A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors

Abstract

In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon on the outer chloroplast membrane) and the TOM (translocon on the outer mitochondrial membrane) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA⁺ adenosine triphosphatase CDC48, after which a previously uncharacterized cytosolic protein, transmembrane domain (TMD)-binding protein for tail-anchored outer membrane proteins (TTOP), binds to the exposed TMDs at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.

Keywords

26S proteasome / CDC48 / SP1 / TOC / TOM / ubiquitination

References

[1] Aoyama, T., and Chua, N.H. (1997). A glucocorticoid-mediated transcriptional induction system in transgenic plants. Plant J. 11: 605–612.

[2] Bae, W., Lee, Y.J., Kim, D.H., Lee, J., Kim, S., Sohn, E.J., and Hwang, I. (2008). AKr2A-mediated import of chloroplast outer membrane proteins is essential for chloroplast biogenesis. Nat. Cell Biol. 10: 220–U101.

[3] Chen X., Randles L., Shi K., Tarasov S.G., Aihara H., Walters K.J. (2016) Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 reveal distinct binding mechanisms between substrate receptors and shuttle factors of the proteasome. Structure 24: 1257–1270

[4] Chio, U.S., Cho, H., and Shan, S.O. (2017). Mechanisms of tail-anchored membrane protein targeting and insertion. Annu. Rev. Cell Dev. Biol. 33: 417–438.

[5] Clough, S.J., and Bent, A.F. (1998). Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. Cell Mol. Biol. 16: 735–743.

[6] Collins, G.A., and Goldberg, A.L. (2020). Proteins containing ubiquitin-like (Ubl) domains not only bind to 26S proteasomes but also induce their activation. Proc. Natl. Acad. Sci. U.S.A. 117, 4664–4674.

[7] Duncan, O., Murcha, M.W., and Whelan, J. (2013). Unique components of the plant mitochondrial protein import apparatus. Biochim. Biophys. Acta Mol. Cell Res. 1833: 304–313.

[8] Eisele, M.R., Reed, R.G., Rudack, T., Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J.M., Baumeister, W., Tomko, Jr., R.J., et al. (2018). Expanded coverage of the 26S proteasome conformational landscape reveals mechanisms of peptidase gating. Cell Rep. 24: 1301–1315.e1305.

[9] Fellerer, C., Schweiger, R., Schongruber, K., Soll, J., and Schwenkert, S. (2011). Cytosolic HSP90 cochaperones HOP and FKBP interact with freshly synthesized chloroplast preproteins of Arabidopsis. Mol. Plant 4: 1133–1145.

[10] Fernández-Bautista, N., Fernández-Calvino, L., Muñoz, A., and Castellano, M.M. (2017). HOP3, a member of the HOP family in Arabidopsis, interacts with BiP and plays a major role in the ER stress response. Plant Cell Environ. 40: 1341–1355.

[11] Ghifari, A.S., Gill-Hille, M., and Murcha, M.W. (2018). Plant mitochondrial protein import: The ins and outs. Biochem. J. 475: 2191–2208.

[12] Guna, A., and Hegde, R.S. (2018). Transmembrane domain recognition during membrane Protein biogenesis and quality control. Curr. Biol. 28: R498–R511.

[13] Hessa, T., Sharma, A., Mariappan, M., Eshleman, H.D., Gutierrez, E., and Hegde, R.S. (2011). Protein targeting and degradation are coupled for elimination of mislocalized proteins. Nature 475: 394–397.

[14] Husnjak, K., Elsasser, S., Zhang, N., Chen, X., Randles, L., Shi, Y., Hofmann, K., Walters, K.J., Finley, D., and Dikic, I. (2008). Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453: 481–488.

[15] Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Zidek, A., Potapenko, A., et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature 596: 583–589.

[16] Kim, J., Na, Y.J., Park, S.J., Baek, S.H., and Kim, D.H. (2019). Biogenesis of chloroplast outer envelope membrane proteins. Plant Cell Rep. 38: 783–792.

[17] Krysztofinska, E.M., Martínez-Lumbreras, S., Thapaliya, A., Evans, N.J., High, S., and Isaacson, R.L. (2016). Structural and functional insights into the E3 ligase, RNF126. Sci. Rep. 6: 26433.

[18] Law, Y.S., Zhang, R., Guan, X., Cheng, S., Sun, F., Duncan, O., Murcha, M., Whelan, J., and Lim, B.L. (2015). Phosphorylation and dephosphorylation of the presequence of pMORF3 during import into mitochondria from Arabidopsis thaliana. Plant Physiol. 169: 1–12.

[19] Ling, Q., and Jarvis, P. (2015). Regulation of chloroplast protein import by the ubiquitin E3 ligase SP1 is important for stress tolerance in plants. Curr. Biol. 25: 2527–2534.

[20] Ling, Q., Huang, W., Baldwin, A., and Jarvis, P. (2012). Chloroplast biogenesis is regulated by direct action of the ubiquitin-proteasome system. Science 338: 655–659.

[21] Ling, Q., Sadali, N.M., Soufi, Z., Zhou, Y., Huang, B., Zeng, Y., Rodriguez-Concepcion, M., and Jarvis, R.P. (2021). The chloroplast-associated protein degradation pathway controls chromoplast development and fruit ripening in tomato. Nat. Plants 7: 655–666.

[22] Ling, Q.H., Broad, W., Trosch, R., Topel, M., Sert, T.D., Lymperopoulos, P., Baldwin, A., and Jarvis, R.P. (2019). Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science 363: aav4467.

[23] Martensson, C.U., Priesnitz, C., Song, J., Ellenrieder, L., Doan, K.N., Boos, F., Floerchinger, A., Zufall, N., Oeljeklaus, S., Warscheid, B., et al. (2019). Mitochondrial protein translocation-associated degradation. Nature 569: 679–683.

[24] Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., and Steinegger, M. (2022). ColabFold: Making protein folding accessible to all. Nat. Methods 19: 679–682.

[25] Mock, J.-Y., Chartron, J.W., Zaslaver, M.a, Xu, Y., Ye, Y., and Clemons, W.M. (2015). Bag6 complex contains a minimal tail-anchor-targeting module and a mock BAG domain. Proc. Natl. Acad. Sci. U.S.A. 112, 106–111.

[26] Mullally, J.E., Chernova, T., and Wilkinson, K.D. (2006). Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain. Mol. Cell. Biol. 26: 822–830.

[27] Nakai, M. (2018). New perspectives on chloroplast protein import. Plant Cell Physiol. 59: 1111–1119.

[28] Pan, R., Satkovich, J., and Hu, J. (2016). E3 ubiquitin ligase SP1 regulates peroxisome biogenesis in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 113: E7307–E7316.

[29] Pan, R.H., and Hu, J.P. (2018). The Arabidopsis E3 ubiquitin ligase SP1 targets to chloroplasts, peroxisomes, and mitochondria. Plant Physiol. 176: 480–482.

[30] Panigrahi, R., Whelan, J., and Vrielink, A. (2014). Exploring ligand recognition, selectivity and dynamics of TPR domains of chloroplast Toc64 and mitochondria Om64 from Arabidopsis thaliana. J. Mol. Recogn. 27: 402–414.

[31] Schuberth, C., and Buchberger, A. (2005). Membrane-bound Ubx2 recruits Cdc48 to ubiquitin ligases and their substrates to ensure efficient ER-associated protein degradation. Nat. Cell Biol. 7: 999–1006.

[32] Shao, S., Rodrigo-Brenni, M.C., Kivlen, M.H., and Hegde, R.S. (2017). Mechanistic basis for a molecular triage reaction. Science 355: 298–302.

[33] Shi, L.-X., and Theg, S.M. (2013). The chloroplast protein import system: From algae to trees. Biochim. Biophys. Acta Mol. Cell Res. 1833: 314–331.

[34] Shi, Y., Chen, X., Elsasser, S., Stocks, B.B., Tian, G., Lee, B.-H., Shi, Y., Zhang, N., Poot, S.A.H.d, Tuebing, F., et al. (2016). Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science 351: aad9421.

[35] Sommer, M., Rudolf, M., Tillmann, B., Tripp, J., Sommer, M.S., and Schleiff, E. (2013). Toc33 and Toc64-III cooperate in precursor protein import into the chloroplasts of Arabidopsis thaliana. Plant Cell Environ. 36: 970–983.

[36] Sun, F., Carrie, C., Law, S., Murcha, M.W., Zhang, R., Law, Y.S., Suen, P.K., Whelan, J., and Lim, B.L. (2012). AtPAP2 is a tail-anchored protein in the outer membrane of chloroplasts and mitochondria. Plant Signaling Behav. 7: 927–932.

[37] Tsutsui, H., and Higashiyama, T. (2017). pKAMA-ITACHI vectors for highly efficient CRISPR/Cas9-mediated gene knockout in Arabidopsis thaliana. Plant Cell Physiol. 58: 46–56.

[38] VanderLinden, R.T., Hemmis, C.W., Yao, T., Robinson, H., and Hill, C.P. (2017). Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. J. Biol. Chem. 292: 9493–9504.

[39] Voon, C.P., Law, Y.S., Guan, X., Lim, S.L., Xu, Z., Chu, W.T., Zhang, R., Sun, F., Labs, M., Leister, D., et al. (2021). Modulating the activities of chloroplasts and mitochondria promotes ATP production and plant growth. Quant. Plant Biol. 2: 1–10.

[40] Wang, Q., Liu, Y., Soetandyo, N., Baek, K., Hegde, R., and Ye, Y. (2011). A ubiquitin ligase-associated chaperone holdase maintains polypeptides in soluble states for proteasome degradation. Mol. Cell 42: 758–770.

[41] Wu, X., Li, L., and Jiang, H. (2016). Doa1 targets ubiquitinated substrates for mitochondria-associated degradation. J. Cell. Biol. 213: 49–63.

[42] Yoo, S.D., Cho, Y.H., and Sheen, J. (2007). Arabidopsis mesophyll protoplasts: A versatile cell system for transient gene expression analysis. Nat. Protoc. 2: 1565–1572.

[43] Zhang, R., Guan, X., Law, Y.S., Sun, F., Chen, S., Wong, K.B., and Lim, B.L. (2016). AtPAP2 modulates the import of the small subunit of Rubisco into chloroplasts. Plant Signaling Behav. 11: e1239687.

[44] Zhang, T., and Ye, Y. (2016). Doa1 is a MAD adaptor for Cdc48. J. Cell. Biol. 213: 7–9.

[45] Zheng, J., Li, L., and Jiang, H. (2019). Molecular pathways of mitochondrial outer membrane protein degradation. Biochem. Soc. Trans. 47: 1437–1447.

RIGHTS & PERMISSIONS

2024 2024 The Authors. Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences.