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

人类和动物的肠道菌群对宿主的健康都至关重要。微生物群的组成可以对健康和疾病产生深远的影响，尽管特定的细菌种类可以变化，但它们编码的生化途径（如维生素合成和碳水化合物降解）大致上是保守的。肠道微生物群的基因组学已经导致了大量的关于居住在人类肠道中的微生物的遗传数据，这些微生物编码了大量功能未知的蛋白质。为这些神秘蛋白分配功能是该领域最重要的挑战之一。这对于增加微生物组研究的关键背景和合理操纵微生物群以造福人类和动物健康至关重要。生活在复杂微生物群落中的一个重要方面是菌株之间对资源的竞争。对于碳水化合物，这可以包括饮食来源、宿主衍生分子或来自其他微生物的物质。我们将细菌生长筛选与组学技术相结合，以鉴定与肠道微生物降解微生物细胞壁聚糖相关的蛋白质。在这个项目中，学生将进行这些未研究的蛋白质的生化和结构表征，以发现新的酶。该学生将接受结构生物学和生物信息学方面的培训，以研究不同细菌中未知功能蛋白质之间的进化关系。该项目最初将专注于一个新的糖苷水解酶结构家族，该家族在细菌细胞壁的聚糖上具有活性，在共生生物和病原体（如屎肠球菌）中具有同源物。这些酶所处的遗传环境表明，这些酶在特异性和靶糖方面存在差异，这将在实验中进行测试。结构和生化数据将用于告知新家族和亚家族的分配，并探索这些酶在人类肠道生存中的作用。在导师1的实验室，学生将学习蛋白质生物化学、糖生物学和晶体学，以表征新的酶，以及细菌遗传学，探索这些酶在细菌生理学中的作用，并拜访导师3学习聚糖分离和化学生物学技术。在导师2的实验室中，他们将接受结构/功能关系的生物信息学分析和底物特异性预测的培训。预测和验证结果将反馈到Pfam和InterPro等数据库中，从而通过自动化管道实现更细致的功能预测。这个项目将导致对健康至关重要的微生物过程的有价值的功能特征。

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.