Mass Spectrometric Studies of Thiotemplate Biosynthesis

硫模板生物合成的质谱研究

基本信息

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
项目类别：
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

项目摘要

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（由适用提供）：随着微生物基因组测序变得更加宽度，微生物生产天然产物的能力变得更好。这种竞争性更新使用最新的计算和表达筛选来调查这种能力，并针对天然产品的特定子类，这些产品从从根本上是从微生物世界中发现天然产品的新平台出现的。此处描述的是对特定天然产物及其基因簇的追求，这些产品及其基因簇是从一种新的方法中出现的，该方法可以实现大规模的生物合成基因簇与它们的小分子进行发现。从178个静脉细菌菌株的库中，使用了一种支持基因组的代谢组学方法（又称“ Metablenomics”）来正确识别天然产物并将其与其生物合成基因簇相关联。拟议的研究扩展了此方法，以检查未知代谢物，tambromycin（AIM 1）和偶氨酰胺（AIM 2），每个酶都表现出各自的簇，表现出异常的生物合成机制和单体，例如新氨基酸，“ Tambromeline”（请参阅AIM 1）。在前两个目的中，将研究并定义这些新天然产物的蛋白质结合靶标的精确结构，生物合成细节以及蛋白质结合靶标。在AIM 3A中，将在硅酸盐中开采一组新的基因集合对，以销售终止在还原域中的人，因此很可能会因降低thiotemplate组装线的卸载而避开了亲电的弹头。 AIM 3B提出了这种基因群集聚焦方法的扩展，以通过靶向矿体数据靶向采矿来发现新的生物活性代谢产物，以促进其他已知会引起生物活性的药物委托书。根据序列数据，提出了一种新的多烯抗生素的特定情况，表明在生物合成簇中存在多个脱氢酶结构域。用“ Metablogenomics”开采微生物世界是从过去的R01赠款中的过去活动的重大转变（在过去的授予期间导致了18个出版物）。借助一组新化合物及其生物合成基因簇，研究人员将以目标模式追求其中的几种。除了该提案的直接影响之外，这项工作为自然产品发现中“ OMICS”驱动的复兴提供了一条主要的途径。这样的复兴有望为基于结构的天然产物发现的更确定性的途径，并以在现场看不到的速率提供这些结构（如最近的文献中所述，“高吞吐量发现”）。从本质上讲，拟议的研究将证明受调节的微生物菌株收集到真正的化合物库中的价值，该化合物被称为表达和潜在的特定子结构（例如，电动弹头）。这些价值建议是促使理由，以合并一种新型的发现管道，其中包含独特的分子结构和生物活性测定法。

项目成果

期刊论文数量（39）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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
影响因子：
0
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.

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
影响因子：
0
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

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.

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.