Understanding the evolution of the membrane trafficking system in diverse eukaryotes through comparative genomics and transcriptomics

• Author / Creator

  Herman, Emily K

• Single-celled organisms represent the majority of eukaryotic diversity. Recent advances in sequencing technologies have been critical for understanding the evolutionary biology and cell biology of microbial eukaryotes. Comparative genomic analyses have shown that many genes that underlie fundamental eukaryotic features (e.g. membrane trafficking, cytoskeleton) are conserved across the diversity of eukaryotes, suggesting that they have also maintained a similar function. However, many microbial eukaryotes have specialized lifestyles or behaviours, the evolutionary pressures of which may be observed in changes to gene content in a lineage; in either gene family expansion, divergence, or loss. Building on analyses of gene presence and absence, gene expression changes in relation to a specific cellular behaviour gives even more insight into the underlying cell biology of that process. The focus of this thesis is the membrane trafficking system, specifically the cellular machinery that underlies intracellular transport, endocytosis, and exocytosis. In the first Results chapter, comparative genomics is used to identify membrane trafficking components in three related organisms, one of which is free-living, while the other two are gut-associated endobionts and/or parasites. The purpose was to determine whether host-association contributes to sculpting of the trafficking system, as is the case in other eukaryotic parasites. In the second Results chapter, comparative genomics and transcriptomics are used to study how membrane trafficking underlies the process of encystation in the gut pathogens Entamoeba invadens and E. histolytica, which is critical for pathogenesis. The third results chapter looks at the biology of a unique behaviour in the haptophyte lineage: the secretion of large organic or calcium carbonate scales. Again, both comparative genomics and transcriptomics are used to understand how the membrane trafficking system contributes to this extensive secretory process. The last Results chapter takes a whole-genome approach to understanding pathogenesis in the free-living neuropathogenic amoeba Naegleria fowleri, as compared with its harmless relative, Naegleria gruberi. The purpose of comparative genomics and transcriptomics of N. fowleri and N. gruberi was primarily to identify pathogenicity factors. Although no single factor was identified that fully explains the difference in pathogenicity between the two Naegleria spp., two major outcomes were achieved. First, this analysis has generated a comprehensive look at the cell biology of N. fowleri during host infection. Secondly, it has produced a list of dozens of potential pathogenicity factors that can now be experimentally tested. An example of how in silico analyses can support functional work concludes this chapter, where evidence of a Golgi body in N. gruberi is shown for the first time. These –omics analyses have contributed significantly to understanding the biology of these lineages. They highlight patterns of retention, loss, and expansion of membrane trafficking machinery that may be related to unusual trafficking pathways or even novel organelles. They also allowed for comparisons of gene complement and expression between different lineages that have similar lifestyles, for example gut-associated parasites or endobionts (Entamoeba spp. and Blastocystis sp., Proteromonas lacertae), or organisms with a heavy secretory load (haptophytes and Entamoeba sp.). Common to all three transcriptomic analyses is the finding that transcriptional responses are complex, often involving differential regulation of paralogous genes. The data presented here have paved the way for future functional work in microbial eukaryotes, improving our depth of knowledge of membrane trafficking function in eukaryotes, and allowing us to fully appreciate unique cell biology in ecologically and medically relevant organisms.

• Subjects / Keywords

  • Eukaryote
  • Evolution
  • Membrane-trafficking

• Graduation date

  Spring 2018

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/R3ZW19755

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.