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Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability

  • Dongkeun Park (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Youngim Yu (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Ji-hyung Kim (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Jongbin Lee (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Jongmin Park (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Kido Hong (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Jeong-Kon Seo (UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology) ;
  • Chunghun Lim (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST)) ;
  • Kyung-Tai Min (Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST))
  • Received : 2022.11.21
  • Accepted : 2023.01.17
  • Published : 2023.06.30

Abstract

Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.

Keywords

Acknowledgement

We thank Franz-Ulrich Hartl, Jeffrey Rothstein, Addgene, and Developmental Studies Hybridoma Bank for reagents. This work was supported by grants from the Suh Kyungbae Foundation (SUHF-17020101); from the National Research Foundation funded by the Ministry of Science and Information & Communication Technology (MSIT), Republic of Korea (NRF-2021R1A2C3011706; NRF-2021M3A9G8022960; NRF-2018R1A5A1024261).

References

  1. Agarwal, S. and Ganesh, S. (2020). Perinuclear mitochondrial clustering, increased ROS levels, and HIF1 are required for the activation of HSF1 by heat stress. J. Cell Sci. 133, jcs245589. 
  2. Alagar Boopathy, L.R., Jacob-Tomas, S., Alecki, C., and Vera, M. (2022). Mechanisms tailoring the expression of heat shock proteins to proteostasis challenges. J. Biol. Chem. 298, 101796. 
  3. Amunts, A., Brown, A., Toots, J., Scheres, S.H.W., and Ramakrishnan, V. (2015). Ribosome. The structure of the human mitochondrial ribosome. Science 348, 95-98.  https://doi.org/10.1126/science.aaa1193
  4. Andreasson, C., Ott, M., and Buttner, S. (2019). Mitochondria orchestrate proteostatic and metabolic stress responses. EMBO Rep. 20, e47865. 
  5. Audas, T.E., Audas, D.E., Jacob, M.D., Ho, J.J.D., Khacho, M., Wang, M., Perera, J.K., Gardiner, C., Bennett, C.A., Head, T., et al. (2016). Adaptation to stressors by systemic protein amyloidogenesis. Dev. Cell 39, 155-168.  https://doi.org/10.1016/j.devcel.2016.09.002
  6. Bennett, C.F., Latorre-Muro, P., and Puigserver, P. (2022). Mechanisms of mitochondrial respiratory adaptation. Nat. Rev. Mol. Cell Biol. 23, 817-835.  https://doi.org/10.1038/s41580-022-00506-6
  7. Bennett, C.F., Vander Wende, H., Simko, M., Klum, S., Barfield, S., Choi, H., Pineda, V.V., and Kaeberlein, M. (2014). Activation of the mitochondrial unfolded protein response does not predict longevity in Caenorhabditis elegans. Nat. Commun. 5, 3483. 
  8. Bohovych, I. and Khalimonchuk, O. (2016). Sending out an SOS: mitochondria as a signaling hub. Front. Cell Dev. Biol. 4, 109. 
  9. Chakrabarty, R.P. and Chandel, N.S. (2022). Beyond ATP, new roles of mitochondria. Biochem. (Lond.) 44, 2-8.  https://doi.org/10.1042/bio_2022_119
  10. Chaudhry, A., Shi, R., and Luciani, D.S. (2020). A pipeline for multidimensional confocal analysis of mitochondrial morphology, function, and dynamics in pancreatic β-cells. Am. J. Physiol. Endocrinol. Metab. 318, E87-E101.  https://doi.org/10.1152/ajpendo.00457.2019
  11. Cipolat, S., de Brito, O.M., Dal Zilio, B., and Scorrano, L. (2004). OPA1 requires mitofusin 1 to promote mitochondrial fusion. Proc. Natl. Acad. Sci. U. S. A. 101, 15927-15932.  https://doi.org/10.1073/pnas.0407043101
  12. D'Angelo, M.A., Gomez-Cavazos, J.S., Mei, A., Lackner, D.H., and Hetzer, M.W. (2012). A change in nuclear pore complex composition regulates cell differentiation. Dev. Cell 22, 446-458.  https://doi.org/10.1016/j.devcel.2011.11.021
  13. Desai, R., East, D.A., Hardy, L., Faccenda, D., Rigon, M., Crosby, J., Alvarez, M.S., Singh, A., Mainenti, M., Hussey, L.K., et al. (2020). Mitochondria form contact sites with the nucleus to couple prosurvival retrograde response. Sci. Adv. 6, eabc9955. 
  14. Divakaruni, A.S. and Jastroch, M. (2022). A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements. Nat. Metab. 4, 978-994.  https://doi.org/10.1038/s42255-022-00619-4
  15. Eckl, E.M., Ziegemann, O., Krumwiede, L., Fessler, E., and Jae, L.T. (2021). Sensing, signaling and surviving mitochondrial stress. Cell. Mol. Life Sci. 78, 5925-5951.  https://doi.org/10.1007/s00018-021-03887-7
  16. Frottin, F., Schueder, F., Tiwary, S., Gupta, R., Korner, R., Schlichthaerle, T., Cox, J., Jungmann, R., Hartl, F.U., and Hipp, M.S. (2019). The nucleolus functions as a phase-separated protein quality control compartment. Science 365, 342-347.  https://doi.org/10.1126/science.aaw9157
  17. Gallagher, P.S., Oeser, M.L., Abraham, A.C., Kaganovich, D., and Gardner, R.G. (2014). Cellular maintenance of nuclear protein homeostasis. Cell. Mol. Life Sci. 71, 1865-1879.  https://doi.org/10.1007/s00018-013-1530-y
  18. Gallardo, P., Real-Calderon, P., Flor-Parra, I., Salas-Pino, S., and Daga, R.R. (2020). Acute heat stress leads to reversible aggregation of nuclear proteins into nucleolar rings in fission yeast. Cell Rep. 33, 108377. 
  19. Gupta, R., Kasturi, P., Bracher, A., Loew, C., Zheng, M., Villella, A., Garza, D., Hartl, F.U., and Raychaudhuri, S. (2011). Firefly luciferase mutants as sensors of proteome stress. Nat. Methods 8, 879-884.  https://doi.org/10.1038/nmeth.1697
  20. Houtkooper, R.H., Mouchiroud, L., Ryu, D., Moullan, N., Katsyuba, E., Knott, G., Williams, R.W., and Auwerx, J. (2013). Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497, 451-457.  https://doi.org/10.1038/nature12188
  21. Kantidze, O.L., Velichko, A.K., Luzhin, A.V., and Razin, S.V. (2016). Heat stress-induced DNA damage. Acta Naturae 8, 75-78.  https://doi.org/10.32607/20758251-2016-8-2-75-78
  22. Kay, M. and Wobbrock, J. (2016). ARTool: aligned rank transform for nonparametric factorial ANOVAs. R package version 0.10 2. 
  23. Kim, J.H., Ki, Y., Lee, H., Hur, M.S., Baik, B., Hur, J.H., Nam, D., and Lim, C. (2020). The voltage-gated potassium channel Shaker promotes sleep via thermosensitive GABA transmission. Commun. Biol. 3, 174. 
  24. Koncha, R.R., Ramachandran, G., Sepuri, N.B.V., and Ramaiah, K.V.A. (2021). CCCP-induced mitochondrial dysfunction - characterization and analysis of integrated stress response to cellular signaling and homeostasis. FEBS J. 288, 5737-5754.  https://doi.org/10.1111/febs.15868
  25. Kovacs, D., Sigmond, T., Hotzi, B., Bohar, B., Fazekas, D., Deak, V., Vellai, T., and Barna, J. (2019). HSF1Base: a comprehensive database of HSF1 (heat shock factor 1) target genes. Int. J. Mol. Sci. 20, 5815. 
  26. Labbadia, J., Brielmann, R.M., Neto, M.F., Lin, Y.F., Haynes, C.M., and Morimoto, R.I. (2017). Mitochondrial stress restores the heat shock response and prevents proteostasis collapse during aging. Cell Rep. 21, 1481-1494.  https://doi.org/10.1016/j.celrep.2017.10.038
  27. Lee, J., Park, J., Kim, J.H., Lee, G., Park, T.E., Yoon, K.J., Kim, Y.K., and Lim, C. (2020). LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient. PLoS Biol. 18, e3001002. 
  28. Lee, Y., Kim, J., Kim, H., Han, J.E., Kim, S., Kang, K.H., Kim, D., Kim, J.M., and Koh, H. (2022). Pyruvate dehydrogenase kinase protects dopaminergic neurons from oxidative stress in Drosophila DJ-1 null mutants. Mol. Cells 45, 454-464.  https://doi.org/10.14348/molcells.2022.5002
  29. Maghames, C.M., Lobato-Gil, S., Perrin, A., Trauchessec, H., Rodriguez, M.S., Urbach, S., Marin, P., and Xirodimas, D.P. (2018). NEDDylation promotes nuclear protein aggregation and protects the Ubiquitin Proteasome System upon proteotoxic stress. Nat. Commun. 9, 4376. 
  30. Martinez-Reyes, I. and Chandel, N.S. (2020). Mitochondrial TCA cycle metabolites control physiology and disease. Nat. Commun. 11, 102. 
  31. Masser, A.E., Kang, W., Roy, J., Mohanakrishnan Kaimal, J., Quintana-Cordero, J., Friedlander, M.R., and Andreasson, C. (2019). Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1. Elife 8, e47791. 
  32. Maxwell, B.A., Gwon, Y., Mishra, A., Peng, J., Nakamura, H., Zhang, K., Kim, H.J., and Taylor, J.P. (2021). Ubiquitination is essential for recovery of cellular activities after heat shock. Science 372, eabc3593. 
  33. Mediani, L., Guillen-Boixet, J., Vinet, J., Franzmann, T.M., Bigi, I., Mateju, D., Carra, A.D., Morelli, F.F., Tiago, T., Poser, I., et al. (2019). Defective ribosomal products challenge nuclear function by impairing nuclear condensate dynamics and immobilizing ubiquitin. EMBO J. 38, e101341. 
  34. Melber, A. and Haynes, C.M. (2018). UPRmt regulation and output: a stress response mediated by mitochondrial-nuclear communication. Cell Res. 28, 281-295.  https://doi.org/10.1038/cr.2018.16
  35. Mottis, A., Herzig, S., and Auwerx, J. (2019). Mitocellular communication: shaping health and disease. Science 366, 827-832.  https://doi.org/10.1126/science.aax3768
  36. Nollen, E.A., Salomons, F.A., Brunsting, J.F., van der Want, J.J., Sibon, O.C., and Kampinga, H.H. (2001). Dynamic changes in the localization of thermally unfolded nuclear proteins associated with chaperone-dependent protection. Proc. Natl. Acad. Sci. U. S. A. 98, 12038-12043.  https://doi.org/10.1073/pnas.201112398
  37. Ogawa, Y. and Imamoto, N. (2018). Nuclear transport adapts to varying heat stress in a multistep mechanism. J. Cell Biol. 217, 2341-2352.  https://doi.org/10.1083/jcb.201712042
  38. Panchal, K. and Tiwari, A.K. (2019). Mitochondrial dynamics, a key executioner in neurodegenerative diseases. Mitochondrion 47, 151-173.  https://doi.org/10.1016/j.mito.2018.11.002
  39. Pelham, H., Lewis, M., and Lindquist, S. (1984). Expression of a Drosophila heat shock protein in mammalian cells: transient association with nucleoli after heat shock. Philos. Trans. R. Soc. Lond. B Biol. Sci. 307, 301-307.  https://doi.org/10.1098/rstb.1984.0131
  40. Pellegrino, M.W., Nargund, A.M., and Haynes, C.M. (2013). Signaling the mitochondrial unfolded protein response. Biochim. Biophys. Acta 1833, 410-416.  https://doi.org/10.1016/j.bbamcr.2012.02.019
  41. Quiros, P.M., Mottis, A., and Auwerx, J. (2016). Mitonuclear communication in homeostasis and stress. Nat. Rev. Mol. Cell Biol. 17, 213-226.  https://doi.org/10.1038/nrm.2016.23
  42. Rackham, O. and Filipovska, A. (2022). Organization and expression of the mammalian mitochondrial genome. Nat. Rev. Genet. 23, 606-623.  https://doi.org/10.1038/s41576-022-00480-x
  43. Richter, U., Lahtinen, T., Marttinen, P., Suomi, F., and Battersby, B.J. (2015). Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness. J. Cell Biol. 211, 373-389.  https://doi.org/10.1083/jcb.201504062
  44. Richter, U., Ng, K.Y., Suomi, F., Marttinen, P., Turunen, T., Jackson, C., Suomalainen, A., Vihinen, H., Jokitalo, E., Nyman, T.A., et al. (2019). Mitochondrial stress response triggered by defects in protein synthesis quality control. Life Sci. Alliance 2, e201800219. 
  45. Riguet, N., Mahul-Mellier, A.L., Maharjan, N., Burtscher, J., Croisier, M., Knott, G., Hastings, J., Patin, A., Reiterer, V., Farhan, H., et al. (2021). Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties. Nat. Commun. 12, 6579. 
  46. Ryu, S.W., Stewart, R., Pectol, D.C., Ender, N.A., Wimalarathne, O., Lee, J.H., Zanini, C.P., Harvey, A., Huibregtse, J.M., Mueller, P., et al. (2020). Proteome-wide identification of HSP70/HSC70 chaperone clients in human cells. PLoS Biol. 18, e3000606. 
  47. Schmidt, U., Weigert, M., Broaddus, C., and Myers, G. (2018). Cell detection with star-convex polygons. In Medical Image Computing and Computer Assisted Intervention - MICCAI 2018, A.F. Frangi, J.A. Schnabel, C. Davatzikos, C. Alberola-Lopez, and G. Fichtinger, eds. (Cham: Springer International Publishing), pp. 265-273. 
  48. Stewart, M. (2007). Molecular mechanism of the nuclear protein import cycle. Nat. Rev. Mol. Cell Biol. 8, 195-208.  https://doi.org/10.1038/nrm2114
  49. Suhm, T., Kaimal, J.M., Dawitz, H., Peselj, C., Masser, A.E., Hanzen, S., Ambrozic, M., Smialowska, A., Bjorck, M.L., Brzezinski, P., et al. (2018). Mitochondrial translation efficiency controls cytoplasmic protein homeostasis. Cell Metab. 27, 1309-1322.e6.  https://doi.org/10.1016/j.cmet.2018.04.011
  50. Theodoridis, P.R., Bokros, M., Marijan, D., Balukoff, N.C., Wang, D., Kirk, C.C., Budine, T.D., Goldsmith, H.D., Wang, M., Audas, T.E., et al. (2021). Local translation in nuclear condensate amyloid bodies. Proc. Natl. Acad. Sci. U. S. A. 118, e2014457118. 
  51. Tulli, S., Del Bondio, A., Baderna, V., Mazza, D., Codazzi, F., Pierson, T.M., Ambrosi, A., Nolte, D., Goizet, C., Toro, C., et al. (2019). Pathogenic variants in the AFG3L2 proteolytic domain cause SCA28 through haploinsufficiency and proteostatic stress-driven OMA1 activation. J. Med. Genet. 56, 499-511.  https://doi.org/10.1136/jmedgenet-2018-105766
  52. Velazquez, J.M. and Lindquist, S. (1984). hsp70: nuclear concentration during environmental stress and cytoplasmic storage during recovery. Cell 36, 655-662.  https://doi.org/10.1016/0092-8674(84)90345-3
  53. Velichko, A.K., Petrova, N.V., Kantidze, O.L., Razin, S.V., and Solomon, M.J. (2012). Dual effect of heat shock on DNA replication and genome integrity. Mol. Biol. Cell 23, 3450-3460.  https://doi.org/10.1091/mbc.e11-12-1009
  54. Wang, L., Schumann, U., Liu, Y., Prokopchuk, O., and Steinacker, J.M. (2012). Heat shock protein 70 (Hsp70) inhibits oxidative phosphorylation and compensates ATP balance through enhanced glycolytic activity. J. Appl. Physiol. (1985) 113, 1669-1676.  https://doi.org/10.1152/japplphysiol.00658.2012
  55. Welch, W.J. and Feramisco, J.R. (1984). Nuclear and nucleolar localization of the 72,000-dalton heat shock protein in heat-shocked mammalian cells. J. Biol. Chem. 259, 4501-4513.  https://doi.org/10.1016/S0021-9258(17)43075-4
  56. Wentink, A.S., Nillegoda, N.B., Feufel, J., Ubartaite, G., Schneider, C.P., De Los Rios, P., Hennig, J., Barducci, A., and Bukau, B. (2020). Molecular dissection of amyloid disaggregation by human HSP70. Nature 587, 483-488.  https://doi.org/10.1038/s41586-020-2904-6
  57. Yun, J. and Finkel, T. (2014). Mitohormesis. Cell Metab. 19, 757-766. https://doi.org/10.1016/j.cmet.2014.01.011
  58. Yusupova, G. and Yusupov, M. (2017). Crystal structure of eukaryotic ribosome and its complexes with inhibitors. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160184. 
  59. Zhang, K., Daigle, J.G., Cunningham, K.M., Coyne, A.N., Ruan, K., Grima, J.C., Bowen, K.E., Wadhwa, H., Yang, P., Rigo, F., et al. (2018). Stress granule assembly disrupts nucleocytoplasmic transport. Cell 173, 958-971.e17.  https://doi.org/10.1016/j.cell.2018.03.025
  60. Zhang, K., Donnelly, C.J., Haeusler, A.R., Grima, J.C., Machamer, J.B., Steinwald, P., Daley, E.L., Miller, S.J., Cunningham, K.M., Vidensky, S., et al. (2015). The C9orf72 repeat expansion disrupts nucleocytoplasmic transport. Nature 525, 56-61.  https://doi.org/10.1038/nature14973
  61. Zhu, D., Li, X., and Tian, Y. (2022). Mitochondrial-to-nuclear communication in aging: an epigenetic perspective. Trends Biochem. Sci. 47, 645-659.  https://doi.org/10.1016/j.tibs.2022.03.008