SAFARI WITH AN ELECTRON GUN: VISUALIZATION OF PROTEIN AND MEMBRANE INTERACTIONS IN MITOCHONDRIA IN THE NATURAL ENVIRONMENT

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

This paper presents new structural data about mitochondria using correlative light and electron microscopy and cryo-electron tomography (cryo-ET). These state-of-the-art structural biology methods allow the study of biological objects at nanometer scales in natural conditions. The non-invasiveness of these methods makes them comparable to observing animals in their natural environment on a safari. The paper highlights two areas of research that can only be accomplished using these methods. The study visualized the location of Aβ42 amyloid aggregates in relation to mitochondria to test a hypothesis for the development of mitochondrial dysfunction in Alzheimer’s disease. The results showed that Aβ42 aggregates do not interact with mitochondria, although some of them are closely located. Therefore, the study demonstrated that mitochondrial dysfunction is not directly influenced by aggregates on mitochondrial structure. The source of mitochondrial dysfunction should be investigated in other processes. Second unique area presented in this work is the high-resolution visualization of mitochondrial membranes and proteins in them. The analysis of cryo-ET data reveals toroidal holes in the lamellar structures of cardiac mitochondrial cristae, where ATP synthases are located. The study proposes a new mechanism for sorting and clustering protein complexes in the membrane based on topology. According to this mechanism, the position of oxidative phosohorylation system proteins in the membrane is determined by its curvature. High-resolution tomography expands and complements existing ideas about the structural and functional organization of mitochondria. This makes it possible to study the previously inaccessible structural interactions of proteins with each other and with membranes in vivo.

About the authors

S. V Nesterov

National Research Center “Kurchatov Institute”

Email: semen.v.nesterov@phystech.edu
123182 Moscow, Russia

K. S Plokhikh

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

Yu. M Chesnokov

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

D. A Mustaphin

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

T. N Goleva

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

A. G Rogov

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

R. G Vasilov

National Research Center “Kurchatov Institute”

123182 Moscow, Russia

L. S Yaguzhinsky

Belozersky Research Institute for Physico Chemical Biology, Lomonosov Moscow State University

119992 Moscow, Russia

References

  1. Saibil, H. R. (2022) Cryo-EM in molecular and cellular biology, Mol. Cell, 82, 274-284, https://doi.org/10.1016/j.molcel.2021.12.016.
  2. Guaita, M., Watters, S. C., and Loerch, S. (2022) Recent advances and current trends in cryo-electron microscopy, Curr. Opin. Struct. Biol., 77, 102484, https://doi.org/10.1016/j.sbi.2022.102484.
  3. Chua, E. Y. D., Mendez, J. H., Rapp, M., Ilca, S. L., Tan, Y. Z., Maruthi, K., Kuang, H., Zimanyi, C. M., Cheng, A., Eng, E. T., Noble, A. J., Potter, C. S., and Carragher, B. (2022) Better, faster, cheaper: recent advances in cryo-electron microscopy, Annu. Rev. Biochem., 91, 1-32, https://doi.org/10.1146/annurev-biochem-032620-110705.
  4. Hoffman, D. P., Shtengel, G., Xu, C. S., Campbell, K. R., Freeman, M., Wang, L., Milkie, D. E., Pasolli, H. A., Iyer, N., Bogovic, J. A., Stabley, D. R., Shirinifard, A., Pang, S., Peale, D., Schaefer, K., Pomp, W., Chang, C.-L., Lippincott-Schwartz, J., Kirchhausen, T., Solecki, D. J., Betzig, E., and Hess, H. F. (2020) Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells, Science, 367, eaaz5357, https://doi.org/10.1126/science.aaz5357.
  5. Liu, T., Stephan, T., Chen, P., Keller-Findeisen, J., Chen, J., Riedel, D., Yang, Z., Jakobs, S., and Chen, Z. (2022) Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain, Proc. Natl. Acad. Sci. USA, 119, e2215799119, https://doi.org/10.1073/pnas.2215799119.
  6. Wang, C., Taki, M., Sato, Y., Tamura, Y., Yaginuma, H., Okada, Y., and Yamaguchi, S. (2019) A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae, Proc. Natl. Acad. Sci. USA, 116, 15817-15822, https://doi.org/10.1073/pnas.1905924116.
  7. Nesterov, S., Chesnokov, Y., Kamyshinsky, R., Panteleeva, A., Lyamzaev, K., Vasilov, R., and Yaguzhinsky, L. (2021) Ordered clusters of the complete oxidative phosphorylation system in cardiac mitochondria, Int. J. Mol. Sci., 22, https://doi.org/10.3390/ijms22031462.
  8. Nesterov, S. V., Yaguzhinsky, L. S., Vasilov, R. G., Kadantsev, V. N., and Goltsov, A. N. (2022) Contribution of the collective excitations to the coupled proton and energy transport along mitochondrial cristae membrane in oxidative phosphorylation system, Entropy, 24, 1813, https://doi.org/10.3390/e24121813.
  9. Epremyan, K. K., Rogov, A. G., Goleva, T. N., Lavrushkina, S. V., Zinovkin, R. A., and Zvyagilskaya, R. A. (2023) Altered mitochondrial morphology and bioenergetics in a new yeast model expressing Aβ42, Int. J. Mol. Sci., 24, https://doi.org/10.3390/ijms24020900.
  10. Bischof, J., Hunt, C. J., Rubinsky, B., Burgess, A., and Pegg, D. E. (1990) Effects of cooling rate and glycerol concentration on the structure of the frozen kidney: Assessment by cryo-scanning electron microscopy, Cryobiology, 27, 301-310, https://doi.org/10.1016/0011-2240(90)90029-4.
  11. Plokhikh, K. S., Nesterov, S. V., Chesnokov, Y. M., Rogov, A. G., Kamyshinsky, R. A., Vasiliev, A. L., Yaguzhinsky, L. S., and Vasilov, R. G. (2024) Association of 2-oxoacid dehydrogenase complexes with respirasomes in mitochondria, FEBS J., 291, 132-141, https://doi.org/10.1111/febs.16965.
  12. Nesterov, S. V., Skorobogatova, Y. A., Panteleeva, A. A., Pavlik, L. L., Mikheeva, I. B., Yaguzhinsky, L. S., and Nartsissov, Y. R. (2018) NMDA and GABA receptor presence in rat heart mitochondria, Chem. Biol. Interact., 291, 40-46, https://doi.org/10.1016/j.cbi.2018.06.004.
  13. Sibarita, J.-B. (2005) Deconvolution microscopy, in Microscopy Techniques (Rietdorf, J., ed) Springer, Berlin, Heidelberg, pp. 201-243.
  14. Kremer, J. R., Mastronarde, D. N., and McIntosh, J. R. (1996) Computer visualization of three-dimensional image data using IMOD, J. Struct. Biol., 116, 71-76, https://doi.org/1047-8477/96.
  15. Wan, W., and Briggs, J. A. G. (2016) Cryo-Electron Tomography and Subtomogram Averaging, 1st Edn, Elsevier.
  16. Nesterov, S. V., Chesnokov, Yu. M., Kamyshinsky, R. A., Yaguzhinsky, L. S., and Vasilov, R. G. (2020) Determining the structure and location of the ATP synthase in the membranes of rat’s heart mitochondria using cryoelectron tomography, Nanotechnol. Russia, 15, 83-89, https://doi.org/10.1134/S1995078020010139.
  17. Liu, Y.-T., Zhang, H., Wang, H., Tao, C.-L., Bi, G.-Q., and Zhou, Z. H. (2022) Isotropic reconstruction for electron tomography with deep learning, Nat. Commun., 13, 6482, https://doi.org/10.1038/s41467-022-33957-8.
  18. Martinez-Sanchez, A., Garcia, I., Asano, S., Lucic, V., and Fernandez, J. J. (2014) Robust membrane detection based on tensor voting for electron tomography, J. Struct. Biol., 186, 49-61, https://doi.org/10.1016/j.jsb.2014.02.015.
  19. Castaño-Díez, D., Kudryashev, M., Arheit, M., and Stahlberg, H. (2012) Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments, J. Struct. Biol., 178, 139-151, https://doi.org/10.1016/j.jsb.2011.12.017.
  20. Tegunov, D., and Cramer, P. (2019) Real-time cryo-electron microscopy data preprocessing with Warp, Nat. Methods, 16, 1146-1152, https://doi.org/10.1038/s41592-019-0580-y.
  21. Bharat, T. A. M., and Scheres, S. H. W. (2016) Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION, Nat. Protoc., 11, 2054-2065, https://doi.org/10.1038/nprot.2016.124.
  22. Asano, S., Fukuda, Y., Beck, F., Aufderheide, A., Förster, F., Danev, R., and Baumeister, W. (2015) A molecular census of 26S proteasomes in intact neurons, Science, 347, 439-442, https://doi.org/10.1126/science.1261197.
  23. Ashleigh, T., Swerdlow, R. H., and Beal, M. F. (2023) The role of mitochondrial dysfunction in Alzheimer’s disease pathogenesis, Alzheimers Dement., 19, 333-342, doi: 10.1002/alz.12683.
  24. Bhatia, S., Rawal, R., Sharma, P., Singh, T., Singh, M., and Singh, V. (2022) Mitochondrial dysfunction in Alzheimer’s disease: opportunities for drug development, Curr. Neuropharmacol., 20, 675-692, https://doi.org/10.2174/1570159X19666210517114016.
  25. Eubel, H., Heinemeyer, J., and Braun, H.-P. (2004) Identification and characterization of respirasomes in potato mitochondria, Plant Physiol., 134, 1450-1459, https://doi.org/10.1104/pp.103.038018.
  26. Chaban, Y., Boekema, E. J., and Dudkina, N. V. (2014) Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilization, Biochim. Biophys. Acta, 1837, 418-426, https://doi.org/10.1016/j.bbabio.2013.10.004
  27. Dudkina, N. V., Kouřil, R., Peters, K., Braun, H.-P., and Boekema, E. J. (2010) Structure and function of mitochondrial supercomplexes, Biochim. Biophys. Acta, 1797, 664-670, https://doi.org/10.1016/j.bbabio.2009.12.013.
  28. Bultema, J. B., Braun, H.-P., Boekema, E. J., and Kouril, R. (2009) Megacomplex organization of the oxidative phosphorylation system by structural analysis of respiratory supercomplexes from potato, Biochim. Biophys. Acta, 1787, 60-67, https://doi.org/10.1016/j.bbabio.2008.10.010.
  29. Dudkina, N. V., Kudryashev, M., Stahlberg, H., and Boekema, E. J. (2011) Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography, Proc. Natl. Acad. Sci. USA, 108, 15196-15200, https://doi.org/10.1073/pnas.1107819108.
  30. Mühleip, A., Flygaard, R. K., Baradaran, R., Haapanen, O., Gruhl, T., Tobiasson, V., Maréchal, A., Sharma, V., and Amunts, A. (2023) Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex, Nature, 615, 934-938, https://doi.org/10.1038/s41586-023-05817-y.
  31. Guo, R., Zong, S., Wu, M., Gu, J., and Yang, M. (2017) Architecture of human mitochondrial respiratory megacomplex I2III2IV2, Cell, 170, 1247-1257.e12, https://doi.org/10.1016/j.cell.2017.07.050.
  32. Gu, J., Wu, M., Guo, R., Yan, K., Lei, J., Gao, N., and Yang, M. (2016) The architecture of the mammalian respirasome, Nature, 537, 639-643, https://doi.org/10.1038/nature19359.
  33. Vercellino, I., and Sazanov, L. A. (2021) Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV, Nature, 598, 364-367, https://doi.org/10.1038/s41586-021-03927-z.
  34. Klusch, N., Dreimann, M., Senkler, J., Rugen, N., Kühlbrandt, W., and Braun, H.-P. (2023) Cryo-EM structure of the respiratory I + III2 supercomplex from Arabidopsis thaliana at 2 Å resolution, Nat Plants., 9, 142-156, https://doi.org/10.1038/s41477-022-01308-6.
  35. Kühlbrandt, W. (2015) Structure and function of mitochondrial membrane protein complexes, BMC Biol., 13, 89, https://doi.org/10.1186/s12915-015-0201-x.
  36. Strauss, M., Hofhaus, G., Schröder, R. R., and Kühlbrandt, W. (2008) Dimer ribbons of ATP synthase shape the inner mitochondrial membrane, EMBO J., 27, 1154-1160, https://doi.org/10.1038/emboj.2008.35.
  37. Garab, G., Yaguzhinsky, L. S., Dlouhý, O., Nesterov, S. V., Špunda, V., and Gasanoff, E. S. (2022) Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes, Prog. Lipid. Res., 86, 101163, https://doi.org/10.1016/j.plipres.2022.101163.
  38. Gasanov, S. E., Kim, A. A., Yaguzhinsky, L. S., and Dagda, R. K. (2018) Non-bilayer structures in mitochondrial membranes regulate ATP synthase activity, Biochim. Biophys. Acta, 1860, 586-599, https://doi.org/10.1016/j.bbamem.2017.11.014.
  39. Paradies, G., Paradies, V., De Benedictis, V., Ruggiero, F. M., and Petrosillo, G. (2014) Functional role of cardiolipin in mitochondrial bioenergetics, Biochim. Biophys. Acta, 1837, 408-417, https://doi.org/10.1016/j.bbabio.2013.10.006.
  40. Epremyan, K. K., Goleva, T. N., Rogov, A. G., Lavrushkina, S. V., Zinovkin, R. A., and Zvyagilskaya, R. A. (2022) The first Yarrowia lipolytica yeast models expressing hepatitis B virus X protein: changes in mitochondrial morphology and functions, Microorganism, 10, 1817, https://doi.org/10.3390/microorganisms10091817.
  41. Völgyi, K., Badics, K., Sialana, F. J., Gulyássy, P., Udvari, E. B., Kis, V., Drahos, L., Lubec, G., Kékesi, K. A., and Juhász, G. (2018) Early presymptomatic changes in the proteome of mitochondria-associated membrane in the APP/PS1 mouse model of Alzheimer’s disease, Mol. Neurobiol., 55, 7839-7857, https://doi.org/10.1007/s12035-018-0955-6.
  42. Buzhynskyy, N., Sens, P., Prima, V., Sturgis, J. N., and Scheuring, S. (2007) Rows of ATP synthase dimers in native mitochondrial inner membranes, Biophys. J., 93, 2870-2876, https://doi.org/10.1529/biophysj.107.109728.
  43. Blum, T. B., Hahn, A., Meier, T., Davies, K. M., and Kühlbrandt, W. (2019) Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows, Proc. Natl. Acad. Sci. USA, 116, 4250-4255, https://doi.org/10.1073/pnas.1816556116.
  44. Davies, K. M., Blum, T. B., and Kühlbrandt, W. (2018) Conserved in situ arrangement of complex I and III2 in mitochondrial respiratory chain supercomplexes of mammals, yeast, and plants, Proc. Natl. Acad. Sci. USA, 115, 3024-3029, https://doi.org/10.1073/pnas.1720702115.
  45. Beltrán-Heredia, E., Tsai, F.-C., Salinas-Almaguer, S., Cao, F. J., Bassereau, P., and Monroy, F. (2019) Membrane curvature induces cardiolipin sorting, Commun. Biol., 2, 1-7, https://doi.org/10.1038/s42003-019-0471-x.
  46. Arias-Cartin, R., Grimaldi, S., Arnoux, P., Guigliarelli, B., and Magalon, A. (2012) Cardiolipin binding in bacterial respiratory complexes: structural and functional implications, Biochim. Biophys. Acta, 1817, 1937-1949, https://doi.org/10.1016/j.bbabio.2012.04.005.
  47. Arnarez, C., Marrink, S. J., and Periole, X. (2013) Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels, Sci. Rep., 3, 1-9, https://doi.org/10.1038/srep01263.
  48. Duncan, A. L., Robinson, A. J., and Walker, J. E. (2016) Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases, Proc. Natl. Acad. Sci. USA, 113, 8687-8692, https://doi.org/10.1073/pnas.1608396113.
  49. Pfeiffer, K., Gohil, V., Stuart, R. A., Hunte, C., Brandt, U., Greenberg, M. L., and Schägger, H. (2003) Cardiolipin stabilizes respiratory chain supercomplexes, J. Biol. Chem., 278, 52873-52880, https://doi.org/10.1074/jbc.M308366200.
  50. Mühleip, A., McComas, S. E., and Amunts, A. (2019) Structure of a mitochondrial ATP synthase with bound native cardiolipin, eLife, 8, e51179, https://doi.org/10.7554/eLife.51179.
  51. Mileykovskaya, E., and Dowhan, W. (2014) Cardiolipin-dependent formation of mitochondrial respiratory supercomplexes, Chem. Phys. Lipids, 179, 42-48, https://doi.org/10.1016/j.chemphyslip.2013.10.012.
  52. Zhang, M., Mileykovskaya, E., and Dowhan, W. (2005) Cardiolipin is essential for organization of complexes III and IV into a supercomplex in intact yeast mitochondria, J. Biol. Chem., 280, 29403-29408, https://doi.org/10.1074/jbc.M504955200.
  53. Zhang, M., Mileykovskaya, E., and Dowhan, W. (2002) Gluing the respiratory chain together. Cardiolipin is required for supercomplex formation in the inner mitochondrial membrane, J. Biol. Chem., 277, 43553-43556, https://doi.org/10.1074/jbc.C200551200.
  54. Mileykovskaya, E., and Dowhan, W. (2009) Cardiolipin membrane domains in prokaryotes and eukaryotes, Biochim. Biophys. Acta, 1788, 2084-2091, https://doi.org/10.1016/j.bbamem.2009.04.003.
  55. Diaz-Rohrer, B., Levental, K. R., and Levental, I. (2014) Rafting through traffic: Membrane domains in cellular logistics, Biochim. Biophys. Acta, 1838, 3003-3013, https://doi.org/10.1016/j.bbamem.2014.07.029.
  56. Zabara, A., Meikle, T. G., Newman, J., Peat, T. S., Conn, C. E., and Drummond, C. J. (2017) The nanoscience behind the art of in meso crystallization of membrane proteins, Nanoscale, 9, 754-763, https://doi.org/10.1039/C6NR07634C.

Copyright (c) 2024 Russian Academy of Sciences

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies