Home LiteratureArticle Details
PMID: 34007035 Published · ppublish English Journal Article

Inducible depletion of PI(4,5)P2 by the synthetic iDePP system in Arabidopsis.

Nature plants ·Vol. 7 ·No. 5 ·2021-00-00 ·Pages 587-597

Doumane M, Lebecq A, Colin L, Fangain A, Stevens FD, Bareille J, Hamant O, Belkhadir Y, Munnik T, Jaillais Y, Caillaud MC

Abstract

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a low-abundance membrane lipid essential for plasma membrane function1,2. In plants, mutations in phosphatidylinositol 4-phosphate (PI4P) 5-kinases (PIP5K) suggest that PI(4,5)P2 production is involved in development, immunity and reproduction3-5. However, phospholipid synthesis is highly intricate6. It is thus likely that steady-state depletion of PI(4,5)P2 triggers confounding indirect effects. Furthermore, inducible tools available in plants allow PI(4,5)P2 to increase7-9 but not decrease, and no PIP5K inhibitors are available. Here, we introduce iDePP (inducible depletion of PI(4,5)P2 in plants), a system for the inducible and tunable depletion of PI(4,5)P2 in plants in less than three hours. Using this strategy, we confirm that PI(4,5)P2 is critical for various aspects of plant development, including root growth, root-hair elongation and organ initiation. We show that PI(4,5)P2 is required to recruit various endocytic proteins, including AP2-µ, to the plasma membrane, and thus to regulate clathrin-mediated endocytosis. Finally, we find that inducible PI(4,5)P2 perturbation impacts the dynamics of the actin cytoskeleton as well as microtubule anisotropy. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P2 in given cellular or developmental responses, and also to evaluate the importance of this lipid in protein localization.

MeSH Terms
Arabidopsis/genetics,growth & development,metabolism Cell Membrane/metabolism Cytoskeleton/metabolism Drosophila Proteins/genetics Inositol Polyphosphate 5-Phosphatases/genetics Phosphatidylinositol 4,5-Diphosphate/metabolism,physiology Phospholipids/metabolism Plant Roots/growth & development,metabolism Plants, Genetically Modified
Chemicals
Drosophila Proteins Phosphatidylinositol 4,5-Diphosphate Phospholipids Inositol Polyphosphate 5-Phosphatases
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Doumane Mehdi ORCID
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Lebecq Alexis ORCID
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Colin Léia
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Fangain Aurélie
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Stevens Floris D ORCID
Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
Bareille Joseph ORCID
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Hamant Olivier ORCID
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.
Belkhadir Youssef ORCID
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
Munnik Teun ORCID
Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
Jaillais Yvon ORCID
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France. yvon.jaillais@ens-lyon.fr.
Caillaud Marie-Cécile
Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France. marie-cecile.caillaud@ens-lyon.fr.
References (51)
51 references, click to expand
  1. Curvature, lipid packing, and electrostatics of membrane organelles: defining cellular territories in determining specificity.
    Bigay, J. & Antonny, B. Curvature, lipid packing, and electrostatics of membrane organelles: defining cellular territories in determining specificity. Dev. Cell 23, 886–895 (2012). PMID: 23153485
  2. Phosphoinositides: tiny lipids with giant impact on cell regulation.
    Balla, T. Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol. Rev. 93, 1019–1137 (2013). PMID: 23899561
  3. Precision targeting by phosphoinositides: how PIs direct endomembrane trafficking in plants.
    Noack, L. C. & Jaillais, Y. Precision targeting by phosphoinositides: how PIs direct endomembrane trafficking in plants. Curr. Opin. Plant Biol. 40, 22–33 (2017). PMID: 28734137
  4. Functions of Anionic Lipids in Plants.
    Noack, L. C. & Jaillais, Y. Functions of anionic lipids in plants. Annu. Rev. Plant Biol. 71, 71–102 (2020). PMID: 32442391
  5. Phosphoinositide signaling in plant development.
    Heilmann, I. Phosphoinositide signaling in plant development. Development 143, 2044–2055 (2016). PMID: 27302395
  6. Phospholipids across scales: lipid patterns and plant development.
    Colin, L. A. & Jaillais, Y. Phospholipids across scales: lipid patterns and plant development. Curr. Opin. Plant Biol. 53, 1–9 (2019). PMID: 31580918
  7. Perturbing phosphoinositide homeostasis oppositely affects vascular differentiation in Arabidopsis thaliana roots.
    Gujas, B. et al. Perturbing phosphoinositide homeostasis oppositely affects vascular differentiation in Arabidopsis thaliana roots. Development 144, 3578–3589 (2017). PMID: 28851711
  8. Type B phosphatidylinositol-4-phosphate 5-kinases mediate Arabidopsis and Nicotiana tabacum pollen tube growth by regulating apical pectin secretion.
    Ischebeck, T., Stenzel, I. & Heilmann, I. Type B phosphatidylinositol-4-phosphate 5-kinases mediate Arabidopsis and Nicotiana tabacum pollen tube growth by regulating apical pectin secretion. Plant Cell 20, 3312–3330 (2008). PMID: 19060112
  9. Phospholipid composition and a polybasic motif determine D6 PROTEIN KINASE polar association with the plasma membrane and tropic responses.
    Barbosa, I. C. et al. Phospholipid composition and a polybasic motif determine D6 PROTEIN KINASE polar association with the plasma membrane and tropic responses. Development 143, 4687–4700 (2016). PMID: 27836964
  10. A multi-colour/multi-affinity marker set to visualize phosphoinositide dynamics in Arabidopsis.
    Simon, M. L. et al. A multi-colour/multi-affinity marker set to visualize phosphoinositide dynamics in Arabidopsis. Plant J. 77, 322–337 (2014). PMID: 24147788
  11. A PtdIns(4)P-driven electrostatic field controls cell membrane identity and signalling in plants.
    Simon, M. L. et al. A PtdIns(4)P-driven electrostatic field controls cell membrane identity and signalling in plants. Nat. Plants 2, 16089 (2016). PMID: 27322096
  12. A Combinatorial Lipid Code Shapes the Electrostatic Landscape of Plant Endomembranes.
    Platre, M. P. et al. A combinatorial lipid code shapes the electrostatic landscape of plant endomembranes. Dev. Cell 45, 465–480 (2018). PMID: 29754803
  13. Phosphoinositides regulate clathrin-dependent endocytosis at the tip of pollen tubes in Arabidopsis and tobacco.
    Zhao, Y. et al. Phosphoinositides regulate clathrin-dependent endocytosis at the tip of pollen tubes in Arabidopsis and tobacco. Plant Cell 22, 4031–4044 (2010). PMID: 21189293
  14. Dejonghe, W. et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nat. Chem. Biol. https://doi.org/10.1038/s41589-019-0262-1 (2019).
  15. Molecular architecture of the endocytic TPLATE complex.
    Yperman, K. et al. Molecular architecture of the endocytic TPLATE complex. Sci. Adv. 7, eabe7999 (2021). PMID: 33637534
  16. Arabidopsis phosphatidylinositol monophosphate 5-kinase 2 is involved in root gravitropism through regulation of polar auxin transport by affecting the cycling of PIN proteins.
    Mei, Y., Jia, W. J., Chu, Y. J. & Xue, H. W. Arabidopsis phosphatidylinositol monophosphate 5-kinase 2 is involved in root gravitropism through regulation of polar auxin transport by affecting the cycling of PIN proteins. Cell Res. 22, 581–597 (2012). PMID: 21894193
  17. Phosphatidylinositol 4,5-bisphosphate influences PIN polarization by controlling clathrin-mediated membrane trafficking in Arabidopsis.
    Ischebeck, T. et al. Phosphatidylinositol 4,5-bisphosphate influences PIN polarization by controlling clathrin-mediated membrane trafficking in Arabidopsis. Plant Cell 25, 4894–4911 (2013). PMID: 24326589
  18. Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic.
    He, K. et al. Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic. Nature 552, 410–414 (2017). PMID: 29236694
  19. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants.
    Gadeyne, A. et al. The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156, 691–704 (2014). PMID: 24529374
  20. Narasimhan, M. et al. Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants. eLife https://doi.org/10.7554/eLife.52067 (2020).
  21. Phosphatidylinositol 4,5-bisphosphate functions as a second messenger that regulates cytoskeleton-plasma membrane adhesion.
    Raucher, D. et al. Phosphatidylinositol 4,5-bisphosphate functions as a second messenger that regulates cytoskeleton-plasma membrane adhesion. Cell 100, 221–228 (2000). PMID: 10660045
  22. Phosphatidic acid regulates microtubule organization by interacting with MAP65-1 in response to salt stress in Arabidopsis.
    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). PMID: 23150630
  23. Green light for polyphosphoinositide signals in plants.
    Munnik, T. & Nielsen, E. Green light for polyphosphoinositide signals in plants. Curr. Opin. Plant Biol. 14, 489–497 (2011). PMID: 21775194
  24. Gungabissoon, R. A., Jiang, C.-J., Drøbak, B. K., Maciver, S. K. & Hussey, P. J. Interaction of maize actin-depolymerising factor with actin and phosphoinositides and its inhibition of plant phospholipase C. Plant J. 16, 689–696 (1998).
  25. SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases.
    Guo, S., Stolz, L. E., Lemrow, S. M. & York, J. D. SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases. J. Biol. Chem. 274, 12990–12995 (1999). PMID: 10224048
  26. Arabidopsis capping protein (AtCP) is a heterodimer that regulates assembly at the barbed ends of actin filaments.
    Huang, S., Blanchoin, L., Kovar, D. R. & Staiger, C. J. Arabidopsis capping protein (AtCP) is a heterodimer that regulates assembly at the barbed ends of actin filaments. J. Biol. Chem. 278, 44832–44842 (2003). PMID: 12947123
  27. Staiger, C. J., Gibbon, B. C., Kovar, D. R. & Zonia, L. E. Profilin and actin-depolymerizing factor: modulators of actin organization in plants. Trends Plant Sci. 2, 275–281 (1997).
  28. Massive actin polymerization induced by phosphatidylinositol-4-phosphate 5-kinase in vivo.
    Shibasaki, Y. et al. Massive actin polymerization induced by phosphatidylinositol-4-phosphate 5-kinase in vivo. J. Biol. Chem. 272, 7578–7581 (1997). PMID: 9065410
  29. Vaughn, L. et al. in The Plant Cytoskeleton. Advances in Plant Biology Vol. 2 (ed. Liu, B.) 307–326 (Springer, 2011).
  30. Imaging and manipulating phosphoinositides in living cells.
    Balla, T. Imaging and manipulating phosphoinositides in living cells. J. Physiol. 582, 927–937 (2007). PMID: 17395624
  31. Identity and functions of inorganic and inositol polyphosphates in plants.
    Lorenzo-Orts, L., Couto, D. & Hothorn, M. Identity and functions of inorganic and inositol polyphosphates in plants. New Phytol. 225, 637–652 (2020). PMID: 31423587
  32. A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis.
    Marques-Bueno, M. M. et al. A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis. Plant J. 85, 320–333 (2016). PMID: 26662936
  33. Saile, S. C. et al. Coiled-coil and RPW8-type immune receptors function at the plasma membrane in a phospholipid dependent manner. Preprint at bioRxiv https://doi.org/10.1101/2020.11.18.388520 (2020).
  34. Compartmentalization of phosphatidylinositol 4,5-bisphosphate signaling evidenced using targeted phosphatases.
    Johnson, C. M., Chichili, G. R. & Rodgers, W. Compartmentalization of phosphatidylinositol 4,5-bisphosphate signaling evidenced using targeted phosphatases. J. Biol. Chem. 283, 29920–29928 (2008). PMID: 18723502
  35. Up-regulation of phosphoinositide metabolism in tobacco cells constitutively expressing the human type I inositol polyphosphate 5-phosphatase.
    Perera, I. Y., Love, J., Heilmann, I., Thompson, W. F. & Boss, W. F. Up-regulation of phosphoinositide metabolism in tobacco cells constitutively expressing the human type I inositol polyphosphate 5-phosphatase. Plant Physiol. 129, 1795–1806 (2002). PMID: 12177493
  36. Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges.
    Christie, J. M. et al. Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science 335, 1492–1496 (2012). PMID: 22323738
  37. Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrane release of its kinase inhibitor.
    Jaillais, Y. et al. Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrane release of its kinase inhibitor. Genes Dev. 25, 232–237 (2011). PMID: 21289069
  38. Recombinational cloning with plant gateway vectors.
    Karimi, M., Depicker, A. & Hilson, P. Recombinational cloning with plant gateway vectors. Plant Physiol. 145, 1144–1154 (2007). PMID: 18056864
  39. Dynamics of Arabidopsis dynamin-related protein 1C and a clathrin light chain at the plasma membrane.
    Konopka, C. A., Backues, S. K. & Bednarek, S. Y. Dynamics of Arabidopsis dynamin-related protein 1C and a clathrin light chain at the plasma membrane. Plant Cell 20, 1363–1380 (2008). PMID: 18502847
  40. Identification and dynamics of Arabidopsis adaptor protein-2 complex and its involvement in floral organ development.
    Yamaoka, S. et al. Identification and dynamics of Arabidopsis adaptor protein-2 complex and its involvement in floral organ development. Plant Cell 25, 2958–2969 (2013). PMID: 23975897
  41. Arabidopsis SH3P2 is an ubiquitin-binding protein that functions together with ESCRT-I and the deubiquitylating enzyme AMSH3.
    Nagel, M.-K. et al. Arabidopsis SH3P2 is an ubiquitin-binding protein that functions together with ESCRT-I and the deubiquitylating enzyme AMSH3. Proc.Natl Acad. Sci. USA 114, E7197–E7204 (2017). PMID: 28784794
  42. In vivo analysis of cell division, cell growth, and differentiation at the shoot apical meristem in Arabidopsis.
    Grandjean, O. et al. In vivo analysis of cell division, cell growth, and differentiation at the shoot apical meristem in Arabidopsis. Plant Cell 16, 74–87 (2004). PMID: 14671026
  43. In-vivo analysis of morphogenesis in plants.
    Stanislas, T., Hamant, O. & Traas, J. In-vivo analysis of morphogenesis in plants. Methods Cell Biol. 139, 203–223 (2017). PMID: 28215337
  44. Doumane, M., Lionnet, C., Bayle, V., Jaillais, Y. & Caillaud, M.-C. Automated tracking of root for confocal time-lapse imaging of cellular processes. Bio Protoc. https://doi.org/10.21769/BioProtoc.2245 (2017).
  45. Lipid kinases PIP5K7 and PIP5K9 are required for polyamine-triggered K+ efflux in Arabidopsis roots.
    Zarza, X. et al. Lipid kinases PIP5K7 and PIP5K9 are required for polyamine-triggered K(+) efflux in Arabidopsis roots. Plant J. 104, 416–432 (2020). PMID: 32666545
  46. Munnik, T. & Zarza, X. in Plant Lipid Signaling Protocols Vol. 1009 (eds Munnik, T. & Heilmann, I.) 3–15 (Humana Press, 2013).
  47. Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
  48. Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. Preprint at https://arxiv.org/abs/1406.5823 (2014).
  49. Fox, J., & Weisberg, S. (2011). Multivariate Linear Models in R. An R Companion to Applied Regression. (SAGE, 2011).
  50. Hothorn, T., Bretz, F., Westfall, P. & Heiberger, R. M. Multcomp: simultaneous inference for general linear hypotheses v.1.0-3 (2008).
  51. Lenth, R. V. Least-squares means: the R package lsmeans. J. Stat. Softw. 69, 1–33 (2016).
Article Info
Journal
Nature plants
Abbr.
Nat Plants
ISSN
2055-0278
DOI
10.1038/s41477-021-00907-z
Email
yvon.jaillais@ens-lyon.fr
marie-cecile.caillaud@ens-lyon.fr
Published
2021-00-00
Epub
2021-00-17
Pages
587-597
Language
English
Region
England
NLM ID
101651677
PMCID
PMC7610831
Subset
IM
Grants
European Research Council · 336360 · International
Corrections
CommentIn
PMID: 34007036
External Links
PubMed source DOI: 10.1038/s41477-021-00907-z PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2