Natural Product Genome Mining

描述（由申请人提供）：属于Salinispora属的海洋放线菌已被证明是新型次级代谢物的丰富来源，包括一种化合物（salinosporamide a），目前正在临床试验中用于治疗癌症。尽管对热带葡萄球菌和沙菌进行了广泛的发酵研究，但最近的基因组测序显示，这两个分类群中都有大量新的生物合成基因簇，其产物尚未被发现。这一新信息提供了明确的证据，即使是这些经过充分研究的环境细菌，也仍然是发现天然产物的重要资源。我们已经从世界各地的许多收集点收集了数千个Salinispora分离物，这些分离物产生不同的次级代谢物组合，表明该属内生物合成多样性的总体广度远远大于以前认识到的。我们现在有了一个独特的机会，可以结合强大的基因组序列分析技术，以及在实验室中对盐孢菌进行基因操作的能力，将细菌遗传学整合到天然产物药物发现过程中。因此，我们提出了一个综合和多学科的计划，其中创新的基因组挖掘技术将被用来有效地加强对这一新的海洋细菌群的天然产物的发现。为了实现本应用程序中概述的广泛目标，Moore和Jensen实验室建立了长期合作关系，无缝集成了两个研究项目的互补专业知识。我们提出两个主要目标。首先，我们将通过基于生物信息学的基因组挖掘技术，从热带葡萄球菌CNB-440和沙尼科葡萄球菌CNS-205中分离、表征和测试新的天然产物的生物活性。从我们对这两种菌株的全面基因组测序和注释中，我们已经确定了五个孤儿基因集，这些基因集很有可能产生具有良好生物学特性的新型代谢物，并在天然产物生物合成中具有新的酶促机制。其次，我们将对四种新的盐孢菌（包括两种新物种S. pacifica和两种地理上和代谢上不同的S. arenicola菌株）的基因组草图进行测序和注释，并挖掘它们以产生新的次生代谢物。公共卫生相关性：天然微生物产品通过提供临床使用的大多数抗生素和抗癌剂以及用于发现和探测细胞过程的重要生物医学研究工具，在医学中发挥着核心作用。随着细菌中新化学实体的发现率随着时间的推移而降低，迫切需要创新的方法来提供新的分子支架，从而开发药物先导物。通过结合一种新的海洋细菌资源，在提供临床相关的候选药物方面有良好的记录，以及一种综合的天然产物发现方法，采用创新的微生物基因组序列分析和最先进的遗传操作，我们的目标是解锁一组选定细菌的生物合成潜力，并为生物测试提供新的化合物。这些分子有可能被开发成新的抗癌剂或抗生素，或者提供开发这些药物的结构基序。公共卫生可能直接受益于这些发现，或者从长远来看，将从这项研究中获得的天然产物发现过程效率的提高。

DESCRIPTION (provided by applicant): Marine actinomycetes belonging to the genus Salinispora have proven to be a rich source of novel secondary metabolites including one compound (salinosporamide A) that is currently in clinical trials for the treatment of cancer. Despite extensive fermentation studies of S. tropica and S. arenicola, recent genome sequencing has revealed an abundance of novel biosynthetic gene clusters in both taxa whose products have yet to be discovered. This new information provides clear evidence that even these well-studied environmental bacteria continue to represent an important resource for natural product discovery. We have amassed a large collection of several thousand Salinispora isolates from numerous worldwide collection sites that produce distinct suites of secondary metabolites indicating that the overall breadth of biosynthetic diversity within the genus is far greater than previously recognized. We are now presented with a unique opportunity to combine the powerful techniques of genome sequence analysis, along with the ability to genetically manipulate Salinispora in the laboratory, to integrate bacterial genetics into the natural product drug discovery process. We therefore propose a comprehensive and multi-disciplinary program in which innovative genome mining techniques will be employed to effectively enhance the discovery of natural products from this new group of marine bacteria. To accomplish the broad goals outlined in this application, the Moore and Jensen laboratories have established a long-term collaboration that seamlessly integrates the complementary expertise of both research programs. We propose two major aims. First, we will isolate, characterize, and test for biological activity new natural products from S. tropica strain CNB-440 and S. arenicola CNS-205 discovered through bioinformatics-based, genome mining techniques. From our comprehensive genome sequencing and annotation of both strains, we have identified five orphan gene sets to explore that have a high probability to yield novel metabolites with promising biological properties and novel enzymatic mechanisms in natural product biosynthesis. Second, we will sequence and annotate draft genomes of four new Salinispora strains, including two phylotypes of the new species S. pacifica and two geographically and metabolically distinct S. arenicola strains, and mine them for the production of novel secondary metabolites. PUBLIC HEALTH RELEVANCE: Natural microbial products occupy a central role in medicine by providing the majority of the antibiotics and anticancer agents employed in the clinic as well as important biomedical research tools used to discover and probe cellular processes. As the discovery rate of new chemical entities from bacteria diminishes over time, innovative methods are urgently needed to provide new molecular scaffolds from which drug leads can be developed. By combining a new marine bacterial resource that has a proven track record in providing clinically relevant drug candidates together with a comprehensive natural product discovery approach that employs innovative analyses of microbial genome sequences and state of the art genetic manipulation, we aim to unlock the biosynthetic potential of a select group of bacteria and provide new compounds for biological testing. These molecules have the potential to be developed into new anticancer agents or antibiotics, or provide the structural motifs from which such drugs can be developed. Public health may directly benefit from these discoveries or, in the long term, from advances in the efficiency of the natural product discovery process that will be gained from this research.