Abstract
Proper stomatal distribution optimizes the balance between acquiring atmospheric CO2 for photosynthesis and minimizing water loss1,2. In Arabidopsis, the EPIDERMAL PATTERNING FACTOR (EPF)–ERECTA family signalling pathway specifies this patterning2,3,4,5,6. Similar to most signalling peptides, EPF1 and EPF2 require proteolytic processing to convert inactive precursor proteins into functional mature peptides7; however, in contrast to the well-characterized signalling cascade downstream of the ERECTA family2, little is known about the mechanisms of proteolytic release of the mature EPF1/2 from precursors. Here we identify a group of subtilisin-like serine proteinases8, designated as EPF-PROCESSING PROTEINASES (EPPs), which play a crucial role in stomatal patterning by processing EPF1 and EPF2 precursors. Loss-of-function mutations in EPPs lead to a dramatic increase and clustering of stomata, resembling the phenotypes observed in epf1/2 and er-105 erl1/2 mutants. Notably, these defects can be mitigated through the exogenous application of mature EPF1/2 peptides. Moreover, mutations of these EPPs inhibit the cleavage of EPF1/2 precursors and attenuate their associated overexpression phenotypes. Furthermore, biochemical assays demonstrate that EPPs cleave EPF1/2 both in vitro and in vivo. Taken together, our findings elucidate the molecular mechanisms underlying EPP-mediated processing of EPF1/2 precursors. This proteolytic release of active peptides is identified as a critical, previously missing link required for establishing proper stomatal patterning in plants.
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All data generated or analysed during this study are included in this Letter and its Supplementary Information. Source data are provided with this paper.
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Acknowledgements
We thank K. Torii for providing the er-105 erl1-2 and er-105 erl2-1 mutants. We are grateful to L. Peng, Y. Gao, L. Guan and Y. Zhao (Core Facility for Life Science Research, Lanzhou University) for technique assistance. This work was supported by the National Natural Science Foundation of China (grant nos. 32370351, 32400291 and 32570400), Fundamental Research Funds for the Central Universities (grant no. lzujbky-2024-ey03), Gansu Provincial Science and Technology Plan Project Foundation (grant nos. 25JRRA637, 25JRRA692 and 22ZD6NA049) and Foundation of the Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations (grant nos. lzujbky-2024-jdzx05 and lzujbky-2025-jdzx05).
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C.H. designed all the experiments, analysed the data and wrote the paper. F.M. performed most of the experiments and prepared and analysed the data. C.H., Y.Z. and F.M revised the paper. S.H., N.L. and C.L. assisted in acquiring the confocal images. S.H., M.L., J.W., S.Z. and Z.W. contributed to the generation of the high-order mutants. X.G. offered many valuable suggestions for this research.
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Nature Plants thanks Michael Mickelbart, Andreas Schaller and Keiko Torii for their contribution to the peer review of this work.
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Extended data
Extended Data Fig. 1 Schematic representation of CRISPR/Cas9-mediated mutations in EPPs, EPF1/2, SDD1, and CRSP.
a, Phylogenetic analysis of members within the SBT subfamily-1 based on their full-length amino acid sequences. The sequences were aligned with CLUSTALW and the phylogenetic reconstruction was performed with MEGA7. b, Schematics show the positions of CRISPR/Cas9-mediated gene editing for each EPP gene. c, Schematics show the positions of CRISPR/Cas9-mediated gene editing for EPF1 and EPF2. d, Schematics show the positions of CRISPR/Cas9-mediated gene editing for SDD1 and CRSP. The black boxes represent exons, the gray boxes represent introns, and the brown boxes represent UTRs. The slash labels the gene editing sites.
Extended Data Fig. 2 The epp1/2/3/4/5/6 mutant exhibits a compact inflorescence architecture.
a–d, Representative images of inflorescences from wild type(a), epp1/2/3/4/5/6 (b), epfl1/2/4/6 (c), and er-105 (d). Scale bar: 2 mm. e, Representative pedicels with fully expanded siliques of wild type, epp1/2/3/4/5/6, epfl1/2/4/6, and er-105. Scale bar, 1 cm. f, Quantitative analyses of the pedicel length from indicated genotypes. For box plots (f), box limits indicate 25th and 75th percentiles; central lines indicate medians; whiskers display minimum and maximum values. Dots represent individual measurements per group. Different lowercase letters indicate statistically significant differences based on one-way ANOVA with Tukey’s multiple comparisons test (P < 0.05). The exact P values for all comparisons are provided in Supplementary Table 2. Sample sizes (number of biological replicates, each representing an independent pedicel): n = 30 (wild type), 52 (epp1/2/3/4/5/6), 57 (epfl1/2/4/6), 55 (er-105).
Extended Data Fig. 3 The epp1/2/3/4/5/6 mutant displays increased stomatal density in the epidermis of all aerial organs.
a–j, Representative SEM images of epidermis of rosette leaves (a, f), cauline leaves (b, g), sepals (c, h), stems (d, i), and pedicels (e, j) from wild type (a–e), and epp1/2/3/4/5/6 (f–j). Scale bar: 25 µm.
Extended Data Fig. 4 The stomatal development defect in epp1/5/6 is less severe than that in epp1/2/3/4/5/6.
a–f, Representative confocal microscopy images of cotyledon abaxial epidermis from 5-day-old seedlings of wild type (a), epp1/2/3/4/5/6 (b), epp1/5/6 (c), epp1 (d), epp5 (e), and epp6 (f). Images were taken under the same magnification. Scale bar, 20 µm. g, Quantification of the stomatal number of indicated genotypes. h, Quantification of the stomatal index of indicated genotypes. For box plots (g, h), box limits indicate 25th and 75th percentiles; central lines indicate medians; whiskers display minimum and maximum values. Dots represent individual measurements per group. Different lowercase letters indicate statistically significant differences based on one-way ANOVA with Tukey’s multiple comparisons test (P < 0.05). The exact P values for all comparisons are provided in Supplementary Table 2. Sample sizes (number of biological replicates, each representing a cotyledon of an independent seedling): n = 15 (wild type), 10 (epp1/2/3/4/5/6), 11 (epp1/5/6), 10 (epp1), 14 (epp5), 13 (epp6).
Extended Data Fig. 5 EPPs are mainly expressed in stomatal lineage cells.
a, Expression patterns of EPPs (green) during stomatal development. EPPs–YFP (green) was driven by the respective native promoter. The experiment was repeated independently three times with similar results. For each experiment, more than six cells were examined per cell type, and consistent expression patterns were observed. b, Expression patterns of EPF1/2 (green) during stomatal development were detected using pEPF1::NLS-YFP and pEPF2::NLS-YFP reporter lines. Representative images for each stage were selected based on cell morphology. Scale bars, 10 µm. c, Expression profiles of the indicated genes in the stomatal lineage, analyzed using published single-cell RNA sequencing data. avg_log2FC, log2 fold-change of the average expression between the given cluster and all the other clusters.
Extended Data Fig. 6 The extremely clustered stomata observed in epp1/2/3/4/5/6 are comparable to those in the epf1/2 double and er-105 erl1/2 triple mutants.
a, Representative confocal microscopy images of cotyledon abaxial epidermis from 7-day-old seedlings of wild type, epf1/2, er-105 erl1/2, and epp1/2/3/4/5/6. Images were taken under the same magnification. Scale bar, 20 µm. b, Quantification of the stomatal number of indicated genotypes. c, Quantification of the stomatal index of indicated genotypes. For box plots (b, c), box limits indicate 25th and 75th percentiles; central lines indicate medians; whiskers display minimum and maximum values. Dots represent individual measurements per group. Different lowercase letters indicate statistically significant differences based on one-way ANOVA with Tukey’s multiple comparisons test (P < 0.05). The exact P values for all comparisons are provided in Supplementary Table 2. Sample sizes (number of biological replicates, each representing a cotyledon of an independent seedling): n = 11 (wild type), 8 (epf1/2), 9 (er-105 erl1/2), 13 (epp1/2/3/4/5/6).
Extended Data Fig. 7 EPPs and SDD1 function in parallel signalling pathways.
a-f, Representative confocal microscopy images of cotyledon abaxial epidermis from 5-day-old seedlings of wild type (a), sdd1-cr1 (b), sdd1-cr2 (c), epp1/2/3/4/5/6 (d), epp1/2/3/4/5/6 sdd1-cr1 (e), and epp1/2/3/4/5/6 sdd1-cr2 (f). Images were taken under the same magnification. Scale bar, 20 µm. g, Quantification of the stomatal number of indicated genotypes. h, Quantification of the stomatal index of indicated genotypes. For box plots (g, h), box limits indicate 25th and 75th percentiles; central lines indicate medians; whiskers display minimum and maximum values. Dots represent individual measurements per group. Different lowercase letters indicate statistically significant differences based on one-way ANOVA with Tukey’s multiple comparisons test (P < 0.05). The exact P values for all comparisons are provided in Supplementary Table 2. Sample sizes (number of biological replicates, each representing a cotyledon of an independent seedling): n = 14 (wild type), 12 (epp1/2/3/4/5/6), 13 (sdd1-cr1), 9 (epp1/2/3/4/5/6 sdd1-cr1), 14 (sdd1-cr2), 14 (epp1/2/3/4/5/6 sdd1-cr2).
Extended Data Fig. 8 Mass spectrometry identification of the cleavage sites in EPF1 and EPF2.
a, Schematic representation of the EPF1 peptide. The putative mature peptide sequence is underlined. Lines indicate the predicted disulfide bonds formed by pairs of cysteine residues. The amino acid residues identified as the subtilase cleavage sites by mass spectrometry are highlighted in red. b, Mass spectrometry analysis of the processed products from the 35S::SP-YFP-PROEPF1 transgenic plants. c, Schematic representation of the EPF2 peptide. The putative mature peptide sequence is underlined. The amino acid residues identified as the subtilase cleavage sites by mass spectrometry are highlighted in red. d, Mass spectrometry analysis of the processed products from the 35S::SP-YFP-PROEPF2 transgenic plants. The identity and sequence of the detected peptides were confirmed by an almost complete series of y-ions (blue) and complementary b-ions (red).
Extended Data Fig. 9 The catalytic activity of EPP5 and EPP6 is essential for their functions.
a, Schematic diagrams of the various domains of the EPP5 and EPP6 proteins. D, H, and S are their catalytic triad. b–i, Representative confocal microscopy images of cotyledon abaxial epidermis from 5-day-old seedlings of wild type (b), epp1/2/3/4/5/6 (c), pEPP5::gEPP5-YFP in epp1/2/3/4/5/6 (d), pEPP6::gEPP6-YFP in epp1/2/3/4/5/6 (e), pEPP5::gEPP5D-A-YFP in epp1/2/3/4/5/6 (f), pEPP5::gEPP5DHS-AAA-YFP in epp1/2/3/4/5/6 (g), pEPP6::gEPP6D-A-YFP in epp1/2/3/4/5/6 (h), and pEPP6::gEPP6DHS-AAA-YFP in epp1/2/3/4/5/6 (i). Images were taken under the same magnification. Scale bar, 20 µm. j, Quantification of the stomatal number of indicated genotypes. k, Quantification of the stomatal index of indicated genotypes. For box plots (j, k), box limits indicate 25th and 75th percentiles; central lines indicate medians; whiskers display minimum and maximum values. Dots represent individual measurements per group. Different lowercase letters indicate statistically significant differences based on one-way ANOVA with Tukey’s multiple comparisons test (P < 0.05). The exact P values for all comparisons are provided in Supplementary Table 2. Sample sizes (number of biological replicates, each representing a cotyledon of an independent seedling): n = 17 (wild type), 8 (epp1/2/3/4/5/6), 8 (pEPP5::gEPP5-YFP in epp1/2/3/4/5/6), 10 (pEPP6::gEPP6-YFP in epp1/2/3/4/5/6), 8 (pEPP5::gEPP5D-A-YFP in epp1/2/3/4/5/6), 12 (pEPP5::gEPP5DHS-AAA-YFP in epp1/2/3/4/5/6), 9 (pEPP6::gEPP6D-A-YFP in epp1/2/3/4/5/6), 9 (pEPP6::gEPP6DHS-AAA-YFP in epp1/2/3/4/5/6). l, Western blot using GFP antibody recognizing the EPP5–YFP, EPP5D-A–YFP, EPP5DHS-AAA–YFP, EPP6–YFP, EPP6D-A–YFP, and EPP6DHS-AAA–YFP in stable transgenic Arabidopsis seedlings. The positions of the zymogen that still retain the inhibitor I9 domain are indicated by a black asterisk, while the mature processed forms of EPP5 and EPP6 are indicated by a red asterisk.
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Meng, F., Huang, S., Liu, N. et al. Subtilase-mediated maturation of EPF1 and EPF2 is crucial for stomatal patterning. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02297-6
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DOI: https://doi.org/10.1038/s41477-026-02297-6


