Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China.
Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China.
Plant J. 2022 Oct;112(2):414-428. doi: 10.1111/tpj.15953. Epub 2022 Sep 12.
Type III polyketide synthases (PKSs) are key enzymes involved in the biosynthesis of a variety of plant specialized metabolites, including flavonoids, stilbenes, and sporopollenin, to name a few. These enzymes likely played vital roles in plant adaptation during their transition from aquatic to terrestrial habitats and their colonization of specific ecological environments. Members of this supergene family have diverse functions, but how type III PKSs and their functions have evolved remains poorly understood. Here, we conducted comprehensive phylogenomics analysis of the type III PKS supergene family in 60 species representing the major plant lineages and elucidated the classification, origin, and evolutionary history of each class. Molecular evolutionary analysis of the typical chalcone synthase and stilbene synthase types revealed evidence for strong positive natural selection in both the Pinaceae and Fabaceae lineages. The positively selected sites of these proteins include residues at the catalytic tunnel entrance and homodimer interface, which might have driven the functional divergence between the two types. Our results also suggest that convergent evolution of enzymes involved in plant flavonoid biosynthesis is quite common. The results of this study provide new insights into the origin, evolution, and functional diversity of plant type III PKSs. In addition, they serve as a guide for the enzymatic engineering of plant polyketides.
III 型聚酮合酶（PKSs）是参与多种植物特化代谢物生物合成的关键酶，包括黄酮类、芪类和孢粉素等。这些酶在植物从水生到陆生环境的过渡以及对特定生态环境的殖民过程中可能发挥了重要作用。这个超基因家族的成员具有多种功能，但 III 型 PKS 及其功能的进化方式仍知之甚少。在这里，我们对代表主要植物谱系的 60 个物种中的 III 型 PKS 超基因家族进行了全面的系统发生基因组学分析，并阐明了每个类别的分类、起源和进化历史。典型查尔酮合酶和芪合酶类型的分子进化分析表明，在松科和豆科两个谱系中都存在强烈的正自然选择证据。这些蛋白质的正选择位点包括催化隧道入口和同源二聚体界面处的残基，这可能导致了这两种类型之间的功能分化。我们的研究结果还表明，参与植物类黄酮生物合成的酶的趋同进化相当普遍。本研究的结果为植物 III 型 PKS 的起源、进化和功能多样性提供了新的见解。此外，它们为植物聚酮的酶工程提供了指导。
