Thesis Jolien V4 20181111 Copy.Indd

Origins and divergence of the eukaryotic kinetochore Jolien van Hooff Jolien van Hooff (2018) Origins and divergence of the eukaryotic kinetochore PhD thesis, Utrecht University Cover and layout by Alessia Peviani (www.photogenicgreen.nl) Printed by Ridderprint BV (www.ridderprint.nl) ISBN 978-94-6375-165-0 Origins and divergence of the eukaryotic kinetochore Oorsprong en divergentie van het eukaryote kinetochoor (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof. dr. H.R.B.M. Kummeling, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op maandag 10 december 2018 des middags te 2.30 uur door Jolien Johanna Elisabeth van Hooff geboren op 10 januari 1988 te Breda Promotoren: Prof. dr. G.J.P.L. Kops Prof. dr. B. Snel Table of Contents 1.Introduction..................................................................................................................... 8 Introduction......................................................................................................... 10 The diversity and origins of eukaryotes........................................................... 11 Cell division and chromosome segregation....................................................... 15 Comparative genomics ...................................................................................... 20 Scope and outline of this thesis.......................................................................... 24 2. Inferring the evolutionary history of your favorite protein: A guide for cell biologists........................................................................................................................... 26 Summary.............................................................................................................. 28 Abstract............................................................................................................... 28 Introduction......................................................................................................... 28 Studying the evolution of a protein: what do we mean?................................... 32 A quick (and dirty) guide to inferring the evolutionary history of a protein...... 33 Life is more complicated..................................................................................... 42 Conclusions & Outlook....................................................................................... 49 Acknowledgments.............................................................................................. 51 Author contributions........................................................................................... 51 3. Evolutionary dynamics of the kinetochore network as revealed by comparative genomics........................................................................................................................... 52 Abstract............................................................................................................... 54 Introduction......................................................................................................... 54 Results................................................................................................................. 56 Discussion............................................................................................................ 70 Materials and Methods....................................................................................... 72 Acknowledgments.............................................................................................. 76 Author contributions........................................................................................... 76 Supplementary Material...................................................................................... 76 4. Unique phylogenetic distributions of the Ska and Dam1 complexes support functional analogy and suggest multiple parallel displacements of Ska by Dam1......................... 82 Abstract ............................................................................................................... 84 Main text.............................................................................................................. 84 Materials and Methods....................................................................................... 93 Acknowledgments.............................................................................................. 97 Author contributions........................................................................................... 97 Supplementary Text............................................................................................ 97 Supplementary Material................................................................................... 100 5. Mosaic origin of the eukaryotic kinetochore............................................................. 106 Abstract............................................................................................................. 108 Introduction....................................................................................................... 108 Results..................................................................................................................109 Discussion.......................................................................................................... 125 Data and Methods............................................................................................ 127 Author contributions......................................................................................... 129 Acknowledgments............................................................................................ 129 Supplementary Text.......................................................................................... 130 Supplementary Material................................................................................... 134 6. Timing large-scale duplications during eukaryogenesis suggests relatively recent origins of eukaryote-specific proteins........................................................................... 142 Abstract............................................................................................................. 144 Introduction....................................................................................................... 144 Results............................................................................................................... 147 Conclusion & Discussion................................................................................... 155 Materials & Methods......................................................................................... 159 Author contributions......................................................................................... 162 Acknowledgments............................................................................................ 162 Supplementary Material.................................................................................... 163 7. Discussion................................................................................................................... 164 Kinetochore as a model for evolution of eukaryotic cellular processes?......... 166 Predictions on non-model kinetochores.......................................................... 170 More data from extant species make more complex ancestors...................... 172 Small- and large-scale studies complement each other in illuminating eukaryogenesis................................................................................................. 173 References....................................................................................................................... 176 Abbreviations.................................................................................................................. 189 Samenvatting.................................................................................................................. 190 Curriculum vitae.............................................................................................................. 194 Publications..................................................................................................................... 195 Acknowledgments.......................................................................................................... 196 1 Introduction 10 Chapter 1 Introduction 11 Introduction 1 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 of more species than ever before, both of eukaryotes and prokaryotes. Extensive analysis of these genomes has taught us that eukaryotic genomes evolve under completely different dynamics than prokaryotic genomes. As a result, these analyses have provided a framework to study the evolution of specifi c proteins encoded by these genomes. In return, small-scale protein evolution studies can uncover new paradigms in genome evolution. Protein evolution studies are regularly

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