Network reduction in metabolic pathway analysis: Elucidation of the key pathways involved in the photoautotrophic growth of the green alga Chlamydomonas reinhardtii

Metabolic Engineering

Volumn 14, Issue 4, 2012, Pages 458-467

  Rügen, Marco ^a   Bockmayr, Alexander ^a   Legrand, Jack ^b   Cogne, Guillaume ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITÉ DE NANTES   (France)

Author keywords

Cellular energetics; Chlamydomonas reinhardtii; Metabolic pathway analysis; Photoautotrophic metabolism

Indexed keywords

ACTIVITY PATTERNS; CELLULAR ENERGETICS; CHLAMYDOMONAS REINHARDTII; ELEMENTARY MODE; ENERGETIC APPROACH; FLUX VECTORS; GREEN ALGA; METABOLIC FLUX DISTRIBUTION; METABOLIC NETWORK; METABOLIC PATHWAY ANALYSIS; NETWORK REDUCTION; OBJECTIVE FUNCTIONS; OPTIMALITY CRITERIA; PHOTOAUTOTROPHIC GROWTH; PHOTOBIORE-ACTOR;

GALLIUM ALLOYS; PHYSIOLOGY;

METABOLISM;

ALGAL GROWTH; ARTICLE; BIOREACTOR; CELL ENERGY; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; DECOMPOSITION; GROWTH RATE; METABOLISM; NONHUMAN; PHOTOAUTOTROPH; PHOTOSYNTHETIC PHOTON FLUX DENSITY; PRIORITY JOURNAL;

CHLAMYDOMONAS REINHARDTII; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PHOTOBIOREACTORS;

CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA;

EID: 84862160168     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2012.01.009     Document Type: Article

References (34)

1. Beard B.A., Babson E., Curtis E., Qian H. Thermodynamic constraints for biochemical networks. J. Theor. Biol. 2004, 228:327-333.
2. Beard B.A., Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 2002, 83:79-86.
3. Boyle N.R., Morgan J.A. Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation. Metab. Eng. 2011, 13:150-158.
4. Cakir T., Kirdar B., Ulgen K.O. Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks. Biotechnol. Bioeng. 2004, 86:251-260.
5. Chang R.L., Ghamsari L., Manichaikul A., Hom E.F.Y., Balaji S., Fu W., Shen Y., Hao T., Palsson B.O., Salehi-Ashtiani K., Papin J.A. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol. Syst. Biol. 2011, 7:518.
6. Chisti Y. Biodiesel from microalgae. Biotechnol. Adv. 2007, 25:294-306.
7. Cogne G., Rügen M., Bockmayr A., Titica M., Dussap C.-G., Cornet J.-F., Legrand J. A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: application to the green alga Chlamydomonas reinhardtii. Biotechnol. Prog. 2011, 27:631-640.
8. Cornet J.-F., Dussap C.-G. A simple and reliable formula for assessment of maximum volumetric productivities in photobioreactors. Biotechnol. Prog. 2009, 25:424-435.
9. Cornet J.-F., Dussap C.-G., Gros J.-B. Kinetics and energetics of photosynthetic micro-organisms in photobioreactors. Adv. Biochem. Eng./Biotechnol. 1998, 59:155-224.
10. Diniz S.C., Voss I., Steinbuchel A. Optimization of cyanophycin production in recombinant strains of Pseudomonas putida and Ralstonia eutropha employing elementary mode analysis and statistical experimental design. Biotechnol. Bioeng. 2006, 93:698-717.
11. Fischer C.R., Klein-Marcuschamer D., Stephanopoulos G. Selection and optimization of microbial hosts for biofuels production. Metab. Eng. 2008, 10:295-304.
12. Gavrilescu M., Chisti Y. Biotechnology-a sustainable alternative for chemical industry. Biotechnol. Adv. 2005, 23:471-499.
13. 2. Trends Biotechnol. 2000, 18:506-511.
14. Jungers R.M., Zamorano F., Blondel V.D., Wouwer A.V., Bastin G. Fast computation of minimal elementary decompositions of metabolic flux vectors. Automatica 2011, 47:1255-1259.
15. Klamt S., Stelling J. Two approaches for metabolic pathway analysis?. Trends Biotechnol. 2003, 21:64-69.
16. Kromer J.O., Wittmann C., Schroder H., Heinzle E. Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab. Eng. 2006, 8:353-369.
17. Li Y., Han D., Hu G., Dauvillée D., Sommerfeld M., Ball S., Hu Q. Chlamydomonas starchless mutant defective in adp-glucose pyrophosphorylase hyper-accumulates triacylglycerol. Metab. Eng. 2010, 12:387-391.
18. Manichaikul A., Ghamsari L., Hom E.F.Y., Lin C., Murray R.R., Chang R.L., Balaji S., Hao T., Shen Y., Chavali A.K., Thiele I., Yang X., Fan C., Mello E., Hill D.E., Vidal M., Salehi-Ashtiani K., Papin J.A. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat. Methods 2009, 6:589-592.
19. Melis A. Green alga hydrogen production: progress, challenges and prospects. Int. J. Hydrogen Energy 2002, 27:1217-1228.
20. Orman M.A., Berthiaume F., Androulakis I.P., Ierapetritou M.G. Pathway analysis of liver metabolism under stressed condition. J. Theor. Biol. 2011, 272:131-140.
21. Papin J.A., Price N.D., Palsson B.O. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 2002, 12:1889-1900.
22. Price N.D., Famili I.F., Beard D.A., Palsson B. Extreme pathways and Kirchoff's second law. Biophys. J. 2002, 83:2879-2882.
23. Rutter M.T., Zufall R.A. Pathway length and evolutionary constraint in amino acid biosynthesis. J. Mol. Evol. 2004, 58:218-224.
24. Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 2000, 203:229-248.
25. Schuster S., Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 1994, 2:165-182.
26. Schwartz J.M., Kanehisa M. A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 2005, 21:204-205.
27. Schwarz R., Musch P., von Kamp A., Engels B., Schirmer H., Schuster S., Dandekar T. Yana-a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinf. 2005, 6.
28. Stelling J., Klamt S., Bettenbrock K., Schuster S., Gilles E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420:190-193.
29. Stucki J.W. The optimal efficiency and the economic degrees of coupling of oxidative phosphorylation. Eur. J. Biochem. 1980, 109:269-283.
30. Takache H., Christophe G., Cornet J.-F., Pruvost J. Experimental and theoretical assessment of maximum productivities for the microalgae Chlamydomonas reinhardtii in two different geometries of photobioreactors. Biotechnol. Prog. 2009, 26:431-440.
31. Terzer M., Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24:2229-2235.
32. Unrean P., Srienc F. Metabolic networks evolve towards states of maximum entropy production. Metab. Eng. 2011, 13:666-673.
33. Wagner C., Urbanczik R. The geometry of the flux cone of a metabolic network. Biophys. J. 2005, 89:3837-3845.
34. Wiback S.J., Mahadevana R., Palsson B.O. Reconstructing metabolic flux vectors from extreme pathways: defining the α-spectrum. J. Theor. Biol. 2003, 224:313-324.