Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana

Abstract

The RPS2 gene in Arabidopsis thaliana governs resistance to strains of the bacterial pathogen, Pseudomonas syringae pv. tomato, that express the avrRpt2 gene. The two loci are involved in a gene-for-gene interaction. Seventeen accessions of A. thaliana were sequenced to explore the diversity present in the coding region of the RPS2 locus. An unusually high level of nucleotide polymorphisms was found (1.26%), with nearly half of the observed polymorphisms resulting in amino acid changes in the RPS2 protein. Seven haplotypes (alleles) were identified and their evolutionary relationships deduced. Several of the alleles conferring resistance were found to be closely related, whereas susceptibility to disease was conferred by widely divergent alleles. The possibility of selection at the RPS2 locus is discussed.

Figure 1

Putative functional motifs found in the predicted RPS2 protein product. The protein is 909 aa long and contains the following motifs: Leu zipper (LZ), nucleotide-binding site (NBS), hydrophobic region (HP), and a series of 14 Leu-rich repeats (LRR). The Leu zipper and Leu-rich repeats are proposed to mediate protein–protein interactions. The position of each motif (amino acid number) is indicated.

Figure 2

Gene tree depicting the nucleotide differences between all haplotypes. Each step represents a point mutation leading to a nucleotide change. Numbers refer to the nucleotide where a change occurred (where number 1 defines the first nucleotide in the coding sequence). Amino acid changes are indicated along with the amino acid number. Nonconservative changes are marked by an asterisk. For convenience, the Col-0 sequence is used as a reference for amino acid changes. The tree is unrooted and no evolutionary direction is implied. Phenotypes corresponding to each haploytpe are classified as follows: ○, susceptible; □, resistant; ⋄, partially resistant.