Starch Glycan Utilization by the Gut Microbiota: Structural and Biochemical Insights Into Starch Digestion and the Role of the Colon Microbiota

Abstract

The human digestive system is resident to a highly populated ecosystem of bacterial species known as the colon microbiota, which contributes significantly to our assimilation of dietary and mucosal carbohydrates. Bacteroides thetaiotaomicron is a member of this diverse colon environment and plays a large role in the break down of dietary complex carbohydrates. The process of sensing and responding to glycans present in the colon lumen is predicted to rely on the mechanisms of proteins that are part of complex gene loci deemed polysaccharide utilization loci. Members of these loci are responsible for acquiring substrates at the cell outer membrane, transporting oligosaccharides into the periplasm, degrading them into simple sugars and importing them into the cell. The objective of this thesis is to investigate specific components of the polysaccharide utilization locus 55 and investigate its role as an alternative starch utilization system in B.thetaiotaomicron. Our analysis of an outer membrane binding protein, a SusD homolog, highlights its contribution to this PUL by acquiring starch-derived glycans from the colon lumen. Through our structural characterization of two Family GH31 α-glucosidases we reveal the adaptability of this bacterium at hydrolyzing a range of starch-derived glycans with the emphasis on branched substrates. To understand the transcriptional control of this PUL, we investigated the interaction of this PUL’s response regulator with B.thetaiotaomicron’s genomic DNA. With these results we demonstrate the predicted function of a locus of genes that is capable of contributing to starch hydrolysis in the human colon and the role this locus could play in upregulating related genes in other loci. Through evolutionary analysis of Family 31 α-glucosidases we were able we are able to observe a number of evolutionary changes that we believe resulted in duplicated genes that provided evidence of the colon microbiota being efficient at utilizing dietary starch. These results provide insight into the complex process of the colon microbiota sensing, acquiring and utilizing dietary glycans in the human colon.