Brett, Christopher L. and Kallay, Laura and Hua, Zhaolin and Green, Richard and Chyou, Anthony and Zhang, Yongqiang and Graham, Todd R. and Donowitz, Mark and Rao, Rajini (2011) Genome-Wide Analysis Reveals the Vacuolar pH-Stat of Saccharomyces cerevisiae. PLoS ONE, 6 (3). e17619. ISSN 1932-6203
- Published Version
Official URL: http://dx.doi.org/10.1371/journal.pone.0017619
Protons, the smallest and most ubiquitous of ions, are central to physiological processes. Transmembrane proton gradients drive ATP synthesis, metabolite transport, receptor recycling and vesicle trafficking, while compartmental pH controls enzyme function. Despite this fundamental importance, the mechanisms underlying pH homeostasis are not entirely accounted for in any organelle or organism. We undertook a genome-wide survey of vacuole pH (pHv) in 4,606 single-gene deletion mutants of Saccharomyces cerevisiae under control, acid and alkali stress conditions to reveal the vacuolar pH-stat. Median pHv (5.27±0.13) was resistant to acid stress (5.28±0.14) but shifted significantly in response to alkali stress (5.83±0.13). Of 107 mutants that displayed aberrant pHv under more than one external pH condition, functional categories of transporters, membrane biogenesis and trafficking machinery were significantly enriched. Phospholipid flippases, encoded by the family of P4-type ATPases, emerged as pH regulators, as did the yeast ortholog of Niemann Pick Type C protein, implicated in sterol trafficking. An independent genetic screen revealed that correction of pHv dysregulation in a neo1ts mutant restored viability whereas cholesterol accumulation in human NPC1−/− fibroblasts diminished upon treatment with a proton ionophore. Furthermore, while it is established that lumenal pH affects trafficking, this study revealed a reciprocal link with many mutants defective in anterograde pathways being hyperacidic and retrograde pathway mutants with alkaline vacuoles. In these and other examples, pH perturbations emerge as a hitherto unrecognized phenotype that may contribute to the cellular basis of disease and offer potential therapeutic intervention through pH modulation.
|Divisions:||Concordia University > Faculty of Arts and Science > Biology|
|Authors:||Brett, Christopher L. and Kallay, Laura and Hua, Zhaolin and Green, Richard and Chyou, Anthony and Zhang, Yongqiang and Graham, Todd R. and Donowitz, Mark and Rao, Rajini|
|Journal or Publication:||PLoS ONE|
|Deposited By:||DANIELLE DENNIE|
|Deposited On:||13 Apr 2011 15:22|
|Last Modified:||13 Apr 2011 15:22|
1.Kaufmann SH (2008) Immunology's foundation: the 100-year anniversary of the Nobel Prize to Paul Ehrlich and Elie Metchnikoff. Nat Immunol 9: 705–712.
2.de Duve C (2005) The lysosome turns fifty. Nat Cell Biol 7: 847–849.
3.Heuser J (1989) Changes in lysosome shape and distribution correlated with changes in cytoplasmic pH. J Cell Biol 108: 855–864.
4.Mellman I (1992) The importance of being acid: the role of acidification in intracellular membrane traffic. J Exp Biol 172: 39–45.
5.Maranda B, Brown D, Bourgoin S, Casanova JE, Vinay P, et al. (2001) Intra-endosomal pH-sensitive recruitment of the Arf-nucleotide exchange factor ARNO and Arf6 from cytoplasm to proximal tubule endosomes. J Biol Chem 276: 18540–18550.
6.Nishi T, Forgac M (2002) The vacuolar (H+)-ATPases–nature's most versatile proton pumps. Nat Rev Mol Cell Biol 3: 94–103.
7.Weisz OA (2003) Organelle acidification and disease. Traffic 4: 57–64.
8.Futerman AH, van Meer G (2004) The cell biology of lysosomal storage disorders. Nat Rev Mol Cell Biol 5: 554–565.
9.Huynh KK, Grinstein S (2007) Regulation of vacuolar pH and its modulation by some microbial species. Microbiol Mol Biol Rev 71: 452–462.
10.Walls KC, Ghosh AP, Franklin AV, Klocke BJ, Ballestas M, et al. Lysosome dysfunction triggers Atg7-dependent neural apoptosis. J Biol Chem 285: 10497–10507.
11.Grabe M, Oster G (2001) Regulation of organelle acidity. J Gen Physiol 117: 329–344.
12.Roos A, Boron WF (1981) Intracellular pH. Physiol Rev 61: 296–434.
13.Steinberg BE, Huynh KK, Brodovitch A, Jabs S, Stauber T, et al. (2010) A cation counterflux supports lysosomal acidification. J Cell Biol 189: 1171–1186.
14.Steinberg BE, Touret N, Vargas-Caballero M, Grinstein S (2007) In situ measurement of the electrical potential across the phagosomal membrane using FRET and its contribution to the proton-motive force. Proc Natl Acad Sci U S A 104: 9523–9528.
15.Graham LA, Flannery AR, Stevens TH (2003) Structure and assembly of the yeast V-ATPase. J Bioenerg Biomembr 35: 301–312.
16.Kane PM (2006) The where, when, and how of organelle acidification by the yeast vacuolar H+-ATPase. Microbiol Mol Biol Rev 70: 177–191.
17.Forgac M (2007) Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology. Nat Rev Mol Cell Biol 8: 917–929.
18.Brett CL, Donowitz M, Rao R (2006) Does the proteome encode organellar pH? FEBS Lett 580: 717–719.
19.Ohgaki R, Matsushita M, Kanazawa H, Ogihara S, Hoekstra D, et al. (2010) The Na+/H+ exchanger NHE6 in the endosomal recycling system is involved in the development of apical bile canalicular surface domains in HepG2 cells. Mol Biol Cell 21: 1293–1304.
20.Brett CL, Tukaye DN, Mukherjee S, Rao R (2005) The yeast endosomal Na+K+/H+ exchanger Nhx1 regulates cellular pH to control vesicle trafficking. Mol Biol Cell 16: 1396–1405.
21.Nakamura N, Tanaka S, Teko Y, Mitsui K, Kanazawa H (2005) Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH regulation. J Biol Chem 280: 1561–1572.
22.Gilfillan GD, Selmer KK, Roxrud I, Smith R, Kyllerman M, et al. (2008) SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome. Am J Hum Genet 82: 1003–1010.
23.Morrow EM, Yoo SY, Flavell SW, Kim TK, Lin Y, et al. (2008) Identifying autism loci and genes by tracing recent shared ancestry. Science 321: 218–223.
24.Franke B, Neale BM, Faraone SV (2009) Genome-wide association studies in ADHD. Hum Genet 126: 13–50.
25.Ali R, Brett CL, Mukherjee S, Rao R (2004) Inhibition of sodium/proton exchange by a Rab-GTPase-activating protein regulates endosomal traffic in yeast. J Biol Chem 279: 4498–4506.
26.Pomorski T, Lombardi R, Riezman H, Devaux PF, van Meer G, et al. (2003) Drs2p-related P-type ATPases Dnf1p and Dnf2p are required for phospholipid translocation across the yeast plasma membrane and serve a role in endocytosis. Mol Biol Cell 14: 1240–1254.
27.Natarajan P, Wang J, Hua Z, Graham TR (2004) Drs2p-coupled aminophospholipid translocase activity in yeast Golgi membranes and relationship to in vivo function. Proc Natl Acad Sci U S A 101: 10614–10619.
28.Zhou X, Graham TR (2009) Reconstitution of phospholipid translocase activity with purified Drs2p, a type-IV P-type ATPase from budding yeast. Proc Natl Acad Sci U S A 106: 16586–16591.
29.Hua Z, Fatheddin P, Graham TR (2002) An essential subfamily of Drs2p-related P-type ATPases is required for protein trafficking between Golgi complex and endosomal/vacuolar system. Mol Biol Cell 13: 3162–3177.
30.Keenan Curtis K, Kane PM (2002) Novel vacuolar H+-ATPase complexes resulting from overproduction of Vma5p and Vma13p. J Biol Chem 277: 2716–2724.
31.Nikawa J, Yonemura K, Yamashita S (1983) Yeast mutant with thermolabile CDP-choline synthesis. Isolation and characterization of a cholinephosphate cytidyltransferase mutant. Eur J Biochem 131: 223–229.
32.Riekhof WR, Wu J, Gijon MA, Zarini S, Murphy RC, et al. (2007) Lysophosphatidylcholine metabolism in Saccharomyces cerevisiae: the role of P-type ATPases in transport and a broad specificity acyltransferase in acylation. J Biol Chem 282: 36853–36861.
33.Muthusamy BP, Raychaudhuri S, Natarajan P, Abe F, Liu K, et al. (2009) Control of protein and sterol trafficking by antagonistic activities of a type IV P-type ATPase and oxysterol binding protein homologue. Mol Biol Cell 20: 2920–2931.
34.Roelants FM, Baltz AG, Trott AE, Fereres S, Thorner J (2010) A protein kinase network regulates the function of aminophospholipid flippases. Proc Natl Acad Sci U S A 107: 34–39.
35.Sakano K (1998) Revision of Biochemical pH-Stat: Involvement of Alternative Pathway Metabolisms. Plant Cell Physiology 39: 467–473. Find this article online
36.Felle HH (2005) pH regulation in anoxic plants. Ann Bot 96: 519–532.
37.Piper P, Mahe Y, Thompson S, Pandjaitan R, Holyoak C, et al. (1998) The pdr12 ABC transporter is required for the development of weak organic acid resistance in yeast. Embo J 17: 4257–4265.
38.Marini AM, Matassi G, Raynal V, Andre B, Cartron JP, et al. (2000) The human Rhesus-associated RhAG protein and a kidney homologue promote ammonium transport in yeast. Nat Genet 26: 341–344.
39.Palma M, Seret ML, Baret PV (2009) Combined phylogenetic and neighbourhood analysis of the hexose transporters and glucose sensors in yeasts. FEMS Yeast Res 9: 526–534.
40.Zhang YQ, Gamarra S, Garcia-Effron G, Park S, Perlin DS, et al. (2010) Requirement for ergosterol in V-ATPase function underlies antifungal activity of azole drugs. PLoS Pathog 6: e1000939.
41.Loftus SK, Morris JA, Carstea ED, Gu JZ, Cummings C, et al. (1997) Murine model of Niemann-Pick C disease: mutation in a cholesterol homeostasis gene. Science 277: 232–235.
42.Berger AC, Hanson PK, Wylie Nichols J, Corbett AH (2005) A yeast model system for functional analysis of the Niemann-Pick type C protein 1 homolog, Ncr1p. Traffic 6: 907–917.
43.Lin M, Grillitsch K, Daum G, Just U, Hofken T (2009) Modulation of sterol homeostasis by the Cdc42p effectors Cla4p and Ste20p in the yeast Saccharomyces cerevisiae. Febs J 276: 7253–7264.
44.Battisti C, Tarugi P, Dotti MT, De Stefano N, Vattimo A, et al. (2003) Adult onset Niemann-Pick type C disease: A clinical, neuroimaging and molecular genetic study. Mov Disord 18: 1405–1409.
45.Liu B, Turley SD, Burns DK, Miller AM, Repa JJ, et al. (2009) Reversal of defective lysosomal transport in NPC disease ameliorates liver dysfunction and neurodegeneration in the npc1−/− mouse. Proc Natl Acad Sci U S A 106: 2377–2382.
46.Bonangelino CJ, Chavez EM, Bonifacino JS (2002) Genomic screen for vacuolar protein sorting genes in Saccharomyces cerevisiae. Mol Biol Cell 13: 2486–2501.
47.Preston RA, Reinagel PS, Jones EW (1992) Genes required for vacuolar acidity in Saccharomyces cerevisiae. Genetics 131: 551–558.
48.Seeley ES, Kato M, Margolis N, Wickner W, Eitzen G (2002) Genomic analysis of homotypic vacuole fusion. Mol Biol Cell 13: 782–794.
49.Nieland TJ, Feng Y, Brown JX, Chuang TD, Buckett PD, et al. (2004) Chemical genetic screening identifies sulfonamides that raise organellar pH and interfere with membrane traffic. Traffic 5: 478–492.
50.Borrelly G, Boyer JC, Touraine B, Szponarski W, Rambier M, et al. (2001) The yeast mutant vps5Delta affected in the recycling of Golgi membrane proteins displays an enhanced vacuolar Mg2+/H+ exchange activity. Proc Natl Acad Sci U S A 98: 9660–9665.
51.Schellmann S, Pimpl P (2009) Coats of endosomal protein sorting: retromer and ESCRT. Curr Opin Plant Biol 12: 670–676.
52.Bowers K, Levi BP, Patel FI, Stevens TH (2000) The sodium/proton exchanger Nhx1p is required for endosomal protein trafficking in the yeast Saccharomyces cerevisiae. Mol Biol Cell 11: 4277–4294.
53.Nickerson DP, Russell MR, Odorizzi G (2007) A concentric circle model of multivesicular body cargo sorting. EMBO Rep 8: 644–650.
54.Jacobs NL, Andemariam B, Underwood KW, Panchalingam K, Sternberg D, et al. (1997) Analysis of a Chinese hamster ovary cell mutant with defective mobilization of cholesterol from the plasma membrane to the endoplasmic reticulum. J Lipid Res 38: 1973–1987.
55.Kiselyov K, Chen J, Rbaibi Y, Oberdick D, Tjon-Kon-Sang S, et al. (2005) TRP-ML1 is a lysosomal monovalent cation channel that undergoes proteolytic cleavage. J Biol Chem 280: 43218–43223.
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