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Chapter 1 Chapter 1: the Gospel According to LUCA UNIVERSITY OF CALIFORNIA, SAN DIEGO The gospel according to LUCA (the last universal common ancestor) A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Ruben Eliezer Meyer Valas Committee in charge: Professor Philip E. Bourne, Chair Professor William F. Loomis, Co-Chair Professor Russell F. Doolittle Professor Richard D. Norris Professor Milton H. Saier Jr. 2010 The Dissertation of Ruben Eliezer Meyer Valas is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ ______________________________________________________________________ Co-chair ______________________________________________________________________ Chair University of California, San Diego 2010 iii DEDICATION I dedicate this work to Alexander “Sasha” Shulgin. Sasha is probably the wisest person I’ve met. He refuses to allow anything other than his own imagination dictates the rules of what is possible. Many of us are just living inside his dreams. This thesis is my attempt at answering the great question of “why are we here?”, and Sasha is one of the few people I’d really listen to if he tried to answer it. iv EPIGRAPH "First they ignore you, then they ridicule you, then they fight you, then you win." Mahatma Gandhi v TABLE OF CONTENTS Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Epigraph .............................................................................................................................. v Table of Contents ............................................................................................................... vi List of Figures .................................................................................................................... xi List of Tables ................................................................................................................... xiii Acknowledgements ........................................................................................................... xv Vita .................................................................................................................................. xvii Abstract of the Disseration .............................................................................................. xix Chapter 1: Introduction to the great tree of life .................................................................. 1 Introduction ..................................................................................................................... 1 Fossils and the origin of life ........................................................................................... 3 The biggest divides in life ............................................................................................... 5 LUCA or the root of the tree of life or the cenancestor or the progenote ....................... 7 Methods of rooting the tree ............................................................................................. 8 Conclusion of the introduction ..................................................................................... 12 Figures .......................................................................................................................... 13 Chapter 2: Save the tree of life or get lost in the woods ................................................... 14 Abstract ......................................................................................................................... 14 Open peer review .......................................................................................................... 15 Background ................................................................................................................... 15 vi Results and Discussion ................................................................................................. 19 The Great Tree of Cellular Function ......................................................................... 19 Placing sequence trees in their cellular context ........................................................ 25 Saving the tree of life ................................................................................................ 31 Reviewers’ Comments .................................................................................................. 35 Reviewer's report 1 ................................................................................................... 35 Reviewer's report 2 ................................................................................................... 60 Figures .......................................................................................................................... 75 Tables ............................................................................................................................ 77 Chapter 3: Nothing about Protein Structure Classification Makes Sense Except in the Light of Evolution ............................................................................................................. 78 Abstract ......................................................................................................................... 78 Introduction ................................................................................................................... 78 Bottom-up Approaches to Protein Structure Classification .......................................... 79 Top-down Approaches to Protein Structure Classification .......................................... 80 The Protein Domain as Today’s Unit of Structural Classification ............................... 81 Domain Distribution in Complete Genomes ................................................................ 82 Is the Domain the Correct Unit of Classification? ........................................................ 85 Subdomain Features ...................................................................................................... 86 Macrodomain Features ................................................................................................. 87 Putting it all Together ................................................................................................... 88 Chapter 4: Critical evaluation of structure based phylogenies ......................................... 92 Introduction ................................................................................................................... 92 vii Problems with the models ............................................................................................. 93 Testing the trees .......................................................................................................... 100 New Algorithms for Building Fake Trees .................................................................. 102 Potential new methods (that didn't work) ................................................................... 105 Directed 1 ................................................................................................................ 105 Directed 2 ................................................................................................................ 105 Hybrid of Song and Gustavo................................................................................... 106 Derived Domain Combinations .............................................................................. 106 Results ......................................................................................................................... 108 Discussion: Why this project failed ............................................................................ 108 Figures ........................................................................................................................ 110 Chapter 5: Rethinking proteasome evolution: Two novel bacterial proteasomes .......... 115 Abstract ....................................................................................................................... 115 Introduction ................................................................................................................. 116 Results ......................................................................................................................... 121 Phylogenetic Analysis ............................................................................................. 121 Structural Analysis .................................................................................................. 125 Function of Anbu and BPH..................................................................................... 128 Discussion ................................................................................................................... 131 Methods ...................................................................................................................... 133 Figures ........................................................................................................................ 135 Tables .........................................................................................................................
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