Quantitative analysis of flux regulation through hierarchical regulation analysis

Methods in Enzymology

Volumn 500, Issue , 2011, Pages 571-595

  Van Eunen, Karen ^a,b   Rossell, Sergio ^c   Bouwman, Jildau ^d   Westerhoff, Hans V ^b,e   Bakker, Barbara M ^a,b  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d TNO   (Netherlands)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Gene expression regulation; Hierarchical regulation analysis; Metabolic regulation; Posttranscriptional regulation; Regulation analysis

Indexed keywords

ARTICLE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GLYCOLYSIS; HIERARCHICAL REGULATION ANALYSIS; METABOLIC REGULATION; METABOLISM; METHODOLOGY; PRIORITY JOURNAL; PROTEIN DEGRADATION; QUANTITATIVE ANALYSIS; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE;

EID: 80053076227     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385118-5.00027-X     Document Type: Chapter

References (67)

1. H.E. Assmus, R. Herwig, K.H. Cho, and O. Wolkenhauer Dynamics of biological systems: Role of systems biology in medical research Expert Rev. Mol. Diagn. 6 2006 891 902 (Pubitemid 44904005)
2. B.M. Bakker, P.A. Michels, F.R. Opperdoes, and H.V. Westerhoff What controls glycolysis in bloodstream form Trypanosoma brucei? J. Biol. Chem. 274 1999 14551 14559
3. F.J. Bruggeman, J. de Haan, H. Hardin, J. Bouwman, S. Rossell, K. van Eunen, B.M. Bakker, and H.V. Westerhoff Time-dependent hierarchical regulation analysis: Deciphering cellular adaptation Syst. Biol. (Stevenage) 153 2006 318 322 (Pubitemid 44227136)
4. F.J. Bruggeman, S. Rossell, K. Van Eunen, J. Bouwman, H.V. Westerhoff, and B. Bakker Systems biology and the reconstruction of the cell: From molecular components to integral function Subcell. Biochem. 43 2007 239 262
5. J.A. Burns, A. Cornishbowden, A.K. Groen, R. Heinrich, H. Kacser, J.W. Porteous, S.M. Rapoport, T.A. Rapoport, J.W. Stucki, J.M. Tager, R.J.A. Wanders, and H.V. Westerhoff Control analysis of metabolic systems Trends Biochem. Sci. 10 1985 16
6. B. Christensen, and J. Nielsen Metabolic network analysis. A powerful tool in metabolic engineering Adv. Biochem. Eng. Biotechnol. 66 2000 209 231
7. A. Clark, J. Dean, C. Tudor, and J. Saklatvala Post-transcriptional gene regulation by MAP kinases via AU-rich elements Front. Biosci. 14 2009 847 871
8. P. Daran-Lapujade, M.L. Jansen, J.M. Daran, W. van Gulik, J.H. de Winde, and J.T. Pronk Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study J. Biol. Chem. 279 2004 9125 9138 (Pubitemid 38304859)
9. P. Daran-Lapujade, S. Rossell, W.M. van Gulik, M.A. Luttik, M.J. de Groot, M. Slijper, A.J. Heck, J.M. Daran, J.H. de Winde, H.V. Westerhoff, J.T. Pronk, and B.M. Bakker The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels Proc. Natl. Acad. Sci. USA 104 2007 15753 15758 (Pubitemid 350035372)
10. M. Dauner From fluxes and isotope labeling patterns towards in silico cells Curr. Opin. Biotechnol. 21 2010 55 62
11. D.A. Day, and M.F. Tuite Post-transcriptional gene regulatory mechanisms in eukaryotes: An overview J. Endocrinol. 157 1998 361 371 (Pubitemid 28275836)
12. J.A. Diderich, B. Teusink, J. Valkier, J. Anjos, I. Spencer-Martins, K. van Dam, and M.C. Walsh Strategies to determine the extent of control exerted by glucose transport on glycolytic flux in the yeast Saccharomyces bayanus Microbiology 145 Pt. 12 1999 3447 3454 (Pubitemid 30018788)
13. R. Eisenthal, and M. Danson Enzyme Assays: A Practical Approach 2002 Oxford University Press, Inc. New York
14. S. Even, N.D. Lindley, and M. Cocaign-Bousquet Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures Microbiology 149 2003 1935 1944 (Pubitemid 36874338)
15. D.A. Fell Metabolic control analysis: A survey of its theoretical and experimental development Biochem. J. 286 Pt. 2 1992 313 330
16. D.A. Fell, and S. Thomas Physiological control of metabolic flux: The requirement for multisite modulation Biochem. J. 311 Pt. 1 1995 35 39
17. E. Fischer, and U. Sauer Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism Nat. Genet. 37 2005 636 640 (Pubitemid 40770420)
18. E. Fischer, N. Zamboni, and U. Sauer High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints Anal. Biochem. 325 2004 308 316 (Pubitemid 38134368)
19. T.M. Franks, and J. Lykke-Andersen The control of mRNA decapping and P-body formation Mol. Cell 32 2008 605 615
20. D. Greenbaum, C. Colangelo, K. Williams, and M. Gerstein Comparing protein abundance and mRNA expression levels on a genomic scale Genome Biol. 4 2003 117
21. T.J. Griffin, S.P. Gygi, T. Ideker, B. Rist, J. Eng, L. Hood, and R. Aebersold Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae Mol. Cell. Proteomics 1 2002 323 333
22. J.R. Haanstra, M. Stewart, V.D. Luu, A. van Tuijl, H.V. Westerhoff, C. Clayton, and B.M. Bakker Control and regulation of gene expression: Quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei J. Biol. Chem. 283 2008 2495 2507
23. T.K. Harris, and M.M. Keshwani Measurement of enzyme activity Methods Enzymol. 463 2009 57 71
24. W. Hilt Targets of programmed destruction: A primer to regulatory proteolysis in yeast Cell. Mol. Life Sci. 61 2004 1615 1632 (Pubitemid 38962044)
25. J.H. Hofmeyr, and A. Cornish-Bowden Co-response analysis: A new experimental strategy for metabolic control analysis J. Theor. Biol. 182 1996 371 380 (Pubitemid 26377425)
26. A. Honda, Y. Mizokami, Y. Matsuzaki, T. Ikegami, M. Doy, and H. Miyazaki Highly sensitive assay of HMG-CoA reductase activity by LC-ESI-MS/MS J. Lipid Res. 48 2007 1212 1220 (Pubitemid 46708688)
27. W. Hu, T.J. Sweet, S. Chamnongpol, K.E. Baker, and J. Coller Co-translational mRNA decay in Saccharomyces cerevisiae Nature 461 2009 225 229
28. F. Jacob, and J. Monod Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 1961 318 356
29. A. Jacobson, and S.W. Peltz Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells Annu. Rev. Biochem. 65 1996 693 739 (Pubitemid 26250623)
30. R. Jaenisch, and A. Bird Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals Nat. Genet. 33 Suppl. 2003 245 254 (Pubitemid 36278835)
31. D. Kahn, and H.V. Westerhoff The regulatory strength: How to be precise about regulation and homeostasis Acta Biotheor. 41 1993 85 96
32. D.J. Klionsky Autophagy: From phenomenology to molecular understanding in less than a decade Nat. Rev. Mol. Cell Biol. 8 2007 931 937 (Pubitemid 47622558)
33. A. Kolkman, P. Daran-Lapujade, A. Fullaondo, M.M. Olsthoorn, J.T. Pronk, M. Slijper, and A.J. Heck Proteome analysis of yeast response to various nutrient limitations Mol. Syst. Biol. 2 2006 0026
34. C. Kraft, A. Deplazes, M. Sohrmann, and M. Peter Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease Nat. Cell Biol. 10 2008 602 610 (Pubitemid 351627380)
35. M. Kranendijk, G.S. Salomons, K.M. Gibson, C. Aktuglu-Zeybek, S. Bekri, E. Christensen, J. Clarke, A. Hahn, S.H. Korman, V. Mejaski-Bosnjak, A. Superti-Furga, and C. Vianey-Saban Development and implementation of a novel assay for L-2-hydroxyglutarate dehydrogenase (L-2-HGDH) in cell lysates: L-2-HGDH deficiency in 15 patients with L-2-hydroxyglutaric aciduria J. Inherit. Metab. Dis. 32 2009 713 719
36. M.R. Larsen, M.B. Trelle, T.E. Thingholm, and O.N. Jensen Analysis of posttranslational modifications of proteins by tandem mass spectrometry Biotechniques 40 2006 790 798 (Pubitemid 46534920)
37. D.D. Licatalosi, and R.B. Darnell RNA processing and its regulation: Global insights into biological networks Nat. Rev. Genet. 11 2010 75 87
38. L. Lindahl, and A. Hinnebusch Diversity of mechanisms in the regulation of translation in prokaryotes and lower eukaryotes Curr. Opin. Genet. Dev. 2 1992 720 726
39. F. Llaneras, and J. Pico Stoichiometric modelling of cell metabolism J. Biosci. Bioeng. 105 2008 1 11 (Pubitemid 351273657)
40. S. Meri, and M. Baumann Proteomics: Posttranslational modifications, immune responses and current analytical tools Biomol. Eng. 18 2001 213 220 (Pubitemid 32939340)
41. N. Mizushima, and D.J. Klionsky Protein turnover via autophagy: Implications for metabolism Annu. Rev. Nutr. 27 2007 19 40 (Pubitemid 351373346)
42. D. Molenaar, R. van Berlo, D. de Ridder, and B. Teusink Shifts in growth strategies reflect tradeoffs in cellular economics Mol. Syst. Biol. 5 2009 323
43. L.C. Myers, and R.D. Kornberg Mediator of transcriptional regulation Annu. Rev. Biochem. 69 2000 729 749
44. H. Nakatogawa, K. Suzuki, Y. Kamada, and Y. Ohsumi Dynamics and diversity in autophagy mechanisms: Lessons from yeast Nat. Rev. Mol. Cell Biol. 10 2009 458 467
45. S.F. Newbury Control of mRNA stability in eukaryotes Biochem. Soc. Trans. 34 2006 30 34 (Pubitemid 43235526)
46. J. Postmus, A.B. Canelas, J. Bouwman, B.M. Bakker, W. van Gulik, M.J. de Mattos, S. Brul, and G.J. Smits Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation J. Biol. Chem. 283 2008 23524 23532
47. K.A. Reijenga, J.L. Snoep, J.A. Diderich, H.W. van Verseveld, H.V. Westerhoff, and B. Teusink Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae Biophys. J. 80 2001 626 634 (Pubitemid 32128317)
48. S. Rossell, C.C. van der Weijden, A.L. Kruckeberg, B.M. Bakker, and H.V. Westerhoff Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae FEMS Yeast Res. 5 2005 611 619 (Pubitemid 40380700)
49. S. Rossell, C.C. van der Weijden, A. Lindenbergh, A. van Tuijl, C. Francke, B.M. Bakker, and H.V. Westerhoff Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 103 2006 2166 2171 (Pubitemid 43271641)
50. S. Rossell, A. Lindenbergh, C.C. van der Weijden, A.L. Kruckeberg, K. van Eunen, H.V. Westerhoff, and B.M. Bakker Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae FEMS Yeast Res. 8 2008 155 164
51. U. Sauer High-throughput phenomics: Experimental methods for mapping fluxomes Curr. Opin. Biotechnol. 15 2004 58 63 (Pubitemid 38224251)
52. U. Sauer Metabolic networks in motion: 13C-based flux analysis Mol. Syst. Biol. 2 2006 62
53. H.M. Sauro Regulatory responses and control analysis: Assessment of the relative importance of internal effectors A. Cornish-Bowden, M.L. Cardenas, Control of Metabolic Processes 1989 Plenum Press New York
54. R.G. Shulman, G. Bloch, and D.L. Rothman In vivo regulation of muscle glycogen synthase and the control of glycogen synthesis Proc. Natl. Acad. Sci. USA 92 1995 8535 8542
55. G. Stephanopoulos Metabolic fluxes and metabolic engineering Metab. Eng. 1 1999 1 11 (Pubitemid 129499367)
56. B.H. ter Kuile, and H.V. Westerhoff Transcriptome meets metabolome: Hierarchical and metabolic regulation of the glycolytic pathway FEBS Lett. 500 2001 169 171 (Pubitemid 32607554)
57. A.M. Tolkovsky Mitophagy Biochim. Biophys. Acta 1793 2009 1508 1515
58. J. van den Brink, A.B. Canelas, W.M. van Gulik, J.T. Pronk, J.J. Heijnen, J.H. de Winde, and P. Daran-Lapujade Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism Appl. Environ. Microbiol. 74 2008 5710 5723
59. K. van Eunen, J. Bouwman, A. Lindenbergh, H.V. Westerhoff, and B.M. Bakker Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast FEBS J. 276 2009 5521 5536
60. K. van Eunen, P. Dool, A.B. Canelas, J. Kiewiet, J. Bouwman, W.M. van Gulik, H.V. Westerhoff, and B.M. Bakker Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history IET Syst. Biol. 4 2010 157 168
61. K. van Eunen, J. Bouwman, P. Daran-Lapujade, J. Postmus, A.B. Canelas, F.I. Mensonides, R. Orij, I. Tuzun, J. van den Brink, G.J. Smits, W.M. van Gulik, and S. Brul Measuring enzyme activities under standardized in vivo-like conditions for systems biology FEBS J. 277 2010 749 760
62. W.A. van Winden, J.C. van Dam, C. Ras, R.J. Kleijn, J.L. Vinke, W.M. van Gulik, and J.J. Heijnen Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites FEMS Yeast Res. 5 2005 559 568 (Pubitemid 40380696)
63. G.W. Welling, A.J. Scheffer, and S. Welling-Wester Determination of enzyme activity by high-performance liquid chromatography J. Chromatogr. B Biomed. Appl. 659 1994 209 225 (Pubitemid 24298818)
64. H.V. Westerhoff, and J.C. Arents Two (completely) rate-limiting steps in one metabolic pathway? The resolution of a paradox using bacteriorhodopsin liposomes and the control theory Biosci. Rep. 4 1984 23 31 (Pubitemid 14143392)
65. W. Wiechert 13C metabolic flux analysis Metab. Eng. 3 2001 195 206
66. G.S. Wilkie, K.S. Dickson, and N.K. Gray Regulation of mRNA translation by 5′- and 3′-UTR-binding factors Trends Biochem. Sci. 28 2003 182 188 (Pubitemid 36507156)
67. S. Zaina, E.L. Perez-Luque, and G. Lund Genetics talks to epigenetics? The interplay between sequence variants and chromatin structure Curr. Genomics 11 2010 359 367