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The Role of Posttranslational Acetylation in the Association of Autophagy Protein ATG8 with Microtubules in Plant Cells

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Abstract

Our study was aimed to anlayze the mechanism of the effect of acetylation of the Lys40 residue in α-tubulin TUBA4 from A. thaliana on its structure and interaction with ATG8a autophagy protein. Reconstruction of the spatial structures of the studied proteins was carried out by homology using experimentally proven crystal structures as a template. Studies of protein–protein interactions and their comparative analysis were performed using in silico methods. It has been demonstrated that acetylation of α-tubulin on the Lys40 residue leads to stabilization of its structure in comparison with its deacetylated form. Also, the analysis of the results of molecular dynamics calculation showed that the replacement of acetylated α-tubulin in complex with ATG8 protein to nonacetylated form leads to a decrease in the number of contact amino acid residues that, as a result, destabilizes the entire complex. Therefore, acetylation of α-tubulin on the Lys40 residue leads to stabilization of the protein itself and its complex with the ATG8 protein.

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REFERENCES

  1. Abraham, M.J. and Gready, J.E., Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5, J. Comp. Chem., 2011, vol. 32, no. 9, pp. 2031–2040.https://doi.org/10.1002/jcc.21773

    Article  CAS  Google Scholar 

  2. Adamakis, I.-D.S., Panteris, E., and Eleftheriou, E.P., Tubulin acetylation mediates bisphenol a effects on the microtubule arrays of Allium cepa and Triticum turgidum, Biomolecules, 2019, vol. 9, no. 5, p. 185. https://doi.org/10.3390/biom9050185

    Article  CAS  PubMed Central  Google Scholar 

  3. Avin-Wittenberg, T., Honig, A., and Galili, G., Variations on a theme: plant autophagy in comparison to yeast and mammals, Protoplasma, 2012, vol. 249, pp. 285–299.

    Article  CAS  Google Scholar 

  4. Benkert, P., Tosatto, S.C.E., and Schomburg, D., QM-EAN: a comprehensive scoring function for model quality assessment, Proteins, 2008, vol. 71, no. 1, pp. 261–277.

    Article  CAS  Google Scholar 

  5. Blume, Y.B., A journey through plant cytoskeleton: hot spots in signaling and functioning, Cell Biol. Int., 2019, vol. 43, no. 9, pp. 978–982. https://doi.org/10.1002/cbin.11210

    Article  PubMed  Google Scholar 

  6. Blume, Y.B., Smertenko, A., Ostapets, N.N., et al., Post-translational modifications of plant tubulin, Cell Biol. Int., 1997, vol. 21, no. 12, pp. 917–920.

    Google Scholar 

  7. Bussi, G., Donadio, D., and Parrinello, M., Canonical sampling through velocity rescaling, J. Chem. Phys., 2007, vol. 126, no. 1, p. 014101.https://doi.org/10.1063/1.2408420

    Article  CAS  PubMed  Google Scholar 

  8. Chu, C.-W., Hou, F., Zhang, J., et al., A novel acetylation of p-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation, Mol. Biol. Cell, 2011, vol. 22, no. 4, pp. 448–456. https://doi.org/10.1091/mbc.e10-03-0203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Eshun-Wilson, L., Zhang, R., Portran, D., et al., Effects of α-tubulin acetylation on microtubule structure and stability, Proc. Natl. Acad. Sci. U. S. A., 2019, vol. 116, no. 21, pp. 10366–10371. https://doi.org/10.1073/pnas.1900441116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fass, E., Shvets, E., Degani, I., et al., Microtubules support production of starvation-induced autophagosomes but not their targeting and fusion with lysosomes, J. Biol. Chem., 2006, vol. 281, pp. 36303–36316.

    Article  CAS  Google Scholar 

  11. Fernandez-Recio, J., Totrov, M., and Abagyan, R., Screened charge electrostatic model in protein–protein docking simulations, Pac. Symp. Biocomput., 2002, vol. 7, pp. 552–563.

    Google Scholar 

  12. Fourest-Lieuvin, A., Peris, L., Gache, V., et al., Microtubule regulation in mitosis: tubulin phosphorylation by the cyclin-dependent kinase Cdk1, Mol. Biol. Cell, 2006, vol. 17, pp. 1041–1050. https://doi.org/10.1091/mbc.E05-07-0621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Freedman, H., Luchko, T., Luduena, R.F., and Tuszynski, J.A., Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface, Proteins, 2011, vol. 79, no. 10, pp. 2968–2982. https://doi.org/10.1002/prot.23155

    Article  CAS  PubMed  Google Scholar 

  14. Gardiner, J., Posttranslational modification of plant microtubules, Plant Signal. Behav., 2019, vol. 14, p. 10. https://doi.org/10.1080/15592324.2019.1654818

    Article  CAS  Google Scholar 

  15. Geeraert, C., Ratier, A., and Pfisterer, S.G., Starvation-induced hyperacetylation of tubulin is required for the stimulation of autophagy by nutrient deprivation, J. Biol. Chem., 2010, vol. 285, no. 31, vol. 24184–24194. https://doi.org/10.1074/jbc.m109.091553

  16. Geeraert, C., Ratier, A., Pfisterer, S.G., et al., Starvation-induced hyperacetylation of tubulin is required for the stimulation of autophagy by nutrient deprivation, J. Biol. Chem., 2010, vol. 285, no. 31, pp. 24184–24194.

    Article  CAS  Google Scholar 

  17. Grauffel, C., Stote, R.H., and Dejaegere, A force field parameters for the simulation of modified histone tails, J. Comput. Chem., 2010, vol. 31, no. 13, pp. 2434–2451. https://doi.org/10.1002/jcc.21536

    Article  CAS  PubMed  Google Scholar 

  18. Grosdidier, S., Totrov, M., and Fernandez-Recio, J., Computer applications for prediction of protein–protein interactions and rational drug design, Adv. Appl. Bioinform. Chem., 2009, vol. 2, pp. 101–123.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Guo, Y., Li, M., Pu, X., et al., PRED_PPI: a server for predicting protein–protein interactions based on sequence data with probability assignment, BMC Res. Notes, 2010, vol. 3, p. 145. https://doi.org/10.1186/1756-0500-3-145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Howes, S.C., Alushin, G.M., Shida, T., et al., Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure, Mol. Biol. Cell, 2014, vol. 25, pp. 2, pp. 257–266.https://doi.org/10.1091/mbc.e13-07-0387

  21. Jahreiss, L., Menzies, F.M., and Rubinsztein, D.C., The itinerary of autophagosomes: from peripheral formation to kiss-and-run fusion with lysosomes, Traffic, 2008, vol. 9, pp. 574–587.

    Article  CAS  Google Scholar 

  22. Janke, C. and Montagnac, G., Causes and consequences of microtubule acetylation, Curr. Biol., 2017, vol. 27, no. 23, pp. 1287–1292. https://doi.org/10.10l6/j.cub.2017.10.044

  23. Janke, C. and Magiera, M.M., The tubulin code and its role in controlling microtubule properties and functions, Nat. Rev. Mol. Cell Biol., 2020, vol. 21, pp. 307–326. https://doi.org/10.1038/s41580-020-0214-3

    Article  CAS  PubMed  Google Scholar 

  24. Ketelaar, T., Voss, C., Dimmock, S.A., et al., Arabidopsis homologues of the autophagy protein Atg8 are a novel family of microtubule binding proteins, FEBS Lett., 2004, vol. 567, nos. 2–3, pp. 302–306. https://doi.org/10.1016/j.febslet.2004.04.088

    Article  CAS  PubMed  Google Scholar 

  25. Kirisako, T., Ichimura, Y., Okada, H., et al., The reversible modification regulates the membranebinding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway, J. Cell Biol., 2000, vol. 151, no. 2, pp. 263–276. https://doi.org/10.1083/jcb.151.2.263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kouno, T., Mizuguchi, M., Tanida, I., et al., Solution structure of microtubule-associated protein light chain 3 and identification of its functional subdomains, J. Biol. Chem., 2005, vol. 280, no. 26, vol. 24610–24617. https://doi.org/10.1074/jbc.m413565200

  27. Kraft, L.J., Manral, P., Dowler, J., and Kenworthy, A.K., Nuclear LC3 associates with slowly diffusing complexes that survey the nucleolus, Traffic, 2016, vol. 17, no. 4, pp. 369–399.https://doi.org/10.1111/tra.12372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lee, J., Cheng, X., Swails, J.M., et al., CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field, J. Chem. Theory Comp., 2015, vol. 12, no. 1, pp. 405–413. https://doi.org/10.1021/acs.jctc.5b00935

    Article  CAS  Google Scholar 

  29. Littauer, U.Z., Giveon, D., Thierauf, M., et al., Common and distinct tubulin binding sites for microtubule-associated proteins, Proc. Natl. Acad. Sci. U. S. A., 1986, vol. 83, no. 19, pp. 7162–7166. https://doi.org/10.1073/pnas.83.19.7162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Liu, Y. and Bassham, D.C., Autophagy: pathways for self-eating in plant cells, Annu. Rev. Plant Biol., 2012, vol. 63, pp. 215–237.

    Article  CAS  Google Scholar 

  31. Lytvyn, D.I. and Blume, Ya.B., Microtubular cytoskeleton in autophagy and programmed cell death development in plants, in Programmed Cell Death in Plants and Animals, Rice, J., Ed., New York: Nova Sci. Publ., pp. 1–26.

  32. Lytvyn, D.I., Olenieva, V.D., Yemets, A.I., and Blume, Y.B., Histochemical analysis of tissue-specific α-tubulin acetylation as a response to autophagy induction by different stress factors in Arabidopsis thaliana, Cytol. Genet., 2018, vol. 52, no. 4, pp. 245–252. https://doi.org/10.3103/s0095452718040059

    Article  Google Scholar 

  33. Mackeh, R., Perdiz, D., Lorin, S., et al., Autophagy and microtubules—new story, old players, J. Cell Sci., 2013, vol. 126, no. 5, pp. 1071–1080. https://doi.org/10.1242/jcs.115626

    Article  CAS  PubMed  Google Scholar 

  34. MacTaggart, B. and Kashina, A., Posttranslational modifications of the cytoskeleton, Cytoskeleton, 2021, pp. 1–32. https://doi.org/10.1002/cm.21679

  35. Maruta, H., The acetylation of alpha-tubulin and its relationship to the assembly and disassembly of microtubules, J. Cell Biol., 1986, vol. 103, no. 2, pp. 571–579. https://doi.org/10.1083/jcb.103.2.571

    Article  CAS  PubMed  Google Scholar 

  36. McEwan, D.G. and Dikic, I., The three musketeers of autophagy: phosphorylation, ubiquitylation and acetylation, Trends Cell Biol., 1986, vol. 21, no. 4, pp. 195–201. https://doi.org/10.1016/j.tcb.2010.12.006

    Article  CAS  Google Scholar 

  37. Merkulova, E.A., Guiboileau, A., Naya, L., et al., Assessment and optimization of autophagy monitoring methods in Arabidopsis roots indicate direct fusion of autophagosomes with vacuoles, Plant Cell Physiol., 2014, vol. 55, no. 4, pp. 715–726. https://doi.org/10.1093/pcp/pcu041

    Article  CAS  PubMed  Google Scholar 

  38. Minoura, I., Hachikubo, Y., Yamakita, Y., et al., Overexpression, purification, and functional analysis of recombinant human tubulin dimer, FEBS Lett., 2013, vol. 587, no. 21, pp. 3450–3455. doihttps://doi.org/10.1016/j.febslet.2013.08.032

    Article  CAS  PubMed  Google Scholar 

  39. Monastyrska, I., Rieter, E., Klionsky, D.J., and Reggiori, F., Multiple roles of the cytoskeleton in autophagy, Biol. Rev. Camb. Philos. Soc., 2009, vol. 84, no. 3, pp. 431–448.

    Article  Google Scholar 

  40. Noda, N.N., Ohsumi, Y., and Inagaki, F., Crystallographic studies on autophagy-related proteins, in Current Trends in X-Ray Crystallography, Chandrasekaran, A., Ed. IntechOpen, 2011. https://doi.org/10.5772/29509

    Book  Google Scholar 

  41. Olenieva, V., Lytvyn, D., Yemets, A., et al., Tubulin acetylation accompanies autophagy development induced by different abiotic stimuli in Arabidopsis thaliana, Cell Biol. Int., 2019, vol. 43, pp. 1056–1064. https://doi.org/10.1002/cbin.10843

    Article  CAS  PubMed  Google Scholar 

  42. Parrinello, M. and Rahman, A., Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys., 1981, vol. 52, no. 12, pp. 7182–7190. https://doi.org/10.1063/1.328693

    Article  CAS  Google Scholar 

  43. Parrotta, L., Cresti, M., and Cai, G., Accumulation and posttranslational modifications of plant tubulins, Plant Biol., 2014, vol. 16, no. 3, pp. 521–527.

    Article  CAS  Google Scholar 

  44. Portran, D., Schaedel, L., Xu, Z., et al., Tubulin acetylation protects long-lived microtubules against mechanical ageing, Nat. Cell Biol., 2017, vol. 19, no. 4, pp. 391–398. https://doi.org/10.1038/ncb3481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Raevsky, A.V., Sharifi, M., Samofalova, D.A., et al., 3D structure prediction of histone acetyltransferase proteins of the MYST family and their interactome in Arabidopsis thaliana, J. Mol. Model., 2016, vol. 22, no. 11, p. 256. https://doi.org/10.1007/s00894-016-3103-0

    Article  CAS  PubMed  Google Scholar 

  46. Ramkumar, A., Jong, B.Y., and Ori-McKenney, K.M., ReMAPping the microtubule landscape: How phosphorylation dictates the activities of microtubule-associated proteins, Dev. Dyn., 2018, vol. 247, pp. 138–155. https://doi.org/10.1002/dvdy.24599

    Article  CAS  PubMed  Google Scholar 

  47. Rayevsky, A., Sharifi, M., Samofalova, D., et al., In silico mechanistic model of microtubule assembly inhibition by selective chromone derivatives, J. Mol. Struct., 2021, p. 1241. https://doi.org/10.1016/j.molstruc.2021.130633

  48. Rayevsky, A.V., Sharifi, M., Samofalova, D.A., et al., Structural and functional features of lysine acetylation of plant and animal tubulins, Cell Biol Int., 2019, vol. 43, art. 10401048. https://doi.org/10.1002/cbin.10887

    Article  CAS  Google Scholar 

  49. Samofalova, D.A., Karpov, P.A., Raevsky, A.V., and Blume, Y.B., Protein phosphatases potentially associated with regulation of microtubules, their spatial structure reconstruction and analysis, Cell Biol. Int., 2019, vol. 43, pp. 1081–1090. https://doi.org/10.1002/cbin.10810

    Article  CAS  PubMed  Google Scholar 

  50. Smertenko, A., Blume, Y.B., Viklicky, V., et al., Posttranslational modifications and multiple isoforms of tubulin in Nicotiana tabacum cells, Planta, 1997, vol. 201, no. 3, pp. 349–358.

    Article  CAS  Google Scholar 

  51. Suzuki, H., Tabata, K., Morita, E., et al., Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism, Structure, 2014, vol. 22, no. 1, pp. 47–58. https://doi.org/10.1016/j.str.2013.09.023

    Article  CAS  PubMed  Google Scholar 

  52. Takemura, R., Okabe, S., Umeyama, T., et al., Increased microtubule stability and alpha tubulin acetylation in cells transfected with microtubule-associated proteins MAP1B, MAP2 or tau, J. Cell Sci., 1992, vol. 103, no. 4, pp. 953–964. https://doi.org/10.1242/jcs.103.4.953

    Article  CAS  PubMed  Google Scholar 

  53. Tran, H.T., Nimick, M., Uhrig, R.G., et al., Arabidopsis thaliana histone deacetylase 14 (HDA14) is an α-tubulin deacetylase that associates with PP2A and enriches in the microtubule fraction with the putative histone acetyltransferase ELP3, Plant J., 2012, vol. 71, pp. 263–272.

    Article  CAS  Google Scholar 

  54. Verhey, K.J. and Gaertig, J., The tubulin code, Cell Cycle, 2007, vol. 6, no. 17, pp. 2152–2160.

    Article  CAS  Google Scholar 

  55. Weiergraber, O.H., Mohrluder, J., and Willbold, D., Atg8 family proteins—autophagy and beyond, in Autophagy—A Double-Edged Sword—Cell Survival or Death?, Bailly, Y., Ed., Rijeka: InTech, 2013, pp. 13–45.

    Google Scholar 

  56. Wloga, D., Joachimiak, E., and Fabczak, H., Tubulin post-translational modifications and microtubule dynamics, Int. J. Mol. Sci., 2017, vol. 18, p. 2207. https://doi.org/10.3390/ijms18102207

    Article  CAS  PubMed Central  Google Scholar 

  57. Xu, Z., Schaedel, L., Portran, D., et al., Microtubules acquire resistance from mechanical breakage through intralumenal acetylation, Science, 2017, vol. 356, no. 6335, pp. 328–332. https://doi.org/10.1126/science.aai8764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Yoshimoto, K., Beginning to understand auto-phagy, an intracellular self-degradation system in plants, Plant Cell Physiol., 2012, vol. 53, pp. 1355–1365.

    Article  CAS  Google Scholar 

  59. Zoete, V., Cuendet, M.A., Grosdidier, A., and Michielin, O., SwissParam: a fast force field generation tool for small organic molecules, J. Comp. Chem., 2012, vol. 32, pp. 11, pp. 2359–2368. https://doi.org/10.1002/jcc.21816

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Authors and Affiliations

  1. Laboratory of Bioinformatics and Structural Biology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123, Kyiv, Ukraine

    A. Rayevsky, D. Samofalova, S. P. Ozheredov, P. A. Karpov & Ya. B. Blume

  2. Taras Shevchenko National University of Kyiv, 01601, Kyiv, Ukraine

    D. S. Ozheredov

  3. TOV Enamine, 02094, Kyiv, Ukraine

    A. Rayevsky

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  1. A. Rayevsky
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  2. D. S. Ozheredov
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Rayevsky, A., Ozheredov, D.S., Samofalova, D. et al. The Role of Posttranslational Acetylation in the Association of Autophagy Protein ATG8 with Microtubules in Plant Cells. Cytol. Genet. 55, 510–518 (2021). https://doi.org/10.3103/S0095452721060128

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