Whi2: a new player in amino acid sensing

  • Xinchen TengEmail author
  • J. Marie HardwickEmail author


A critical function of human, yeast, and bacterial cells is the ability to sense and respond to available nutrients such as glucose and amino acids. Cells must also detect declining nutrient levels to adequately prepare for starvation conditions by inhibiting cell growth and activating autophagy. The evolutionarily conserved protein complex TORC1 regulates these cellular responses to nutrients, and in particular to amino acid availability. Recently, we found that yeast Whi2 (Saccharomyces cerevisiae) and a human counterpart, KCTD11, that shares a conserved BTB structural domain, are required to suppress TORC1 activity under low amino acid conditions. Using yeast, the mechanisms were more readily dissected. Unexpectedly, Whi2 suppresses TORC1 activity independently of the well-known SEACIT–GTR pathway, analogous to the GATOR1–RAG pathway in mammals. Instead, Whi2 requires the plasma membrane-associated phosphatases Psr1 and Psr2, which were known to bind Whi2, although their role was unknown. Yeast WHI2 was previously reported to be involved in regulating several fundamental cellular processes including cell cycle arrest, general stress responses, the Ras–cAMP–PKA pathway, autophagy, and mitophagy, and to be frequently mutated in the yeast knockout collections and in genome evolution studies. Most of these observations are likely explained by the ability of Whi2 to inhibit TORC1. Thus, understanding the function of yeast Whi2 will provide deeper insights into the disease-related KCTD family proteins and the pathogenesis of plant and human fungal infections.


Whi2 TORC1 Amino acid sensing RAG/GTR-independent KCTD KCTD11 



Supported by the National Natural Science Foundation of China 31401197 and Jiangsu Key Laboratory of Neuropsychiatric Diseases BM2013003 to X. T., and National Institutes of Health USA Grants R01NS083373 and R01GM077875, and the Wendy Klag Center to J. M. H.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Bachmann RA, Kim JH, Wu AL, Park IH, Chen J (2006) A nuclear transport signal in mammalian target of rapamycin is critical for its cytoplasmic signaling to S6 kinase 1. J Biol Chem 281:7357–7363. CrossRefGoogle Scholar
  2. Beck T, Hall MN (1999) The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402:689–692. CrossRefGoogle Scholar
  3. 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. CrossRefGoogle Scholar
  4. Bockler S, Westermann B (2014) Mitochondrial ER contacts are crucial for mitophagy in yeast. Dev Cell 28:450–458. CrossRefGoogle Scholar
  5. Boeckstaens M, Llinares E, Van Vooren P, Marini AM (2014) The TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium transport protein. Nat Commun 5:3101. CrossRefGoogle Scholar
  6. Bonfils G, Jaquenoud M, Bontron S, Ostrowicz C, Ungermann C, De Virgilio C (2012) Leucyl-tRNA synthetase controls TORC1 via the EGO complex. Mol Cell 46:105–110. CrossRefGoogle Scholar
  7. Chen X, Wang G, Zhang Y, Dayhoff-Brannigan M, Diny NL, Zhao M, He G, Sing CN, Metz KA, Stolp ZD, Aouacheria A, Cheng WC, Hardwick JM, Teng X (2018) Whi2 is a conserved negative regulator of TORC1 in response to low amino acids. PLoS Genet 14:e1007592. CrossRefGoogle Scholar
  8. Cheng WC, Teng X, Park HK, Tucker CM, Dunham MJ, Hardwick JM (2008) Fis1 deficiency selects for compensatory mutations responsible for cell death and growth control defects. Cell Death Differ 15:1838–1846. CrossRefGoogle Scholar
  9. Comyn SA, Flibotte S, Mayor T (2017) Recurrent background mutations in WHI2 impair proteostasis and degradation of misfolded cytosolic proteins in Saccharomyces cerevisiae. Sci Rep 7:4183. CrossRefGoogle Scholar
  10. Das S, Samant RS, Shevde LA (2013) Nonclassical activation of Hedgehog signaling enhances multidrug resistance and makes cancer cells refractory to Smoothened-targeting Hedgehog inhibition. J Biol Chem 288:11824–11833. CrossRefGoogle Scholar
  11. De Virgilio C, Loewith R (2006) Cell growth control: little eukaryotes make big contributions. Oncogene 25:6392–6415. CrossRefGoogle Scholar
  12. De Smaele E, Di Marcotullio L, Ferretti E, Screpanti I, Alesse E, Gulino A (2004) Chromosome 17p deletion in human medulloblastoma: a missing checkpoint in the Hedgehog pathway. Cell cycle 3:1263–1266. CrossRefGoogle Scholar
  13. Desai BN, Myers BR, Schreiber SL (2002) FKBP12-rapamycin-associated protein associates with mitochondria and senses osmotic stress via mitochondrial dysfunction. Proc Natl Acad Sci USA 99:4319–4324. CrossRefGoogle Scholar
  14. Di Marcotullio L, Ferretti E, De Smaele E, Argenti B, Mincione C, Zazzeroni F, Gallo R, Masuelli L, Napolitano M, Maroder M, Modesti A, Giangaspero F, Screpanti I, Alesse E, Gulino A (2004) REN(KCTD11) is a suppressor of Hedgehog signaling and is deleted in human medulloblastoma. Proc Natl Acad Sci USA 101:10833–10838. CrossRefGoogle Scholar
  15. Dokudovskaya S, Rout MP (2015) SEA you later alli-GATOR—a dynamic regulator of the TORC1 stress response pathway. J Cell Sci 128:2219–2228. CrossRefGoogle Scholar
  16. Drenan RM, Liu X, Bertram PG, Zheng XF (2004) FKBP12–rapamycin-associated protein or mammalian target of rapamycin (FRAP/mTOR) localization in the endoplasmic reticulum and the Golgi apparatus. J Biol Chem 279:772–778. CrossRefGoogle Scholar
  17. Ejzykowicz DE, Locken KM, Ruiz FJ, Manandhar SP, Olson DK, Gharakhanian E (2017) Hygromycin B hypersensitive (hhy) mutants implicate an intact trans-Golgi and late endosome interface in efficient Tor1 vacuolar localization and TORC1 function. Curr Genet 63:531–551. CrossRefGoogle Scholar
  18. Fannjiang Y, Cheng WC, Lee SJ, Qi B, Pevsner J, McCaffery JM, Hill RB, Basanez G, Hardwick JM (2004) Mitochondrial fission proteins regulate programmed cell death in yeast. Genes Dev 18:2785–2797. CrossRefGoogle Scholar
  19. Goberdhan DC, Wilson C, Harris AL (2016) Amino acid sensing by mTORC1: intracellular transporters mark the spot. Cell Metab 23:580–589. CrossRefGoogle Scholar
  20. Gonzalez A, Hall MN (2017) Nutrient sensing and TOR signaling in yeast and mammals. EMBO J 36:397–408. CrossRefGoogle Scholar
  21. Han JM, Jeong SJ, Park MC, Kim G, Kwon NH, Kim HK, Ha SH, Ryu SH, Kim S (2012) Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149:410–424. CrossRefGoogle Scholar
  22. Harata K, Nishiuchi T, Kubo Y (2016) Colletotrichum orbiculare WHI2, a yeast stress-response regulator homolog, controls the biotrophic stage of hemibiotrophic infection through TOR signaling. Mol Plant Microbe Interact MPMI 29:468–483. CrossRefGoogle Scholar
  23. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183. CrossRefGoogle Scholar
  24. Hong J, Gresham D (2014) Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments. PLoS Genet 10:e1004041. CrossRefGoogle Scholar
  25. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98:4569–4574. CrossRefGoogle Scholar
  26. Ivanovska I, Hardwick JM (2005) Viruses activate a genetically conserved cell death pathway in a unicellular organism. J Cell Biol 170:391–399. CrossRefGoogle Scholar
  27. Jewell JL, Kim YC, Russell RC, Yu FX, Park HW, Plouffe SW, Tagliabracci VS, Guan KL (2015) Metabolism. Differential regulation of mTORC1 by leucine and glutamine. Science 347:194–198. CrossRefGoogle Scholar
  28. Jung CH, Ro SH, Cao J, Otto NM, Kim DH (2010) mTOR regulation of autophagy. FEBS Lett 584:1287–1295. CrossRefGoogle Scholar
  29. Kaida D, Yashiroda H, Toh-e A, Kikuchi Y (2002) Yeast Whi2 and Psr1-phosphatase form a complex and regulate STRE-mediated gene expression. Genes Cells Devot Mol Cell Mech 7:543–552CrossRefGoogle Scholar
  30. 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. CrossRefGoogle Scholar
  31. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O’Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–643. CrossRefGoogle Scholar
  32. Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, Desai MM (2013) Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500:571–574. CrossRefGoogle Scholar
  33. Leadsham JE, Miller K, Ayscough KR, Colombo S, Martegani E, Sudbery P, Gourlay CW (2009) Whi2p links nutritional sensing to actin-dependent Ras–Camp–PKA regulation and apoptosis in yeast. J Cell Sci 122:706–715. CrossRefGoogle Scholar
  34. Mao K, Wang K, Liu X, Klionsky DJ (2013) The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev Cell 26:9–18. CrossRefGoogle Scholar
  35. Mendl N, Occhipinti A, Muller M, Wild P, Dikic I, Reichert AS (2011) Mitophagy in yeast is independent of mitochondrial fission and requires the stress response gene WHI2. J Cell Sci 124:1339–1350. CrossRefGoogle Scholar
  36. Metcalfe C, Alicke B, Crow A, Lamoureux M, Dijkgraaf GJ, Peale F, Gould SE, de Sauvage FJ (2013) PTEN loss mitigates the response of medulloblastoma to Hedgehog pathway inhibition. Cancer Res 73:7034–7042. CrossRefGoogle Scholar
  37. Metz KA, Teng X, Coppens I, Lamb HM, Wagner BE, Rosenfeld JA, Chen X, Zhang Y, Kim HJ, Meadow ME, Wang TS, Haberlandt ED, Anderson GW, Leshinsky-Silver E, Bi W, Markello TC, Pratt M, Makhseed N, Garnica A, Danylchuk NR, Burrow TA, Jayakar P, McKnight D, Agadi S, Gbedawo H, Stanley C, Alber M, Prehl I, Peariso K, Ong MT, Mordekar SR, Parker MJ, Crooks D, Agrawal PB, Berry GT, Loddenkemper T, Yang Y, Maegawa GHB, Aouacheria A, Markle JG, Wohlschlegel JA, Hartman AL, Hardwick JM (2018) KCTD7 deficiency defines a distinct neurodegenerative disorder with a conserved autophagy-lysosome defect. Ann Neurol. Google Scholar
  38. Michel AH, Hatakeyama R, Kimmig P, Arter M, Peter M, Matos J, De Virgilio C, Kornmann B (2017) Functional mapping of yeast genomes by saturated transposition. eLife. Google Scholar
  39. Moreno-Torres M, Jaquenoud M, De Virgilio C (2015) TORC1 controls G1-S cell cycle transition in yeast via Mpk1 and the greatwall kinase pathway. Nat Commun 6:8256. CrossRefGoogle Scholar
  40. Panchaud N, Peli-Gulli MP, De Virgilio C (2013a) Amino acid deprivation inhibits TORC1 through a GTPase-activating protein complex for the Rag family GTPase Gtr1. Sci Signal 6:ra42. CrossRefGoogle Scholar
  41. Panchaud N, Peli-Gulli MP, De Virgilio C (2013b) SEACing the GAP that nEGOCiates TORC1 activation: evolutionary conservation of Rag GTPase regulation. Cell Cycle 12:2948–2952. CrossRefGoogle Scholar
  42. Parzych KR, Klionsky DJ (2014) An overview of autophagy: morphology, mechanism, and regulation. Antioxidants Redox Signal 20:460–473. CrossRefGoogle Scholar
  43. Peli-Gulli MP, Sardu A, Panchaud N, Raucci S, De Virgilio C (2015) Amino acids stimulate TORC1 through Lst4–Lst7, a GTPase-activating protein complex for the Rag family GTPase Gtr2. Cell Rep 13:1–7. CrossRefGoogle Scholar
  44. Radcliffe P, Trevethick J, Tyers M, Sudbery P (1997) Deregulation of CLN1 and CLN2 in the Saccharomyces cerevisiae whi2 mutant. Yeast 13:707–715 doCrossRefGoogle Scholar
  45. Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM (2008) The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320:1496–1501. CrossRefGoogle Scholar
  46. 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. CrossRefGoogle Scholar
  47. Siniossoglou S, Hurt EC, Pelham HR (2000) Psr1p/Psr2p, two plasma membrane phosphatases with an essential DXDX(T/V) motif required for sodium stress response in yeast. J Biol Chem 275:19352–19360. CrossRefGoogle Scholar
  48. Skoblov M, Marakhonov A, Marakasova E, Guskova A, Chandhoke V, Birerdinc A, Baranova A (2013) Protein partners of KCTD proteins provide insights about their functional roles in cell differentiation and vertebrate development. BioEssays News Rev Mol Cell Dev Biol 35:586–596. CrossRefGoogle Scholar
  49. Stecca B, Mas C, Clement V, Zbinden M, Correa R, Piguet V, Beermann F, Ruiz IAA (2007) Melanomas require HEDGEHOG–GLI signaling regulated by interactions between GLI1 and the RAS–MEK/AKT pathways. Proc Natl Acad Sci USA 104:5895–5900. CrossRefGoogle Scholar
  50. Stracka D, Jozefczuk S, Rudroff F, Sauer U, Hall MN (2014) Nitrogen source activates TOR (target of rapamycin) complex 1 via glutamine and independently of Gtr/Rag proteins. J Biol Chem 289:25010–25020. CrossRefGoogle Scholar
  51. Sudbery PE, Goodey AR, Carter BL (1980) Genes which control cell proliferation in the yeast Saccharomyces cerevisiae. Nature 288:401–404CrossRefGoogle Scholar
  52. Sutter BM, Wu X, Laxman S, Tu BP (2013) Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell 154:403–415. CrossRefGoogle Scholar
  53. Szamecz B, Boross G, Kalapis D, Kovacs K, Fekete G, Farkas Z, Lazar V, Hrtyan M, Kemmeren P, Groot Koerkamp MJ, Rutkai E, Holstege FC, Papp B, Pal C (2014) The genomic landscape of compensatory evolution. PLoS Biol 12:e1001935. CrossRefGoogle Scholar
  54. Tanigawa M, Maeda T (2017) An in vitro TORC1 kinase assay that recapitulates the gtr-independent glutamine-responsive TORC1 activation mechanism on yeast vacuoles. Mol Cell Biol. Google Scholar
  55. Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM (2013) Genome-wide consequences of deleting any single gene. Mol Cell 52:485–494. CrossRefGoogle Scholar
  56. Teng X, Yau E, Sing C, Hardwick JM (2018) Whi2 signals low leucine availability to halt yeast growth and cell death. FEMS Yeast Res. Google Scholar
  57. Thomas JD, Zhang YJ, Wei YH, Cho JH, Morris LE, Wang HY, Zheng XF (2014) Rab1A is an mTORC1 activator and a colorectal oncogene. Cancer Cell 26:754–769. CrossRefGoogle Scholar
  58. Timpano H, Chan Ho Tong L, Gautier V, Lalucque H, Silar P (2016) The PaPsr1 and PaWhi2 genes are members of the regulatory network that connect stationary phase to mycelium differentiation and reproduction in Podospora anserina. Fungal Genet Biol FG & B 94:1–10. CrossRefGoogle Scholar
  59. Tong R, Yang B, Xiao H, Peng C, Hu W, Weng X, Cheng S, Du C, Lv Z, Ding C, Zhou L, Xie H, Wu J, Zheng S (2017) KCTD11 inhibits growth and metastasis of hepatocellular carcinoma through activating Hippo signaling. Oncotarget 8:37717–37729. Google Scholar
  60. Ukai H, Araki Y, Kira S, Oikawa Y, May AI, Noda T (2018) Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane. PLoS Genet 14:e1007334. CrossRefGoogle Scholar
  61. van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Usaj MM, Pechlaner M, Takar M, Usaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C (2016) Exploring genetic suppression interactions on a global scale. Science. Google Scholar
  62. Wei L, Xu Z (2011) Cross-signaling among phosphinositide-3 kinase, mitogen-activated protein kinase and sonic hedgehog pathways exists in esophageal cancer. Int J Cancer 129:275–284. CrossRefGoogle Scholar
  63. Wen X, Klionsky DJ (2016) An overview of macroautophagy in yeast. J Mol Biol 428:1681–1699. CrossRefGoogle Scholar
  64. Wolfson RL, Sabatini DM (2017) The dawn of the age of amino acid sensors for the mTORC1 pathway. Cell Metab 26:301–309. CrossRefGoogle Scholar
  65. Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O, Ben-Dor S, Schutze C, Wiedemann N, Knop M, Khmelinskii A, Schuldiner M (2016) One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods 13:371–378. CrossRefGoogle Scholar
  66. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi AL, Tavernier J, Hill DE, Vidal M (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322:104–110. CrossRefGoogle Scholar
  67. Zazzeroni F, Nicosia D, Tessitore A, Gallo R, Verzella D, Fischietti M, Vecchiotti D, Ventura L, Capece D, Gulino A, Alesse E (2014) KCTD11 tumor suppressor gene expression is reduced in prostate adenocarcinoma. BioMed Res Int 2014:380398. CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
  2. 2.W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins University Bloomberg School of Public HealthBaltimoreUSA

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