Skip to main content

Nutritional Control of Cell Growth via TOR Signaling in Budding Yeast

  • Protocol
  • First Online:
Yeast Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 759))

Abstract

Cell growth is highly regulated and its deregulation is related to many human diseases such as cancer. Nutritional cues stimulate cell growth through modulation of TOR (target of rapamycin) signaling pathway. At the center of this pathway is a large serine/threonine protein kinase TOR, which forms two distinct functional complexes TORC1 and TORC2 in a cell. TORC1 senses the environmental nutrient quality/quantity and transmits the growth signals to multiple effectors to regulate a broad spectrum of biological processes including translation initiation, ribosome biogenesis, autophagy, nutrient uptake, and metabolism. By using budding yeast as a model, recent studies began to elucidate the complexity of the TOR signaling pathway.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Hall, M. N. (1996) The TOR signalling pathway and growth control in yeast. Biochem. Soc. Trans. 24, 234–239.

    PubMed  CAS  Google Scholar 

  2. Thomas, G., and Hall, M. N. (1997) TOR signalling and control of cell growth. Curr. Opin. Cell Biol. 9, 782–787.

    Article  PubMed  CAS  Google Scholar 

  3. Tsang, C. K., Qi, H., Liu, L. F., and Zheng, X. F. (2007) Targeting mammalian target of rapamycin (mTOR) for health and diseases. Drug Discov. Today 12, 112–124.

    Article  PubMed  CAS  Google Scholar 

  4. De Virgilio, C., and Loewith, R. (2006) Cell growth control: little eukaryotes make big contributions. Oncogene 25, 6392–6415.

    Article  PubMed  Google Scholar 

  5. Tsang, C. K., and Zheng, X. F. (2007) TOR-in(g) the nucleus. Cell Cycle 6, 25–29.

    Article  PubMed  CAS  Google Scholar 

  6. Keith, C. T., and Schreiber, S. L. (1995) PIK-related kinases: DNA repair, recombination, and cell cycle checkpoints. Science 270, 50–51.

    Article  PubMed  CAS  Google Scholar 

  7. Wullschleger, S., Loewith, R., and Hall, M. N. (2006) TOR signaling in growth and metabolism. Cell 124, 471–484.

    Article  PubMed  CAS  Google Scholar 

  8. Zheng, X. F., Florentino, D., Chen, J., Crabtree, G. R., and Schreiber, S. L. (1995) TOR kinase domains are required for two distinct functions, only one of which is inhibited by rapamycin. Cell 82, 121–130.

    Article  PubMed  CAS  Google Scholar 

  9. Loewith, R., Jacinto, E., Wullschleger, S., et al. (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol. Cell 10, 457–468.

    Article  PubMed  CAS  Google Scholar 

  10. Barbet, N. C., Schneider, U., Helliwell, S. B., Stansfield, I., Tuite, M. F., and Hall, M. N. (1996) TOR controls translation initiation and early G1 progression in yeast. Mol. Biol. Cell 7, 25–42.

    PubMed  CAS  Google Scholar 

  11. Hay, N., and Sonenberg, N. (2004) Upstream and downstream of mTOR. Genes Dev. 18, 1926–1945.

    Article  PubMed  CAS  Google Scholar 

  12. Urban, J., Soulard, A., Huber, A., et al. (2007) Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol. Cell 26, 663–674.

    Article  PubMed  CAS  Google Scholar 

  13. Cosentino, G. P., Schmelzle, T., Haghighat, A., Helliwell, S. B., Hall, M. N., and Sonenberg, N. (2000) Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 20, 4604–4613.

    Article  PubMed  CAS  Google Scholar 

  14. Cherkasova, V. A., and Hinnebusch, A. G. (2003) Translational control by TOR and TAP42 through dephosphorylation of eIF2alpha kinase GCN2. Genes Dev. 17, 859–872.

    Article  PubMed  CAS  Google Scholar 

  15. Hardwick, J. S., Kuruvilla, F. G., Tong, J. K., Shamji, A. F., and Schreiber, S. L. (1999) Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc. Natl. Acad. Sci. USA 96, 14866–14870.

    Article  PubMed  CAS  Google Scholar 

  16. Powers, T., and Walter, P. (1999) Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol. Biol. Cell 10, 987–1000.

    PubMed  CAS  Google Scholar 

  17. Wei, Y., Tsang, C. K., and Zheng, X. F. (2009) Mechanisms of regulation of RNA polymerase III-dependent transcription by TORC1. EMBO J. 28, 2220–2230.

    Article  PubMed  CAS  Google Scholar 

  18. Li, H., Tsang, C. K., Watkins, M., Bertram, P. G., and Zheng, X. F. (2006) Nutrient regulates Tor1 nuclear localization and association with rDNA promoter. Nature 442, 1058–1061.

    Article  PubMed  CAS  Google Scholar 

  19. Zaragoza, D., Ghavidel, A., Heitman, J., and Schultz, M. C. (1998) Rapamycin induces the G0 program of transcriptional repression in yeast by interfering with the TOR signaling pathway. Mol. Cell. Biol. 18, 4463–4470.

    PubMed  CAS  Google Scholar 

  20. Warner, J. R. (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437–440.

    Article  PubMed  CAS  Google Scholar 

  21. Cardenas, M. E., Cutler, N. S., Lorenz, M. C., Di Como, C. J., and Heitman, J. (1999) The TOR signaling cascade regulates gene expression in response to nutrients. Genes Dev. 13, 3271–3279.

    Article  PubMed  CAS  Google Scholar 

  22. Moss, T., and Stefanovsky, V. Y. (2002) At the center of eukaryotic life. Cell 109, 545–548.

    Article  PubMed  CAS  Google Scholar 

  23. Jorgensen, P., Rupes, I., Sharom, J. R., Schneper, L., Broach, J. R., and Tyers, M. (2004) A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18, 2491–2505.

    Article  PubMed  CAS  Google Scholar 

  24. Martin, D. E., Soulard, A., and Hall, M. N. (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119, 969–979.

    Article  PubMed  CAS  Google Scholar 

  25. Lempiainen, H., Uotila, A., Urban, J., et al. (2009) Sfp1 interaction with TORC1 and Mrs6 reveals feedback regulation on TOR signaling. Mol. Cell 33, 704–716.

    Article  PubMed  CAS  Google Scholar 

  26. Pascual-Ahuir, A., and Proft, M. (2007) The Sch9 kinase is a chromatin-associated transcriptional activator of osmostress-responsive genes. EMBO J. 26, 3098–3108.

    Article  PubMed  CAS  Google Scholar 

  27. Rohde, J. R., and Cardenas, M. E. (2003) The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. Mol. Cell. Biol. 23, 629–635.

    Article  PubMed  CAS  Google Scholar 

  28. Humphrey, E. L., Shamji, A. F., Bernstein, B. E., and Schreiber, S. L. (2004) Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem. Biol. 11, 295–299.

    Article  PubMed  CAS  Google Scholar 

  29. Claypool, J. A., French, S. L., Johzuka, K., et al. (2004) Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol. Biol. Cell 15, 946–956.

    Article  PubMed  CAS  Google Scholar 

  30. Mayer, C., Zhao, J., Yuan, X., and Grummt, I. (2004) mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev. 18, 423–434.

    Article  PubMed  CAS  Google Scholar 

  31. Tsang, C. K., Bertram, P. G., Ai, W., Drenan, R., and Zheng, X. F. (2003) Chromatin-mediated regulation of nucleolar structure and RNA Pol I localization by TOR. EMBO J. 22, 6045–6056.

    Article  PubMed  CAS  Google Scholar 

  32. Yorimitsu, T., and Klionsky, D. J. (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ. 12(Suppl 2), 1542–1552.

    Article  PubMed  CAS  Google Scholar 

  33. Kamada, Y., Sekito, T., and Ohsumi, Y. (2004) Autophagy in yeast: a TOR-mediated response to nutrient starvation. Curr. Top. Microbiol. Immunol. 279, 73–84.

    Article  PubMed  CAS  Google Scholar 

  34. Kamada, Y., Funakoshi, T., Shintani, T., Nagano, K., Ohsumi, M., and Ohsumi, Y. (2000) Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J. Cell Biol. 150, 1507–1513.

    Article  PubMed  CAS  Google Scholar 

  35. Jung, C. H., Jun, C. B., Ro, S. H., et al. (2009) ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol. Biol. Cell 20, 1992–2003.

    Article  PubMed  CAS  Google Scholar 

  36. Chan, T. F., Bertram, P. G., Ai, W., and Zheng, X. F. (2001) Regulation of APG14 expression by the GATA-type transcription factor Gln3p. J. Biol. Chem. 276, 6463–6467.

    Article  PubMed  CAS  Google Scholar 

  37. Magasanik, B., and Kaiser, C. A. (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290, 1–18.

    Article  PubMed  CAS  Google Scholar 

  38. Ozcan, S., and Johnston, M. (1999) Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63, 554–569.

    PubMed  CAS  Google Scholar 

  39. Schmidt, A., Beck, T., Koller, A., Kunz, J., and Hall, M. N. (1998) The TOR nutrient signalling pathway phosphorylates NPR1 and inhibits turnover of the tryptophan permease. EMBO J. 17, 6924–6931.

    Article  PubMed  CAS  Google Scholar 

  40. De Craene, J. O., Soetens, O., and Andre, B. (2001) The Npr1 kinase controls biosynthetic and endocytic sorting of the yeast Gap1 permease. J. Biol. Chem. 276, 43939–43948.

    Article  PubMed  Google Scholar 

  41. Carvalho, J., and Zheng, X. F. (2003) Domains of Gln3p interacting with karyopherins, Ure2p, and the target of rapamycin protein. J. Biol. Chem. 278, 16878–16886.

    Article  PubMed  CAS  Google Scholar 

  42. Bertram, P. G., Choi, J. H., Carvalho, J., et al. (2000) Tripartite regulation of Gln3p by TOR, Ure2p, and phosphatases. J. Biol. Chem. 275, 35727–35733.

    Article  PubMed  CAS  Google Scholar 

  43. Kuruvilla, F. G., Shamji, A. F., and Schreiber, S. L. (2001) Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc. Natl. Acad. Sci. USA 98, 7283–7288.

    Article  PubMed  CAS  Google Scholar 

  44. Liu, Z., and Butow, R. A. (2006) Mitochondrial retrograde signaling. Annu. Rev. Genet. 40, 159–185.

    Article  PubMed  CAS  Google Scholar 

  45. Beck, T., and Hall, M. N. (1999) The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402, 689–692.

    Article  PubMed  CAS  Google Scholar 

  46. Mayordomo, I., Estruch, F., and Sanz, P. (2002) Convergence of the target of rapamycin and the Snf1 protein kinase pathways in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes. J. Biol. Chem. 277, 35650–35656.

    Article  PubMed  CAS  Google Scholar 

  47. Pedruzzi, I., Dubouloz, F., Cameroni, E., et al. (2003) TOR and PKA signaling pathways converge on the protein kinase Rim15 to control entry into G0. Mol. Cell 12, 1607–1613.

    Article  PubMed  CAS  Google Scholar 

  48. Swinnen, E., Wanke, V., Roosen, J., et al. (2006) Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae. Cell Div. 1, 3.

    Article  PubMed  Google Scholar 

  49. Wanke, V., Cameroni, E., Uotila, A., et al. (2008) Caffeine extends yeast lifespan by targeting TORC1. Mol. Microbiol. 69, 277–285.

    Article  PubMed  CAS  Google Scholar 

  50. De Wever, V., Reiter, W., Ballarini, A., Ammerer, G., and Brocard, C. (2005) A dual role for PP1 in shaping the Msn2-dependent transcriptional response to glucose starvation. EMBO J. 24, 4115–4123.

    Article  PubMed  Google Scholar 

  51. Goberdhan, D. C., Ogmundsdottir, M. H., Kazi, S., et al. (2009) Amino acid sensing and mTOR regulation: inside or out? Biochem. Soc. Trans. 37, 248–252.

    Article  PubMed  CAS  Google Scholar 

  52. Nicklin, P., Bergman, P., Zhang, B., et al. (2009) Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136, 521–534.

    Article  PubMed  CAS  Google Scholar 

  53. Schneper, L., Duvel, K., and Broach, J. R. (2004) Sense and sensibility: nutritional response and signal integration in yeast. Curr. Opin. Microbiol. 7, 624–630.

    Article  PubMed  CAS  Google Scholar 

  54. Dubouloz, F., Deloche, O., Wanke, V., Cameroni, E., and De Virgilio, C. (2005) The TOR and EGO protein complexes orchestrate microautophagy in yeast. Mol. Cell 19, 15–26.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to X.F. Steven Zheng .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Humana Press

About this protocol

Cite this protocol

Wei, Y., Zheng, X.S. (2011). Nutritional Control of Cell Growth via TOR Signaling in Budding Yeast. In: Castrillo, J., Oliver, S. (eds) Yeast Systems Biology. Methods in Molecular Biology, vol 759. Humana Press. https://doi.org/10.1007/978-1-61779-173-4_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-173-4_18

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-172-7

  • Online ISBN: 978-1-61779-173-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics