Accessing the hidden biosynthetic capabilities of fungi

获取真菌隐藏的生物合成能力

• 批准号: 10188555
• 负责人: NANCY P KELLER
• 金额: $ 35.13万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-15 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10188555
• 关键词: Address; Agriculture; Algorithmic Software; Algorithms; Alkaloids; Alleles; Amino Acids; Architecture; Area; Aspergillus fumigatus; Bacteria; Biochemistry; Bioinformatics; Biological; Biology; Birth; Carbon; Chemicals; Chemistry; Computer software; Coupled; Couples; Cytostatics; Development; Dioxygenases; Enzymes; Exhibits; Family; Foundations; Gene Cluster; Gene Expression; Gene Family; Genes; Genetic; Genetic Recombination; Genetic Transcription; Genome; Genomics; Glycols; Grant; Horizontal Gene Transfer; Hot Spot; Immunosuppressive Agents; Laboratories; Lipids; Medicine; Methodology; Methods; Mining; Molds; Natural Products; Nature; Pathway interactions; Peptides; Pharmaceutical Preparations; Plants; Process; Production; Property; Proteins; Public Health; Research; Signal Induction; Signal Transduction; Signaling Molecule; Structural Chemistry; Structure; Technology; Terpenes; Testing; Work; antimicrobial; base; comparative; design; fungal genetics; fungus; genome sequencing; grasp; hybrid protein; innovation; insight; isocyanide; metabolomics; novel; promoter; tool; transcriptome sequencing; transcriptomics

ABSTRACT Filamentous fungi produce a vast universe of secondary metabolites (SM) with biological activities that are of central importance for progress in medicine and agriculture. For example, fungal SMs exhibit cytostatic, immunosuppressant, lipid lowering, or antimicrobial properties. Rapid progress in sequencing the genomes of filamentous fungi has revealed a very large number of putative biosynthetic pathways with no known metabolites, suggesting a vast potential for the discovery of new compounds and activities. However, significant impediments to full characterization of fungal BGC diversity exist: (a) many SMs are synthesized by ‘non-canonical’ biosynthetic gene clusters (BGCs) not recognized by bioinformatic algorithms, (b) many BGCs are not expressed in standard laboratory conditions (e.g. ‘cryptic’ BGCs), and (c) genes for some biosynthetic pathways are not all clustered and involve more than one locus. Further, there is (d) little understanding of the genesis of functional BGCs. Our recent results clearly indicate that non-canonical BGCs reveal genuinely novel structures or unusual biochemistry, that specific fungal differentiation signals induce global BGC expression and that “hot spots” of recombination generate BGC diversity. In this grant, we will (i) characterize isocyanide synthase (ICS) BGCs, a recently discovered family of noncanonical fungal BGCs not recognized by current software algorithms for which we have preliminary results demonstrating new and exciting biochemistry, (ii) use a fungal differentiation signal for transcriptomic identification of ‘invisible' BGCs across diverse fungal taxa and (iii) address the hypothesis that genomic “hot spots” of recombination and horizontal transfer give birth to new BGCs. Based on the premise that non-canonical gene clusters are particularly likely to produce chemical entities with a high degree of structural and functional novelty coupled with two advances able to identify active BGCs and how BGC are formed, our tool set of comparative transcriptomics, advanced endogenous and heterologous expression platforms and a recently developed platform for comparative metabolomics will provide a wealth of new structures, biosynthetic pathways, and biological activities through expansion of the biology, genetics and chemistry of fungal BGCs. Moreover, insight into BGC genesis and identification of global BGC induction signals present genuinely new processes to further the scope of fungal BGC discovery and functional annotation.

摘要 丝状真菌产生大量具有生物活性的次级代谢产物 这对医学和农业的发展至关重要。例如，真菌SM 表现出细胞生长抑制、免疫抑制、降脂或抗微生物特性。迅速进展 在丝状真菌的基因组测序中， 生物合成途径，没有已知的代谢产物，这表明发现的巨大潜力， 新化合物和活性。然而，全面表征真菌存在重大障碍 BGC存在多样性：（a）许多SM是由“非典型”生物合成基因簇合成的 （b）许多BGC不被生物信息学算法识别，（B）许多BGC不以标准表达。 实验室条件下（例如“隐蔽”BGC），以及（c）某些生物合成途径的基因不 都聚集在一起并涉及不止一个基因座。（d）对《公约》的理解不多。 功能性BGC的发生。我们最近的研究结果清楚地表明，非典型的BGC揭示了 真正新颖的结构或不寻常的生物化学，特定的真菌分化信号， 诱导整体BGC表达和重组“热点”产生BGC多样性。在 这项赠款，我们将（i）表征异氰合酶（ICS）BGC，最近发现的 家族的非典型真菌BGC不承认目前的软件算法，我们 有初步结果表明新的和令人兴奋的生物化学，（ii）使用真菌 不同转录组中“隐形”BGC识别的分化信号 真菌分类群和（iii）解决的假设，基因组“热点”的重组和 横向迁移催生了新BGC。基于非典型基因 簇特别可能产生具有高度结构和 功能新奇加上两个进步，能够识别活跃的BGC和BGC是如何 我们的比较转录组学工具集，先进的内源性和异源性 表达平台和最近开发的比较代谢组学平台将 提供了丰富的新结构、生物合成途径和生物活性， 扩展真菌BGC的生物学、遗传学和化学。此外，深入了解BGC 全球BGC诱导信号的发生和鉴定提出了真正的新过程， 进一步扩大了真菌BGC发现和功能注释的范围。