One of the major challenges in biology is to discover ways to convert renewable plant-based material into commodity chemicals and fuels. For this process to be economically feasible, valuable products must be made from lignin, a portion of plant material that now remains mostly unused. Lignin is abundant and its chemical composition holds great potential for bioenergy production and biotechnology. This project seeks to use newly developed tools in computational and experimental biology to manipulate bacterial pathways for improved lignin degradation with the ultimate goal of developing effective methods of generating energy in a renewable fashion. A soil bacterium, Acinetobacter baylyi ADP1, that already degrades a vast array of plant derived compounds will be used in these studies. The degradation capability of this bacterium will be expanded by introducing new genes into the chromosome and by optimizing the expression of the catabolic genes for the desired applications. This integrative project will be accomplished via a multi-disciplinary collaboration, including an international component. Training opportunities will enable students to visit and conduct some of the research in the laboratories of different collaborators. All collaborators have a strong commitment to training students at the undergraduate, graduate and postdoctoral levels. This project will be used to enhance diversity and inclusiveness in the scientific community.
Building on the conceptual framework of synthetic biology, this project will develop A. baylyi as the recipient cell (the chassis) to incorporate genetic modules (devices) to expand bacterial pathways for aromatic compound catabolism. To overcome obstacles that may arise from differences between idealized concepts and biological realities, a novel method of experimental evolution that relies on gene amplification will help optimize metabolic functions. This method exploits the exceptionally high efficiency of natural transformation and homologous recombination in A. baylyi. This bacterium is an ideal chassis for lignin biodegradation because of its powerful genetic system and ability to degrade many aromatic compounds, including those that are toxic to Escherichia coli. Experimental flux analysis and kinetic studies will be used to build dynamical models for the design, optimization, and synthetic expansion of aromatic compound catabolic abilities. Advanced computational tools, developed by a member of this research team, in collaboration with others, will also be applied: Biochemical Network Integrated Computational Explorer (BNICE). To complement these approaches, biochemical, biophysical, and structural studies will examine how the spatial orientation of enzymes can be used to improve catalytic efficiency, target metabolite flow, and prevent toxic intermediates from accumulating.
This collaborative US/UK project is supported by the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council.