A Phytophthora receptor-like kinase regulates oospore development and can activate pattern-triggered plant immunity

Pei, Yong; Ji, Peiyun; Si, Jierui; Zhao, Hanqing; Zhang, Sicong; Xu, Ruofei; Qiao, Huijun; Duan, Weiwei; Shen, Danyu; Yin, Zhiyuan; Dou, Daolong

doi:10.1038/s41467-023-40171-7

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Published: 31 July 2023

A Phytophthora receptor-like kinase regulates oospore development and can activate pattern-triggered plant immunity

Yong Pei¹,
Peiyun Ji¹,
Jierui Si¹,
Hanqing Zhao¹,
Sicong Zhang¹,
Ruofei Xu¹,
Huijun Qiao¹,
Weiwei Duan¹,
Danyu Shen¹,
Zhiyuan Yin ORCID: orcid.org/0000-0002-7189-895X¹ &
…
Daolong Dou ORCID: orcid.org/0000-0001-5226-6642^1,2

Nature Communications volume 14, Article number: 4593 (2023) Cite this article

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Abstract

Plant cell-surface leucine-rich repeat receptor-like kinases (LRR-RLKs) and receptor-like proteins (LRR-RLPs) form dynamic complexes to receive a variety of extracellular signals. LRR-RLKs are also widespread in oomycete pathogens, whereas it remains enigmatic whether plant and oomycete LRR-RLKs could mediate cell-to-cell communications between pathogen and host. Here, we report that an LRR-RLK from the soybean root and stem rot pathogen Phytophthora sojae, PsRLK6, can activate typical pattern-triggered immunity in host soybean and nonhost tomato and Nicotiana benthamiana plants. PsRLK6 homologs are conserved in oomycetes and also exhibit immunity-inducing activity. A small region (LRR5-6) in the extracellular domain of PsRLK6 is sufficient to activate BAK1- and SOBIR1-dependent immune responses, suggesting that PsRLK6 is likely recognized by a plant LRR-RLP. Moreover, PsRLK6 is shown to be up-regulated during oospore maturation and essential for the oospore development of P. sojae. Our data provide a novel type of microbe-associated molecular pattern that functions in the sexual reproduction of oomycete, and a scenario in which a pathogen LRR-RLK could be sensed by a plant LRR-RLP to mount plant immunity.

Introduction

Plant transmembrane receptor-like kinases (RLKs) and receptor-like proteins (RLPs) play important roles in growth, development, and defense responses^1,2. The various extracellular domains (ECDs) can sense microbe-associated molecular patterns (MAMPs) during interaction to mount pattern-triggered immunity (PTI). Microbe-associated molecular patterns (MAMPs) are generally considered to be highly conserved throughout classes of microbes and contribute to microbial fitness³. The majority of currently characterized MAMPs are molecules secreted by microbes or cell components of microbes that are released by plants^4,5. For example, plant enzymes target the bacterial flagella and fungal cell wall to release flagellin⁶ and chitin⁷ respectively, while Nep1-like proteins⁸ and glycoside hydrolases⁹ are virulence factors that are also recognized as MAMPs by plants. MAMP-receptor pairs are useful for guiding plant-resistance breeding. Recently, transgenic wheat expressing the Nicotiana benthamiana receptor RXEG1 exhibited enhanced resistance to Fusarium graminearum by recognizing glycoside hydrolase 12 MAMPs¹⁰. There are hundreds of RLKs and RLPs on the plant cell surface, but only dozens of MAMPs were found up till now².

Oomycetes resemble filamentous fungi in morphology but belong to Stramenopiles. Phytophthora is an oomycete genus that includes ~200 destructive plant pathogens, causing a variety of agricultural losses worldwide as well as environmental damage in natural ecosystems¹¹. For example, potato late blight caused by P. infestans, which was one of the causes of the Irish famine of the 19th century and which still threatens the safe production of potatoes and tomatoes¹². P. sojae causes soybean root and stem rot and has been developed as a model species for the study of oomycete development and pathogenesis owing to the availability of abundant genomic data and well-established gene editing technique^11,13,14. The leucine-rich repeat (LRR) RLKs form the largest family of plant cell-surface receptors. Interestingly, LRR-RLKs with a similar domain structure are also widespread in oomycetes although they are evolutionarily distant to plants^15,16. We previously reported that PcLRR-RK1 regulates the growth, development, and virulence of P. capsici¹⁷ and several P. sojae LRR-RLKs play pivotal roles in zoospore production and virulence¹⁶.

LRR-containing proteins may interact with each other to regulate different biological processes. For MAMPs (microbe-associated molecular patterns) recognition, interactions between ECDs of LRR-RLKs are a prerequisite for ligand signal activation¹⁸. In Arabidopsis, an extracellular network consisting of 567 interactions among ECDs of 225 LRR-RLKs was identified¹⁹. A similar extracellular interactome of LRR proteins was revealed in Drosophila melanogaster²⁰. Similar to plants and metazoans, P. sojae also has a complicated interaction network of LRR-RLKs¹⁶. Importantly, it is worth to notice that receptors with LRR ECDs between adjacent cells can also establish contacts and mediate cell-to-cell communication in metazoans²¹.

Given that both P. sojae and the host plant possess many LRR-RLKs that are essential for virulence or resistance, we hypothesized that they could mediate cell-to-cell communications during interaction. To test it, we systematically expressed 24 P. sojae LRR-RLKs and found that PsRLK6 could elicit immune responses in Nicotiana benthamiana. PsRLK6 is conserved and widespread across Peronosporales, whose homologs exhibited immune-inducing activity in the plant as well. Moreover, the immunity activated by PsRLK6 required two co-receptors BAK1 and SOBIR1, suggesting that an LRR-RLP binds PsRLK6 to mount plant immunity. Our data provide a novel type of microbe-associated molecular patterns (MAMP) that is a cell surface-localized RLK and a scenario showing plants and pathogens communicate with each other via cell-surface receptors.

Results

P. sojae PsRLK6 can activate typical pattern-triggered immunity (PTI) in Nicotiana benthamiana

In our previous study, a total of 24 LRR-RLK genes (PsRLKs) were identified in the P. sojae genome¹⁶. We hypothesized that some PsRLKs could interact with plant receptors to induce plant immunity during infection. Thus, extracellular domains (ECDs) of all 24 PsRLKs were cloned and then transiently expressed in N. benthamiana by agroinfiltration. The DAB (3,3-diaminobenzidine) staining assay revealed that PsRLK6^ECD and PsRLK7^ECD could induce reactive oxygen species (ROS) accumulation in N. benthamiana, while other PsRLKs and the negative control GFP could not (Fig. 1a). To further examine the effect of PsRLK6^ECD and PsRLK7^ECD on plant resistance to pathogen, N. benthamiana leaves that expressed PsRLK6^ECD, PsRLK7^ECD, or GFP for 24 h were inoculated with P. capsici. Leaf regions expressing PsRLK6^ECD or PsRLK7^ECD showed significantly smaller lesion areas and less P. capsici biomass, compared to that expressing GFP (Supplementary Fig. 1a, b). Western blot analysis showed that GFP, PsRLK6^ECD, and PsRLK7^ECD were successfully expressed at the expected size in N. benthamiana (Supplementary Figs. 1c, d). These results suggest that P. sojae PsRLKs could enhance plant resistance in N. benthamiana.

**Fig. 1: PsRLK6 can induce PTI responses in *N. benthamiana*.**

To further confirm that PsRLK6^ECD and PsRLK7^ECD could induce immune responses in N. benthamiana, we initially expressed and purified His-tagged PsRLK6^ECD and PsRLK7^ECD from Pichia pastoris (Supplementary Fig. 2). The recombinant proteins were used to test for a series of PTI (pattern-triggered immunity) responses, including ROS burst, MAPK activation, and up-regulation of two PTI marker genes (PR1a and CYP71D20). As shown in Fig. 1b, 1 μM PsRLK6^ECD protein treatment increased ROS levels after about 5 min upon elicitation, reaching the maximum levels at 30 min. However, PsRLK7^ECD protein failed to induce detectable ROS production even at 60 min, similar to GFP protein (Fig. 1b). Therefore, PsRLK6^ECD was selected for further studies. To test whether PsRLK6^ECD-induced ROS burst is concentration-dependent, different concentrations of PsRLK6^ECD proteins ranging from 0.01 μM to 5 μM were examined. The result showed that the total ROS production of 60 min increased with higher concentrations (Fig. 1c).

MAPK activation is another early PTI (pattern-triggered immunity) signaling event. As shown in Fig. 1d, PsRLK6^ECD protein treatment triggered MAPK activation at 5, 10, and 15 min in N. benthamiana as detected by immunoblot with the α-pTEpY antibody. We also observed that the expressions of PTI marker gene PR1a and CYP71D20 were greatly activated by PsRLK6^ECD protein for 6 h (Fig. 1e, f). Finally, to examine the effect of PsRLK6^ECD protein on plant resistance to pathogen, N. benthamiana leaves were pre-treated with 1 μM PsRLK6^ECD or GFP proteins, respectively, and were inoculated with P. capsici 24 h later. Consistent with the above results, pre-treatment with PsRLK6^ECD protein resulted in significantly smaller lesions and less P. capsici biomass compared to GFP (Fig. 1g–i). Collectively, these findings show that PsRLK6^ECD can activate PTI (pattern-triggered immunity) responses in N. benthamiana.

BAK1 and SOBIR1 are required for PsRLK6-induced immune responses in N. benthamiana

LRR-RLKs BAK1 and SOBIR1 are two co-receptors of most LRR-RLK and LRR-RLP receptors for signaling activation⁴. To determine whether PsRLK6^ECD-induced immune responses are BAK1- and SOBIR1-dependent in N. benthamiana, we used the virus-induced gene silencing (VIGS) construct to silence BAK1. The sobir1 mutant was generated by CRISPR/Cas9 previously²². PsRLK6^ECD-induced ROS production, activation of MAPK and the PTI marker gene CYP71D20 were measured in BAK1-silenced and sobir1 plants. The results showed that the ROS production was remarkably compromised in BAK1-silenced plants and sobir1 mutants compared to GFP-silenced and wild-type plants (Fig. 2a–d). The relative expressions of CYP71D20 induced by PsRLK6^ECD protein were reduced by about 12-fold in BAK1-silenced plants and 40-fold in sobir1 mutants, respectively (Fig. 2e, f). Similarly, the MAPK activation was also remarkably compromised in BAK1-silenced plants and sobir1 mutants (Fig. 2g, h). We next evaluated whether BAK1 and SOBIR1 are also required for PsRLK6^ECD-induced resistance to P. capsici. Compared with leaves treated with TRV2:GFP, BAK1-silenced leaves are more susceptible to P. capsici and PsRLK6^ECD-induced resistance was blocked through monitoring lesion areas and relative pathogen biomass in BAK1-silenced plants (Supplementary Fig. 3a–d). Similar results were observed in the sobir1 mutant, which showed increased disease severity and comprised plant resistance induced by PsRLK6^ECD (Supplementary Fig. 3e–g). Collectively, these results showed that BAK1 and SOBIR1 are both required for PsRLK6-triggered immunity in N. benthamiana.

**Fig. 2: Immune responses triggered by PsRLK6 require coreceptors BAK1 and SOBIR1.**

PsRLK6 can trigger immune responses in soybean and tomato

We also tested the elicitor activity of PsRLK6^ECD in the cognate host soybean (Glycine max) along with two nonhost plants tomato and Arabidopsis thaliana. The results showed that 1 μM PsRLK6^ECD protein could trigger ROS burst in soybean and tomato, but not in A. thaliana (Fig. 3a–c). Similarly, the marker gene PR1a was up-regulated in soybean and tomato but not in A. thaliana after being pre-treated for 6 h with PsRLK6^ECD compared to GFP protein (Fig. 3d–f). To further evaluate the contribution of PsRLK6^ECD to disease resistance in soybean, the etiolated soybean hypocotyls were placed into 50 nM PsRLK6^ECD and GFP protein solution respectively. Twelve hours later, soybean hypocotyls were taken out from the protein solution and inoculated with a piece of mycelium of P. sojae. Compared to the GFP control, pre-treatment with PsRLK6^ECD resulted in lighter symptoms in plants (Fig. 3g). Similarly, 50 nM GFP and PsRLK6^ECD protein were used to treat tomato and A. thaliana, and PsRLK6^ECD could induce resistance to P. capsici in tomato (Fig. 3h) but not in A. thaliana (Fig. 3i). These results suggest that PsRLK6^ECD could induce immune responses in multiple plants including the host plant soybean.

**Fig. 3: PsRLK6 can induce immune responses in soybean and tomato.**

A small region (LRR5-6) of PsRLK6 is sufficient to elicit immune responses in plants

To identify the critical area of the PsRLK6 for elicitor activity, we firstly predicted the 3D structure of PsRLK6^ECD by AlphaFold 2²³. Total of five generated models were provided, and the pLDDT coloring was displayed in Fig. 4a. The best predicted structure of PsRLK6^ECD was presented, wherein the ECD forms a single continuous structure in an arc shaped conformation (Fig. 4a). The inner face of the arc forms a concave surface, the majority of which contain an extended parallel β-sheet. The outer face forms a convex side mostly consisting of various secondary structures such as α-helices, loops and turns. According to the predicted structure, PsRLK6^ECD contains an N-terminal signal peptide domain, an LRR capping domain, seven atypical LRR domains, and an LRR C-terminal domain (Fig. 4b). To test whether the elicitor activity of PsRLK6^ECD is heat stable, we treated the PsRLK6^ECD protein by boiling at 100 °C for 10 min. The results showed that boiled PsRLK6^ECD protein still could induce ROS accumulation (Fig. 4c) and disease resistance to P. capsici in N. benthamiana (Supplementary Fig. 4). So, we hypothesized an epitope might be recognized by plants to elicit immune responses. To map the PsRLK6^ECD epitope that is responsible for the elicitor activity, we generated truncated mutant variants of PsRLK6^ECD that carried an intact signal peptide and tested their ability to test the ROS accumulation in N. benthamiana by agroinfiltration (Fig. 4b). As shown in Fig. 4b, the region containing residues 237–281 (M7), corresponding to LRR5-6, fully triggered ROS accumulation in N. benthamiana leaves (Fig. 4b). Furthermore, pathogen inoculation assays confirmed that expression of LRR5-6 in N. benthamiana was sufficient to enhance plant resistance to P. capsici (Fig. 4b). These results indicate that the LRR5-6 of PsRLK6^ECD is the key region for elicitor function. To further verify whether the immunogenic epitope LRR5-6 could trigger plant immunity, the peptide was chemically synthesized. However, we failed to obtain the final peptide after trying three times. Furthermore, we expressed and purified the LRR5-6 region using E. coli to investigate whether it could elicit immune responses in different plants. The results demonstrated that LRR5-6 could induce ROS burst in N. benthamiana (Fig. 4d), and subsequent experiments confirmed its ability to trigger ROS burst in soybean (Fig. 4e) and tomato (Fig. 4f). In conclusion, these results demonstrate that two LRR motif of PsRLK6^ECD is sufficient to elicit immune response in multiple plants.

**Fig. 4: Two LRR motifs of PsRLK6 are sufficient to induce immune responses in plants.**

The elicitor function of RLK6 could be conserved in oomycetes

Since LRR-RLKs are widespread in oomycetes and plants, but not in diatoms, fungi, or metazoans¹⁶, to investigate the phylogenetic distribution of PsRLK6 homologs, we queried the genomes of twenty-six oomycete, three fungal, two bacterial, and two plant species. A total of 53 homologous protein sequences were obtained in different oomycete species, while no homologs were found in others (Fig. 5a, b, Supplementary Data 1). Interestingly, PsRLK6 homologs were only found in the Peronosporales but not in Saprolegniales (Fig. 5a, b). Most oomycetes contain no more than three PsRLK6 homologs, while Phytophthora fragariae and Phytophthora cactorum have much more homologs than other species (Fig. 5b). Additionally, the Consurf server²⁴ was used to analyze the conservation of the structure of obtained 53 homologous protein sequences with PsRLK6^ECD. The results showed that they share a high similarity at the protein level (Supplementary Fig. 5a). The enlarged image of the key region for elicitor function LRR5-6 also showed a high similarity (Supplementary Fig. 5b).

**Fig. 5: Conserved PsRLK6 homologs that exhibit elicitor function in *N. benthamiana* are widely distributed in oomycetes.**

To investigate whether the PsRLK6 homologs from diverse Phytophthora and Pythium species could induce immune responses, we cloned the ECDs of six homologous genes from Phytophthora infestans, Phytophthora capsici, Phytophthora parasitica, Phytophthora nicotianae, Phytophthora cactorum, and Pythium oligandrum (Supplementary Fig. 5c). These homologs were transiently expressed in N. benthamiana to test for their ability to induce ROS accumulation. Similar to PsRLK6^ECD, DAB staining assays showed that all six PsRLK6^ECD homologs could induce ROS accumulation in N. benthamiana (Fig. 5c). Western blot analysis confirmed that all the proteins were successfully expressed at the expected size in N. benthamiana (Fig. 5d). Moreover, expression of these six homologs in N. benthamiana all resulted in remarkably reduced P. capsici biomass compared to the GFP control (Fig. 5e). These results indicated that conserved PsRLK6 homologs from diverse oomycetes could be recognized by N. benthamiana to mount plant immunity.

PsRLK6 can trigger immune responses during P. sojae-soybean interaction

MAMPs often play important roles in the growth, development, and virulence of microbes. However, we previously reported that the PsRLK6 knockout mutants have no obvious phenotypes on growth, zoospore development, and virulence¹⁶. A transcriptome data showed that PsRLK6 was up-regulated during infection stages²⁵, suggesting its potential role during interaction. Therefore, we over-expressed PsRLK6-GFP by PEG-mediated transformation²⁶. Immunoblotting analysis using the α-GFP antibody confirmed that the protein was expressed in the mycelia of the OT24 and OT36 lines (Supplementary Fig. 6a). All transformants showed normal filamentous growth compared with WT (Supplementary Fig. 6b, c). To assay the virulence of the transformants, zoospores were inoculated onto etiolated seedlings of soybean. The knockout mutant ΔPsRLK6 showed unchanged lesion length as reported previously¹⁶, while overexpression of PsRLK6-GFP showed significantly reduced virulence on soybean (Supplementary Fig. 6d). Determination of the P. sojae DNA biomass confirmed that virulence of OT24 and OT36 transformants was severely attenuated compared to that of WT and ΔPsRLK6 (Supplementary Fig. 6e, f). These results indicate that overexpression of PsRLK6 could limit P. sojae infection, likely by inducing defense responses.

Furthermore, we conducted a series of experiments to investigate whether PsRLK6 could elicit PTI immune responses during P. sojae-soybean interaction, including ROS burst, up-regulation of PR1a and MAPK activation. At 24 h post-inoculation (hpi), PsRLK6 overexpression line OT24 exhibited a higher level of ROS accumulation compared to both the WT and knockout mutant, which displayed similar levels of ROS staining as the WT after DAB staining (Fig. 6a). Next, the ROS burst in soybean leaves triggered by different strains was quantified, revealing that PsRLK6 knockout mutants produced a slightly reduced amount of ROS compared to the WT, while overexpression lines generated significantly higher levels of ROS (Fig. 6b, c). Similarly, the fold change of PR1a expression was lower than that induced by the WT, whereas OT24 overexpression line exhibited an opposite trend (Fig. 6d). Further experiments on MAPK activation of different strains revealed that OT24 exhibited greater MAPK activation compared to WT and ΔPsRLK6 exhibited a little less (Fig. 6e), indicating a potential role of PsRLK6 in inducing MAPK activation of soybean. Taken together, these results show that PsRLK6 can trigger defense responses, though the extent to which it does so during infection of plants with wild-type Phytophthora remains to be determined.

**Fig. 6: PsRLK6 could induce PTI immune responses during infection.**

PsRLK6 is required for the oospore development of P. sojae

In nature, survival and dispersal of spores are essential for the success of many plant pathogens. The sexual reproduction of P. sojae produces thick-walled oospores, which are important inoculum to trigger a new epidemic in the next growing season²⁷. Sexual reproduction is particularly relevant for the homothallic P. sojae²⁸. To further explore the biological role of PsRLK6 during the sexual cycle of P. sojae, we firstly investigated the number and morphology of oospores produced by PsRLK6 knockout and overexpression transformants. Interestingly, after culturing on LBA (lima bean agar) medium for 14 days, the knockout mutant generated considerably reduced oospores, while overexpression lines produced slightly more oospores than WT (Fig. 7a, b). The oospores produced by ΔPsRLK6 showed more abnormal morphological oospores while overexpression lines showed less (Fig. 7c). We further determined whether PsRLK6 could up-regulate in oospore development stages. The mycelia grown on the LBA medium for 6, 12, and 20 days produced no oospores, immature oospores and mature oospores, respectively. We found that PsRLK6 is up-regulated about 3-fold and 12-fold in the stages of immature and mature oospores respectively (Fig. 7d). Furthermore, we investigated oospore number and morphology produced by different strains during infection. Due to phenotype of two overexpression lines grown on LBA medium was consistent, we selected OT24 for further study. Oospores were generated on infected root tissue with mycelia at 48 hpi (top row) and 96 hpi (bottom row) stained with lactophenol-trypan blue. The results showed that oospores produced in infected soybean hypocotyl tissue by PsRLK6 knockout mutant was less than WT, while PsRLK6 overexpression transformant (OT24) produced more oospores (Fig. 7e, f). Similar to that grown on the LBA medium, the oospores produced by ΔPsRLK6 during infection showed more abnormal morphological oospores, while overexpression line (OT24) showed less (Fig. 7g). We further determined whether PsRLK6 could up-regulate in infection stages when oospores could be produced. In the late stages of infection, the oospores became mature gradually, and the expression levels of PsRLK6 were significantly increased (Fig. 7h). Taken together, these results indicate that PsRLK6 is essential for the oospore development of P. sojae.

**Fig. 7: PsRLK6 regulates the oospore development of *P. sojae*.**

Discussion

To overcome pathogen attacks, plants have evolved an excellent system to recognize non-self MAMPs (microbe-associated molecular patterns) through cell-surface receptors, among which LRR-RLKs are the largest family of RLKs in plants²⁹. Interestingly, LRR-RLKs are also widespread in oomycetes and play important roles in development and stress^15,16,17. Remarkably, here we found a P. sojae LRR-RLK (PsRLK6) and its homologs could be detected by plants to activate pattern-triggered immunity.

Sexual reproduction is a key process in the infection cycle of oomycetes, which produce oospores that are important inoculum to trigger a new epidemic in the next growing season³⁰. However, the molecular mechanism of sexual reproduction in oomycetes is poorly understood. Only very few genes have been reported to regulate the oospore development of oomycetes. In Pythium ultimum, knockout mutants of PuM90, a Puf family RNA-binding protein, showed significantly defective in oospore formation with empty oogonia or oospores larger in size with thinner oospore walls³¹. Further study indicated that a tripartite recognition motif in the Puf domain of PuM90 could specifically bind to the 3’-untranslated region region of PuFLP, which encodes a flavodoxin-like protein and thereby repress PuFLP mRNA level to facilitate oospore formation³¹. In P. infestans, silencing of a gene that encodes loricrin-like protein blocked oospore wall formation³². As for P. sojae, YPK1 (a serine/threonine protein kinase-encoding gene)³³, YKT6 (a soluble N-ethylmaleimide-sensitive factor attachment protein receptors)³⁴, GK5 (a G-protein-coupled receptor with a phosphatidylinositol phosphate kinase domain)³⁵, IMPA1 (a conserved importin α)³⁶, and N-glycosylation in HSP70³⁷ also play important roles in oospore production while the mechanisms of regulating oospore development remain largely elusive. Here, we showed that PsRLK6 plays an indispensable role in oospore production and morphological development. Knockout of PsRLK6 led to reduced oospore number, increased ratio of abnormal oospores. During infecting soybean, ΔPsRLK6 produced much less mature oospores compared to WT. Although knockout of PsRLK6 does not affect the zoospore development and virulence¹⁶, impaired oospore production and survival rate in soybean residues likely could not guarantee sufficient inoculum to trigger a new epidemic in the next growing season in the field.

Microbe-associated molecular patterns (MAMPs) are highly conserved molecules and have an essential function in microbial fitness or survival within the microbiome³. These molecules are usually involved in the growth, development, or pathogenicity of microbes. Classical MAMPs are usually structural molecules, such as bacterial flagellin, peptidoglycan, lipopolysaccharides, oomycete glucans, and fungal chitin³. Many virulence secretory proteins are also MAMPs, such as NLP³⁸, XEG1³⁹ PcEXLX1⁴⁰. The reproduction of fungi and oomycetes is vital for the infection cycle and virulence variation, but only a few reports indicate that molecules involved in this process were identified as MAMPs. Zoospore of Phytophthora and conidiospore of fungi could directly elicit plant defense during infection^41,42. Meanwhile, the MAMPs VmE02⁴³ and VdNLP1³⁸ regulate the conidiation of fungal pathogens Valsa mali and Verticillium dahliae, respectively. In this study, we first reported a protein that regulates the sexual reproduction of Phytophthora was recognized by plants. And we reveal that the transmembrane protein of pathogens also could be recognized as a MAMP.

The formation of heteromeric PRR complexes is important to activate intracellular signaling for immunity⁴⁴. LRR-RLKs recruit the co-receptor BAK1 upon ligand binding, while LRR-RLPs require another co-receptor SOBIR1 besides BAK1⁴⁵. PsRLK6-triggered immune responses depend on both BAK1 and SOBIR1 in N. benthamiana, suggesting that PsRLK6 is likely recognized by a plant LRR-RLP. In animals, transmembrane LRR proteins regulate synapse formation and function in the vertebrate nervous system by directly interacting with membrane proteins of neighboring cells⁴⁶. During infection, pathogens release cell-wall degrading enzymes to enter the host’s apoplast, and host plants also secret enzymes to degrade the cell wall of pathogens to limit infection^47,48. In pathogen-host interactions, LRR-containing proteins could also mediate the infection cycle. For example, Listeria monocytogenes, a bacterial pathogen that causes gastroenteritis, abortions, and meningitis, produces about 25 different LRR-containing internalin proteins⁴⁹. Biochemical and structural analyses demonstrated that the LRR domains of cell-surface located internalin proteins bind directly to distinct human receptors to promote the internalization of bacteria into mammalian cells⁴⁹. Thus, in the plant apoplast battleground, P. sojae LRR-RLKs might interact with plant receptors to mediate cell-to-cell communications.

Another possible scenario is that the ECD of PsRLK6 is cleaved by the plant and then released into the apoplast. In animals, controlled proteolysis is a well-known general mechanism that regulates the function of transmembrane receptors. Proteolytic cleavage of the extracellular portion of transmembrane proteins at or near the cell surface is referred as ectodomain shedding. It can be either constitutive or stimulus-induced and has been demonstrated for a lot of animal proteins, including cell adhesion molecules, growth factors, and receptors^50,51. Prominent examples are receptor tyrosine kinases epidermal growth factor receptors (EGFRs), which are structurally similar to plant RLKs and their ligands. Both EGFRs and EGFR ligands are synthesized as membrane-anchored precursors and their soluble ectodomains are released by proteolysis⁵². Moreover, numerous MAMPs need to be processed by plants before being recognized, such as bacterial flagellin processed by BGAL into flg22, fungal chitin and pectin are degraded into oligomers, and the oomycete-derived ceramide cleaved by plant apoplastic ceramidase into sphingoid base^5,53. Taken together, we speculate that PsRLK6^ECD might be released into the host’s apoplast to be detected by the plant immune receptor.

Plant RLKs and RLPs form dynamic complexes in a ligand-dependent manner, which is essential for signaling activation^54,55. The Arabidopsis LRR-RLKs show a complicated interaction network revealed by a high-throughput screen¹⁹. Likewise, we previously showed that P. sojae LRR-RLKs could form various complexes by split-luciferase assay¹⁶. Indeed, cell surface transmembrane proteins of animals interact directly to mediate cell-to-cell communications⁴⁶. Here, we reveal that a P. sojae LRR-RLK is likely sensed by a plant LRR-RLP that forms a complex with LRR-RLKs BAK1 and SOBIR1 to activate plant immunity, suggesting that the pathogen receptor could also form complexes with plant receptors. The parasitic weed Striga gesnerioides produces an LRR effector to promote host colonization⁵⁶. Therefore, it’s interesting to further determine other P. sojae LRR-RLKs that could interact with plant receptors to disturb plant immunity.

The primary way to control plant diseases is using chemical fungicides, however, which threaten the environment and food safety. Microbe-associated molecular patterns (MAMPs) are environmentally friendly biological factors that enhance plant resistance to pathogens⁵⁷. Here, we show that PsRLK6 induces immune responses in soybean and tomato, and the elicitor activity is heat-stable. Thus, PsRLK6 is a promising bio-stimulant for the control of plant diseases. Moreover, immune receptors that recognize MAMPs can be used for plant-resistance breeding. For instance, interfamily transfer of the LRR-RLK EFR that recognizes bacterial EF-Tu proteins in tomato and rice confers broad-spectrum resistance to bacteria⁵⁷. Since RLK6 homologs that have elicitor activity are widespread in oomycete pathogens, further characterization of the corresponding receptor of RLK6 will provide resistance to these pathogens.

In summary, we report that an LRR-RLK from the oomycete pathogen P. sojae is essential for sexual reproduction by regulating oospore development. PsRLK6 triggers BAK1- and SOBIR1-dependent immune responses, representing a novel type of MAMP that shows the cell communication between cell surface receptors from plant and pathogen.

Methods

Microbial cultures

The Phytophthora sojae strains (P6497 and transformants), P. capsici, P. parasitica, P. nicotianae, P. cactorum, and Pythium oligandrum were routinely grown on 10% vegetable (V8) juice agar medium at 25 °C in the dark. The P. infestans strain T30-4 was routinely cultured on the solid RSA/V8 medium at 18 °C in the dark. P. sojae mycelia and zoospores were prepared as previously described¹⁶. PsRLK6 overexpression transformants were generated using the PEG-mediated protoplast transformation²⁶. Overexpression lines were confirmed by immunoblot.

Plant growth conditions and infection assays

In this study, Nicotiana benthamiana plants were grown in soil at 23 °C with a 16 h light and 8 h dark photoperiod. Soybean plants (Hefeng 47) were grown in soil at 23 °C with a 16 h light and 8 h dark photoperiod. Tomato seeds were germinated on a Petri dish lined with moist filter paper at 25 °C. After 5 days, the germinating sprouting seeds were transferred to soil and grown at 25 °C under a 16 h light and 8 h dark photoperiod. Arabidopsis plants were grown at 23 °C with a 10 h light and 14 h dark photoperiod.

For the P. capsici infection assay in N. benthamiana, leaves with different treatments were collected. Agar plugs of 5 mm diameter excised from fully grown mycelium of P. capsici were placed on adaxial surface of the leaves and incubated in darkness at 25 °C. The inoculated leaves were kept in transparent plastic boxes with high humidity and placed in a climate chamber. Lesion areas were measured at 36 h post-inoculation (hpi).

For the P. capsici infection assay in tomato. Tomato plants were sprayed with GFP and PsRLK6^ECD proteins. After 12 h, leaves were excised. Agar plugs of 5 mm diameter excised from fully grown mycelium of P. capsici were placed on the adaxial surface of the leaves and incubated in darkness at 25 °C. After three days post inoculation, disease severity and in planta P. capsici biomass was quantified.

For the P. capsici infection assay in Arabidopsis. Arabidopsis Col-0 plants were sprayed with GFP and PsRLK6^ECD protein. After 12 h, leaves were excised. About 150 zoospores of P. capsici were inoculated onto the center of a detached leaves and incubated in a growth room in dark at 25 °C. Inoculated leaves were photographed under UV light and the lesion areas were measured at 24 hpi. Relative quantification of P. capsici biomass in infected Arabidopsis leaves was performed to evaluate disease development.

For the P. sojae infection assay, ~200 zoospores of each transformant and the wild-type strain were inoculated onto the hypocotyls of etiolated soybean seedlings (susceptible Hefeng47 cultivar). Disease symptoms were scored at 48 h post-inoculation (hpi). At least three replications were performed for infected seedlings of each transformant. All assays were repeated at least three times.

P. sojae growth, oospore production, and staining assays

To determine the growth rate, all tested strains were cultured on 10% V8 agar medium at 25 °C in the dark. Colony diameters were measured and photographed after seven days. To quantify oospore production, all tested strains were cultured on LBA agar medium in 7 cm petri plates at 25 °C in the dark. The oospores produced by different strains were photographed and counted with at least 30 images per strain. The different morphology of oospores was photographed, and the content ratio was calculated.

Oospores of the homothallic species P. sojae were collected and separated by following the techniques as described previously⁵⁸. Briefly, a polytron was used to homogenize the mating tissues collected from five dishes. The tissues were washed by 50 ml of sterile deionized water using five intervals of 2 min each at 4 °C. Then, oospores and hyphae were concentrated by centrifugation for 10 min at 4000 × g, and washed three times in water by spinning at 650 × g for 5 min. To assess the colonization of soybean tissues by oospores, infected epidermal cells were collected at 48 and 96 hpi and soaked in lactophenol-trypan blue [(10 mL lactic acid, 10 mL glycerol, 10 g phenol, and 10 mg trypan blue (purchased from Beijing Solarbio Science & Technology Co., Ltd.), dissolved in 10 mL distilled water], and then the infected epidermal cells were examined under an inverted microscope.

To examine colonization of soybean tissues by oospores of different strains, infected epidermal cells were collected at 6, 12, 24, 48, 72, 84, 96, 168 hpi and then soaked in lactophenol-trypan blue to stain for 2 h. After destaining in chloral hydrate and water, cells were examined under a light microscope. The morphology of oospores was observed and the number was measured. Each strain was tested using at least two different preparations of mycelia and five plants for infection. The lesion areas of plants infected by pathogen are measured by ImageJ v1.52 and the figures are made by GraphPad Prism 9 software.

Bioinformatics

The proteomes of different organisms used in this study were obtained from National Center for Biotechnology Information (NCBI) databases with following accession numbers: Phytophthora sojae (GCA_000149755.2), P. infestans (GCA_000142945.1), P. nicotianae (GCA_001483015.1), P. aleatoria (GCA_018873745.1), P. pseudosyringae (GCA_019155715.1), P. fragariae (GCA_009733025.1), P. rubi (GCA_009732945.1), P. capsici (GCA_000325885.1), P. idaei (GCA_016880175.1), P. cactorum (GCA_003287315.1), P. kernoviae (GCA_001712705.2), P. parasitica (GCA_000509465.1), Hyaloperonospora arabidopsis (GCA_000173235.2), Bremia lactucae (GCA_004359215.2), Plasmopara halstedii (GCA_900000015.1), Pythium ultimum (GCA_000143045.1), Pythium oligandrum (GCA_005966545.1), Pythium aphanidermatum (GCA_000387445.2), Globisporangium splendens (GCA_006386115.1), Albugo laibachii (GCA_902706625.1), Albugo candida (GCA_001078535.1), Aphanomyces invadans (GCA_000520115.1), Aphanomyces astaci (GCA_003546625.1), Saprolegnia diclina (GCA_000281045.1), Saprolegnia parasitica (GCA_000151545.2), Thalassiosira pseudonana (GCA_000149405.2), Botrytis cinerea (GCA_000143535.4), Magnaporthe oryzae (GCA_000002495.2), Sclerotinia sclerotiorum (GCA_001857865.1), Pseudomonas syringae (GCA_002905815.2), Xanthomonas oryzae (GCA_008370835.2), Arabidopsis thaliana (GCA_001651475.1), and Glycine max (GCA_000004515.5). To determine the phylogenetic relationships of selected organisms, BLASTP (v2.5.0) comparisons (E value < 1e-5) of all the protein sequences derived from above organisms were used as input into TribeMCL v14.137⁵⁹ using an inflation value of 2.0 for clustering. Protein sequence clusters with only one member from each organism were defined as single-copy core proteins (Fig. 5a). The multigene phylogenetic tree was conducted by MEGA 11⁶⁰ following the maximum-likelihood based method with 1,000 bootstrap replicates based on the concatenated sequences of single-copy core proteins. Single copy genes used in the phylogenetic analysis was as listed in Supplementary Data 2. To search for PsRLK6 orthologs in other organisms, PsRLK6 was used as the query to search against proteomes above by reciprocal BLASTP with an E-value cut-off of 1e-5. A phylogenetic tree of PsRLK6 and its homologous proteins was constructed following the neighbor-joining algorithm with 1,000 bootstrap replicates using MEGA 11 software to identify PsRLK6 orthologs (Fig. 5b). The multiple sequence alignment analysis was performed using MUSCLE (v3.8.31) tool with default parameters. To analyze the amino acid conservation, we used the Consurf server (https://consurf.tau.ac.il/consurf_index.php) with the default parameters except uploading a multiple sequence alignment of obtained 53 homologous protein sequences²⁴ (Supplementary Figs. 5a and b). The structures were visualized in the PyMOL v2.4.0 program.

Protein structure prediction. The structure of PsRLK6^ECD is predicted by ColabFold²³ v1.5.2: AlphaFold2 using MMseqs2 and the detect templates in pdb70 (Fig. 4a). All the ColabFold output was included with the Supplementary Data 3. The structures were visualized in the PyMOL v2.4.0 program.

Plasmid construction

A mixture of cDNAs from P. sojae collected at different infection stages was used as a template to amplify the coding sequences of P. sojae genes using the Phanta Super-Fidelity DNA Polymerase (P501-d1, Vazyme). Genes were cloned into vectors based on homologous recombination technology using the Vazyme ClonExpress II One Step Cloning Kit (C112, Vazyme). For Agrobacterium-mediated transient expression in N. benthamiana, the coding sequences of P. sojae LRR-RLKs, PsRLK6^ECD homologs and truncated versions of PsRLK6^ECD were cloned into the vector pBIN-3xHA. pBIN:INF1 and pBIN:GFP plasmid constructs served as positive and negative controls, respectively. For expression of the protein in Pichia pastoris, PsRLK6^ECD and PsRLK7^ECD without the signal peptide were cloned into pPICZaA vector. For expression of the protein in E. coli, LRR5-6 region of PsRLK6^ECD were cloned into pCold TF vector. To generate overexpression transformants, PsRLK6 was cloned into the pTOR-GFP vector. The primers and constructs used in this study are listed in Supplementary Table 1.

Transient expression in N. benthamiana and DAB staining

Agrobacterium-mediated transient expression assays were performed to test the ROS-inducing activity. The indicated constructs were transformed into A. tumefaciens strain GV3101. The Agrobacterium strains carrying a plasmid were cultured in the LB medium containing antibiotics at 28 °C for 16–18 h. And then cells were collected by centrifugation and resuspended in infiltration buffer (10 mM magnesium chloride (MgCl₂), 10 mM MES, 200 μM acetosyringone, pH 5.7) in the dark at 28 °C for 2 h. The Agrobacterium cell suspension was infiltrated into N. benthamiana leaves using a needleless syringe at a concentration of 0.5 OD₆₀₀. After N. benthamiana leaves were infiltrated with Agrobacterium for 24 h, the infiltrated leaves were soaked and stained with 3,3-diaminobenzidine (DAB, Sigma-Aldrich) solution for 8 h in the dark and then were destained with ethanol before observation.

VIGS Assays in N. benthamiana

For VIGS assays, pTRV1, pTRV2:BAK1, or pTRV2:GFP plasmid constructs were introduced into A. tumefaciens GV3101. The cultured Agrobacterium cells were harvested and resuspended in infiltration buffer to an 0.5 OD₆₀₀. Agrobacterium strains harboring pTRV2:BAK1 or pTRV2:GFP vector combining with that harboring pTRV1 vector were mixed in a 1:1 ratio. The cocultures were then infiltrated into two primary leaves of N. benthamiana at the four-leaf stage. The effectiveness of the VIGS assay was evaluated using the PDS gene as described⁶¹. The silencing efficiency of BAK1 was validated using RT-qPCR analysis.

Western blot analysis

For western blotting, protein extraction buffer (10 mM Tris/Cl [pH 7.5], 0.5 mM EDTA, 150 mM NaCl, 1% Triton X-100, 1% deoxycholate, 1% SDS) supplemented with protease inhibitor cocktail (Sigma) was used to extract the total proteins from plants. Anti-HA antibody (1:5,000; Sigma) was used for immunoblotting protein with an HA tag. Anti-GFP antibody (1:5000; Abmart) was used for immunoblotting protein with an GFP tag.

Expression and purification of recombinant proteins

The expression host Pichia pastoris KM71H (Muts) (Invitrogen) was cultured on yeast extract-peptone-dextrose medium. BMGY (buffered glycerol-complex medium) at pH 6.5 was used for yeast growth and BMMY (buffered methanol-complex medium) at pH 6.5 was used for induction (Easy Select Pichia expression kit; Invitrogen). P. pastoris transformants were screened for protein induction in 24-well plates as described⁶². Induction of protein expression was performed according to the manufacturer’s instructions. Purification of recombinant GFP, PsRLK6^ECD, and PsRLK7^ECD protein from the culture supernatant was performed by affinity chromatography using Ni-NTA Superflow resin. LRR5-6 region were recombinant expressed using E. coli strain BL21 (DE3) followed by induction with isopropyl β-d-1-thiogalactopyranoside (IPTG, 0.5 mM; Sangon Biotech, A600168) at 18 °C for 16 h. Then purification of recombinant LRR5-6 TF protein from the culture supernatant was performed by affinity chromatography using Ni-NTA Superflow resin. Subsequently, HRV 3 C Protease (Takara, 7360) was employed to cleave the labeled LRR5-6 protein and produce unlabeled LRR5-6 protein.

Measurement of reactive oxygen species

Reactive oxygen species (ROS) production was monitored with an L-012/peroxidase-based assay on leaf discs collected from N. benthamiana, soybean, tomato, and Arabidopsis plants. The leaf discs were floated overnight on 200 μL of ddH₂O in a 96-well plate. The ddH₂O was replaced with a working solution [20 μM L-012 (Waco), 20 μg/mL peroxidase (Sigma-Aldrich), 1 μM flg22 (Sangon), or 1 μM purified protein reaction solution]. After the addition of the working solution, the plate was immediately moved to a GLOMAX96 microplate luminometer (Promega, Madison, WI, USA) for measurement of luminescence.

ROS detection in soybean leaves in response to zoospores of different P. sojae strains was monitored with an L-012 /peroxidase-based assays as previous reported with some minor modifications⁶³. Briefly, Leaf discs was collected from 2-week-old soybean plants and then floated overnight on 200 μL of ddH₂O in a 96-well plate. The ddH₂O was replaced with a working solution [20 μM L-012 (Waco), 20 μg/mL peroxidase (Sigma-Aldrich), zoospores (10000 zoospores per mL) of WT, PsRLK6-knockout (ΔPsRLK6) or PsRLK6-GFP overexpression transformants (OT-24). After the addition of the working solution, the plate was immediately moved to a GLOMAX96 microplate luminometer (Promega, Madison, WI, USA) for measurement of luminescence.

RNA extraction and quantitative PCR assays

Total RNA of all samples was extracted using a PureLink RNA mini kit. Approximately 900 ng RNA was used for reverse transcription with oligo (dT) primers. Then, the cDNA reaction mixture was diluted three times and 2 μL was used as the template in a 20 μL PCR reaction with SYBR qPCR Master Mix (Vazyme). qPCR was performed using an ABI Prism 7500 Fast Real-Time PCR system as per the manufacturer’s instructions. The relative quantitative method (2^−ΔΔCt) was used to evaluate the quantitative variation.

MAPK assays

Proteins were extracted from 5-week-old N. benthamiana leaves after treatment with purified protein. The leaves were then frozen in liquid nitrogen and stored at −80 °C. The frozen leaves were ground in liquid nitrogen and homogenized in protein extraction buffer (50 mM Tris–HCl, pH 7.5, 5 mM EDTA, 5 mM EGTA, 2 mM DTT, 10 mM sodium fluoride, 50 mM β-glycerolphosphate, 10% [v/v] glycerol, complete proteinase inhibitor cocktail [Roche, Mannheim, Germany], and Phosstop phosphatase inhibitor cocktail (Roche). Phosphorylation of MAPK proteins was detected by immunoblotting with anti-phospho-p44/42 MAPK antibody (1:5,000, Cell Signaling Technology, Danvers, Massachusetts, USA; #9101) according to the manufacturer’s protocol. Western blots were stained with Ponceau S to verify equal loading.

MAPK assays were conducted in soybean leaves in response to zoospores (10,000/mL) produced by different P. sojae strains. Leaf discs was collected from 2-week-old soybean plants and then floated overnight on 200 μL of ddH₂O in a 96-well plate. The ddH₂O was substiuted with either fresh ddH₂O or zoospores (10,000 zoospores per mL) of WT, PsRLK6-knockout (ΔPsRLK6) or PsRLK6-GFP overexpression transformants (OT-24) and incubated for 10 min, 20 min, 30 min. Subsequently, protein extraction and MAPK detection were performed as described above.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

Data availability

All data are available within the article and supplementary Files. The proteomes of different organisms used in this study can be obtained from National Center for Biotechnology Information (NCBI) databases with following accession numbers: Phytophthora sojae (GCA_000149755.2) [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000149755.1/], P. infestans (GCA_000142945.1), P. nicotianae (GCA_001483015.1), P. pseudosyringae (GCA_019155715.1), P. fragariae (GCA_009733025.1), P. rubi (GCA_009732945.1), P. capsici (GCA_000325885.1), P. idaei (GCA_016880175.1), P. cactorum (GCA_003287315.1), P. kernoviae (GCA_001712705.2), P. parasitica (GCA_000509465.1), Hyaloperonospora rabidopsis (GCA_000173235.2), Bremia lactucae (GCA_004359215.2), Plasmopara halstedii (GCA_900000015.1), Pythium ultimum (GCA_000143045.1), Pythium oligandrum (GCA_005966545.1), Pythium aphanidermatum (GCA_000387445.2), Globisporangium splendens (GCA_006386115.1), Albugo laibachii (GCA_902706625.1), Albugo candida (GCA_001078535.1), Aphanomyces invadans (GCA_000520115.1), Aphanomyces astaci (GCA_003546625.1), Saprolegnia diclina (GCA_000281045.1), Saprolegnia parasitica (GCA_000151545.2), Thalassiosira pseudonana (GCA_000149405.2), Botrytis cinerea (GCA_000143535.4), Magnaporthe oryzae (GCA_000002495.2), Sclerotinia sclerotiorum (GCA_001857865.1), Pseudomonas syringae (GCA_002905815.2), Xanthomonas oryzae (GCA_008370835.2), Arabidopsis thaliana (GCA_001651475.1), and Glycine max (GCA_000004515.5) [https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000004515.6/]. Source data are provided with this paper.

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Acknowledgements

The work was supported by the Natural Science Foundation of Jiangsu Province (BK20221000 to Z.Y.), the National Natural Science Foundation of China (32230089 to D.D. and 32202251 to Z.Y.), the China Agriculture Research System (CARS-21 to D.D.), and the Jiangsu Funding Program for Excellent Postdoctoral Talent (2022ZB343 to Z.Y.).

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Authors and Affiliations

College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
Yong Pei, Peiyun Ji, Jierui Si, Hanqing Zhao, Sicong Zhang, Ruofei Xu, Huijun Qiao, Weiwei Duan, Danyu Shen, Zhiyuan Yin & Daolong Dou
Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
Daolong Dou

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Yong Pei
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Peiyun Ji
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Jierui Si
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Hanqing Zhao
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Sicong Zhang
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Ruofei Xu
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Huijun Qiao
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Weiwei Duan
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Danyu Shen
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Zhiyuan Yin
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Daolong Dou
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Contributions

D.D. and Z.Y. conceived and designed the research. H.Z. and D.S. performed bioinformatics analyses. Y.P., P.J., J.S., S.Z., R.X., H.Q., and W.D. performed experiments. Y.P. and P.J. analyzed data. Y.P., Z.Y., and D.D. wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Zhiyuan Yin or Daolong Dou.

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Nature Communications thanks Edouard Evangelistx, Yuelin Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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Pei, Y., Ji, P., Si, J. et al. A Phytophthora receptor-like kinase regulates oospore development and can activate pattern-triggered plant immunity. Nat Commun 14, 4593 (2023). https://doi.org/10.1038/s41467-023-40171-7

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Received: 13 January 2023
Accepted: 05 July 2023
Published: 31 July 2023
DOI: https://doi.org/10.1038/s41467-023-40171-7

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