Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector

Abstract

Studies focused solely on single organisms can fail to identify the networks underlying host–pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic coevolution between an NLR integrated domain and multiple families of effector proteins.

TheNRC0gene cluster of sensor and helper NLR immune receptors is functionally conserved across asterid plants

“…Thus, the NRC0 gene cluster may have been lost as a consequence of selection against potential autoimmunity. Notably, five campanulids (Lactuca pathogen effectors (Sarris et al, 2015;Le Roux et al, 2015;Césari et al, 2014;Maqbool et al, 2015;Shimizu et al, 2022;Sugihara et al, 2023). Furthermore, in the Solanaceae NRC networks, about half of the NRC-S subclade members acquired N-terminal domain extensions that are often involved in effector recognition (Saur et al, 2015;Li et al, 2019;Adachi et al, 2019;Seong et al, 2020).…”

“…Both NRC0 and NRC0-S across asterids have a typical CC-NB-LRR domain architecture. In the case of well-studied NLR pairs, Arabidopsis RRS1/RPS4, rice RGA5/RGA4 and Pik-1/Pik-2, the sensor NLRs acquired additional integrated domains that function as decoys to bait pathogen effectors (Sarris et al, 2015; Le Roux et al, 2015; Césari et al, 2014; Maqbool et al, 2015; Shimizu et al, 2022; Sugihara et al, 2023). Furthermore, in the Solanaceae NRC networks, about half of the NRC-S subclade members acquired N-terminal domain extensions that are often involved in effector recognition (Saur et al, 2015; Li et al, 2019; Adachi et al, 2019; Seong et al, 2020).…”

“…For example, in Arabidopsis, RESISTANCE TO RALSTONIA SOLANACEARUM 1 ( RRS1 ) / RESISTANCE TO PSEUDOMONAS SYRINGAE 4 ( RPS4 ) (Narusaka et al, 2009; Sarris et al, 2015; Le Roux et al, 2015), Chilling Sensitive 1 ( CHS1 ) / Suppressors of chs1-2, 3 ( SOC3 ) and TIR-NB 2 ( TN2 ) (Zhang et al, 2017; Liang et al, 2019), CONSTITUTIVE SHADE-AVOIDANCE 1 ( CSA1 ) / CHILLING SENSITIVE 3 ( CHS3 ) (Xu et al, 2015; Yang et al, 2022), SUPRESSOR OF NPR1, CONSTITUTIVE 1 ( SNC1 ) / SIDEKICK SNC1 1 ( SIKIC1 ), SIKIC2 and SIKIC3 (Dong et al, 2018), form genetically linked pairs or clusters that function together in immune responses. In rice, RESISTANCE GENE ANALOG 5 ( RGA5 ) / RGA4 and PYRICULARIA ORYZAE RESISTANCE K-1 ( Pik-1 ) / Pik-2 are two sensor-helper NLR pairs that are found in head-to-head orientation in the genome (Césari et al, 2014; Maqbool et al, 2015; Shimizu et al, 2022; Sugihara et al, 2023).…”

Functional divergence shaped the network architecture of plant immune receptors

“…In rice, the helper NLR Pias-1 can also function with the sensor NLR RGA5 to respond to AVR-Pia, indicating that Pias-1 is not specialized to its own linked sensor NLR Pias-2 ( 31 ). In contrast, helper-sensor specialization was observed in allelic Pik-1/Pik-2 rice NLR pairs ( 32 ). For Pikm-1/Pikm-2 and Pikp-1/Pikp-2, this helper-sensor specialization was mapped to a single amino acid polymorphism on Pik-2 that determines its preferential association between matching pairs ( 33 ).…”

The blast effector Pwl2 is a virulence factor that modifies the cellular localisation of host protein HIPP43 to suppress immunity

“…However, effectors are also recognised by plant intracellular nucleotide-binding leucine rich repeat (NLR) immune receptors to activate disease resistance. For example, in rice, the paired NLRs RGA5/RGA4, Pik-1/Pik-2, and Piks-1/Piks-2 confer resistance to M. oryzae strains that secrete AVR1-CO39/AVR-Pia, AVR-Pik or AVR-Mgk1 effectors, respectively (5)(6)(7)(8)(9). Each of these proteins are members of the Magnaporthe Avrs and ToxB-like (MAX) effector family that are sequence unrelated, but structurally conserved (10), and are overrepresented among effectors recognised by rice NLR immune receptors (6,7,11,12).…”