Constraint-based genome-scale metabolic modeling of Clostridium acetobutylicum behavior in an immobilized column

Bioresource Technology

Volumn 142, Issue , 2013, Pages 603-610

  Wallenius, Janne ^a   Viikilä, Matti ^a   Survase, Shrikant ^a   Ojamo, Heikki ^a   Eerikäinen, Tero ^a  

^a AALTO UNIVERSITY   (Finland)

Author keywords

Cell immobilization; Clostridia; Continuous fermentation; Flux balance analysis; Genome scale metabolic modeling

Indexed keywords

ACETONE; CELL IMMOBILIZATION; CLOSTRIDIUM; ETHANOL; FERMENTATION; GENES;

CLOSTRIDIUM ACETOBUTYLICUM; CONTINUOUS FERMENTATION; EXPERIMENTAL DATUM; FLUX BALANCE ANALYSIS; GENOME-SCALE METABOLIC MODELING; MEAN ABSOLUTE ERROR; OPTIMIZATION PROCEDURES; SOLVENT PRODUCTION;

METABOLISM;

ACETONE; ALCOHOL; BUTANOL; SUGAR;

BACTERIUM; CELL ORGANELLE; DATA SET; FERMENTATION; GENOME; IMMOBILIZATION; METABOLISM; NUMERICAL MODEL; SOLVENT; SUGAR;

ARTICLE; BACTERIAL GENOME; BACTERIAL METABOLISM; BEHAVIOR; CLOSTRIDIUM ACETOBUTYLICUM; FERMENTATION; IMMOBILIZATION; IMMOBILIZED CELL; NONHUMAN; PRIORITY JOURNAL;

CLOSTRIDIA; CLOSTRIDIUM ACETOBUTYLICUM;

EID: 84879427882     PISSN: 09608524     EISSN: 18732976     Source Type: Journal    
DOI: 10.1016/j.biortech.2013.05.085     Document Type: Article

References (35)

1. Amador-Noguez D., Feng X.J., Fan J., Roquet N., Rabitz H., Rabinowitz J.D. Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum. J. Bacteriol. 2010, 192:4452-4461.
2. Amador-Noguez D., Brasg I.A., Feng X.J., Roquet N., Rabinowitz J.D. Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum. Appl. Environ. Microbiol. 2011, 77:7984-7997.
3. Becker S.A., Feist A.M., Mo M.L., Hannum G., Palsson B.O., Herrgard M.J. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat. Protoc. 2007, 2:727-738.
4. Cheng C.L., Che P.Y., Chen B.Y., Lee W.J., Chien L.J., Chang J.S. High yield bio-butanol production by solvent-producing bacterial microflora. Bioresour. Technol. 2012, 113:58-64.
5. Hanly T., Urello M., Henson M. Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures. Appl. Microbiol. Biotechnol. 2012, 93:2529-2541.
6. Harris L.M., Desai R.P., Welker N.E., Papoutsakis E.T. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?. Biotechnol. Bioeng. 2000, 67:1-11.
7. Jang Y.S., Malaviya A., Cho C., Lee J., Lee S.Y. Butanol production from renewable biomass by clostridia. Bioresour. Technol. 2012, 123:653-663.
8. Jurgens G., Survase S., Berezina O., Sklavounos E., Linnekoski J., Kurkijarvi A., Vakeva M., van Heiningen A., Granstrom T. Butanol production from lignocellulosics. Biotechnol. Lett. 2012, 34:1415-1434.
9. Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
10. Kim H.U., Kim S.Y., Jeong H., Kim T.Y., Kim J.J., Choy H.E., Yi K.Y., Rhee J.H., Lee S.Y. Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol. Syst. Biol. 2011, 7.
11. Lee J., Yun H., Feist A.M., Palsson B.O., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol. 2008, 80:849-862.
12. Lewis N.E., Nagarajan H., Palsson B.O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 2012, 10:291-305.
13. Lutke-Eversloh T., Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr. Opin. Biotechnol. 2011, 22:634-647.
14. McAnulty M.J., Yen J.Y., Freedman B.G., Senger R.S. Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. BMC Syst. Biol. 2012, 6. 42-0509-6-42.
15. Milne C., Eddy J., Raju R., Ardekani S., Kim P., Senger R., Jin Y., Blaschek H., Price N. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst. Biol. 2011, 5:1-15.
16. Napoli F., Olivieri G., Russo M.E., Marzocchella A., Salatino P. Butanol production by Clostridium acetobutylicum in a continuous packed bed reactor. J. Ind. Microbiol. Biotechnol. 2010, 37:603-608.
17. Palsson B. Finding Functional States, in Systems Biology: Properties of Reconstructed Networks 2006, Cambridge University Press, New York, pp. 244-264.
18. Price N.D., Famili I., Beard D.A., Palsson B.O. Extreme pathways and Kirchhoff's second law. Biophys. J. 2002, 83:2879-2882.
19. Qureshi N., Maddox I.S. Continuous production of acetone-butanol-ethanol using immobilized cells of Clostridium acetobutylicum and integration with product removal by liquid-liquid extraction. J. Ferment. Bioeng. 1995, 80:185-189.
20. Qureshi N., Schripsema J., Lienhardt J., Blaschek H.P. Continuous solvent production by Clostridium beijerinckii BA101 immobilized by adsorption onto brick. World J. Microbiol. Biotechnol. 2000, 16:377-382.
21. Reed J.L. Shrinking the metabolic solution space using experimental datasets. PLoS Comput. Biol. 2012, 8:1-5.
22. Reed J.L., Patel T.R., Chen K.H., Joyce A.R., Applebee M.K., Herring C.D., Bui O.T., Knight E.M., Fong S.S., Palsson B.O. Systems approach to refining genome annotation. Proc. Natl. Acad. Sci. USA 2006, 103:17480-17484.
23. Roberts S., Gowen C., Brooks J.P., Fong S. Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst. Biol. 2010, 4:31.
24. Rogers P. Genetics and biochemistry of clostridium relevant to development of fermentation processes. Advances in Applied Microbiology 1984, 1-60. Academic Press.
25. Salimi F., Zhuang K., Mahadevan R. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol. J. 2010, 5:726-738.
26. Schellenberger J., Que R., Fleming R.M.T., Thiele I., Orth J.D., Feist A.M., Zielinski D.C., Bordbar A., Lewis N.E., Rahmanian S., Kang J., Hyduke D.R., Palsson B.O. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 2011, 6:1290-1307.
27. Schuetz R., Kuepfer L., Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 2007, 3.
28. Senger R.S., Papoutsakis E.T. Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol. Bioeng. 2008, 101:1036-1052.
29. Senger R.S., Papoutsakis E.T. Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol. Bioeng. 2008, 101:1053-1071.
30. Survase S.A., van Heiningen A., Granstrom T. Continuous bio-catalytic conversion of sugar mixture to acetone-butanol-ethanol by immobilized Clostridium acetobutylicum DSM 792. Appl. Microbiol. Biotechnol. 2012, 93:2309-2316.
31. Swann W.H. A survey of non-linear optimization techniques. FEBS Lett. 1969, 2(Suppl. 1):S39-S55.
32. Teusink B., Wiersma A., Molenaar D., Francke C., de Vos W.M., Siezen R.J., Smid E.J. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 2006, 281:40041-40048.
33. Van Hecke W., Hofmann T., De Wever H. Pervaporative recovery of ABE during continuous cultivation: enhancement of performance. Bioresour. Technol. 2013, 129:421-429.
34. Xu C., Liu L., Zhang Z., Jin D., Qiu J., Chen M. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl. Microbiol. Biotechnol. 2013, 97:519-539.
35. Zhang Y., Ma Y., Yang F., Zhang C. Continuous acetone-butanol-ethanol production by corn stalk immobilized cells. J. Ind. Microbiol. Biotechnol. 2009, 36:1117-1121.