Graduate Studies, UNL

 

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

First Advisor

Rajib Saha

Degree Name

Doctor of Philosophy (Ph.D.)

Committee Members

Kevin Van Cott, Nicole Buan, William Velander

Department

Chemical and Biomolecular Engineering

Date of this Version

2025

Document Type

Dissertation

Citation

A dissertation presented to the faculty of the Graduate College of the University of Nebraska in partial fulfillment of requirements for the degree Doctor of Philosophy (Ph.D.)

Major: Chemical and Biomolecular Engineering

Under the supervision of Professor

Lincoln, Nebraska, December 2025

Comments

Copyright 2025, the author. Used by permission

Abstract

Metabolic engineering has made it possible to develop biological processes that were once considered economically unfeasible or uncompetitive. This field has enabled both a robust niche market, whereby products, such as pharmaceutical substances like monoclonal antibodies, are produced exclusively through biological means, as well as an emerging commodity production market. Nonetheless, significant challenges remain in harnessing the unique metabolic capabilities of genetically non-tractable organisms. This dissertation focuses on Rhodopseudomonas palustris CGA009 as a potential chassis for metabolic engineering. To address the issue of genetic intractability, a synthetic biology toolkit was developed to facilitate the expression of heterologous proteins in R. palustris. Leveraging its unique capacity to degrade lignin, a multi-omics approach was employed to explore ligninolytic pathways and identify key enzymes involved in processing different lignin-derived feedstocks. The most significant finding is the hypothesis that R. palustris employs a shared catabolic pathway, utilizing the same set of enzymes to degrade all three major lignin types—H, G, and S. This work also covers the construction of an optimized plasmid-based expression system for R. palustris. This organism's potential application in bioremediation was also assessed, revealing its ability to remove 44% of a 50 ppm dose of perfluorooctanoic acid. Finally, the plasmid retention effects of a relaxase-like mobilization protein, MobV, on R. palustris were investigated. Collectively, this research enhances the ability to metabolically engineer R. palustris, laying the groundwork for its broader application in sustainable biotechnology.

Advisor: Rajib Saha

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