Abstract
Covering 40–50% of world’s arable lands, acidic soils pose a major constraint on global crop productivity by severely restricting root development and nutrient acquisition. The Arabidopsis C2H2-type transcription factor STOP1 plays a fundamental role in mitigating acid stress by activating H+/NO3− symport via NRT1.1, thereby driving rhizosphere alkalinization to protect root growth and improving nitrogen use efficiency (NUE). However, the upstream regulation of this pH-responsive STOP1-NRT1.1 pathway remains poorly defined. Here, we identify the central SWI2/SNF2-type ATPase BRAHMA (BRM) as a key suppressor of the STOP1 pathway. BRM physically interacts with STOP1 and occupies the genomic region of NRT1.1, repressing the STOP1-dependent activation of NRT1.1 expression and consequently limiting NO3− uptake and rhizosphere alkalization under chronic acidity. Genetic epistasis analysis using brm stop1 and brm nrt1.1 double mutants establish BRM as an upstream regulator of this signaling module. Notably, low pH rapidly triggers BRM degradation independent of NO3− availability, thereby relieving its repression on the STOP1-NRT1.1 pathway. This dynamic BRM disintegration enables robust induction of H+-coupled NO3− uptake, remodeling the rhizosphere pH landscape to foster optimal root growth under acidity. Collectively, our findings uncover the BRM-STOP1-NRT1.1 axis as a central regulatory module integrating NO3− acquisition with pH homeostasis, offering a dual-benefit strategy for enhancing crop resilience to acid soils and reducing fertilizer-driven acidification through improved NUE.
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All data are available in the main text or the supplementary materials. Source data are provided with this paper.
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Acknowledgements
We thank Dr. She Long Zhang (the Instrument Platform of College of Life Sciences, Zhejiang University) for his assistant in Confocal measurement, Prof. Ming Guang Lei (Hangzhou Normal University, Hangzhou, China), Dr. Thierry Desnos (CEA Cadarache), Prof. Yi Kun He (Capital Normal University, Beijing, China), Prof. Zhi Ye Wang (Zhejiang University), and Prof. Ai Wu Dong (Fudan University, Shanghai, China) for providing seeds. This study was supported by the National Key Research and Development Program of China (grant no. 2022YFA1303402 to Z.J.D. and S.J.Z.), the National Natural Science Foundation of China (grant no. 31970272 to Z.J.D., 32500240 to J.Y.Y., and 32201702 to W.H.T.), the Postdoctoral Fellowship Program of CPSF (grant no. GZC20232327 to J.Y.Y.), the China Postdoctoral Science Foundation (2023M743048 to J.Y.Y.), the Ministry of Education and Bureau of Foreign Experts of China (grant no. B14027) and the Fundamental Research Funds for the Central Universities, the Central Public-interest Scientific Institution Basal Research Fund (grant no, Y2023QC21 to W.H.T.).
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S.J.Z., W.H.T., Z.J.D., and J.Y.Y. conceived and designed the experiments. J.Y.Y., W.H.T., and D.R.Z. performed the experiments. Q.Y.Y., J.M.X., G.X.L. and J.Y.Y. (Jing Ying Yan) assisted in plant material generation. J.Y.Y. and W.T.H. analyzed the data and generated the figures. W.N.D., C.W.J., and M.B. provided suggestions and revised the manuscript. J.Y.Y., Z.J.D., and S.J.Z. wrote the manuscript.
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Ye, J.Y., Tian, W.H., Zhang, D.R. et al. BRAHMA represses STOP1-NRT1.1 module to control plant rhizosphere alkalization and acid stress adaptation. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69905-z
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DOI: https://doi.org/10.1038/s41467-026-69905-z
