Abstract
Root development involves the maintenance of longitudinal cell division, cell expansion, and maturation, which is coordinated by signaling networks composed of peptide ligand-receptor complexes and reactive oxygen species (ROS) homeostasis, and is coupled with dynamic cell-wall remodeling. However, these regulatory modules remain disconnected, and the systematic mechanisms that efficiently orchestrate root development remain elusive. Here, we uncover an intrinsic regulatory hub in rice that coordinates root development by integrating ROS transmembrane signaling with pectin structural organization. THESEUS3, a receptor-like kinase, interacts and phosphorylates RbohB to promote superoxide anion (O2−) generation, negatively regulating pectin demethylesterification in the meristem. Rice RAPID ALKALINIZATION FACTOR4 (OsRALF4), functioning as a ligand, balances O2− homeostasis through inhibiting THESEUS3-RbohB signaling in the meristem and modulates pectin demethylesterification. Demethylesterified pectin subsequently binds with OsRALF4 to mediate pectin bundling into a condensed structure, marking the onset of cell expansion. Our study establishes the integrated mechanistic framework underlying root development.
Data availability
The RNA-seq data generated in this work has been deposited in the Genome Sequence Archive database under accession CRA040099 in the National Genomics Data Center, China National Center for Bioinformation. The mass spectrometry proteomics data has been deposited in the ProteomeXchange Consortium under accession PXD075847. The gene sequences can be obtained from PLAZA 3.0 database (https://bioinformatics.psb.ugent.be/plaza/) and rice genome database (https://rice.plantbiology.msu.edu) under accession numbers: LOC_Os01g25820 (RbohB), LOC_Os05g45210 (RbohC), LOC_Os06g22810 (THE3), LOC_Os11g07090 (OsPME30), LOC_Os12g35670 (OsRALF4), LOC_Os01g70690 (OsRALF1), LOC_Os01g25540 (OsRALF6), and LOC_Os03g22440 (OsRALF15). Source data are provided with this paper.
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Acknowledgements
We thank Prof. Kunming Chen for the kindly providing us the seeds of RbohB-OE and rbohb mutant, and Dr. Jiasong Mei for the contribution in generation of the the3 mutant. We thank Xuefen Zhang and Dong Qi for the assistance in STED microscopy. We thank Yunqi Liu (Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance) and Longfei Zheng [Bapu (Shanghai) Information Sci. &Tech. Co.,Ltd.] for technical assistance in the apoplast pH measurement. This work was supported by the National Natural Science Foundation of China (W2412131 to Y.Z. and 32201711 to M.J.), the Youth Innovation Promotion Association CAS (2023104 to M.J.), CAS Project for Young Scientists in Basic Research (YSBR-078 to B.Z.) and China Postdoctoral Science Foundation (2024M763520 to H.Y.).
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Y.Z. designed the experiments. M.J. performed the most of the experiments with the help of H.Y. B.L. performed MST assay and PME30 purification. Z.X. and L.P. performed dSTORM analysis. S.C. performed NBT staining in the3. M.J., H.Y., B.L., Z.X., B.Z., and Y.Z. analyzed the data. Y.Z., M.J., and B.Z. wrote the paper. All authors read and commented on the manuscript.
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Jia, M., Yang, H., Li, B. et al. Root development progression involves RALF peptide-mediated ROS signaling and pectin dynamics in rice. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71645-z
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DOI: https://doi.org/10.1038/s41467-026-71645-z
