A User Guide for the Identification of New RiPP Biosynthetic Gene Clusters Using a RiPPER-Based Workflow.
A User Guide for the Identification of New RiPP Biosynthetic Gene Clusters Using a RiPPER-Based Workflow.
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使用基于 RiPPER 的工作流程鉴定新 RiPP 生物合成基因簇的用户指南。
DOI：
10.1007/978-1-0716-1358-0_14
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Moffat AD
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文献类型：
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作者：
Moffat AD
近年来，基因组挖掘已成为从微生物中发现新的特化代谢产物的有力策略。然而，发现新组的核糖体合成和后修饰肽（RIPPs），通过采用目前可用的基因组挖掘工具已被证明具有挑战性，由于其固有的偏见，以前已知的RIPPs家族。在本章中，我们提供了使用RiPPER的详细指南，这是一种最近开发的面向RiPP的基因组挖掘工具，旨在以灵活的方式探索基因组数据库的多样性，从而发现真正新的RiPP化学。此外，使用TfuA蛋白的Alphaproteobacteria作为一个例子，我们提出了一个完整的工作流程，集成功能的RiPPER与现有的生物信息学工具到一个完整的基因组挖掘策略。这包括对RiPPER的一些关键更新（更新到1.1版），这些更新大大简化了此工作流的实现。
In recent years, genome mining has become a powerful strategy for the discovery of new specialized metabolites from microorganisms. However, the discovery of new groups ofribosomally synthesized andpost-translationally modifiedpeptides (RiPPs) by employing the currently available genome mining tools has proven challenging due to their inherent biases towards previously known RiPP families. In this chapter we provide detailed guidelines on using RiPPER, a recently developed RiPP-oriented genome mining tool conceived for the exploration of genomic database diversity in a flexible manner, thus allowing the discovery of truly new RiPP chemistry. In addition, using TfuA proteins of Alphaproteobacteria as an example, we present a complete workflow which integrates the functionalities of RiPPER with existing bioinformatic tools into a complete genome mining strategy. This includes some key updates to RiPPER (updated to version 1.1), which substantially simplify implementing this workflow.