Mechanistic studies to develop a polysaccharide degradation signature (PDS) and its application in improving host health

开发多糖降解特征（PDS）的机制研究及其在改善宿主健康中的应用

• 批准号: 10260593
• 负责人: ISAAC CANN
• 金额: $ 51.12万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-15 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10260593
• 关键词: Adult; Aminoglycoside Antibiotics; Anaerobic Bacteria; Antioxidants; Avena sativa; Bacteria; Bacteriodetes; Bacteroides; Bacteroidetes; Barley; Biochemical; Bioinformatics; Biological; Biological Assay; Biological Availability; Cells; Chemopreventive Agent; Cisplatin; Colon; Communities; Complex; Cytoprotection; Data; Databases; Deposition; Development; Diet; Dietary Component; Dietary Fiber; Dietary Polysaccharide; Distal; Environment; Enzymes; Family; Fermentation; Fiber; Firmicutes; Gene Cluster; Gene Expression; Genes; Genome; Genomics; Germ-Free; Gnotobiotic; Goals; Growth; Hair; Hair Cells; Harvest; Health; Health Benefit; Health Promotion; Human; Hydrolysis; Individual; Link; Mediating; Metabolism; Microbe; Modeling; Molecular; Molecular Profiling; Mucins; Noise; Nutritional; Oligosaccharides; Pectins; Pharmaceutical Preparations; Pharmacology; Phenols; Phylogenetic Analysis; Phytochemical; Plants; Polysaccharides; Prevotella; Proteins; Proxy; Reporting; Rice; Sensory Hair; Structure; System; Trees; Volatile Fatty Acids; Wheat; X-Ray Crystallography; Zebrafish; base; colon microbiome; ferulic acid; improved; in vivo; member; microbial; microbiome; microorganism; multiple omics; nutrition; polypeptide; predictive signature; protein complex; response; search engine; sensor; sugar; transcriptomics; yeast two hybrid system

PROJECT SUMMARY/ABSTRACT The human colon harbors a large number of microorganisms that collectively are referred to as the colonic microbiome. The microbes in the colonic microbiome are dominated by bacteria of the phyla Bacteroidetes and Firmicutes. Among the Bacteriodetes, Prevotella spp. and Bacteroides spp. abound in the colonic environment and have evolved a complex protein machinery that allows them to harvest energy from both host undegradable polysaccharides in the diet and host derived-glycans, such as mucin. Central to the mechanism underlying polysaccharide degradation by the Bacteroidetes is the Polysaccharide Degradation Locus (PUL) or Loci (PULs) present on their genomes. The PULs are composed of gene clusters that encode proteins that enable the Bacteroidetes to sense, transport, and degrade diverse polysaccharides to their unit sugars for fermentation. A large protein, known as the Hybrid Two Component System (HTCS), is conserved in the PULs of the Bacteroidetes and functions by sensing either a polysaccharide or its oligosaccharides to turn on the expression of the hydrolytic enzymes and their associated transporters. In this proposal, we demonstrate that indeed the Bacteroidetes HTCS contain sensor modules that sense unique polysaccharides or their degradative products in the colonic environment. Thus, we hypothesized that the diverse sensors in the HTCS polypeptides collectively can serve as a proxy for polysaccharide sensing in the colon of an individual. We have designated this proxy as the Polysaccharide Degradation Signature or PDS. By using more than 3000 HTCS sequences in the publicly available databases, we constructed a phylogenetic tree that appeared to cluster the sensor modules into different branches. Among host undegradable polysaccharides found in human diets, such as wheat, barley, rice and oats, is arabinoxylan. We, therefore, used growth on arabinoxylan and transcriptomic analysis to determine the PULs that target soluble arabinoxylan and insoluble arabinoxylan degradation, respectively, in three members of the human colonic Bacteroidetes. Our data showed that clusters in our phylogenetic tree or PDS can be matched to arabinoxylan sensing and metabolism. Interestingly, we also discovered that the Bacteroides spp that metabolize complex arabinoxylan release the plant phenolic compound ferulic acid and that the compound accumulates in the spent medium. Ferulic acid is known to have antioxidant effects and also to protect against mechanosensory hair loss. We will, therefore, determine whether a synbiotic of complex arabinoxylan and arabinoxylan-metabolizing Bacteroidetes has the capacity to confer protection against mechanosensory hair loss in germ-free zebrafish. Confirmation of this observation will allow us, through transcriptomics analysis, to determine the underlying molecular mechanisms for this protection. Furthermore, we will use biochemical and structural analyses to completely characterize the mechanism of arabinoxylan degradation by the human colonic Bacteroidetes. We also anticipate that our development of the PDS will allow rational manipulation of the polysaccharides sensed by an individual’s microbiome for health and nutritional benefits.

项目摘要/摘要 人类结肠拥有大量的微生物，共同称为结肠 微生物组。结肠微生物组中的微生物以门类细菌和 公司。在细菌中，prevotella spp。和细菌属。在结肠环境中比比皆是 并发展了一种复杂的蛋白质机械，使他们能够从两个宿主那里收集能量 饮食中的多糖和宿主衍生的聚糖，例如粘蛋白。基础机制的中心 细菌植物的多糖降解是多糖降解基因座（PUL）或基因座（puls） 存在于其基因组上。脉冲由编码蛋白质的基因簇组成 细菌植物感知，运输和降解潜水员多糖以发酵的单位糖。一个 大型蛋白质，称为杂交两个组分系统（HTC），在脉冲中保守 细菌群和通过灵敏度的多糖或其寡糖来打开表达的功能 水解酶及其相关转运蛋白。在这一提议中，我们证明了 细菌植物HTC含有传感器模块，这些模块具有独特的多糖或其降解产物 在结肠环境中。这就是我们假设HTCS多肽中的潜水员传感器 可以作为个体结肠中多糖传感的代理。我们已将这个代理称为 多糖降解签名或PDS。通过在公开中使用3000多个HTCS序列 可用的数据库，我们构建了一个似乎将传感器模块聚集到的系统发育树 不同的分支。在人类饮食中发现的宿主无法基因多糖，例如小麦，大麦，大米 燕麦是阿拉伯素。因此，我们在阿拉伯素和转录组分析上使用生长来确定 靶向可溶性阿拉伯素和不溶性阿拉伯素降解的脉冲在三个 人类结肠杆菌的成员。我们的数据显示，系统发育或PDS中的簇 可以与阿拉伯素的传感和代谢相匹配。有趣的是，我们还发现了杀菌剂 代谢复杂阿拉伯素的SPP释放植物酚类化合物阿拉列酸，并 化合物在支出介质中积聚。血腥酸已知具有抗氧化作用，也可以保护 反对机理感觉脱发。因此，我们将确定是否合成复杂的阿拉伯素的合成 和阿拉伯素氧化物 - 代谢细菌植物具有赋予机理感知头发的保护能力 无菌斑马鱼的损失。确认此观察结果将使我们通过转录组学分析， 确定该保护的基本分子机制。此外，我们将使用生化和 结构分析以完全表征人类结肠的阿拉伯素降解机制 细菌植物。我们还预计，我们的PDS发展将允许合理地操纵 一个人的微生物组感受到多糖，以实现健康和营养益处。