Abstract
Malate transporters play pivotal roles in plant aluminum tolerance mechanisms. In the classic aluminum tolerance pathway, Al3+ induces ALMT, which promotes malate exudation to chelate Al3+ to enhance aluminum tolerance. However, in tomato, SlALMT was inhibited by Al3+, but Al3+ still induced malate exudation. We found that SlSLAH2, upon induction by Al3+, can transport malate and is required for full activation of malate exudation by Al3+ stress. SlWRKY37 contributes to SlSLAH2 induction by Al3+. Moreover, SlSLAH2 is phosphorylated in response to Al3+. We identify SlCDPK21 and SlPP2C72 as putative upstream kinase and phosphatase that could potentially facilitate phosphorylation homeostasis. SlCDPK21 can interact with SlSLAH2 in a heterologous system, phosphorylate SlSLAH2 at Thr167 in vitro and is also required for full malate exudation. SlPP2C72 can dephosphorylate SlSLAH2 in vitro and knock-out leads to increased malate exudation. Furthermore, Al3+ downregulated SlPP2C72, and Al3+ treated seedling extracts can suppress SlPP2C72 phosphatase activity. We propose a synergistic transcription-phosphorylation cascade that can ensure a robust malate exudation across Al3+ environments.
Data availability
The authors declare that the data supporting the findings of this study are available within the paper and its supplementary information files. Source data are provided with this paper.
References
von Uexküll, H. R. & Mutert, E. Global extent, development and economic impact of acid soils. Plant Soil 171, 1–15 (1995).
Kochian, L. V. Cellular mechanisms of aluminum toxicity and resistance in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46, 237–260 (1995).
Jiang, X. et al. Aluminum-tolerant, growth-promoting rhizosphere bacteria improve growth and alleviate aluminum stress in tea plants. Hortic. Plant J. https://doi.org/10.1016/j.hpj.2024.12.008 (2025).
Huang, D. et al. CsWRKY17 enhances Al accumulation by promoting pectin deesterification in tea plant. Hortic. Res. 12, uhaf085 (2025).
Yan, L., Riaz, M., Liu, J., Yu, M. & Cuncang, J. The aluminum tolerance and detoxification mechanisms in plants; recent advances and prospects. Crit. Rev. Environ. Sci. Technol. 52, 1491–1527 (2022).
Kochian, L. V., Piñeros, M. A., Liu, J. & Magalhaes, J. V. Plant adaptation to acid soils: the molecular basis for crop aluminum resistance. Annu. Rev. Plant Biol. 66, 571–598 (2015).
Jifu, L., Jing, T., Min, Z., Jiang, T. & Cuiyue, L. Research progress on the physiological and molecular mechanisms underlying soybean aluminum resistance. N. Crops 2, 100034 (2025).
Sasaki, T. et al. A wheat gene encoding an aluminum-activated malate transporter. Plant J. 37, 645–653 (2004).
Hoekenga, O. A. et al. AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis. Proc. Natl. Acad. Sci. USA 103, 9738–9743 (2006).
Chen, Q. et al. Overexpression of MsALMT1, from the aluminum-sensitive medicago sativa, enhances malate exudation and aluminum resistance in tobacco. Plant Mol. Biol. Rep. 31, 769–774 (2013).
Liang, C. et al. Low pH, aluminum, and phosphorus coordinately regulate malate exudation through GmALMT1 to improve Soybean adaptation to acid soils. Plant Physiol. 161, 1347–1361 (2013).
Kobayashi, Y. et al. Characterization of AtALMT1 expression in aluminum-inducible malate release and its role for rhizotoxic stress tolerance in Arabidopsis. Plant Physiol. 145, 843–852 (2007).
Iuchi, S. et al. Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proc. Natl. Acad. Sci. USA 104, 9900–9905 (2007).
Ding, Z. J., Yan, J. Y., Xu, X. Y., Li, G. X. & Zheng, S. J. WRKY46 functions as a transcriptional repressor of ALMT1, regulating aluminum-induced malate secretion in Arabidopsis. Plant J. 76, 825–835 (2013).
Li, Q. et al. Aluminum-activated malate transporter family member CsALMT6 mediates fluoride resistance in tea plants (Camellia sinensis). Hortic. Res. 12, uhae353 (2025).
Heng, Y. et al. OsALMT7 maintains panicle size and grain yield in rice by mediating malate transport. Plant Cell 30, 889–906 (2018).
Meyer, S. et al. AtALMT12 represents an R-type anion channel required for stomatal movement in Arabidopsis guard cells. Plant J. 63, 1054–1062 (2010).
Schroeder, J. I. & Keller, B. U. Two types of anion channel currents in guard cells with distinct voltage regulation. Proc. Natl. Acad. Sci. USA 89, 5025–5029 (1992).
Linder, B. & Raschke, K. A slow anion channel in guard-cells, activating at large hyperpolarization, may be principal for stomatal closing. FEBS Lett. 313, 27–30 (1992).
Barbier-Brygoo, H. et al. Anion channels/transporters in plants: from molecular bases to regulatory networks. Annu Rev. Plant Biol. 62, 25–51 (2011).
Negi, J. et al. CO2 regulator SLAC1 and its homologues are essential for anion homeostasis in plant cells. Nature 452, 483–486 (2008).
Vahisalu, T. et al. SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature 452, 487–491 (2008).
Qin, L. et al. Mechanistic insights into phosphoactivation of SLAC1 in guard cell signaling. Proc. Natl. Acad. Sci. USA 121, e2323040121 (2024).
Schroeder, J. I. & Hagiwara, S. Cytosolic calcium regulates ion channels in the plasma-membrane of vicia-faba guard-cells. Nature 338, 427–430 (1989).
Schmidt, C., Schelle, I., Liao, Y. J. & Schroeder, J. I. Strong regulation of slow anion channels and abscisic acid signaling in guard cells by phosphorylation and dephosphorylation events. Proc. Natl. Acad. Sci. USA 92, 9535–9539 (1995).
Lehmann, J. et al. Acidosis-induced activation of anion channel SLAH3 in the flooding-related stress response of Arabidopsis. Curr. Biol. 31, 3575–3585.e3579 (2021).
Liu, Y. et al. Anion channel SLAH3 is a regulatory target of chitin receptor-associated kinase PBL27 in microbial stomatal closure. eLife 8, e44474 (2019).
Xiao, C. et al. Nitrate transporter NRT1.1 and anion channel SLAH3 form a functional unit to regulate nitrate-dependent alleviation of ammonium toxicity. J. Integr. Plant Biol. 64, 942–957 (2022).
Sun, D. et al. Kinase SnRK1.1 regulates nitrate channel SLAH3 engaged in nitrate-dependent alleviation of ammonium toxicity. Plant Physiol. 186, 731–749 (2021).
Zheng, X., He, K., Kleist, T., Chen, F. & Luan, S. Anion channel SLAH3 functions in nitrate-dependent alleviation of ammonium toxicity in Arabidopsis. Plant Cell Environ. 38, 474–486 (2015).
Gutermuth, T. et al. Pollen tube growth regulation by free anions depends on the interaction between the anion channel SLAH3 and calcium-dependent protein kinases CPK2 and CPK20. Plant Cell 25, 4525–4543 (2013).
Liu, B. et al. The anion channel SLAH3 interacts with potassium channels to regulate nitrogen–potassium homeostasis and the membrane potential in Arabidopsis. Plant Cell 35, 1259–1280 (2023).
Wang, N. et al. Early ABA-stimulated maintenance of Cl- homeostasis by mepiquat chloride priming confers salt tolerance in cotton seeds. Crop J. 9, 387–399 (2021).
Schmidt, C. & Schroeder, J. I. Anion selectivity of slow anion channels in the plasma membrane of guard cells (large nitrate permeability). Plant Physiol. 106, 383–391 (1994).
Keller, B. U., Hedrich, R. & Raschke, K. Voltage-dependent anion channels in the plasma-membrane of guard-cells. Nature 341, 450–453 (1989).
Ye, J. et al. An InDel in the promoter of Al-ACTIVATED MALATE TRANSPORTER 9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. Plant Cell 29, 2249–2268 (2017).
Zhang, L. et al. A zinc finger protein SlSZP1 protects SlSTOP1 from SlRAE1mediated degradation to modulate aluminum resistance. New Phytol. 236, 165–181 (2022).
Jeong, J. et al. A nodule-specific dicarboxylate transporter from alder is a member of the peptide transporter family. Plant Physiol. 134, 969–978 (2004).
Deng, Y. N. et al. Structure and activity of SLAC1 channels for stomatal signaling in leaves. Proc. Natl. Acad. Sci. USA 118, e2015151118 (2021).
Li, Y. et al. Structure of the Arabidopsis guard cell anion channel SLAC1 suggests activation mechanism by phosphorylation. Nat. Commun. 13, 2511 (2022).
Dong, D. et al. SlSLAH1 defines SlSTOP1-activated malate exudation pathway for aluminium tolerance in tomato. Plant Cell Environ. https://doi.org/10.1111/pce.70416 (2026).
Wang, Z. et al. Jasmonate and aluminum crosstalk in tomato: Identification and expression analysis of WRKYs and ALMTs during JA/Al-regulated root growth. Plant Physiol. Biochem 154, 409–418 (2020).
Wang, Z. et al. The transcription factor SlWRKY37 positively regulates jasmonic acid- and dark-induced leaf senescence in tomato. J. Exp. Bot. 73, 6207–6225 (2022).
Geiger, D. et al. Guard cell anion channel SLAC1 is regulated by CDPK protein kinases with distinct Ca2+ affinities. Proc. Natl. Acad. Sci. USA 107, 8023–8028 (2010).
Brandt, B. et al. Reconstitution of abscisic acid activation of SLAC1 anion channel by CPK6 and OST1 kinases and branched ABI1 PP2C phosphatase action. Proc. Natl. Acad. Sci. USA 109, 10593–10598 (2012).
Maierhofer, T. et al. Site- and kinase-specific phosphorylation-mediated activation of SLAC1, a guard cell anion channel stimulated by abscisic acid. Sci. Signal 7, ra86 (2014).
Jones, D. L., Gilroy, S., Larsen, P. B., Howell, S. H. & Kochian, L. V. Effect of aluminum on cytoplasmic Ca2+ homeostasis in root hairs of Arabidopsis thaliana (L.). Planta 206, 378–387 (1998).
Zhu, X. et al. Calmodulin-like protein CML24 interacts with CAMTA2 and WRKY46 to regulate ALMT1-dependent Al resistance in Arabidopsis thaliana. New Phytol. 233, 2471–2487 (2022).
Cao H. R. et al. Ca-dependent cytoplasmic and nuclear phosphorylation of STOP1 by CPK21 and CPK23 confers ALMT1-dependent aluminum resistance. Nat. Commun. 16, 5225 (2025).
Li, Y. et al. MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle. Mol. Plant 13, 1203–1218 (2020).
Liu, Y. et al. Integrated multi-omics dissects receptor-mediated phytomelatonin signaling. Hortic. Plant J. 12, 485-488 (2026).
Guo, Y. et al. The clade F PP2C phosphatase ZmPP84 negatively regulates drought tolerance by repressing stomatal closure in maize. New Phytol. 237, 1728–1744 (2023).
Fu, H. et al. SALT OVERLY SENSITIVE 1 is inhibited by clade D Protein phosphatase 2C D6 and D7 in Arabidopsis thaliana. Plant Cell 35, 279–297 (2023).
Zhu, H. H. et al. SlSTOP1-regulated SlHAK5 expression confers Al tolerance in tomato by facilitating citrate secretion from roots. Hortic. Res. 11, uhae282 (2024).
Kovermann, P. et al. The Arabidopsis vacuolar malate channel is a member of the ALMT family. Plant J. 52, 1169–1180 (2007).
Zhao, H. et al. AtALMT9 modulates leaf development and disease resistance in Arabidopsis thaliana. Plant Cell Environ. 48, 6509–6523 (2025).
Sasaki, T. et al. Two members of the aluminum-activated malate transporter family, SlALMT4 and SlALMT5, are expressed during fruit development, and the overexpression of SlALMT5 alters organic acid contents in seeds in tomato (Solanum lycopersicum). Plant Cell Physiol. 57, 2367–2379 (2016).
Doireau, R. et al. AtALMT5 mediates vacuolar fumarate import and regulates the malate/fumarate balance in Arabidopsis. New Phytol. 244, 811–824 (2024).
Meyer, S. et al. Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation. Plant J. 67, 247–257 (2011).
Cubero-Font, P. et al. Silent s-type anion channel subunit SLAH1 gates SLAH3 open for chloride root-to-shoot translocation. Curr. Biol. 26, 2213–2220 (2016).
Ramesh, S. A. et al. GABA signalling modulates plant growth by directly regulating the activity of plant-specific anion transporters. Nat. Commun. 6, 7879 (2015).
Ligaba-Osena, A. et al. Loss-of-function mutation of the calcium sensor CBL1 increases aluminum sensitivity in Arabidopsis. New Phytol. 214, 830–841 (2017).
Batistič, O. & Kudla, J. Analysis of calcium signaling pathways in plants. Biochim. Biophys. Acta 1820, 1283–1293 (2012).
Harper, J. F. et al. A calcium-dependent protein kinase with a regulatory domain similar to calmodulin. Science 252, 951–954 (1991).
Harmon, A. C., Gribskov, M. & Harper, J. F. CDPKs - a kinase for every Ca2+ signal? Trends Plant Sci. 5, 154–159 (2000).
Kiselev, K. V. & Dubrovina, A. S. The role of calcium-dependent protein kinase (CDPK) genes in plant stress resistance and secondary metabolism regulation. Plant Growth Regul. 105, 535–552 (2025).
Delhaize, E., Ryan, P. R. & Randall, P. J. Aluminum tolerance in wheat (Triticum aestivum L.) (II. Aluminum-stimulated excretion of malic acid from root apices). Plant Physiol. 103, 695–702 (1993).
Schweighofer, A., Hirt, H. & Meskiene, L. Plant PP2C phosphatases: emerging functions in stress signaling. Trends Plant Sci. 9, 236–243 (2004).
Miao, J. et al. OsPP2C09, a negative regulatory factor in abscisic acid signalling, plays an essential role in balancing plant growth and drought tolerance in rice. New Phytol. 227, 1417–1433 (2020).
Bai, Z. et al. A Kinase–phosphatase–transcription factor module regulates adventitious root emergence in arabidopsis root–hypocotyl junctions. Mol. Plant 13, 1162–1177 (2020).
Couto, D. et al. The arabidopsis protein phosphatase PP2C38 negatively regulates the central immune kinase BIK1. PLoS Pathog. 12, e1005811 (2016).
Geiger, D. et al. Activity of guard cell anion channel SLAC1 is controlled by drought-stress signaling kinase-phosphatase pair. Proc. Natl. Acad. Sci. USA 106, 21425–21430 (2009).
Geiger, D. et al. Stomatal closure by fast abscisic acid signaling is mediated by the guard cell anion channel SLAH3 and the receptor RCAR1. Sci. Signal 4, ra32–ra32 (2011).
Wang, X. et al. Chloroplast acetyltransferase GNAT2 acts as a redox-regulated switch for state transitions in tomato. Mol. Hortic. 5, 39 (2025).
Liu, Y. et al. Integration of phytomelatonin signaling with jasmonic acid in wound-induced adventitious root regeneration. Adv. Sci. 12, e2413485 (2025).
Dong, D. et al. Transcription factor SlSTOP1 regulates Small Auxin-Up RNA Genes for tomato root elongation under aluminum stress. Plant Physiol. 196, 2654–2668 (2024).
Zhang, J. et al. Fine-tuning of MYC2-mediated Botrytis defense response by the LBD40/42-CRL3BPM4 module in tomato. Plant Cell 37, koaf258 (2025).
Li, Y. et al. Protein phosphatase PP2C2 dephosphorylates transcription factor ZAT5 and modulates tomato fruit ripening. Plant Physiol. 197, kiaf017 (2024).
Takita, E., Koyama, H. & Hara, T. Organic acid metabolism in aluminum-phosphate utilizing cells of carrot (Daucus carota L.). Plant Cell Physiol. 40, 489–495 (1999).
Acknowledgements
We thank Professor Jianmin Wan (State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University) for providing Escherichia coli wild type strain K12 (CGSC4401), Escherichia coli dicarboxylate transport mutant strain CBT315 (CGSC5269) and pKK223-3 vector. We thank Professor Yi Wang (State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University) for providing pGEMHE vector. This work was supported by the grants from National Natural Science Foundation of China (32172599 to Y-DG), the Open Research Fund of State Key Laboratory of Efficient Utilization of Agricultural Water Resources (SKLAWR-2025Y-03 to NZ), Beijing Rural Revitalization Agricultural Science and Technology Project (NY2401080000 to Y-DG), Beijing Agriculture Innovation Consortium (BAIC01-2026 to Y-DG) and the 2115 Talent Development Program of China Agricultural University (to Y-DG and NZ).
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Y.-D.G., N.Z., and D.D. designed this project and wrote the manuscript. D.D. performed most of the experiments. D.D., C.J., and J.Z. analyzed the data. W.Y., G.M., J.G., S.C., W.Z., and Z.L. participated in this work. TL and JY provided valuable assistance during revision. All authors read and approved the final manuscript.
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Dong, D., Jia, C., Zhang, J. et al. SlSLAH2 mediates malate exudation and contributes to aluminum tolerance. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71651-1
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DOI: https://doi.org/10.1038/s41467-026-71651-1