Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis

Abstract

The tomato (Lycopersicon esculentum) Cf-9 resistance gene encodes the first characterized member of the plant receptor-like protein (RLP) family. Other RLPs such as CLAVATA2 and TOO MANY MOUTHS are known to regulate development. The domain structure of RLPs consists of extracellular leucine-rich repeats, a transmembrane helix, and a short cytoplasmic region. Here, we identify 90 RLPs in rice (Oryza sativa) and compare them with functionally characterized RLPs from different plant species and with 56 Arabidopsis (Arabidopsis thaliana) RLPs, including the downy mildew resistance protein RPP27. Many RLPs cluster into four distinct superclades, three of which include RLPs known to be involved in plant defense. Sequence comparisons reveal diagnostic amino acid residues that may specify different molecular functions in different RLP subtypes. This analysis of rice RLPs thus identified at least 73 candidate resistance genes and four genes potentially involved in development. Due to the synteny between rice and other Gramineae, this analysis should provide valuable tools for experimental studies in rice and other cereals.

Figure 1.

Canonical Cf-9-like RLP, RLK, and PGIP domain structures. Domain A contains a putative signal peptide. Domain B contains one or two pairs of Cys that may play structural roles. Domain C contains multiple LRRs, and contains a variable “loop-out” C2 region in some RLPs and RLKs. Domain D is a linker domain between C and the acidic domain E. Domain F contains the TM helix, and domain G corresponds to the cytoplasmic region. M, Membrane.

Figure 2.

Representation of genomic loci of rice RLPs. The numbered gray bars represent the 12 rice chromosomes. The black bar on the chromosome represents the centromere; gene positions on chromosomes are indicated by the scale at top. RLPs are represented by rectangles colored according to their GHG classification. Positions of putative rice orthologs of the Arabidopsis genes CLV2 (OsPDO3) and TMM (OsPDO4) along with OsPDO1 and OsPDO2 are highlighted.

Figure 3.

Features of GHGs. Shown in this figure are GHGs containing a minimum of three sequences. The striped rectangles represent the PGIP-like N-terminal regions.

Figure 4.

Phylogenetic relationships of RLPs and selected RLKs and PGIPs. A, Neighbor-joining tree built using 1,000 bootstrap replicates, based on an alignment of the C3-F region of Arabidopsis, rice, and characterized RLPs, as well as LRR-RLKs and PGIPs. Superclades are shaded. B, Clades-superclades-GHG relationships. The 16 clades are divided into four major superclades (shown boxed in gray). Rice sequences found in large genomic clusters are indicated with an asterisk. See Table I for details.

Figure 4.

Phylogenetic relationships of RLPs and selected RLKs and PGIPs. A, Neighbor-joining tree built using 1,000 bootstrap replicates, based on an alignment of the C3-F region of Arabidopsis, rice, and characterized RLPs, as well as LRR-RLKs and PGIPs. Superclades are shaded. B, Clades-superclades-GHG relationships. The 16 clades are divided into four major superclades (shown boxed in gray). Rice sequences found in large genomic clusters are indicated with an asterisk. See Table I for details.

Figure 5.

Multiple sequence alignments of OsPDO2 (A) and OsPDO1 (B) and their homologs from other plants species. The protein sequences of the homologs are entire translated predicted open reading frames of ESTs from various plant species. LRRs are boxed, and the predicted TM domains are indicated with asterisks.

Figure 6.

Cf-RLP conserved motifs. A, Alignment of the B domain of Cf-RLPs to the N terminus of PGIP. 1OGQA is the Protein Data Bank identifier of the solved PGIP structure. Columns with highly conserved amino acids are highlighted in gray. Conserved Cys are marked with asterisks. B, Alignment of the C2 region of Cf-RLPs highlighting the Yx(n)KG motif. The conserved residues are indicated with asterisks and the columns are shaded as in A. C, Alignment of the TM regions of functionally characterized RLPs, RLKs, and PDOs that contain GXXXG-type motifs. The conserved Gly (or Ser) in the GXXXG-type motifs are highlighted in gray and are marked with asterisks.