mechanism is at least partly responsible for generating organelle diversity across eukaryotes. It is expected that similar future studies will allow this model to be expanded and refined.

• Subjects / Keywords

  • organellogenesis
  • Apicomplexa
  • membrane-trafficking
  • paralogous
  • evolution

• Graduation date

  Fall 2019

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/r3-3wvm-2063

• License

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