Engineering new enzymes for synthesis and biosynthesis A dissertation submitted to The University of Manchester for the degree of Master of Science by Research in the Faculty of Science and Engineering 2018 Varvara Androulaki School of Chemistry Contents List of Figures ............................................................................................................................. 6 List of Tables ............................................................................................................................ 10 List of Schemes......................................................................................................................... 11 List of Abbreviations ................................................................................................................ 12 Abstract .................................................................................................................................... 14 Declaration ............................................................................................................................... 15 Copyright Statement ................................................................................................................ 15 Acknowledgments.................................................................................................................... 16 1 Introduction ...................................................................................................................... 17 2 Halogenases ...................................................................................................................... 20 2.1 Haloperoxidases ........................................................................................................ 20 2.1.1 Heme dependent halogenases .......................................................................... 20 2.1.2 Vanadium Haloperoxidase ................................................................................. 21 2.2 FeII/α-ketoglutarate-dependent Halogenases .......................................................... 21 2.3 Flavin-Dependent Halogenases ................................................................................. 23 2.3.1 Tryptophan FAD dependent halogenases ......................................................... 25 2.4 Flavin-Dependent Halogenases as Biocatalysts ........................................................ 27 2.5 Suzuki Cross-coupling using halogenase enzymes .................................................... 29 2.6 Ochratoxin Halogenase ............................................................................................. 31 3 Aims of the project ........................................................................................................... 35 4 Results and discussion ...................................................................................................... 37 4.1 Halogenase enzymes ................................................................................................. 37 4.1.1 Vmax™ cells ........................................................................................................ 37 4.2 Chromo Halogenase .................................................................................................. 43 2 | P a g e 4.2.1 Expression and purification of Chromo-Hal and Fre.......................................... 43 4.2.2 Chromo-Hal Assays with Tryptophan (Trp)........................................................ 44 4.2.3 Scaled up Biohalogenation ................................................................................ 59 4.2.4 Chromo-Hal assays with new substrates ........................................................... 64 4.3 Ochratoxin Halogenase ............................................................................................. 69 4.3.1 Expression of Ochratoxin Halogenase using E. coli BL21 competent cells ........ 69 4.3.2 In vitro-transcription of pET-28a-Ochra-Hl ........................................................ 70 4.3.3 Expression of Ochratoxin Halogenase using different E. coli strains and temperatures .................................................................................................................... 70 4.3.4 Restriction digest and ligation of the synthetic genes....................................... 72 4.3.5 Expression of Ochratoxin Halogenase using different vectors .......................... 74 4.3.6 Restriction digest and ligation of the synthetic genes into pET-28a ................. 76 4.3.7 HiFi DNA Assembly ............................................................................................. 77 4.3.8 Expression and purification of Ochra-P450 and Ochratoxin Hl ......................... 79 4.3.9 Expression of the truncated Ochra-P450 ........................................................... 79 5 Conclusions ....................................................................................................................... 82 6 Experimental Section ........................................................................................................ 84 6.1 Buffer preparations ................................................................................................... 84 6.1.1 Preparation of 100 mM KPi buffers ................................................................... 84 6.1.2 Preparation of 10 mM KPi buffer ....................................................................... 84 6.1.3 Preparation of 100 mM sodium phosphate buffer ........................................... 84 6.1.4 Protein storage buffer ........................................................................................ 84 6.2 Preparation of Growth Media ................................................................................... 84 6.2.1 Lysogeny Broth (LB) ........................................................................................... 85 6.2.2 Enhanced 2xYT medium ..................................................................................... 85 6.2.3 Lysogeny Broth Agar .......................................................................................... 85 3 | P a g e 6.3 Preparation of agar plates ......................................................................................... 85 6.4 Competent cell preparation ...................................................................................... 85 6.4.1 Competent cell preparation solution (KMES I) .................................................. 85 6.4.2 Competent cell storage solution (KMES II) ........................................................ 85 6.4.3 Competent E. coli cells preparation ................................................................... 86 6.4.4 General method for cell transformation and gene inoculation ........................ 86 6.5 SDS-PAGE electrophoresis ......................................................................................... 86 6.5.1 X10 SDS running buffer ...................................................................................... 86 6.5.2 X4 Loading dye ................................................................................................... 86 6.5.3 SDS-PAGE analysis .............................................................................................. 87 6.5.4 General method for Flavin Reductase (Fre) Expression .................................... 87 6.6 General method for halogenases expression in E. coli Arctic Express (DE3) ............ 87 6.7 General method for halogenases expression in E. coli BL21 (DE3) pGro7 ............... 88 6.8 General method for Ochra-Hl expression in E. coli Rosetta 2 (DE3) ......................... 88 6.9 Gateway Cloning ....................................................................................................... 89 6.10 General method for halogenases expression in Vmax™ Express cells ..................... 90 6.11 Protein Purification ................................................................................................... 91 6.12 General method for cross-linked enzyme aggregates formation (CLEA) ................. 91 6.13 Assay conditions with purified WT halogenases ....................................................... 92 6.14 General method for analytical scale biohalogenation with pure enzymes (ADH recycling system) .................................................................................................................. 92 6.15 General method for preparative scale biohalogenation with cross-linked enzyme aggregates ............................................................................................................................ 92 6.16 Whole cells reaction in Vmax™ cells ......................................................................... 93 6.17 Lysate reaction in Vmax™ cells ................................................................................. 93 6.18 HPLC Method ............................................................................................................ 93 4 | P a g e 6.19 Restriction Digest ...................................................................................................... 94 6.20 DNA gel – Agarose electrophoresis ........................................................................... 94 6.21 Plasmid ligation ......................................................................................................... 94 6.22 Polymerase Chain Reaction (PCR) ............................................................................