Design and construction of modular genetic devices and the enzymatic hydrolysis of lignocellulosic biomass

Abstract

The enzymatic deconstruction of lignocellulosic plant biomass is performed by specialist microbial species. It is a ubiquitous process within nature and central to the global recycling of carbon and energy. Lignocellulose is a complex heteropolymer, highly recalcitrant and resistant to hydrolysis due to the major polysaccharide cellulose existing as a crystalline lattice, intimately associated with a disordered sheath of hemicellulosic polysaccharides and lignin. In this thesis I aim to transfer the highly efficient cellulolytic mechanism of the bacterium Cellulomonas fimi, to that of a suitably amenable and genetically tractable expression host, in the hopes of better understanding the enzymatic hydrolysis of lignocellulose. Using tools and concepts from molecular biology and synthetic biology, I constructed a library of standardised genetic parts derived from C. fimi, each encoding a known enzymatic activity involved in the hydrolysis of cellulose, mannan or xylan; three of the major polysaccharides present in lignocellulose. Characterization assays were performed on individual parts to confirm enzymatic activity and compare efficiencies against a range of substrates. Results then informed the rational design and construction of parts into modular devices. The resultant genetic devices were introduced into the expression hosts Escherichia coli and Citrobacter freundii, and transformed strains were assayed for the ability to utilize various forms of xylan, mannan and cellulose as a sole carbon source. Results identified devices which when expressed by either host showed growth on the respective carbon sources. Notably, devices with improved activity against amorphous cellulose, crystalline cellulose, mannan and xylan were determined. Recombinant cellulase expressing strains of E. coli and C. freundii were shown capable of both deconstruction and utilization of pure cellulose paper as a sole carbon source. Moreover, this capacity was shown to be entirely unhindered when C. freundii strains were cultured in saline media. These findings show promise in developing C. freundii for bioprocessing of biomass in sea water, so as to reduce the use of fresh water resources and improve sustainability as well as process economics. Work presented in this thesis contributes towards understanding the complementarities and synergies of the enzymes responsible for lignocellulose hydrolysis. Moreover, the research emphasizes the merits of standardizing genetic parts used within metabolic engineering projects and how adopting such design principles can expedite the research process.