Natural Product Genome Mining

描述(申请人提供)：属于盐生孢属的海洋放线菌已被证明是一种新的次生代谢物的丰富来源，包括一种化合物(盐孢酰胺A)，该化合物目前正处于治疗癌症的临床试验中。尽管对热带葡萄球菌和花生葡萄球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，表明即使是这些经过充分研究的环境细菌也仍然是天然产品发现的重要资源。我们已经从世界各地的许多采集点收集了数千个盐生孢子菌分离物，这些分离物产生了不同的次生代谢物套件，这表明该属内生物合成多样性的总体广度远远大于先前认识的。我们现在面临着一个独特的机会，可以将强大的基因组序列分析技术与在实验室中对盐霉进行基因操作的能力结合起来，将细菌遗传学整合到天然产品的药物发现过程中。因此，我们提出了一个全面的、多学科的计划，其中将使用创新的基因组挖掘技术，以有效地促进从这一新的海洋细菌群中发现天然产物。为了实现本申请中概述的广泛目标，摩尔和延森实验室建立了长期合作关系，无缝地整合了两个研究项目的互补专业知识。我们提出了两个主要目标。首先，我们将从通过基于生物信息学的基因组挖掘技术发现的热带链霉菌株CNB-440和链霉菌CNS-205中分离、鉴定和检测新的天然产物。从我们对这两个菌株的全面基因组测序和注释中，我们已经确定了五个孤立的基因集，以探索在天然产物生物合成中产生具有良好生物学特性和新的酶机制的新代谢物的可能性。其次，我们将对四个新的盐霉菌菌株的基因组草稿进行测序和注释，其中包括两个新物种太平洋盐霉的系统模式和两个地理和代谢上不同的盐生孢子菌菌株，并对它们进行挖掘，以产生新的次生代谢产物。与公共健康相关：天然微生物产品在医学中发挥着核心作用，它提供了临床上使用的大多数抗生素和抗癌剂，以及用于发现和探索细胞过程的重要生物医学研究工具。随着从细菌中发现新化学实体的速度随着时间的推移而减少，迫切需要创新的方法来提供新的分子支架，以开发药物先导。通过将一种在提供临床相关候选药物方面具有良好记录的新海洋细菌资源与一种全面的天然产品发现方法相结合，该方法采用了对微生物基因组序列和最先进的基因操作的创新分析，我们的目标是释放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药物或抗生素，或者提供开发此类药物的结构基序。公共卫生可能直接受益于这些发现，或者从长远来看，受益于这项研究将获得的天然产品发现过程效率的进步。

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.