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A membrane trafficking pathway regulated by the plant-specific RAB GTPase ARA6

Abstract

Endosomal trafficking plays an integral role in various eukaryotic cell activities and serves as a basis for higher-order functions in multicellular organisms. An understanding of the importance of endosomal trafficking in plants is rapidly developing1,2, but its molecular mechanism is mostly unknown. Several key regulators of endosomal trafficking, including RAB5, which regulates diverse endocytic events in animal cells3,4, are highly conserved. However, the identification of lineage-specific regulators in eukaryotes indicates that endosomal trafficking is diversified according to distinct body plans and lifestyles. In addition to orthologues of metazoan RAB5, land plants possess a unique RAB5 molecule, which is one of the most prominent features of plant RAB GTPase organization5,6. Plants have also evolved a unique repertoire of SNAREs, the most distinctive of which are diverse VAMP7-related longins, including plant-unique VAMP72 derivatives7. Here, we demonstrate that a plant-unique RAB5 protein, ARA6, acts in an endosomal trafficking pathway in Arabidopsis thaliana. ARA6 modulates the assembly of a distinct SNARE complex from conventional RAB5, and has a functional role in the salinity stress response. Our results indicate that plants possess a unique endosomal trafficking network and provide the first indication of a functional link between a specific RAB and a specific SNARE complex in plants.

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Figure 1: The land-plant-unique RAB5 (ARA6) and conventional RAB5 proteins localize to different endosomes.
Figure 2: Genetic interactions between SYP22 and RAB5 genes.
Figure 3: ARA6 and VAMP727 act at the plasma membrane.
Figure 4: ARA6 promotes VAMP727–SYP121 complex formation at the plasma membrane.
Figure 5: ARA6 is required for salinity stress tolerance.

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References

  1. Otegui, M. S. & Spitzer, C. Endosomal functions in plants. Traffic 9, 1589–1598 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Richter, S., Voss, U. & Jurgens, G. Post-Golgi traffic in plants. Traffic 10, 819–828 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. Benmerah, A. Endocytosis: signaling from endocytic membranes to the nucleus. Curr. Biol. 14, R314–316 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. Somsel Rodman, J. & Wandinger-Ness, A. Rab GTPases coordinate endocytosis. J. Cell Sci. 113, 183–192 (2000).

    PubMed  Google Scholar 

  5. Rutherford, S. & Moore, I. The Arabidopsis Rab GTPase family: another enigma variation. Curr. Opin. Plant Biol. 5, 518–528 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Ueda, T., Yamaguchi, M., Uchimiya, H. & Nakano, A. Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana. EMBO J. 20, 4730–4741 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Sanderfoot, A. Increases in the number of SNARE genes parallels the rise of multicellularity among the green plants. Plant Physiol. 144, 6–17 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Saito, C. & Ueda, T. Chapter 4: functions of RAB and SNARE proteins in plant life. Int. Rev. Cell Mol. Biol. 274, 183–233 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Wickner, W. & Schekman, R. Membrane fusion. Nat. Struct. Mol. Biol. 15, 658–664 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Brennwald, P. & Novick, P. Interactions of three domains distinguishing the Ras-related GTP-binding proteins Ypt1 and Sec4. Nature 362, 560–563 (1993).

    Article  CAS  PubMed  Google Scholar 

  11. Chavrier, P. et al. Hypervariable C-terminal domain of rab proteins acts as a targeting signal. Nature 353, 769–772 (1991).

    Article  CAS  PubMed  Google Scholar 

  12. Dhonukshe, P. et al. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Dev. Cell 10, 137–150 (2006).

    Article  CAS  PubMed  Google Scholar 

  13. Kotzer, A. M. et al. AtRabF2b (Ara7) acts on the vacuolar trafficking pathway in tobacco leaf epidermal cells. J. Cell Sci. 117, 6377–6389 (2004).

    Article  CAS  PubMed  Google Scholar 

  14. Sohn, E. J. et al. Rha1, an Arabidopsis Rab5 homolog, plays a critical role in the vacuolar trafficking of soluble cargo proteins. Plant Cell 15, 1057–1070 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ueda, T., Uemura, T., Sato, M. H. & Nakano, A. Functional differentiation of endosomes in Arabidopsis cells. Plant J. 40, 783–789 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Jaillais, Y., Fobis-Loisy, I., Miege, C. & Gaude, T. Evidence for a sorting endosome in Arabidopsis root cells. Plant J. 53, 237–247 (2008).

    Article  CAS  PubMed  Google Scholar 

  17. Geldner, N. et al. The Arabidopsis GNOM ARF-GEF mediates endosomal recycling, auxin transport, and auxin-dependent plant growth. Cell 112, 219–230 (2003).

    Article  CAS  PubMed  Google Scholar 

  18. Takano, J., Miwa, K., Yuan, L., von Wiren, N. & Fujiwara, T. Endocytosis and degradation of BOR1, a boron transporter of Arabidopsis thaliana, regulated by boron availability. Proc. Natl Acad. Sci. USA 102, 12276–12281 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ueda, H. et al. AtVAM3 is required for normal specification of idioblasts, myrosin cells. Plant Cell Physiol. 47, 164–175 (2006).

    Article  CAS  PubMed  Google Scholar 

  20. Goh, T. et al. VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana. Plant Cell 19, 3504–3515 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Nishizawa, K. et al. A C-terminal sequence of soybean β-conglycinin α′ subunit acts as a vacuolar sorting determinant in seed cells. Plant J. 34, 647–659 (2003).

    Article  CAS  PubMed  Google Scholar 

  22. Emans, N., Zimmermann, S. & Fischer, R. Uptake of a fluorescent marker in plant cells is sensitive to brefeldin A and wortmannin. Plant Cell 14, 71–86 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Fujimoto, M., Arimura, S.-i., Nakazono, M. & Tsutsumi, N. Imaging of plant dynamin-related proteins and clathrin around the plasma membrane by variable incidence angle fluorescence microscopy. Plant Biotechnol. 24, 449–455 (2007).

    Article  CAS  Google Scholar 

  24. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Collins, N. C. et al. SNARE-protein-mediated disease resistance at the plant cell wall. Nature 425, 973–977 (2003).

    Article  CAS  PubMed  Google Scholar 

  26. Kwon, C. et al. Co-option of a default secretory pathway for plant immune responses. Nature 451, 835–840 (2008).

    Article  CAS  PubMed  Google Scholar 

  27. Ebine, K. & Ueda, T. Unique mechanism of plant endocytic/vacuolar transport pathways. J. Plant Res. 122, 21–30 (2009).

    Article  PubMed  Google Scholar 

  28. Ebine, K. et al. A SNARE complex unique to seed plants is required for protein storage vacuole biogenesis and seed development of Arabidopsis thaliana. Plant Cell 20, 3006–3021 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Uemura, T. et al. Systematic analysis of SNARE molecules in Arabidopsis: dissection of the post-Golgi network in plant cells. Cell Struct. Funct. 29, 49–65 (2004).

    Article  CAS  PubMed  Google Scholar 

  30. Banbury, D. N., Oakley, J. D., Sessions, R. B. & Banting, G. Tyrphostin A23 inhibits internalization of the transferrin receptor by perturbing the interaction between tyrosine motifs and the medium chain subunit of the AP-2 adaptor complex. J. Biol. Chem. 278, 12022–12028 (2003).

    Article  CAS  PubMed  Google Scholar 

  31. Alonso, J. M. et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653–657 (2003).

    Article  PubMed  Google Scholar 

  32. Rosso, M. G. et al. An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol. Biol. 53, 247–259 (2003).

    Article  CAS  PubMed  Google Scholar 

  33. Enami, K. et al. Differential expression control and polarized distribution of plasma membrane-resident SYP1 SNAREs in Arabidopsis thaliana. Plant Cell Physiol. 50, 280–289 (2009).

    Article  CAS  PubMed  Google Scholar 

  34. Tian, G. W. et al. High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. Plant Physiol. 135, 25–38 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Batoko, H., Zheng, H. Q., Hawes, C. & Moore, I. A Rab1 GTPase is required for transport between the endoplasmic reticulum and Golgi apparatus and for normal Golgi movement in plants. Plant Cell 12, 2201–2218 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Takeuchi, M. et al. A dominant negative mutant of sar1 GTPase inhibits protein transport from the endoplasmic reticulum to the Golgi apparatus in tobacco and Arabidopsis cultured cells. Plant J. 23, 517–525 (2000).

    Article  CAS  PubMed  Google Scholar 

  37. Haas, T. J. et al. The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. Plant Cell 19, 1295–1312 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Yano, D. et al. A SNARE complex containing SGR3/AtVAM3 and ZIG/VTI11 in gravity-sensing cells is important for Arabidopsis shoot gravitropism. Proc. Natl Acad. Sci. USA 100, 8589–8594 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhang, Z. et al. A SNARE-protein has opposing functions in penetration resistance and defence signalling pathways. Plant J. 49, 302–312 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Altschul, S. F et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275–282 (1992).

    CAS  PubMed  Google Scholar 

  43. Adachi, J. & Hasegawa, M. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28, 1–150 (1996).

    Google Scholar 

  44. Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987).

    CAS  PubMed  Google Scholar 

  45. Felsenstein, J. PHYLIP (phylogeny inference package), Version 3.65. Distributed by the author, Department of Genetics, University of Washington, Seattle. (2005).

  46. Tamura, K. et al. Why green fluorescent fusion proteins have not been observed in the vacuoles of higher plants. Plant J. 35, 545–555 (2003).

    Article  CAS  PubMed  Google Scholar 

  47. Miyawaki, A. & Tsien, R. Y. Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein. Methods Enzymol. 327, 472–500 (2000).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank T. Fujiwara, S. Utsumi, I. Hara-Nishimura, Y. Wada, J. Takano and M. T. Morita for sharing materials; E. Furuyama for technical support; and the SALK Institute, Max Planck Institute and ABRC for providing A. thaliana mutants. Sequence data for Selagninella moellendorffii and Volvox carterii were generated by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/). This work was supported by Grants-in-Aid for Scientific Research and the Targeted Proteins Research Program (TPRP) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and Grant-in-Aid for JSPS Fellows (K.E., 195010).

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Contributions

T. Ueda designed the study; K.E. carried out the main parts of the genetic, biochemical and confocal microscopy experiments; M.F. and N.T. conducted TIRFM; T.G. carried out the experiments presented in Fig. 2c; T.N. carried out the phylogenetic analysis; Y.O., T.D., E.I., A. Nishitani, M.H.S. and T. Uemura constructed the transgenic plants used in this study; H.T-C. prepared the anti-SYP121 antibody; and A. Nakano and T. Ueda supervised the study.

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Correspondence to Takashi Ueda.

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Ebine, K., Fujimoto, M., Okatani, Y. et al. A membrane trafficking pathway regulated by the plant-specific RAB GTPase ARA6. Nat Cell Biol 13, 853–859 (2011). https://doi.org/10.1038/ncb2270

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