Assigning activity to proteins of unknown function - enzyme discovery in the gut microbiota

The gut microbiota of both human and animals is critical to host health. The composition of the microbiota can have profound effects on health and disease, and though specific bacterial species can vary, the biochemical pathways they encode such as vitamin synthesis and carbohydrate degradation are broadly conserved. Genomics of the gut microbiota has led to a wealth of genetic data about the microbes that inhabit the human gut which encode large numbers of proteins of unknown function. Assigning functions to these mystery proteins is one of the most important challenges in the field. This is essential to add critical context to microbiome studies and enable rational manipulation of the microbiota to benefit human and animal health.
One important aspect of living in complex microbial communities is the competition amongst strains for resources. For carbohydrates, this can include dietary sources, host-derived molecules or materials derived from other microbes. We have combined bacterial growth screens with 'omics technologies to identify proteins associated with the degradation of microbial cell wall glycans by gut microbes. In this project the student will undertake biochemical and structural characterisation of these unstudied proteins, to discover novel enzymes. The student will receive training in structural biology and bioinformatics to study the evolutionary relationships between proteins of unknown function across diverse bacteria. The project will initially focus on a new structural family of glycoside hydrolases, active on glycans from bacterial cell walls, with homologs in both commensals and pathogens such as Enterococcus faecium. The genetic context the enzymes are found in suggests differences in specificity and target sugars for these enzymes, which will be tested experimentally. Structural and biochemical data will be used to inform assignments to new families and subfamilies, and to explore the role of these enzymes in survival in the human gut. In Supervisor 1's lab, the student will learn protein biochemistry, glycobiology and crystallography to characterise new enzymes, and bacterial genetics to explore the role of these enzymes in bacterial physiology, with visits to supervisor 3 to learn glycan isolation and chemical biology techniques. In supervisor 2's lab they will be trained in bioinformatic analysis of structure/function relationships and develop of predictions of substrate specificity. Predictions and validated results will be fed back to databases like Pfam and InterPro to enable more nuanced functional prediction by automated pipelines. This project will result in valuable functional characterisation of microbial processes essential for health.