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Structural and Functional Characterization of Rubisco Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig–Maximilians–Universität München Structural and functional characterization of Rubisco assembly chaperones Thomas Hauser aus Tübingen, Deutschland 2016 Erklärung Diese Dissertation wurde im Sinne von §7 der Promotionsordnung vom 28. November 2011 von Herrn Prof. Dr. F. Ulrich Hartl betreut. Eidesstattliche Versicherung Diese Dissertation wurde eigenständig und ohne unerlaubte Hilfe erarbeitet. München, 03.02.2016 _______________________ Thomas Hauser Dissertation eingereicht am: 25.02.2016 1. Gutachter: Prof. Dr. F. Ulrich Hartl 2. Gutachter: Prof. Dr. Jörg Nickelsen Mündliche Prüfung am 28.04.2016 Acknowledgements Acknowledgements First of all, I am very thankful to Prof. Dr. F. Ulrich Hartl and Dr. Manajit Hayer-Hartl for giving me the opportunity to conduct my PhD in their department at the Max Planck Institute of Biochemistry. This work has benefited greatly from their scientific expertise and experience together with their intellectual ability to tackle fundamental scientific questions comprehensively. Their way of approaching complex projects has shaped my idea on how to perform science. I am very greatful to Dr. Andreas Bracher for giving crucial input and collaborating on many aspects on my work conducted in the department. His extensive crystallographic expertise was of great importance during my time as a PhD student. Furthermore, I want to thank Oliver Müller-Cajar for introducing me into the field of Rubisco and supporting me with help and suggestions in the beginning of my PhD. His enthusiasm about conducting science was of great importance to me and influenced my motivation to work and live science on a day- by-day lab basis enormously. Thanks to all the people in the Hartl lab, especially the “Rubisco group”, represented by Oliver Müller- Cajar, Mathias Stotz, Candace Tsai, Cuimin Liu and Amanda Windhof for the friendly, sophisticated and open-minded atmosphere. Their comments on my work have been inspiring for my study. It was always a pleasure being with them, in work as well as in private. I am thankful for the discussions with my thesis advisory committee members Prof. Dr. Jörg Nickelsen and Prof. Dr. Ute Vothknecht and for the support of the IMPRS organisation team Dr. Hans Joerg Schaeffer, Dr. Ingrid Wolf and Maximiliane Reif. I especially want to thank all collaborators within and outside of the Department. Dr. Petra Wendler and Goran Milicic for performing negative stain electron microscopy, Dr. Javaid Bhat for mass spectrometry, Karina Valer and the MPIB Crystallization facility. Thank you to Evelyn Frey-Royston, Silke Leuze-Bütün and Andrea Obermayr-Rauter for their administrative support as well as Emmanuel Burghardt, Romy Lange, Nadine Wischnewski, Elisabeth Schreil, Albert Ries and especially Anastacia Jungclaus for their technical support. I want to thank the members of my PhD comittee Prof. Dr. Jörg Nickelsen, Prof. Dr. Ute Vothknecht, Dr. Petra Wendler, Dr. Dietmar Martin, and Prof. Dr. Elena Conti for critical evaluation of this thesis. Of great importance during my stay in Munich were Amit Gupta, Timm Hassemer, Leonhardt Popilka, Tobias Neudegger, David Balchin, Christian Löw, and Mark Hipp. I am deeply obliged for countless memorable moments; they were colleagues and became friends. A special thank goes to my family. I am deeply grateful for their unlimited support since the beginning of my studies until the end of my PhD. Finally, I want to express my strongest gratitude to my darling Tanja for her invaluable support and love. You are most important to me and make my life meaningful. II Table of content Table of content Summary .................................................................................................................................. 1 1. Introduction ........................................................................................................................... 3 1.1 Protein Folding ................................................................................................................ 3 1.2 Molecular Chaperones .................................................................................................... 4 1.2.1 The chaperone concept ........................................................................................... 4 1.2.2 The Hsp70 system ................................................................................................... 7 1.2.3 Chaperonins ........................................................................................................... 10 1.2.4 Assembly chaperones ............................................................................................ 13 1.2.4.1 Nucleosome assembly ................................................................................... 13 1.2.4.2 Proteasome assembly .................................................................................... 14 1.2.4.3 Ribosome assembly ....................................................................................... 14 1.2.4.4 Pilus assembly ................................................................................................ 15 1.3 Photosynthesis ............................................................................................................. 16 1.3.1 Light-dependent reactions ...................................................................................... 17 1.3.2 Light-independent reactions / Calvin Benson Bassham cycle ............................... 19 1.3.3 Photorespiration ..................................................................................................... 21 1.3.4 Carbon concentrating mechamisms ....................................................................... 22 1.3.4.1 The Carboxysome .......................................................................................... 22 1.3.4.2 The pyrenoid ................................................................................................... 24 1.3.4.3 C4 and crassulacean acid metabolism (CAM) photosynthesis....................... 24 1.4 Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) .................................... 25 1.4.1 Structure of Rubisco ............................................................................................... 25 1.4.2 Catalytic mechanism and regulation of Rubisco activity ........................................ 29 1.4.3 Rubisco: synthesis, folding and assembly ............................................................. 33 1.4.4 Role of auxiliary proteins in Rubisco biogenesis and function ............................... 38 1.5 Aim of the study ............................................................................................................ 50 2. Publications ........................................................................................................................ 51 2.1 Structure and mechanism of the Rubisco-assembly chaperone Raf1 .......................... 51 III Table of content 2.2 Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii ............................................................................................................................ 81 3. Additional unpublished results ............................................................................................ 99 3.1 Analysis of Raf1-RbcL interaction by RbcL peptide membrane ................................... 99 3.2 Raf1-RbcL binding is not affected by Mg2+, ATP and RuBP ....................................... 103 3.3 RbcS displaces Raf1 from RbcL8 at equimolar concentrations .................................. 105 3.4 Interaction of Raf1 with RbcS ..................................................................................... 106 3.5 Interaction of Raf1, Raf2 and RbcS ............................................................................ 108 3.6 In vitro reconstitution of plant Rubisco ........................................................................ 111 3.7 Analysis of eukaryotic RbcX-RbcL interaction ............................................................ 113 3.8 Functional analysis of eukaryotic RbcX ...................................................................... 116 3.9 A potential role for RbcX in Rubisco assembly in Chlamydomonas reinhardtii .......... 117 3.10 Interplay of Raf1 and RbcX in Rubisco assembly ..................................................... 119 4. Discussion ........................................................................................................................ 122 4.1 A new model for Raf1-mediated Rubisco assembly ................................................... 123 4.2 The role of eukaryotic RbcX in Rubisco assembly ..................................................... 123 4.3 Functional interplay between Raf1 and RbcX in Rubisco assembly ........................... 125 4.4 Plant Rubisco in vitro reconstitution ............................................................................ 128 5. Outlook ............................................................................................................................. 131 6. Material and Methods ....................................................................................................... 132 6.1 Materials ..................................................................................................................... 132 6.1.1 Chemicals ...........................................................................................................
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