Genomewide Profiling of Rapamycin Sensitivity in Saccharomyces cerevisiae on Synthetic Medium |
Chang, Yeon-Ji
(School of Biological Sciences, and Research Center for Functional Cellulomics, Institute of Microbiology, Seoul National University)
Shin, Chun-Shik (School of Biological Sciences, and Research Center for Functional Cellulomics, Institute of Microbiology, Seoul National University) Han, Dong-Hun (Korea Science Academy) Kim, Ji-Yun (Korea Science Academy) Kim, Kang-In (Korea Science Academy) Kwon, Yong-Min (Korea Science Academy) Huh, Won-Ki (School of Biological Sciences, and Research Center for Functional Cellulomics, Institute of Microbiology, Seoul National University) |
1 | Wu, J., Tolstykh, T., Lee, J., Boyd, K., Stock, J.B., and Broach, J.R. (2000). Carboxyl methylation of the phosphoprotein phosphatase 2A catalytic subunit promotes its functional association with regulatory subunits in vivo. EMBO J. 19, 5672-5681. DOI |
2 | Xie, M.W., Jin, F., Hwang, H., Hwang, S., Anand, V., Duncan, M.C., and Huang, J. (2005). Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method. Proc. Natl. Acad. Sci. USA 102, 7215-7220. DOI |
3 | Rohde, J., Heitman, J., and Cardenas, M.E. (2001). The TOR kinases link nutrient sensing to cell growth. J. Biol. Chem. 276, 9583-9586. DOI |
4 | Rohde, J.R., Campbell, S., Zurita-Martinez, S.A., Cutler, N.S., Ashe, M., and Cardenas, M.E. (2004). TOR controls transcriptional and translational programs via Sap-Sit4 protein phosphatase signaling effectors. Mol. Cell Biol. 24, 8332-8341. DOI |
5 | Sherman, F. (2002). Getting started with yeast. Methods Enzymol 350, 3-41. DOI |
6 | Snowdon, C., Hlynialuk, C., and van der Merwe, G. (2008). Components of the Vid30c are needed for the rapamycin-induced degradation of the high-affinity hexose transporter Hxt7p in Saccharomyces cerevisiae. FEMS Yeast Res. 8, 204-216. DOI |
7 | Takeda, M., Chen, W.J., Saltzgaber, J., and Douglas, M.G. (1986). Nuclear genes encoding the yeast mitochondrial ATPase complex. Analysis of ATP1 coding the F1-ATPase alpha-subunit and its assembly. J. Biol. Chem. 261, 15126-15133. |
8 | von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. (2003). STRING: a database of predicted functional associations between proteins. Nucl. Acids Res. 31, 258-261. DOI ScienceOn |
9 | Weinberger, M., Mesquita, A., Caroll, T., Marks, L., Yang, H., Zhang, Z., Ludovico, P., and Burhans, W.C. (2010). Growth signaling promotes chronological aging in budding yeast by inducing superoxide anions that inhibit quiescence. Aging (Albany NY) 2, 709-726. DOI |
10 | Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., El Bakkoury, M., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Liebundguth, N., Lockhart, D.J., Lucau-Danila, A., Lussier, M., M'Rabet, N., Menard, P., Mittmann, M., Pai, C., Rebischung, C., Revuelta, J.L., Riles, L., Roberts, C.J., Ross-MacDonald, P., Scherens, B., Snyder, M., Sookhai-Mahadeo, S., Storms, R.K., Veronneau, S., Voet, M., Volckaert, G., Ward, T.R., Wysocki, R., Yen, G.S., Yu, K., Zimmermann, K., Philippsen, P., Johnston, M., and Davis, R.W. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906. DOI |
11 | Koltin, Y., Faucette, L., Bergsma, D.J., Levy, M.A., Cafferkey, R., Koser, P.L., Johnson, R.K., and Livi, G.P. (1991). Rapamycin sensitivity in Saccharomyces cerevisiae is mediated by a peptidyl-prolyl cis-trans isomerase related to human FK506-binding protein. Mol. Cell Biol. 11, 1718-1723. DOI |
12 | Kaeberlein, M., Powers, R.W., 3rd, Steffen, K.K., Westman, E.A., Hu, D., Dang, N., Kerr, E.O., Kirkland, K.T., Fields, S., and Kennedy, B.K. (2005). Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 310, 1193-1196. DOI |
13 | 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. DOI |
14 | Kim, D.H., Sarbassov, D.D., Ali, S.M., King, J.E., Latek, R.R., Erdjument-Bromage, H., Tempst, P., and Sabatini, D.M. (2002). mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110, 163-175. DOI |
15 | Lastauskiene, E., and Citavicius, D. (2008). Influence of RAS genes on yeast Saccharomyces cerevisiae cell viability in acid environment. Biologija 54, 150-155. DOI |
16 | Leidel, S., Pedrioli, P.G., Bucher, T., Brost, R., Costanzo, M., Schmidt, A., Aebersold, R., Boone, C., Hofmann, K., and Peter, M. (2009). Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature 458, 228-232. DOI |
17 | Liu, Z., and Butow, R.A. (2006). Mitochondrial retrograde signaling. Annu. Rev. Genet. 40, 159-185. DOI |
18 | Loewith, R., Jacinto, E., Wullschleger, S., Lorberg, A., Crespo, J.L., Bonenfant, D., Oppliger, W., Jenoe, P., and Hall, M.N. (2002). Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol. Cell 10, 457-468. DOI |
19 | Parsons, A.B., Brost, R.L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G.W., Kane, P.M., Hughes, T.R., and Boone, C. (2004). Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22, 62-69. DOI |
20 | Mayer, C., and Grummt, I. (2006). Ribosome biogenesis and cell growth: mTOR coordinates transcription by all three classes of nuclear RNA polymerases. Oncogene 25, 6384-6391. DOI |
21 | Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A.P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K.D., Flaherty, P., Foury, F., Garfinkel, D.J., Gerstein, M., Gotte, D., Guldener, U., Hegemann, J.H., Hempel, S., Herman, Z., Jaramillo, D.F., Kelly, D.E., Kelly, S.L., Kotter, P., LaBonte, D., Lamb, D.C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi, S.L., Revuelta, J.L., Roberts, C.J., Rose, M., Ross-Macdonald, P., Scherens, B., Schimmack, G., Shafer, B., Shoemaker, D.D., Sookhai-Mahadeo, S., Storms, R.K., Strathern, J.N., Valle, G., Voet, M., Volckaert, G., Wang, C.Y., Ward, T.R., Wilhelmy, J., Winzeler, E.A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J.D., Snyder, M., Philippsen, P., Davis, R.W., and Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391. DOI |
22 | Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C., Avruch, J., and Yonezawa, K. (2002). Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177-189. DOI |
23 | Heitman, J., Movva, N.R., Hiestand, P.C., and Hall, M.N. (1991). FK 506-binding protein proline rotamase is a target for the immunosuppressive agent FK 506 in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88, 1948-1952. DOI |
24 | Huber, A., Bodenmiller, B., Uotila, A., Stahl, M., Wanka, S., Gerrits, B., Aebersold, R., and Loewith, R. (2009). Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23, 1929-1943. DOI |
25 | Abe, F., and Minegishi, H. (2008). Global screening of genes essential for growth in high-pressure and cold environments: searching for basic adaptive strategies using a yeast deletion library. Genetics 178, 851-872. DOI |
26 | Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S., and O'Shea, E.K. (2003). Global analysis of protein localization in budding yeast. Nature 425, 686-691. DOI |
27 | Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P., and von Mering, C. (2009). STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucl. Acids Res. 37, D412-416. DOI |
28 | Kaeberlein, M., and Guarente, L. (2002). Saccharomyces cerevisiae MPT5 and SSD1 function in parallel pathways to promote cell wall integrity. Genetics 160, 83-95. |
29 | Beck, T., and Hall, M.N. (1999). The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402, 689-692. DOI |
30 | 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. DOI |
31 | Chan, T.F., Carvalho, J., Riles, L., and Zheng, X.F. (2000). A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc. Natl. Acad. Sci. USA 97, 13227-13232. DOI |
32 | Fournier, M.L., Paulson, A., Pavelka, N., Mosley, A.L., Gaudenz, K., Bradford, W.D., Glynn, E., Li, H., Sardiu, M.E., Fleharty, B., Seidel, C., Florens, L., and Washburn, M.P. (2010). Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol. Cell Proteomics 9, 271-284. DOI |
33 | Di Como, C.J., and Arndt, K.T. (1996). Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev. 10, 1904-1916. DOI |
34 | Dudley, A.M., Janse, D.M., Tanay, A., Shamir, R., and Church, G.M. (2005). A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Syst. Biol. 1, 2005.0001. |
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