Metabolic flux balance analysis of an industrially useful microorganism Corynebacerium glutamicum by a genome-scale reconstructed model

Microorganisms have multi-hierarchical networks such as gene, protein and metabolites in the cells. In silico genome-scale metabolic models allow us to analyze characteristics of metabolic systems of organisms. In this study, we newly reconstructed a genome-scale metabolic model of an industrially useful microorganism, Corynebacterium glutamicum, based on genome sequence annotation and physiological data. The metabolic characteristics were analyzed using flux balance analysis (FBA). We simulated the metabolic fluxes both under aerobic and oxygen deprivation conditions. The predicted growth rates and production rates of organic acids as lactate and succinate exhibited good agreement with experimental data reported in the literatures. The genome-scale metabolic model provides a better understanding for evaluating metabolic capabilities and predicting metabolic characteristics of C. glutamicum. This can be a basis for in silico analyses of metabolic network.

[1]  M. Inui,et al.  Production of organic acids by Corynebacterium glutamicum under oxygen deprivation , 2005, Applied Microbiology and Biotechnology.

[2]  P. Gounon,et al.  Importance of mycoloyltransferases on the physiology of Corynebacterium glutamicum. , 2004, Microbiology.

[3]  U. Sauer,et al.  Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism , 1999, Journal of bacteriology.

[4]  S. Lee,et al.  Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation , 2005, Applied and Environmental Microbiology.

[5]  C. Ouzounis,et al.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes , 2005, Nucleic acids research.

[6]  C. Furusawa,et al.  Zipf's law in gene expression. , 2002, Physical review letters.

[7]  B. Palsson,et al.  The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[9]  A. Barabasi,et al.  Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.

[10]  M. Ikeda,et al.  The Corynebacterium glutamicum genome: features and impacts on biotechnological processes , 2003, Applied Microbiology and Biotechnology.

[11]  S. Udaka,et al.  STUDIES ON THE AMINO ACID FERMENTATION , 1957 .

[12]  B. Palsson,et al.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.

[13]  G. Stephanopoulos,et al.  Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction , 2000, Biotechnology and bioengineering.

[14]  Gregory Stephanopoulos,et al.  Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets , 2005, Nature Biotechnology.

[15]  Adam M. Feist,et al.  Modeling methanogenesis with a genome‐scale metabolic reconstruction of Methanosarcina barkeri , 2006 .

[16]  Jochen Förster,et al.  Modeling Lactococcus lactis using a genome-scale flux model , 2005, BMC Microbiology.

[17]  P. Brennan,et al.  Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis. , 2001, Glycobiology.

[18]  A. Goesmann,et al.  The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. , 2003, Journal of biotechnology.

[19]  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.

[20]  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.

[21]  Markus J. Herrgård,et al.  Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. , 2004, Genome research.

[22]  A. Barabasi,et al.  Global organization of metabolic fluxes , 2004 .

[23]  M. Inui,et al.  Production of d-lactic acid by Corynebacterium glutamicum under oxygen deprivation , 2005, Applied Microbiology and Biotechnology.

[24]  M. Cocaign-Bousquet,et al.  Growth Rate-Dependent Modulation of Carbon Flux through Central Metabolism and the Kinetic Consequences for Glucose-Limited Chemostat Cultures of Corynebacterium glutamicum , 1996, Applied and environmental microbiology.

[25]  B. Palsson,et al.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.

[26]  W. Leuchtenberger,et al.  Biotechnological production of amino acids and derivatives: current status and prospects , 2005, Applied Microbiology and Biotechnology.

[27]  Suteaki Shioya,et al.  Study on roles of anaplerotic pathways in glutamate overproduction of Corynebacterium glutamicum by metabolic flux analysis , 2007, Microbial cell factories.

[28]  B. Palsson,et al.  Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants , 2005, Journal of bacteriology.

[29]  F. Rainey,et al.  A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre. , 1999, International journal of systematic bacteriology.

[30]  C. Hoischen,et al.  Membrane alteration is necessary but not sufficient for effective glutamate secretion in Corynebacterium glutamicum , 1990, Journal of bacteriology.

[31]  G. Stephanopoulos.  Metabolic fluxes and metabolic engineering. , 1999, Metabolic engineering.

[32]  B. Palsson,et al.  Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data* , 2007, Journal of Biological Chemistry.

[33]  L. Nielsen,et al.  Modeling Hybridoma Cell Metabolism Using a Generic Genome‐Scale Metabolic Model of Mus musculus , 2008, Biotechnology progress.

[34]  S. Kinoshita,et al.  STUDIES ON LYSINE FERMENTATION I. , 1961 .

[35]  F. Neidhardt,et al.  Growth of the bacterial cell , 1983 .

[36]  H Sahm,et al.  Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing , 1996, Biotechnology and bioengineering.

[37]  Stephen S Fong,et al.  Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes , 2004, Nature Genetics.

[38]  Takashi Gojobori,et al.  Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria. , 2005, Metabolic engineering.

[39]  L. Eggeling,et al.  Handbook of Corynebacterium glutamicum , 2005 .