Biochemical mapping of a ligand-binding domain within Arabidopsis BAM1 reveals diversified ligand recognition mechanisms of plant LRR-RKs

Plant J. 2012 Jun;70(5):845-54. doi: 10.1111/j.1365-313X.2012.04934.x. Epub 2012 Mar 31.


Leucine-rich repeat receptor kinases (LRR-RKs) are the largest sub-family of transmembrane receptor kinases in plants. In several LRR-RKs, a loop-out region called an 'island domain', which intercepts the extracellular tandem LRRs at a position near the transmembrane domain, constitutes the ligand-binding pocket, but the absence of the island domain in numerous LRR-RKs raises questions about which domain recognizes the ligand in non-island domain LRR-RKs. Here, we used photoaffinity labeling followed by chemical and enzymatic digestion to show that BAM1, a CLV1/BAM-family LRR-RK whose extracellular domain comprises 22 consecutive LRRs, directly interacts with the small peptide ligand CLE9 at the LRR6-LRR8 region that is relatively distal from the transmembrane domain. Multiple sequence alignment and homology modeling revealed that the inner concave side of LRR6-LRR8 of CLV1/BAM-family LRR-RKs deviates slightly from the LRR consensus. In support of our findings, the clv1-4 mutant carries a missense mutation at the inner concave side of LRR6 of CLV1, and introduction of the corresponding mutation in BAM1 resulted in complete loss of ligand binding activity. Our results indicate that the ligand recognition mechanisms of plant LRR-RKs are more complex and diverse than anticipated.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Binding Sites
  • Consensus Sequence
  • Electrophoresis, Polyacrylamide Gel
  • Leucine / metabolism*
  • Ligands
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Mutation, Missense
  • Peptide Fragments / metabolism
  • Photoaffinity Labels / metabolism
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Protein Structure, Tertiary
  • Protein-Serine-Threonine Kinases / genetics
  • Protein-Serine-Threonine Kinases / metabolism*
  • Receptor Protein-Tyrosine Kinases / genetics
  • Receptor Protein-Tyrosine Kinases / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Tobacco / genetics
  • Tobacco / metabolism


  • Arabidopsis Proteins
  • Ligands
  • Peptide Fragments
  • Photoaffinity Labels
  • Receptor Protein-Tyrosine Kinases
  • BAM1 protein, Arabidopsis
  • CLV1 protein, Arabidopsis
  • Protein-Serine-Threonine Kinases
  • Leucine

Associated data

  • PDB/3RGX
  • PDB/3RIZ