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Discovery and Functional Characterization of Novel Soil-Metagenome Derived Phosphatases

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Discovery and Functional Characterization of Novel Soil-Metagenome Derived Phosphatases Discovery and Functional Characterization of Novel Soil-metagenome Derived Phosphatases Dissertation for the award of the degree "Doctor rerum naturalium" (Dr.rer.nat.) of the Georg-August-Universität Göttingen within the doctoral program Biology of the Georg-August University School of Science (GAUSS) submitted by Genis Andrés Castillo Villamizar from Bucaramanga, Colombia Göttingen, 2019 Thesis Committee Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen PD Dr. Michael Hoppert, Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen Members of the Examination Board Referent: Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen Coreferent: PD Dr. Michael Hoppert, Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen Further Members of the Examination Board Prof. Dr. Stefanie Pöggeler, Department of Genetics of Eukaryotic Microorganisms, Institute of Microbiology and Genetics, Georg-August University Göttingen Prof. Dr. Fabian Commichau, Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen Prof. Dr. Kai Heimel Department of Molecular Microbiology and Genetics , Institute of Microbiology and Genetics, Georg-August University Göttingen Prof. Dr. Gerhard Braus, Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August University Göttingen Prof. Dr. Wolfgang Streit, Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg Date of oral examination: 28.03.2019 I List of Publications 1. Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity Genis A. Castillo Villamizar, Heiko Nacke, Rolf Daniel. Methods Mol Biol. (2017). 1539:249-260. DOI: 10.1007/978-1-4939-6691-2_16 2. Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases Genis Andrés Castillo Villamizar, Heiko Nacke, Marc Boehning, Kristin Herz, Rolf Daniel. mbio (2019). DOI: 10:e01966-18, DOI:10.1128/mBio.01966-18 3. Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome Genis Andrés Castillo Villamizar, Heiko Nacke, Laura Griese, Lydia Tabernero, Katrina Funkner and Rolf Daniel. Genes (2019). 10:101. DOI: 10.3390/genes10020101 4. Functional metagenomics unwraps a new catalytic domain associated to phytase activity: the metallo-β-lactamase superfamily domain Genis Andrés Castillo Villamizar, Katrina Funkner, Heiko Nacke, Karolin Foerster and Rolf Daniel. accepted mSphere DOI: 10.1128/mSphere.00167-19 5. Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce Heiko Nacke, Kezia Goldmann, Ingo Schöning, Birgit Pfeiffer, Kristin Kaiser, Genis Andrés Castillo-Villamizar, Marion Schrumpf, François Buscot, Rolf Daniel, Tesfaye Wubet. Fine spatial scale variation of soil microbial communities under european beech and norway spruce. Front Microbiol (2017):2067. DOI: 10.3389/fmicb.2016.02067 6. Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T Genis Andrés Castillo-Villamizar, Anja Poehlein. Genome Announc. (2016). 4, e00444- 00416. DOI: 10.1128/genomeA.00444-16 7. First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic Sporomusa sphaeroides Strain E (DSM 2875) Genis Andrés Castillo-Villamizar, Rolf Daniel, Anja Poehlein. Genome Announc. (2017). 4, e00444-00416. DOI: 10.1128/genomeA.00037-17 II Table of Contents Thesis Committee ................................................................................................................................................ I List of Publications ............................................................................................................................................ II 1 General Introduction ...................................................................................... 1 1.1. Phosphorus “the essential element” .................................................................................... 1 1.2. Factors Disturbing the Phosphorus Cycle ......................................................................... 1 1.3. Phytate as Alternative Source of Phosphorus ................................................................. 5 1.4. Phytases are Key Biocatalysts with Still Unknown Potential ................................... 6 1.5. Histidine Acid Phytases ............................................................................................................. 9 1.6. -propeller Phytases ............................................................................................................... 11 1.7. βProtein Tyrosin Phytases ...................................................................................................... 12 1.8. Purple Acid Phytases ............................................................................................................... 13 1.9. Soil Metagenomes as Source of Novel Phytases .......................................................... 14 1.10. Aim of the Thesis ....................................................................................................................... 16 1.11. References .................................................................................................................................... 18 2 Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity ................................................................................... 24 3 Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases ........................................................................................................... 37 Supplemental Information for Chapter 3 ................................................................................... 53 4 Characteristics of the First Protein Tyrosine Phosphatase with Phytase Activity from a Soil Metagenome ............................................ 60 Supplemental Information for Chapter 4 ................................................................................... 77 5 Functional Metagenomics Unwraps a New Catalytic Domain Associated to Phytase Activity: the Metallo-β-lactamase Superfamily Domain .................................................................................... 81 5.1. Abstract ......................................................................................................................................... 82 5.2. Importance .................................................................................................................................. 82 5.3. Introduction ................................................................................................................................ 83 5.4. Results ........................................................................................................................................... 84 5.5. Discussion .................................................................................................................................... 92 5.6. References ................................................................................................................................. 101 5.7. Supplemental Information for Chapter 5 .................................................................... 105 6 General Discussion .....................................................................................117 6.1. Soil as Source of Metagenome-Derived Biocatalysts .............................................. 117 6.2. Phosphatases in Metagenome Surveys ........................................................................ 118 6.3. Metagenomics for the Recovery of New Phytases ................................................... 119 6.4. A Simple and Effective Function-Based Method for the Retrieval of Novel Phosphatases/Phytases .................................................................................................................. 123 6.5. The Metagenome Input to Phytase Research ............................................................ 126 6.6. Function-Based Metagenomics Reveals Classic Phytases with Special Characteristics and New Phosphatases ................................................................................... 127 6.7. References ................................................................................................................................. 130 7 Summary ........................................................................................................134 8 Appendix ........................................................................................................136 8.1. Thesis Declaration ................................................................................................................. 136 8.2. Additional Publications ....................................................................................................... 137 8.2.1. Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce ............................................................................................................
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