Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.

中文翻译：

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序列相似性网络证实了绿色细胞色素 P450 的层次关系

陆地植物具有多种酶家族。其中最突出的之一是细胞色素 P450（CYP 或 CYP450）家族。CYP 在生命树中对超过 443,000 个 CYP 蛋白进行了测序，在古细菌、细菌和真核生物中无处不在。在这里，我们重点关注陆地植物和藻类来研究 CYP 多样化的作用。CYP 作为单加氧酶，催化羟基化反应，这对于特殊的植物代谢途径至关重要，包括解毒和植物激素的产生；CYPome 由一个庞大的超级家族组成，该家族又分为氏族和家族。它们的进化史表明了高度的基质混杂性。辐射和功能多样化产生了众多的 CYP 家族。为了了解 CYP 内的进化关系，我们采用了序列相似性网络分析。我们恢复了代表不同 CYP 家族的不同簇，反映了我们将其与功能预测联系起来的多样化序列。层次聚类和系统发育分析进一步阐明了 CYP 家族之间的关系，揭示了它们共同的深层进化历史。我们探索了 CYP 亚家族在植物和藻类谱系中的分布和多样性，发现了新的候选酶并提供了对这些酶家族进化的见解。这确定了 CYP 家族之间意想不到的关系，例如 CYP82 和 CYP74 之间的联系，揭示了它们在植物防御信号通路中的作用。我们的方法提供了一种方法论，可以深入了解 CYP450 家族中新功能的出现，为植物和藻类的进化史做出贡献。这些见解可以通过各种外部条件下的实验设置进一步验证和实施。