Molecular basis of lipo-chitooligosaccharide recognition by the lysin motif receptor-like kinase LYR3 in legumes.

LYR3 (Lysin Motif (LysM) Receptor-Like Kinase 3) of Medicago truncatula is a high affinity binding protein for symbiotic lipo-chitooligosaccharidic (LCO) signals, produced by Rhizobia bacteria and arbuscular mycorrhizal fungi. This work shows that LYR3 from several other legumes, but not from two Lupinus species which are incapable of forming the mycorrhizal symbiosis, bind LCOs with high affinity and discriminate them from chitooligosaccharides (COs). The biodiversity of these proteins and the lack of binding to the Lupinus proteins were used to identify features required for high affinity LCO binding. Swapping experiments between each of the three LysMs of the extracellular domain of the M. truncatula and Lupinus angustifolius LYR3 proteins revealed the crucial role of the third LysM in LCO binding. Site directed mutagenesis identified a Tyr residue, highly conserved in all the LYR3 LCO-binding proteins, which is essential for high-affinity binding. Molecular modeling suggests that it may be part of a hydrophobic tunnel able to accommodate the LCO acyl chain. The lack of conservation of these features in the binding site of plant LysM proteins binding COs, provides a mechanistic explanation of how LCO recognition might differ from CO perception by structurally-related LysM receptors.