Origins and divergence of the eukaryotic kinetochore

Abstract

Virtually all life we can see by eye is eukaryotic. Eukaryotes are a group of organisms that encompasses animals, plants and fungi. In addition to large, multicellular organisms, eukaryotes also include many unicellular organisms, such as the causal agent of malaria and the photosynthetic symbiont of corals. Compared to prokaryotes, which are all non-eukaryotic cellular life forms, eukaryotes are characterized by their intracellular complexity. We can presently access the genomes and (predicted) proteomes of more species than ever before, both of eukaryotes and prokaryotes. These allow for large scale as well as in-depth studies on the evolution of proteins and of the processes these proteins are involved in. In the case of eukaryotes, proteins subject to such analyses often participate in the intricate cellular structures, processes and machineries that separate eukaryotes from prokaryotes. One of these typical eukaryotic features is the mitotic spindle. This is a complex machinery that eukaryotes use to segregate their duplicated DNA during cell division. The mitotic spindle pulls apart duplicated chromosomes towards the opposite ends of the cell, after which the cell is ready to divide. The spindle consists of hundreds of proteins. Among these are the pulling elements known as microtubules and the protein complex that links microtubules to the chromosomes. This latter complex is known as the kinetochore, and it is essential for proper cell division. In the work described in this thesis, I studied the evolution of eukaryotic proteins since and before the last eukaryotic common ancestor (LECA), specifically those proteins that constitute the kinetochore. I mainly applied comparative genomics on a small scale, by manually studying the evolution of individual proteins. In Chapter 2, I expose how I approach this type of study. Thereby, this chapter serves as a guide for other researchers who want to investigate the evolution of a particular protein of interest. Moreover, this chapter reveals how I examined the evolution of various kinetochore proteins in Chapters 3, 4, and 5. In Chapter 3, I report the overall presences and absences of characterized kinetochore proteins across eukaryotes. I try to explain what (co-)evolutionary dynamics are responsible for these presences and absences. This inventory revealed the unique presence-absence patterns of the analogous outer kinetochore complexes Ska and Dam1. In Chapter 4, I discuss our in-depth study on the evolution of these complexes. I propose they arose from ancient gene duplications and that Dam1 spread via horizontal gene transfer and displaced Ska in the recipient lineages. Chapter 5 uncovers the ancient origins of kinetochore proteins and reveals that the kinetochore is of mosaic origin and that duplication played an important role in its expansion.. In Chapter 6, I generalize the latter by investigating how gene duplications contributed to the complex genome of LECA. I studied the prokaryotic origins and the duplication histories of LECA’s genes through phylogenomics. In Chapter 7, I end this thesis with a discussion on the evolutionary phenomena I encountered, their impact on kinetochore evolution and why investigating them can be a challenge.