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从植物到微生物的基因簇:它们在基因组结构、生物体发育、特殊代谢及药物发现中的作用。

Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery.

作者信息

Chakraborty Prasanta

机构信息

Kalpana Chawla Center for Space and Nanoscience, Kolkata, Indian Institute of Chemical Biology (retd.), Kolkata, 700032, India.

出版信息

Biochimie. 2022 Feb;193:1-15. doi: 10.1016/j.biochi.2021.12.001. Epub 2021 Dec 8.

Abstract

Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organized in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.

摘要

植物和微生物通过不同的高价值化学物质满足我们的日常需求,例如营养保健品、药品、化妆品,以及各种水果、农作物、蔬菜等等。因此,对于这些重要作物、药用植物和微生物的生长、发育和可持续性将给予 utmost care。同源异型框基因和 HOX 簇及其最近被表征的扩展家族成员,包括从药用植物人参中新发现的同源异型框 WOX 基因,对这些生物体的生长和发育有显著贡献。另一方面,植物和微生物通过次生代谢产生的次生代谢产物既用作生物体的防御物质,也用作人类的药物/类药物分子。发育性 HOX 簇和次生代谢产物的生物合成基因簇(BGC)都在生物体基因组中组织排列。对这些基因簇进行基因组挖掘和全基因组分析肯定会从未被探索的植物和微生物以及未被充分研究的人类微生物群中鉴定和表征更多重要分子,并且这些基因簇的进化研究将揭示它们的起源。尽管基因组学革命目前仍在持续推进,但到目前为止仅有几百个植物基因组序列可供使用。然而,目前市场上的下一代测序(NGS)技术甚至可应用于基因组难以处理的植物,最终可能会发现环境和微生物群中各种植物和微生物产生次生代谢产物的基因组潜力。此外,还将讨论用于基因组挖掘的工具的开发,例如 antiSMASH、plantiSMASH 以及越来越多预测数百个次生代谢产物 BGC 的计算方法。

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