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

• 批准号: 8448101
• 负责人: PIETER C DORRESTEIN
• 金额: $ 45.26万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 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/8448101
• 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; 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; screening; tandem mass spectrometry; therapeutic development; tool

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.

描述（由申请人提供）：核糖体编码的天然产物曾经被认为结构多样性有限，在微生物中并不常见。然而，在过去的几年中，由于RNPs具有新描述的结构基序的发现率的增加，这种观点已经发生了变化，这些结构基序以前被归因于它们的非核糖体对偶体。几乎每一个测序的基因组，包括无脊椎动物，都含有生物合成核糖体编码、翻译后修饰的天然产物的遗传能力，如抗生素、细菌素、微素、蓝藻素、硫肽和套索肽，从而使这类未被重视的天然产物可能是自然界中最具优势的。然而，缺乏的是一种系统的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RNPs的困难可归因于它们不仅超出了大多数治疗筛选程序的范围，而且由于它们较大的尺寸，结构多样性和大量的翻译后修饰，它们也超出了代谢组学或蛋白质组学方法的范围。本提案概述了发展战略，以创建一套工具，利用核糖体编码的天然产物的生物合成潜力，通过质谱为基础的基因组挖掘。这项工作所创造的技术和方法不仅对治疗性先导化合物的检测很重要，而且对病原菌（如金黄色葡萄球菌、蜡样芽孢杆菌和艰难梭菌）分泌的核糖体编码毒素以及高等真核生物（如海洋蜗牛、灵长类动物和人类）产生的防御素的有效表征也很重要。