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.

项目概要/摘要 人类结肠中含有大量的微生物，这些微生物统称为结肠微生物。 微生物组。结肠微生物组中的微生物以拟杆菌门和拟杆菌门细菌为主。 厚壁菌门。在拟杆菌门中，普雷沃氏菌属（Prevotella spp.）。和拟杆菌属。大量存在于结肠环境中 并进化出了一种复杂的蛋白质机制，使它们能够从宿主和不可降解的物质中获取能量 饮食中的多糖和宿主衍生的聚糖，例如粘蛋白。底层机制的核心 拟杆菌属的多糖降解是多糖降解位点 (PUL) 或位点 (PUL) 存在于他们的基因组上。 PUL 由编码蛋白质的基因簇组成，这些蛋白质使 拟杆菌能够感知、运输多种多糖并将其降解为其单位糖以进行发酵。一个 大蛋白质，称为混合双组分系统 (HTCS)，保存在 PUL 中 拟杆菌门通过感知多糖或其寡糖来开启表达来发挥作用 水解酶及其相关转运蛋白。在本提案中，我们证明确实 Bacteroidetes HTCS 包含可感知独特多糖或其降解产物的传感器模块 在结肠环境中。因此，我们假设 HTCS 多肽中的不同传感器共同作用 可以作为个体结肠中多糖传感的代理。我们已将此代理指定为 多糖降解特征或 PDS。通过公开使用 3000 多个 HTCS 序列 根据可用的数据库，我们构建了一个系统发育树，该树似乎将传感器模块聚类为 不同的分支机构。人类饮食中发现的宿主不可降解多糖，例如小麦、大麦、大米 和燕麦一样，是阿拉伯木聚糖。因此，我们利用阿拉伯木聚糖的生长和转录组分析来确定 PUL 分别以三种方式降解可溶性阿拉伯木聚糖和不溶性阿拉伯木聚糖： 人类结肠拟杆菌门的成员。我们的数据表明，我们的系统发育树或 PDS 中的簇 可与阿拉伯木聚糖传感和代谢相匹配。有趣的是，我们还发现拟杆菌 代谢复杂的阿拉伯木聚糖并释放植物酚类化合物阿魏酸的 spp 化合物在用过的介质中积累。众所周知，阿魏酸具有抗氧化作用，还可以保护 防止机械感觉脱发。因此，我们将确定复合阿拉伯木聚糖是否是一种合生元 阿拉伯木聚糖代谢拟杆菌具有针对机械感觉毛发提供保护的能力 无菌斑马鱼的损失。这一观察的证实将使我们能够通过转录组学分析 确定这种保护的潜在分子机制。此外，我们将使用生化和 结构分析以完全表征人类结肠降解阿拉伯木聚糖的机制 拟杆菌门。我们还预计，我们开发的 PDS 将允许合理操纵 个体微生物组感知的多糖对健康和营养有益。