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Considerations in Evolutionary Biochemistry Van Der Gulik, P.T.S UvA-DARE (Digital Academic Repository) Considerations in evolutionary biochemistry van der Gulik, P.T.S. Link to publication Creative Commons License (see https://creativecommons.org/use-remix/cc-licenses): Other Citation for published version (APA): van der Gulik, P. T. S. (2019). Considerations in evolutionary biochemistry. Amsterdam: Institute for Logic, Language and Computation. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (http://dare.uva.nl) Download date: 28 sep 2020 Considerations in Evolutionary Biochemistry Peter T. S. van der Gulik Considerations in Evolutionary Biochemistry ILLC Dissertation Series DS-2019-06 For further information about ILLC-publications, please contact Institute for Logic, Language and Computation Universiteit van Amsterdam Science Park 107 1098 XG Amsterdam phone: +31-20-525 6051 e-mail: [email protected] homepage: http://www.illc.uva.nl/ These investigations were supported by Centrum Wiskunde & Informatica (CWI), Vici grant 639-023-302 from the Netherlands Organization for Scientific Research (NWO), and the QuSoft Research Center for Quantum Software. Copyright c 2019 by Peter T.S. van der Gulik Printed and bound by Ipskamp Drukkers. ISBN: 978{94{028{1569{6 Considerations in Evolutionary Biochemistry Academisch Proefschrift ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam op gezag van de Rector Magnificus prof. dr. ir. K.I.J. Maex ten overstaan van een door het College voor Promoties ingestelde commissie, in het openbaar te verdedigen in de Aula der Universiteit op woensdag 18 september 2019, te 13.00 uur door Petrus Theodorus Simon van der Gulik geboren te Amsterdam. Promotiecommissie Promotores: Prof. dr. H.M. Buhrman Universiteit van Amsterdam Prof. dr. W.D. Hoff Oklahoma State University Copromotor: Dr. D. Speijer Universiteit van Amsterdam Overige leden: Prof. dr. M.A. Haring Universiteit van Amsterdam Prof. dr. A.T. Groot Universiteit van Amsterdam Prof. dr. L. Stougie Vrije Universiteit Amsterdam Prof. dr. S.A. Massar Universit´elibre de Bruxelles Dr. C.J.M. Egas Universiteit van Amsterdam Faculteit der Natuurwetenschappen, Wiskunde en Informatica dedicated to the memory of Christian de Duve v Contents Acknowledgments ix 1 Evolutionary Biochemistry 1 1.1 The first peptides . .6 1.2 The genetic code . .9 1.3 Linkage selection . 17 2 Searching for primordial peptides 19 2.1 From philosophical speculations to rigorous scientific enquiry . 19 2.2 State of the art: Prebiotic amino acids . 21 2.3 Search for traces of prebiotic peptides . 22 2.4 Prebiotic peptide candidates . 25 2.5 The origin of life and the first peptides . 33 2.6 How to validate our findings? . 38 3 Error minimization in the genetic code 39 3.1 Mathematical formulation of genetic code spaces . 39 3.2 The global minimum and four larger spaces . 42 3.2.1 Goldman's best solution is the global minimum . 42 3.2.2 Incorporating stop codons . 43 3.2.3 Enlarging the \possible code space" . 48 3.3 Implications for genetic code evolution . 52 3.3.1 Selection for error minimization . 53 3.3.2 The Sequential \2-1-3" Model . 55 3.3.3 The Frozen Accident Theory . 56 3.3.4 The Stereochemical Theory . 58 3.3.5 A Four-Column Theory . 58 3.3.6 Consequence of the error robustness . 59 vii viii Contents 4 Unassigned codons in the genetic code 61 4.1 Potential lethality of unassigned codons . 61 4.2 Unassigned codons and suppression . 62 4.3 Suppression in primordial organisms . 63 4.4 Codon reassignments are difficult . 65 4.5 Role of anticodon modifications in the SGC . 67 4.6 Unmodified anticodon wobble rules . 68 4.6.1 Wobble rules and family boxes . 68 4.6.2 Unmodified-G-starting anticodons . 69 4.6.3 Unmodified-C-starting anticodons . 70 4.6.4 Wobble rules in early evolution . 70 4.7 Small sets without anticodon modifications . 72 4.8 No codon reassignments required . 75 4.9 Agmatidine and Lysidine . 76 4.10 A novel regularity in the genetic code . 77 5 Aptamers and the genetic code 79 5.1 The three \faces" of the genetic code . 79 5.1.1 Polar Requirement . 80 5.1.2 Aptamers . 81 5.1.3 Gradual Growth . 83 5.1.4 Integration of assumptions . 84 5.2 Optimality of the genetic code . 84 5.3 Different stages of code development . 87 5.4 Molecular Structure Matrix . 91 5.5 Why these twenty? . 95 6 The danger of losing information 99 6.1 Shrinking pressure and large deletions . 99 6.2 Trypanosoma mitochondrial DNA . 100 6.3 Modeling Trypanosoma mitochondrial DNA . 102 6.3.1 The replication advantage function . 103 6.3.2 The graph of the Markov chain . 104 6.3.3 State Space Reduction . 105 6.3.4 Results . 108 6.4 Linkage selection and batch selection . 109 Bibliography 113 Samenvatting 143 Abstract 149 Acknowledgments My debt to my promotor, Harry Buhrman, can hardly be exaggerated. It is very improbable that a 39-year old without a Ph.D. will get the opportunity to pursue his great scientific \queeste". I sincerely thank Harry for believing in me as a scientist, and creating the environment in which I could build my new life. Working at CWI is an exciting and rewarding experience. I vividly remember the excitement when we realized that our histograms, without the \peaks" and the \throughs" were the \real histograms", and the beautiful patterns in the pub- lished literature turned out to be artefacts. I have to admit that Harry was right when he said that suddenly the beauty of the complicated figure was gone, and it started to look awful. Since those early days we have published three articles in this field, and went through many meetings, discussions, and more casual con- versations. Sometimes the thinking had to be hard and the work became very difficult. Without doubt, completing this effort was the most difficult thing I did in my life, up to now. Seeing the articles being accepted has been very rewarding. I am extremely thankful for understanding the SGC on a much deeper level than I did twenty years ago, and for functioning on a different level than I used to do. What I remember too, is the necessity to quantify things I was seeing, a necessity brought to my attention by Harry. Without this advice, I would not have thought of making the Molecular Structure Matrix we published in 2013. I am also very thankful to Harry for putting on the brake when I was close to irresponsibly neglect my RSI problems in my autistic way, and continue working towards finishing the thesis without taking summer holiday. I am happy that I followed his advice, and started late August with a fresh mind. As for my job, now, at CWI: I remember a conversation in the train from Brussels to Amster- dam, and realize I am a flower which can thrive in an environment created and maintained by Harry; and I am very thankful for that. Thank you very much, Harry! Next, I want to thank my wonderful copromotor, Dave Speijer. Right from the start of my time at CWI, Dave was my biological reality-check support-pillar, ix x Acknowledgments during the days when we established our AMC-CWI cooperation on sleeping sickness genetics. It was a huge relief for me when the \GCC" (Leen's \Genetic Code Club", Harry's \Bio-Club", Dave's \Codon Club", and my own \little RNA Tie Club") grew from five to six, and I could share the burden of being \guardian of biological reliability" (that's how I saw myself at A&C) with a fellow evolu- tionary biochemist. Dave was especially important during the first half of 2013, when I had trouble with writing. I want to thank especially my second promotor: Wouter Hoff. When Harry and Dave suggested that I should write the article on nonsense suppression as a solo effort, I was faced by my inability to write in scientific style. I also had difficulty to remain in high spirit, when working all alone. I was very happy when Wouter accepted my invitation to be a co-author. Looking back to the trouble it gave us to get the message across, I am sure the article would not have been published if I had remained alone on this project. Wouter's viewpoint that, with a ma- jor expansion, the thing would be understandable and acceptable for Journal of Molecular Evolution, proved correct. My interaction with Wouter in the scientific field is not something young and recent: we were already discussing biochemistry and evolution during the eighties. I thank Wouter for keeping me on board of the ship of evolutionary biochemistry throughout the years. I thank the members of the Doctoral Committee, Michel Haring, Astrid Groot, Leen Stougie, Serge Massar and Martijn Egas, for spending their precious time on investigation of our research.
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