Carbohydrate sensing in a human gut symbiont

The human gut contains a vast number of what are known as symbiotic microorganisms. These are microbes that have co-evolved with humans and are part of our normal, healthy digestive tract. Several different species of these microorganisms have been shown to be beneficial to our health. Indeed, having the correct balance of beneficial bacteria is critical to the prevention of a range of intestinal disorders, the most well known being irritable bowel syndrome (IBS). The mechanisms used by these beneficial bacteria to enable them to survive and flourish in the such a competitive environment are currently not well understood. The genome sequence of a prominent member of our gut bacterial community, Bacteroides thetaiotaomicron has paved the way for a fuller understanding of these important processes. The bacterium contains a large number of proteins and enzymes specifically tailored for sensing different carbohydrates in its environment and using them as a source of nutrients. This may be how B. thetaiotaomicron is able to survive so well in the human gut which contains a wide range of complex plant derived carbohydrates from our diet (often called dietary fibre) as well as those produced by our own bodies. Microbes are able to sense changes in their environment, such as the presence of nutrients, by binding specific signalling molecules to proteins on the surface of the cell. The recognition of these extracellular molecules activates gene expression changes in the bacteria that enable them to respond to the change in their environment. However, the identity of these signalling molecules and the mechanism by which they are recognised is currently unclear. The aim of this project is to identify the important environmental signalling molecules that recognised by B. thetaiotaomicron and further our understanding of how they are sensed by the bacterium and the changes in gene expression that result. The prospective outcomes of this research are a fuller understanding of the mechanisms symbiotic bacteria have evolved to survive in the human intestine and possibly some insight into what dietary supplements we could use to encourage the growth of these beneficial organisms over harmful ones, thus benefiting human health.

Regulation of gene expression in response to changes in the external environment is critical to the survival of all cells. In bacteria, responses to changes in the extracellular milieu are often mediated by two-component systems (TCS). Although the basic biochemistry of TCS is quite well understood, several important issues are less clear. In particular there is a paucity of data on the identity and complexity of the signalling molecules that activate TCS. Bacteroides thetaiotaomicron, a prominent member of the human gut microbiota which plays an important role in human health and nutrition, synthesises an extensive repertoire of catabolic enzymes that enable the organism to utilise both plant and host-derived polysaccharides and is critical to its ability to survive in the highly competitive community of the large intestine. Recently it has been shown that the polysaccharide degrading apparatus of B. thetaiotaomicron is regulated by novel hybrid two-component systems (HTCS), which contain all of the domains of a canonical TCS in a single polypeptide. In view of the role of B. thetaiotaomicron in the maintenance of human health it is important that the molecules which regulate expression of the enzymes that enable the bacterium to access complex carbohydrates are identified and the mechanism of signal perception is understood. Recent studies by the applicant and his collaborators have identified the HTCS that activate the expression of different polysaccharide utilisation loci in response to specific carbohydrate polymers, and the periplasmic sensory domains of several HTCS have been expressed in a recombinant form. In this project we will use a combined biochemical and transcriptomics based approach to identify the precise ligands that activate specific HTCS, and provide a fuller understanding of the mechanisms of signal recognition in these generic prokaryotic regulatory systems.