三萜 RDF:使用资源描述框架开发三萜生物合成过程中涉及的植物酶和转录因子数据库。

IF 1.4 4区 生物学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Keita Tamura, Hirokazu Chiba, Hidemasa Bono
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引用次数: 0

摘要

植物产生结构多样的三萜(三萜和类固醇)。它们的生物合成发生在一个共同的前体,即2,3-氧化角鲨烯,然后由氧化角鲨烯环化酶(OSCs)催化环化,产生各种三萜骨架。类固醇由环蒿烯醇或羊毛甾醇生物合成,是大多数植物必不可少的初级代谢物,此外还有谱系特异性类固醇,如在茄属植物中发现的甾体糖生物碱。其他不同的三萜骨架被转化为三萜,通常被归类为专门的化合物,仅在有限数量的植物物种中生物合成,在植物中具有组织或细胞类型特异性积累。最近的研究已经确定了参与三萜结构多样化的各种剪裁酶以及调节这些酶表达的转录因子。然而,这些蛋白质的覆盖范围在公开的蛋白质或酶数据库中是稀缺的,这使得新组装的基因组或转录组序列的功能注释变得复杂。在这里,我们创建了三萜RDF,这是一个人工整理的涉及植物三萜生物合成的酶和转录因子的数据库。该数据库(https://github.com/ktamura2021/triterpene_rdf/)包含532种蛋白质,可链接到UniProt知识库或NCBI蛋白质数据库,并可直接下载一组按蛋白质类型或分类过滤的蛋白质序列。三萜RDF将增强对三萜生物合成的酶和调控元件的功能注释,在当前各种植物基因组信息的可用性扩展中。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework.

Plants produce structurally diverse triterpenes (triterpenoids and steroids). Their biosynthesis occurs from a common precursor, namely 2,3-oxidosqualene, followed by cyclization catalyzed by oxidosqualene cyclases (OSCs) to yield various triterpene skeletons. Steroids, which are biosynthesized from cycloartenol or lanosterol, are essential primary metabolites in most plant species, along with lineage-specific steroids, such as steroidal glycoalkaloids found in the Solanum species. Other diverse triterpene skeletons are converted into triterpenoids, often classified as specialized compounds that are biosynthesized only in a limited number of plant species with tissue- or cell-type-specific accumulation in plants. Recent studies have identified various tailoring enzymes involved in the structural diversification of triterpenes as well as transcription factors that regulate the expression of these enzymes. However, the coverage of these proteins is scarce in publicly available databases for curated proteins or enzymes, which complicates the functional annotation of newly assembled genomes or transcriptome sequences. Here, we created the Triterpene RDF, a manually curated database of enzymes and transcription factors involved in plant triterpene biosynthesis. The database (https://github.com/ktamura2021/triterpene_rdf/) contains 532 proteins, with links to the UniProt Knowledgebase or NCBI protein database, and it enables direct download of a set of protein sequences filtered by protein type or taxonomy. Triterpene RDF will enhance the functional annotation of enzymes and regulatory elements for triterpene biosynthesis, in a current expansion of availability of genomic information on various plant species.

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来源期刊
Plant Biotechnology
Plant Biotechnology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-PLANT SCIENCES
CiteScore
2.90
自引率
18.80%
发文量
45
审稿时长
6-12 weeks
期刊介绍: Plant Biotechnology is an international, open-access, and online journal, published every three months by the Japanese Society for Plant Biotechnology. The journal, first published in 1984 as the predecessor journal, “Plant Tissue Culture Letters” and became its present form in 1997 when the society name was renamed to Japanese Society for Plant Cell and Molecular Biology, publishes findings in the areas from basic- to application research of plant biotechnology. The aim of Plant Biotechnology is to publish original and high-impact papers, in the most rapid turnaround time for reviewing, on the plant biotechnology including tissue culture, production of specialized metabolites, transgenic technology, and genome editing technology, and also on the related research fields including molecular biology, cell biology, genetics, plant breeding, plant physiology and biochemistry, metabolic engineering, synthetic biology, and bioinformatics.
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