Noncanonical ATG8–ABS3 interaction controls senescence in plants

Abstract

Protein homeostasis is essential for cellular functions and longevity, and the loss of proteostasis is one of the hallmarks of senescence. Autophagy is an evolutionarily conserved cellular degradation pathway that is critical for the maintenance of proteostasis. Paradoxically, autophagy deficiency leads to accelerated protein loss by unknown mechanisms. We discover that the ABNORMAL SHOOT3 (ABS3) subfamily of multidrug and toxic compound extrusion transporters promote senescence under natural and carbon-deprivation conditions in Arabidopsis thaliana. The senescence-promoting ABS3 pathway functions in parallel with the longevity-promoting autophagy to balance plant senescence and survival. Surprisingly, ABS3 subfamily multidrug and toxic compound extrusion proteins interact with AUTOPHAGY-RELATED PROTEIN 8 (ATG8) at the late endosome to promote senescence and protein degradation without canonical cleavage and lipidation of ATG8. This non-autophagic ATG8–ABS3 interaction paradigm is probably conserved among dicots and monocots. Our findings uncover a previously unknown non-autophagic function of ATG8 and an unrecognized senescence regulatory pathway controlled by ATG8–ABS3-mediated proteostasis.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: ABS3 subfamily MATEs promote plant senescence.
Fig. 2: Genetic interaction between abs3-1D, mateq and the autophagy mutant atg7-3.
Fig. 3: Physical interaction between ABS3 and ATG8e.
Fig. 4: The ATG8–ABS3 interaction is independent of ABS3 transporter activity or ATG8-PE conjugation.
Fig. 5: ABS3-mediated senescence requires ATG8–ABS3 interaction.
Fig. 6: Conserved ATG8–ABS3 interactions in wheat.
Fig. 7: Model for the ATG8–ABS3 interaction in controlling senescence in plants.

Data availability

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

References

  1. 1.

    Riera, C. E., Merkwirth, C., De Magalhaes Filho, C. D. & Dillin, A. Signaling networks determining life span. Annu. Rev. Biochem. 85, 35–64 (2016).

    CAS  Article  Google Scholar 

  2. 2.

    Li, F. & Vierstra, R. D. Autophagy: a multifaceted intracellular system for bulk and selective recycling. Trends Plant Sci. 17, 526–537 (2012).

    CAS  Article  Google Scholar 

  3. 3.

    Liu, Y. & Bassham, D. C. Autophagy: pathways for self-eating in plant cells. Annu. Rev. Plant Biol. 63, 215–237 (2012).

    CAS  Article  Google Scholar 

  4. 4.

    Xiong, Y. et al. Glucose-TOR signalling reprograms the transcriptome and activates meristems. Nature 496, 181–186 (2013).

    CAS  Article  Google Scholar 

  5. 5.

    Sheen, J. Master regulators in plant glucose signaling networks. J. Plant Biol. 57, 67–79 (2014).

    CAS  Article  Google Scholar 

  6. 6.

    Xiong, Y. & Sheen, J. Novel links in the plant TOR kinase signaling network. Curr. Opin. Plant Biol. 28, 83–91 (2015).

    CAS  Article  Google Scholar 

  7. 7.

    Baena-González, E., Rolland, F., Thevelein, J. M. & Sheen, J. A central integrator of transcription networks in plant stress and energy signalling. Nature 448, 938–942 (2007).

    Article  Google Scholar 

  8. 8.

    Lim, P. O., Kim, H. J. & Nam, H. G. Leaf senescence. Annu. Rev. Plant Biol. 58, 115–136 (2007).

    CAS  Article  Google Scholar 

  9. 9.

    Thomas, H. Senescence, ageing and death of the whole plant. New Phytol. 197, 696–711 (2013).

    Article  Google Scholar 

  10. 10.

    Woo, H. R., Kim, H. J., Nam, H. G. & Lim, P. O. Plant leaf senescence and death—regulation by multiple layers of control and implications for aging in general. J. Cell Sci. 126, 4823–4833 (2013).

    CAS  Article  Google Scholar 

  11. 11.

    Kim, J., Woo, H. R. & Nam, H. G. Toward systems understanding of leaf senescence: an integrated multi-omics perspective on leaf senescence research. Mol. Plant 9, 813–825 (2016).

    CAS  Article  Google Scholar 

  12. 12.

    Guo, Y. & Gan, S.-S. Convergence and divergence in gene expression profiles induced by leaf senescence and 27 senescence-promoting hormonal, pathological and environmental stress treatments. Plant Cell Environ. 35, 644–655 (2012).

    CAS  Article  Google Scholar 

  13. 13.

    Liebsch, D. & Keech, O. Dark-induced leaf senescence: new insights into a complex light-dependent regulatory pathway. New Phytol. 212, 563–570 (2016).

    CAS  Article  Google Scholar 

  14. 14.

    Kaur, J. & Debnath, J. Autophagy at the crossroads of catabolism and anabolism. Nat. Rev. Mol. Cell Biol. 16, 461–472 (2015).

    CAS  Article  Google Scholar 

  15. 15.

    Xie, Z. & Klionsky, D. J. Autophagosome formation: core machinery and adaptations. Nat. Cell Biol. 9, 1102–1109 (2007).

    CAS  Article  Google Scholar 

  16. 16.

    Michaeli, S., Galili, G., Genschik, P., Fernie, A. R. & Avin-Wittenberg, T. Autophagy in plants—what's new on the menu?. Trends Plant Sci. 21, 134–144 (2016).

    CAS  Article  Google Scholar 

  17. 17.

    Soto-Burgos, J., Zhuang, X., Jiang, L. & Bassham, D. C. Dynamics of autophagosome formation. Plant Physiol. 176, 219–229 (2018).

    CAS  Article  Google Scholar 

  18. 18.

    Morita, Y., Kataoka, A., Shiota, S., Mizushima, T. & Tsuchiya, T. NorM of Vibrio parahaemolyticus is an Na+-driven multidrug efflux pump. J. Bacteriol. 182, 6694–6697 (2000).

    CAS  Article  Google Scholar 

  19. 19.

    Ogawa, T. et al. Stimulating S-adenosyl-l-methionine synthesis extends lifespan via activation of AMPK. Proc. Natl Acad. Sci. USA 113, 11913–11918 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Otsuka, M. et al. A human transporter protein that mediates the final excretion step for toxic organic cations. Proc. Natl Acad. Sci. USA 102, 17923–17928 (2005).

    CAS  Article  Google Scholar 

  21. 21.

    Li, L., He, Z., Pandey, G. K., Tsuchiya, T. & Luan, S. Functional cloning and characterization of a plant efflux carrier for multidrug and heavy metal detoxification. J. Biol. Chem. 277, 5360–5368 (2002).

    CAS  Article  Google Scholar 

  22. 22.

    Diener, A. C., Gaxiola, R. A. & Fink, G. R. Arabidopsis ALF5, a multidrug efflux transporter gene family member, confers resistance to toxins. Plant Cell 13, 1625–1638 (2001).

    CAS  Article  Google Scholar 

  23. 23.

    Rogers, E. E. & Guerinot, M. L. FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. Plant Cell 14, 1787–1799 (2002).

    CAS  Article  Google Scholar 

  24. 24.

    Magalhaes, J. V. et al. A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat. Genet. 39, 1156–1161 (2007).

    CAS  Article  Google Scholar 

  25. 25.

    Marinova, K. et al. The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+-antiporter active in proanthocyanidin-accumulating cells of the seed coat. Plant Cell 19, 2023–2038 (2007).

    CAS  Article  Google Scholar 

  26. 26.

    Serrano, M. et al. Export of salicylic acid from the chloroplast requires the multidrug and toxin extrusion-like transporter EDS5. Plant Physiol. 162, 1815–1821 (2013).

    CAS  Article  Google Scholar 

  27. 27.

    Li, R. et al. ADP1 affects plant architecture by regulating local auxin biosynthesis. PLoS Genet. 10, e1003954 (2014).

    Article  Google Scholar 

  28. 28.

    Zhang, H. et al. A DTX/MATE-type transporter facilitates abscisic acid efflux and modulates ABA sensitivity and drought tolerance in Arabidopsis. Mol. Plant 7, 1522–1532 (2014).

    CAS  Article  Google Scholar 

  29. 29.

    Tian, W. et al. A molecular pathway for CO2 response in Arabidopsis guard cells. Nat. Commun. 6, 6057 (2015).

    CAS  Article  Google Scholar 

  30. 30.

    Wang, R. et al. A subgroup of MATE transporter genes regulates hypocotyl cell elongation in Arabidopsis. J. Exp. Bot. 66, 6327–6343 (2015).

    CAS  Article  Google Scholar 

  31. 31.

    Zhang, H. et al. Two tonoplast mate proteins function as turgor-regulating chloride channels in Arabidopsis. Proc. Natl Acad. Sci. USA 114, E2036–E2045 (2017).

    CAS  Article  Google Scholar 

  32. 32.

    Dobritzsch, M. et al. MATE transporter-dependent export of hydroxycinnamic acid amides. Plant Cell 28, 583–596 (2016).

    CAS  Article  Google Scholar 

  33. 33.

    Kim, J. H. et al. Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science 323, 1053–1057 (2009).

    CAS  Article  Google Scholar 

  34. 34.

    Sato, Y., Morita, R., Nishimura, M., Yamaguchi, H. & Kusaba, M. Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl Acad. Sci. USA 104, 14169–14174 (2007).

    CAS  Article  Google Scholar 

  35. 35.

    Hanaoka, H. et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol. 129, 1181–1193 (2002).

    CAS  Article  Google Scholar 

  36. 36.

    Doelling, J. H., Walker, J. M., Friedman, E. M., Thompson, A. R. & Vierstra, R. D. The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J. Biol. Chem. 277, 33105–33114 (2002).

    CAS  Article  Google Scholar 

  37. 37.

    Thompson, A. R., Doelling, J. H., Suttangkakul, A. & Vierstra, R. D. Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol. 138, 2097–2110 (2005).

    CAS  Article  Google Scholar 

  38. 38.

    Phillips, A. R., Suttangkakul, A. & Vierstra, R. D. The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics 178, 1339–1353 (2008).

    CAS  Article  Google Scholar 

  39. 39.

    Svenning, S., Lamark, T., Krause, K. & Johansen, T. Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1. Autophagy 7, 993–1010 (2011).

    CAS  Article  Google Scholar 

  40. 40.

    Cui, Y. et al. Biogenesis of plant prevacuolar multivesicular bodies. Mol. Plant 9, 774–786 (2016).

    CAS  Article  Google Scholar 

  41. 41.

    Lee, G.-J., Sohn, E. J., Lee, M. H. & Hwang, I. The Arabidopsis rab5 homologs rha1 and ara7 localize to the prevacuolar compartment. Plant Cell Physiol. 45, 1211–1220 (2004).

    CAS  Article  Google Scholar 

  42. 42.

    Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2017).

    CAS  Article  Google Scholar 

  43. 43.

    Waadt, R. et al. Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant J. 56, 505–516 (2008).

    CAS  Article  Google Scholar 

  44. 44.

    Bashline, L. & Gu, Y. Using the split-ubiquitin yeast two-hybrid system to test protein–protein interactions of transmembrane proteins. Methods Mol. Biol. 1242, 143–158 (2015).

    CAS  Article  Google Scholar 

  45. 45.

    Tanaka, Y. et al. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 496, 247–251 (2013).

    CAS  Article  Google Scholar 

  46. 46.

    Miyauchi, H. et al. Structural basis for xenobiotic extrusion by eukaryotic MATE transporter. Nat. Commun. 8, 1633 (2017).

    Article  Google Scholar 

  47. 47.

    Birgisdottir, Å. B., Lamark, T. & Johansen, T. The LIR motif—crucial for selective autophagy. J. Cell Sci. 126, 3237–3247 (2013).

    CAS  PubMed  Google Scholar 

  48. 48.

    Jacomin, A.-C., Samavedam, S., Charles, H. & Nezis, I. P. iLIR@viral: a web resource for LIR motif-containing proteins in viruses. Autophagy 13, 1782–1789 (2017).

    CAS  Article  Google Scholar 

  49. 49.

    Subramani, S. & Malhotra, V. Non-autophagic roles of autophagy-related proteins. EMBO Rep. 14, 143–151 (2013).

    CAS  Article  Google Scholar 

  50. 50.

    Schaaf, M. B. E., Keulers, T. G., Vooijs, M. A. & Rouschop, K. M. A. LC3/GABARAP family proteins: autophagy-(un)related functions. FASEB J. 30, 3961–3978 (2016).

    CAS  Article  Google Scholar 

  51. 51.

    Kriegenburg, F., Ungermann, C. & Reggiori, F. Coordination of autophagosome–lysosome fusion by ATG8 family members. Curr. Biol. 28, R512–R518 (2018).

    CAS  Article  Google Scholar 

  52. 52.

    Wild, P., McEwan, D. G. & Dikic, I. The LC3 interactome at a glance. J. Cell Sci. 127, 3–9 (2014).

    CAS  Article  Google Scholar 

  53. 53.

    Cullen, P. J. & Steinberg, F. To degrade or not to degrade: mechanisms and significance of endocytic recycling. Nat. Rev. Mol. Cell Biol. 19, 679–696 (2018).

    CAS  Article  Google Scholar 

  54. 54.

    Lai, Z., Wang, F., Zheng, Z., Fan, B. & Chen, Z. A critical role of autophagy in plant resistance to necrotrophic fungal pathogens. Plant J. 66, 953–968 (2011).

    CAS  Article  Google Scholar 

  55. 55.

    Geldner, N. et al. Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set. Plant J. 59, 169–178 (2009).

    CAS  Article  Google Scholar 

  56. 56.

    Yu, F., Park, S. & Rodermel, S. R. The Arabidopsis FtsH metalloprotease gene family: interchangeability of subunits in chloroplast oligomeric complexes. Plant J. 37, 864–876 (2004).

    CAS  Article  Google Scholar 

  57. 57.

    Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).

    CAS  Article  Google Scholar 

  58. 58.

    Lichtenthaler, H. K. [34] Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. Methods Enzymol. 148, 350–382 (1987).

    CAS  Article  Google Scholar 

  59. 59.

    Schägger, H. & von Jagow, G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166, 368–379 (1987).

    Article  Google Scholar 

  60. 60.

    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).

    CAS  Article  Google Scholar 

  61. 61.

    Yoo, S.-D., Cho, Y.-H. & Sheen, J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1572 (2007).

    CAS  Article  Google Scholar 

  62. 62.

    Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    CAS  Article  Google Scholar 

  63. 63.

    Avila, J. R., Lee, J. S. & Torii, K. U. Co-immunoprecipitation of membrane-bound receptors. Arabidopsis Book 13, e0180 (2015).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31570267 to F.Y., 31770205 to X.L. and 31741010 to Y.Q.) and Northwest A&F University (2452016001 to F.Y.). Y.W., L.S. and J.S. were supported by US National Institute of Health grant R01GM06493. We thank the Teaching and Research Core Facility at the College of Life Sciences, NWAFU for support in this work. We thank members of the Sheen Laboratory and K. Mao of Massachusetts General Hospital and Harvard Medical School, USA for stimulating discussions and critical reading of the manuscript.

Author information

Affiliations

Authors

Contributions

X.L., J.Sheen and F.Y. conceived the study and designed the experiments. M.J., H.X, R.W., Y.C., N.X., J.Z., J.Shao and Y.Q. performed the experiments. M.J., X.L., Y.W., L.S. and L.A. analysed the data. M.J., X.L., J.Sheen and F.Y. wrote the manuscript with contributions from all authors.

Corresponding author

Correspondence to Fei Yu.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Supplementary information

Supplementary Information

Supplementary Figures 1–7 and Supplementary Tables 1 and 2.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jia, M., Liu, X., Xue, H. et al. Noncanonical ATG8–ABS3 interaction controls senescence in plants. Nature Plants 5, 212–224 (2019). https://doi.org/10.1038/s41477-018-0348-x

Download citation

Further reading