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Thesis Format

Integrated Article

Degree

Doctor of Philosophy

Program

Biochemistry

Supervisor

Edgell, David R.

Abstract

Harnessing organisms for protein and chemical production is useful to the scientific community and has applications in the fuel, food, and pharmaceutical industries. Biological systems commonly used for industrial chemical production include yeast and bacteria due to their fast growth rates and potential for high product yields. However, biologically active proteins, such as for human therapeutics, usually require production in mammalian and insect systems that are prohibitively expensive to grow at scale. Recently, photoautotrophic microalgae have emerged as promising platforms, as some species can be grown quickly and inexpensively at large scales and have the potential to produce biologically active proteins that mimic those produced in mammalian systems. Thus, they combine advantages from several traditional biological systems, but require further genetic and biotechnological development for their full potential to be unlocked.

Ideal biological production systems generally possess a variety of genetic tools to enable foreign gene expression, and genome editing systems to create desired genetic modifications. Here I present a robust gene editing system, novel genetic tools, and valuable strains for the microalga Phaeodactylum tricornutum. First, I identify novel endogenous regulatory elements that can drive expression of foreign genes in P. tricornutum, and design a plasmid-based Cas9 gene editing system for this species. Next, I demonstrate the utility of these tools with the generation of auxotrophic P. tricornutum strains through the genetic knockout of key enzymes in the uracil and histidine biosynthesis pathways. I complement the phenotype of the auxotrophs by introducing intact versions of these genes on replicating plasmids and demonstrate that these genes function as selective markers for transformation of their respective auxotrophic strain. Finally, I highlight the potential of these tools by creating a P. tricornutum expression system for the production of SARS-CoV-2 antigens. This will potentially address the need for a cheap, scalable source of serologically-active antigens for population-wide serological testing to combat the SARS-CoV-2 pandemic, and this system can be rapidly adapted to tackle future pandemics. I hope that these novel tools and strains will broaden the potential applications of P. tricornutum for industrial production of high-value products, and further the study of diatom biology.

Summary for Lay Audience

There is a growing demand for methods to produce food, drugs, and fuels cheaply and in an environmentally sustainable way. One promising solution is to exploit organisms through genetic engineering to synthesize these products for us. Yeast, bacteria, and mammalian cell cultures are commonly used for this purpose but aren’t suitable for all applications, such as large-scale production of pharmaceutical compounds that require special modifications to be functional. Microalgae are promising alternative platforms for these applications as many microalgal species are photosynthetic, making them inexpensive to grow at large scales, and several species have been deemed safe to eat. Some microalgae have also shown the potential to perform the special modifications that are required to produce functional pharmaceuticals. However, many promising microalgae species lack the proper development and tools required to engineer them for these purposes. Here, I develop genetic tools and strains of the marine microalga Phaeodactylum tricornutum to enable industrial-scale production of high-value products in this species.

First, I create novel plasmid-based expression tools, and a CRISPR/Cas9 gene-editing system for P. tricornutum. I then use these tools to generate auxotrophic strains of this species by knocking out key genes in the P. tricornutum uracil and histidine biosynthesis pathways. I show that the auxotroph phenotypes can be complemented by plasmid-encoded intact versions of these genes, providing an antibiotic-free plasmid selection system. Finally, I use these tools and strains to engineer P. tricornutum to produce the SARS-CoV-2 spike protein to potentially address the need for a cheap, abundant source of viral proteins required for serological testing. This expression system can be easily adapted to address future pandemics or produce human therapeutics. The tools and strains generated here will enable industrial-scale production of valuable products in P. tricornutum, and further the study of diatom biology.

Creative Commons License

Creative Commons Attribution-Noncommercial 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License

Available for download on Tuesday, November 30, 2021

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