Cited by 559Genetics, Aging, and Longevity in Model OrganismsAutophagy in Disease and TherapyMitochondrial Function and Pathology

An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast

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Hughes, Adam L., Gottschling, Daniel E.·2012·Nature

Abstract

Mitochondria have a central role in ageing. They are considered to be both a target of the ageing process and a contributor to it. Alterations in mitochondrial structure and function are evident during ageing in most eukaryotes, but how this occurs is poorly understood. Here we identify a functional link between the lysosome-like vacuole and mitochondria in Saccharomyces cerevisiae, and show that mitochondrial dysfunction in replicatively aged yeast arises from altered vacuolar pH. We found that vacuolar acidity declines during the early asymmetric divisions of a mother cell, and that preventing this decline suppresses mitochondrial dysfunction and extends lifespan. Surprisingly, changes in vacuolar pH do not limit mitochondrial function by disrupting vacuolar protein degradation, but rather by reducing pH-dependent amino acid storage in the vacuolar lumen. We also found that calorie restriction promotes lifespan extension at least in part by increasing vacuolar acidity via conserved nutrient-sensing pathways. Interestingly, although vacuolar acidity is reduced in aged mother cells, acidic vacuoles are regenerated in newborn daughters, coinciding with daughter cells having a renewed lifespan potential. Overall, our results identify vacuolar pH as a critical regulator of ageing and mitochondrial function, and outline a potentially conserved mechanism by which calorie restriction delays the ageing process. Because the functions of the vacuole are highly conserved throughout evolution, we propose that lysosomal pH may modulate mitochondrial function and lifespan in other eukaryotic cells.

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  • Dementia with Lewy Bodies presents with frontal executive dysfunction and cognitive fluctuations associated with Lewy body inclusions in the amygdala and cortex.

    “In contrast to PD, dementia with Lewy Bodies (DLB) presents with frontal executive dysfunction and cognitive fluctuations associated with Lewy body inclusions in the amygdala and cortex.76”

    From The lysosome and proteostatic stress at the intersection of pediatric neurological disorders and adult neurodegenerative diseases (2025) · cites this paper as [76]

    The paper’s ageing and mitochondrial-function passages concern yeast cells, not dementia with Lewy bodies. Searches for the claimed cognitive symptoms and Lewy body inclusions found no passage addressing them; the cited source therefore does not verify this claim. (LLM, conf=0.76)

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  1. [3]Bishop NA Guarente L Genetic links between diet and lifespan: shared mechanisms from yeast to humans Nat Rev Genet 8 835 2007 17909538
  2. [4]Steinkraus KA Kaeberlein M Kennedy BK Replicative aging in yeast: the means to the end Annu Rev Cell Dev Biol 24 29 2008 18616424 PMC2730916
  3. [5]Li SC Kane PM The yeast lysosome-like vacuole: endpoint and crossroads Biochim Biophys Acta 1793 650 2009 18786576 PMC2906225
  4. [6]Scheckhuber CQ Reducing mitochondrial fission results in increased life span and fitness of two fungal ageing models Nat Cell Biol 9 99 2007 17173038
  5. [7]Lam YT Aung-Htut MT Lim YL Yang H Dawes IW Changes in reactive oxygen species begin early during replicative aging of Saccharomyces cerevisiae cells Free Radic Biol Med 50 963 2011 21255640
  6. [8]Mcfaline-Figueroa JR Mitochondrial quality control during inheritance is associated with lifespan and mother-daughter age asymmetry in budding yeast Aging Cell 10 885 2011 21726403 PMC3173513
  7. [9]Veatch JR Mcmurray MA Nelson ZW Gottschling DE Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect Cell 137 1247 2009 19563757 PMC2759275
  8. [10]Lindstrom DL Gottschling DE The Mother Enrichment Program: A Genetic System for Facile Replicative Life Span Analysis in Saccharomyces cerevisiae Genetics 183 413 2009 19652178 PMC2766306
  9. [11]Pringle JR Fluorescence microscopy methods for yeast Methods Cell Biol 31 357 1989 2476649
  10. [12]Dimmer KS Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae Mol Biol Cell 13 847 2002 11907266 PMC99603
  11. [13]Altmann K Westermann B Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae Mol Biol Cell 16 5410 2005 16135527 PMC1266436
  12. [14]Hirata R Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae J Biol Chem 265 6726 1990 2139027
  13. [15]Jackson DD Stevens TH VMA12 encodes a yeast endoplasmic reticulum protein required for vacuolar H+-ATPase assembly J Biol Chem 272 25928 1997 9325326
  14. [16]Drose S Inhibitory effect of modified bafilomycins and concanamycins on P- and V-type adenosinetriphosphatases Biochemistry 32 3902 1993 8385991
  15. [17]Weisman LS Bacallao R Wickner W Multiple methods of visualizing the yeast vacuole permit evaluation of its morphology and inheritance during the cell cycle The Journal of Cell Biology 105 1539 1987 2444598 PMC2114659
  16. [18]Sankaranarayanan S De Angelis D Rothman JE Ryan TA The use of pHluorins for optical measurements of presynaptic activity Biophys J 79 2199 2000 11023924 PMC1301110
  17. [19]Lin SJ Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration Nature 418 344 2002 12124627
  18. [20]Kaeberlein M Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients Science 310 1193 2005 16293764
  19. [21]Parr CL Keates RA Bryksa BC Ogawa M Yada RY The structure and function of Saccharomyces cerevisiae proteinase A Yeast 24 467 2007 17447722
  20. [22]Shimazu M Sekito T Akiyama K Ohsumi Y Kakinuma Y A family of basic amino acid transporters of the vacuolar membrane from Saccharomyces cerevisiae J Biol Chem 280 4851 2005 15572352
  21. [23]Miseta A Kellermayer R Aiello DP Fu L Bedwell DM The vacuolar Ca2+/H+ exchanger Vcx1p/Hum1p tightly controls cytosolic Ca2+ levels in S. cerevisiae FEBS Lett 451 132 1999 10371152
  22. [24]Nass R Cunningham KW Rao R Intracellular sequestration of sodium by a novel Na+/H+ exchanger in yeast is enhanced by mutations in the plasma membrane H+-ATPase. Insights into mechanisms of sodium tolerance J Biol Chem 272 26145 1997 9334180
  23. [25]Russnak R Konczal D Mcintire SL A family of yeast proteins mediating bidirectional vacuolar amino acid transport J Biol Chem 276 23849 2001 11274162
  24. [27]Kaeberlein M Kirkland KT Fields S Kennedy BK Sir2-independent life span extension by calorie restriction in yeast PLoS Biol 2 E296 2004 15328540 PMC514491
  25. [28]Tanaka K S. cerevisiae genes IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein Cell 60 803 1990 2178777
  26. [29]Palmieri F Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins Biochim Biophys Acta 1757 1249 2006 16844075
  27. [30]Piper MD Partridge L Raubenheimer D Simpson SJ Dietary restriction and aging: a unifying perspective Cell Metab 14 154 2011 21803286 PMC4445606
  28. [31]Brachmann CB Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications Yeast 14 115 1998 9483801
  29. [32]Sheff MA Thorn KS Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae Yeast 21 661 2004 15197731
  30. [35]Alberti S Gitler AD Lindquist S A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae Yeast 24 913 2007 17583893 PMC2190539
  31. [36]Hu Y Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae Genome Research 17 536 2007 17322287 PMC1832101
  32. [37]Van Leeuwen F Gottschling DE Assays for gene silencing in yeast Meth Enzymol 350 165 2002 12073311
  33. [38]Lindstrom DL Leverich CK Henderson KA Gottschling DE Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae PLoS Genet 7 e1002015 2011 21436897 PMC3060066
  34. [39]Morano KA Klionsky DJ Differential effects of compartment deacidification on the targeting of membrane and soluble proteins to the vacuole in yeast J Cell Sci 107 2813 1994 7876349
  35. [40]Plant PJ Manolson MF Grinstein S Demaurex N Alternative mechanisms of vacuolar acidification in H(+)-ATPase-deficient yeast J Biol Chem 274 37270 1999 10601292
  36. [41]Jones GM A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae Nat Methods 5 239 2008 18246075

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Authors
Hughes, A. L., & Gottschling, D. E.
Affiliations
Fred Hutch Cancer Center (US)
Corresponding author
Gottschling, Daniel E.
Venue
Nature
Published
2012-11-21
Volume
492
Issue
7428
Pages
261-265
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W2154164675
Cited by
559
References
5
Citations by year
2026: 32 · 2025: 43 · 2024: 42 · 2023: 39 · 2022: 49 · 2021: 47 · 2020: 41 · 2019: 39 · 2018: 32 · 2017: 35 · 2016: 42 · 2015: 45 · 2014: 44 · 2013: 25 · 2012: 3
FWCI
12.16
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Helen Hay Whitney Foundation
  • National Institutes of Health
  • National Institute on Aging (T32AG000057, P01AG001751, R01AG037512, R01AG023779, R37AG023779, AG023779, AG037512)
  • National Cancer Institute (P30CA015704)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
Keywords
vacuolar pH, mitochondrial dysfunction, lifespan extension, aging, Saccharomyces cerevisiae, caloric restriction, nutrient sensing, amino acid storage, lysosomes, asymmetric cell division, glucose limitation
MeSH terms
Amino Acids, Proton-Translocating ATPases, Homeostasis, Hydrogen-Ion Concentration, Lysosomes, Mitochondria, Saccharomyces cerevisiae, Vacuoles, Gene Expression, Saccharomyces cerevisiae Proteins, Microbial Viability

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