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  • Letter
  • Published:

Subtilase-mediated maturation of EPF1 and EPF2 is crucial for stomatal patterning

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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Fig. 1: EPPs function in regulating stomatal density and clustering.
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Fig. 2: EPPs function in the EPF1/2–ERf signalling pathway in stomatal development.
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Fig. 3: The stomatal patterning defects of epp1/2/3/4/5/6 can be ameliorated by mature EPF1/2 peptides.
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Fig. 4: Loss of EPPs inhibits EPF1/2 maturation and attenuates the associated overexpression phenotypes.
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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.

References

  1. Torii, K. U. Mix-and-match: ligand–receptor pairs in stomatal development and beyond. Trends Plant Sci.17, 711–719 (2012).

    Article  CAS  PubMed  Google Scholar 

  2. Pillitteri, L. J. & Torii, K. U. Mechanisms of stomatal development. Annu. Rev. Plant Biol. 63, 591–614 (2012).

    Article  CAS  PubMed  Google Scholar 

  3. Hunt, L. & Gray, J. E. The signaling peptide EPF2 controls asymmetric cell divisions during stomatal development. Curr. Biol. 19, 864–869 (2009).

    Article  CAS  PubMed  Google Scholar 

  4. Hara, K., Kajita, R., Torii, K. U., Bergmann, D. C. & Kakimoto, T. The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule. Genes Dev. 21, 1720–1725 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hara, K. et al. Epidermal cell density is autoregulated via a secretory peptide, EPIDERMAL PATTERNING FACTOR 2 in Arabidopsis leaves. Plant Cell Physiol. 50, 1019–1031 (2009).

    Article  CAS  PubMed  Google Scholar 

  6. Shpak, E. D., McAbee, J. M., Pillitteri, L. J. & Torii, K. U. Stomatal patterning and differentiation by synergistic interactions of receptor kinases. Science 309, 290–293 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Olsson, V. et al. Look closely, the beautiful may be small: precursor-derived peptides in plants. Annu. Rev. Plant Biol. 70, 153–186 (2019).

    Article  CAS  PubMed  Google Scholar 

  8. van der Hoorn, R. A. Plant proteases: from phenotypes to molecular mechanisms. Annu. Rev. Plant Biol. 59, 191–223 (2008).

    Article  PubMed  Google Scholar 

  9. Yang, M. & Sack, F. D. The too many mouths and four lips mutations affect stomatal production in Arabidopsis. Plant Cell 7, 2227–2239 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Geisler, M., Nadeau, J. & Sack, F. D. Oriented asymmetric divisions that generate the stomatal spacing pattern in Arabidopsis are disrupted by the too many mouths mutation. Plant Cell 12, 2075–2086 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Meng, X. et al. Differential function of Arabidopsis SERK family receptor-like kinases in stomatal patterning. Curr. Biol. 25, 2361–2372 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bergmann, D. C., Lukowitz, W. & Somerville, C. R. Stomatal development and pattern controlled by a MAPKK kinase. Science 304, 1494–1497 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Wang, H., Ngwenyama, N., Liu, Y., Walker, J. C. & Zhang, S. Stomatal development and patterning are regulated by environmentally responsive mitogen-activated protein kinases in Arabidopsis. Plant Cell 19, 63–73 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  14. MacAlister, C. A., Ohashi-Ito, K. & Bergmann, D. C. Transcription factor control of asymmetric cell divisions that establish the stomatal lineage. Nature 445, 537–540 (2007).

    Article  CAS  PubMed  Google Scholar 

  15. Pillitteri, L. J., Sloan, D. B., Bogenschutz, N. L. & Torii, K. U. Termination of asymmetric cell division and differentiation of stomata. Nature 445, 501–505 (2007).

    Article  CAS  PubMed  Google Scholar 

  16. Ohashi-Ito, K. & Bergmann, D. C. Arabidopsis FAMA controls the final proliferation/differentiation switch during stomatal development. Plant Cell 18, 2493–2505 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Schardon, K. et al. Precursor processing for plant peptide hormone maturation by subtilisin-like serine proteinases. Science 354, 1594–1597 (2016).

    Article  CAS  PubMed  Google Scholar 

  18. Reichardt, S., Piepho, H. P., Stintzi, A. & Schaller, A. Peptide signaling for drought-induced tomato flower drop. Science 367, 1482–1485 (2020).

    Article  CAS  PubMed  Google Scholar 

  19. Doll, N. M. et al. A two-way molecular dialogue between embryo and endosperm is required for seed development. Science 367, 431–435 (2020).

    Article  CAS  PubMed  Google Scholar 

  20. Royek, S. et al. Processing of a plant peptide hormone precursor facilitated by posttranslational tyrosine sulfation. Proc. Natl Acad. Sci. USA 119, e2201195119 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Stührwohldt, N. et al. The biogenesis of CLEL peptides involves several processing events in consecutive compartments of the secretory pathway. eLife 9, e55580 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Yang, H. et al. Subtilase-mediated biogenesis of the expanded family of SERINE RICH ENDOGENOUS PEPTIDES. Nat. Plants 9, 2085–2094 (2023).

    Article  CAS  PubMed  Google Scholar 

  23. Matsui, S. et al. Arabidopsis SBT5.2 and SBT1.7 subtilases mediate C-terminal cleavage of flg22 epitope from bacterial flagellin. Nat. Commun. 15, 3762 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Berger, D. & Altmann, T. A subtilisin-like serine protease involved in the regulation of stomatal density and distribution in Arabidopsis thaliana. Genes Dev. 14, 1119–1131 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. von Groll, U., Berger, D. & Altmann, T. The subtilisin-like serine protease SDD1 mediates cell-to-cell signaling during Arabidopsis stomatal development. Plant Cell 14, 1527–1539 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Engineer, C. B. et al. Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development. Nature 513, 246–250 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Uchida, N. et al. Regulation of inflorescence architecture by intertissue layer ligand-receptor communication between endodermis and phloem. Proc. Natl Acad. Sci. USA 109, 6337–6342 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Kim, E. J. et al. Cell type-specific attenuation of brassinosteroid signaling precedes stomatal asymmetric cell division. Proc. Natl Acad. Sci. USA 120, e2303758120 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bemis, S. M., Lee, J. S., Shpak, E. D. & Torii, K. U. Regulation of floral patterning and organ identity by Arabidopsis ERECTA-family receptor kinase genes. J. Exp. Bot. 64, 5323–5333 (2013).

    Article  CAS  PubMed  Google Scholar 

  30. Lee, J. S. et al. Competitive binding of antagonistic peptides fine-tunes stomatal patterning. Nature 522, 439–443 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Lee, J. S. et al. Direct interaction of ligand-receptor pairs specifying stomatal patterning. Genes Dev. 26, 126–136 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Ottmann, C. et al. Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase3. Proc. Natl Acad. Sci. USA 106, 17223–17228 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Cedzich, A. et al. The protease-associated domain and C-terminal extension are required for zymogen processing, sorting within the secretory pathway, and activity of tomato subtilase 3 (SlSBT3). J. Biol. Chem. 284, 14068–14078 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Shpak, E. D., Berthiaume, C. T., Hill, E. J. & Torii, K. U. Synergistic interaction of three ERECTA-family receptor-like kinases controls Arabidopsis organ growth and flower development by promoting cell proliferation. Development 131, 1491–1501 (2004).

    Article  CAS  PubMed  Google Scholar 

  35. Wang, Z. et al. Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol. 16, 144 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Li, M. et al. The EPFL–ERf–SERK signaling controls integument development in Arabidopsis. New Phytol. 238, 186–201 (2023).

    Article  CAS  PubMed  Google Scholar 

  37. Li, H. et al. SERK receptor-like kinases control division patterns of vascular precursors and ground tissue stem cells during embryo development in Arabidopsis. Mol. Plant 12, 984–1002 (2019).

    Article  CAS  PubMed  Google Scholar 

  38. Wang, W. et al. Receptor-like cytoplasmic kinases PBL34/35/36 are required for CLE peptide-mediated signaling to maintain shoot apical meristem and root apical meristem homeostasis in Arabidopsis. Plant Cell 34, 1289–1307 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

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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).

Author information

Authors and Affiliations

Authors

Contributions

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.

Corresponding author

Correspondence to Chong Hu.

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The authors declare no competing interests.

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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).

Source data

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 (ae), and epp1/2/3/4/5/6 (fj). 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).

Source data

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).

Source data

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).

Source data

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).

Source data

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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