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Reconstruction of a Genome-Scale Metabolic Model to Simulate Uncoupled Growth of Zymomonas mobilis
Abstract:Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1125485Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 768
 Lee, K.Y., et al., The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microbial cell factories, 2010. 9(1): p. 94.
 Kalnenieks, U., Physiology of Zymomonas mobilis: Some Unanswered Questions. Advances in microbial physiology, 2006. 51: p. 73-117.
 Rutkis, R., et al., The inefficient aerobic energetics of Zymomonas mobilis: Identifying the bottleneck. Journal of basic microbiology, 2014.
 Kalnenieks, U., et al., Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies. Frontiers in microbiology, 2014. 5.
 Widiastuti, H., et al., Genome‐scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis. Biotechnology and bioengineering, 2011. 108(3): p. 655-665.
 Orth, J.D., et al., A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011. Molecular systems biology, 2011. 7(1).
 Thiele, I., and B.Ø. Palsson, A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols, 2010. 5(1): p. 93-121.
 Feist, A.M., and B.Ø. Palsson, The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature biotechnology, 2008. 26(6): p. 659-667.
 Seo, J.-S., et al., The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nature biotechnology, 2004. 23(1): p. 63-68.
 Yang, S., et al., Improved genome annotation for Zymomonas mobilis. Nature biotechnology, 2009. 27(10): p. 893-894.
 Pentjuss, A., et al., Biotechnological potential of respiring< i> Zymomonas mobilis: A stoichiometric analysis of its central metabolism. Journal of biotechnology, 2013. 165(1): p. 1-10.
 Keating, S.M., et al., SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics, 2006. 22(10): p. 1275-1277.
 Becker, S.A., et al., Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature protocols, 2007. 2(3): p. 727-738.
 Kanehisa, M., et al., KEGG for integration and interpretation of largescale molecular data sets. Nucleic acids research, 2011: p. gkr988.
 Karp, P.D., et al., Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic acids research, 2005. 33(19): p. 6083-6089.
 Schomburg, I., et al., BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic acids research, 2012: p. gks1049.
 Ren, Q., K. Chen, and I.T. Paulsen, TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic acids research, 2007. 35(suppl 1): p. D274-D279.
 Carey, V.C. and L. Ingram, Lipid composition of Zymomonas mobilis: effects of ethanol and glucose. Journal of bacteriology, 1983. 154(3): p. 1291-1300.
 Sahm, H., S. Bringer-Meyer, and G.A. Sprenger, The genus Zymomonas, in The prokaryotes. 2006, Springer. p. 201-221.
 Vincent, S.P., P. Sinay, and M. Rohmer, Composite hopanoid biosynthesis in Zymomonas mobilis: N-acetyl-D-glucosamine as precursor for the cyclopentane ring linked to bacteriohopanetetrol. Chemical Communications, 2003(6): p. 782-783.
 Welander, P.V., et al., Identification and characterization of Rhodopseudomonas palustris TIE‐1 hopanoid biosynthesis mutants. Geobiology, 2012. 10(2): p. 163-177.
 Hayashi, T., T. Kato, and K. Furukawa, Respiratory chain analysis of Zymomonas mobilis mutants producing high levels of ethanol. Applied and environmental microbiology, 2012. 78(16): p. 5622-5629.
 Goodman, A.E., P.L. Rogers, and M.L. Skotnicki, Minimal medium for isolation of auxotrophic Zymomonas mutants. Applied and environmental microbiology, 1982. 44(2): p. 496.
 De Graaf, A.A., et al., Metabolic state of Zymomonas mobilis in glucose- , fructose-, and xylose-fed continuous cultures as analysed by 13C-and 31P-NMR spectroscopy. Archives of microbiology, 1999. 171(6): p. 371-385.