MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities
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DOI：
10.1016/j.cels.2019.09.004
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发表时间：
2019-12-18
期刊：
影响因子：
9.3
通讯作者：
Mohimani, Hosein
中科院分区：
文献类型：
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作者：
Cao, Liu;Gurevich, Alexey;Mohimani, Hosein
核糖体合成和后修饰肽（Ribosomally synthesized and post-deletionally modified peptides，RIPPs）是一类重要的天然产物，含有抗生素和多种其他生物活性化合物。现有的通过结合基因组挖掘和计算质谱来发现RIPPs的方法仅限于从小数据集中发现特定类别的RIPPs，并且这些方法无法处理未知的翻译后修饰。在这里，我们提出了MetaMiner，一个软件工具，用于解决这些挑战，是兼容的大规模筛选平台的天然产物发现。在全球天然产物社会（GNPS）分子网络基础设施中对8个基因组和宏基因组数据集搜索了数百万个光谱后，MetaMiner从不同的微生物群落中发现了31个已知和7个未知的RIPP，包括人类微生物组和地衣微生物组，以及从国际空间站分离的微生物。
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.