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Identification, Characterization and Engineering of Glutathione-Dependent, Lignin-Degrading Enzymes

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Identification, Characterization and Engineering of Glutathione-Dependent, Lignin-Degrading Enzymes Identification, characterization and engineering of glutathione-dependent, lignin-degrading enzymes Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Hauke Voß aus Neumünster 1. Referentin: Professorin Dr. Anett Schallmey 2. Referent: Professor Dr. Dieter Jahn eingereicht am: 21.10.2019 mündliche Prüfung (Disputation) am: 18.12.2019 Druckjahr 2020 Vorveröffentlichungen der Dissertation Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch die Mentorin der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen J. Husarcíková, H. Voß, P. Domínguez de María, A. Schallmey, “Microbial β-etherases and glutathione lyases for lignin valorisationin biorefineries: current state and future perspectives”, Applied Microbiology and Biotechnology, Vol 102, 5391–5401, (2018). H. Voß, C. A. Heck, M. Schallmey, A. Schallmey, “Database mining for novel bacterial - etherases, glutathione-dependent lignin-degrading enzymes”, Applied and Environmental Microbiology, Vol 86, No 2, (2020). Posterbeiträge H. Voß, P. Picart, C. Diederich, A. Schallmey, “Application of β-etherases and glutathione lyases in lignin valorization”, Biocat 2016, 8th International Congress of Biocatalysis, Hamburg, Germany, (2016). H. Voß, C.Diederich, A. Schallmey, “PROTEIN ENGINEERING OF LIG-TD, A GLUTATHTION LYASE”, BioTrans 2017, 13th International Symposium on Biocatalysis and Biotransformation, Budapest, Hungary, (2017). H. Voß, C. A. Heck, A. Schallmey, “IDENTIFICATION OF NEW β-ETHERASES BY PEPTIDE PATTERN RECOGNITION”, ICRC 2018, International CeBiTec Research Conference 2018 Reaction Concepts for Industrial Biocatalysis, Bielefeld, Germany, (2018). H. Voß, C. A. Heck, A. Schallmey, “IDENTIFICATION OF NEW β-ETHERASES BY PEPTIDE PATTERN RECOGNITION”, Biocat 2018, 9th International Congress of Biocatalysis, Hamburg, Germany, (2018). H. Voß, C. A. Heck, A. Schallmey, “IDENTIFICATION OF NEW β-ETHERASES BY PEPTIDE PATTERN RECOGNITION”, Procompas PhD Symposium 2018, Braunschweig, Germany, (2018). i Table of contents Table of contents Vorveröffentlichungen der Dissertation ............................................................... i Table of contents................................................................................................ ii Abstract ............................................................................................................. 1 Zusammenfassung .............................................................................................. 2 1 Introduction ....................................................................................................... 3 1.1 Renewable resources ................................................................................................. 3 1.2 Lignin .......................................................................................................................... 3 1.3 Lignin synthesis and structure ................................................................................... 4 1.4 Lignin pretreatment and isolation ............................................................................. 5 1.5 Lignin model compounds ........................................................................................... 8 1.6 Lignin degradation using chemical and thermal methods....................................... 10 1.7 Lignin-degrading enzymes ....................................................................................... 11 1.8 Glutathione-dependent lignin degradation ............................................................. 13 1.8.1 Glutathione S-transferases ............................................................................................ 14 1.8.2 GSH-dependent lignin degradation pathway ................................................................ 14 1.8.3 β-Etherases .................................................................................................................... 16 1.8.4 Glutathione lyases ......................................................................................................... 19 1.8.5 Applications of GSH-dependent lignin-degrading enzymes .......................................... 22 1.9 Peptide pattern recognition ..................................................................................... 25 1.10 Protein engineering .................................................................................................. 26 1.10.1 Biocatalysis in nature and industry ............................................................................... 26 1.10.2 Random mutagenesis and directed evolution............................................................... 27 1.10.3 Rational and semi-rational design ................................................................................. 29 1.11 Aim of this thesis ...................................................................................................... 30 2 Materials and Methods .................................................................................... 32 2.1 Materials .................................................................................................................. 32 2.1.1 Chemicals ....................................................................................................................... 32 2.1.2 Equipment ..................................................................................................................... 32 ii Table of Contents 2.2 Computer programs and web servers ...................................................................... 33 2.2.1 Bacterial strains and plasmids ....................................................................................... 34 2.2.2 Primer ............................................................................................................................ 34 2.2.3 Antibiotics...................................................................................................................... 36 2.2.4 Buffer and media ........................................................................................................... 37 2.2.5 Proteins ......................................................................................................................... 38 2.2.6 Kits and standards ......................................................................................................... 39 2.3 Methods .................................................................................................................... 39 2.3.1 Substrate synthesis ....................................................................................................... 39 2.3.1.1 Synthesis of 2-bromo-1-(3,4-dimethoxyphenyl)ethan-1-one (1) ........................................... 41 2.3.1.2 Synthesis of β-keto-ethers (2, 4, 6, 8) ..................................................................................... 41 2.3.1.3 Hydroxy methylation of β-keto-ethers (3, 5, 7, 9) .................................................................. 44 2.3.1.4 Inhibitor synthesis ................................................................................................................... 46 2.3.2 GSH specific dye L2 synthesis ......................................................................................... 48 2.3.3 Bioinformatical Methods ............................................................................................... 48 2.3.3.1 BLASTP and PHI-BLAST ............................................................................................................ 48 2.3.3.2 Peptide pattern recognition ................................................................................................... 49 2.3.3.3 Alignments and phylogenetic trees ........................................................................................ 49 2.3.3.4 Docking ................................................................................................................................... 49 2.3.4 Molecular biological methods ....................................................................................... 50 2.3.4.1 Gene synthesis ........................................................................................................................ 50 2.3.4.2 Restriction digest .................................................................................................................... 50 2.3.4.3 Ligation ................................................................................................................................... 51 2.3.4.4 Heat shock transformation and preparation of chemo competent cells ............................... 51 2.3.4.5 PCR reactions .......................................................................................................................... 52 2.3.4.6 Plasmid isolation ..................................................................................................................... 56 2.3.4.7 Sequencing .............................................................................................................................. 56 2.3.5 Cultivation of bacteria and enzyme expression ............................................................ 56 2.3.5.1 Overnight cultures .................................................................................................................
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