UBC Theses and Dissertations
The functional diversity and evolution of nuclear processes Irwin, Nicholas A. T.
The nucleus is a defining characteristic of eukaryotic cells which not only houses the genome but a myriad of processes that function synergistically to regulate cellular activity. Nuclear proteins are key in facilitating core eukaryotic processes such as genome compaction, nucleocytoplasmic exchange, and DNA replication, but the interconnectedness of these processes makes them challenging to dissect mechanistically. Moreover, the antiquity of the nucleus complicates evolutionary analyses, limiting our view of nuclear evolution. Despite this, a comprehensive understanding of the function and evolution of nuclear processes is essential given their central importance in disease, basic cell biology, and eukaryotic evolution. In this dissertation, I argue that insights into nuclear biology and evolution can be obtained by examining eukaryotic diversity rather than relying solely on traditional model organisms. I begin by presenting an introduction to nuclear evolution and diversity, highlighting the existence of nuclear variation across eukaryotes from a systems perspective and underscoring the potential utility of biodiversity in studying nuclear processes (Chapter 1). In the following chapters, I test my hypothesis by examining the function and evolution of different processes in a subset of divergent nuclear systems: namely, chromatin in the dinoflagellate dinokaryon, nuclear pore complexes (NPCs) in the nucleomorphs of chlorarachniophytes and cryptophytes, and DNA replication in the ciliate macronucleus. In Chapter 2, I use an experimental evolutionary approach to investigate the drivers of histone depletion in dinoflagellates, revealing the capacity for viruses to shape cellular evolution and raising questions regarding the subfunctionalization of remnant dinoflagellate histones. In Chapter 3, I reconstruct the NPCs of endosymbiotically acquired nuclei, termed nucleomorphs, in silico, and predict a highly reduced pore structure, suggesting that a complex NPC may not be required for baseline nuclear function. Lastly, in Chapter 4, I examine the diversity of motile DNA replication systems in ciliates, highlighting new models for studying DNA replication and the capacity of cytoskeletal elements to coordinate nuclear organization and processes. Ultimately this work confirms the efficacy of examining diverse nuclear systems, provides insights into the biology and evolution of nuclear processes, and encourages a re-evaluation of how we view and select model organisms.
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