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Strategies for Synthetic Activation of Translation Elongation Factor P

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Strategies for Synthetic Activation of Translation Elongation Factor P Strategies for synthetic activation of translation elongation factor P DISSERTATION der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Wolfram Johannes Volkwein München, November 2019 Gutachter: 1. Prof. Dr. Jürgen Lassak 2. Prof. Dr. Andreas Klingl Datum der Abgabe: 07.11.2019 Datum der mündlichen Prüfung: 10.01.2020 II Eidesstattliche Erklärung Eidesstattliche Erklärung Ich versichere hiermit an Eides statt, dass die vorgelegte Dissertation von mir selbstständig und ohne unerlaubte Hilfe angefertigt wurde. Des Weiteren erkläre ich, dass ich nicht anderweitig ohne Erfolg versucht habe, eine Dissertation einzureichen oder mich der Doktorprüfung zu unterziehen. Die folgende Dissertation liegt weder ganz, noch in wesentlichen Teilen einer anderen Prüfungskommission vor. München, 07.11.2019 Wolfram Volkwein Statutory Declaration I declare that I have authored this thesis independently, that I have not used other than the declared sources/resources. As well I declare, that I have not submitted a dissertation without success and not passed the oral exam. The present dissertation (neither the entire dissertation nor parts) has not been presented to another examination board. Munich, 07.11.2019 Wolfram Volkwein III Table of Content Table of Content Eidesstattliche Erklärung ........................................................................................ III Statutory Declaration .............................................................................................. III Table of Content ...................................................................................................... IV Nomenclature ........................................................................................................... VI Abbreviations .......................................................................................................... VII Publications and Manuscripts Originating from this Thesis ............................. VIII Contributions to Publications and Manuscripts Presented in this Thesis ......... IX Summary .................................................................................................................. XI Zusammenfassung ................................................................................................. XII 1. Introduction .................................................................................................... 1 1.1 The non-uniformity of translation ...................................................................... 1 1.2 The discovery of EF-P and its molecular function ............................................ 1 1.3 EF-P resolves polyproline (PPP) mediated ribosome stalling .......................... 3 1.4 EF-P resolves diprolyl (PP) mediated ribosome stalling................................... 3 1.5 The larger upstream amino acid context of the arrest motif also influences its stalling strength ........................................................................................... 4 1.6 Additional factors influencing the translation of proteins containing consecutive prolines......................................................................................... 4 1.7 Post-translational modifications of EF-P .......................................................... 5 1.7.1 β-Lysylation of lysine type EF-P by the EpmABC pathway .............................. 5 1.7.2 5-Amino-pentanolylation of lysine type EF-P by an unknown pathway ............ 6 1.7.3 Rhamnosylation of arginine type EF-P by the RmlABCD/EarP pathway.......... 7 1.8 Motivation and strategies for the synthetic activation of EF-P .......................... 9 1.8.1 Strategy one: Translational activation of E. coli EF-P using the amber suppression system ......................................................................................... 9 1.8.2 Strategy two: Non-cognate post-translational activation of E. coli EF-P ........ 10 2 Strategy for the Translational Activation of EF-P Using the Amber Suppression System .................................................................................... 11 3 A Versatile Toolbox for the Control of Protein Levels Using Nε-Acetyl-L-lysine Dependent Amber Suppression .................................. 20 3.1 Supplementary Material ................................................................................. 32 4 Switching the Post-translational Modification of Elongation Factor EF-P ................................................................................................... 44 4.1 Supplementary Material ................................................................................. 61 IV Table of Content 5 Exceptionally Versatile – Arginine in Bacterial Post-translational Protein Modifications ................................................................................... 82 6 Concluding Discussion and Outlook ......................................................... 83 6.1 Strategy one: Translational activation of EF-P using the amber suppression system ............................................................................................................ 83 6.1.1 Alternative strategy to activate EF-P synthetically with different ncAAs ......... 85 6.2 The amber suppression system as a tool to regulate bacterial protein levels ....................................................................................................................... 87 6.2.1 Strategies to improve the uptake of ncAAs into the cell ................................. 87 6.2.2 The Nε-acetyl-lysine metabolism .................................................................... 89 6.3 Strategy two: Post-translational activation of EF-P by non-cognate rhamnosylation ............................................................................................... 90 6.3.1 Synthetic rhamnosylation of EF-P .................................................................. 90 6.3.2 Glycoengineering of EarP .............................................................................. 91 6.3.3 Synthetic activation of EF-P ........................................................................... 91 Danksagung ............................................................................................................ 94 References .............................................................................................................. 96 V Nomenclature Nomenclature Amino acids are given in the one-letter code (e.g. K). The positions of amino acids within a protein are indicated by numbers. The numbering starts with “1” at the first methionine/valine of the wild-type protein. Amino acid substitutions are termed as follows: The native amino acid is designated in one letter code first, followed by its position in the protein, and the one-letter code for the amino acid substitution introduced. (Example: EF-P K34R, here, lysine at position 34 of EF-P is replaced by an arginine). Deletions are marked with “Δ”. VI Abbreviations Abbreviations AcKRS acetyl lysyl-tRNA synthetase A-site aminoacyl-site BTH bacterial two-hybrid β3Ωβ4 loop between beta-strands β3/β4 CAT chloramphenicol acetyltransferase EF-P elongation factor P eIF5A eukaryotic translation initiation factor 5A E-site exit-site fMet fMet-tRNAi initiator transfer RNA N-formyl-methionyl-tRNAi GFP green fluorescent protein LysRS lysyl-tRNA synthetase mRNA messenger RNA ncAA non-canonical amino acid ORF open reading frame PTM post-translational modification PylRS pyrrolysyl-tRNA synthetase P-site peptidyl-site tRNACUA pyrrolysyl-transfer RNA tRNALys lysyl-transfer RNA VII Publications and Manuscripts Originating from this Thesis Publications and Manuscripts Originating from this Thesis Chapter 2: Wolfram Volkwein, Sabine Peschek, Benedikt Frederik Camille Graf von Armansperg, Kirsten Jung and Jürgen Lassak (2019). Strategy for the translational activation of EF-P using the amber suppression system. (Manuscript). Chapter 3: Wolfram Volkwein, Christopher Maier, Ralph Krafczyk, Kirsten Jung and Jürgen Lassak (2017). A versatile toolbox for the control of protein levels using Nε-acetyl-L-lysine dependent amber suppression. ACS Synth. Biol. 6, 1892-1902. Chapter 4: Wolfram Volkwein*, Ralph Krafczyk*, Pravin Kumar Ankush Jagtap, Marina Parr, Elena Mankina, Jakub Macošek, Zhenghuan Guo, Maximilian Josef Ludwig Johannes Fürst, Miriam Pfab, Dmitrij Frishman, Janosch Hennig, Kirsten Jung and Jürgen Lassak (2019). Switching the post-translational modification of translation elongation factor EF-P. Front. Microbiol. 10. *Authors contributed equally Chapter 5: Jürgen Lassak, Franziska Koller, Ralph Krafczyk and Wolfram Volkwein (2019). Exceptionally versatile – Arginine in bacterial post-translational protein modifications. Biol. Chem. 400, 1397-1427. (Review Article) Manuscripts in preparation: Miriam Pfab, Pavel Kielkowski, Ralph Krafczyk, Wolfram Volkwein, Stephan Sieber, Jürgen Lassak and Kirsten Jung. Synthetic post-translational modifications of elongation factor P using the ligase EpmA. Ralph Krafczyk, Fei Qi, Alina Sieber, Wolfram Volkwein, Kirsten Jung, Dmitrij Frishman and Jürgen Lassak. Codon choice affects translation efficiency of consecutive prolines in bacteria. VIII Contributions to Publications and Manuscripts Presented in this Thesis Contributions to Publications and Manuscripts Presented in this Thesis Chapter 2: The study was designed by Wolfram Volkwein, Kirsten Jung and Jürgen Lassak. The study was directed by Kirsten Jung and Jürgen Lassak. Wolfram Volkwein, Sabine
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