MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-09-26 DOI:10.1093/nar/gkaf969

Adriano Rutz, Daniel Probst, César Aguilar, Daniel Y Akiyama, Fabrizio Alberti, Hannah E Augustijn, Nicole E Avalon, Christine Beemelmanns, Hellen Bertoletti Barbieri, Friederike Biermann, Alan J Bridge, Esteban Charria Girón, Russell Cox, Max Crüsemann, Paul M D’Agostino, Marc Feuermann, Jennifer Gerke, Karina Gutiérrez García, Jonathan E Holme, Ji-Yeon Hwang, Riccardo Iacovelli, Júlio César Jeronimo Barbosa, Navneet Kaur, Martin Klapper, Anna M Köhler, Aleksandra Korenskaia, Noel Kubach, Byung T Lee, Catarina Loureiro, Shrikant Mantri, Simran Narula, David Meijer, Jorge C Navarro-Muñoz, Giang-Son Nguyen, Sunaina Paliyal, Mohit Panghal, Latika Rao, Simon Sieber, Nika Sokolova, Sven T Sowa, Judit Szenei, Barbara R Terlouw, Heiner G Weddeling, Jingwei Yu, Nadine Ziemert, Tilmann Weber, Kai Blin, Justin J J van der Hooft, Marnix H Medema, Mitja M Zdouc

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引用次数: 0

Abstract

Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core ‘scaffold’, which is subsequently modified by tailoring enzymes to define the molecule’s final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.

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关于捕获专门代谢物生物合成的裁剪酶数据库的最小信息

次生或特化代谢物表现出非凡的结构多样性和与临床和工业应用相关的强有力的生物活性。这些代谢物的生物合成通常从核心“支架”的组装开始，随后通过剪裁酶来修饰它，以确定分子的最终结构，进而确定其生物活性概况。关于裁剪酶的反应和底物特异性的知识对于理解和计算预测代谢物的生物合成是必不可少的，但这些信息通常分散在文献中。在这里，我们提出了关于裁剪酶数据库的最小信息。MITE使用一套全面的参数来注释裁剪酶，通过表达反应的SMARTS（简化分子输入线输入系统任意目标规范）化学模式语言来定义底物和反应特异性。人类和机器都可读，MITE可以用作知识库，用于硅生物合成，或训练机器学习应用程序，并与现有资源紧密集成。作为一个社区驱动的开放资源，MITE采用数据管理和专家评审的滚动发布模式。可以在https://mite.bioinformatics.nl/上免费访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.