Computational tools and analytical methods for effective metabolic engineering of microbial cell factories

Research output: Book/ReportPh.D. thesis

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Abstract

Biomanufacturing of chemical and natural products is set to improve environmental sustainability and increase reliability of the production processes. Using microbial cell factories for biomanufacturing opens up a large range of potential products, especially considering the ability to produce non-native products through metabolic engineering.While possible, metabolic engineering remains challenging due to the inherent complexity of microbial metabolism. Metabolic engineering addresses this challenge by following an iterative design-build-test-learn (DBTL) cycle, where the design and the build phase have seen the most advancements in recent years. The full cycle would benefit from high-throughput and automated strategies, which can be implemented both in the laboratory and digitally. In this thesis, two computational tools and two analytical methods were developed to improve the performance and throughput of the test and learn phases. Regarding the test phase, a high-throughput workflow for absolute quantitative proteomics was established and integrated into an automated data analysis tool. An optimised sample preparation protocol for membrane proteomics was developed, which results in a more representative membrane fraction for proteome-wide analysis. As a tool for the learn phase, a kinetic model was constructed to investigate the inner workings of metabolism through integration of proteomics, metabolomics and fluxomics data. Altogether, the computational tools and analytical methods presented here could be applied to improve future development of microbial cell factories.
Original languageEnglish
Place of PublicationKongens Lyngby
PublisherTechnical University of Denmark
Number of pages172
Publication statusPublished - 2023

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