Abstract
In eukaryotic cells, cellular homeostasis requires that different organelles respond to intracellular as well as environmental signals and modulate their behavior as conditions demand. Understanding the molecular mechanisms required for these changes remains an outstanding goal. One such organelle is the lysosome/vacuole, which undergoes alterations in size and number in response to environmental and physiological stimuli. Changes in the morphology of this organelle are mediated in part by the equilibrium between fusion and fission processes. While the fusion of the yeast vacuole has been studied intensively, the regulation of vacuolar fission remains poorly characterized by comparison. In recent years, a number of studies have incorporated genome-wide visual screens and high-throughput microscopy to identify factors required for vacuolar fission in response to diverse cellular insults, including hyperosmotic and endoplasmic reticulum stress. Available evidence now demonstrates that the rapamycin-sensitive TOR network, a master regulator of cell growth, is required for vacuolar fragmentation in response to stress. Importantly, many of the genes identified in these studies provide new insights into potential links between the vacuolar fission machinery and TOR signaling. Together these advances both extend our understanding of the regulation of vacuolar fragmentation in yeast as well as underscore the role of analogous events in mammalian cells.
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References
Aronova S, Wedaman K, Anderson S, Yates J 3rd, Powers T (2007) Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in Saccharomyces cerevisiae. Mol Biol Cell 18:2779–2794
Baars TL, Petri S, Peters C, Mayer A (2007) Role of the V-ATPase in regulation of the vacuolar fission–fusion equilibrium. Mol Biol Cell 18:3873–3882
Baba M, Takeshige K, Baba N, Ohsumi Y (1994) Ultrastructural analysis of the autophagic process in yeast: detection of autophagosomes and their characterization. J Cell Biol 124:903–913
Bachhawat AK, Manolson MF, Murdock DG, Garman JD, Jones EW (1993) The VPH2 gene encodes a 25 kDa protein required for activity of the yeast vacuolar H(+)-ATPase. Yeast 9:175–184
Balderhaar HJ, Lachmann J, Yavavli E, Brocker C, Lurick A, Ungermann C (2013) The CORVET complex promotes tethering and fusion of Rab5/Vps21-positive membranes. Proc Natl Acad Sci USA 110:3823–3828
Banta LM, Robinson JS, Klionsky DJ, Emr SD (1988) Organelle assembly in yeast: characterization of yeast mutants defective in vacuolar biogenesis and protein sorting. J Cell Biol 107:1369–1383
Barbet NC, Schneider U, Helliwell SB, Stansfield I, Tuite MF, Hall MN (1996) TOR controls translation initiation and early G1 progression in yeast. Mol Biol Cell 7:25–42
Betz C, Hall MN (2013) Where is mTOR and what is it doing there? J Cell Biol 203:563–574
Binda M, Peli-Gulli MP, Bonfils G, Panchaud N, Urban J, Sturgill TW, Loewith R, De Virgilio C (2009) The Vam6 GEF controls TORC1 by activating the EGO complex. Mol Cell 35:563–573
Bonangelino CJ, Nau JJ, Duex JE, Brinkman M, Wurmser AE, Gary JD, Emr SD, Weisman LS (2002) Osmotic stress-induced increase of phosphatidylinositol 3,5-bisphosphate requires Vac14p, an activator of the lipid kinase Fab1p. J Cell Biol 156:1015–1028
Bridges D, Fisher K, Zolov SN, Xiong T, Inoki K, Weisman LS, Saltiel AR (2012a) Rab5 proteins regulate activation and localization of target of rapamycin complex 1. J Biol Chem 287:20913–20921
Bridges D, Ma JT, Park S, Inoki K, Weisman LS, Saltiel AR (2012b) Phosphatidylinositol 3,5-bisphosphate plays a role in the activation and subcellular localization of mechanistic target of rapamycin 1. Mol Biol Cell 23:2955–2962
Coonrod EM, Graham LA, Carpp LN, Carr TM, Stirrat L, Bowers K, Bryant NJ, Stevens TH (2013) Homotypic vacuole fusion in yeast requires organelle acidification and not the V-ATPase membrane domain. Dev Cell 27:462–468
Gao M, Kaiser CA (2006) A conserved GTPase-containing complex is required for intracellular sorting of the general amino-acid permease in yeast. Nat Cell Biol 8:657–667
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391
Gomes de Mesquita DS, van den Hazel HB, Bouwman J, Woldringh CL (1996) Characterization of new vacuolar segregation mutants, isolated by screening for loss of proteinase B self-activation. Eur J Cell Biol 71:237–247
Ho YH, Gasch AP (2015) Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 61:503–511
Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R (2009) Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev 23:1929–1943
Jiang Y (2016) Regulation of TORC1 by ubiquitin through non-covalent binding. Curr Genet. doi:10.1007/s00294-016-0581-7
Jin N, Mao K, Jin Y, Tevzadze G, Kauffman EJ, Park S, Bridges D, Loewith R, Saltiel AR, Klionsky DJ et al (2014) Roles for PI(3,5)P2 in nutrient sensing through TORC1. Mol Biol Cell 25:1171–1185
Kim A, Cunningham KW (2015) A LAPF/phafin1-like protein regulates TORC1 and lysosomal membrane permeabilization in response to endoplasmic reticulum membrane stress. Mol Biol Cell 26:4631–4645
Kim H, Kim A, Cunningham KW (2012) Vacuolar H+-ATPase (V-ATPase) promotes vacuolar membrane permeabilization and nonapoptotic death in stressed yeast. J Biol Chem 287:19029–19039
Kingsbury JM, Sen ND, Maeda T, Heitman J, Cardenas ME (2014) Endolysosomal membrane trafficking complexes drive nutrient-dependent TORC1 signaling to control cell growth in Saccharomyces cerevisiae. Genetics 196:1077–1089
Kirkegaard T, Jaattela M (2009) Lysosomal involvement in cell death and cancer. Biochim Biophys Acta 1793:746–754
Kuranda K, Leberre V, Sokol S, Palamarczyk G, Francois J (2006) Investigating the caffeine effects in the yeast Saccharomyces cerevisiae brings new insights into the connection between TOR, PKC and Ras/cAMP signalling pathways. Mol Microbiol 61:1147–1166
Li SC, Kane PM (2009) The yeast lysosome-like vacuole: endpoint and crossroads. Biochim Biophys Acta 1793:650–663
Li SC, Diakov TT, Xu T, Tarsio M, Zhu W, Couoh-Cardel S, Weisman LS, Kane PM (2014) The signaling lipid PI(3,5)P(2) stabilizes V(1)-V(o) sector interactions and activates the V-ATPase. Mol Biol Cell 25:1251–1262
Loewith R, Hall MN (2011) Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 189:1177–1201
Luzio JP, Pryor PR, Bright NA (2007) Lysosomes: fusion and function. Nat Rev Mol Cell Biol 8:622–632
Michaillat L, Mayer A (2013) Identification of genes affecting vacuole membrane fragmentation in Saccharomyces cerevisiae. PLoS One 8:e54160
Michaillat L, Baars TL, Mayer A (2012) Cell-free reconstitution of vacuole membrane fragmentation reveals regulation of vacuole size and number by TORC1. Mol Biol Cell 23:881–895
Murley A, Sarsam RD, Toulmay A, Yamada J, Prinz WA, Nunnari J (2015) Ltc1 is an ER-localized sterol transporter and a component of ER-mitochondria and ER-vacuole contacts. J Cell Biol 209(4):539–548. doi:10.1083/jcb.201502033
Okamura K, Kimata Y, Higashio H, Tsuru A, Kohno K (2000) Dissociation of Kar2p/BiP from an ER sensory molecule, Ire1p, triggers the unfolded protein response in yeast. Biochem Biophys Res Commun 279:445–450
Powers T, Walter P (1999) Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol Biol Cell 10:987–1000
Powis K, Zhang T, Panchaud N, Wang R, Virgilio CD, Ding J (2015) Crystal structure of the Ego1-Ego2-Ego3 complex and its role in promoting Rag GTPase-dependent TORC1 signaling. Cell Res 25:1043–1059
Reinke A, Anderson S, McCaffery JM, Yates J 3rd, Aronova S, Chu S, Fairclough S, Iverson C, Wedaman KP, Powers T (2004) TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae. J Biol Chem 279:14752–14762
Reinke A, Chen JC, Aronova S, Powers T (2006) Caffeine targets TOR complex I and provides evidence for a regulatory link between the FRB and kinase domains of Tor1p. J Biol Chem 281:31616–31626
Roberts P, Moshitch-Moshkovitz S, Kvam E, O’Toole E, Winey M, Goldfarb DS (2003) Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Mol Biol Cell 14:129–141
Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM (2010) Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141:290–303
Shaw JM, Wickner WT (1991) vac2: a yeast mutant which distinguishes vacuole segregation from Golgi-to-vacuole protein targeting. EMBO J 10:1741–1748
Sidrauski C, Walter P (1997) The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 90:1031–1039
Stauffer B, Powers T (2015) Target of rapamycin signaling mediates vacuolar fission caused by endoplasmic reticulum stress in Saccharomyces cerevisiae. Mol Biol Cell 26:4618–4630
Sturgill TW, Cohen A, Diefenbacher M, Trautwein M, Martin DE, Hall MN (2008) TOR1 and TOR2 have distinct locations in live cells. Eukaryot Cell 7:1819–1830
Suzuki T, Sugiyama M, Wakazono K, Kaneko Y, Harashima S (2012) Lactic-acid stress causes vacuolar fragmentation and impairs intracellular amino-acid homeostasis in Saccharomyces cerevisiae. J Biosci Bioeng 113:421–430
Takahara T, Maeda T (2012) Transient sequestration of TORC1 into stress granules during heat stress. Mol Cell 47:242–252
Urban J, Soulard A, Huber A, Lippman S, Mukhopadhyay D, Deloche O, Wanke V, Anrather D, Ammerer G, Riezman H et al (2007) Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 26:663–674
Wang YX, Zhao H, Harding TM, Gomes de Mesquita DS, Woldringh CL, Klionsky DJ, Munn AL, Weisman LS (1996) Multiple classes of yeast mutants are defective in vacuole partitioning yet target vacuole proteins correctly. Mol Biol Cell 7:1375–1389
Weisman LS (2003) Yeast vacuole inheritance and dynamics. Annu Rev Genet 37:435–460
Weisman LS, Emr SD, Wickner WT (1990) Mutants of Saccharomyces cerevisiae that block intervacuole vesicular traffic and vacuole division and segregation. Proc Natl Acad Sci USA 87:1076–1080
Zhang L, Sheng R, Qin Z (2009) The lysosome and neurodegenerative diseases. Acta Biochim Biophys Sin (Shanghai) 41:437–445
Zieger M, Mayer A (2012) Yeast vacuoles fragment in an asymmetrical two-phase process with distinct protein requirements. Mol Biol Cell 23:3438–3449
Zoncu R, Bar-Peled L, Efeyan A, Wang S, Sancak Y, Sabatini DM (2011) mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. Science 334:678–683
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This work was supported by the National Institutes of Health Grant GM086387 to Ted Powers.
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Communicated by M. Kupiec.
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Stauffer, B., Powers, T. Target of rapamycin signaling mediates vacuolar fragmentation. Curr Genet 63, 35–42 (2017). https://doi.org/10.1007/s00294-016-0616-0
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DOI: https://doi.org/10.1007/s00294-016-0616-0