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A fungal nuclease effector subverts the chloroplast genome and triggers cell death to promote infection

Nature Plants (2026)Cite this article

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Abstract

The hemibiotrophic fungus Magnaporthe oryzae causes rice blast, a devastating plant disease, by transitioning from biotrophic to necrotrophic growth, which triggers host cell death. This trophic shift is essential for nutrient acquisition and disease progression, culminating in conidiation. However, the molecular mechanisms underlying this transition are not well understood. Here, by screening 298 candidate effector proteins upregulated during late infection stages, we identified six necrotrophic effectors (NEEs) from M. oryzae, with MoNee6 exhibiting a particularly important role in virulence. MoNee6 functions as a nuclease that specifically localizes to rice chloroplasts and degrades chloroplast DNA, directly inducing host cell death. Nevertheless, MoNee6 is unstable within the chloroplast and is degraded by the rice chloroplast caseinolytic protease (Clp). To improve host resistance, we engineered OsClpP1 as a nuclear-encoded, chloroplast-targeted protein by fusing it to a chloroplast transit peptide, thereby enabling its expression independent of the native chloroplast-genome-encoded function. This modification enhanced Clp-mediated degradation of MoNee6 and substantially reduced the severity of rice blast. Our findings reveal a previously unrecognized interaction between an effector and the chloroplast that drives the biotrophic-to-necrotrophic transition, and they demonstrate an effective strategy for engineering chloroplast-targeted defence mechanisms against M. oryzae.

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Fig. 1: MoNee1 to MoNee6 are potential necrotrophic effectors in M. oryzae.
Fig. 2: Chloroplast-localized MoNee6 is important in infection by M. oryzae.
Fig. 3: MoNee6 degrades chloroplast DNA within rice cells.
Fig. 4: The Clp protease mediates the degradation of MoNee6 in rice chloroplasts.
Fig. 5: Nuclear-genome-expressed OsClpP1 enhances rice resistance to M. oryzae.
Fig. 6: Summary of MoNee6 and Clp function during M. oryzae and rice interaction.

Data availability

The primary high-throughput sequencing data generated in this study have been deposited in GEO under the accession code GSE322726. The plant materials generated in this study are available from the corresponding author upon reasonable request. Source data are provided with this paper. All other data supporting the findings of this study are available in the Article and Supplementary Information.

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Acknowledgements

This research was supported by the Revitalization Foundation of Seed Industry of Jiangsu (grant no. JBGS(2021-005)), the Young Elite Scientists Sponsorship Program by CAST (grant no. 2022QNRC001), the Jiangsu Agriculture Science & Technology Innovation Fund Program (grant no. CX(23)1032) and NSCF (grant no. 32272496). We thank Y. Wang from Nanjing Agricultural University for providing the bak1, pad4 and eds1 knockout mutants.

Author information

Author notes

  1. These authors contributed equally: Xinyu Liu, Zhengguang Zhang.

Authors and Affiliations

  1. State Key Laboratory of Agricultural and Forestry Biosecurity, Sanya Institute of Nanjing Agricultural University, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China

    Jintao Wang, Xinyu Liu, Xiu Wu, Zhao Hu, Chang’an Ji, Lei Su, Xinhua Zhang, Chen Chen, Jiangtao Liu, Jiexiong Hu, Zhixiang Yang, Gang Li, Haifeng Zhang, Muxing Liu, Leiyun Yang & Zhengguang Zhang

  2. Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA

    Ping Wang

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Contributions

J.W., X.L., X.W., Z.H., C.J., L.S., X.Z., C.C., J.L. and J.H. performed the experiments. J.W., X.L. and X.W. analysed the data. J.W., X.L., Z.Y., G.L., H.Z., M.L., L.Y., P.W. and Z.Z. supervised the study and designed the experiments. J.W., X.L. and Z.Z. wrote the paper.

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Correspondence to Xinyu Liu or Zhengguang Zhang.

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Extended data

Extended Data Fig. 1 Comparative analysis and functional validation of necrotrophic effector proteins in M. oryzae.

(a) Heatmap of homology comparison for the entire set of secreted effector proteins from M. oryzae across different nutritional-type pathogens (biotrophic, hemibiotrophic, and necrotrophic fungi), based on sequence alignment, with color scale indicating homology (darker colors represent higher similarity). (b) Relative expression levels of candidate necrotrophic effectors (MoNee1 to MoNee9) in M. oryzae at different infection time points (12, 24, 36, 48, 72, and 96 hpi), quantified by qRT-PCR with HY phase as the control. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant. (c) Necrotic response in tobacco leaves after Agrobacterium-mediated transient expression of MoNee1-6 constructs with and without signal peptides, observed under UV illumination at 4 dpi, with necrosis intensity assessed visually, color scale indicates live cells (red) and severe necrosis (green).

Source Data

Extended Data Fig. 2 MoNee6 triggers cell death in a nuclease-dependent manner.

(a) Relative transcript levels of GUN1, HDS, and nuclear-encoded photosynthesis-associated genes in Est::MoNEE6Δsp-OE treated with Est, quantified by qRT-PCR. Data are presented as mean ± SD. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant. (b) Structural schematic of MoNee6 and its predicted 3D structure by AlphaFold3, with yellow indicating the signal peptide, blue representing the DUF1524 nuclease domain, and pink highlighting the active nuclease site. (c) Alignment of AlphaFold3-predicted 3D structures of MoNee6 and its inactive mutant MoNee62A, with RMSD (root-mean-square deviation) indicating positional deviation between the two structures. (d) Confidence scores of the AlphaFold3-predicted structure of MoNee6, visualized as a per-residue confidence metric. (e) Western blot analysis of MoNee6Δsp and MoNee6Δsp,2A proteins expressed in Pichia pastoris. The experiment was independently repeated three times. (f) Nuclease activity assay of MoNee6Δsp and MoNee6Δsp,2A proteins incubated with phage λDNA, detected by agarose gel electrophoresis; DNase I as a positive control, EDTA and empty His-tag protein as negative controls. The experiment was independently repeated three times. (g) Nuclease activity assay of purified MoNee6Δsp and MoNee6Δsp,2A proteins incubated with isolated rice nuclear DNA, detected by agarose gel electrophoresis; DNase I as a positive control, EDTA as a negative control. The experiment was independently repeated three times. (h) Confocal microscopy images of wild-type rice protoplasts expressing empty vector, MoNee6Δsp, and MoNee6Δsp,2A proteins, stained with FDA (live cells, green) and PI (dead cells, pink), showing cellular viability (scale bar = 10 μm). (i) Quantification of dead cell percentage from (h), based on PI staining intensity. Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. Error bars, ± SD (n = 3 independent biological replicates, over 50 cells were analyzed per replicate). NS, not significant. (j) Phenotypic comparison of rice leaves from wild-type plants and lines expressing MoNee6Δsp or MoNee6Δsp,2A under an Est-inducible promoter, with and without Est treatment, observed at 7 dpi.

Source Data

Extended Data Fig. 3 MoNee6 suppresses chloroplast genome-encoded gene expression during M. oryzae mid-to-late infection.

(a) Confocal microscopy images of rice protoplasts expressing MoNee6Δsp and MoNee6Δsp,2A, showing GFP signal and chlorophyll autofluorescence (scale bar = 1 μm). The experiment was independently repeated three times. (b) Subcellular localization of MoNee62A-GFP in rice sheath cells infected with ΔMonee6/MoNEE6-GFP strain (scale bar = 20 μm). The experiment was independently repeated three times. (c) Relative transcript levels of chloroplast genome-encoded genes in rice infected with Guy11 and ΔMonee6 at 12 and 48 hpi, quantified by RNA-seq (mean ± SD, n=3 biological replicates, p<0.001, one-way ANOVA), with each gene’s transcript levels normalized to the mock treatment at the corresponding time point. (d) Venn diagram of downregulated genes in rice at 12 hpi (n=113 unique to Guy11, n=177 unique to ΔMonee6, n=75 shared) and 48 hpi (n=293 unique to Guy11, n=261 unique to ΔMonee6, n=20 shared), overlapping with chloroplast genome-encoded genes. (e) qRT-PCR validation of 4 chloroplast genome-encoded genes specifically affected by MoNee6 from RNA-seq data in (c-d). Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant.

Source Data

Extended Data Fig. 4 MoNee6 degrades cpDNA in tobacco to induce cell death.

(a) Confocal microscopy images of GFP, chlorophyll autofluorescence, DIC, and merged channels in tobacco leaves transiently expressing MoNee6Δsp, MoNee6Δsp,2A, and empty GFP, showing co-localization of MoNee6Δsp and MoNee6Δsp,2A with tobacco chloroplasts (scale bar = 10 μm). The experiment was independently repeated three times. (b) Western blot analysis of MoNee6Δsp distribution in chloroplast and extrachloroplast fractions from tobacco leaves transiently expressing MoNee6Δsp or empty vector control, with Actin as an extrachloroplast loading control and RBCL as a chloroplast loading control (from three separate gels). The experiment was independently repeated three times. (c) Necrotic response in tobacco leaves after Agrobacterium-mediated transient expression of MoNee6Δsp, MoNee6Δsp,2A, empty GFP (negative control), and XEG1 (positive control), observed at 6 dpi, showing lesion development. (d) Western blot analysis of MoNee6Δsp, MoNee6Δsp,2A, and XEG1 proteins from infiltrated tobacco leaves at 6 dpi. The experiment was independently repeated three times. (e) Detection of MoNee6Δsp-induced necrosis in tobacco mutant backgrounds. Agrobacterium-mediated transient expression was performed in leaves of WT and mutant (bak1, eds1, pad4) tobacco plants, with observations at 6 dpi. (f) Chloroplast DNA was stained with SYTO42 after isolating and purifying chloroplasts from tobacco leaves, where expressed MoNee6Δsp, MoNee6Δsp,2A, or GFP for 2 days (scale bar = 10 μm). The experiment was independently repeated three times. (g) Flow cytometry analysis of SYTO42-stained chloroplasts isolated from tobacco leaves expressing MoNee6Δsp, MoNee6Δsp,2A, and empty GFP; the left panel shows cell population gating based on SYTO42 fluorescence and chloroplast autofluorescence; the right panel shows SYTO42 fluorescence intensity histograms for each group, indicating cpDNA integrity.

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Extended Data Fig. 5 Conserved distribution and functional characterization of MoNee6 homologs in fungal pathogens.

(a) Phylogenetic tree and presence/absence heatmap of MoNee1-6 homologs across isolates of pathogens with different trophic modes (biotrophic, hemibiotrophic and necrotrophic). (b) SDS-PAGE analysis of recombinant MoNee6 and its homologs from Fusarium graminearum PH-1 (FgNee6), Colletotrichum higginsianum IMI 349063 (ChNee6), and Botrytis cinerea B05.10 (BcNee6) expressed in and purified from Pichia pastoris. The experiment was independently repeated three times. (c) Nuclease activity assay. Purified proteins were incubated with λDNA and analyzed by agarose gel electrophoresis. His was used as a negative control. The experiment was independently repeated three times. (d) Cell death induction in tobacco leaves. Necrosis was recorded at 4 days post Agrobacterium-mediated transient expression of the indicated proteins. XEG1 and GFP served as positive and negative controls, respectively.

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Extended Data Fig. 6 MoNee6 undergoes light-dependent degradation and interacts with Clp protease subunits.

(a) Western blot analysis of MoNee6Δsp protein levels in tobacco leaves transiently expressing MoNee6Δsp at different time points (36, 48, 60, and 72 hpi), with light exposure at 36-48 h and 60-72 h, and dark exposure at 48-60 h. The experiment was independently repeated three times. (b) Relative MoNee6Δsp protein abundance from (a), quantified by densitometry. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by different letters. 36 hpi vs. 48 hpi, P = 2.07E-04; 48 hpi vs. 60 hpi, P = 2.02E-02; 60 hpi vs. 72 hpi, P = 4.51E-04. The experiment was independently repeated three times. (c) Western blot analysis of MoNee6Δsp protein levels in tobacco leaves transiently expressing MoNee6Δsp at 36 hpi, followed by 12 h light exposure with sampling every 4 h; right panel shows CHX treatment, with Actin as loading control (from two separate gels). The experiment was independently repeated three times. (d) Relative MoNee6Δsp protein abundance from (c), quantified by densitometry, normalized to Actin, and compared to 36 h levels. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by different letters. MoNee6Δsp: 36 hpi vs. 40 hpi, P = 1.36E-09; 40 hpi vs. 44 hpi, P = 3.07E-06; 44 hpi vs. 48 hpi, P = 3.08E-08. MoNee6Δsp + CHX: 36 hpi vs. 40 hpi, P = 5.10E-14; 40 hpi vs. 44 hpi, P = 1.34E-02; 44 hpi vs. 48 hpi, P = 9.99E-01. The experiment was independently repeated three times. (e) BiFC assay in rice protoplasts co-expressing YFPn-tagged OsClpP5 or OsClpP6 with YFPc-tagged MoNee6, or controls (YFPn-OsClpP5/6 with empty YFPc, YFPc-MoNee6 with empty YFPn, empty YFPn/YFPc), observed for YFP fluorescence at 8-12 h post-transfection (scale bar = 1 μm). The experiment was independently repeated three times. (f) Yeast two-hybrid assay in the yeast strain co-transformed with AD-OsClpP1/5/6 and BD-MoNee6, or controls (AD-OsClpP1/5/6 with empty BD, BD-MoNee6 with empty AD, positive/negative controls), on SD-Leu-Trp (input) and SD-Leu-Trp-His-Ade (output) plates to assess growth and interaction. (g) Confocal microscopy images of GFP-tagged MoNee6 and RFP-tagged OsClpP5 or OsClpP6 in rice protoplasts, showing co-localization (scale bar = 1 μm). The experiment was independently repeated three times. (h) Fluorescence intensity profile of MoNee6-GFP co-localization with OsClpP5/6-RFP and chlorophyll autofluorescence from (g), plotted along a 4-6 μm transect. (i) The plant chloroplast Clp protease complex is a stromal degradation machine composed of a double-barrel proteolytic core capped by a single hexameric/heptameric chaperone ring and accessorized by two adaptors and two stabilizing ‘feet’. The protease core, endowed with proteolytic activity, comprises a 14-subunit double-ring structure formed by ClpP (ClpP1/3/4/5/6) and ClpR (ClpR1-4) subunits, where substrate proteins are progressively degraded within the internal chamber. (j) Western blot detection of Clp protease subunit expression in rice. The experiment was independently repeated three times. (k) In vitro incubation of MoNee6 with purified Clp protease subunits at different time points (0, 4, 8, 12, and 20 h), detected by Western blot. The experiment was independently repeated three times. (l) Relative MoNee6Δsp abundance from (k), quantified by densitometry and normalized to 0 h levels. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by different letters. Trt 1: 0 h vs. 4 h, P = 3.98E-02; 4 h vs. 8 h, P = 4.77E-04; 8 h vs. 12 h, P = 6.69E-01. Trt 2: 0 h vs. 4 h, P = 6.61E-01; 4 h vs. 8 h, P = 1.60E-04; 8 h vs. 12 h, P = 3.29E-01. Trt 3: 0 h vs. 4 h, P = 6.81E-04; 4 h vs. 8 h, P = 9.74E-01; 8 h vs. 12 h, P = 6.10E-03. Trt 4: 0 h vs. 4 h, P = 3.18E-02; 4 h vs. 8 h, P = 4.61E-01; 8 h vs. 12 h, P = 5.75E-02. Trt 4: 0 h vs. 4 h, P = 9.86E-01; 4 h vs. 8 h, P = 2.80E-03; 8 h vs. 12 h, P = 4.02E-05. The experiment was independently repeated three times.

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Extended Data Fig. 7 Overexpression of Clp protease subunits does not affect rice agronomic traits, whereas their silencing induces leaf yellowing.

(a) Phenotypic comparison of ZH11 and Ubi::OsCLPP5-GFP lines (#1, #2, and #3), Ubi::OsCLPP6-GFP lines (#1, #2, and #3) showing plant height and overall growth at 120 days post-germination (scale bar = 7 cm). (b) Western blot analysis of GFP-tagged OsClpP5/6 protein levels in Ubi::OsCLPP5/6-GFP lines (#1, #2, #3) with Ponceau S (PS) staining for total protein loading. (c) Plant height measurement of ZH11 and Ubi::OsCLPP5/6-GFP lines from (a) at 120 days post-germination. Error bars, ± SD (n = 3 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (d) Tiller number measurement of ZH11 and Ubi::OsCLPP5/6-GFP lines from (a) at 120 days post-germination. Error bars, ± SD (n = 3 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (e) Seed morphology of ZH11 and Ubi::OsCLPP5/6-GFP lines, showing random 2 panicles per line, with left side filled grains and right-side empty grains (scale bar = 7 mm). (f) Number of grains per panicle from (e), for ZH11 and Ubi::OsCLPP5/6-GFP lines. Error bars, ± SD (n = 10 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (g) Number of empty grains per 300 seeds from (e), for ZH11 and Ubi::OsCLPP5/6-GFP lines. Error bars, ± SD (n = 3 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (h) 1000-grain weight from (e), for ZH11 and Ubi::OsCLPP5/6-GFP lines. Error bars, ± SD (n = 10 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (i-j) Morphology of 10 grains per line from ZH11 and Ubi::OsCLPP5/6-GFP lines, showing length and width (scale bar = 7 mm). (k-l) Grain length and width measurement from (i), for ZH11 and Ubi::OsCLPP5/6-GFP lines. Error bars, ± SD (n = 10 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (m) Phenotypic comparison of ZH11 and Est:: OsCLPP1/6-RNAi lines (#1, #2, #3) after Est induction of OsCLPP1/6 silencing, showing plant height and growth defects at 15 days post-germination (scale bar = 12 cm). (n-o) Relative OsCLPP1/6 transcript levels in Est:: OsCLPP1/6-RNAi lines (#1, #2, #3) before and after Est induction, quantified by qRT-PCR. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant.

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Extended Data Fig. 8 Overexpression of individual Clp protease subunits fails to enhance rice resistance to M. oryzae.

(a) Disease symptoms on rice leaves (ZH11 and Ubi::OsCLPP5/6-OE) after wound inoculation with Guy11 and ΔMonee6 at 5 dpi. (b) Quantification of lesion length from (a), expressed as relative lesion area. Error bars, ± SD (ZH11 infected by ΔMonee6, n = 5, and n = 6 for others). Statistical differences were determined using two-sided Student’s t-tests. Exact P values are shown in the figure. The experiment was independently repeated three times. (c) Western blot analysis of MoNee6-RFP protein levels in MoNee6-RFP complemented strains inoculated on ZH11 and Ubi::OsCLPP5/6-OE lines at different time points (48, 52, 56, 60 hpi), with Actin as loading control (from two separate gels). The experiment was independently repeated three times. (d) Relative protein abundance of MoNee6 from (c), quantified by densitometry, normalized to Actin, and expressed relative to 48 hpi as control. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by different letters. ZH11: 48 hpi vs. 52 hpi, P = 1.70E-01; 52 hpi vs. 56 hpi, P = 9.46E-01; 56 hpi vs. 60 hpi, P = 5.34E-05. Ubi::OsCLPP5-OE: 48 hpi vs. 52 hpi, P = 1.22E-01; 52 hpi vs. 56 hpi, P= 1.58E-02; 56 hpi vs. 60 hpi, P = 9.49E-04. Ubi::OsCLPP6-OE: 48 hpi vs. 52 hpi, P = 5.40E-01; 52 hpi vs. 56 hpi, P = 1.02E-04; 56 hpi vs. 60 hpi, P = 2.01E-06. The experiment was independently repeated three times. (e) Western blot analysis of MoNee6-RFP protein levels in MoNee6-RFP complemented strains inoculated on ZH11 and Est::OsCLPP1/6-RNAi lines after Est induction of OsCLPP1 and OsCLPP6 silencing, at different time points (48, 52, 56, and 60 hpi), with Actin as a loading control (from two separate gels). The experiment was independently repeated three times. (f) Relative protein abundance of MoNee6 from (e), quantified by densitometry, normalized to Actin, and expressed relative to 48 hpi as control. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by different letters. ZH11: 48 hpi vs. 52 hpi, P = 7.59E-12; 52 hpi vs. 56 hpi, P = 2.60E-01; 56 hpi vs. 60 hpi, P = 4.00E-09. Est::OsCLPP1-RNAi: 48 hpi vs. 52 hpi, P = 1.29E-01; 52 hpi vs. 56 hpi, P= 2.48E-01; 56 hpi vs. 60 hpi, P = 5.30E-01. Est::OsCLPP6-RNAi: 48 hpi vs. 52 hpi, P = 6.48E-01; 52 hpi vs. 56 hpi, P = 7.96E-01; 56 hpi vs. 60 hpi, P = 5.80E-02. The experiment was independently repeated three times. (g-j) Relative transcript levels of OsCLPP5, OsCLPP6, OsCLPP1, and MoNEE6 in rice leaves infected with Guy11 and ΔMonee6 strains at 12, 24, 36, 48, 72, and 96 hpi, quantified by qRT-PCR. Error bars, ± SD (n = 3 independent experiment). Statistical differences were determined using two-sided Student’s t-tests. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant.

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Extended Data Fig. 9 Modified OsClpP1 blocks MoNee6-mediated transcriptional arrest of chloroplast genes and cell death.

(a) Relative OsCLPP1 transcript levels in ZH11 and Ubi::CTP2/3-OsCLPP1-OE lines after M. oryzae inoculation, normalized to OsCLPP1 in uninfected ZH11. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant. (b) Confocal microscopy images of FDA/PI-stained rice protoplasts from wild-type ZH11 and Ubi::CTP1/2/3-OsCLPP1-OE lines expressing empty vector or MoNee6Δsp, showing cell viability (green) and death (pink) at 8-12 h p-transfection (scale bar = 10 μm). (c) Percentage of dead cells from (b). Statistical differences were determined using two-sided Student’s t-tests. Exact P values are shown in the figure. Error bars, ± SD (n = 3 independent biological replicates, over 50 cells were analyzed per replicate). NS, not significant. (d) Necrotic response in tobacco leaves after co-infiltration of GFP with XEG1, MoNee6Δsp, or MoNee6Δsp,2A, and MoNee6 with OsClpP1, CTP2-OsClpP1, or CTP3-OsClpP1, observed at 4 dpi, showing lesion development. (e) Relative transcript levels of chloroplast genome-encoded genes OsATPB and OsPETB in ZH11 and Ubi::CTPs-OsCLPP1-OE rice infected with Guy11 and ΔMonee6 at 12 and 48 hpi. Error bars, ± SD (n = 3 independent experiment). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. Exact P values are shown in the figure. The experiment was independently repeated three times. NS, not significant.

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Extended Data Fig. 10 Modified OsClpP1 does not affect rice agronomic traits.

(a) Phenotypic comparison of ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines at 120 days post-germination, showing plant height and tillering (scale bar = 10 cm). (b-c) Plant height and tiller number measurements from (a), for ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines. Error bars, ± SD (n = 3 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (d) Panicle morphology of wild-type ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines at maturity, showing grain filling (scale bar = 2 cm). (e-g) Number of grains per panicle, empty grains per 300 seeds, and 1000-grain weight from (d), for ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines. Error bars, ± SD (n=10 independent panicles for grains per panicle, n=10 independent batches for empty grains and n=3 independent biological replicates for 1000-grain weight). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant. (h-i) Morphology of 10 grains per line from ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines, showing length and width (scale bar = 2 mm). (j-k) Grain length and width measurements from (h-i), for ZH11, Ubi::OsCLPP1-OE, and Ubi::CTP2/3-OsCLPP1-OE lines. Error bars, ± SD (n = 10 independent biological replicates). Statistical significance was determined by one-way ANOVA followed by Dunnett’s multiple comparisons test. The experiment was independently repeated three times. NS, not significant.

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Wang, J., Liu, X., Wu, X. et al. A fungal nuclease effector subverts the chloroplast genome and triggers cell death to promote infection. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02276-x

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