Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model.

A genome-scale metabolic model of Bacillus megaterium WSH002, an industrial bacterium widely used in the vitamin C industry, was reconstructed on the basis of the genome annotation and data from the literature and biochemical databases. It comprises 1112 reactions, 993 metabolites, and 1055 genes, including 43 new annotated genes. This model was able to predict qualitatively and quantitatively the growth of B. megaterium on a range of carbon and nitrogen sources, and the results agreed well with experimental data. A gene essentiality analysis predicted a core metabolic essential gene set of 57 genes on three different media. Furthermore, constraint-based analysis revealed that B. megaterium WSH002 is capable of producing and exporting several key metabolites, which could promote the growth of Ketogulonicigenium vulgare and 2-keto-l-gulonic acid (2-KLG) production. Here, the model represents a helpful tool for understanding and exploring this important industrial organism.

[1]  D. Ellar,et al.  Morphogenesis of the membrane-bound electron-transport system in sporulating Bacillus megaterium KM. , 1975, European journal of biochemistry.

[2]  D. Jahn,et al.  Metabolic engineering of cobalamin (vitamin B12) production in Bacillus megaterium , 2009, Microbial biotechnology.

[3]  Jens Nielsen,et al.  Use of genome‐scale metabolic models for understanding microbial physiology , 2010, FEBS letters.

[4]  Rick L Stevens,et al.  iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations , 2009, Genome Biology.

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

[6]  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.

[7]  F. Kawamura,et al.  Cloning of oxetanocin A biosynthetic and resistance genes that reside on a plasmid of Bacillus megaterium strain NK84-0128. , 1999, Bioscience, biotechnology, and biochemistry.

[8]  M. Vihinen,et al.  Microbial amylolytic enzymes. , 1989, Critical reviews in biochemistry and molecular biology.

[9]  Weiwen Zhang,et al.  Proteomic Analysis of Ketogulonicigenium vulgare under Glutathione Reveals High Demand for Thiamin Transport and Antioxidant Protection , 2012, PloS one.

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

[11]  Metabolomic profiling elucidates community dynamics of the Ketogulonicigenium vulgare–Bacillus megaterium consortium , 2012, Metabolomics.

[12]  Zhemin Zhou,et al.  Complete Genome Sequence of the Industrial Strain Bacillus megaterium WSH-002 , 2011, Journal of Bacteriology.

[13]  A. Wieczorek,et al.  Isolation of microorganisms capable fo styrene degradation , 2006 .

[14]  P. Vary.  Prime time for Bacillus megaterium. , 1994, Microbiology.

[15]  Rick L. Stevens,et al.  High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.

[16]  H. S. Levinson,et al.  EFFECT OF SUGARS AND OTHER CARBON COMPOUNDS ON GERMINATION AND POSTGERMINATIVE DEVELOPMENT OF BACILLUS MEGATERIUM SPORES , 1964, Journal of bacteriology.

[17]  Jörg Stülke,et al.  Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. , 2003, Metabolic engineering.

[18]  P. Vary.  Development of genetic engineering in Bacillus megaterium. , 1992, Biotechnology.

[19]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[20]  C. Wittmann,et al.  Effect of different carbon sources on central metabolic fluxes and the recombinant production of a hydrolase from Thermobifida fusca in Bacillus megaterium. , 2007, Journal of biotechnology.

[21]  Junwei Sun,et al.  Integrated Proteomic and Metabolomic Analysis of an Artificial Microbial Community for Two-Step Production of Vitamin C , 2011, PloS one.

[22]  Hao Song,et al.  Metabolome Profiling Reveals Metabolic Cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during Induced Swarm Motility , 2011, Applied and Environmental Microbiology.

[23]  R. Crawford.  Degradation of 3-hydroxybenzoate by bacteria of the genus Bacillus. , 1975, Applied microbiology.

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

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

[26]  B. Palsson,et al.  Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods , 2012, Nature Reviews Microbiology.

[27]  C. Thermes,et al.  Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. , 1998, The Biochemical journal.

[28]  Dieter Jahn,et al.  Genome Sequences of the Biotechnologically Important Bacillus megaterium Strains QM B1551 and DSM319 , 2011, Journal of bacteriology.

[29]  Laura Marina Pinotti,et al.  The penicillin G acylase production by B. megaterium is amino acid consumption dependent , 2007, Biotechnology and bioengineering.

[30]  C. Wittmann,et al.  Comparative study on central metabolic fluxes of Bacillus megaterium strains in continuous culture using 13C labelled substrates , 2006, Bioprocess and biosystems engineering.

[31]  Peter B. McGarvey,et al.  Infrastructure for the life sciences: design and implementation of the UniProt website , 2009, BMC Bioinformatics.

[32]  Akiyasu C. Yoshizawa,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Environmental health perspectives.

[33]  W. Deckwer,et al.  Bacillus megaterium—from simple soil bacterium to industrial protein production host , 2007, Applied Microbiology and Biotechnology.

[34]  W. Deckwer,et al.  Codon optimized Thermobifida fusca hydrolase secreted by Bacillus megaterium , 2007, Biotechnology and bioengineering.

[35]  Liming Liu,et al.  Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001. , 2012, Journal of biotechnology.

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

[37]  Liming Liu,et al.  Structure, mechanism and regulation of an artificial microbial ecosystem for vitamin C production , 2013, Critical reviews in microbiology.