Kim Colin Y, Kastner David W, Mitchell Andrew J, Gutierrez Michael A, Yao Jocelyn S, Neumann Edwin N, Kulik Heather J, Weng Jing-Ke
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Sci Adv. 2025 Aug 15;11(33):eadv6898. doi: 10.1126/sciadv.adv6898. Epub 2025 Aug 13.
Biohalogenation is rare in plant metabolism, with the Menispermaceae's chloroalkaloid acutumine being an exception. This involves a specialized dechloroacutumine halogenase (DAH) from the iron- and 2-oxoglutarate-dependent dioxygenase (2ODD) family. While DAH is presumed to have evolved from an ancestral 2ODD, how enzyme specialization arises through Darwinian processes remains a fundamental question in understanding metabolic evolution. Here, we investigate the evolutionary history of DAH using the chromosomal-level genome of . Phylogenomic dating and synteny analyses reveal DAH evolution through tandem duplication of an ancestral flavonol synthase (FLS) gene, followed by neofunctionalization and gene loss events. Structural modeling, molecular dynamics, and site-directed mutagenesis identify mutations enabling the catalytic switch from FLS to DAH. This required traversing a complex evolutionary landscape with deep fitness valleys separating intermediate states captured in the genome. Our findings illustrate how enzymatic functions evolve through lineage-specific pathways, reshaping active sites and enabling catalytic mechanism-switching mutations.
生物卤化在植物代谢中很少见，防己科的氯生物碱尖防己碱是个例外。这涉及一种来自铁和2-氧代戊二酸依赖性双加氧酶（2ODD）家族的特殊的去氯尖防己碱卤化酶（DAH）。虽然推测DAH是从一个祖先2ODD进化而来的，但通过达尔文过程酶的特化是如何产生的，仍然是理解代谢进化的一个基本问题。在这里，我们利用……的染色体水平基因组研究了DAH的进化历史。系统发育年代测定和共线性分析揭示了DAH通过一个祖先黄酮醇合酶（FLS）基因的串联重复进化而来，随后是新功能化和基因丢失事件。结构建模、分子动力学和定点诱变确定了使催化从FLS转变为DAH的突变。这需要穿越一个复杂的进化景观，其中有深深的适应性低谷将在……基因组中捕获的中间状态分隔开。我们的研究结果说明了酶功能是如何通过特定谱系的途径进化的，重塑活性位点并实现催化机制转换突变。
