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Genomics, Proteomics and Secondary Metabolites Biosynthesis Research on Streptomyces Asterosporus DSM 41452

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Genomics, Proteomics and Secondary Metabolites Biosynthesis Research on Streptomyces Asterosporus DSM 41452 - 1 - Genomics, Proteomics and Secondary Metabolites Biosynthesis Research on Streptomyces asterosporus DSM 41452 Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Albert-Ludwigs-Universität Freiburg im Breisgau Vorgelegt von Songya Zhang Aus Zhengzhou, China 2018 - 2 - Dekan: Prof. Dr. Manfred Jung Vorsitzender des Promotionsausschusses: Prof. Dr. Stefan Weber Referent: Prof. Dr. Andreas Bechthold Korreferent: Prof. Dr. Irmgard Merfort Drittprüfer: Prof. Dr. Oliver Einsle Datum der Promotion: 20.04.2018 - 3 - Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbstständig und nur unter Verwendung der angegebenen Literatur und Hilfsmittel angefertigt sowie Zitate kenntlich gemacht habe. - 4 - Acknowledgements I would like to take this opportunity to express my appreciation to my supervisor, Prof. Dr. Andreas Bechthold, for his support, encouragement and guidance throughout my study in this outstanding research environment at the Fakultät für Chemie und Pharmazie in Freiburg University. His enthusiasm and attitude towards science and research will definitely affect my life. I am particularly thankful to my co-advisor Prof. Dr. Irmgard Merfort for kindly reviewing this thesis, her generous help during my study, for being the supervisor of my doctoral committee. I desire to convey my earnest appreciation to Prof. Dr. Oliver Einsle for being the member of my doctoral committee. In addition, I feel grateful to Dr. Lin Zhang for his help to determine protein structure and professional advice on my research project. I would also wish to thank Prof. Dr. Stefan Günther for reviewing the manuscript. I also want to express my greatest thanks to Dennis Klementz for his reliable help in terms of bioinformatics analysis and for helping revise my manuscript. My deep gratitude as well goes to Prof. Dr. David Zechel for his discussion about my research project, review my paper in earnest. His attitude toward academic research really motivates me a lot. I desire to thank Dr. Claudia Jessen-Trefzer for her kind help about my project and her helpful discussions, and for her amendment to the manuscript. Also, I am grateful to Dr. Thomas Pauluat for the NMR data analysis and his professional suggestion on the manuscript. I am really grateful to Dr. Max Cryle from Monash University for his kindly providing substrate and earnest guidance on the P450 project. In addition, I want to thank Dr. Greule Anja for her suggestion and effort to solve this interesting scientific question. I also want to express my greatest gratitude to Dr. Verónica I. Dumit and Dr. Mingjian Wang from Center for Biological Systems Analysis in Freiburg University for their assistance, professional suggestion and guidance on proteomics analysis. I want to thank Prof. Dr. Jun Yin from Georgia State University, Dr. Stephen G. Bell from University of Adelaide, Mr. Gunter Stier from Heidelberg University for their kindness of providing plasmids. - 5 - I am appreciated Prof. Dr. Xin-zhuan Su and Dr. Richard Eastman from National Center for Advancing Translational Sciences/NIH for helping compound activity test and manuscript review. I would like to thank all my colleagues who helped me throughout my PhD study. I would like to thank Dr. Gabriele Weitnauer for her kind help and unselfish assistance in many ways. I would like to express my warmest gratitude to Marcus Essing, Sandra Groß, Elizabeth Welle and Frau Weber for their contribution to the lab. Especially, I like to thank Marcus Essing for strong technician support for maintaining equipment running in the lab. My gratitude also goes to Sandra Groß for tireless help in the lab, and for reviewing my thesis. I also want to thank Elizabeth Welle for strong technician assistance on the LCMS, HPLC system in the lab. I want to thank Sandra Cabrera, Dr. Susanne Elfert, Tanja Herbstritt and Judy Wang for their kind help. I would like to thank Dr. Roman Makitrynskyy for his kind help during my study. In the meanwhile, I would like to thank all my current and previous colleagues working in the lab of AG Bechthold for their selfless help and for sharing me various kinds of perspectives and outlook to the life, world. I wish all of them have a wealthier and more successful future. Last but not the least I would like to show my gratitude to my family for their backing, especially my loving wife: Jing Zhu, for her unconditional support and passion. I owe all the success of my PhD study to my family. - 6 - Wissenschaftliche Publikationen und Akademische Aktivitäten Wissenschaftliche Publikationen I. Songya Zhang, Andreas Bechthold. Iteratively Acting Glycosyltransferases, 2nd edition of Handbook of Carbohydrate-Modifying Biocatalysts, 2016, Pages 321-348, Pan Stanford Publishing. II. Songya Zhang, Jing Zhu, Tao Liu, Suzan Samra, Huaqi Pan, Jiao Bai, Huiming Hua, Andreas Bechthold, a Novel Glycosylated Polyketide from the Terrestrial Fungus Myrothecium sp. GS-17. Helvetica Chimica Acta, 2016, 99 (3), 215-219. III. Songya Zhang, Jing Zhu, David Zechel, Claudia Jessen-Trefzer, Richard T. Eastman, Thomas Paululat, Andreas Bechthold. Novel WS9326A derivatives and one novel Annimycin derivative with antimalarial activity are produced by S. asterosporus DSM 41452 and its mutant, ChemBioChem, 2017, 19(3), 272-279. IV. Arne Gessner, Tanja Heitzler, Songya Zhang (cofirst), Christine Klaus, Renato Murillo, Hanna Zhao, Stephanie Vanner, David L. Zechel, Andreas Bechthold. Changing Biosynthetic Profiles by Expressing bldA in Streptomyces Strains. ChemBioChem, 2015, 16(15):2244-2252. V. Greule Anja, Songya Zhang, Thomas Paululat, Andreas Bechthold. From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028. Journal of visualized experiments: JoVE, 2017, (119): 54952. VI. Anja Greule, Marija Marolt, Denise Deubel, Iris Peintner, Songya Zhang, Claudia Jessen- Trefzer, Christian De Ford, Sabrina Burschel, Shu-Ming Li, Thorsten Friedrich, Irmgard Merfort, Steffen Lüdeke, Philippe Bisel, Michael Müller, Thomas Paululat, Andreas Bechthold. Wide distribution of foxicin biosynthetic gene clusters in Streptomyces strains-an unusual secondary metabolite with various properties. Frontiers in microbiology, 2017, 8:221. VII. Songya Zhang, Dennis Klementz, Jing Zhu, Stefan Günther, Andreas Bechthold. The complete genome sequence of S. asterosporus DSM 41452, a high producer of the - 7 - neurokinin A antagonist WS9326As. Journal of Biotechnology (under review). VIII. Arslan Sarwar, Zakia Latif, Songya Zhang, Andreas Bechthold, Biological control of potato common scab with rare Isatropolone C compound produced by Streptomyces sp. A1RT, Frontiers in microbiology (under review). IX. Songya Zhang, Mingjian Wang, Dennis Klementz, Jing Zhu, Verónica I. Dumit, Andreas Bechthold. Comparative Proteomic Analysis of S. asterosporus DSM 41452 reveals the AdpA regulon in a native non-sporulating Streptomyces species by SILAC. Applied microbiology and Biotechnology (in preparation). X. Songya Zhang, Lin Zhang, Anja Greule, Jing Zhu, Oliver Einsle, Max Cryle, Andreas Bechthold, Structural Characterization of Cytochrome P450WS9326A, mediates the formation of the olefinic bond to generate the dehydrotyrosine formation in WS9326A Biosynthesis, ACS chemical biology (in preparation). Poster Präsentation I. Songya Zhang, Lin Zhang, Anja Greule, Jing Zhu, Max Cryle, Oliver Einsle, Andreas Bechthold. Structural Characterization of Cytochrome P450 Sas16, mediates the formation of the olefinic bond to generate the dehydrotyrosine formation in WS9326As Biosynthesis. RTG 1976 Symposium 2017: Unique Cofactor-dependent Enzymes in Microbes, 10/2017, Freiburg, Germany II. Songya Zhang, Dennis Klementz, Mingjian Wang, Jing Zhu, Stefan Günther, Verónica I. Dumit, Andreas Bechthold. Complete genome sequencing and comparative Proteomic Analysis of S. asterosporus DSM 41452 reveals the AdpA regulon in a native non- sporulating Streptomyces species. International VAAM-Workshop 2017: Biology of Bacteria Producing Natural Products, 09/2017, Tübingen, Germany. III. Songya Zhang, Jing Zhu, Andreas Bechthold. WS9326A Derivatives from S. asterosporus DSM 41152: Chemical Structure and Biosynthesis. International VAAM-Workshop 2016: Biology of Bacteria Producing Natural Products, 09/2016, Freiburg, Germany IV. Songya Zhang, Jing Zhu, Roman Makitrynskyy, Olga Tsypik, Andreas Bechthold. Connecting Chemotype, Phenotype and Genotype, revealing the Gene Regulatory Mechanism of Morphological Development and Secondray Metabolism in S. asterosporus - 8 - DSM 41452.Tag der Forschung der Universität Freiburg 2016, 07/2016, Freiburg, Germany V. Songya Zhang, Jing Zhu, Tao Liu, Suzan Samra, Huiming Hua, Andreas Bechthold. Exploiting and Elucidation of a new Glycosylated Polyketide from Fungus Myrothecium sp., 2016 VAAM Annual Conference, 03/2016, Jena, Germany VI. Jing Zhu, Songya Zhang, Andreas Bechthold. Revealing the Hidden “domain skipping” Biosynthetic Mechanism in the Annimycin Polyketide Synthase from S. asterosporus DSMZ 41452. VAAM workshop, 09/2016, Freiburg, Germany VII. Jing Zhu, Xiaohui Yan, Anja Greule, Songya Zhang, Andreas Bechthold. Exploring the Biosynthetic Capability of Ganefromycin by Direct Cloning and Heterologous Expression, Annual Conference 2016 of the Association for General and Applied Microbiology (VAAM), 03/2016, Jena, Germany VIII. Anja Greule, Songya Zhang, Andreas Bechthold. Foxicins: Ortho-Quinone Derivates produced by Polyketomycin Producer Streptomyces diastatochromogenes
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