Abstract Karrikins (KARs), smoke-derived butenolides, are perceived by the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and are thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting diversification and co-evolution of ligand-receptor relationships. In legumes, which comprise a number of important crops with protein-rich, nutritious seed, KAI2 has duplicated. We report sub-functionalization of KAI2a and KAI2b in the model legume Lotus japonicus and demonstrate that their ability to bind the synthetic ligand GR24 ent -5DS differs in vitro as well as in genetic assays in Lotus japonicus and in the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which occured independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. Unexpectedly, L. japonicus responds to diverse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl development responds to KAR 1 , KAR 2 and rac -GR24, while root system development responds only to KAR 1 . This organ-specificity cannot be explained by receptor-ligand preferences alone, because Lj KAI2a is sufficient for karrikin responses in the hypocotyl, while Lj KAI2a and Lj KAI2b operate redundantly in roots. Our findings open novel research avenues into the evolution and diversity of butenolide ligand-receptor relationships, their ecological significance and the mechanisms controlling diverse developmental responses to different KAI2 ligands.

Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy