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A Systematic Method for Enhanced Expression of Alcohol Dehydrogenases in Escherichia coli


Type

Thesis

Change log

Authors

Mital, Suraj 

Abstract

Expression of recombinant enzymes in bacteria – principally E. coli - is an important method to generate high yields of industrially valuable proteins in short manufacturing timescales. While an extensive understanding of recombinant protein expression at industrial scale in E. coli has been achieved, challenges such as the formation of inclusion bodies, present limitations that inhibit streamlined manufacturing of recombinant enzymes. The lack of consistent workflows to address enzyme solubility issues often results in difficulties in producing high quantities of catalytically active protein. Commercial alcohol dehydrogenases are enzymes often produced in recombinant systems that are primarily employed in industrial chemical catalysis; the formation of inclusion bodies currently limits product yield of these enzymes. The primary aim of the work described in this thesis was to develop a robust strategy for heterologous expression of aggregate-prone industrially relevant alcohol dehydrogenases to improve their solubility in E. coli, thereby alleviating time-consuming troubleshooting steps in the future. A systematic literature analysis was first carried out to identify routinely adopted strategies used to minimise the likelihood of inclusion body formation in E. coli. This revealed that expression methods typically relied upon ad hoc, trial-and-error approaches with limited guarantees of success. This led to the emergence of the need to develop a systematic approach to handle this problem. Select identified strategies were then used to guide a more systematic experimental approach to cytosolic protein expression, which considered the impact of parameters such as plasmid design, strain variation, media formulation, and expression conditions. Protein expression at relatively high medium pH (pH = 9) led to a 4.47-fold and 5.46-fold improvement in soluble yield for two alcohol dehydrogenase models. The experimental design was further developed to improve the cellular density of the high pH system through fitness modifications to the E. coli strains of interest via adaptive laboratory evolution; the final evolved strain provided a further 4.15-fold and 4.87-fold improvement to the soluble yield of the system for the two alcohol dehydrogenase models. The evolved expression strain, E. coli ALE strain ‘D9’, showed key biological differences compared to the parental strain, E. coli BL21 (DE3). While E. coli BL21 (DE3) responded to protein expression at high pH by reducing/modifying its ribosomal profile and translational processes, the evolved strain reduced pathways related to energy intensive metabolic processes to maintain cytoplasmic pH in alkaline growth conditions. This evolved strain contained seven key mutations that conferred changes to cell envelope stress responses, morphology, and transcriptional/translational regulation that contributed to its fitness. The final E. coli expression system developed in this thesis ultimately improved the soluble yield of two model ‘difficult to express’ alcohol dehydrogenases. At the same time, the work exemplified an alternative view to protein expression that stresses the importance of understanding how E. coli biology, enzyme physicochemical properties, and fermentation conditions can affect the solubility of a DtE enzyme; furthermore, this work highlights the importance matching the requirements of an enzyme of interest with the characteristics of the expression host employed.

Description

Date

2022-10-22

Advisors

Christie, Graham

Keywords

Adaptive Laboratory Evolution, E. coli, Enzymes, Inclusion Bodies, Recombinant Protein Expression, RNA-Sequencing, Whole Genome Sequencing

Qualification

Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
Sponsorship
Johnson Matthey Cambridge. Grant: NQAG/260
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