Revising the representation of fatty acid, glycerolipid, and glycerophospholipid metabolism in the consensus model of yeast metabolism

Industrial Biotechnology

Volumn 9, Issue 4, 2013, Pages 215-228

  Aung, Hnin W ^a   Henry, Susan A ^b   Walker, Larry P ^a  

^a Department of Biological and Environmental Engineering   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOME-SCALE METABOLIC MODELS; GLYCEROPHOSPHOLIPIDS; INCREASE PRODUCTIONS; INCREASED PRODUCTIVITY; METABOLIC ENZYMES; METABOLIC NETWORK; OXIDATION PATHWAY; SUPPLEMENTARY DATA;

ASSOCIATION REACTIONS; FATTY ACIDS; GENES; METABOLISM; METABOLITES; PHYSIOLOGY; SYNTHESIS (CHEMICAL); YEAST;

COMPUTER SIMULATION;

EID: 84881540727     PISSN: 15509087     EISSN: None     Source Type: Journal    
DOI: 10.1089/ind.2013.0013     Document Type: Article

References (57)

1. US Environmental Protection Agency. Biofuels and the environment: First triennial report to Congress. EPA/600/R-10/183F (2011).
2. Kosa M, Ragauskas AJ. Lipids from heterotrophic microbes: Advances in metabolism research. Trends Biotechnol 2011;29(2):53-61.
3. Oberhardt MA, Palsson BO, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 2009;5: doi:10.1038/msb.2009.77.
4. Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010;5(1):93-121.
5. Herrgard MJ, Swainston N, Dobson P, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26(10):1155-1160.
6. Schellenberger J, Que R, Fleming RMT, et al. Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat Protoc 2011;6(9):1290-1307.
7. Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: An API library for SBML. Bioinformatics 2008;24(6):880-881. (Pubitemid 351386935)
8. Keating SM, Bornstein BJ, Finney A, Hucka M. SBMLToolbox: An SBML toolbox for MATLAB users. Bioinformatics 2006;22(10):1275-1277. (Pubitemid 43779023)
9. Henry SA, Kohlwein SD, Carman GM. Metabolism and regulation of glycerolipids in the yeast Saccharomyces cerevisiae. Genetics 2012;190(2):317-349.
10. Heavner B, Smallbone K, Barker B, et al. Yeast 5-an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 2012; 6(1)55.
11. Tehlivets O, Scheuringer K, Kohlwein SD. Fatty acid synthesis and elongation in yeast. BBA-Mol Cell Biol L 2007;1771(3):255-270. (Pubitemid 46428612)
12. Lomakin IB, Xiong Y, Steitz TA. The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell 2007;129(2):319-332. (Pubitemid 46574968)
13. Hiltunen JK, Schonauer MS, Autio KJ, et al. Mitochondrial fatty acid synthesis type II: More than just fatty acids. J Biol Chem 2009;284(14):9011- 9015.
14. Oh C-S, Toke DA, Mandala S, Martin CE. ELO2 and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. J Biol Chem 1997;272(28):17376-17384. (Pubitemid 27311164)
15. Toke DA, Martin CE. Isolation and characterization of a gene affecting fatty acid elongation in Saccharomyces cerevisiae. J Biol Chem 1996;271(31):18413-18422. (Pubitemid 26322697)
16. Han G, Gable K, Kohlwein SD, et al. The Saccharomyces cerevisiae YBR159w gene encodes the 3-ketoreductase of the microsomal fatty acid elongase. J Biol Chem 2002;277(38):35440-35449.
17. Denic V, Weissman JS. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell 2007;130(4):663-677. (Pubitemid 47268053)
18. Kohlwein SD, Eder S, Oh C-S, et al. 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(1):109-125.
19. Paul S, Gable K, Dunn TM. A six-membrane-spanning topology for yeast and Arabidopsis Tsc13p, the enoyl reductases of the microsomal fatty acid elongating system. J Biol Chem 2007;282(26):19237-19246. (Pubitemid 47100163)
20. Rossler H, Rieck C, Delong T, et al. Functional differentiation and selective inactivation of multiple Saccharomyces cerevisiae genes involved in very-longchain fatty acid synthesis. Mol Genet Genomics 2003;269(2):290-298. (Pubitemid 36693793)
21. Stukey JE, McDonough VM, Martin CE. The OLE1 gene of Saccharomyces cerevisiae encodes the delta 9 fatty acid desaturase and can be functionally replaced by the rat stearoyl-CoA desaturase gene. J Biol Chem 1990;265(33):20144-20149. (Pubitemid 120013987)
22. Martin CE, Oh C-S, Jiang Y. Regulation of long chain unsaturated fatty acid synthesis in yeast. BBA-Mol Cell Biol L 2007;1771(3):271-285. (Pubitemid 46428610)
23. Hiltunen JK, Mursula AM, Rottensteiner H, et al. The biochemistry of peroxisomal b-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2003;27(1):35-64. (Pubitemid 36412186)
24. van Roermund CW, Elgersma Y, Singh N, et al. The membrane of peroxisomes in Saccharomyces cerevisiae is impermeable to NAD(H) and acetyl-CoA under in vivo conditions. EMBO J 1995;14(14):3480-3486.
25. Athenstaedt K, Daum G. 1-Acyldihydroxyacetone-phosphate reductase (Ayr1p) of the yeast Saccharomyces cerevisiae encoded by the open reading frame yil124w is a major component of lipid particles. J Biol Chem 2000;275(1):235-240. (Pubitemid 30038977)
26. Han G-S, Wu W-I, Carman GM. The Saccharomyces cerevisiae lipin homolog is a Mg2 + -dependent phosphatidate phosphatase enzyme. J Biol Chem 2006;281(14):9210-9218. (Pubitemid 43864636)
27. Carman GM, Han G-S. Roles of phosphatidate phosphatase enzymes in lipid metabolism. Trends Biochem Sci 2006;31(12):694-699. (Pubitemid 44791946)
28. Oelkers P, Cromley D, Padamsee M, et al. The DGA1 gene determines a second triglyceride synthetic pathway in yeast. J Biol Chem 2002;277(11): 8877-8881. (Pubitemid 34952956)
29. Sandager L, Gustavsson MH, Stahl U, et al. Storage lipid synthesis is nonessential in yeast. J Biol Chem 2002;277(8):6478-6482. (Pubitemid 34968444)
30. Sorger D, Daum G. Synthesis of triacylglycerols by the acyl-coenzyme A:diacylglycerol acyltransferase Dga1p in lipid particles of the yeast Saccharomyces cerevisiae. J Bacteriol 2002;184(2):519-524. (Pubitemid 34027393)
31. Oelkers P, Tinkelenberg A, Erdeniz N, et al. A lecithin cholesterol acyltransferaselike gene mediates diacylglycerol esterification in yeast. J Biol Chem 200;275(21):15609-15612.
32. Dahlqvist A, Stahl U, Lenman M, et al. Phospholipid:diacylglycerol acyltransferase: An enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants. Proc Natl Acad Sci 2000;97(12):6487-6492. (Pubitemid 30412740)
33. Ham HJ, Rho HJ, Shin SK, Yoon H-J. The TGL2 gene of Saccharomyces cerevisiae encodes an active acylglycerol lipase located in the mitochondria. J Biol Chem 2010;285(5):3005-3013.
34. Grillitsch K, Daum G. Triacylglycerol lipases of the yeast. Front Biol 2011;6(3):219-230.
35. Debelyy MO, Thoms S, Connerth M, et al. Involvement of the Saccharomyces cerevisiae hydrolase Ldh1p in lipid homeostasis. Eukaryot Cell 2011;10(6): 776-781.
36. Fakas S, Konstantinou C, Carman GM. DGK1-encoded diacylglycerol kinase activity is required for phospholipid synthesis during growth resumption from stationary phase in Saccharomyces cerevisiae. J Biol Chem 2010;286(2): 1464-1474.
37. Kurat CF, Natter K, Petschnigg J, et al. Obese yeast: Triglyceride lipolysis is functionally conserved frommammals to yeast. J Biol Chem 2006;281(1):491-500. (Pubitemid 43671212)
38. Heier C, Taschler U, Rengachari S, et al. Identification of Yju3p as functional orthologue of mammalian monoglyceride lipase in the yeast Saccharomyces cerevisiae. BBA-Mol Cell Biol L 2010;1801(9):1063-1071.
39. de Kroon AIPM. Metabolism of phosphatidylcholine and its implications for lipid acyl chain composition in Saccharomyces cerevisiae. BBA-Mol Cell Biol L 2007;1771(3):343-352.
40. You KM, Rosenfield C-L, Knipple DC. Ethanol tolerance in the yeast Saccharomyces cerevisiae Is dependent on cellular oleic acid content. Appl Environ Microbiol 2003;69(3):1499-1503. (Pubitemid 36314287)
41. Rodriguez-Vargas S, Sanchez-Garcia A, Martinez-Rivas JM, et al. Fluidization of membrane lipids enhances the tolerance of Saccharomyces cerevisiae to freezing and salt stress. Appl Environ Microbiol 2007;73(1):110-116. (Pubitemid 46079941)
42. Forster J, Famili I, Fu P, et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003;13(2): 244-253. (Pubitemid 36581837)
43. Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005;15(10):1421-1430. (Pubitemid 41400909)
44. Mo M, Palsson B, Herrgard M. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol 2009; 3(1):37.
45. Duarte NC, Herrgard MJ, Palsson BO. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004;14(7):1298-1309. (Pubitemid 39036129)
46. Heavner BD, Henry SA, Walker LP. Evaluating sphingolipid biochemistry in the consensus reconstruction of yeast metabolism. Ind Biotechnol 2012;8(2):72-78.
47. Wagner S, Paltauf F. Generation of glycerophospholipid molecular species in the yeast Saccharomyces cerevisiae. Fatty acid pattern of phospholipid classes and selective acyl turnover at sn-1 and sn-2 positions. Yeast 1994;10(11):1429-1437. (Pubitemid 24347996)
48. Schweizer E, Hofmann J. Microbial type I fatty acid synthases (FAS): Major players in a network of cellular FAS systems. Microbiol Mol Biol Rev 2004;68(3):501-517. (Pubitemid 39238280)
49. Osman C, Voelker DR, Langer T. Making heads or tails of phospholipids in mitochondria. J Cell Biol 2011;192(1):7-16.
50. Strahl T, Thorner J. Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae. BBA-Mol Cell Biol L 2007;1771(3):353-404. (Pubitemid 46428617)
51. Choi J-Y, Martin CE. The Saccharomyces cerevisiae FAT1 gene encodes an acyl- CoA synthetase that is required for maintenance of very long chain fatty acid levels. J Biol Chem 1999;274(8):4671-4683.
52. Marobbio CMT, Di noia MA, Palmieri F. Identification of a mitochondrial transporter for pyrimidine nucleotides in Saccharomyces cerevisiae: Bacterial expression, reconstitution and functional characterization. Biochem J 2006;393(2):441-446. (Pubitemid 43099083)
53. Marobbio CMT, Agrimi G, Lasorsa FM, Palmieri F. Identification and functional reconstitution of yeast mitochondrial carrier for S-adenosylmethionine. EMBO J 2003;22(22):5975-5982. (Pubitemid 37463241)
54. Stukey JE, McDonough VM, Martin CE. Isolation and characterization of OLE1, a gene affecting fatty acid desaturation from Saccharomyces cerevisiae. J Biol Chem 1989;264(28):16537-16544. (Pubitemid 19243545)
55. Osterlund T, Nookaew I, Bordel S, Nielsen J. Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst Biol 2013;7(1):36.
56. Nookaew I, Jewett M, Meechai A, et al. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: A scaffold to query lipid metabolism. BMC Syst Biol 2008;2(1):71.
57. Stobbe MD, Houten SM, van Kampen AHC, et al. Improving the description of metabolic networks: The TCA cycle as example. FASEB J 2012;26(9):3625-3636.