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

Article metrics


Mitochondria have a central role in ageing. They are considered to be both a target of the ageing process and a contributor to it1. Alterations in mitochondrial structure and function are evident during ageing in most eukaryotes2, 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 pathways3. 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 potential4. 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 evolution5, we propose that lysosomal pH may modulate mitochondrial function and lifespan in other eukaryotic cells.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Age-induced mitochondrial dysfunction is suppressed by VMA1 overexpression.
Figure 2: Vacuolar acidity is reduced in ageing cells and regulates mitochondrial function and lifespan.
Figure 3: Reduced vacuolar acidity causes mitochondrial dysfunction by disrupting amino acid homeostasis.
Figure 4: Calorie restriction extends lifespan by regulating vacuolar acidity.


  1. 1

    Guarente, L. Mitochondria—a nexus for aging, calorie restriction, and sirtuins? Cell 132, 171–176 (2008)

  2. 2

    Seo, A. Y. et al. New insights into the role of mitochondria in aging: mitochondrial dynamics and more. J. Cell Sci. 123, 2533–2542 (2010)

  3. 3

    Bishop, N. A. & Guarente, L. Genetic links between diet and lifespan: shared mechanisms from yeast to humans. Nature Rev. Genet. 8, 835–844 (2007)

  4. 4

    Steinkraus, K. A., Kaeberlein, M. & Kennedy, B. K. Replicative aging in yeast: the means to the end. Annu. Rev. Cell Dev. Biol. 24, 29–54 (2008)

  5. 5

    Li, S. C. & Kane, P. M. The yeast lysosome-like vacuole: endpoint and crossroads. Biochim. Biophys. Acta 1793, 650–663 (2009)

  6. 6

    Scheckhuber, C. Q. et al. Reducing mitochondrial fission results in increased life span and fitness of two fungal ageing models. Nature Cell Biol. 9, 99–105 (2007)

  7. 7

    Lam, Y. T., Aung-Htut, M. T., Lim, Y. L., Yang, H. & Dawes, I. W. Changes in reactive oxygen species begin early during replicative aging of Saccharomyces cerevisiae cells. Free Radic. Biol. Med. 50, 963–970 (2011)

  8. 8

    McFaline-Figueroa, J. R. et al. Mitochondrial quality control during inheritance is associated with lifespan and mother–daughter age asymmetry in budding yeast. Aging Cell 10, 885–895 (2011)

  9. 9

    Veatch, J. R., McMurray, M. A., Nelson, Z. W. & Gottschling, D. E. Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect. Cell 137, 1247–1258 (2009)

  10. 10

    Lindstrom, D. L. & Gottschling, D. E. The mother enrichment program: a genetic system for facile replicative life span analysis in Saccharomyces cerevisiae. Genetics 183, 413–422 (2009)

  11. 11

    Pringle, J. R. et al. Fluorescence microscopy methods for yeast. Methods Cell Biol. 31, 357–435 (1989)

  12. 12

    Dimmer, K. S. et al. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol. Biol. Cell 13, 847–853 (2002)

  13. 13

    Altmann, K. & Westermann, B. Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. Mol. Biol. Cell 16, 5410–5417 (2005)

  14. 14

    Hirata, R. et al. 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, 6726–6733 (1990)

  15. 15

    Jackson, D. D. & Stevens, T. H. VMA12 encodes a yeast endoplasmic reticulum protein required for vacuolar H+-ATPase assembly. J. Biol. Chem. 272, 25928–25934 (1997)

  16. 16

    Droese, S. et al. Inhibitory effect of modified bafilomycins and concanamycins on P- and V-type adenosinetriphosphatases. Biochemistry 32, 3902–3906 (1993)

  17. 17

    Weisman, L. S., Bacallao, R. & Wickner, W. Multiple methods of visualizing the yeast vacuole permit evaluation of its morphology and inheritance during the cell cycle. J. Cell Biol. 105, 1539–1547 (1987)

  18. 18

    Sankaranarayanan, S., De Angelis, D., Rothman, J. E. & Ryan, T. A. The use of pHluorins for optical measurements of presynaptic activity. Biophys. J. 79, 2199–2208 (2000)

  19. 19

    Lin, S. J. et al. Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration. Nature 418, 344–348 (2002)

  20. 20

    Kaeberlein, M. et al. Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 310, 1193–1196 (2005)

  21. 21

    Parr, C. L., Keates, R. A., Bryksa, B. C., Ogawa, M. & Yada, R. Y. The structure and function of Saccharomyces cerevisiae proteinase A. Yeast 24, 467–480 (2007)

  22. 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, 4851–4857 (2005)

  23. 23

    Miseta, A., Kellermayer, R., Aiello, D. P., Fu, L. & Bedwell, D. M. The vacuolar Ca2+/H+ exchanger Vcx1p/Hum1p tightly controls cytosolic Ca2+ levels in S. cerevisiae. FEBS Lett. 451, 132–136 (1999)

  24. 24

    Nass, R., Cunningham, K. W. & 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, 26145–26152 (1997)

  25. 25

    Russnak, R., Konczal, D. & Mcintire, S. L. A family of yeast proteins mediating bidirectional vacuolar amino acid transport. J. Biol. Chem. 276, 23849–23857 (2001)

  26. 26

    Lin, S. J., Defossez, P. A. & Guarente, L. Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae. Science 289, 2126–2128 (2000)

  27. 27

    Kaeberlein, M., Kirkland, K. T., Fields, S. & Kennedy, B. K. Sir2-independent life span extension by calorie restriction in yeast. PLoS Biol. 2, e296 (2004)

  28. 28

    Tanaka, K. et al. cerevisiae genes IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein. Cell 60, 803–807 (1990)

  29. 29

    Palmieri, F. et al. Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins. Biochim. Biophys. Acta 1757, 1249–1262 (2006)

  30. 30

    Piper, M. D., Partridge, L., Raubenheimer, D. & Simpson, S. J. Dietary restriction and aging: a unifying perspective. Cell Metab. 14, 154–160 (2011)

  31. 31

    Baker Brachmann, C. et al. 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, 115–132 (1998)

  32. 32

    Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661–670 (2004)

  33. 33

    Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nature Biotechnol. 22, 1567–1572 (2004)

  34. 34

    Huh, W.-K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003)

  35. 35

    Alberti, S., Gitler, A. D. & Lindquist, S. A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24, 913–919 (2007)

  36. 36

    Hu, Y. et al. Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Res. 17, 536–543 (2007)

  37. 37

    Van Leeuwen, F. & Gottschling, D. E. Assays for gene silencing in yeast. Methods Enzymol. 350, 165–186 (2002)

  38. 38

    Lindstrom, D. L., Leverich, C. K., Henderson, K. A. & Gottschling, D. E. Replicative age induces mitotic recombination in the ribosomal RNA gene cluster of Saccharomyces cerevisiae. PLoS Genet. 7, e1002015 (2011)

  39. 39

    Morano, K. A. & Klionsky, D. J. Differential effects of compartment deacidification on the targeting of membrane and soluble proteins to the vacuole in yeast. J. Cell Sci. 107, 2813–2824 (1994)

  40. 40

    Plant, P. J., Manolson, M. F., Grinstein, S. & Demaurex, N. Alternative mechanisms of vacuolar acidification in H+-ATPase-deficient yeast. J. Biol. Chem. 274, 37270–37279 (1999)

  41. 41

    Jones, G. M. et al. A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae. Nature Methods 5, 239–241 (2008)

Download references


We thank L. Pallanck and members of the Gottschling laboratory for reviewing the manuscript; K. Henderson for helpful discussions; G. Miesenbock, D. Lindstrom and J. Hsu for reagents; and L. Dimitrov for technical assistance. This work was supported by National Institutes of Health grants AG037512 and AG023779, and a Glenn Award for Research in Biological Mechanisms of Aging to D.E.G., and by fellowships from the Helen Hay Whitney Foundation and Genetic Approaches to Aging Training Grant (T32 AG000057) to A.L.H.

Author information

A.L.H. designed and carried out the experiments. D.E.G. provided experimental guidance and supervision. Both authors discussed the results and implications of the experiments. The paper was written by A.L.H. and edited by D.E.G.

Correspondence to Daniel E. Gottschling.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-1 and Supplementary Tables 1-2. (PDF 11915 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hughes, A., Gottschling, D. An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast. Nature 492, 261–265 (2012) doi:10.1038/nature11654

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.