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.

New insights into receptor-like protein functions in Arabidopsis

“…20 Most AtRLP genes were proposed to be involved in disease resistance based on the hypothesis that disease resistance genes are likely to be duplicated and underwent diversifying selection. 11,12,20 The notion is thus reinforced by our expression study showing that the majority of AtRLP genes exhibited altered responses to a broad series of abiotic and biotic stress treatments. 20 With the availability of the collection of AtRLP overexpressors generated in our study, more AtRLP genes are expected to be assigned biological functions in future.…”

“…We found that the most homologous AtRLP genes resided at the same locus and AtRLP genes are underwent massive duplications. 11,12,20 The comparision of AtRLP phylogeny and their transcriptional profile indicates that there is no signifiant correlation between AtRLP phylogeny and the expression patterns, although culstered AtRLP genes with similar expression profiles are observed. This implies that the duplicated AtRLP homologs could acquire different functions through the diversification in their gene expression.…”

“…12,19 In addition, it is nearly impossible for genetically crossing individual T-DNA insertion lines to obtain high-order knockout mutants because many AtRLP genes are clustered at the same locus. 11,12,20 Also it is difficult to elucidate the function of AtRLPs due to the high diversity and extremely low abundance of their putative ligands. Particularly, no phenotypic changes were found for a number of RNAi lines that were generated to knockdown the expression of several sets of AtRLP genes.…”

“…9,10 Genome-wide sequence analyses identified a total of 57 AtRLPs in Arabidopsis. 11,12 Although the biological functions of most AtRLP genes still remain unknown, a number of AtRLP genes have been assigned functions. In addition to CLV2 and TMM, the functionally characterized AtRLP proteins comprise AtRLP1/ReMAX that mediates recognition of eMAX, 13 AtRLP3/RFO that involves in resistance to the vascular wilt fungus Fusarium oxysporum, 14 AtRLP23 that perceives a conserved fragment present in most necrosis and ethyleneinducing peptide (NEP) 1-like proteins and subsequently activate the immunity, 15 AtRLP30 that implicates in resistance against Pseudomonas syringae pv.…”

Gene silencing to investigate the roles of receptor-like proteins in Arabidopsis

“…14,19 Often, the most homologous AtRLP genes reside at the same locus, 14,19 and therefore crossing individual T-DNA insertion lines to obtain knock-out lines for multiple AtRLP genes is nearly impossible. RNAi-mediated gene silencing currently is the most suitable strategy to target expression of several highly homologous genes simultaneously.…”