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。 结肠微生物组中的微生物以拟杆菌门和 拟杆菌门中，普氏菌属和拟杆菌属在结肠环境中大量存在。 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，是潜在机制的核心。 拟杆菌属的多糖降解是多糖降解位点 (PUL) 或位点 (PUL) PUL 存在于它们的基因组上，由编码蛋白质的基因簇组成。 拟杆菌能够感知、运输各种多糖并将其降解为其单位糖用于发酵。 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 在这个提案中，我们证明了水解酶及其相关转运蛋白确实存在。 Bacteroidetes HTCS 包含可感知独特多糖或其降解产物的传感器模块 因此，我们加强了 HTCS 多肽中的多种传感器的结合。 可以作为个体结肠中多糖传感的代理，我们将该代理指定为 多糖降解特征 (PDS) 通过使用公开的 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 人类饮食中发现的宿主不可降解的多糖，如小麦、大麦、大米。 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： 我们的数据显示，我们的系统发育树或 PDS 中存在簇。 可以隐式地匹配阿拉伯木聚糖的传感和代谢，我们还发现了拟杆菌。 代谢复杂的阿拉伯木聚糖的 spp 会释放植物酚类化合物阿魏酸，并且 已知阿魏酸化合物在用过的培养基中积累具有抗氧化作用并具有保护作用。 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 这一观察结果的确认将使我们能够通过转录组学分析来确定无菌斑马鱼的损失。 此外，我们将使用生物化学和方法来确定这种保护的潜在分子机制。 结构分析以完全表征人类结肠降解阿拉伯木聚糖的机制 我们还预计 PDS 的开发将允许对拟杆菌进行合理的操纵。 个体微生物组感知的多糖对健康和营养有益。