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

PLoS Genet. 2020 Dec 28;16(12):e1009249. doi: 10.1371/journal.pgen.1009249. eCollection 2020 Dec.


Karrikins (KARs), smoke-derived butenolides, are perceived by the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and 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. We found that the genomes of legumes, comprising a number of important crops with protein-rich, nutritious seed, contain two or more KAI2 copies. We uncover sub-functionalization of the two KAI2 versions in the model legume Lotus japonicus and demonstrate differences in their ability to bind the synthetic ligand GR24ent-5DS in vitro and in genetic assays with Lotus japonicus and 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 arose 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. The diversification of KAI2 binding pockets suggests the occurrence of several different KLs acting in non-fire following plants, or an escape from possible antagonistic exogenous molecules. Unexpectedly, L. japonicus responds to diverse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl growth responds to KAR1, KAR2 and rac-GR24, while root system development responds only to KAR1. This differential responsiveness cannot be explained by receptor-ligand preferences alone, because LjKAI2a is sufficient for karrikin responses in the hypocotyl, while LjKAI2a and LjKAI2b operate redundantly in roots. Instead, it likely reflects differences between plant organs in their ability to transport or metabolise the synthetic KLs. Our findings provide new insights into the evolution and diversity of butenolide ligand-receptor relationships, and open novel research avenues into their ecological significance and the mechanisms controlling developmental responses to divergent KLs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Furans / chemistry
  • Furans / metabolism*
  • Gene Duplication
  • Gene Expression Regulation, Plant / genetics
  • Heterocyclic Compounds, 3-Ring / metabolism
  • Hydrolases / genetics*
  • Hydrolases / metabolism
  • Hypocotyl / growth & development*
  • Hypocotyl / metabolism
  • Lactones / metabolism
  • Ligands
  • Lotus / genetics
  • Lotus / metabolism*
  • Microarray Analysis
  • Phylogeny
  • Plant Growth Regulators / chemistry
  • Plant Growth Regulators / genetics
  • Plant Growth Regulators / metabolism*
  • Plant Roots / growth & development*
  • Plant Roots / metabolism
  • Pyrans / chemistry
  • Pyrans / metabolism*


  • 3-methyl-2H-furo(2,3-c)pyran-2-one
  • Arabidopsis Proteins
  • Furans
  • GR24 strigolactone
  • Heterocyclic Compounds, 3-Ring
  • Lactones
  • Ligands
  • Plant Growth Regulators
  • Pyrans
  • HTL protein, Arabidopsis
  • Hydrolases

Grants and funding

The study was supported by an Australian Research Council Future Fellowship (FT150100162) to MTW and initially by the SFB924 of the DFG to CG and subsequently by the Emmy Noether program of the DFG, grant GU1423/1-1 to CG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.