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Tissue-specific accumulation of pH-sensing phosphatidic acid determines plant stress tolerance


The signalling lipid phosphatidic acid (PA) is involved in regulating various fundamental biological processes in plants. However, the mechanisms of PA action remain poorly understood because currently available methods for monitoring PA fail to determine the precise spatio-temporal dynamics of this messenger in living cells and tissues of plants. Here, we have developed PAleon, a PA-specific optogenetic biosensor that reports the concentration and dynamics of bioactive PA at the plasma membrane based on Förster resonance energy transfer (FRET). PAleon was sensitive enough to monitor physiological concentrations of PA in living cells and to visualize PA dynamics at subcellular resolution in tissues when they were challenged with abscisic acid (ABA) and salt stress. PAleon bioimaging revealed kinetics and tissue specificity of salt stress-triggered PA accumulation. Compared with wild-type Arabidopsis, the pldα1 mutant lacking phospholipase Dα1 (PLDα1) for PA generation showed delayed and reduced PA accumulation. Comparative analysis of wild type and pldα1 mutant indicated that cellular pH-modulated PA interaction with target proteins and PLD/PA-mediated salt tolerance. Application of the PA biosensor PAleon uncovered specific spatio-temporal PA dynamics in plant tissues. Our findings suggest that PA signalling integrates with cellular pH dynamics to mediate plant response to salt stress.

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Fig. 1: Design of PA biosensor.
Fig. 2: PAleon specifically responds to PA based on FRET principles.
Fig. 3: PA generation at the PM on ABA stimulation.
Fig. 4: PA changes in root zones in response to salt stress.
Fig. 5: Loss of PLDα1 function impairs PA accumulation at the PM of roots exposed to stress.
Fig. 6: Interconnection between PA and pH homoeostasis in salt response.

Data availability

The data that support the findings of this study are available within the paper and its Supplementary Information or from the corresponding authors upon request.


  1. 1.

    Pokotylo, I., Kravets, V., Martinecc, J. & Ruelland, E. The phosphatidic acid paradox: too many actions for one molecule class? Lessons from plants. Prog. Lipid Res. 71, 43–53 (2018).

    CAS  Article  Google Scholar 

  2. 2.

    Young, B. P. et al. Phosphatidic acid is a pH biosensor that links membrane biogenesis to metabolism. Science 329, 1085–1088 (2010).

    CAS  Article  Google Scholar 

  3. 3.

    Wang, X., Su, Y., Liu, Y., Kim, S. C. & Fanella, B. Signaling and Communication in Plants (ed. Wang, X.) 69–92 (Springer, 2014).

  4. 4.

    Kassas, N. et al. Comparative characterization of phosphatidic acid sensors and their localization during frustrated phagocytosis. J. Biol. Chem. 292, 4266–4279 (2017).

    CAS  Article  Google Scholar 

  5. 5.

    Jacob, T., Ritchie, S., Assmann, S. & Gilroy, S. Abscisic acid signal transduction in guard cells is mediated by phospholipase D activity. Proc. Natl Acad. Sci. USA 96, 12192–12197 (1999).

    CAS  Article  Google Scholar 

  6. 6.

    Mishra, G., Zhang, W., Deng, F., Zhao, J. & Wang, X. A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis. Science 312, 264–266 (2006).

    CAS  Article  Google Scholar 

  7. 7.

    Zhang, Y. et al. Phospholipase Dα1 and phosphatidic acid regulate NADPH oxidase activity and production of reactive oxygen species in ABA-mediated stomatal closure in Arabidopsis. Plant Cell 21, 2357–2377 (2009).

    CAS  Article  Google Scholar 

  8. 8.

    Zhang, Q. et al. Phosphatidic acid regulates microtubule organization by interacting with MAP65-1 in response to salt stress in Arabidopsis. Plant Cell 24, 4555–4576 (2012).

    CAS  Article  Google Scholar 

  9. 9.

    Galvan-Ampudia, C. S. et al. Halotropism is a response of plant roots to avoid a saline environment. Curr. Biol. 23, 2044–2050 (2013).

    CAS  Article  Google Scholar 

  10. 10.

    Wang, P. et al. Phosphatidic acid directly regulates PINOID-dependent phosphorylation and activation of the PIN-FORMED 2 auxin efflux transporter in response to salt stress. Plant Cell 31, 250–271 (2019).

    CAS  Article  Google Scholar 

  11. 11.

    McLoughlin, F. et al. The Snf1-related protein kinases SnRK2.4 and SnRK2.10 are involved in maintenance of root system architecture during salt stress. Plant J. 72, 436–449 (2012).

    CAS  Article  Google Scholar 

  12. 12.

    Testerink, C. & Munnik, T. Molecular, cellular, and physiological responses to phosphatidic acid formation in plants. J. Exp. Bot. 62, 2349–2361 (2011).

    CAS  Article  Google Scholar 

  13. 13.

    Welti, R. et al. Profiling membrane lipids in plant stress responses. Role of phospholipase Dα in freezing-induced lipid changes in Arabidopsis. J. Biol. Chem. 277, 31994–32002 (2002).

    CAS  Article  Google Scholar 

  14. 14.

    Shadyro, O., Yurkova, I., Kisel, M., Brede, O. & Arnhold, J. Formation of phosphatidic acid, ceramide, and diglyceride on radiolysis of lipids: identification by MALDI-TOF mass spectrometry. Free Radic. Biol. Med. 36, 1612–1624 (2004).

    CAS  Article  Google Scholar 

  15. 15.

    Bargmann, B. O. R. et al. Multiple PLDs required for high salinity and water deficit tolerance in plants. Plant Cell Physiol. 50, 78–89 (2009).

    CAS  Article  Google Scholar 

  16. 16.

    An, N., Rudge, S. A., Zhang, Q. & Wakelam, M. J. Using lipidomics analysis to determine signalling and metabolic changes in cells. Curr. Opin. Biotech. 43, 96–103 (2017).

    Article  Google Scholar 

  17. 17.

    Nakanishi, H., Santos, P. D. L. & Neiman, A. M. Positive and negative regulation of a SNARE protein by control of intracellular localization. Mol. Biol. Cell 15, 1802–1815 (2004).

    CAS  Article  Google Scholar 

  18. 18.

    Rizzo, M. A., Shome, K., Watkins, S. C. & Romero, G. The recruitment of Raf-1 to membranes is mediated by direct interaction with phosphatidic acid and is independent of association with Ras. J. Biol. Chem. 275, 23911–23918 (2000).

    CAS  Article  Google Scholar 

  19. 19.

    Potocký, M. et al. Live-cell imaging of phosphatidic acid dynamics in pollen tubes visualized by Spo20p-derived biosensor. New Phytol. 203, 483–494 (2014).

    Article  Google Scholar 

  20. 20.

    Platre, M. P. et al. A combinatorial lipid code shapes the electrostatic landscape of plant endomembranes. Dev. Cell 45, 465–480 (2018).

    CAS  Article  Google Scholar 

  21. 21.

    Tavare, J. M., Fletcher, L. M. & Welsh, G. I. Using green fluorescent protein to study intracellular signaling. J. Endocrinol. 170, 297–306 (2001).

    CAS  Article  Google Scholar 

  22. 22.

    Wang, X., Devaiah, S. P., Zhang, W. & Welti, R. Signaling functions of phosphatidic acid. Prog. Lipid Res. 45, 250–278 (2006).

    CAS  Article  Google Scholar 

  23. 23.

    Zhang, W., Qin, C., Zhao, J. & Wang, X. Phospholipase Dα1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and regulates abscisic acid signaling. Proc. Natl Acad. Sci. USA 101, 9508–9513 (2004).

    CAS  Article  Google Scholar 

  24. 24.

    Nishioka, T., Frohman, M. A., Matsuda, M. & Kiyokawa, E. Heterogeneity of phosphatidic acid levels and distribution at the plasma membrane in living cells as visualized by a Förster resonance energy transfer (FRET) biosensor. J. Biol. Chem. 285, 35979–35987 (2010).

    CAS  Article  Google Scholar 

  25. 25.

    Yu, L. et al. Phosphatidic acid mediates salt stress response by regulation of MPK6 in Arabidopsis thaliana. New Phytol. 188, 762–773 (2010).

    CAS  Article  Google Scholar 

  26. 26.

    Devaiah, S. P. et al. Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Dα1 knockout mutant. Phytochemistry 67, 1907–1924 (2006).

    CAS  Article  Google Scholar 

  27. 27.

    Ni, M. et al. Strength and tissue specificity of chimeric promoters derived from the octopine and mannopine synthase genes. Plant J. 7, 661–676 (1995).

    CAS  Article  Google Scholar 

  28. 28.

    Simon, M. L. et al. A PtdIns(4)P-deriven electrostatic field controls cell membrane identity and signaling in plants. Nat. Plants 2, 16089–16098 (2016).

    CAS  Article  Google Scholar 

  29. 29.

    Waadt, R. et al. FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis. eLife 3, e01739 (2014).

    Article  Google Scholar 

  30. 30.

    Behera, S. et al. Cellular Ca2+ signals generate defined pH signatures in plants. Plant Cell 30, 2704–2719 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Wilkins, K. A. et al. Self-incompatibility-induced programmed cell death in field poppy pollen involves dramatic acidification of the incompatible pollen tube cytosol. Plant Physiol. 167, 766–779 (2015).

    CAS  Article  Google Scholar 

  32. 32.

    Darwish, E., Testerink, C., Khalil, M., Elshihy, O. & Munnik, T. Phospholipid signaling responses in salt-stressed rice leaves. Plant Cell Physiol. 50, 986–997 (2009).

    CAS  Article  Google Scholar 

  33. 33.

    Jones, A. M. et al. Abscisic acid dynamics in roots detected with genetically encoded FRET sensors. eLife 3, e01741 (2014).

    Article  Google Scholar 

  34. 34.

    Petersen, E. N., Chung, H. W., Nayebosadri, A. & Hansen, S. B. Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D. Nat. Commun. 7, 13873 (2016).

    CAS  Article  Google Scholar 

  35. 35.

    Basu, D. & Haswell, E. S. Plant mechanosensitive ion channels: an ocean of possibilities. Curr. Opin. Plant Biol. 40, 43–48 (2017).

    CAS  Article  Google Scholar 

  36. 36.

    Zhao, J. & Wang, X. Arabidopsis phospholipase Dα1 interacts with the heterotrimeric G-protein α-subunit through a motif analogous to the DRY motif in G-protein-coupled receptors. J. Biol. Chem. 279, 1794–1800 (2004).

    CAS  Article  Google Scholar 

  37. 37.

    Martinière, A. et al. Uncovering pH at both sides of the root plasma membrane interface using noninvasive imaging. Proc. Natl Acad. Sci. USA 115, 6488–6493 (2018).

    Article  Google Scholar 

  38. 38.

    Rocks, O., Peyker, A. & Bastiaens, P. I. H. Spatio-temporal segregation of Ras signals: one ship, three anchors, many harbors. Curr. Opin. Cell Biol. 18, 351–357 (2006).

    CAS  Article  Google Scholar 

  39. 39.

    Munns, R. & Tester, M. Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 59, 651–681 (2008).

    CAS  Article  Google Scholar 

  40. 40.

    Yang., Y. & Guo, Y. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol. 217, 523–539 (2018).

    CAS  Article  Google Scholar 

  41. 41.

    Gevaudant, F. et al. Expression of a constitutively activated plasma membrane H+-ATPase alters plant development and increases salt tolerance. Plant Physiol. 144, 1763–1776 (2007).

    CAS  Article  Google Scholar 

  42. 42.

    Wang, X. Multiple forms of phospholipase D in plants: the gene family, catalytic and regulatory properties, and cellular functions. Prog. Lipid Res. 39, 109–149 (2000).

    CAS  Article  Google Scholar 

  43. 43.

    Hong, Y., Pan, X., Welti, R. & Wang, X. Phospholipase Dα3 is involved in the hyperosmotic response in Arabidopsis. Plant Cell 20, 803–816 (2008).

    CAS  Article  Google Scholar 

  44. 44.

    Krebs, M. et al. FRET-based genetically encoded sensors allow high-resolution live cell imaging of Ca2+ dynamics. Plant J. 69, 181–192 (2012).

    CAS  Article  Google Scholar 

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We thank E. Kiyokawa (Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University) for the generous gift of the Pii vector. We thank J. Chen and X. Liu for their assistance in using confocals. The research was supported by grants from National Natural Science Foundation of China (grant nos. 31770294 and 31570270) to W.Z. and from the Deutsche Forschungsgemeinschaft (grant no. DFG, KU931/14-1).

Author information




W.L. and W.Z. designed experiments, analysed data and wrote the manuscript. W.L. performed most of the experiments and prepared the data. T.S. and L.W. helped with the experiments. J.K., L.W. and X.W. discussed the data and revised the manuscript.

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Correspondence to Wenhua Zhang.

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Li, W., Song, T., Wallrad, L. et al. Tissue-specific accumulation of pH-sensing phosphatidic acid determines plant stress tolerance. Nat. Plants 5, 1012–1021 (2019).

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