Tracing the stepwise Darwinian evolution of a plant halogenase

Halogenation chemistry is rare in plant metabolism, with the chloroalkaloid acutumine produced by Menispermaceae species being the only well characterized example, involving a specialized dechloroacutumine halogenase (DAH) from the iron(II)- and 2-oxoglutarate-dependent dioxygenase (2ODD) superfamily. While DAH is presumed to have evolved from an ancestral 2ODD enzyme, the broader question of how new enzymes arise through Darwinian processes, such as the birth of DAH in Menispermaceae, remains a fundamental challenge in understanding metabolic evolution. Here, we investigate DAHs evolutionary trajectory using the chromosomal-level genome assembly of Menispermum canadense. By analyzing the genomic context of DAH in M. canadense and syntenic regions in related plants, we show that DAH evolved through tandem duplication of an ancestral flavonol synthase (FLS) gene, followed by a series of neofunctionalization and gene loss events. Through structural modeling, molecular dynamics simulations, and site-directed mutagenesis, we identify residue changes enabling the transition from FLS to DAH. This functional switch required traversing a complex evolutionary landscape where adaptive peaks were separated by deep fitness valleys. Our work illustrates how new enzymatic functions can arise through lineage-specific evolutionary pathways that gradually reshape the active site architecture through permissive mutations, ultimately enabling mechanism-switching mutations that establish novel catalytic activities.