Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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Metabolic analysis of antibody producing Chinese hamster ovary cell culture under different stresses conditions Reviewed

Badsha M., Kurata H., Onitsuka M., Oga T., Omasa T.

Journal of Bioscience and Bioengineering 122 ( 1 ) 117 - 124 2016.07

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

© 2015 The Society for Biotechnology, Japan. Chinese hamster ovary (CHO) cells are commonly used as the host cell lines concerning their ability to produce therapeutic proteins with complex post-translational modifications. In this study, we have investigated the time course extra- and intracellular metabolome data of the CHO-K1 cell line, under a control and stress conditions. The addition of NaCl and trehalose greatly suppressed cell growth, where the maximum viable cell density of NaCl and trehalose cultures were 2.2-fold and 2.8-fold less than that of a control culture. Contrariwise, the antibody production of both the NaCl and trehalose cultures was sustained for a longer time to surpass that of the control culture. The NaCl and trehalose cultures showed relatively similar dynamics of cell growth, antibody production, and substrate/product concentrations, while they indicated different dynamics from the control culture. The principal component analysis of extra- and intracellular metabolome dynamics indicated that their dynamic behaviors were consistent with biological functions. The qualitative pattern matching classification and hierarchical clustering analyses for the intracellular metabolome identified the metabolite clusters whose dynamic behaviors depend on NaCl and trehalose. The volcano plot revealed several reporter metabolites whose dynamics greatly change between in the NaCl and trehalose cultures. The elastic net identified some critical, intracellular metabolites that are distinct between the NaCl and trehalose. While a relatively small number of intracellular metabolites related to the cell growth, glucose, glutamine, lactate and ammonium ion concentrations, the mechanism of antibody production was suggested to be very complicated or not to be explained by elastic net regression analysis.

DOI： 10.1016/j.jbiosc.2015.12.013

Scopus

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Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli Reviewed International journal

Jahan N., Maeda K., Matsuoka Y., Sugimoto Y., Kurata H.

Microbial Cell Factories 15 ( 1 ) 2016.06

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

© 2016 The Author(s).Background: A kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters. Results: In this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture. Conclusions: This model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes.

DOI： 10.1186/s12934-016-0511-x

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84975299249&origin=inward

S-system-based Analysis of the Robust Properties Common to Many Biochemical Network Models Reviewed

Yu Matsuoka, Nusrat Jahan, Hiroyuki Kurata

Bioprocess and Biosystems Engineering 2016.03

Metabolic analysis of antibody producing CHO cell culture under different stresses conditions Reviewed

Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

Journal of Bioscience and Bioengineering 2016.03

Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants. Reviewed International journal

Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kazuhiro Maeda, Hiroyuki Kurata

Journal of Bioscience and Bioengineering 2016.03

Developing a kinetic model of the E. coli ammonium assimilation network International journal

Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, Hiroyuki Kurata

Proceedings of the 16th International Conference on Systems Biology 2015.11

A detailed kinetic model of E. coli central metabolism in a batch culture Reviewed International journal

Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata,

Proceedings of Asian Congress on Biotechnology 2015 (ACB2015) 2015.11

Effect of NaCl and Trehalose Condition on Antibody Producing CHO Cell Culture Reviewed International journal

Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

Proceedings of Asian Congress on Biotechnology 2015 (ACB2015) 2015.11

Synthesis and decomposition approach for rational design of a biochemical network International journal

Hiroyuki Kurata

Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human 2015.03

Toward a quantitative in silico model for the E. coli ammonium assimilation system

Kazuhiro Maeda, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, Hiroyuki Kurata

Proceedings of the Third BMIRC International Symposium for Virtual Physiological Human 2015.03

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity Reviewed International journal

Kazuhiro Maeda, Hiroyuki Kurata

BMC Syst. Biol. 8 ( Suppl 5 ) S1 - S12 2014.12

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity Reviewed

Kazuhiro Maeda, Hiroyuki Kurata

GIW/ISCB-Asia 2014 2014.12

Complementary elementary modes for fast and efficient analysis of metabolic networks Reviewed

Md. Bahadur Badsha, Hiroyuki Kurata

Biochem Eng J. 90 121 - 130 2014.06

Integration of omics into metabolic flux distribution by complementary elementary mode analysis for large-scale metabolic networks Reviewed

Md Bahadur Badsha, Hiroyuki Kurata

3rd International Conference and Exhibition on Metabolomics & Systems Biology 2014.03

CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis, Reviewed

Bioproc. Biosys. Eng. 2014.03

S-systemを用いた代謝反応モデルの感度解析 Reviewed

松岡結 , NusratJahan , 倉田博之

IPSJ SIG technical reports ( Information Processing Society of Japan (IPSJ) ) 2014 ( 1 ) 1 - 2 2014.02

Aim and scope of the BMIRC at Kyutech

Hiroyuki Kurata

Proceedings of the Second BMIRC International Symposium on Advances in Bioinformatics and Medical Engineering 2014.02

Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes Reviewed

Journal of Chemical Engineering of Japan 47 1 - 9 2014.01

バイオテクノロジー Reviewed

神谷典穂, 田中孝明, 宮坂武寛, 倉田博之, 近藤昭彦, 市川創作

化学工学 = Chemical engineering 77 ( 10 ) 719 - 724 2013.10

大腸菌アンモニア同化制御機構のダイナミックモデルの構築 Reviewed

前田和勲 , FredC.Boogerd , FrankJ.Bruggeman , HansV.Westerhoff , 倉田博之

IPSJ SIG technical reports ( Information Processing Society of Japan (IPSJ) ) 2013 ( 7 ) 1 - 6 2013.09

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Papers - KURATA Hiroyuki