Abstract

Microbial specialized metabolites are pervasive in their use as natural products. From antibiotics and anticancer drugs to food additives and cosmetic products – human have benefitted immensely from small, specialized metabolites produced by microscopic organisms. Production of such molecules is typically encoded by biosynthetic gene clusters (BGCs), which can be identified during computational analysis of genetic sequencing data. Global analysis of genomic data suggests that despite almost 100 years of discovering antibiotics from microbes, the majority of BGCs encode the production of novel, undiscovered bioactive chemistry. Two major questions arise when mining genomes for BGCs: How do we prioritize BGCs to discover novel natural products? How do we increase the expression of BGCs to facilitate the encoded production of bioactive chemistry? To help answer these big questions, I investigate the diversity and regulation of a class of specialized metabolites called polycyclic tetramate macrolactams (PTMs) as a model system. I systematically classified BGCs using comparisons of BGC architecture and evolutionary models of encoded enzymes, paired with metabolomics data and biosynthetic mutants. This critical analysis provides a map of PTM diversity but also contains several vignettes illustrating the limitations of predicting genes-to-molecules. After laying out the landscape of all PTM BGCs, I characterized one of the PTM BGC groups further. Group 6 PTM BGCs are found in two different genera, Streptomyces and Kitasatospora. Despite BGCs from members of each genus containing the same gene content with a high degree of sequence identity, I showed that Kitasatospora produced PTMs not made by Streptomyces, leading to the discovery of novel specialized metabolites and further exemplifying the limitations of genome mining. Finally, I sought to understand the regulation of Group 6 PTM BGCs. By mapping transcript start sites and measuring reporter expression of promoter bashing mutants, I characterized the promoters that drive expression of these BGCs. I showed that despite a common evolutionary history and ability to function in their native hosts, Group 6 promoters exhibited different functionality from each other in a heterologous host. The results presented across this dissertation showcase the unexpected diversity of specialized metabolic pathways on multiple levels. By presenting correlations of genetic, chemical, and transcriptional diversity amongst PTM BGCs, I have helped shed light on an intriguing family of specialized metabolites, though many of the lessons learned can be applied to other families of natural products.

Committee Chair

Joshua Blodgett

Committee Members

Arpita Bose; Christina Stallings; Joseph Jez; Rebecca Bart; Timothy Wencewicz

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Plant & Microbial Biosciences)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

8-11-2026

Language

English (en)

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Available for download on Monday, August 07, 2028

Included in

Microbiology Commons

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