Genome-scale reconstruction of a metabolic network for Gluconobacter oxydans 621H

Gluconobacter oxydans is a Gram-negative bacterium with a number of biotechnological applications. Although the genome of G. oxydans has been reported in 2005, the systematical cellular metabolism in this high-value bacterium, however, remains unclear. In this study, a genome-scale metabolic network of G. oxydans 621H, iXW433, was reconstructed and validated on the basis of the known genome annotations and biochemical information. This reconstructed model included 433 genes, 859 reactions, and 985 metabolites. To test the capability of the model, gene and reaction essentiality analysis, flux variability analysis, and robustness analysis simulations were performed. The metabolic states predicted by the model were highly consistent with the experimental data of G. oxydans. According to the result, 92 genes and 137 reactions were identified to be essential, 194 reactions were found to be variable by flux variability analysis, and 2 possible genetically modified targets were determined. The model would be valuable for further research on G. oxydans and thereby expanding its application.

[1]  J. Edwards,et al.  Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* , 1999, The Journal of Biological Chemistry.

[2]  W. Olijve,et al.  An analysis of the growth of Gluconobacter oxydans in chemostat cultures , 1979, Archives of Microbiology.

[3]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[4]  E. Ruppin,et al.  Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D. Heefner,et al.  Change in quantity of lipids and cell size during intracytoplasmic membrane formation in Gluconobacter oxydans , 1976, Journal of bacteriology.

[6]  H. Sahm,et al.  The use of microorganisms in L-ascorbic acid production. , 2006, Journal of biotechnology.

[7]  Adam M. Feist,et al.  Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.

[8]  J. Nielsen,et al.  Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. , 2005, Genome research.

[9]  B. Palsson,et al.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.

[10]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[11]  Jeong-Sun Seo,et al.  Genome‐scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis , 2011, Biotechnology and bioengineering.

[12]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[13]  J. Edwards,et al.  Robustness Analysis of the Escherichiacoli Metabolic Network , 2000, Biotechnology progress.

[14]  Antje Chang,et al.  BRENDA, the enzyme information system in 2011 , 2010, Nucleic Acids Res..

[15]  An-Ping Zeng,et al.  Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms , 2003, Bioinform..

[16]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[17]  S. Lee,et al.  Metabolic flux analysis and metabolic engineering of microorganisms. , 2008, Molecular bioSystems.

[18]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[19]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[20]  R. Mahadevan,et al.  The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.

[21]  R. Sharan,et al.  A genome-scale computational study of the interplay between transcriptional regulation and metabolism , 2007, Molecular systems biology.

[22]  J. Tkáč,et al.  A novel microbial biosensor based on cells of Gluconobacter oxydans for the selective determination of 1,3-propanediol in the presence of glycerol and its application to bioprocess monitoring , 2007, Analytical and bioanalytical chemistry.

[23]  A. Bories,et al.  Glycerol inhibition of growth and dihydroxyacetone production byGluconobacter oxydans , 1992, Current Microbiology.

[24]  D. Heefner,et al.  Lipid and fatty acid composition of Gluconobacter oxydans before and after intracytoplasmic membrane formation , 1978, Journal of bacteriology.

[25]  U. Deppenmeier,et al.  Biochemistry and biotechnological applications of Gluconobacter strains , 2002, Applied Microbiology and Biotechnology.

[26]  Özlem Ates,et al.  Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043 , 2011, BMC Systems Biology.

[27]  W. Soetaert,et al.  The Genus Gluconobacter Oxydans: Comprehensive Overview of Biochemistry and Biotechnological Applications , 2007, Critical reviews in biotechnology.

[28]  C. Maranas,et al.  Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism , 2011, PloS one.

[29]  Wei Dongzhi,et al.  Asymmetric oxidation by Gluconobacter oxydans , 2006, Applied Microbiology and Biotechnology.

[30]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[31]  H. Sahm,et al.  High-yield 5-keto-d-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5-dehydrogenases of Gluconobacter oxydans , 2006, Applied Microbiology and Biotechnology.

[32]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[33]  H. Sahm,et al.  An easy cloning and expression vector system for Gluconobacter oxydans. , 2008, International journal of food microbiology.

[34]  W. F. Fricke,et al.  Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans , 2005, Nature Biotechnology.

[35]  Yuguo Zheng,et al.  Use of glycerol for producing 1,3-dihydroxyacetone by Gluconobacter oxydans in an airlift bioreactor. , 2011, Bioresource technology.

[36]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[37]  F. Lichtenthaler,et al.  Unsaturated O- and N-heterocycles from carbohydrate feedstocks. , 2002, Accounts of chemical research.