Genome-Scale Metabolic Models of Saccharomyces cerevisiae

Methods in Molecular Biology

Volumn 759, Issue , 2011, Pages 445-463

  Nookaew, Intawat ^a   Olivares Hernández, Roberto ^a   Bhumiratana, Sakarindr ^b   Nielsen, Jens ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

genome scale metabolic model (GSM); metabolic network reconstruction; metabolism; Saccharomyces cerevisiae; systems biology; yeast

Indexed keywords

BASIC RESEARCH; CELL FUNCTION; COMPUTER SIMULATION; NONHUMAN; SACCHAROMYCES CEREVISIAE; SIMULATION; SYSTEMS BIOLOGY; YEAST; ARTICLE; BIOLOGICAL MODEL; FUNGAL GENOME; GENETICS; GENOMICS; HUMAN; METABOLISM; METHODOLOGY;

GENOME, FUNGAL; GENOMICS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 80054755690     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-173-4_25     Document Type: Chapter

References (96)

1. Nielsen, J., and Jewett, M. C. (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res. 8, 122–131.
2. Spier, R. E. (2000) Yeast as a cell factory. Enzyme Microb. Technol. 26, 639.
3. Goffeau, A., Barrell, B. G., Bussey, H., et al. (1996) Life with 6000 genes. Science 274, 546, 563–567.
4. Botstein, D., Chervitz, S. A., and Cherry, J. M. (1997) Yeast as a model organism. Science 277, 1259–1260.
5. Steinmetz, L. M., Scharfe, C., Deutschbauer, A. M., et al. (2002) Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400–404.
6. Bassett, D. E., Jr., Boguski, M. S., and Hieter, P. (1996) Yeast genes and human disease. Nature 379, 589–590.
7. Foury, F. (1997) Human genetic diseases: a cross-talk between man and yeast. Gene 195, 1–10.
8. Perocchi, F., Mancera, E., and Steinmetz, L. M. (2008) Systematic screens for human disease genes, from yeast to human and back. Mol. Biosyst. 4, 18–29.
9. Petranovic, D., and Nielsen, J. (2008) Can yeast systems biology contribute to the understanding of human disease? Trends Biotechnol. 26, 584–590.
10. Sturgeon, C. M., Kemmer, D., Anderson, H. J, and Roberge, M. (2006) Yeast as a tool to uncover the cellular targets of drugs. Biotechnol. J. 1, 289–298.
11. Mutka, S. C., Bondi, S. M., Carney, J. R., Da Silva, N. A., and Kealey J. T. (2006) Metabolic pathway engineering for complex polyketide biosynthesis in Saccharomyces cerevisiae. FEMS Yeast Res. 6, 40–47.
12. Wattanachaisaereekul, S., Lantz, A. E., Nielsen, M. L., and Nielsen, J. (2008) Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply. Metab. Eng. 10, 246–254.
13. Ro, D. K., and Douglas, C. J. (2004) Reconstitution of the entry point of plant phenylpropanoid metabolism in yeast (Saccha-romyces cerevisiae): implications for control of metabolic flux into the phenylpropanoid pathway. J. Biol. Chem. 279, 2600–2607.
14. Asadollahi, M. A., Maury, J., Moller, K., et al. (2008) Production of plant sesquiter-penes in Saccharomyces cerevisiae: effect of ERG9 repression on sesquiterpene biosynthesis. Biotechnol. Bioeng. 99, 666–677.
15. Yamano, S., Ishii, T., Nakagawa, M., Ike-naga, H., and Misawa, N. (1994) Metabolic engineering for production of beta-carotene and lycopene in Saccharomyces cerevisiae. Biosci. Biotechnol. Biochem. 58, 1112–1114.
16. Dejong, J. M., Liu, Y., Bollon, A. P., et al. (2006) Genetic engineering of taxol biosynthetic genes in Saccharomyces cerevisiae. Biotechnol. Bioeng. 93, 212–224.
17. Thim, L., Hansen, M. T., Norris, K., et al. (1986) Secretion and processing of insulin precursors in yeast. Proc. Natl. Acad. Sci. USA 83, 6766–6770.
18. Thim, L., Hansen, M. T., and Sorensen, A. R. (1987) Secretion of human insulin by a transformed yeast cell. FEBS Lett. 212, 307–312.
19. Bro, C., Regenberg, B., Förster, J., and Nielsen, J. (2006) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab. Eng. 8, 102–111.
20. Guo, Z. P., Zhang, L., Ding, Z. Y., Wang, Z. X., and Shi, G. Y. (2009) Interruption of glycerol pathway in industrial alcoholic yeasts to improve the ethanol production. Appl. Microbiol. Biotechnol. 82, 287–292.
21. Boros, L. G., and Boros, T. F. (2007) Use of metabolic pathway flux information in anti-cancer drug design. Ernst Schering Found. Symp. Proc. 4, 189–203.
22. Biochemical Pathways– Metabolic Pathways. (http://www.expasy.ch/cgi-bin/show_thumbnails.pl).
23. Covert, M. W., Schilling, C. H., Famili, I., et al. (2001) Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26, 179–186.
24. Weng, S., Dong, Q., Balakrishnan, R., et al. (2003) Saccharomyces Genome database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 31, 216–218.
25. Guldener, U., Munsterkotter, M., Kasten-muller, G., et al. (2005) CYGD: the comprehensive yeast genome database. Nucleic Acids Res. 33, D364–D368.
26. Godzik, A., Jambon, M., and Friedberg, I. (2007) Computational protein function prediction: are we making progress? Cell. Mol. Life Sci. 64, 2505–2511.
27. Kanehisa, M., and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30.
28. Joshi-Tope, G., Gillespie, M., Vastrik, I., et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33, D428–D432.
29. Vastrik, I., D’Eustachio, P., Schmidt, E., et al. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 8, R39.
30. Caspi, R., Foerster, H., Fulcher, C. A., et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36, D623–D631.
31. Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., and Palsson, B. Ø. (2009) Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 7, 129–143.
32. Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M., and Palsson, B. Ø. (2001) Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17, 286–287.
33. Tomita, M. (2001) Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19, 205–210.
34. Tomita, M., Hashimoto, K., Takahashi, K., et al. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72–84.
35. Ohno, H., Naito, Y., Nakajima, H., and Tomita, M. (2008) Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule. Artif. Life 14, 3–28.
36. Stephanopoulos, G., Aristidou, A. A., and Nielsen, J. (1998) Metabolic Engineering: Principles and Methodologies. Academics, San Diego, California, USA.
37. Iwatani, S., Yamada, Y., and Usuda, Y. (2008) Metabolic flux analysis in biotechnology processes. Biotechnol. Lett. 30, 791–799.
38. Schilling, C. H., Schuster, S., Palsson, B. Ø., and Heinrich, R. (1999) Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296–303.
39. Schuster, S., Dandekar, T., and Fell, D. A. (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53–60.
40. Schuster, S., Fell, D. A., and Dandekar, T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18, 326–332.
41. Papin, J. A., Price, N. D., Edwards, J. S., and Palsson, B. B. Ø. (2002) The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215, 67–82.
42. Papin, J. A, Price, N. D, and Palsson, B. Ø. (2002) Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12, 1889–1900.
43. Price, N. D., Papin, J. A., and Palsson, B. Ø. (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12, 760–769.
44. Wiback, S. J., and Palsson, B. Ø. (2002) Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83, 808–818.
45. Varma, A., and Palsson, B. Ø. (1994) Stoichiometric flux balance models quantita-tively predict growth and metabolic byproduct secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60, 3724–3731.
46. Edwards, J. S., and Palsson, B. Ø. (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97, 5528–5533.
47. Famili, I., Förster, J., Nielsen, J., and Palsson, B. Ø. (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 100, 13134–13139.
48. van Gulik, W. M., and Heijnen, J. J. (1995) A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnol. Bioeng. 48, 681–698.
49. Ramakrishna, R., Edwards, J. S., McCulloch, A., and Palsson, B. Ø. (2001) Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am. J. Physiol. Regul. Integr. Comp. Physiol. 280, R695–R704.
50. Knorr, A. L., Jain, R., and Srivastava, R. (2007) Bayesian-based selection of metabolic objective functions. Bioinformatics 23, 351–357.
51. Ebenhoh, O., and Heinrich, R. (2001) Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bull. Math. Biol. 63, 21–55.
52. Oliveira, A. P., Nielsen, J., and Förster, J. (2005) Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5, 39.
53. Nookaew, I., Jewett, M. C., Meechai, A., et al. (2008) The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst. Biol. 2, 71.
54. Segre, D., Vitkup, D., and Church, G. M. (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112–15117.
55. Shlomi, T., Berkman, O., and Ruppin, E. (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 102, 7695–7700.
56. Covert, M. W., Schilling, C. H., and Palsson, B. (2001) Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213, 73–88.
57. Shlomi, T., Eisenberg, Y., Sharan, R., and Ruppin, E. (2007) A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol. Syst. Biol. 3, 101.
58. Covert, M. W., Xiao, N., Chen, T. J., and Karr, J. R. (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24, 2044–2050.
59. Lee, J. M., Gianchandani, E. P., Eddy, J. A., and Papin, J. A. (2008) Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4, e1000086.
60. Becker, S. A., Feist, A. M., Mo, M. L., Han-num, G., Palsson, B. Ø., and Herrgård, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat. Protoc. 2, 727–738.
61. Hucka, M., Finney, A., Sauro, H. M., et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531.
62. Keating, S. M., Bornstein, B. J., Finney, A., and Hucka, M. (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 22, 1275–1277.
63. Winzeler, E. A., Shoemaker, D. D., Astro-moff, A., et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906.
64. Förster, J., Famili, I., Palsson, B. Ø., and Nielsen, J. (2003) Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS 7, 193–202.
65. Kuepfer, L., Sauer, U., and Blank, L. M. (2005) Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15, 1421–1430.
66. Duarte, N. C., Herrgård, M. J., and Palsson, B. Ø. (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14, 1298–1309.
67. Duarte, N. C., Palsson, B. Ø., and Fu, P. (2004) Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. BMC Genomics 5, 63.
68. Edwards, J. S., and Palsson, B. Ø. (2000) Robustness analysis of the Escherichia coli metabolic network. Biotechnol. Progr. 16, 927–939.
69. Varma, A., Boesch, B. W., and Palsson, B. Ø. (1993) Biochemical production capabilities of Escherichia coli. Biotechnol. Bioeng. 42, 59–73.
70. Vallino, J., and Stephanopoulos, G. (1993) Metabolic flux distributions in Corynebac-terium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 41, 633–646.
71. Vanrolleghem, P. A., Jong-Gubbels, P., van Gulik, W. M., Pronk, J. T., van Dijken, J. P., and Heijnen, S. (1996) Validation of a metabolic network for Saccharomyces cerevisiae using mixed substrate studies. Biotechnol. Progr. 12, 434–448.
72. Nissen, T. L., Schulze, U., Nielsen, J., and Villadsen, J. (1997) Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143, 203–218.
73. Jin, S., Ye, K., and Shimizu, K. (1997) Metabolic flux distribution in recombinant Saccharromyces cerevisiae during foreign protein production. J. Biotechnol. 54, 161–174.
74. Nissen, T. L., Kielland-Brandt, M. C., Nielsen, J., and Villadsen, J. (2000) Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation. Metabolic Eng. 2, 69–77.
75. Gombert, A. K., Moreira dos Santos, M., Christensen, B., and Nielsen, J. (2001) Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183, 1441–1451.
76. Jouhten, P., Rintala, E., Huuskonen, A., et al. (2008) Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113–1A. BMC Syst. Biol. 2, 60.
77. van Winden, W. A., van Dam, J. C., Ras, C., et al. (2005) Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113–7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. FEMS Yeast Res. 5, 559–568.
78. 13 C flux analysis. Microb. Cell Fact. 4, 30.
79. Carlson, R., Fell, D., and Srienc, F. (2002) Metabolic Pathway analysis of a recombinat yeast for rational strain development. Biotechnol. Bioeng. 79, 121–134.
80. Förster, J., Gombert, K. A., and Nielsen, J. (2002) A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioeng. 79, 703–712.
81. Nookaew, I., Meechai, A., Tham-marongtham, C., et al. (2007) Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Biotechnol. Bioeng. 97, 1535–1549.
82. Förster, J., Famili, I., Fu, P., Palsson, B. Ø., and Nielsen, J. (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13, 244–253.
83. Herrgård, M. J., Lee, B. S., Portnoy, V., and Palsson, B. Ø. (2006) Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res. 16, 627–635.
84. Mo, M. L., Palsson, B. Ø., and Heijnen, J. J. (2009) Connecting extracellular meta-bolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 3, 1–17.
85. Herrgård, M. J., Swainston, N., Dobson, P., et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol. 26, 1155–1160.
86. Asadollahi, M. A., Maury, J., Patil, K. R., Schalk, M., Clark, A., and Nielsen, J. (2009) Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 11, 328–334.
87. Åkesson, M., Förster, J., and Nielsen, J. (2004) Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6, 285–293.
88. Patil, K. R., Rocha, I., Förster, J., and Nielsen, J. (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6, 1–12.
89. Patil, K. R., and Nielsen, J. (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. USA 102, 2685–2689.
90. Cakır, T., Patil, K. R., Onsan, I., Ulgen, K. O., Kirdar, B., and Nielsen, J. (2006) Integration of metabolome data with metabolic networks reveals reporter reactions. Mol. Syst. Biol. 2, 1–11.
91. Oliveira, A. P., Patil, K. R., and Nielsen, J. (2008) Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol. 2, 17.
92. Pizarro, F. J., Jewett M. C., Nielsen, J., and Agosin, E. (2008) Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 74, 6358–6368.
93. Vemuri, G. N., Eiteman, M. A., McEwen, J. E., Olsson, L., and Nielsen, J. (2007) Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 104, 2402–2407.
94. Cimini. D., Patil, K. R., Schiraldi, C., and Nielsen J. (2009) Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. BMC Syst. Biol. 3, 17.
95. Usaite, R., Patil, K. R., Grotkjaer, T., Nielsen, J., and Regenberg, B. (2006) Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation. Appl. Environ. Microbiol. 72, 6194–6203.
96. 13 C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6, R49.