Genome mining for natural product biosynthesis: Amino acids, nonribosomal peptides, and ribosomal peptides with posttranslational modifications

Natural products, secondary metabolites produced by microbial species, have served as privileged drug scaffolds in human medicine. Their complex structures are biosynthesized by enzymes encoded in the microbial genome, often referred to as biosynthetic gene clusters (BGCs). Despite the importance of natural products, many biosynthetic pathways of known natural products and related enzymatic mechanisms remain poorly understood. In addition, advances in genome sequencing have revealed numerous orphan BGCs, where either the structure of the natural product or the function of encoded enzymes cannot be reliably predicted. These unresolved questions in natural product biosynthesis motivated my research to explore genome mining for discovering biosynthetic pathways with novel biosynthetic logic and enzymatic mechanisms. In Chapter 1, I introduce the biosynthetic machinery responsible for three classes of natural products: nonribosomal peptides (NRPs), ribosomally synthesized and post-translationally modified peptides (RiPPs), and single amino acid-derived natural products, termed pearlins. Chapter 2 describes a carrier peptide-mediated biosynthesis of the pearlin 3-thiahomoleucine and the reconstitution of a cobalamin-dependent radical S-adenosylmethionine enzyme that catalyzes C-isopropylation. Chapter 3 details the discovery of the nonribosomal peptide threopeptin and the biochemical study of a novel peptide extension machinery. Chapter 4 demonstrates how genome mining of enzymes annotated as ‘domain of unknown function’ led to the discovery of new post-translational modifications in peptide natural products. Overall, these studies revealed unexpected enzyme functions and novel biosynthetic strategies, providing new insights into natural product biosynthesis and new opportunities for future bioengineering applications in drug development.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Yu, Yue

Contributors dc:contributor

• van der Donk, Wilfred
• Zhao, Huimin
• Nair, Satish
• Mehta, Angad

• natural product
• biosynthesis
• enzymes

Statement dc:rights

• Copyright 2025 Yue Yu

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/129669

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F129669