Doctoral Dissertations

Date of Award

5-2025

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemistry

Major Professor

Constance B. Bailey, Bhavya Sharma,

Committee Members

Ziling Xue

Abstract

Omics techniques such as proteomics and metabolomics are uniquely suited to systemically investigate the metabolism of microbes at a molecular level and provide mechanistic clues to their response under relevant conditions. Microbial communities, such as bacteria, archaea, fungi, and viruses, are vital for ecosystems, biotechnological processes, and human health. For example, they play key roles in processes like microbial fermentation for producing antibiotics, vaccines, pharmaceuticals and also bioremediation for degrading environmental pollutants, such as oil spills, heavy metals, and contaminated groundwater.

Mass spectrometry (MS) enables high-throughput, precise identification, and quantification of proteins and metabolites, facilitating the exploration of microbial physiology and interactions at an unprecedented resolution. This dissertation leverages these advanced techniques to explore microbial community dynamics and unravel cellular processes with high resolution and throughput.

This dissertation employs HPLC-MS and bioinformatics to analyze 6-deoxyerythronolide B synthase expression in heterologous microbial hosts, using analytical and computational approaches to uncover mechanisms and evaluate host effectiveness in supporting protein expression. We found that although P. putida shows distinct N-terminal truncation patterns compared to E. coli BAP1, it is not necessarily a superior host for PKS production. The findings suggest that a more closely related heterologous host may be required for successful full-length protein translation.

Concurrently, the final study of this dissertation employs high resolution mass-spectrometry based metabolomics for developing a standard operating procedure (SOP) of best practices in metabolomic field sampling by utilizing SDC-9, a chlorinated solvent detoxifying bioaugmentation consortia. Through analyzing environmental samples under various storage and extraction conditions, we identified optimal protocols that preserve sample integrity and enhance metabolite detection in field applications by experimenting with different filter types.

This work highlights the significance of mass spectrometry-based proteomics and metabolomics in microbial research, enabling innovative discoveries and applications across disciplines. Through continued advancements in methodologies, omics approaches hold promise for a deeper understanding of microbial life and its myriad implications for science and society.

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