Characterization of LYM genes in Medicago truncatula.
M. truncatula contains a large family of genes encoding LysM-domain containing receptor-like proteins (Arrighi et al., 2006). In addition, several proteins containing single or multiple LysM domains can be predicted from available sequencing resources. Among these, two transcripts encoding proteins with structural homology to the chitin elicitor-binding protein CEBiP from rice (Oryza sativa (Kaku et al., 2006)) were identified, MtLYM1 and MtLYM2 (Arrighi et al., 2006). The proteins deduced from these transcripts featured signal peptides, indicating an extracellular localization (Fig. 1). Moreover, both proteins were predicted to be modified by glycosylphosphatidylinositol (GPI) for anchorage at the cell surface after removal of the C-terminal transmembrane domain. The genes encoding MtLYM1 and 2 contained five exons/four introns and four exons/three introns, respectively (Fig. 1), from which only one intron position was conserved between both genes. Interestingly, a small intron was present in MtLYM2 inside of the region encoding the three LysM domains, which was never observed for other genes encoding LysM-containing proteins in M. truncatula (Arrighi et al., 2006)
We analyzed the phylogeny of LYMs by performing a consensus search of fully sequenced plant genomes for encoded proteins with similarity to LYMs from M. truncatula. Proteins, which were not predicted to contain a signal peptide or which were shorter than 300 residues were removed to obtain a list of 53 LYMs (suppl Table xx). In contrast to LYPs, which are defined, less stringently, as LysM-containing extracellular proteins and were detected in the moss Physcomitrella patens (Zhang et al., 2009), LYMs are present in vascular plants only. Interestingly, most of the annotated genomes contain at least two LYM-type proteins, with the exception of Mimulus guttatus for which in the present release (JGI release v1.0) only one could be found. For all other genomes, always at least one LYM1-like and one LYM2-like protein was detected. They were named, in accordance with the designation for the LYMs from M. truncatula and Arabidopsis thaliana, LYM1 or LYM2 if a GPI-anchor was predicted, or LYM3 and LYM4 for LYM1-like and LYM2-like if no GPI attachment could be predicted (suppl Table xx). Alignment of the amino acid sequences enabled the mapping of three putative LysM domains for each protein, separated by cystein pairs (Fig. 2; suppl Fig xxx [alignment]). Phylogenetic analysis of the full length proteins showed a clear separation of LYM1/3 (clade I in Zhang et al., 2009) versus LYM2/4 (clade III) (Fig. 3). Interestingly, LYM1/3 proteins showed a higher overall sequence conservation in comparison to LYM2/4 proteins, which are generally more divergent from each other.
RNA interference of MtLYM1 and MtLYM2.
CEBiP, the only LYM protein, for which the function was established, proved to be a chitin elicitor-binding protein, necessary for...