Discovery of novel natural products from plant-associated bacteria

Tian, Qiqi

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https://hdl.handle.net/2142/117553 Copy

Description

Title

Discovery of novel natural products from plant-associated bacteria

Author(s)

Tian, Qiqi

Issue Date

2022-11-22

Director of Research (if dissertation) or Advisor (if thesis)

Zhao, Huimin

Doctoral Committee Chair(s)

Zhao, Huimin

Committee Member(s)

• van der Donk, Wilfred A
• Nair, Satish K
• Ort, Donald R

Department of Study

Biochemistry

Discipline

Biochemistry

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

Synthetic biology, natural product discovery, genomic data mining, plant microbiome.

Abstract

Natural products represent invaluable presents from nature that have inspired the development of numerous medical agents and agrochemicals. The diversity and intricacy of the chemicals conceived by nature are far beyond human being’s imagination. With the advance of DNA sequencing techniques, the chemical spaces hidden in the bacterial genomes but not detectable under routine cultivation were realized, thus incited a new era for natural product discovery via the genome-mining approach. Rapid accumulation of genomic data has led to an exponential increasement of candidate biosynthetic gene clusters (BGCs) awaiting exploration. To that end, target BGC prioritization and high-throughput discovery of novel natural product are desired. In this dissertation, I sought to solve this dilemma from both ends using plant-associated bacteria as a case study. For target BGC prioritization, I proposed, conducted, and validated two new approaches to search for important natural product BGCs in plant ecology, both took the advantage of the advance of sequencing technology. The first approach was based on comparative genomics, which identified hundreds of BGCs whose analogs were enriched in plant-associated bacterial genomes compared to bacteria from other living niches. In addition, new insights were gained into the bacterial secondary metabolisms that are important in plant-associated ecosystems. This work shed lights on the future direction of natural product discovery from plant-associated bacteria. The second approach utilized metagenomic information to prioritize the BGCs that are highly abundant in plant-associated environments. It successfully identified a few BGCs producing compounds that are essential in plant ecology, along with a list of unexplored BGCs. These two approaches have their own limitations and therefore served as complements to each other. Taken together, a road map for natural product discovery from plant-associated bacteria was generated for future experimental validation. To reach rapid characterization of novel natural products, a modular pathway refactoring approach with the potential of uncovering natural products in a high-throughput format was developed based on a published method. Compared to the previous one, the new approach was able to accommodate more genes from more complex BGCs. Two assembly strategies were designed, developed, and tested, using ten BGCs with different sizes as case studies. Lastly, a workflow that can rapidly assay the antibacterial activity of one major type of natural products was described, which can be used for discovery of novel natural products and engineering of known natural products with enhanced bioactivity. The workflow was featured by a sophisticated synthetic biology design to produce, secret, and bioassay natural products and their analogs in Escherichia coli. The bioactivity screening on the analogs of a known natural product was performed, leading to insights to its structure-activity relationship.

Graduation Semester

2022-12

Type of Resource

Thesis

Copyright and License Information

Copyright 2022 Qiqi Tian

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