Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis

Journal of Cell Biology

Volumn 181, Issue 2, 2008, Pages 281-292

  Saleem, Ramsey A ^a   Knoblach, Barbara ^b   Mast, Fred D ^b   Smith, Jennifer J ^a   Boyle, John ^a   Dobson, C Melissa ^b   Long O'Donnell, Rose ^a   Rachubinski, Richard A ^b   Aitchison, John D ^a,b  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL COENZYME A ACETYLTRANSFERASE; FATTY ACID; FUNGAL PROTEIN; GLUCOSE; GREEN FLUORESCENT PROTEIN; OLEIC ACID; PHOSPHATASE; PHOSPHOTRANSFERASE; PROTEIN PHO85P; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; CHIMERA; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME PHOSPHORYLATION; FUNGAL STRAIN; GENE EXPRESSION; GENE REPRESSION; GENOME; NONHUMAN; PEROXISOME; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; CELL ORGANELLE; DRUG EFFECT; GENE DELETION; GENE EXPRESSION REGULATION; GENETICS; REPORTER GENE; ULTRASTRUCTURE;

SACCHAROMYCES CEREVISIAE;

FATTY ACIDS; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; GENES, REPORTER; GENOME, FUNGAL; GREEN FLUORESCENT PROTEINS; ORGANELLES; PEROXISOMES; SACCHAROMYCES CEREVISIAE;

EID: 42449096382     PISSN: 00219525     EISSN: 00219525     Source Type: Journal    
DOI: 10.1083/jcb.200710009     Document Type: Article

References (45)

1. 6 transcription factors Oaf1p and Pip2p. Different roles in fatty acid induction of β-oxidation in Saccharomyces cerevisiae. J. Biol. Chem. 274:22208-22216.
2. Boukh-Viner, T., T. Guo, A. Alexandrian, A. Cerracchio, C. Gregg, S. Haile, R. Kyskan, S. Milijevic, D. Oren, J. Solomon, et al. 2005. Dynamic ergosterol-and ceramide-rich domains in the peroxisomal membrane serve as an organizing platform for peroxisome fusion. J. Cell Biol. 168: 761-773.
3. Chang, C.C., S. South, D. Warren, J. Jones, A.B. Moser, H.W. Moser, and S.J. Gould. 1999. Metabolic control of peroxisome abundance. J. Cell Sci. 112:1579-1590.
4. Einerhand, A.W., T.M. Voorn-Brouwer, R. Erdmann, W.H. Kunau, and H.F. Tabak. 1991. Regulation of transcription of the gene coding for peroxisomal 3-oxoacyl-CoA thiolase of Saccharomyces cerevisiae. Eur. J. Biochem. 200:113-122.
5. Eitzen, G.A., R.K. Szilard, and R.A. Rachubinski. 1997. Enlarged peroxisomes are present in oleic acid-grown Yarrowia lipolytica overexpressing the PEX16 gene encoding an intraperoxisomal peripheral membrane peroxin. J. Cell Biol. 137:1265-1278.
6. Elbing, K., E.M. Rubenstein, R.R. McCartney, and M.C. Schmidt. 2006. Subunits of the Snf1 kinase heterotrimer show interdependence for association and activity. J. Biol. Chem. 281:26170-26180.
7. Erdmann, R., and W. Schliebs. 2005. Peroxisomal matrix protein import: the transient pore model. Nat. Rev. Mol. Cell Biol. 6:738-742.
8. Fernandis, A.Z., and M.R. Wenk. 2007. Membrane lipids as signaling molecules. Curr. Opin. Lipidol. 18:121-128.
9. Gurvitz, A., and H. Rottensteiner. 2006. The biochemistry of oleate induction: transcriptional upregulation and peroxisome proliferation. Biochim. Biophys. Acta. 1763:1392-1402.
10. Hannun, Y.A., and L.M. Obeid. 2002. The ceramide-centric universe of lipid-mediated cell regulation: stress encounters of the lipid kind. J. Biol. Chem. 277:25847-25850.
11. Hengartner, C.J., V.E. Myer, S.M. Liao, C.J. Wilson, S.S. Koh, and R.A. Young. 1998. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol. Cell. 2:43-53.
12. Hiltunen, J.K., A.M. Mursula, H. Rottensteiner, R.K. Wierenga, A.J. Kastaniotis, and A. Gurvitz. 2003. The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol. Rev. 27:35-64.
13. Hoepfner, D., D. Schildknegt, I. Braakman, P. Philippsen, and H.F. Tabak. 2005. Contribution of the endoplasmic reticulum to peroxisome formation. Cell. 122: 85-95.
14. Huh, W.K., J.V. F alvo, L.C. Gerke, A.S. Carroll, R.W. H owson, J.S. Weissman, and E.K. O'Shea. 2003. Global analysis of protein localization in budding yeast. Nature. 425:686-691.
15. Igual, J.C., C. Gonzalez-Bosch, L. Franco, and J.E. Perez-Ortin. 1992. The POT1 gene for yeast peroxisomal thiolase is subject to three different mechanisms of regulation. Mol. Microbiol. 6:1867-1875.
16. Kaida, D., H. Yashiroda, A. Toh-e, and Y. Kikuchi. 2002. Yeast Whi2 and Psr1-phosphatase form a complex and regulate STRE-mediated gene expression. Genes Cells. 7:543-552.
17. Karpichev, I.V., and G.M. Small. 1998. Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:6560-6570.
18. Koerkamp, M.G., M. Rep, H.J. Bussemaker, G.P. Hardy, A. Mul, K. Piekarska, C.A. Szigyarto, J.M. De Mattos, and H.F. Tabak. 2002. Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays. Mol. Biol. Cell. 13:2783-2794.
19. Kumar, A., S. Agarwal, J.A. Heyman, S. Matson, M. Heidtman, S. Piccirillo, L. Umansky, A. Drawid, R. Jansen, Y. Liu, et al. 2002. Subcellular localization of the yeast proteome. Genes Dev. 16:707-719.
20. Leon, S., J.M. Goodman, and S. Subramani. 2006. Uniqueness of the mechanism of protein import into the peroxisome matrix: transport of folded, co-factor-bound and oligomeric proteins by shuttling receptors. Biochim. Biophys. Acta. 1763:1552-1564.
21. Liao, S.M., J. Zhang, D.A. Jeffery, A.J. Koleske, C.M. Thompson, D.M. Chao, M. Viljoen, H.J. van Vuuren, and R.A. Young. 1995. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 374:193-196.
22. Marelli, M., J.J. Smith, S. Jung, E. Yi, A.I. Nesvizhskii, R.H. Christmas, R.A. Saleem, Y.Y. Tam, A. Fagarasanu, D.R. Goodlett, et al. 2004. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J. Cell Biol. 167:1099-1112.
23. Navarro, B., and J.C. Igual. 1994. ADR1 and SNF1 mediate different mechanisms in transcriptional regulation of yeast POT1 gene. Biochem. Biophys. Res. Commun. 202:960-966.
24. Pelkmans, L., E. Fava, H. Grabner, M. Hannus, B. Habermann, E. Krausz, and M. Zerial. 2005. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature. 436:78-86.
25. Phelps, C., V. Gburcik, E. Suslova, P. Dudek, F. Forafonov, N. Bot, M. MacLean, R.J. Fagan, and D. Picard. 2006. Fungi and animals may share a common ancestor to nuclear receptors. Proc. Natl. Acad. Sci. USA. 103: 7077-7081.
26. Platta, H.W., and R. Erdmann. 2007. The peroxisomal protein import machinery. FEBS Lett. 581:2811-2819.
27. Ptacek, J., G. Devgan, G. Michaud, H. Zhu, X. Zhu, J. Fasolo, H. Guo, G. Jona, A. Breitkreutz, R. Sopko, et al. 2005. Global analysis of protein phosphorylation in yeast. Nature. 438:679-684.
28. Rayapuram, N., and S. Subramani. 2006. The importomer - a peroxisomal membrane complex involved in protein translocation into the peroxisome matrix. Biochim. Biophys. Acta. 1763:1613-1619.
29. Roth, A.F., J. Wan, A.O. Bailey, B. Sun, J.A. Kuchar, W.N. Green, B.S. Phinney, J.R. Yates III, and N.G. Davis. 2006. Global analysis of protein palmitoylation in yeast. Cell. 125:1003-1013.
30. Rottensteiner, H., A.J. Kal, M. Filipits, M. Binder, B. Hamilton, H.F. Tabak, and H. Ruis. 1996. Pip2p: a transcriptional regulator of peroxisome proliferation in the yeast Saccharomyces cerevisiae. EMBO J. 15:2924-2934.
31. Rottensteiner, H., L. Wabnegger, R. Erdmann, B. Hamilton, H. Ruis, A. Hartig, and A. Gurvitz. 2003. Saccharomyces cerevisiae PIP2 mediating oleic acid induction and peroxisome proliferation is regulated by Adr1p and Pip2p-Oaf1p. J. Biol. Chem. 278:27605-27611.
32. Saeed, A.I., V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Klapa, T. Currier, M. Thiagarajan, et al. 2003. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 34: 374-378.
33. Saeed, A.I., N.K. Bhagabati, J.C. Braisted, W. Liang, V. Sharov, E.A. Howe, J. Li, M. Thiagarajan, J.A. White, and J. Quackenbush. 2006. TM4 microarray software suite. Methods Enzymol. 411:134-193.
34. Scholz, O., A. Thiel, W. Hillen, and M. Niederweis. 2000. Quantitative analysis of gene expression with an improved green fluorescent protein. Eur. J. Biochem. 267:1565-1570.
35. Shannon, P., A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-2504.
36. Simon, M., M. Binder, G. Adam, A. Hartig, and H. Ruis. 1992. Control of peroxisome proliferation in Saccharomyces cerevisiae by ADR1, SNF1 (CAT1, CCR1) and SNF4 (CAT3). Yeast. 8:303-309.
37. Smith, J.J., T.W. Brown, G.A. Eitzen, and R.A. Rachubinski. 2000. Regulation of peroxisome size and number by fatty acid β-oxidation in the yeast Yarrowia lipolytica. J. Biol. Chem. 275:20168-20178.
38. Smith, J.J., M. Marelli, R.H. Christmas, F.J. Vizeacoumar, D.J. Dilworth, T. Ideker, T. Galitski, K. Dimitrov, R.A. Rachubinski, and J.D. Aitchison. 2002. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J. Cell Biol. 158:259-271.
39. Smith, J.J., Y. Sydorskyy, M. Marelli, D. Hwang, H. Bolouri, R.A. Rachubinski, and J.D. Aitchison. 2006. Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Mol. Syst. Biol. 2:2006.
40. Smith, J.J., S.A. Ramsey, M. Marelli, B. Marzolf, D. Hwang, R.A. Saleem, R.A. Rachubinski, and J.D. Aitchison. 2007. Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol. Syst. Biol. 3:115.
41. Strahl, T., and J. Thorner. 2007. Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1771: 353-404.
42. Tam, Y.Y.C., A. Fagarasanu, M. Fagarasanu, and R.A. Rachubinski. 2005. Pex3p initiates the formation of a preperoxisomal compartment from a subdomain of the endoplasmic reticulum in Saccharomyces cerevisiae. J. Biol. Chem. 280:34933-34939.
43. van Roermund, C.W.T., H.F. Tabak, M. van Den Berg, R.J.A. Wanders, and E.H. Hettema. 2000. Pex11p plays a primary role in medium-chain fatty acid oxidation, a process that affects peroxisome number and size in Saccharomyces cerevisiae. J. Cell Biol. 150:489-498.
44. Voronkova, V., N. Kacherovsky, C. Tachibana, D. Yu, and E.T. Young. 2006. Snf1-dependent and Snf1-independent pathways of constitutive ADH2 expression in Saccharomyces cerevisiae. Genetics. 172:2123-2138.
45. Zhu, H., J.F. Klemic, S. Chang, P. Bertone, A. Casamayor, K.G. Klemic, D. Smith, M. Gerstein, M.A. Reed, and M. Snyder. 2000. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:283-289.