Natural Product Genome Mining

描述（由申请人提供）：属于放线菌目的细菌，通常称为放线菌，占人类治疗中使用的微生物天然产物的约75%。虽然主要的制药公司已经远离天然产物作为小分子药物发现的资源，但最近已经认识到，来自海洋来源的放线菌是结构多样的天然产物的重要新来源。特别是，属于Salinispora属的海洋放线菌已被证明是生物活性次级代谢物的丰富来源，包括最近完成治疗癌症的I期临床试验的salinosporamide A。由这种化学多产属产生的化合物几乎跨越所有已知的生物合成类，并导致越来越多的前所未有的生物合成范例的表征。经过二十多年的广泛海洋采样，我们已经收集了5,000多种不同的盐孢菌菌株。这个集合提供了前所未有的机会，进一步探索这种非凡的分类群的生物合成潜力，并解决有关机械生物化学和产生新的结构多样性的进化过程的基本问题。在这里，我们提出了一个基因组挖掘项目，这是不到四年前开始分析六Salinispora基因组序列的延续。该更新申请建立在摩尔（生物合成/基因组挖掘）、詹森（生物信息学/微生物学）和威廉·芬尼克（天然产物化学）实验室之间建立的富有成效的合作基础上。在这次更新中，我们特别提出了五个主要目标： 1)101个盐孢属基因组序列的生物信息学分析，2）新的、具有生物活性的盐孢属天然产物的基因组引导的分离和表征，3）通过转化相关重组克隆表达盐孢属生物合成基因簇，4）通过调控操作激活“沉默”生物合成途径，以及5）盐孢属mTOR抑制剂淋巴抑制素的生物合成分析。这些目标解决了与次级代谢物生物合成途径在一个明确的分类群中的多样性和分布以及产生新的小分子多样性的进化过程有关的根本性重要问题。

DESCRIPTION (provided by applicant): Bacteria belonging to the Order Actinomycetales, commonly called actinomycetes, account for approximately 75% of the microbial natural products used in human therapy. While major pharmaceutical companies have moved en masse away from natural products as a resource for small molecule drug discovery, it has recently become recognized that actinomycetes derived from marine sources represent an important new source of structurally diverse natural products. In particular, marine actinomycetes belonging to the genus Salinispora have proven to be a rich source of biologically active secondary metabolites including salinosporamide A, which recently completed phase I clinical trials for the treatment of cancer. The compounds produced by this chemically prolific genus span virtually all known biosynthetic classes and have led to the characterization of a growing number of unprecedented biosynthetic paradigms. After more than two decades of extensive marine sampling, we have amassed a collection of more than 5,000 diverse Salinispora strains. This collection provides unprecedented opportunities to further explore the biosynthetic potential of this extraordinary taxon and to address fundamental questions about mechanistic biochemistry and the evolutionary processes that generate new structural diversity. Here we propose the continuation of a genome-mining project that was initiated less than four years ago to analyze six Salinispora genome sequences. This renewal application builds upon the productive collaboration established between the Moore (biosynthesis/genome mining), Jensen (bioinformatics/microbiology) and William Fenical (natural product chemistry) laboratories. In this renewal, we specifically address five major aims: 1) the bioinformatic analysis of 101 Salinispora genome sequences, 2) the genome guided isolation and characterization of new, biologically active Salinispora natural products, 3) the expression of Salinispora biosynthetic gene clusters by transformation-associated recombination cloning, 4) the activation of 'silent' biosynthetic pathways by regulatory manipulation, and 5) the biosynthetic analysis of the Salinispora mTOR inhibitor lymphostin. These aims address fundamentally important questions related to the diversity and distributions of secondary metabolite biosynthetic pathways in a well-defined taxon and the evolutionary processes that generate new small molecule diversity.