Expression profiling of kinesins, involved in the development of autophagy in Arabidopsis thaliana, and the role of tubulin acetylation in the interaction of Atg8 protein with microtubules

  • V. D. Olenieva
  • D. I. Lytvyn
  • A. I. Yemets
  • Ya. B. Blume
DOI: https://doi.org/10.7124/FEEO.v22.942

Abstract

Aim. To investigate the interrelation between changes in the expression levels of kinesin genes that are potentially involved in the development of stress-induced autophagy in Arabidopsis thaliana by means of microtubules, and the structural biology analysis of the role of α-tubulin acetylation in the regulation of interaction of α-tubulin with Atg8. Methods. The simulation of the influence of abiotic stresses. PCR analysis of changes in expression levels of kinesin genes. The molecular dynamics simulations of α-tubulin and Atg8 complexes were performed using the GROMACS 4.5.5 program. Results. It was shown that the changes in expression levels were caused by the influence of stressful stimuli. A significant increase in the transcriptional activity of the KIN5B, KIN12B, KIN12F genes after UV-B irradiation, the KIN6, KIN7O, KIN7D, KIN12B genes under osmotic-, and KIN6, KIN12B under salt stress was detected. By means of bioinformatics it was demonstrated that α-tubulin acetylation provides an enhanced interaction of α-tubulin and Atg8 protein. Conclusions. Obtained data point out the important role of kinesins and α-tubulin acetylation in realization of microtubules’ partaking in the development of stress-induced autophagy in plants.

Keywords: microtubules, α-tubulin, kinesins, Atg8 protein, stress-induced autophagy.

References

Wang P., Mugume Y., Bassham D.C. New advances in autophagy in plants: Regulation, selectivity and function. Semin. Cell Dev. Biol. 2017. pii: S1084-9521(17)30129-5. doi: 10.1016/j.semcdb.2017.07.018.

Mackeh R., Perdiz D., Lorin S., Codogno P., Poüs C. Autophagy and microtubules - new story, old players, J. Cell Sci, 2013. Vol. 126. P. 1071–1080. doi: 10.1242/jcs.115626.

Monastyrska I., Rieter E., Klionsky D.J., Reggiori F. Multiple roles of the cytoskeleton in autophagy. Biol Rev Camb Philos Soc. 2009. Vol. 84 (3). P. 431–448. doi: 10.1111/j.1469-185X.2009.00082.x.

Perdiz D., Mackeh R., Poüs C., Baillet A. The ins and outs of tubulin acetylation: More than just a post-translational modi fi cation? Cell. Signal. 2011. Vol. 23 (5). P. 763–771. doi: 10.1016/j.cellsig.2010.10.014.

Olenieva V., Lytvyn D., Yemets A., Bergounioux C., Blume Y. Tubulin acetylation accompanies autophagy development induced by different abiotic stimuli in Arabidopsis thaliana. Cell Biol. Int. 2017. doi: 10.1002/cbin.10842.

Olenieva V., Lytvyn D., Yemets A., Blume Ya.B. Influence of UV-B on expression profiles of genes involved in the development of autophagy by means of microtubules. Reports Natl. Acad. Sci. Ukraine. 2018. Vol. 1. P. 100–109 (in Ukr). doi: 10.15407/dopovidi2018.01.100

Olenieva V., Lytvyn D., Yemets A., Blume Ya.B. Influence of sucrose starvation, osmotic and salt stresses on expression profiles of genes involved in the development of autophagy by means of microtubules. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2018. Vol. 16 (2). P. 174–180. doi: 10.7124/visnyk.utgis.15.2.876

Endow S.A. Determinants of molecular motor directionality. Nat Cell Biol. 1999. Vol. 1 (6). P. 163–167. doi: 10.1038/14113.

Li J., Xu Y., Chong K. The novel functions of kinesin motor proteins in plants. Protoplasma. 2012. Vol. 249. P. S95–100. doi: 10.1007/s00709-011-0357-3.

Biasini M., Bienert S., Waterhouse A., Arnold K., Studer G., Schmidt T., Kiefer F., Gallo Cassarino T., Bertoni M., Bordoli L., Schwede T. SWISS-MODEL: modeling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014. Vol. 42. P. W252–258. doi: 10.1093/nar/gku340.

Kutzner C., Páll S., Fechner M., Esztermann A., De Groot B. L., Grubmüller H. Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. 2015. Vol. 36 (26). P. 1990–2008. doi: 10.1002/jcc.24030.

Guo Y., Li M., Pu X., Li G., Guang X., Xiong W., Li J. PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes. 2010. Vol. 3 (1). P. 145. doi: 10.1186/1756-0500-3-145.

Dominguez C., Boelens R., Bonvin A.M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003. Vol. 125 (7). P. 1731–1737. doi: 10.1021/ja026939x.

Fedyna V.D., Lytvyn D.I., Blume Y.B. α The role of miclotubules in the development of plant autophagy, induced by abiotic stresses. Factors Exp. Evol. Organisms. 2016. Vol. 19. P. 47–49 (in Ukr.).

Walter W.J., Beránek V., Fischermeier E., Diez S. tubulin acetylation alone does not affect kinesin-1 velocity and run length in vitro. PLoS ONE. 2012. Vol. 7 (8). e42218. doi: 10.1371/journal.pone.0042218.

Balabanian L., Berger C.L., Hendricks A.G. Acetylated microtubules are preferentially bundled leading to enhanced kinesin-1 motility. Biophys. J. 2017. Vol. 113 (7). P. 1551–1560. doi: 10.1016/j.bpj.2017.08.009

Howes S.C., Alushin G.M., Shida T., Nachury M.V., Nogales E. Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure. Mol. Biol Cell. 2014. Vol. 25 (2). P. 257–266. doi: 10.1091/mbc.E13-07-0387

Janke C., Montagnac G. Causes and consequences of microtubule acetylation. Curr. Biol. 2017. Vol. 27 (23). P. R1287–R1292. doi: 10.1016/j.cub.2017.10.044

Sadoul K., Khochbin S. The growing landscape of tubulin acetylation: lysine 40 and many more. Biochem. J. 2016. Vol. 473. P. 1859–1868. doi: 10.1042/BCJ20160172