Mass Spectrometric Studies of Thiotemplate Biosynthesis

硫模板生物合成的质谱研究

• 批准号: 9905491
• 负责人: NEIL L KELLEHER
• 金额: $ 32.73万
• 依托单位: NORTHWESTERN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2022-08-04
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9905491
• 关键词: Actinobacteria class; Amino Acids; Anabolism; Antibiotics; Bacteria; Basic Science; Binding Proteins; Biological Assay; Chemicals; Collection; Communities; Country; Data; Development; Exhibits; Family; Gene Cluster; Genome; Genomics; Goals; Grant; Hand; Harvest; Health; Hospitals; Human; Hybrids; Investigation; Joints; Laboratories; Left; Libraries; Literature; Medicine; Methods; Microbial Genome Sequencing; Mining; Modeling; Molecular Structure; Molecular Target; Natural Products; Nature; Oxidoreductase; Pharmacologic Substance; Polyenes; Process; Productivity; Proteomics; Public Health; Publications; Research; Research Personnel; Resources; Solid; Source; Stream; Structure; Surveys; Synthesis Chemistry; Work; base; complex biological systems; drug development; human disease; in silico; innovation; insight; interdisciplinary approach; metabolomics; microbial; microorganism; monomer; novel; novel strategies; novel therapeutics; pharmacophore; public health relevance; screening; small molecule

 DESCRIPTION (provided by applicant): As microbial genome sequencing becomes more widespread, the capacity of microorganisms to produce natural products is coming into better view. This competing renewal surveys this capacity using the latest in computational and expression screening and targets specific sub-classes of natural products that emerge from a fundamentally new platform for discovery of natural products from the microbial world. Described here is the pursuit of specific set of natural products and their gene clusters which have emerged from a new approach that achieves large-scale pairing of biosynthetic gene clusters with their small molecules for discovery. From a library of 178 actinobacteria strains, a genome-enabled metabolomics approach was used (a.k.a., "metabologenomics") to correctly identify natural products and correlate them with their biosynthetic gene clusters. The proposed research extends this method to examine unknown metabolites, tambromycin (Aim 1) and rimosamides (Aim 2), each with their respective clusters exhibiting unusual biosynthetic mechanisms and monomers, such as the new amino acid, "tambroline" (see Aim 1). In the first two aims, the precise structures, biosynthetic details and in the case of tambromycin-the protein binding target(s) of these new natural products will be studied and defined. In Aim 3a, a set of new gene cluster-compound pairs will be mined in silico for those that terminate in reductase domains, and therefore likely harbor electrophilic warheads from reductive off-loading from thiotemplate assembly lines. Aim 3b proposes an expansion of this gene-cluster focused approach to discovering new bioactive metabolites by targeted mining of metabologenomics data for other pharmacophores known to elicit bioactivity. The specific case of a new polyene antibiotic is put forth based on sequence data indicating the presence of multiple dehydrogenase domains within the biosynthetic cluster. Mining the microbial world with "metabologenomics" represents a major shift from past activities in this R01 grant (which led to 18 publications over the past granting period). With a set of new compounds and their biosynthetic gene clusters in hand, the investigators will pursue several of these in targeted mode. Beyond the direct impact of this proposal, the work provides a major path forward for an 'omics'-driven resurgence in natural products discovery. Such a resurgence promises a more deterministic path for structure- based discovery of natural products and to provide these structures at a rate not seen before in the field (a.k.a. "high throughput discovery" as described in recent literature). In essence, the proposed research will demonstrate the value of regularizing a microbial strain collection into a bona fide library of compounds, which are known to be expressed and possess particular sub-structures (e.g., an electrophilic warhead). These value propositions serve as motivating rationales to merge a new kind of discovery pipeline containing unique molecular structures with assays for bioactivity.

 描述（由申请人提供）：随着微生物基因组测序变得越来越普遍，微生物产生天然产物的能力越来越受到关注。这种竞争性的更新使用最新的计算和表达筛选来调查这种能力，并针对从微生物世界发现天然产物的全新平台中出现的天然产物的特定子类。这里描述的是追求特定的一组天然产物及其基因簇，这些天然产物及其基因簇是从一种新的方法中出现的，该方法实现了生物合成基因簇与其小分子的大规模配对以用于发现。从178个放线菌菌株的文库中，使用基因组使能代谢组学方法（a.k.a.，“代谢基因组学”），以正确识别天然产物并将其与其生物合成基因簇相关联。拟议的研究扩展了这种方法，以检查未知的代谢物，坦布霉素（目标1）和rimosamides（目标2），每个与其各自的集群表现出不寻常的生物合成机制和单体，如新的氨基酸，“tambroline”（见目标1）。在前两个目标中，将研究和定义这些新天然产物的精确结构、生物合成细节以及坦溴霉素的蛋白质结合靶点。在目标3a中，一组新的基因簇-化合物对将被计算机挖掘，用于那些终止于还原酶结构域的基因簇-化合物对，因此可能含有来自硫模板组装线还原卸载的亲电子弹头。目标3b提出了一种扩展的基因簇为重点的方法，发现新的生物活性代谢物的代谢基因组学数据的有针对性的挖掘其他药效团已知的生物活性。一个新的多烯抗生素的具体情况下提出的序列数据表明存在多个脱氢酶结构域内的生物合成集群的基础上。用“代谢基因组学”挖掘微生物世界代表了R 01资助（在过去的资助期内发表了18篇论文）过去活动的重大转变。随着一系列新化合物及其生物合成基因簇的掌握，研究人员将以靶向模式研究其中的几种。除了这一提议的直接影响外，这项工作还为“组学”驱动的天然产品发现复兴提供了一条重要的前进道路。这样的复苏为基于结构的天然产物的发现提供了一条更确定性的道路，并以该领域以前从未见过的速度提供这些结构（也称为“结构”）。“高通量发现”，如最近文献中所述）。本质上，所提出的研究将证明将微生物菌株集合正规化为真正的化合物库的价值，已知这些化合物被表达并具有特定的子结构（例如，亲电子弹头）。这些价值主张是将含有独特分子结构的新型发现管道与生物活性测定相结合的激励理由。

项目成果

Gobichelin A and B: Mixed-Ligand Siderophores Discovered Using Proteomics.

Gobichelin A 和 B：利用蛋白质组学发现的混合配体铁载体。

• DOI: 10.1039/c2md20232h
• 发表时间: 2013-01-01
• 期刊: MedChemComm
• 作者: Chen Y;Unger M;Ntai I;McClure RA;Albright JC;Thomson RJ;Kelleher NL
• 通讯作者: Kelleher NL

A roadmap for natural product discovery based on large-scale genomics and metabolomics.

基于大规模基因组学和代谢组学的自然产品发现的路线图。

• DOI: 10.1038/nchembio.1659
• 发表时间: 2014-11
• 期刊: NATURE CHEMICAL BIOLOGY
• 影响因子: 14.8
• 作者: Doroghazi, James R.;Albright, Jessica C.;Goering, Anthony W.;Ju, Kou-San;Haines, Robert R.;Tchalukov, Konstantin A.;Labeda, David P.;Kelleher, Neil L.;Metcalf, William W.
• 通讯作者: Metcalf, William W.

Redox metabolites signal polymicrobial biofilm development via the NapA oxidative stress cascade in Aspergillus.

• DOI: 10.1016/j.cub.2014.11.018
• 发表时间: 2015-01-05
• 期刊: Current biology : CB
• 作者: Zheng H;Kim J;Liew M;Yan JK;Herrera O;Bok JW;Kelleher NL;Keller NP;Wang Y
• 通讯作者: Wang Y

A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria.

• DOI: 10.1021/pr2009115
• 发表时间: 2012-01-01
• 期刊: JOURNAL OF PROTEOME RESEARCH
• 影响因子: 4.4
• 作者: Chen, Yunqiu;Ntai, Ioanna;Ju, Kou-San;Unger, Michelle;Zamdborg, Leonid;Robinson, Sarah J.;Doroghazi, James R.;Labeda, David P.;Metcalf, William W.;Kelleher, Neil L.
• 通讯作者: Kelleher, Neil L.

Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation.

• DOI: 10.1021/acschembio.5b00025
• 发表时间: 2015-06-19
• 期刊: ACS CHEMICAL BIOLOGY
• 影响因子: 4
• 作者: Albright, Jessica C.;Henke, Matthew T.;Soukup, Alexandra A.;McClure, Ryan A.;Thomson, Regan J.;Keller, Nancy P.;Kelleher, Neil L.
• 通讯作者: Kelleher, Neil L.