Bioinformatic analysis of microbial type terpene synthase genes in plants.

4区生物学 Q3 Biochemistry, Genetics and Molecular Biology

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-03-12 DOI:10.1016/bs.mie.2024.02.014

Xinlu Chen, Jin Han, Feng Chen

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引用次数: 0

Abstract

Plants are prolific producers of terpenoids. Terpenoid biosynthesis is initiated by terpene synthases (TPS). In plants, two types of terpenes synthase genes are recognized: typical plant TPS genes and microbial-terpene synthase like-genes (MTPSL). While TPS genes are ubiquitous in land plants, MTPSL genes appear to be restricted to non-seed land plants. Evolutionarily, TPS genes are specific to land plants, whereas MTPSL genes have related counterparts in other organisms, especially fungi and bacteria. The presence of microbial type TPS in plants, fungi and bacteria, with the latter two often being associated with plants, poses a challenge in accurately identifying bona fide MTPSL genes in plants. In this chapter, we present bioinformatic procedures designed to identify MTPSL genes in sequenced plant genomes and/or transcriptomes. Additionally, we outline validation methods for confirming the identified microbial-type TPS genes as genuine plant genes. The method described in this chapter can also be adopted to analyze microbial type TPS in organisms other than plants.

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植物中微生物型萜烯合成酶基因的生物信息学分析。

植物是多产的萜类化合物生产者。萜类化合物的生物合成是由萜烯合成酶（TPS）启动的。植物中有两种萜烯合成酶基因：典型的植物 TPS 基因和类似微生物萜烯合成酶的基因（MTPSL）。TPS 基因在陆生植物中普遍存在，而 MTPSL 基因似乎仅限于非种子陆生植物。在进化过程中，TPS 基因是陆地植物所特有的，而 MTPSL 基因在其他生物，尤其是真菌和细菌中也有相关的对应基因。植物、真菌和细菌中都存在微生物类型的 TPS，而后两者往往与植物相关联，这给准确鉴定植物中真正的 MTPSL 基因带来了挑战。在本章中，我们将介绍生物信息学程序，旨在识别测序植物基因组和/或转录组中的 MTPSL 基因。此外，我们还概述了确认已鉴定的微生物型 TPS 基因为真正植物基因的验证方法。本章介绍的方法也可用于分析植物以外的微生物型 TPS。

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

Methods in enzymology 生物-生化研究方法

CiteScore

2.90

自引率

0.00%

发文量

308

审稿时长

3-6 weeks

期刊介绍： The critically acclaimed laboratory standard for almost 50 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 500 volumes the series contains much material still relevant today and is truly an essential publication for researchers in all fields of life sciences, including microbiology, biochemistry, cancer research and genetics-just to name a few. Five of the 2013 Nobel Laureates have edited or contributed to volumes of MIE.