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Distinct immune sensor systems for fungal endopolygalacturonases in closely related Brassicaceae

Nature Plants volume 7, pages 1254–1263 (2021)Cite this article

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Abstract

Plant pattern recognition receptors (PRRs) facilitate recognition of microbial patterns and mediate activation of plant immunity. Arabidopsis thaliana RLP42 senses fungal endopolygalacturonases (PGs) and triggers plant defence through complex formation with SOBIR1 and SERK co-receptors. Here, we show that a conserved 9-amino-acid fragment pg9(At) within PGs is sufficient to activate RLP42-dependent plant immunity. Structure–function analysis reveals essential roles of amino acid residues within the RLP42 leucine-rich repeat and island domains for ligand binding and PRR complex assembly. Sensitivity to pg9(At), which is restricted to A. thaliana and exhibits scattered accession specificity, is unusual for known PRRs. Arabidopsis arenosa and Brassica rapa, two Brassicaceae species closely related to A. thaliana, respectively perceive immunogenic PG fragments pg20(Aa) and pg36(Bra), which are structurally distinct from pg9(At). Our study provides evidence for rapid evolution of polymorphic PG sensors with distinct pattern specificities within a single plant family.

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Fig. 1: Identification of an A. thaliana defence-stimulating structural motif in B. cinerea polygalacturonase 6.
Fig. 2: RLP42 binds to pg9(At) and forms a complex with SERK family proteins to activate plant immunity.
Fig. 3: Structure–function analysis of RLP42.
Fig. 4: Immunogenic activity of PG6 and pg13(At) in A. thaliana accessions and in various plant species.
Fig. 5: Identification of PG epitopes triggering immunity in A. arenosa and B. rapa.

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All data are available in the main text, extended data or the Supplementary Information. Source data are provided with this paper.

Code availability

The protein structures shown in Fig. 3e (PDB ID: 3RGX) and in Fig. 5d (PDB ID: 1HG8) are available from the Protein Data Bank (https://www.rcsb.org/).

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Acknowledgements

We thank R. Schwab (Max Planck Institute for Developmental Biology, Tübingen) for providing A. arenosa and A. lyrata seeds, M. Collenberg and D. Weigel (Max Planck Institute for Developmental Biology, Tübingen) for bioinformatic analysis of A. arenosa genome. This work was supported by Deutsche Forschungsgemeinschaft (DFG) grants Nu70/9-2, Nu 70/15-1, Nu70/16-1 and Nu70/17-1 to T.N.

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Authors and Affiliations

  1. Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), Eberhard-Karls-University of Tübingen, Tübingen, Germany

    Lisha Zhang, Chenlei Hua, Rory N. Pruitt, Si Qin, Isabell Albert & Thorsten Nürnberger

  2. Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

    Si Qin & Jan A. L. van Kan

  3. Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China

    Lei Wang

  4. Institute of Molecular Plant Physiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany

    Isabell Albert & Markus Albert

  5. Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa

    Thorsten Nürnberger

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  1. Lisha Zhang
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Contributions

L.Z. and T.N. conceived and designed the experiments; L.Z., C.H., S.Q. and L.W. conducted experiments; L.Z., C.H., R.N.P., I.A., M.A., J.A.L.v.K. and T.N. analysed data; and L.Z., C.H., R.N.P. and T.N. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Lisha Zhang or Thorsten Nürnberger.

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The authors declare no competing interests.

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Peer review information Nature Plants thanks Yusuke Saijo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Ethylene-inducing activity of Botrytis cinerea PGs and peptides derived from PGs.

Ethylene accumulation in A. thaliana Col-0 was measured 4 h after treatment with the following elicitors. a, water (mock), 5 mM DTT, or 60 nM DTT untreated/treated PG3/PG6. b,c, water (mock), Glu-C (b)/Lys-C (c), or 100 nM Glu-C (b) or Lys-C (c) untreated/treated PG3/PG6. d, water (mock), 50 nM PG6, or 1 or 10 µM synthetic peptides pep1-4. e, water (mock), 10 nM pg9(At) alone or together with 100 µM mutagenized pg13N186A, pg13D188A, pg13D188K, pg13F190A, or pg13F190W. f, water (mock), 1 µM pg9(At), Oom-pg9 (AKNTDGFDL, derived from PGs of Phytophthora sp.), or Bac-pg9 (AKNTDGFDP, derived from PGs of Xanthomonas sp.). Bars represent means ± standard deviation of three replicates. Data points are indicated as black dots. Statistically significant differences to mock treatments are indicated (two-sided Student’s t-test). ns, no significant difference to pg9(At) treatment.

Extended Data Fig. 2 Pg13(At)/pg9(At) activates plant immunity in RLP42-expressing A. thaliana.

a,b, Reactive oxygen species (ROS) production in Col-0 (a), PG-insensitive accession Br-0 and Br-0 overexpressing RLP42 (Br-0 + RLP42) (b) after treatment with water (mock) or the elicitors indicated. For a, bars represent means ± standard deviation (n = 6) of relative light units (RLU). For b, total ROS production over 50 min was monitored. c,d, Col-0 (c), Br-0 and Br-0 + RLP42 (d) were infiltrated with water (mock) or 1 µM of the elicitors indicated, and harvested at the indicated time points. Activated MAPKs were detected by immunoblot using anti-p44/42 MAP kinase antibody. Ponceau S staining served as loading control. Assays were performed in triplicate with similar results. e,f, Transcript levels of FRK1 and PAD3 were determined by quantitative real-time PCR (qRT-PCR). Col-0 (e), Br-0 and Br-0 + RLP42 (f) were infiltrated with water (mock) or 1 µM of the elicitor indicated and sampled 6 h after treatment. Relative expression of the indicated genes was normalized to the levels of EF-1α transcript and calibrated to the levels of the mock treatment. For b,e,f, data points are indicated as grey dots and plotted as box plots (centre line: median, bounds of box: the first and third quartiles, whiskers: 1.5x the interquartile range, error bar: minima and maxima) (f, n = 3). Statistically significant differences to mock treatments are indicated (two-sided Student’s t-test). g,h, Cell death-inducing activity of peptides derived from PG6. g, A. thaliana Col-0 leaves were infiltrated with 10 µM of the indicated peptides (left panel). Cell death symptoms were scored at 7 days post infiltration (dpi), and the incidence of cell death (number of leaves showing cell death/total number of leaves infiltrated with peptide) was calculated (right panel). h, The cell-death inducing activity of pg23(At) is associated with its immunogenic activity. Sequences of pg23(At) and mutagenized peptides (pg23m1 and pg23m2) are indicated. EC50 values for elicitor-induced ethylene production were obtained from dose-response experiments conducted with synthetic peptides (middle panel). Leaves infiltrated with the indicated peptides were photographed at 7 dpi (right panel).

Source data

Extended Data Fig. 3 Ethylene-inducing activity of biotinylated pg13(At) peptide in A. thaliana (a) and of pg9(At) in N. benthamiana (b).

a, Ethylene accumulation in Col-0 was measured 4 h after treatment with pg13(At), or biotinylated pg13(At) [pg13(At)-bio]. EC50 values were obtained from dose-response experiments. b, Ethylene accumulation in N. benthamiana leaves transiently expressing RLP42 was measured 4 h after treatment with pg9(At). Bars represent means ± standard deviation of two/three replicates. Assays were performed in triplicate with similar results.

Extended Data Fig. 4 BAK1 and BKK1 are required for RLP42-pg9(At) signalling.

a, ROS production (relative light units, RLU) in leaf discs of Col-0 and bak1-5/bkk1-1 mutant treated with 1 µM pg9(At). Bars represent means ± standard deviation (n = 8) of relative light units (RLU). b, Hypersensitive response-like cell death in leaves of Col-0 and bak1-5/bkk1-1 mutant infiltrated with 10 µM pg23(At) or pg23m1, and visualized at 7 days post infiltration.

Extended Data Fig. 5 Structure-function analysis of RLP42 required for pg9(At) recognition.

a, Immunoblot analysis using anti-GFP antibody of protein extracts from N. benthamiana leaves alone or transiently expressing GFP or RLP42 chimeric and mutant proteins. The relative band intensities of GFP to loading (Ponceau S staining) were calculated and shown at the bottom of the blot. b, Total ROS production (relative light units, RLU) in N. benthamiana leaf discs transiently transformed with chimeric constructs or mutant constructs as indicated and treated with water (mock), 1 µM flg22, or 1 µM pg9(At). Data points are indicated as grey dots from three independent experiments (n with exact numbers are indicated on top of the box plots) and plotted as box plots (centre line: median, bounds of box: the first and third quartiles, whiskers: 1.5x the interquartile range, error bar: minima and maxima). Statistically significant differences to the response observed in RLP42-expressing plant are indicated (two-sided Student’s t-test). c, Summary of RLP42 chimeric and mutant proteins used in this study. d, Ethylene accumulation after treatment with serial dilutions of pg9(At) in N. benthamiana leaves transiently transformed with RLP42, and RLP42 D153V, H321S, or E696K mutant constructs. Bars represent means ± standard deviation of three replicates. Assays were performed in triplicate with similar results. e, BAK1 recruitment to RLP42 receptor mutant proteins. Proteins extracted from N. benthamiana leaves co-expressing RLP42/mutant-GFP and BAK1-Myc treated with water (-) or 1 µM pg9(At) (+) for 5 min were used for co-immunoprecipitation with GFP-trap beads, and immunoblotting with tag-specific antibodies. Assays were performed in triplicate with similar results.

Source data

Extended Data Fig. 6 Pattern sensitivity in A. thaliana accessions and different plant species.

a, Ethylene accumulation in A. thaliana accessions after 4 h treatment with water (mock), 1 µM flg22, or 1 µM pg13(At). b, Ethylene accumulation in Col-0 and 17 pg13(At)-insensitive accessions after 4 h treatment with water (mock), 1 µM flg22, 50 nM PG6, or 1 µM pg13(At). c, Ethylene accumulation in different plant species after 4 h treatment with water (mock), 1 µM flg22, 1 µM nlp20, or 1 µM pg13(At). Data points are indicated as grey dots from two independent experiments (a, n = 4; b,c, n = 6) and plotted as box plots (centre line: median, bounds of box: the first and third quartiles, whiskers: 1.5x the interquartile range, error bar: minima and maxima). Statistically significant differences to mock treatments in the respective plant are indicated (two-sided Student’s t-test).

Extended Data Fig. 7 Phylogenetic analysis based on the available amino acid sequences of RLP39-RLP42 from 23 A. thaliana accessions.

The evolutionary history was inferred using the Neighbour-Joining method. The optimal tree with the sum of branch length = 0.54412429 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and the evolutionary analyses were conducted in MEGA X. Pg13(At)-sensitive and pg13(At)-insensitive accessions are indicated as + and -, respectively. *, “Z”s [RLP42 (Ct-1)] indicate unknown amino acids.

Extended Data Fig. 8 Expression of RLP42 gene and function analysis of RLP42 alleles from selected A. thaliana accessions.

a, Quantitative (upper panel, qRT-PCR) and semi-quantitative (lower panel) real-time PCR analysis of RLP42 expression. Ciste-1, Gu-0, Shigu-1, and Col-0 are sensitive (+) to pg13(At), whereas Dobra-1, Ler-1, NFA-10, Petro-1, Ts-5, and Tsu-1 are insensitive (-) to pg13(At). For qRT-PCR, relative expression of RLP42 was normalized to the levels of EF-1α transcript. Genomic DNA (gDNA) from Col-0 served as positive control. Bars represent means ± standard deviation of three replicates. Data points are indicated as black dots. Assays were performed in duplicate with similar results. b, Ethylene accumulation after 4 h treatment with water (mock), 1 µM flg22, or 1 µM pg9(At) in N. benthamiana leaves transiently transformed with RLP42 (Col-0) derivatives carrying RLP42 (Petro-1)-specific point mutations or RLP42 alleles from accessions Petro-1 and Dobra-1. Data points are indicated as grey dots from three independent experiments [n = 9, except for RLP42, RLP42 (Petro-1), n = 12] and plotted as box plots (centre line: median, bounds of box: the first and third quartiles, whiskers: 1.5x the interquartile range, error bar: minima and maxima). Statistically significant differences to the response observed in RLP42-expressing plant are indicated (two-sided Student’s t-test). c, Immunoblot analysis using anti-GFP antibody of protein extracts from N. benthamiana leaves transiently expressing RLP42 mutant and allelic proteins. Assays were performed in duplicate with similar results.

Source data

Extended Data Fig. 9 Pg20(Aa) and pg36(Bra) activate plant immune responses in Arabidopsis arenosa and Brassica rapa, respectively.

a, Peptides 1-3 derived from PG6 do not activate ethylene production in A. arenosa and B. rapa. Ethylene accumulation after 4 h treatment with water (mock), or 1 µM pep1-3 in A. arenosa and B. rapa. b,d, Ethylene-inducing activity of pg20(Aa) (b) and pg36(Bra) (d) and the corresponding mutant peptides in A. arenosa (b) or B. rapa (d). EC50 values were obtained from dose-response experiments using synthetic peptides. Peptide sequences are indicated at the left. Mutant residues are indicated in red. At the right panel, bars represent means ± standard deviation on a logarithmic scale. Data points are indicated as black dots. The peptide with low EC50 value has high elicitor activity. The peptides that did not induce any or residual ethylene production only at 10 µM are defined as inactive peptide (stars). c,e, Total ROS production in leaf discs of A. arenosa treated with water (mock), 100 nM flg22, 1 µM pg20, or 1 µM pg20G236A (c) or of B. rapa treated with water (mock), or 1 µM of the given elicitor (e) over 120 min. RLU, relative light unit. For a,c,e, data points are indicated as grey dots from three or two independent experiments (a, A. arenosa, n = 9; B. rapa, n = 6; c, n = 24) and plotted as box plots (centre line: median, bounds of box: the first and third quartiles, whiskers: 1.5x the interquartile range, error bar: minima and maxima). Statistically significant differences to mock treatments in the respective plant are indicated (two-sided Student’s t-test). f, Hypersensitive response-like cell death in B. rapa leaves infiltrated with water (mock), 1 µM pg36(Bra), or 1 µM pg36Q208G, and visualized at 7 days post infiltration. Assays were performed in triplicate with similar results.

Extended Data Fig. 10 Synteny analysis of genomic regions flanking the RLP39-RLP40-RLP-41-RLP42 locus in A. thaliana, A. arenosa, and B. rapa.

Coloured boxes indicate individual genes with their sequence identifiers (except for RLP39-42). Syntenic genes are indicated by the same colours and syntenic gene blocks between species are linked with black lines.

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Zhang, L., Hua, C., Pruitt, R.N. et al. Distinct immune sensor systems for fungal endopolygalacturonases in closely related Brassicaceae. Nat. Plants 7, 1254–1263 (2021). https://doi.org/10.1038/s41477-021-00982-2

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