Metabolic flux analysis in complex isotopolog space. Recycling of glucose in tobacco plants

Phytochemistry

Volumn 66, Issue 3, 2005, Pages 323-335

  Ettenhuber, Christian ^a   Radykewicz, Tanja ^a   Kofer, Waltraud ^b   Koop, Hans Ulrich ^b   Bacher, Adelbert ^a   Eisenreich, Wolfgang ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b Department I   (Germany)

Author keywords

Carbon flux; In silico modelling; Isotopolog; Metabolism; Nicotiana tabacum; NMR

Indexed keywords

GLUCOSE; SUCROSE; WATER;

ARTICLE; CARBOHYDRATE METABOLISM; CARBON DIOXIDE FIXATION; CARBON NUCLEAR MAGNETIC RESONANCE; CATABOLISM; CITRIC ACID CYCLE; COMPUTER MODEL; EXTRACTION; GENETIC ALGORITHM; GLYCOLYSIS; ISOTOPE LABELING; PENTOSE PHOSPHATE CYCLE; PLANT GROWTH; PLANT LEAF; PLANT METABOLISM; PLANT ROOT; TOBACCO;

ALGORITHMS; CARBON; CARBON ISOTOPES; GLUCOSE; ISOMERISM; MAGNETIC RESONANCE SPECTROSCOPY; PLANT LEAVES; TOBACCO; ZEA MAYS;

NICOTIANA; NICOTIANA OBTUSIFOLIA; NICOTIANA TABACUM;

EID: 12844253308     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2004.12.014     Document Type: Article

References (46)

1. Arabidopsis Genome Initiative, 2001. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815
2. A. Bacher, C. Rieder, D. Eichinger, G. Fuchs, D. Arigoni, and W. Eisenreich Elucidation of biosynthetic pathways and metabolic flux patterns via retrobiosynthetic NMR analysis FEMS Microbiol. Rev. 22 1999 567 598
3. R. Bligny, and R. Douce NMR and plant metabolism Curr. Opin. Plant. Biol. 4 2001 191 196
4. D. Bray Molecular networks: the top-down view Science 301 2003 1864 1866
5. H. Brunengraber, J.K. Kelleher, and C. Des Rosiers Applications of mass isotopomer analysis to nutrition research Annu. Rev. Nutr. 17 1997 559 596
6. S.W. Clifton, and B.A. Roe The beautifully simple but intriguingly complex world of small genomes Genome Res. 8 1998 331 333
7. C. Cobelli, G. Toffolo, and D.M. Foster Tracer-to-tracee ratio for analysis of stable isotope tracer data: link with radioactive kinetic formalism Am. J. Physiol. 262 1992 968 975
8. D. Eisenberg, E.M. Marcotte, I. Xenarios, and T.O. Yeates Protein function in the post-genomic era Nature 405 2000 823 826
9. W. Eisenreich, C. Ettenhuber, R. Laupitz, C. Theus, and A. Bacher Isotopolog perturbation techniques for metabolic networks: Metabolic recycling of nutritional glucose in Drosophila melanogaster Proc. Natl. Acad. Sci. USA 101 2004 6764 6769
10. W. Eisenreich, G. Strauß, U. Werz, A. Bacher, and G. Fuchs Retrobiosynthetic analysis of 1 carbon fixation in the phototrophic eubacterium Chloroflexus aurantiacus Eur. J. Biochem. 215 1993 619 632
11. Ettenhuber, C., Eisenreich, W., 2004. 4F service 1.0. Available from: http://xsystem.org.chemie.tu-muenchen.de
12. S.J. Fey, A. Nawrocki, M.R. Larsen, A. Gorg, P. Roepstorff, G.N. Skews, R. Williams, and P.M. Larsen Proteome analysis of Saccharomyces cerevisiae: a methodological outline Electrophoresis 18 1997 1361 1372
13. 13C NMR flux ratio analysis of Escherichia coli central carbon metabolism in microaerobic bioprocesses J. Am. Chem. Soc. 121 1999 1407 1408
14. O. Fiehn, J. Kopka, P. Dormann, T. Altmann, R.N. Trethewey, and L. Willmitzer Metabolite profiling for plant functional genomics Nat. Biotechnol. 18 2000 1157 1161
15. B.D. Follstadt, and G. Stephanopoulos Effect of reversible reaction on isotope label redistribution. Analysis of the pentose phosphate pathway Eur. J. Biochem. 202 1998 360 371
16. C.M. Fraser The minimal gene complement of Mycoplasma genitalium Science 270 1995 397 403
17. D.T. Gillespie Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 1977 2340 2361
18. D.T. Gillespie, and L.R. Petzold Improved leap-size selection for accelerated stochastic simulation J. Chem. Phys. 119 2004 8229 8234
19. E. Glawischnig, A. Gierl, A. Tomas, A. Bacher, and W. Eisenreich Retrobiosynthetic nuclear magnetic resonance analysis of amino acid biosynthesis and intermediary metabolism. Metabolic flux in developing maize kernels Plant Physiol. 130 2002 1717 1727
20. 13C content of primary and secondary plant products in different cell compartments and that in decomposing Basidiomycetes Plant Physiol. 4 1993 1287 1290
21. S.A. Goff A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 296 2002 92 100
22. Holland, J.H., 1975. Adaptation in natural and artificial systems. Ph.D. Thesis, University of Michigan
23. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
24. N.J. Kruger, R.G. Ratcliffe, and A. Roscher Quantitative approaches for analysing fluxes through plant metabolic networks using NMR and stable isotope labelling Phytochem. Rev. 2 2003 17 30
25. D.J. Lockhart, and E.A. Winzeler Genomics, gene expression and DNA arrays Nature 405 2000 827 836
26. A. Manandhar, and P.M. Gresshoff Blue spruce (Picea pungens) tissue and cell culture Cytobiosphere 29 1980 175 182
27. W. Müller, H. Fricke, A.N. Halliday, M.T. McCulloch, and J.A. Wartho Origin and migration of the Alpine Iceman Science 203 2003 862 866
28. S.M. Park, M.I. Klapa, A.J. Sinskey, and G. Stephanopoulos Metabolite and isotopomer balancing in the analysis of metabolic cycles: II Appl. Biotechnol. Bioeng. 62 1999 392 401
29. B. Powel-Douglass Real Time UML third ed. 2004 Addison-Wesley
30. R.G. Ratcliffe, A. Roscher, and Y. Shachar-Hill Plant NMR spectroscopy Prog. Nucl. Magn. Reson. Spectrosc. 39 2001 267 300
31. Rechenberg, I., 1973. Evolution strategies. Ph.D. Thesis, University of Stuttgart
32. Rice Chromosome 10 Sequencing Consortium, 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566-1569
33. A. Roscher, N.J. Kruger, and R.G. Ratcliffe Strategies for metabolic flux analysis in plants using isotope labelling J. Biotechnol. 77 2000 81 102
34. A. Rossmann, M. Butzenlechner, and H.L. Schmidt Evidence for a nonstatistical carbon isotope distribution in natural glucose Plant Physiol. 96 1991 609 614
35. H.L. Schmidt Fundamentals and systematics of the non-statistical distributions of isotopes in natural compounds Naturwissenschaften 90 2003 537 552
36. K. Schmidt, M. Carlsen, J. Nielsen, and J. Villadsen Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices Biotechnol. Bioeng. 55 1997 831 840
37. 13C Tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches Biotechnol. Bioeng. 58 1998 254 257
38. G. Sriram, and J.V. Shanks Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping Metab. Eng. 6 2004 116 132
39. 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism Eur. J. Biochem. 232 1995 433 438
40. 13C, 1H COSY NMR data Biotechn. Bioeng. 80 2002 731 745
41. W. Wiechert, M. Möllney, N. Isermann, M. Murzel, and A.A. de Graaf Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems Biotechnol. Bioeng. 66 1999 69 85
42. W. Wiechert, and M. Murzel Metabolic isotopomer labeling systems. Part I: global dynamic behaviour Math. Biosci. 169 2001 173 205
43. W. Wiechert, and A.A. de Graaf Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments Biotechnol. Bioeng. 55 1997 101 117
44. W. Wiechert, C. Siefke, A.A. de Graaf, and A. Marx Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis Biotechnol. Bioeng. 55 1997 118 135
45. K. Yamada, J. Lim, J.M. Dale, H. Chen, P. Shinn, C.J. Palm, A.M. Southwick, H.C. Wu, C. Kim, M. Nguyen, P. Pham, R. Cheuk, G. Karlin-Newmann, S.X. Liu, B. Lam, H. Sakano, T. Wu, G. Yu, M. Miranda, H.L. Quach, M. Tripp, C.H. Chang, J.M. Lee, M. Toriumi, M.M. Chan, C.C. Tang, C.S. Onodera, J.M. Deng, K. Akiyama, Y. Ansari, T. Arakawa, J. Banh, F. Banno, L. Bowser, S. Brooks, P. Carninci, Q. Chao, N. Choy, A. Enju, A.D. Goldsmith, M. Gurjal, N.F. Hansen, Y. Hayashizaki, C. Johnson-Hopson, V.W. Hsuan, K. Iida, M. Karnes, S. Khan, E. Koesema, J. Ishida, P.X. Jiang, T. Jones, J. Kawai, A. Kamiya, C. Meyers, M. Nakajima, M. Narusaka, M. Seki, T. Sakurai, M. Satou, R. Tamse, M. Vaysberg, E.K. Wallender, C. Wong, Y. Yamamura, S. Yuan, K. Shinozaki, R.W. Davis, A. Theologis, and J.R. Ecker Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 2003 842 846
46. E. Yourdon Modern Structured Systems Analysis 1989 Prentice-Hall Englewood Cliffs, NJ