Functional divergence shaped the network architecture of plant immune receptors

Abstract

In solanaceous plants, several sensor NLRs and their helper NLRs, known as NRC, form a complex network to confer immunity against pathogens. While the sensor NLRs and downstream NRC helpers display diverse genetic compatibility, the evolution and molecular basis of the complex network structure remained elusive. Here we demonstrated that functional divergence of NRC3 variants has shaped the genetic architecture of the NLR network. Natural NRC3 variants form three allelic groups displaying distinct compatibilities with sensor NLRs. Ancestral sequence reconstruction and analyses of natural and chimeric variants identified six key amino acids involved in sensor-helper compatibility, with two residues critical for subfunctionalization. Co-functioning Rpi-blb2 and NRC3 variants showed stronger transient interactions upon effector detection, with NRC3 membrane-associated complexes forming subsequently. Our findings reveal how mutations in helper NLRs, particularly NRC3, have driven the evolution of their transient interactions with sensor NLRs, leading to subfunctionalization and contributing significantly to the complexity of the NRC network in plant immunity.TeaserHelper NLR subfunctionalization alters transient interactions with sensor NLRs, enhancing plant immune system complexity.

The nucleotide‐binding domain of NRC‐dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling

“…To date, conclusive evidence that NRC-dependent sensors and their NRC helpers form stable complexes has not been obtained. This is largely due to sensor-helper co-immunoprecipitation studies being notoriously difficult to control properly, as was shown recently by Huang et al in their recent study (Huang et al, 2023). In this same study, however, Huang et al leveraged Turbo-ID to reveal that NRC-dependent sensors specifically show enhanced interactions with their corresponding downstream helpers following activation, in support of a model in which NRC activation is mediated by transient sensor-helper interactions.…”

Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector

“…Ancestral sequence reconstruction statistically infers intermediate sequences at phylogenetic nodes, enabling the identification of key evolutionary mutations. It is increasingly being applied to plant-pathogen coevolutionary systems (Bentham et al, 2021; Białas et al, 2021; Huang et al, 2023; Schornack and Kamoun, 2023). For instance, this method was used to explore when the rice sensor NLR Pik-1 evolved to detect the AVR-PikD effector of the pathogenic fungus Magnaporthe oryzae (syn.…”

“…Similarly, ancestral sequence reconstruction was applied to the AVR-Pik effector family to understand the directionality of evolutionary changes, determining whether the effector family expanded host-target binding or host immunity evaded the effector family (Bentham et al, 2021). Moreover, a recent study employed this technique on NRC3 to examine the evolutionary history of sensor-helper compatibility (Huang et al, 2023). In our study, we applied ancestral sequence reconstruction to NRC3 and reconstructed the coevolutionary dynamics between NLRs and pathogen immunosuppressors.…”

“…One possible explanation is a trade-off between functional NLR activation and evasion of pathogen immunosuppression. In NLRs, mutations in the NB-ARC module are known to cause autoimmunity, loss-of-function, or sensor-helper incompatibility (De la Concepcion et al, 2021b; Huang et al, 2023; Sueldo et al, 2015; Williams et al, 2011). Since E316K is located in the NB-ARC module, this polymorphism could affect NLR activity or autoimmunity, and plants carrying K316 might be subject to negative selection in the absence of parasite pressure.…”

“…NRC0 helpers have been genetically and functionally conserved across asterids for more than 100 million years, predating the massive expansion and diversification of NRC-H and NRC-S into lineage- or species-specific NRC networks in lamiids, notably in the Solanaceae family (Goh et al, 2023; Oh et al, 2023; Sakai et al, 2024). Throughout their expansion and diversification, NRC proteins have subfunctionalised from the larger NRC network, resulting in organ-specialised subnetworks or in partial genetic redundancy as well as evolving specificity to different sensor NLRs (Huang et al, 2023; Lüdke et al, 2023). Notably, NRC3 of solanaceous species is required not only by sensor NLRs but also by the tomato cell-surface receptors Cf-2, Cf-4, Cf-5 and Cf-9, which trigger hypersensitive cell death response upon the recognition of the fungal pathogen Cladosporium fulvum (syn.…”