Experiment based genome mining of ribosomal natural products

基于实验的核糖体天然产物基因组挖掘

基本信息

批准号：
8297118
负责人：
PIETER C DORRESTEIN
金额：
$ 46.87万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-04-01 至 2016-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8297118
关键词：
Algorithms Amino Acids Bacillus cereus Biochemistry Biological Factors Biology Chemistry Cholesterol Chronic Disease Clostridium difficile Coculture Techniques Data Defensins Detection Development Eukaryota Future Genetic Genetic Identity Genome Genomics Harvest Human Image In Vitro Infection Invertebrates Lasso Lead Malignant Neoplasms Marines Mass Spectrum Analysis Metabolic Diseases Methodology Microbe Mining Multi-Drug Resistance Nature Organism Penicillins Peptides Pharmaceutical Preparations Post-Translational Protein Processing Prevalence Primates Property Proteomics Published Comment RNA Screening procedure Snails Source Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization Staging Staphylococcus aureus Structure Structure-Activity Relationship Techniques Therapeutic Toxin Translations Viral Work analog antimicrobial drug bacteriocin base falls genome sequencing interest metabolomics microbial microcin novel novel therapeutics pathogenic bacteria programs reconstitution research study response tandem mass spectrometry therapeutic development tool

项目摘要

DESCRIPTION (provided by applicant): Ribosomally encoded natural products were once thought to be of limited structural diversity and uncommon amongst microbes. Over the past few years, however, this viewpoint has changed due to the increased discovery rate of RNPs possessing newly described structural motifs previously ascribed to their nonribosomal counterparts. Nearly every sequenced genome, including invertebrates, contains the genetic capacity to biosynthesize ribosomally- encoded, post-translationally modified natural products such as lantibiotics, bacteriocins, microcins, cyanobactins, thiopeptides, and lasso peptides, thereby making this class of underappreciated natural products perhaps the most dominant in all of nature. What is lacking, however, is a systematic approach to harvest this ubiquitous class of natural products and assess their unique biosynthetic capacity. The difficulty associated with characterizing RNPs in a systematic fashion can be attributed to their falling outside the scope of not only most therapeutic screening programs but also metabolomic or proteomic approaches due to their larger size, structural diversity and extraordinary number of post-translational modifications. This proposal outlines the developmental strategies to create a set of tools for harnessing the biosynthetic potential of ribosomally encoded natural products through mass spectrometry based genome mining. The techniques and methodologies created as a result of the proposed work will not only be important for the detection of therapeutic lead compounds, but also for the efficient characterization of ribosomally encoded toxins secreted by pathogenic bacteria such as Staphylococcus aureus, Bacillus cereus and Clostridium difficile as well as defensins produced by higher eukaryotes such as marine snails, primates and humans. PUBLIC HEALTH RELEVANCE: This work outlines an approach that experimentally mines genome sequences for genetically encoded molecules that control biology. Such molecules serve as great lead compounds for therapeutic development.

描述（由申请人提供）：核糖体编码的天然产物曾经被认为具有有限的结构多样性并且在微生物中并不常见。然而，在过去几年中，由于具有新描述的结构基序（之前归因于其非核糖体对应物）的 RNP 的发现率增加，这种观点发生了变化。几乎每个已测序的基因组，包括无脊椎动物，都含有生物合成核糖体编码的、翻译后修饰的天然产物的遗传能力，例如羊毛硫抗生素、细菌素、小菌素、蓝细菌素、硫肽和套索肽，从而使这类未被充分重视的天然产物可能成为最受重视的天然产物。在自然界中占主导地位。然而，缺乏的是一种系统方法来收获这种普遍存在的天然产物并评估其独特的生物合成能力。以系统方式表征 RNP 的困难可归因于它们不仅超出了大多数治疗筛选计划的范围，而且由于其较大的尺寸、结构多样性和大量的翻译后修饰，也超出了代谢组学或蛋白质组学方法的范围。该提案概述了创建一套工具的开发策略，通过基于质谱的基因组挖掘来利用核糖体编码的天然产物的生物合成潜力。拟议工作所创建的技术和方法不仅对于检测治疗先导化合物很重要，而且对于有效表征由金黄色葡萄球菌、蜡样芽孢杆菌和艰难梭菌等病原菌分泌的核糖体编码毒素也很重要。以及高等真核生物（如海螺、灵长类动物和人类）产生的防御素。公共卫生相关性：这项工作概述了一种通过实验挖掘基因组序列以获取控制生物学的基因编码分子的方法。这些分子是治疗开发的重要先导化合物。