Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

The plant ESCRT component FREE1 shuttles to the nucleus to attenuate abscisic acid signalling

Nature Plants volume 5, pages 512–524 (2019)Cite this article

Subjects

An Author Correction to this article was published on 20 July 2021

This article has been updated

Abstract

The endosomal sorting complex required for transport (ESCRT) machinery has been well documented for its function in endosomal sorting in eukaryotes. Here, we demonstrate an up-to-now unknown and non-endosomal function of the ESCRT component in plants. We show that FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), a recently identified plant-specific ESCRT component essential for multivesicular body biogenesis, plays additional functions in the nucleus in transcriptional inhibition of abscisic acid (ABA) signalling. Following ABA treatment, SNF1-related protein kinase 2 (SnRK2) kinases phosphorylate FREE1, a step requisite for ABA-induced FREE1 nuclear import. In the nucleus, FREE1 interacts with the basic leucine zipper transcription factors ABA-RESPONSIVE ELEMENTS BINDING FACTOR4 and ABA-INSENSITIVE5 to reduce their binding to the cis-regulatory sequences of downstream genes. Collectively, our study demonstrates the crosstalk between endomembrane trafficking and ABA signalling at the transcriptional level and highlights the moonlighting properties of the plant ESCRT subunit FREE1, which has evolved unique non-endosomal functions in the nucleus besides its roles in membrane trafficking in the cytoplasm.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: free1-ctmut is a newly identified free1 weak allele and is hypersensitive to ABA treatment.
Fig. 2: ABA treatment induces nuclear shuttling of FREE1.
Fig. 3: SnRK2 kinases interact with and phosphorylate the FREE1 protein.
Fig. 4: Identification of the phosphorylation sites located in the C terminus of FREE1.
Fig. 5: FREE1 interacts with and supresses the transcriptional activation activities of ABF4 and ABI5.
Fig. 6: Genetic interactions between FREE1 and ABF4 or ABI5.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available from the corresponding authors on reasonable request.

Change history

References

  1. Henne, W. M., Buchkovich, N. J. & Emr, S. D. The ESCRT pathway. Dev. Cell 21, 77–91 (2011).

    Article  PubMed  CAS  Google Scholar 

  2. Liu, C., Shen, W., Yang, C., Zeng, L. & Gao, C. Knowns and unknowns of plasma membrane protein degradation in plants. Plant Sci. 272, 55–61 (2018).

    Article  PubMed  CAS  Google Scholar 

  3. Leung, K. F., Dacks, J. B. & Field, M. C. Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage. Traffic 9, 1698–1716 (2008).

    Article  PubMed  CAS  Google Scholar 

  4. Valencia, J. P., Goodman, K. & Otegui, M. S. Endocytosis and endosomal trafficking in plants. Annu. Rev. Plant Biol. 67, 309–335 (2016).

    Article  CAS  Google Scholar 

  5. Gao, C., Zhuang, X., Shen, J. & Jiang, L. Plant ESCRT complexes: moving beyond endosomal sorting. Trends Plant Sci. 22, 986–998 (2017).

    Article  PubMed  CAS  Google Scholar 

  6. Otegui, M. S. ESCRT-mediated sorting and intralumenal vesicle concatenation in plants. Biochem. Soc. Trans. 46, 537–545 (2018).

    Article  PubMed  CAS  Google Scholar 

  7. Buono, R. A. et al. ESCRT-mediated vesicle concatenation in plant endosomes. J. Cell Biol. 216, 2167–2177 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Gao, C. et al. A unique plant ESCRT component, FREE1, regulates multivesicular body protein sorting and plant growth. Curr. Biol. 24, 2556–2563 (2014).

    Article  PubMed  CAS  Google Scholar 

  9. Kolb, C. et al. FYVE1 is essential for vacuole biogenesis and intracellular trafficking in Arabidopsis. Plant Physiol. 167, 1361–1373 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Shen, J. B. et al. AtBRO1 functions in ESCRT-I complex to regulate multivesicular body protein sorting. Mol. Plant 9, 760–763 (2016).

    Article  PubMed  CAS  Google Scholar 

  11. Zhuang, X. et al. A BAR-domain protein SH3P2, which binds to phosphatidylinositol 3-phosphate and ATG8, regulates autophagosome formation in Arabidopsis. Plant Cell 25, 4596–4615 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Gao, C. et al. Dual roles of an Arabidopsis ESCRT component FREE1 in regulating vacuolar protein transport and autophagic degradation. Proc. Natl Acad. Sci. USA 112, 1886–1891 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Barberon, M. et al. Polarization of IRON-REGULATED TRANSPORTER 1 (IRT1) to the plant–soil interface plays crucial role in metal homeostasis. Proc. Natl Acad. Sci. USA 111, 8293–8298 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Miyakawa, T., Fujita, Y., Yamaguchi-Shinozaki, K. & Tanokura, M. Structure and function of abscisic acid receptors. Trends Plant Sci. 18, 259–266 (2013).

    Article  PubMed  CAS  Google Scholar 

  15. Yu, F. & Xie, Q. Non-26S proteasome endomembrane trafficking pathways in ABA signaling. Trends Plant Sci. 22, 976–985 (2017).

    Article  PubMed  CAS  Google Scholar 

  16. Yu, F., Wu, Y. R. & Xie, Q. Precise protein post-translational modifications modulate ABI5 activity. Trends Plant Sci. 20, 569–575 (2015).

    Article  PubMed  CAS  Google Scholar 

  17. Kong, L. et al. Degradation of the ABA co-receptor ABI1 by PUB12/13 U-box E3 ligases. Nat. Commun. 6, 8630 (2015).

    Article  PubMed  CAS  Google Scholar 

  18. Belda-Palazon, B. et al. FYVE1/FREE1 interacts with the PYL4 ABA receptor and mediates its delivery to the vacuolar degradation pathway. Plant Cell 28, 2291–2311 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Yu, F. F. et al. ESCRT-I component VPS23A affects ABA signaling by recognizing ABA receptors for endosomal degradation. Mol. Plant 9, 1570–1582 (2016).

    Article  PubMed  CAS  Google Scholar 

  20. Bueso, E. et al. The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling. Plant J. 80, 1057–1071 (2014).

    Article  PubMed  CAS  Google Scholar 

  21. Rodriguez, L. et al. C2-domain abscisic acid-related proteins mediate the interaction of PYR/PYL/RCAR abscisic acid receptors with the plasma membrane and regulate abscisic acid sensitivity in Arabidopsis. Plant Cell 26, 4802–4820 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Zhao, Q. et al. Fast-suppressor screening for new components in protein trafficking, organelle biogenesis and silencing pathway in Arabidopsis thaliana using DEX-inducible FREE1-RNAi plants. J. Genet. Genomics 42, 319–330 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Shen, J. et al. A plant Bro1 domain protein BRAF regulates multivesicular body biogenesis and membrane protein homeostasis. Nat. Commun. 9, 3784 (2018).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  24. Gao, X., Chen, J., Dai, X., Zhang, D. & Zhao, Y. An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing. Plant Physiol. 171, 1794–1800 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Gao, Y. B. & Zhao, Y. D. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J. Integr. Plant Biol. 56, 343–349 (2014).

    Article  PubMed  CAS  Google Scholar 

  26. Raghavendra, A. S., Gonugunta, V. K., Christmann, A. & Grill, E. ABA perception and signalling. Trends Plant Sci. 15, 395–401 (2010).

    Article  PubMed  CAS  Google Scholar 

  27. Planes, M. D. et al. A mechanism of growth inhibition by abscisic acid in germinating seeds of Arabidopsis thaliana based on inhibition of plasma membrane H+-ATPase and decreased cytosolic pH, K+, and anions. J. Exp. Bot. 66, 813–825 (2015).

    Article  PubMed  CAS  Google Scholar 

  28. Ng, L. M. et al. Structural basis for basal activity and autoactivation of abscisic acid (ABA) signaling SnRK2 kinases. Proc. Natl Acad. Sci. USA 108, 21259–21264 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Gao, S. et al. ABF2, ABF3, and ABF4 promote ABA-mediated chlorophyll degradation and leaf senescence by transcriptional activation of chlorophyll catabolic genes and senescence-associated genes in Arabidopsis. Mol. Plant 9, 1272–1285 (2016).

    Article  PubMed  CAS  Google Scholar 

  30. Nardozzi, J. D., Lott, K. & Cingolani, G. Phosphorylation meets nuclear import: a review. Cell Commun. Signal. 8, 32 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Liu, Z. Y. et al. Plasma membrane CRPK1-mediated phosphorylation of 14-3-3 proteins induces their nuclear import to fine-tune CBF signaling during cold response. Mol. Cell 66, 117–128 (2017).

    Article  PubMed  CAS  Google Scholar 

  32. Nishino, T. G. et al. 14-3-3 regulates the nuclear import of class IIa histone deacetylases. Biochem. Biophys. Res. Commun. 377, 852–856 (2008).

    Article  PubMed  CAS  Google Scholar 

  33. Zhang, Z. et al. KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis. Proc. Natl Acad. Sci. USA 114, 4011–4016 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Takeo, K. & Ito, T. Subcellular localization of VIP1 is regulated by phosphorylation and 14-3-3 proteins. FEBS Lett. 591, 1972–1981 (2017).

    Article  PubMed  CAS  Google Scholar 

  35. Yoshida, T. et al. Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress. Plant Cell Environ. 38, 35–49 (2015).

    Article  PubMed  CAS  Google Scholar 

  36. Skubacz, A., Daszkowska-Golec, A. & Szarejko, I. The role and regulation of ABI5 (ABA-Insensitive 5) in plant development, abiotic stress responses and phytohormone crosstalk. Front. Plant Sci. 7, 1884 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Kagale, S. & Rozwadowski, K. EAR motif-mediated transcriptional repression in plants: an underlying mechanism for epigenetic regulation of gene expression. Epigenetics 6, 141–146 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Reynolds, N., O’Shaughnessy, A. & Hendrich, B. Transcriptional repressors: multifaceted regulators of gene expression. Development 140, 505–512 (2013).

    Article  PubMed  CAS  Google Scholar 

  39. Yoshida, H. et al. DELLA protein functions as a transcriptional activator through the DNA binding of the INDETERMINATE DOMAIN family proteins. Proc. Natl Acad. Sci. USA 111, 7861–7866 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Pauwels, L. & Goossens, A. The JAZ proteins: a crucial interface in the jasmonate signaling cascade. Plant Cell 23, 3089–3100 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Pauwels, L. et al. NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature 464, 788–791 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Bunney, T. D. et al. Association of phosphatidylinositol 3-kinase with nuclear transcription sites in higher plants. Plant Cell 12, 1679–1688 (2000).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Drobak, B. K. & Heras, B. Nuclear phosphoinositides could bring FYVE alive. Trends Plant Sci. 7, 132–138 (2002).

    Article  PubMed  CAS  Google Scholar 

  44. Zhou, X. N. et al. SOS2-LIKE PROTEIN KINASE5, an SNF1-RELATED PROTEIN KINASE3-type protein kinase, is important for abscisic acid responses in Arabidopsis through phosphorylation of ABSCISIC ACID-INSENSITIVE5. Plant Physiol. 168, 659–676 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Nakashima, K. et al. Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol. 50, 1345–1363 (2009).

    Article  PubMed  CAS  Google Scholar 

  46. Benedetti, C. E. & Arruda, P. Altering the expression of the chlorophyllase gene ATHCOR1 in transgenic Arabidopsis caused changes in the chlorophyll-to-chlorophyllide ratio. Plant Physiol. 128, 1255–1263 (2002).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Song, S. et al. Interaction between MYC2 and ETHYLENE INSENSITIVE3 modulates antagonism between jasmonate and ethylene signaling in Arabidopsis. Plant Cell 26, 263–279 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Gao, C. et al. The Golgi-localized Arabidopsis endomembrane protein 12 contains both endoplasmic reticulum export and Golgi retention signals at its C terminus. Plant Cell 24, 2086–2104 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Yamaguchi, N. et al. Protocols: chromatin immunoprecipitation from Arabidopsis tissues. Arabidopsis Book 12, e0170 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31671467 and 31870171), the China 1000-Talents Plan for young researchers (C83025) to C.G., the National Natural Science Foundation of China (31701246) to W.S., the China Postdoctoral Science Foundation (2018M630963) and the National Science Foundation of Guangdong Province (2018A030310505) to C.Y., the National Natural Science Foundation of China (91854201) and the Research Grants Council of Hong Kong (C4011-14R, C4012-16E, C4002-17G and AoE/M-05/12) to L.J. We thank H. Deng for her assistance on the EMSA experiments.

Author information

Author notes

  1. These authors contributed equally: Hongbo Li, Yingzhu Li, Qiong Zhao.

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University (SCNU), Guangzhou, China

    Hongbo Li, Yingzhu Li, Tingting Li, Juan Wei, Wenjin Shen, Chao Yang, Xiaojing Wang & Caiji Gao

  2. School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China

    Qiong Zhao, Baiying Li, Yonglun Zeng & Liwen Jiang

  3. Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain

    Pedro L. Rodriguez

  4. Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA

    Yunde Zhao

Authors
  1. Hongbo Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yingzhu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qiong Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tingting Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Juan Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Baiying Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Wenjin Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chao Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yonglun Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Pedro L. Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Yunde Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Liwen Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Xiaojing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Caiji Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

H.L., Y.L., Q.Z. and C.G. designed the project. H.L., Y.L., Q.Z., T.L., J.W., B.L. and Y.Z. performed the experiments. H.L., Y.L., Q.Z., W.S., C.Y., P.L.R., Y.Z., L.J., X.W. and C.G. analysed the results. H.L., Q.Z., R.L.R., L.J., X.W. and C.G. wrote the manuscript.

Corresponding authors

Correspondence to Liwen Jiang, Xiaojing Wang or Caiji Gao.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Journal peer review information: Nature Plants thanks Masa Sato and other anonymous reviewers for their contribution to the peer review of this work.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–15, Supplementary Methods, Supplementary Table 1 and Supplementary References.

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, H., Li, Y., Zhao, Q. et al. The plant ESCRT component FREE1 shuttles to the nucleus to attenuate abscisic acid signalling. Nat. Plants 5, 512–524 (2019). https://doi.org/10.1038/s41477-019-0400-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-019-0400-5

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing