Alloactinosynnema Sp

University of New Mexico UNM Digital Repository Chemistry ETDs Electronic Theses and Dissertations Summer 7-11-2017 AN INTEGRATED BIOINFORMATIC/ EXPERIMENTAL APPROACH FOR DISCOVERING NOVEL TYPE II POLYKETIDES ENCODED IN ACTINOBACTERIAL GENOMES Wubin Gao University of New Mexico Follow this and additional works at: https://digitalrepository.unm.edu/chem_etds Part of the Bioinformatics Commons, Chemistry Commons, and the Other Microbiology Commons Recommended Citation Gao, Wubin. "AN INTEGRATED BIOINFORMATIC/EXPERIMENTAL APPROACH FOR DISCOVERING NOVEL TYPE II POLYKETIDES ENCODED IN ACTINOBACTERIAL GENOMES." (2017). https://digitalrepository.unm.edu/chem_etds/73 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Chemistry ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Wubin Gao Candidate Chemistry and Chemical Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Jeremy S. Edwards, Chairperson Charles E. Melançon III, Advisor Lina Cui Changjian (Jim) Feng i AN INTEGRATED BIOINFORMATIC/EXPERIMENTAL APPROACH FOR DISCOVERING NOVEL TYPE II POLYKETIDES ENCODED IN ACTINOBACTERIAL GENOMES by WUBIN GAO B.S., Bioengineering, China University of Mining and Technology, Beijing, 2012 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Chemistry The University of New Mexico Albuquerque, New Mexico July 2017 ii DEDICATION This dissertation is dedicated to my altruistic parents, Wannian Gao and Saifeng Li, who never stopped encouraging me to learn more and always supported my decisions on study and life. I also dedicate this work to my loving wife Mengqin Cai, who has accompanied me throughout the whole PhD period, as a sincere friend, girlfriend and supportive spouse. In addition, I hope this work could be dedicated to my great country, China, where I grew up and was educated for more than twenty years. Lastly, I want to dedicate this work to Buddha, whose teachings of wisdom guided me to continually improve. iii ACKNOWLEDGMENTS Time flies! It seems yesterday when I started at UNM as a naive freshman who wholeheartedly thirsted for knowledge, research, and foreign culture. However, looking back, immense vivid pictures — laughs, joy, anxiety, struggles, disappointments, persistence, bitter tears, and happiness for the harvest — all emerged in my mind in a moment. In the summer of 2011, I got my first taste of scientific research by doing my graduation project as undergraduate in Keqian Yang’s group. I did not expect that this involvement, an ordinary event as it seemed at that time, would be a turning point in my life. During those two years, I became enthusiastic about doing research. Yang’s and other lab members’ dedication to their work and the harmonious environment inspired me to pursue a PhD in the United States. When I submitted my applications to a number of universities in the United States, Dr. Melançon’s ideas about doing research on natural product discovery using a combination of computational tools and experimental methods attracted me immediately. The feeling about Dr. Melançon’s group was like when I placed my feet into the right shoes. My inner voice said “Yes! This is exactly the group I am looking for!” In the Melançon group, I have learned much about natural product discovery while receiving a rigorous, professional training. From literature reading and presenting to progress reports, all have been conducive to my growth and development as a scientist. Dr. Melançon always encouraged me to develop and test my own ideas and to work independently. This freedom has forced me to think independently and work hard. In addition, I met several awesome lab members, Yasushi Ogasawara, Benjamin Yackley, iv Shijie Huang, Jingxuan He, Han Nguyen, and Xuechen Zhu, who became my good friends and influential teachers. The things I have learned during my PhD studies have been tremendous and have changed me immeasurably, from my ways of thinking to my habits in handling things. For example, I tend to take some things for granted. “Be rigorous, well organized!” is what I learned from Dr. Melançon. These words immediately came into my mind when I was lazy or was considering skipping some experimental steps. All the things I have learned here will surely continue to influence me for the remainder of my life. I am also sincerely grateful to my committee members, Dr. Jeremy Edwards, Dr. Lina Cui and Dr. Changjian (Jim) Feng for their insightful suggestions in writing the research proposal and their assistance in completing my research projects. All those who have helped me and have been influential in my life will remain in my memory. I owe them a great debt for all the kind help they have offered to me. I wish everyone who played an indispensable role in my life much happiness in the future. v AN INTEGRATED BIOINFORMATIC/EXPERIMENTAL APPROACH FOR DISCOVERING NOVEL TYPE II POLYKETIDES ENCODED IN ACTINOBACTERIAL GENOMES by Wubin Gao B.S., Bioengineering, China University of Mining and Technology, Beijing, 2012 Ph.D., Chemistry, University of New Mexico, 2017 ABSTRACT Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs produced by these BGCs. First, new degenerate primers were designed to amplify the region containing key “fingerprint residues” used as predictive indicators of the KSα/β gene product novelty. This work resulted in identification of several BGCs encoding potentially novel PK-IIs in the genomes of 54 Actinobacteria, including 38 unique environmental strains. Next, complete vi PK-II BGCs were obtained through whole genome sequencing of 5 strains of high priority. Through combined core structure prediction and bioinformatic analysis, Alloactinosynnema sp. L-07 was chosen for compound isolation. By optimizing fermentation conditions, we purified 3.8 mg of sample to elucidate the structure of this compound, a pentangular PK-II which we named alloactinomicin. In another route, we bioinformatically identified over 500 PK-II BGCs from the NCBI databank, and selected 28 of these predicted to produce structurally novel PK-IIs for experimental characterization by a combined genetic/metabolic approach. As a proof of concept, the CRISPR/Cas9-based genome editing was utilized to achieve KSα gene inactivation in two Streptomyces PK-II BGCs. Comparison of wild-type and mutant metabolite profiles led to identification of new putative PK-IIs and correlation of genotype to chemotype for the PK-II BGC being characterized. Finally, we purified one of the metabolites identified and obtained uv-visible and mass spectral evidences consistent with an angucycline-type PK-II, which we named flavochromycin. This work demonstrates two routes for discovery of novel PK-IIs using genomics- driven bioinformatic/experimental approaches. Results from both routes have laid the foundation for more targeted and efficient ways to discover novel NPs for drug and agrochemical development. vii Table of Contents List of Tables .................................................................................................................. xiii List of Figures ...................................................................................................................xv List of Abbreviations ..................................................................................................... xix Chapter 1. Background and Significance ........................................................................1 1. Introduction ........................................................................................................................... 1 2. Natural Products Produced by Actinobacteria ................................................................. 13 3. Biosynthesis of Type II Polyketides ................................................................................... 16 4. Genomics-driven Discovery of Natural Products ............................................................. 23 5. Summary and Thesis Statement ......................................................................................... 32 6. References ............................................................................................................................ 35 Chapter 2. Automated KSα/β Amplicon-based Identification and Chemotyping of Type II Polyketide BGCs.................................................................................................43 1. Introduction ......................................................................................................................... 43 2. Experimental Materials and Methods ............................................................................... 48 General. ................................................................................................................................

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