Genomic and synthetic biology tools for expressing natural product gene clusters

用于表达天然产物基因簇的基因组和合成生物学工具

• 批准号: 9316665
• 负责人: Ronald Wayne Davis
• 金额: $ 214.6万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9316665
• 关键词: Address; Anabolism; Animal Model; Anti-Bacterial Agents; Antineoplastic Agents; Biological; Biosensor; Bypass; Chemicals; Collection; Communities; Coupled; Couples; DNA; DNA biosynthesis; Data; Directed Molecular Evolution; Distant; Engineering; Ensure; Evolution; Explosion; Fungal Genes; Fungal Genome; Gene Cluster; Gene Library; Genes; Genetic; Genetic Transcription; Genome; Genomic Library; Genomics; Growth; Health; Human; Impairment; Introns; Laboratories; Libraries; Location; Measures; Methods; Molds; Molecular Chaperones; Mutagenesis; Mutation; Natural Product Drug; Natural Products; Nature; Oligonucleotides; Organism; Pathway interactions; Peptide Hydrolases; Pharmacology; Problem Solving; Process; Production; Productivity; Proteins; RNA Splicing; Saccharomyces cerevisiae; Series; Spliceosomes; Structure; Technology; Therapeutic; Translating; Translations; Yeasts; base; cost; design; functional genomics; fungus; gene product; genetic selection; genome sequencing; genome-wide; genome-wide analysis; genomic data; improved; interest; next generation; novel; overexpression; programs; promoter; protein degradation; protein expression; public health relevance; response; scaffold; screening; success; synthetic biology; tool; whole genome

DESCRIPTION (provided by applicant): The untapped chemical diversity in nature holds tremendous promise of biological and pharmacological relevance. Indeed, as highlighted in this RFA, roughly 75% of antibacterial and anticancer drugs are natural products or inspired by natural products (NPs). However, discovery of secondary metabolite NPs has historically been a laborious and costly process involving producer species that are often difficult to impossible to cultivate. The recent explosion in genome sequence data has additionally revealed that only a fraction of the secondary metabolites from even well-studied species have actually been discovered, due to the clusters being transcriptionally silent under laboratory conditions. Efforts to activate these cryptic or silent gene clusters have been laborious and not scalable to high-throughput discovery. We propose to address this bottleneck in NP discovery by altogether bypassing native, uncultivable hosts and instead developing yeast as a "super-host" capable of expressing a large variety of NP gene clusters. We propose to achieve this objective through four specific aims. Aim 1. Tools for NP DNA design and synthesis. We will use de novo DNA synthesis and develop new synthetic biology tools and genomic technologies to allow heterologous expression of diverse NP pathways in yeast. We will develop this host and its tools while performing heterologous expression of ~600 natural product gene clusters mined from 10 filamentous fungi of diverse ecological origin. Aim 2. Tools to improve yeast as a host for heterologous transcription of fungal NP gene clusters. We will characterize promoter libraries and engineer a fungal spliceosome in S. cerevisiae to allow proper intron splicing. Aim 3. Tools to improve yeast as a host for heterologous translation of fungal NP gene clusters. We will identify yeast strains that serve as improved hosts for heterologous protein expression by screening genome-wide yeast and fungal gene libraries and performing directed in-lab evolution, coupled with a high-throughput readout for protein expression. Aim 4. Tools to improve yeast as a host for heterologous NP production. We will use the library and in-lab evolution screening developed in Aim 3, here applied to a screen for improved NP production. We will also develop tools that users can use to improve expression their own NP pathways of interest. Our proposal addresses all aspects of the genome to NP process, starting with genomic sequence and ending with NPs. The strategy outlined here will allow discovery of an unprecedented number of new NPs.

描述（由申请人提供）：自然界中未开发的化学多样性具有巨大的生物学和药理学意义。事实上，正如RFA所强调的那样，大约75%的抗菌药物和抗癌药物是天然产物或受天然产物（NP）的启发。然而，次级代谢物NP的发现在历史上是一个费力且昂贵的过程，涉及通常难以甚至不可能培养的生产者物种。基因组序列数据最近的爆炸还表明，即使是研究充分的物种，实际上也只发现了一小部分次级代谢产物，因为这些簇在实验室条件下是转录沉默的。努力 激活这些隐藏的或沉默的基因簇是费力的，并且不能扩展到高通量发现。我们建议通过完全绕过原生的、不可培养的宿主，而是开发酵母作为能够表达大量NP基因簇的“超级宿主”来解决NP发现中的这一瓶颈。我们建议通过四个具体目标来实现这一目标。目标1. NP DNA设计和合成工具。我们将使用从头DNA合成，并开发新的合成生物学工具和基因组技术，以允许在酵母中异源表达不同的NP途径。我们将开发这种宿主及其工具，同时对从10种不同生态来源的丝状真菌中开采的~600个天然产物基因簇进行异源表达。目标2.用于改进酵母作为真菌NP基因簇的异源转录宿主的工具。我们将鉴定启动子文库并在S.酿酒酵母允许适当的内含子剪接。目标3.用于改进酵母作为真菌NP基因簇的异源翻译宿主的工具。我们将通过筛选全基因组酵母和真菌基因文库并进行定向实验室内进化，结合蛋白质表达的高通量读数，来鉴定作为异源蛋白表达的改良宿主的酵母菌株。目标4。改进酵母作为异源NP生产宿主的工具。我们将使用目标3中开发的文库和实验室内进化筛选，在此应用于筛选改进的NP生产。我们还将开发工具，用户可以使用它来改善表达自己感兴趣的NP途径。我们的提案涉及基因组到NP过程的所有方面，从基因组序列开始，以NP结束。这里概述的策略将允许发现前所未有数量的新NP。