Research in the Gardner lab uses an interdisciplinary approach including systems biology (transcriptomics and proteomics), classical bacterial genetics (making targeted and random gene disruptions), and biochemistry (enzyme purification and assay) to understand the regulation and mechanisms of plant cell wall degradation by bacteria. We use the soil bacterium Cellvibrio japonicus because of the sophisticated genetic tools to manipulate the microorganism, and because this bacterium has the incredible ability to completely depolymerize all plant cell wall constituents to obtain carbon and energy. We have four fundamental questions that drive our research:
How do bacteria sense the environment and detect lignocellulose?
The crystalline and hydrophobic nature of the polymers that comprise plant cell walls make them largely insoluble and inaccessible to most bacteria. Our microarray data shows that C. japonicus is not only able to detect lignocellulose, but can alter the composition of degradative enzymes over time as it depolymerizes the substrate. Currently, our lab is dissecting what signals cause these physiological and metabolic changes necessary for insoluble polysaccharids degradation.
What proteins are needed for complete consumption of lignocellulose?
There are several hundred genes predicted to be involved in degrading lignocellulose in C. japonicus. But it is unclear which genes encode proteins with functions that are absolutely critical for degradation. Work in our lab has identified several gene products that are critical for the degradation of the plant polymer cellulose. Through mutational analysis and enzymatic assay we are expanding our understanding of what proteins are essential for plant cell wall degradation in C. japonicus.
With several hundred proteins to synthesize and export to degrade lignocellulose, it is unclear how this process is regulated. Our transcriptomic and genetic data suggest that degradation is done in a coordinated manner, and we have identified several pathways critical for plant cell wall degradation. Further analysis of the physiological and metabolic changes that take place during the course of plant cell wall degradation will elucidate how this complex process unfolds.
We have previously engineered an ethanol production pathway into C. japonicus and shown that when grown on the plant polymer cellulose, C. japonicus can produce bio-ethanol. Future work in our lab will use synthetic biology (i.e. metabolic engineering) to examine the possibility of incorporating novel metabolic pathways into bacteria with useful industrial properties.