Investigations of lanthipeptides derived from human gut microbiome

项目总结/摘要 抗生素耐药性的出现对人类、动物和环境构成了严重的全球性威胁， 和环境健康。因此，迫切需要发现新抗生素的替代来源 以对抗病原性感染，同时限制细菌耐药性的出现。货车德顿克集团 主要研究lanthipeptides，一类核糖体合成和后修饰的 肽（RiPP）天然产物，其特征在于具有潜在的作为 新的药物和抗微生物剂。事实上，羊毛硫肽乳链菌肽已被美国利用。 食品工业作为防腐剂，以打击食源性病原体超过50年，几乎没有 细菌耐药性的发展。人类微生物组是新型RIPP样继发性 代谢产物具有有效的抗菌特性。然而，几乎所有这些天然产品的特性都是 未知，其生物学作用知之甚少。因此，更深入地分析人类微生物组来源的 天然产物不仅会导致新的抗菌化合物的发现， 寻求调节人类微生物群以影响人类健康的疗法。通过基因组挖掘， 来自毛螺菌科细菌C6 A11（lah）的三个新型梭菌RiPP生物合成基因簇（BGC）， 经鉴定为梭菌属（Clostridium indicum）和梭菌属（Clostridium sp.）AF 15 - 17 LB（cls）。毛螺菌C6 A11 定植于人类肠道，其他毛螺菌科细菌与2型糖尿病和耐药性有关 艰难梭菌的肠道定植-医院内寄生虫相关性腹泻的主要原因。BGC 是独特的，因为它们编码一个有趣的翻译后修饰酶（PTM）的星座， 与天然产物所来源的几种不同的前体肽结合。但 所有这些天然产物的特性都是未知的，它们的生物合成也知之甚少。因此 本文提出的研究旨在通过首先开发一种新的普遍适用的 为从E. coli和/或C.用于表征的产孢菌， 生物活性筛选此外，每个PTM酶的作用将通过系统基因检测， 删除。PTM酶的结构-功能关系将通过蛋白质晶体学检查 一部分将被生物工程改造成新的功能完成拟议的研究将导致 发现多达11种具有潜在治疗应用/干预的新型RiPP天然产物 并开发了一个新的普遍适用的平台，用于从 人类肠道微生物组。此外，这项研究的结果将提供一个工具、知识的平台 和技术，将延伸到未来发现新的抗生素，并将形成一个蓝图，预测 鉴定来自人类肠道微生物组的其他类似复杂的BGC。

Project Summary/Abstract The emergence of antibiotic resistance poses a serious global threat of growing concern to human, animal and environmental health. Therefore, there is an urgent need to discover alternative sources of new antibiotics to combat pathogenic infections while limiting the emergence of bacterial resistance. The van der Donk group focuses on the study of lanthipeptides, a class of ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products characterized by lanthionine and methyllanthionine rings that have potential as novel pharmaceuticals and antimicrobial agents. Indeed, the lanthipeptide nisin has been utilized by the U.S. food industry as a preservative to combat food-borne pathogens for more than 50 years with little to no development of bacterial resistance. The human microbiome is a rich source of novel RiPP-like secondary metabolites with potent antimicrobial properties. However, the identities of nearly all these natural products are unknown, and their biological roles are poorly understood. Thus, a deeper analysis of human microbiome-derived natural products would not only lead to the discovery of new antimicrobial compounds but also guide new therapies that seek to modulate the human microbiota in order to impact human health. Through genome mining, three novel Clostridiales RiPP biosynthetic gene clusters (BGC) from Lachnospiraceae bacterium C6A11 (lah), Clostridium indicum (cli) and Clostridium sp. AF15-17LB (cls) were identified. Lachnospiraceae bacterium C6A11 colonizes the human gut and other Lachnospiraceae bacterium are linked to type 2 diabetes, and resistance to gut colonization by Clostridium difficile - a leading cause of nosocomial antibiotic-associated diarrhea. The BGCs are unique in that they encode an intriguing constellation of posttranslational modification enzymes (PTM) in conjunction with several distinct precursor peptides from which the natural products are derived. However, the identities of all these natural products are unknown and their biosynthesis poorly understood. Therefore, the research proposed herein is designed to examine all three BGCs by first developing a new generally applicable platform for accessing these natural products from E. coli and/or C. sporogenes for characterization and bioactivity screening. In addition, the role of each PTM enzyme will be examined through systematic gene deletions. The structure-function relationships of the PTM enzymes will be examined via protein crystallography and a subset will be bioengineered towards new functionalities. Completion of the proposed research will lead to the discovery of up to eleven novel RiPP natural products with potential therapeutic applications/interventions and the development of a new generally applicable platform for accessing other RiPP-like natural products from the human gut microbiome. In addition, the findings from this research will provide a platform of tools, knowledge and techniques that will extend to future discovery of new antibiotics and will form a blueprint for predicting the identity other similarly complicated BGCs from the human gut microbiome.