Publications
Genetic dissection of isoprenoid biosynthesis pathways in Mycobacterium
Abstract
This doctoral dissertation focuses on two parallel, biosynthetic pathways by which bacteria generate a critical isoprenoid precursor molecule. The introduction provides critical background of how these two pathways—the mevalonate (MEV) and the methylerythritol (MEP) pathways— are differentially distributed across the domains of life. More specifically, the introduction highlights the extensive inter- and intra-genus heterogeneity of bacterial isoprenoid synthesis and acquisition strategies, including bacteria that encode either, neither, or both pathways. This thesis uses the genus Mycobacterium to explore pathway diversity, as all bacteria in this genus use the MEP pathway and one exceptional species additionally uses the MEV pathway. In chapter 1, I investigate each of these pathways in the dual pathway-encoding Mycobacterium marinum (Mm). Prior to this work, it was unknown why Mm encodes both pathways and whether either was essential or functional. In this chapter, I leveraged a genetic approach to demonstrate that the MEP pathway is essential for growth and survival, while the MEV pathway is nonessential. Using liquid-chromatography-mass spectrometry (LC-MS), we found that both pathways are functional and interact at the metabolic level. Further I demonstrated that while a deletion of the MEV pathway does not impact growth of the bacterium, it impaired its ability to compete with other bacteria. In vitro macrophage infections and in vivo zebrafish infection revealed that the MEV pathway does not play a role in infection, although engineering the MEV pathway had functional consequences on the survival of Mm upon UV and H2O2 damage. Taken together, this chapter presents the first study to investigate these pathways in Mm. In chapter 2, I focus on the MEP pathway in Mycobacterium bovis BCG, the vaccine strain against tuberculosis. I leveraged a synthetic biology approach to boost the ability of BCG to produce HMBPP, an intermediate of the MEP pathway and a potent activator of human Vγ9Vδ2 T cells, which are protective in the context of Mycobacterium tuberculosis infection. I used bioinformatic analyses to design a synthetic locus of MEP genes, which does not exist in nature. Using an in vitro stimulation assay using peripheral blood mononuclear cells (PBMCs) from human donors, I tested my engineered strains for their ability to induce Vγ9Vδ2 expansion and observed mild expansion over the wild-type vaccine strain. Although much remains to be done, this chapter 2 presents the first work to attempt reengineering of the MEP pathway in the BCG vaccine platform to improve its efficacy. Finally, in chapter 3 I explore the experience of a doctoral program through the lens of equity. Section 1 highlights campus- and department-level DEI initiatives including qualifying exam guidelines that were adopted by the Department of Plant & Microbial Biology at UC Berkeley, as well as the Financial Needs Census I administered to the entire graduate student body as part of the Graduate Assembly. Section 2 outlines grassroots DEI programming at a more local level, including a discussion series that was built and facilitated by students in my lab supergroup. This section serves to outline this initiative as a case study and model for future iterations to approach meaningful integration of DEI work in an academic workplace. Section 3 draws on my experience as a mentor to undergraduates on campus through the L&S Mentors program, as well as in the lab as a research mentor. This section presents research-informed best practices for mentors, providing a flexible framework for graduate students to apply to their mentoring relationships. While these guidelines will no doubt benefit all mentors and mentees, my work centers students of colour by highlighting inclusive practices and rooting my research and writing in the principles of diversity, equity, and inclusion (DEI). Further, I share a mentorship toolkit developed specifically to support the undergraduate experience, which can be applied to mentoring an undergraduate in the lab. Taken together, these local initiatives and best practices can be employed to support equity and retention of marginalized students on an individual basis.
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Genes
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