Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001

Zou, Wei; Liu, Li; Zhang, Jing; Yang, Hao-Ru; Zhou, M.; Hua, Qiang; Chen, Jian

doi:10.1016/j.jbiotec.2012.05.015

Cited by 38 publications

(24 citation statements)

References 34 publications

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“…Recent studies demonstrated that Bacillus sp. could release metabolites in amino acid biosynthesis (Liu et al, 2011a;Zhou et al, 2011) and purine during cell lysis upon sporulation Ma et al, 2011;Zhang et al, 2010), which can be used to compensate the deficient metabolism of K. vulgare (Zou et al, 2012). In this study, our results showed that the blank plasmid did not impair the growth and 2-KLG production in the consortium of K. vulgare-B.…”

Section: Effect Of Overexpression Of Endogenous L-sorbose Pathway On mentioning

confidence: 52%

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

Du¹,

Bai²,

Song³

et al. 2013

Metabolic Engineering

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Section: Effect Of Overexpression Of Endogenous L-sorbose Pathway On mentioning

confidence: 52%

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

Du¹,

Bai²,

Song³

et al. 2013

Metabolic Engineering

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“…Overexpressions of ZWF1, SOL3, MDH1, and GDH3 were positive for improved recombinant protein production, which demonstrated the high accuracy of prediction by GEM for heterologous enzyme production. Based on the successful application of GEMs in the metabolic engineering of model microorganism such as like E. coli and Saccharomyces cerevisiae (McCloskey et al 2013;Xu et al 2012Xu et al , 2013a, the GEMs of industrially important strains such as Candida glabrata, Ketogulonicigenium vulgare WSH-001, and Bacillus megaterium WSH002 have also been reconstructed (Xu et al 2013b;Zou et al 2012Zou et al , 2013. In silico metabolic engineering has further enhanced their cellular properties for industrial production.…”

Section: Gem-guided Metabolic Engineeringmentioning

confidence: 99%

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

Liu

Shin

et al. 2014

Appl Microbiol Biotechnol

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Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.

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“…The potential of such models for the investigation of optimal processing is now acknowledged and practiced 5,32–35 . Examples for applicative use include the optimal production or utilization of industrial compounds such as xylose 36 , biofuels 37 ,vitamins 38 and drug development 39 . In bioremediation, genome scale metabolic modeling approaches were applied for the design of Geobacter sulfurreducens strain capable of increased electron transfer and a higher Fe(III) respiratory that was beneficial for environmental bioremediation 40 .…”

Section: Introductionmentioning

confidence: 99%

Genome-Scale reconstruction ofPaenarthrobacter aurescensTC1 metabolic model towards the study of atrazine bioremediation

Ofaim

Zarecki

Porob

et al. 2019

Preprint

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Atrazine is an herbicide and pollutant of great environmental concern that is naturally biodegraded by microbial communities. The efficiency of biodegradation can be improved through the stimulating addition of fertilizers, electron acceptors, etc. In recent years, metabolic modelling approaches have become widely used as an in silico tool for organism-level phenotyping and the subsequent development of metabolic engineering strategies including biodegradation improvement. Here, we constructed a genome scale metabolic model, iRZ960, for Paenarthrobacter aurescens TC1 – a widely studied atrazine degrader - aiming at simulating its degradation activity. A mathematical stoichiometric metabolic model was constructed based on a published genome sequence of P. aurescens TC1. An Initial draft model was automatically constructed using the RAST and KBase servers. The draft was developed into a predictive model through semi-automatic gap-filling procedures including manual curation. In addition to growth predictions under different conditions, model simulations were used to identify optimized media for enhancing the natural degradation of atrazine without a need in strain design via genetic modifications. Model predictions for growth and atrazine degradation efficiency were tested in myriad of media supplemented with different combinations of carbon and nitrogen sources that were verified in vitro. Experimental validations support the reliability of the model’s predictions for both bacterial growth (biomass accumulation) and atrazine degradation. Predictive tools, such as the presented model, can be applied for achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation in changing environments.

show abstract

Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001

Cited by 38 publications

References 34 publications

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

Genome-Scale reconstruction ofPaenarthrobacter aurescensTC1 metabolic model towards the study of atrazine bioremediation

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