Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis

Abstract

Receptor-like kinases (RLKs) are a family of transmembrane proteins with versatile N-terminal extracellular domains and C-terminal intracellular kinases. They control a wide range of physiological responses in plants and belong to one of the largest gene families in the Arabidopsis genome with more than 600 members. Interestingly, this gene family constitutes 60% of all kinases in Arabidopsis and accounts for nearly all transmembrane kinases in Arabidopsis. Analysis of four fungal, six metazoan, and two Plasmodium sp. genomes indicates that the family was represented in all but fungal genomes, indicating an ancient origin for the family with a more recent expansion only in the plant lineages. The RLK/Pelle family can be divided into several subfamilies based on three independent criteria: the phylogeny based on kinase domain sequences, the extracellular domain identities, and intron locations and phases. A large number of receptor-like proteins (RLPs) resembling the extracellular domains of RLKs are also found in the Arabidopsis genome. However, not all RLK subfamilies have corresponding RLPs. Several RLK/Pelle subfamilies have undergone differential expansions. More than 33% of the RLK/Pelle members are found in tandem clusters, substantially higher than the genome average. In addition, 470 of the RLK/Pelle family members are located within the segmentally duplicated regions in the Arabidopsis genome and 268 of them have a close relative in the corresponding regions. Therefore, tandem duplications and segmental/whole-genome duplications represent two of the major mechanisms for the expansion of the RLK/Pelle family in Arabidopsis.

Figure 1.

Relationships among Arabidopsis protein kinases. The kinase sequences were identified from the Arabidopsis genome, and an alignment was generated using the kinase domain amino acid sequence. The phylogeny was inferred from the alignment using the neighbor-joining method with 100 bootstrap replicates (bootstrap values shown in Supplement B). The tentative kinase families were assigned based on nodes with more than 30% bootstrap support. The family names were given based on known sequences in each family. In the context of all kinases, representative RLK/Pelle members all fall into a monophyletic group as predicted. Interestingly, a group of kinases is found to form a sister group to the RLK/Pelle family (arrowhead a). In addition to RLKs in the RLK/Pelle family, the IRE1-like genes are the only other receptor kinases found in Arabidopsis (arrowhead b). The IRE1 family genes are not the closest relatives to RLK/Pelle members, suggesting that the receptor kinase configurations have arisen independently between these two kinase families. CDPK, Calcium-dependent protein kinase; CaMK, calmodulin-dependent kinase; SnRK2, SNF-related protein kinase 2; PvPK, bean protein kinase; NPH1, non-phototropic hypocotyl 1; S6K, ribosomal protein S6 kinase; LeSPAK, tomato self-pruning-associated kinase; NIMA, never in mitosis A; CDK, cyclin-dependent kinase; GSK3, glycogen synthase kinase 3; CK2, casein kinase 2; NtNPK1L, Nicotiana protein kinase 1 like; HsWNKL, human with no Lys kinase-like; RTK, receptor Tyr kinase; MAPK, mitogen-associated protein kinase; MAPKK, MAPK kinase; MAPKKK, MAPKK kinase.

Figure 2.

The RLK/Pelle family members from Arabidopsis and other eukaryotic genomes. The kinase domains of the Arabidopsis representatives listed in Table II are aligned with putative RLK/Pelle members from the genomes listed in Table I. The phylogeny inferred based on the alignments is shown on the left with branches leading to Arabidopsis sequences in green, to animal sequences in red, and to Plasmodium sp. in blue. The numbers on the base on the branch indicate bootstrap support out of 1,000 replicates. Branches with than 5% support are collapsed. All genomes except Arabidopsis have few RLK/Pelle members. The identifiers for Arabidopsis follow the convention: gene name, subfamily designation, and synonym (if available). For the other genomes, the identifier follows: species abbreviation, sequence name from the source database (see Table I), synonym (if available). AG, A. gambiae; DM, D. melanogaster; CE, C. elegans; CI, C. intestinalis; FR, F. rubripes; HS, Homo sapiens; MM, M. musculus.

Figure 3.

The relationships between IRE1-like genes and RLK/Pelle family kinases. The kinase domain amino acid sequences of IRE1-like genes and kinase family representatives from Arabidopsis and human were used for generating the neighboring-joining tree with 1,000 bootstrap replicates. The RLK/Pelle family forms a close relationship to Raf kinases and human receptor Tyr kinases (arrowhead b). The Arabidopsis IRE1-like genes are closely related to human IRE1 with high bootstrap support (arrowhead b). The identifiers follow the convention: species abbreviation followed by gene name. RSK, Metazoan receptor Ser/Thr kinase. RTK, Animal receptor Tyr kinase.

Figure 4.

The relationships between the kinase phylogeny, the extracellular domains, and the number of exons. The phylogenetic trees in (A) and (B) were generated from an alignment of 610 RLK/Pelle family members previously published (Shiu and Bleecker, 2001). A, Branches of the phylogenetic tree were colored according to the identity of the extracellular domains as predicted by SMART and Pfam databases. RLKs with similar extracellular domains are generally clustered together. RLCKs are clustered into several groups also. Exceptions are the CrRLK1-like genes (arrow a), the LRK10-like genes (arrow b), and the S-domain RLKs (arrow c). For detailed domain organization for all genes, see Supplement C. B, Branches of the phylogenetic tree were colored according to the number of exons based on the predicted gene model of RLK/Pelle members. Related RLK/Pelle members as defined by the kinase phylogeny or extracellular domain identities, in general, have identical or similar numbers of exons. For the locations, placements, and phases of introns, see Supplement C.

Figure 5.

Similarity clustering and domain organization of RLPs from Arabidopsis. On the basis of pair wise comparison of putative RLPs and the extracellular domain sequences of representative RLKs with BLAST, a distance matrix is generated with transformed E values and used for clustering with the UPGMA algorithm implemented in MEGA2. The clustering diagram is a representation of relatedness between sequences. More closely related sequence pairs are joined together with branches of shorter length. The domain organizations as predicted by SMART/Pfam are shown on the left of the clustering diagram. The identifiers for the representative sequences follow the convention: gene name, subfamily, and synonym (if available). The intracellular domains of all representative RLKs are not shown. The classification of RLPs is shown right to the domain organizations. Red arrows indicate sequences representing misannotated RLKs. Branches are colored in three RLP classes: green, TMM-like; red, LRR II-like; and blue, LRR-I-like.