This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. A genomics‑guided study of the biosynthesis of microbial secondary metabolites Chakrabortti, Alolika 2016 Chakrabortti, A. (2016). A genomics‑guided study of the biosynthesis of microbial secondary metabolites. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/68357 https://doi.org/10.32657/10356/68357 Downloaded on 09 Oct 2021 19:21:04 SGT GENOMICS STUDY OF BIOSYNTHESIS OF MICROBIAL SECONDARY METABOLITES 2016 A GENOMICS-GUIDED STUDY OF THE BIOSYNTHESIS OF MICROBIAL SECONDARY METABOLITES A CHAKRABORTTI ALOLIKA CHAKRABORTTI SCHOOL OF BIOLOGICAL SCIENCES 2016 2016 A GENOMICS-GUIDED STUDY OF THE BIOSYNTHESIS OF MICROBIAL SECONDARY METABOLITES A CHAKRABORTTI ALOLIKA CHAKRABORTTI School of Biological Sciences A thesis submitted to the Nanyang Technological University in partial fulfillment of the requirement for the degree of Doctor of Philosophy 2016 Acknowledgement While submitting this doctoral thesis, I would like to take the opportunity of thanking a few people who stood by me and extended their support and assistance to me at all times during the last few years. First and foremost, I would like to thank my Ph.D-Supervisor Assoc. Prof. Liang Zhao- Xun for being such a source of motivation and encouragement. I am immensely thankful to him for giving me the opportunity and freedom to grow as an independent researcher and take up new challenges. At the same time, I am indebted to him for his invaluable insights and inputs on my research. It has been a complete privilege for me to work under his tutelage. I am deeply thankful to my ex-colleagues – Dr. Ho Chun Loong and Dr. Yang Lifeng for their constant guidance and most importantly for standing by me through thick and thin in the last four years. I would also like to extend my gratitude to my ex-labmate and mentor Dr. Mary Chuah for her guidance. I would like to thank and acknowledge the support of Yeo Qin Yi, Denise Seow, Leow Min Li, Ding Yichen, Huang Peng and Cheang Qing Wei for working with me on this project at various stages. I want to express my gratitude towards all my other former and present lab-mates - Prabhadevi Venkataramani, Amanda Tan, Dr. Sun Hui Hua, Ishin Soehano, Swathi Pasunooti, Koh Siew Lee, Dr. Xu Ling Hui, Jamila Oppong, Yong Grace, Xin Lingyi, Pang Li Mei and Low Zhen Zie for their continuous and unfailing camaraderie. I would also like to thank Dr. Nishanth V. Menon, Dr. Manisha Mukherjee, Areetha D’Souza and Dr. Tan Jiazi for their help and support. I am thankful to all my collaborators; Dr. Yoganathan Kanagasundaram (Bioinformatic Institute, A*STAR, Singapore), A/P Liu Xuewei (School of Physical and Mathematical Sciences, Nanyang Technological University), Asst/P Yang Liang (Singapore Centre on Environmental Life Science Engineering, Singapore), Jinming Li (Southern Medical University, China) and A/P Mark Turner (School of Agriculture and Food Sciences, University of Queensland). I would like to express my sincere gratitude to Dr. Yit Heng Chooi, Research fellow, (College of Medicine, Biology and Environment, Autralian National University) for his advice on the bioinformatic analysis during the early days of the project. Page | i I am extremely thankful to my Thesis Advisory Committee (TAC) members Prof. James Tam, A/P Liu Chuan Fa, Dr. Tang Kai and Dr. Peter Cheung from the School of Biological Sciences, NTU for their valuable inputs and guidance. I am indebted to Nanyang Technological University and Ministry of Education, Singapore for providing me with the NTU research scholarship and grants necessary for my research. Last but not the least a special thanks to my family and friends. I am eternally thankful to my parents for being my biggest source of strength and inspiration at all times. Words are enough to express how grateful I am to all my friends for their being a part of my support- system in such a huge way. This acknowledgement would be incomplete without the mention of Dr. Arnab Kapat, my mentor at Reliance Life Sciences, India, for I would have probably not been here without his constant encouragement and nudging. I am thankful to him for always having some kind words to inspire and motivate me. Page | ii Table of contents Acknowledgement .............................................................................................................. i Table of contents .............................................................................................................. iii List of figures .................................................................................................................... vi List of Tables .................................................................................................................... ix Abbreviations .....................................................................................................................x Abstract .................................................................................................................... xiii Chapter 1 Introduction ..................................................................................................1 1.1 Microbial secondary metabolites .........................................................................1 1.2 Key concepts .......................................................................................................4 Classes of secondary metabolites .........................................................................................5 Biosynthetic mechanisms and enzymes ...............................................................................6 Regulation of secondary metabolism .................................................................................10 1.3 Genomics guided approach to study secondary metabolism .............................12 1.4 Which microbes to choose for genome-mining? ...............................................17 1.5 Leveraging genomics with other techniques .....................................................18 1.6 Genomics and combinatorial biosynthesis of novel compounds ......................22 1.7 Synthetic biology, metabolomics and secondary metabolism ...........................24 1.8 Genomics and future of secondary metabolism research ..................................26 1.9 Naturally occurring dihydroisocoumarins and their biosynthetic mechanism ..27 1.10 Objectives ..........................................................................................................28 Chapter 2 The complete genome of Aspergillus westerdijkiae and secondary metabolism ......................................................................................................................31 2.1 Introduction .......................................................................................................31 2.2 Materials and methods .......................................................................................35 2.3 Results ...............................................................................................................38 2.4 Discussion .........................................................................................................47 Page | iii Chapter 3 Biosynthesis of ochratoxin A in A. westerdijkiae ....................................49 3.1 Introduction .......................................................................................................49 3.2 Materials and methods .......................................................................................54 3.3 Results ...............................................................................................................59 3.4 Discussion .........................................................................................................64 Chapter 4 Biosynthesis of circumdatins and other peptidyl alkaloids in A. westerdijkiae .................................................................................................................69 4.1 Introduction .......................................................................................................69 4.2 Materials and method ........................................................................................72 4.3 Results ...............................................................................................................72 4.4 Discussion .........................................................................................................80 Chapter 5 Genome sequence and biosynthetic potential of Nocardia jinanensis ...83 5.1 Introduction .......................................................................................................83 5.2 Materials and method ........................................................................................87 5.3 Results ...............................................................................................................89 5.4 Discussion .........................................................................................................98 Reference ....................................................................................................................101 Appendix ....................................................................................................................129 Appendix I: Summary of antiSMASH predictions for A. westerdijkiae genome. ...........129 Appendix II: Summary of NRPS and PKS genes in A. westerdijkiae genome………..132