ORCID

http://orcid.org/0000-0002-0150-1777

Date of Award

Spring 5-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Plant & Microbial Biosciences)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

Streptomyces are Gram-positive and filamentous bacteria with high-G+C genomes, which have yielded over half of all clinically used antibiotics plus many other useful compounds. Genome analyses indicate that these bacteria possess biosynthetic gene clusters (BGCs) encoding for many more antibiotic-like compounds than they are known to produce. The apparent silence of many BGCs poses a significant roadblock to genome-mining efforts for novel drugs. To understand BGC silence, I compared several Streptomyces that harbor the widespread BGC for polycyclic tetramate macrolactam (PTM) antibiotics to explore the genetic variations that differentiate robustly expressed BGCs from silent BGCs. To test the prevalent hypothesis that silent BGCs are transcriptionally downregulated, I specifically compared the promoters of the PTM BGCs encoded within closely related members of the S. griseus clade. I found that PTM production by S. griseus clade strains indeed varies due to differences in the strengths of their PftdA promoters that drive PTM production. A key finding from these experiments was an ‘AG’ indel that differentiated strong and ‘silent’ PftdA promoters. This ‘AG’ indel tuned PTM production by strongly changing PftdA strength when deleted or reintroduced in wild-type PftdA sequences. I also showed that the global quorum-responsive transcription regulator, AdpA, upregulated S. griseus clade PftdA promoters. Unexpectedly, I also found that PTM expression in the S. griseus clade strain JV180 was dependent on the griseorhodin BGC, which was only present in the genomes of S. griseus clade strains having robust PTM expression. This finding suggested that strain-to-strain differences in PTM expression is caused by more complex factors than just promoter sequence variations alone. Finally, I also explored the diversity of biosynthetic genes in PTM BGCs, and the effects of these genes on the structures of PTM molecules. These results demonstrate a clear utility for PTM biosynthesis as a model system for understanding how genetic variations ranging from the short indels to entire BGCs can tune antibiotic production in Streptomyces.

Language

English (en)

Chair and Committee

Joshua A. Blodgett

Committee Members

Joseph Jez, Barbara Kunkel, Petra Levin, Timothy Wencewicz,

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