Our lab is focused on understanding the metabolism and physiology of bacteria, specifically how they sense their environment and obtain energy. We use the soil bacterium Cellvibrio japonicus to study how microbes in the soil detect and degrade plant cell walls. Our lab uses the interdisciplinary approaches of molecular genetics (transcriptomics), classical bacterial genetics, and biochemistry. By uncovering the mechanisms of plant cell wall degradation by bacteria we hope to (1) determine how bacteria are able to sense plant cell walls as nutrients, (2) understand how the degradation of plant material is regulated, (3) elucidate unknown gene function in the context of plant cell wall degradation, and (4) engineer useful properties into bacteria that may have industrial applications.
Enzymes are proteins that help accelerate chemical reactions. My research group studies enzymes that degrade polysaccharides, which are long chains of sugar molecules. Enzymes that can degrade polysaccharides are used in detergents, food and drink production, and for making nutritional supplements. In order to have the best enzymes to make these types of products, researchers are looking to the natural world to find bacteria that can degrade polysaccharides with very high efficiency. The idea is that if we understand how these bacteria degrade polysaccharides in nature, we will be able to use similar methods in a laboratory or factory to make better commercial products.
Recent research has shown that certain bacteria can have hundreds of enzymes that degrade polysaccharides, so how do you find which ones are the best? One trick my research group has used is to feed the bacteria only one specific type of polysaccharide. For example, if we wanted to find new enzymes that would be useful in detergents, we would feed the bacteria only starch and then study the enzymes the bacteria produced. This approach can be used for different polysaccharides, and the resulting mix of enzymes we discover can be used to manufacturer renewable fuels, biodegradable plastics, and even poultry feed.
Discovering and characterizing enzymes from nature that have uses in biotechnology or medicine is called bio-prospecting. In order for enzyme bio-prospecting to be effective, many types of bacteria need to be studied, so this type of research not only provides an opportunity to make better consumer products, but also helps us understand the natural world.