Cited by 73Mitochondrial Function and PathologyGenetics, Aging, and Longevity in Model OrganismsAutophagy in Disease and Therapy

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain

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Krishna, Shefali, Arrojo e Drigo, Rafael, Capitanio, Juliana S., Ramachandra, Ranjan, Ellisman, Mark, Hetzer, Martin W.·2021·Developmental Cell

Abstract

In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.

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Crossref · 10.1016/j.devcel.2021.10.008

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  • The half-life of mitochondria is a couple of weeks in several cell types.

    “The half-life of mitochondria is known to be a couple of weeks in several cell types,20”

    From ApoE4-dependent lysosomal cholesterol accumulation impairs mitochondrial homeostasis and oxidative phosphorylation in human astrocytes (2023) · cites this paper as [20]

    The Results section reports mitochondrial-protein half-lives in two cell types: 7 days in neurons and 5.5 days in myotubes. That supports the broader point that mitochondrial turnover varies by cell type, but it does not establish a roughly two-week half-life for mitochondria themselves; the paper says the lifespan of individual mitochondria is unknown. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 51

  1. Acin-Perez R, Bayona-Bafaluy MP, Fernandez-Silva P, Moreno-Loshuertos R, Perez-Martos A, Bruno C, Moraes CT, and Enriquez JA (2004). Respiratory complex III is required to maintain complex I in mammalian mitochondria. Mol Cell 13, 805– 815. 15053874 PMC3164363
  2. Adams SR, Mackey MR, Ramachandra R, Palida Lemieux SF, Steinbach P, Bushong EA, Butko MT, Giepmans BNG, Ellisman MH, and Tsien RY (2016). Multicolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species. Cell Chem Biol 23, 1417– 1427. 27818300 PMC5127401
  3. Benninghoven A, Rudenauer FG & Werner HW (1987). Secondary ion mass spectrometry: basic concepts, instrumental aspects, applications, and trends. Wiley.
  4. Bezawork-Geleta A, Brodie EJ, Dougan DA, and Truscott KN (2015). LON is the master protease that protects against protein aggregation in human mitochondria through direct degradation of misfolded proteins. Sci Rep 5, 17397. 26627475 PMC4667172
  5. Buchwalter A, Schulte R, Tsai H, Capitanio J, and Hetzer M (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. Elife 8. PMC6802967 31599721
  6. Clayton DA, and Shadel GS (2014). Isolation of mitochondria from cells and tissues. Cold Spring Harb Protoc 2014, pdb top074542. 25275115
  7. Cogliati S, Calvo E, Loureiro M, Guaras AM, Nieto-Arellano R, Garcia-Poyatos C, Ezkurdia I, Mercader N, Vazquez J, and Enriquez JA (2016). Mechanism of super-assembly of respiratory complexes III and IV. Nature 539, 579– 582. 27775717
  8. D’Angelo MA, Raices M, Panowski SH, and Hetzer MW (2009). Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell 136, 284– 295. 19167330 PMC2805151
  9. David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, and Kenyon C (2010). Widespread protein aggregation as an inherent part of aging in C. elegans. PLoS Biol 8, e1000450. 20711477 PMC2919420
  10. Diaz F, Fukui H, Garcia S, and Moraes CT (2006). Cytochrome c oxidase is required for the assembly/stability of respiratory complex I in mouse fibroblasts. Mol Cell Biol 26, 4872– 4881. 16782876 PMC1489173
  11. Dzeja PP, Bortolon R, Perez-Terzic C, Holmuhamedov EL, and Terzic A (2002). Energetic communication between mitochondria and nucleus directed by catalyzed phosphotransfer. Proc Natl Acad Sci U S A 99, 10156– 10161. 12119406 PMC126640
  12. Fedor JG, and Hirst J (2018). Mitochondrial Supercomplexes Do Not Enhance Catalysis by Quinone Channeling. Cell Metab 28, 525– 531 e524. 29937372 PMC6125145
  13. Fellmann C, Hoffmann T, Sridhar V, Hopfgartner B, Muhar M, Roth M, Lai DY, Barbosa IA, Kwon JS, Guan Y, (2013). An optimized microRNA backbone for effective single-copy RNAi. Cell Rep 5, 1704– 1713. 24332856
  14. Fornasiero EF, Mandad S, Wildhagen H, Alevra M, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Sakib MS, (2018). Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions. Nat Commun 9, 4230. 30315172 PMC6185916
  15. 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. 27654917
  16. He L, Diedrich J, Chu YY, and Yates JR 3rd (2015). Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter. Anal Chem 87, 11361– 11367. 26499134 PMC4777630
  17. Hipp MS, Kasturi P, and Hartl FU (2019). The proteostasis network and its decline in ageing. Nat Rev Mol Cell Biol 20, 421– 435. 30733602
  18. Hofmann AD, Beyer M, Krause-Buchholz U, Wobus M, Bornhauser M, and Rodel G (2012). OXPHOS supercomplexes as a hallmark of the mitochondrial phenotype of adipogenic differentiated human MSCs. PLoS One 7, e35160. 22523573 PMC3327658
  19. Jha P, Wang X, and Auwerx J (2016). Analysis of Mitochondrial Respiratory Chain Supercomplexes Using Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE). Curr Protoc Mouse Biol 6, 1– 14. 26928661 PMC4823378
  20. Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, (2015). Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments. FASEB J 29, 3582– 3592. 25977255 PMC4511201
  21. Katajisto P, Dohla J, Chaffer CL, Pentinmikko N, Marjanovic N, Iqbal S, Zoncu R, Chen W, Weinberg RA, and Sabatini DM (2015). Stem cells. Asymmetric apportioning of aged mitochondria between daughter cells is required for stemness. Science 348, 340– 343. 25837514 PMC4405120
  22. Keene DR (2015). A review of color blindness for microscopists: guidelines and tools for accommodating and coping with color vision deficiency. Microsc Microanal 21, 279– 289. 25739321
  23. Knott SRV, Maceli A, Erard N, Chang K, Marran K, Zhou X, Gordon A, Demerdash OE, Wagenblast E, Kim S, (2014). A computational algorithm to predict shRNA potency. Mol Cell 56, 796– 807. 25435137 PMC4272634
  24. Kuznetsov AV, and Margreiter R (2009). Heterogeneity of mitochondria and mitochondrial function within cells as another level of mitochondrial complexity. Int J Mol Sci 10, 1911– 1929. 19468346 PMC2680654
  25. Letts JA, Fiedorczuk K, and Sazanov LA (2016). The architecture of respiratory supercomplexes. Nature 537, 644– 648. 27654913
  26. Letts JA, and Sazanov LA (2017). Clarifying the supercomplex: the higher-order organization of the mitochondrial electron transport chain. Nat Struct Mol Biol 24, 800– 808. 28981073
  27. Lobo-Jarne T, Nyvltova E, Perez-Perez R, Timon-Gomez A, Molinie T, Choi A, Mourier A, Fontanesi F, Ugalde C, and Barrientos A (2018). Human COX7A2L Regulates Complex III Biogenesis and Promotes Supercomplex Organization Remodeling without Affecting Mitochondrial Bioenergetics. Cell Rep 25, 1786– 1799 e1784. 30428348 PMC6286155
  28. Lopez-Otin C, Blasco MA, Partridge L, Serrano M, and Kroemer G (2013). The hallmarks of aging. Cell 153, 1194– 1217. 23746838 PMC3836174
  29. Mahat DB, Salamanca HH, Duarte FM, Danko CG, and Lis JT (2016). Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation. Mol Cell 62, 63– 78. 27052732 PMC4826300
  30. Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, (2018). Systematic analysis of protein turnover in primary cells. Nat Commun 9, 689. 29449567 PMC5814408
  31. Moehle EA, Shen K, and Dillin A (2019). Mitochondrial proteostasis in the context of cellular and organismal health and aging. J Biol Chem 294, 5396– 5407. 29622680 PMC6462515
  32. Pain VM (1994). Translational control during amino acid starvation. Biochimie 76, 718– 728. 7893822
  33. Palikaras K, Lionaki E, and Tavernarakis N (2018). Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat Cell Biol 20, 1013– 1022. 30154567
  34. Park SK, Aslanian A, McClatchy DB, Han X, Shah H, Singh M, Rauniyar N, Moresco JJ, Pinto AF, Diedrich JK, (2014). Census 2: isobaric labeling data analysis. Bioinformatics 30, 2208– 2209. 24681903 PMC4155478
  35. Peng J, Elias JE, Thoreen CC, Licklider LJ, and Gygi SP (2003). Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2, 43– 50. 12643542
  36. Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, (2019). The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res 47, D442– D450. 30395289 PMC6323896
  37. Picca A, Guerra F, Calvani R, Coelho-Junior HJ, Bossola M, Landi F, Bernabei R, Bucci C, and Marzetti E (2020). Generation and Release of Mitochondrial-Derived Vesicles in Health, Aging and Disease. J Clin Med 9. PMC7290979 32408624
  38. Schneider CA, Rasband WS, and Eliceiri KW (2012). NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671– 675. 22930834 PMC5554542
  39. Shpilka T, and Haynes CM (2018). The mitochondrial UPR: mechanisms, physiological functions and implications in ageing. Nat Rev Mol Cell Biol 19, 109– 120. 29165426
  40. Song J, Herrmann JM, and Becker T (2021). Quality control of the mitochondrial proteome. Nat Rev Mol Cell Biol 22, 54– 70. 33093673
  41. Sorzano CO, Thevenaz P, and Unser M (2005). Elastic registration of biological images using vector-spline regularization. IEEE Trans Biomed Eng 52, 652– 663. 15825867
  42. Sosinsky GE, Deerinck TJ, Greco R, Buitenhuys CH, Bartol TM, and Ellisman MH (2005). Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography. Neuroinformatics 3, 133– 162. 15988042
  43. Steinhauser ML, Bailey AP, Senyo SE, Guillermier C, Perlstein TS, Gould AP, Lee RT, and Lechene CP (2012). Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism. Nature 481, 516– 519. 22246326 PMC3267887
  44. Su J, Ekman C, Oskolkov N, Lahti L, Strom K, Brazma A, Groop L, Rung J, and Hansson O (2015). A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging. Skelet Muscle 5, 35. 26457177 PMC4600214
  45. Tabb DL, McDonald WH, and Yates JR 3rd (2002). DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1, 21– 26. 12643522 PMC2811961
  46. Toyama BH, Arrojo EDR, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, and Hetzer MW (2019). Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. J Cell Biol 218, 433– 444. 30552100 PMC6363465
  47. Toyama BH, and Hetzer MW (2013). Protein homeostasis: live long, won’t prosper. Nat Rev Mol Cell Biol 14, 55– 61. 23258296 PMC3570024
  48. Vazquez-Calvo C, Suhm T, Buttner S, and Ott M (2020). The basic machineries for mitochondrial protein quality control. Mitochondrion 50, 121– 131. 31669238
  49. Wirth C, Brandt U, Hunte C, and Zickermann V (2016). Structure and function of mitochondrial complex I. Biochim Biophys Acta 1857, 902– 914. 26921811
  50. Yin H, Price F, and Rudnicki MA (2013). Satellite cells and the muscle stem cell niche. Physiol Rev 93, 23– 67. 23303905 PMC4073943
  51. Zhang DS, Piazza V, Perrin BJ, Rzadzinska AK, Poczatek JC, Wang M, Prosser HM, Ervasti JM, Corey DP, and Lechene CP (2012). Multi-isotope imaging mass spectrometry reveals slow protein turnover in hair-cell stereocilia. Nature 481, 520– 524. 22246323 PMC3267870

Cited by

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Authors
Krishna, S., Arrojo e Drigo, R., Capitanio, J. S., Ramachandra, R., Ellisman, M., & Hetzer, M. W.
Affiliations
  • Salk Institute for Biological Studies (US)
  • University of California San Diego (US)
Corresponding author
Hetzer, Martin W.
Venue
Developmental Cell
Publisher
Elsevier BV
Published
2021-11
Volume
56
Issue
21
Pages
2952-2965.e9
ISSN
1534-5807 (ISSN-L)
OpenAlex
W3203222983
Cited by
73
References
9
Citations by year
2026: 14 · 2025: 22 · 2024: 19 · 2023: 8 · 2022: 9 · 2021: 1
FWCI
2.90
Type
journal article
Language
en
Open access
Locations
  • Developmental Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • W. M. Keck Foundation
  • Compton Foundation
  • Leona M. and Harry B. Helmsley Charitable Trust
  • National Science Foundation
  • NOMIS Stiftung
  • National Cancer Institute (P30 014195)
  • National Institutes of Health (R01 NS096786)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
Keywords
long-lived proteins, mitochondrial proteins, protein stability, electron transport chain, respiratory supercomplexes, post-transcriptional regulation, brain mitochondria, age-related decline
MeSH terms
Animals, Electron Transport Complex IV, Electron Transport, Mitochondria, Oxidative Phosphorylation, Mitochondrial Proteins, Electron Transport Complex I, Mitochondrial Membranes, Mice

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