Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation

BioSystems

Volumn 104, Issue 1, 2011, Pages 63-75

  Kavun Ozbayraktar, Fatma Betul ^a   Ulgen, Kutlu O ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Calcium sensitivity; Cancer; Computational systems biology; Drug targeting; Flux balance analysis; Yeast sphingolipid metabolism

Indexed keywords

ADENOSINE TRIPHOSPHATE; CALCIUM; DIACYLGLYCEROL; PHOSPHATIDIC ACID; PHOSPHOLIPID; SPHINGOLIPID;

ALCOHOL; CALCIUM; CANCER; CELL ORGANELLE; COMPUTER SIMULATION; FATTY ACID; GENE EXPRESSION; LIPID; MEMBRANE; METABOLISM; METABOLITE; MUTATION; NUMERICAL MODEL; PHENOTYPE; PLASMA; RECONSTRUCTION; SENSITIVITY ANALYSIS; SILICON; STOCHASTICITY; YEAST;

ARTICLE; BACTERIAL GENE; CELL DEATH; CELL MEMBRANE; CELL VIABILITY; CSG1 BACTERIAL GENE; CSG2 BACTERIAL GENE; FATTY ACID METABOLISM; GENE DELETION; HYDROXYLATION; LIPID METABOLISM; MOLECULAR MODEL; NONHUMAN; PHENOTYPE; PHOSPHOLIPID METABOLISM; SACCHAROMYCES CEREVISIAE; STOICHIOMETRY; YEAST;

SACCHAROMYCES CEREVISIAE;

EID: 79952317819     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2011.01.001     Document Type: Article

References (56)

1. Alvarez-Vasquez F., Sims K.J., Hannun Y.A., Voit E.O. Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models. J. Theor. Biol. 2004, 226:265-291.
2. Alvarez-Vasquez F., Sims K.J., Cowart L.A., Okamoto Y., Voit E.O., Hannun Y.A. Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 2005, 433:425-430.
3. Beeler T., Bacikova D., Gable K., Hopkins L., Johnson C., Slife H., Dunn T. The Saccharomyces cerevisiae TSC10/YBR265w gene encoding 3-ketosphinganine reductase is identified in a screen for temperature-sensitive suppressors of the Ca2+-sensitive csg2Δ mutant. J. Biol. Chem. 1998, 273:30688-30694.
4. Bonarius H.P.J., Hatzimanikatis V., Meesters K.P.H., de Gooijer C.D., Schmid G., Tramper J. Metabolic flux analysis of hybridoma cells in different culture media using mass balances. Biotechnol. Bioeng. 1996, 50:299-318.
5. Bonarius H.P.J., Schmid G., Tramper J. Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends Biotechnol. 1997, 15:308-314.
6. Cakir T., Alsan S., Saybasili H., Akin A., Ulgen K.O. Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia. Theor. Biol. Med. Model. 2007, 4.
7. Cuvillier O., Levade T. Enzymes of sphingosine metabolism as potential pharmacological targets for therapeutic intervention in cancer. Pharmacol. Res. 2003, 47:439-445.
8. Dickson R.C., Lester R.L. Metabolism and selected functions of sphingolipids in the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta 1999, 1438:305-321.
9. Dickson R.C., Lester R.L. Sphingolipid functions in Saccharomyces cerevisiae. Biochim. Biophys. Acta 2002, 1583:13-25.
10. Dickson R.C., Sumanasekera C., Lester R.L. Functions and metabolism of sphingolipids in Saccharomyces cerevisiae. Prog. Lipid Res. 2006, 45:447-465.
11. Dominguez A., Elorza M.V., Santos E., Villanueva J.R., Sentandreu R. Inositol deficiency in yeast: metabolic, enzymatic and autoradiographic studies. Antonie Van Leeuwenhoek 1978, 44:341-352.
12. Duarte N.C., Herrgard M.J., Palsson B.O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004, 14:1298-1309.
13. Dunn T.M., Haak D., Monaghan E., Beeler T.J. Synthesis of monohydroxylated inositolphosphorylceramide (IPC-C) in Saccharomyces cerevisiae requires Scs7p, a protein with both a cytochrome b5-like domain and a hydroxylase/desaturase domain. Yeast 1998, 14:311-321.
14. Edwards J.S., Palsson B.O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:5528-5533.
15. Edwards J.S., Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 2000, 1.
16. Fell D.A., Small J.R. Fat synthesis in adipose tissue. An examination of stoichiometric constraints. Biochem. J. 1986, 238:781-786.
17. Förster J., Famili I., Fu P., Palsson B.O., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13:244-253.
18. Gomez-Munoz A. Modulation of cell signalling by ceramides. Biochim. Biophys. Acta 1998, 1391:92-109.
19. Guilllas I., Kirchman P.A., Chuard R., Pfefferli M., Jiang J.C., Jazwinski S.M., Conzelmann A. C26-CoA-dependent ceramide synthesis of Saccharomyces cerevisiae is operated by Lag1p and Lac1p. EMBO J. 2001, 20:2655-2665.
20. Haak D., Gable K., Beeler T., Dunn T. Hydroxylation of Saccharomyces cerevisiae ceramides requires Sur2p and Scs7p. J. Biol. Chem. 1997, 272:29704-29710.
21. Hannun Y.A., Luberto C., Argraves K.M. Enzymes of sphingolipid metabolism: from modular to integrative signaling. Biochemistry 2001, 40:4893-4903.
22. Holzhutter H.G. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 2004, 271:2905-2922.
23. Hwang O., Kim G., Jang Y.J., Kim S.W., Choi G., Choi H.J., Jeon S.Y., Lee D.G., Lee J.D. Synthetic phytoceramides induce apoptosis with higher potency than ceramides. Mol. Pharmacol. 2001, 59:1249-1255.
24. Kauffman K.J., Prakash P., Edwards J.S. Advances in flux balance analysis. Curr. Opin. Biotechnol. 2003, 14:491-496.
25. Kavun Ozbayraktar F.B., Ulgen K.O. Molecular facets of sphingolipids: mediators of diseases. Biotechnol. J. 2009, 4:1028-1041.
26. Kavun Ozbayraktar F.B., Ulgen K.O. Drug target identification in sphingolipid metabolism by computational systems biology tools: metabolic control analysis and metabolic pathway analysis. J. Biomed. Inform. 2010, 43:537-549.
27. Klamt S. Generalized concept of minimal cut sets in biochemical networks. BioSystems 2006, 83:233-247.
28. Klamt S., Saez-Rodriguez J., Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 2007, 1.
29. Kohlwein S.D., Eder S., Oh C.S., Martin C.E., Gable K., Bacikova D., Dunn T. Tsc13p is required for fatty acid elongation and localizes to a novel structure at the nuclear-vacuolar interface in Saccharomyces cerevisiae. Mol. Cell. Biol. 2001, 21:109-125.
30. Kuepfer L., Sauer U., Blank L.M. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 2005, 15:1421-1430.
31. Mahadevan R., Schilling C.H. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 2003, 5:264-276.
32. Mandala S.M. Sphingosine-1-phosphate phosphatases. Prostaglandins Other Lipid Mediat. 2001, 64:143-156.
33. Mao C., Wadleigh M., Jenkins G.M., Hannun Y.A., Obeid L.M. Identification and characterization of Saccharomyces cerevisiae dihydrosphingosine-1-phosphate phosphatase. J. Biol. Chem. 1997, 272:28690-28694.
34. Mathias S., Penna L.A., Kolesnick R.N. Signal transduction of stress via ceramide. Biochem. J. 1998, 335:465-480.
35. Modrak D.E., Gold D.V., Goldenberg D.M. Sphingolipid targets in cancer therapy. Mol. Cancer Ther. 2006, 5:200-208.
36. Obeid L.M., Okamoto Y., Mao C. Yeast sphingolipids: metabolism and biology. Biochim. Biophys. Acta 2002, 1585:163-171.
37. Ogretmen B., Hannun Y.A. Updates on functions of ceramide in chemotherapy-induced cell death and in multidrug resistance. Drug Resist. Updat. 2002, 4:368-377.
38. Ohanian J., Ohanian V. Sphingolipids in mammalian cell signalling. Cell. Mol. Life Sci. 2001, 58:2053-2068.
39. Ohanian J., Ohanian V. Lipid second messenger regulation: the role of diacylglycerol kinases and their relevance to hypertension. J. Hum. Hypertens. 2001, 15:93-98.
40. Perry R.J., Ridgway N.D. Molecular mechanisms and regulation of ceramide transport. Biochim. Biophys. Acta 2005, 1734:220-234.
41. Ramakrishna R., Edwards J.S., Mcculloch A., Palsson B.O. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am. J. Physiol. Regul. Integr. Comp. Physiol. 2001, 280:695-704.
42. Reggiori F., Conzelmann A. Biosynthesis of inositol phosphoceramides and remodeling of glycosylphosphatidylinositol anchors in Saccharomyces cerevisiae are mediated by different enzymes. J. Biol. Chem. 1998, 273:30550-30559.
43. Reynolds C.P., Maurera B.J., Kolesnick R.N. Ceramide synthesis and metabolism as a target for cancer therapy. Cancer Lett. 2004, 206:169-180.
44. Saba J.D., Obeid L.M., Hannun Y.A. Ceramide: an intracellular mediator of apoptosis and growth suppression. Philos. Trans. R. Soc. Lond., B: Biol. Sci. 1996, 351:233-241.
45. Schneiter R. Brave little yeast, please guide us to Thebes: sphingolipid function in S. cerevisiae. Bioessays 1999, 21:1004-1010.
46. Shaldubina A., Ju S., Vaden D.L., Ding D., Belmaker R.H., Greenberg M.L. Epi-inositol regulates expression of the yeast INO1 gene encoding inositol-1-P synthase. Mol. Psychiatry 2002, 7:174-180.
47. Sims K.J., Spassieva S.D., Voit E.O., Obeid L.M. Yeast sphingolipid metabolism: clues and connections. Biochem. Cell Biol. 2004, 82:45-61.
48. Spiegel S., Milstien S. Sphingosine 1-phosphate, a key cell signaling molecule. J. Biol. Chem. 2002, 277:25851-25854.
49. Stephanopoulos G., Aristidou A.A., Nielsen J. Metabolic Engineering: Principles and Methodologies 1998, Academic Press, San Diego.
50. Stunff H., Galve-Roperh I., Peterson C., Milstien S., Spiegel S. Sphingosine-1-phosphate phosphohydrolase in regulation of sphingolipid metabolism and apoptosis. J. Cell Biol. 2002, 158:1039-1049.
51. Taha T.A., Mullen T.D., Obeid L.M. A house divided: ceramide, sphingosine, and sphingosine-1-phosphate in programmed cell death. Biochim. Biophys. Acta 2006, 1758:2027-2036.
52. Trawick J.D., Schilling C.H. Use of constraint-based modeling for the prediction and validation of antimicrobial targets. Biochem. Pharmacol. 2006, 71:1026-1035.
53. Vallee B., Riezman H. Lip1p: a novel subunit of acyl-CoA ceramide synthase. EMBO J. 2005, 24:730-741.
54. Varma A., Palsson B.O. Metabolic flux balancing: basic concepts, scientific and practical use. Biotechnology (N.Y.) 1994, 12:994-998.
55. Vo T.D., Greenberg H.J., Palsson B.O. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 2004, 279:39532-39540.
56. Zeidan Y.H., Hannun Y.A. Translational aspects of sphingolipid metabolism. Trends Mol. Med. 2007, 13:327-336.