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Modeling and Robustness Analysis of Biochemical Networks of Glycerol Metabolism by Klebsiella Pneumoniae [chapter]

Jianxiong Ye, Enmin Feng, Lei Wang, Zhilong Xiu, Yaqin Sun
2009 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Glycerol bioconversion to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae (K. pneumoniae) can be characterized by an intricate network of interactions among biochemical fluxes, metabolic compounds, key  ...  To determine the most reasonable metabolic network from all possible ones, we establish a quantitative definition of biological robustness and undertake parameter identification and robustness analysis  ...  and Discussions Metabolic network of glycerol enzyme-catalytic dissimilation by K. pneumoniae includes some uncertain factors since the transport mechanisms of glycerol and 1,3-PD across the cell membrane  ... 
doi:10.1007/978-3-642-02466-5_44 fatcat:5hwh45lvxza6vpzmjonrx4qd44

Computational method for inferring objective function of glycerol metabolism in Klebsiella pneumoniae

Zhaohua Gong, Chongyang Liu, Enmin Feng, Qingrui Zhang
2009 Computational biology and chemistry  
Flux balance analysis (FBA) is an effective tool in the analysis of metabolic network.  ...  In this work, we propose two nonlinear bilevel programming models on anaerobic glycerol metabolism in Klebsiella pneumoniae (K. pneumoniae) for 1,3-propanediol (1,3-PD) production.  ...  Acknowledgements This research is supported by National Natural Science Foundation of China (No. 10671126) and National Basic Research Program of China (No. 2007AA02Z208).  ... 
doi:10.1016/j.compbiolchem.2008.06.005 pmid:18804419 fatcat:b5dthfb6vfbb3l4lafra7j5fge

Contemplating 3-Hydroxypropionic Acid Biosynthesis in Klebsiella pneumoniae

Ying Li, Pingfang Tian
2015 Indian Journal of Microbiology  
Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, here we advocate protocols for overproducing 3-HP in K. pneumoniae.  ...  To surmount this problem, this review aims to portray a picture of 3-HP biosynthesis, involving 3-HP-synthesizing strains, biochemical attributes, metabolic pathways and key enzymes.  ...  Klebsiella pneumoniae and Glycerol Dissimilation Among 3-HP-synthesizing strains, Klebsiella pneumoniae is of great attractiveness due to its biochemical attributes, including remarkable capacity to metabolize  ... 
doi:10.1007/s12088-015-0513-0 pmid:25805899 pmcid:PMC4363255 fatcat:csonomlqvngwdamsefp3i3q7ze

Metabolic Changes in Klebsiella oxytoca in Response to Low Oxidoreduction Potential, as Revealed by Comparative Proteomic Profiling Integrated with Flux Balance Analysis

Y. Zhu, D. Li, G. Bao, S. Wang, S. Mao, J. Song, Y. Li, Y. Zhang
2014 Applied and Environmental Microbiology  
As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism.  ...  Here we characterized the effect of altering ORP in a 1,3-propanediol producer, Klebsiella oxytoca, by comparative proteomic profiling combined with flux balance analysis.  ...  The working model was Klebsiella oxytoca.  ... 
doi:10.1128/aem.03327-13 pmid:24584239 pmcid:PMC3993281 fatcat:iwpkq37bjjbofnndphxojicqge

Identification and robustness analysis of nonlinear hybrid dynamical system of genetic regulation in continuous culture

Qi Yang, Lei Wang, Enmin Feng, Hongchao Yin, Zhilong Xiu
2017 Journal of Industrial and Management Optimization  
Numerical results indicate that the most likely transmembrane mode of transport is active transport coupling with passive diffusion for glycerol and 1,3-propanediol. 2010 Mathematics Subject Classification  ...  A novel quantitative definition of biological robustness is proposed to characterize the system's resilience when system parameters were perturbed.  ...  Over the past years, a number of models have been proposed to describe the bio-dissimilation process of glycerol to 1,3-PD by Klebsiella pneumoniae (K. pneumoniae).  ... 
doi:10.3934/jimo.2018168 fatcat:gqeq4e3tjrcudb7anyqhccjw7m

Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1

Amanda Oliveira Dos Santos Melo-Nascimento, Brena Mota Moitinho Sant Anna, Carolyne Caetano Gonçalves, Giovanna Santos, Eliane Noronha, Nádia Parachin, Milton Ricardo de Abreu Roque, Thiago Bruce
2020 PLoS ONE  
These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.  ...  We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization  ...  Ricardo Kruger and Dr. Sonia Maria de Freitas (head and former head of Molecular Biology Department of Universidade de Brasília) for all the support for developing research in the department.  ... 
doi:10.1371/journal.pone.0243739 pmid:33351813 pmcid:PMC7755216 fatcat:gsjffcc3qfejraiy7rthyavssy

Cofactor Engineering Enhances the Physiological Function of an Industrial Strain [chapter]

Liming Liu, Jian Che
2011 Progress in Molecular and Environmental Bioengineering - From Analysis and Modeling to Technology Applications  
By inactivating aldehyde dehydrogenase (ALDH) in Klebsiella pneumonia, an enzyme that competes with 1,3-PD oxidoreductase for NADH, the final titer, the productivity of 1,3-PD and the yield of 1,3-PD relative  ...  (e.g. the intracellular energy charge and the interior redox potential and intracellular pH) on the phenotype, based on an accurate analysis of the metabolic network structure.  ...  Cofactor Engineering Enhances the Physiological Function of an Industrial Strain, Progress in Molecular and Environmental Bioengineering -From Analysis and Modeling to Technology Applications, Prof.  ... 
doi:10.5772/18249 fatcat:armdwcmjrzddrp6yxadz7b6nlu

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Miguel A. Campodonico, Barbara A. Andrews, Juan A. Asenjo, Bernhard O. Palsson, Adam M. Feist
2014 Metabolic Engineering  
In this study, we extended this analysis for non-native compounds by using an integrated approach through heterologous pathway integration and growth-coupled metabolite production design.  ...  The production of 75% of the current drug molecules and 35% of all chemicals could be achieved through bioprocessing (Arundel and Sawaya, 2009) .  ...  Funding for this work was provided by the Novo Nordisk Foundation.  ... 
doi:10.1016/j.ymben.2014.07.009 pmid:25080239 fatcat:ylnnzwxpizadjab7pz5qydq6xm

Advances in industrial microbiome based on microbial consortium for biorefinery

Li-Li Jiang, Jin-Jie Zhou, Chun-Shan Quan, Zhi-Long Xiu
2017 Bioresources and Bioprocessing  
Comparison of 1,3-propanediol production by mixed and pure cultures were then introduced, and interaction relationships between cells in microbial consortium were summarized.  ...  One of the important targets of industrial biotechnology is using cheap biomass resources. The traditional strategy is microbial fermentations with single strain.  ...  Metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organism, but also to capture growth parameters and composition of simple bacterial  ... 
doi:10.1186/s40643-017-0141-0 pmid:28251041 pmcid:PMC5306255 fatcat:nhhfdy76wnghfeija2t4rz3o7e

Industrial biotechnology: Tools and applications

Weng Lin Tang, Huimin Zhao
2009 Biotechnology Journal  
A Ab bb br re ev vi ia at ti io on ns s: : ISPR, in situ product removal; MFA, metabolic flux analysis; 1 1, ,3 3--P PD D, 1,3-propanediol  ...  Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing.  ...  In another study, the metabolic network of glycerol metabolism in K. pneumoniae was extended, and elementary flux modes (EFM) analysis incorporating oxygen regulatory systems was carried out for 1,3-PD  ... 
doi:10.1002/biot.200900127 pmid:19844915 fatcat:4wjc2x4eibdg5d3hdvzcuucj7m

Industrial biotechnology: Tools and applications

Huimin Zhao, Tianwei Tan
2015 Biotechnology Advances  
A Ab bb br re ev vi ia at ti io on ns s: : ISPR, in situ product removal; MFA, metabolic flux analysis; 1 1, ,3 3--P PD D, 1,3-propanediol  ...  Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing.  ...  In another study, the metabolic network of glycerol metabolism in K. pneumoniae was extended, and elementary flux modes (EFM) analysis incorporating oxygen regulatory systems was carried out for 1,3-PD  ... 
doi:10.1016/j.biotechadv.2015.10.012 pmid:26598053 fatcat:lkv7wjbikjbw5g5bba7fpyjs6m

A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products

Gillian O. Bruni, Evan Terrell
2022 Fermentation  
This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted  ...  upgrading of sugar crop products/by-products.  ...  One study reported using elementary mode analysis with clustering to examine the M. succiniciproducens metabolic networks and predicted that overexpression of the zwf gene would increase succinic acid  ... 
doi:10.3390/fermentation8050216 fatcat:3jbhwdrhtfe6fj7qbtavs6eeyi

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Ines Thiele, Ronan M. T. Fleming, Richard Que, Aarash Bordbar, Dinh Diep, Bernhard O. Palsson, Tamir Tuller
2012 PLoS ONE  
Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria.  ...  The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly.  ...  Designed and performed the computations with ME-matrix: IT RMTF.  ... 
doi:10.1371/journal.pone.0045635 pmid:23029152 pmcid:PMC3461016 fatcat:umwo6aegezej7l3vxwjkzikfvm

Metabolic Design and Control for Production in Prokaryotes [chapter]

S.R. Chhabra, J.D. Keasling
2011 Comprehensive Biotechnology  
Synopsis Prokaryotic life on earth is manifested by its diversity and omnipresence.  ...  Major drivers of this trend include recombinant DNA technology, high throughput characterization of macromolecular cellular components, quantitative modeling for metabolic engineering, targeted combinatorial  ...  The applications of genome--scale models span beyond metabolic engineering into the realms of bacterial evolution, network analysis, phenotypic behavior, biological discovery and synthetic biology.  ... 
doi:10.1016/b978-0-08-088504-9.00031-3 fatcat:t37oxhcgpraaxo5btrqhilaina

Mammalian Cell Culture Process for Monoclonal Antibody Production: Nonlinear Modelling and Parameter Estimation

Dan Selişteanu, Dorin Șendrescu, Vlad Georgeanu, Monica Roman
2015 BioMed Research International  
By using a dynamical model of such kind of processes, an optimization-based technique for estimation of kinetic parameters in the model of mammalian cell culture process is developed.  ...  The nonlinearity of these processes and the absence of suitable instrumentation require an enhanced modelling effort and modern kinetic parameter estimation strategies.  ...  Most of the reported works were focused on the process of glycerol fermentation by Klebsiella pneumoniae in batch, fed-batch, and continuous cultures [37] [38] [39] [40] [41] . Shen et al.  ... 
doi:10.1155/2015/598721 pmid:25685797 pmcid:PMC4313526 fatcat:izvjmb4k6zf6jexcaatqefblca
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