Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Abstract

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant–pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the “Guard-Hypothesis,” R proteins (the “guards”) can sense modification of target molecules in the host (the “guardees”) by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the “guardee-effector” interface for pathogen recognition, natural selection acts on the “guard-guardee” interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen.

Subfamily-Specific Fluorescent Probes for Cysteine Proteases Display Dynamic Protease Activities during Seed Germination

“…This probe was subsequently used to monitor PLCP activities during immunity and senescence (Martínez et al, 2007a;Shabab et al, 2008), to study protease activation (Gilroy et al, 2007;Wang et al, 2008;Gu et al, 2012), and to reveal the selectivity of endogenous and pathogen-derived protease inhibitors (Rooney et al, 2005;Tian et al, 2007;Shabab et al, 2008;van Esse et al, 2008;Song et al, 2009;Kaschani et al, 2010;Lampl et al, 2010;Hörger et al, 2012;Lozano-Torres et al, 2012;van der Linde et al, 2012;Mueller et al, 2013;Dong et al, 2014). Although powerful, a disadvantage of DCG-04 profiling is that this biotinylated probe involves an indirect detection using streptavidin-horseradish peroxidase, which reduces throughput and resolution.…”

Functional Divergence of Two Secreted Immune Proteases of Tomato

“…Indeed, unrelated effector proteins (Avr2, EpiCs, and Vap1) target secreted tomato proteases [2,19,29]. This process is associated with the accumulation of variant residues on the surface of Rcr3 and Pip1, some of which affect inhibitor affinity [3,[29][30][31]. Next, gene duplication and diversification of the duplicates occurred, probably driven by the arms race with pathogenderived inhibitors ( Figure 4C).…”

Plastic Transcriptomes Stabilize Immunity to Pathogen Diversity: The Jasmonic Acid and Salicylic Acid Networks within the Arabidopsis/Botrytis Pathosystem

“…These attacks can lead to strong selective forces on the plant genome in wild ecosystems and can cause significant financial and yield losses in agricultural crops (Bergelson et al, 2001; Van der Hoorn et al, 2002;Mauricio et al, 2003;Rose et al, 2007;Fisher et al, 2012;Hörger et al, 2012;Züst et al, 2012;Karasov et al, 2014). In turn, pathogens have evolved an array of virulence mechanisms based on their infection strategy that causes a prolonged selection pressure on plants to evolve complex and coherent innate immune systems.…”