Biochemical and Biomolecular Engineering Commons^™

Elucidating Mechanisms And Genotypes Underlying Robust Phenotypes In Yarrowia Lipolytica, Caleb M. Walker

Doctoral Dissertations

Robustness is an important phenotype for bioenergy microbes to acquire but is difficult to engineer. Hence, tools for engineering microbial robustness are critical to unlock novel phenotypes for innovative bioprocessing strategies. The oleaginous yeast, Yarrowia lipolytica, is an exceptionally robust microbe that can tolerate stressful environments, assimilate a wide range of substrates, and produce high-value chemicals. In this doctoral dissertation, the impacts of systems biology and metabolic engineering to reveal mechanisms and identify genotypes- underlying robust phenotypes are addressed.

The first approach employs adaptive laboratory engineering to generate a platform strain by which to study superior robust mechanisms. This …

Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo

Doctoral Dissertations

Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …

Metabolic Engineering Of Serratia Marcescens, Qiang Yan

Theses and Dissertations

The potential value of the chitin biomass (e.g. food waste) is recently considered being ignored by landfill. Chitin can be a potential cheap carbon source for converting into value-added chemicals by microorganisms. Serratia marcescens is a chitinolytic bacterium that harbors endogenous chitinase systems. With goals of characterzing S. marcescens chitinolytic capabilities and applying S. marcescens to chemical production from chitin, my dissertation main content includes five chapters: 1) Chapter 1 highlights background information of chitin source, S. marcescens and potential metabolic engineering targets using chitin as a substrate; 2) Chapter 2 demonstrates that ChiR is a key regulator in regulating …

In Silico Driven Metabolic Engineering Towards Enhancing Biofuel And Biochemical Production, Richard Adam Thompson

Doctoral Dissertations

The development of a secure and sustainable energy economy is likely to require the production of fuels and commodity chemicals in a renewable manner. There has been renewed interest in biological commodity chemical production recently, in particular focusing on non-edible feedstocks. The fields of metabolic engineering and synthetic biology have arisen in the past 20 years to address the challenge of chemical production from biological feedstocks. Metabolic modeling is a powerful tool for studying the metabolism of an organism and predicting the effects of metabolic engineering strategies. Various techniques have been developed for modeling cellular metabolism, with the underlying principle …

Exploiting Issatchenkia Orientalis Sd108 For Succinic Acid Production, Han Xiao, Zengyi Shao, Yu Jiang, Sudhanshu Dole, Huimin Zhao

Zengyi Shao

Background: Recent advances in synthesizing valuable chemicals such as organic acids from low-cost renewable biomass through microbial fermentation have attracted great attention. However, the toxicity of organic acids presents a key challenge to the development of an economically viable fermentation process. Therefore, a platform organism that not only produces organic acids but also tolerates the associated toxicity is highly desirable. Results: Here we report the discovery, characterization, and engineering of a yeast strain, Issatchenkia orientalis SD108, that is tolerant to low pH and high concentration of organic acids. This strain demonstrated a higher tolerance compared to I. orientalis ATCC 24210 …

Predicting Enzyme Targets For Optimization Of Metabolic Networks Under Uncertainty, David Christopher Flowers

Masters Theses

Recently, ensemble modeling was applied to metabolic networks for the sake of predicting the effects of genetic manipulations on the observed phenotype of the system. The ensemble of models is generated from experimental wild-type flux data and screened using phenotypic data from gene overexpression and knockout experiments, leaving predictive models. The need for data from multiple genetic perturbation experiments is an inherent limitation to this approach. In this investigation, ensemble modeling is used alongside elementary mode analysis to attempt to predict those enzymatic perturbations that are most likely to result in an increase in a target yield and a target …

Dna Assembler, An In Vivo Genetic Method For Rapid Construction Of Biochemical Pathways, Zengyi Shao, Hua Zhao, Huimin Zhao

Zengyi Shao

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional d-xylose utilization pathway (∼9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (∼11 kb DNA consisting of five genes) and a functional combined d-xylose utilization and zeaxanthin biosynthesis pathway (∼19 kb consisting of eight genes) with high efficiencies (70 - 100%) …