Arabidopsis thaliana genes encoding defense signaling and recognition proteins exhibit contrasting evolutionary dynamics

Abstract

The interplay between pathogen effectors, their host targets, and cognate recognition proteins provides various opportunities for antagonistic cycles of selection acting on plant and pathogen to achieve or abrogate resistance, respectively. Selection has previously been shown to maintain diversity in plant proteins involved in pathogen recognition and some of their cognate pathogen effectors. We analyzed the signatures of selection on 10 Arabidopsis thaliana genes encoding defense signal transduction proteins in plants, which are potential targets of pathogen effectors. There was insufficient evidence to reject neutral evolution for 6 genes encoding signaling components consistent with these proteins not being targets of effectors and/or indicative of constraints on their ability to coevolve with pathogen effectors. Functional constraints on effector targets may have provided the driving selective force for the evolution of guard proteins. PBS1, a known target of an effector, showed little variation but is known to be monitored by a variable guard protein. Evidence of selection maintaining diversity was present at NPR1, PAD4, and EDS1. Differences in the signatures of selection observed may reflect the numbers of effectors that target a particular protein, the presence or absence of a cognate guard protein, as well as functional constraints imposed by biochemical activities or interactions with plant proteins.

Figure 1.—

Position of proteins involved in the defense signal transduction pathways. Proteins encoded by the genes analyzed in this study are circled. The signaling molecules, salicylic acid (SA), jasmonic acid (JA), and ethylene (C₂H₄), are boxed. The positions of PBS1 and RIN4 in these pathways are not currently known.

Figure 2.—

Sliding-window plots of the polymorphism-to-divergence ratio of NPR1, PAD4, and EDS1. The proportion of polymorphic changes within A. thaliana relative to fixed differences between A. thaliana and A. lyrata were plotted for each window of 20 variable sites (40 for PAD4). Note that the plots in the second column are not the same for each gene. Corresponding gene structure is shown at the bottom of the plots: exons are indicated by boxes and noncoding regions by lines.

Figure 3.—

Sliding-window analysis of silent site divergence between the two major allelic classes at NPR1. Values plotted are the midpoints of windows 150 silent-sites wide at 10-bp increments. Corresponding gene structure is shown at the bottom of the plots: exons are indicated by boxes and noncoding regions by lines.

Figure 4.—

TASSEL plots of pairwise association. r² values are above the diagonal. P-values are below the diagonal. Sites located in exons are indicated by black bars above and to the right of the matrix. Exon 3 of EDS1 was monomorphic and, therefore, is not represented. Arrows indicate consensus positions of nonsynonymous substitutions: NPR1 398, 406, 653, 667, 1002, 1298, 1416, 1939, and 1940; PAD4 208, 210, 248, 266, 299, 1512, and 1713; and EDS1 119, 639, 667, 734, 780, 781, 811, 849, 982, 1075, 1119, 1443, 1482, 1620, 1673, 1815, 2019, 2028, 2044, 2058, 2059, 2060, 2119, and 2147.