Biochemical Characterization of Specificity for Family 3 Glycoside Hydrolases

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DESCRIPTION (provided by applicant): The human distal gut microbiome is an extraordinary example of a mutualistic relationship wherein trillions of microbes ferment dietary and host-derived carbohydrates and the products of fermentation contribute to nutrient acquisition, gut epithelial health, and immune system development. The NIH-funded human microbiome project will generate nearly 1000 reference genomes from cultured and non-cultured microbes, and will supplement this data with DNA sequencing of microbial samples taken from human subjects. Glycoside hydrolases (GHs) comprise a significant proportion of the genes encoded by microbial genomes within the human distal gut microbiome and contribute to the depolymerization of recalcitrant dietary polysaccharides. A recent metagenomic analysis of the human distal gut microbiome revealed that of the 81 GH families present in the distal gut microbiome, GH family 3 was the most highly represented, which indicates that this gene family is important for carbohydrate utilization by the gut microflora. A number of different functional activities have been described for GH family 3 enzymes although the molecular determinants that define substrate specificity for these enzymes have not been elucidated. The long-term goal of the proposed research is to provide insight into the role of the GH family 3 genes in the metabolic repertoire of human gut microorganisms. In aim 1 we will characterize the substrate specificities of four GH family 3 enzymes from the bacterium Prevotella bryantii Bi4 using a library of natural plant cell wall derived oligosaccharides. In aim 2 we will employ a directed evolution approach for identifying amino acid residues that contribute to substrate specificity for one of these GH family 3 enzymes from P. bryantii Bi4. Results from the proposed studies will provide insight into the molecular determinants of substrate specificity for GH family 3 genes and will allow us to place this important gene family in the context of the metabolic repertoire of the gut-associated microflora.