基因组挖掘是一种从基因组数据中自动检测和注释生物合成基因簇(BGC)的计算方法。由于现在可用的大量测序数据,这种方法已经越来越多地用于天然产物(NP)发现。核糖体合成和翻译后修饰的肽(RiPP)是一类具有多种生物活性的结构复杂的NP。RiPP最近被证明占据了比以前想象的更大的基因组和化学空间,这表明RiPPBGC在基因组中的注释在过去可能被忽视了。这篇综述概述了专门开发的基因组挖掘工具,以帮助发现RiPPBGC,它们是由越来越多的RiPP结构和生物合成知识库建立起来的。鉴于这些最近的进步,靶向基因组挖掘的应用具有巨大的潜力,可以加速重要分子的发现,例如抗微生物剂和抗癌剂,同时增加我们对这些化合物如何在自然界中生物合成的理解。
Genome mining is a computational method for the automatic detection and annotation of biosynthetic gene clusters (BGCs) from genomic data. This approach has been increasingly utilised in natural product (NP) discovery due to the large amount of sequencing data that is now available. Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of structurally complex NP with diverse bioactivities. RiPPs have recently been shown to occupy a much larger expanse of genomic and chemical space than previously appreciated, indicating that annotation of RiPP BGCs in genomes may have been overlooked in the past. This review provides an overview of the genome mining tools that have been specifically developed to aid in the discovery of RiPP BGCs, which have been built from an increasing knowledgebase of RiPP structures and biosynthesis. Given these recent advances, the application of targeted genome mining has great potential to accelerate the discovery of important molecules such as antimicrobial and anticancer agents whilst increasing our understanding about how these compounds are biosynthesised in nature.