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Hosoda S, Iwata H, Miura T, Tanabe M, Okada T, Mochizuki A, Sato M. BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks. BMC Bioinformatics 2024; 25:297. [PMID: 39256657 DOI: 10.1186/s12859-024-05921-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 09/04/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Chemical bioproduction has attracted attention as a key technology in a decarbonized society. In computational design for chemical bioproduction, it is necessary to predict changes in metabolic fluxes when up-/down-regulating enzymatic reactions, that is, responses of the system to enzyme perturbations. Structural sensitivity analysis (SSA) was previously developed as a method to predict qualitative responses to enzyme perturbations on the basis of the structural information of the reaction network. However, the network structural information can sometimes be insufficient to predict qualitative responses unambiguously, which is a practical issue in bioproduction applications. To address this, in this study, we propose BayesianSSA, a Bayesian statistical model based on SSA. BayesianSSA extracts environmental information from perturbation datasets collected in environments of interest and integrates it into SSA predictions. RESULTS We applied BayesianSSA to synthetic and real datasets of the central metabolic pathway of Escherichia coli. Our result demonstrates that BayesianSSA can successfully integrate environmental information extracted from perturbation data into SSA predictions. In addition, the posterior distribution estimated by BayesianSSA can be associated with the known pathway reported to enhance succinate export flux in previous studies. CONCLUSIONS We believe that BayesianSSA will accelerate the chemical bioproduction process and contribute to advancements in the field.
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Affiliation(s)
- Shion Hosoda
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., Kokubunji-shi, Tokyo, 185-8601, Japan.
| | - Hisashi Iwata
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Takuya Miura
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Maiko Tanabe
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Takashi Okada
- Laboratory of Mathematical Biology, Institute for Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Life and Medical Sciences, Kyoto University, Kyoto-shi, Kyoto, 606-8507, Japan
| | - Miwa Sato
- Center for Exploratory Research, Research and Development Group, Hitachi, Ltd., Kokubunji-shi, Tokyo, 185-8601, Japan
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2
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Garfinkel AM, Ilker E, Miyazawa H, Schmeisser K, Tennessen JM. Historic obstacles and emerging opportunities in the field of developmental metabolism - lessons from Heidelberg. Development 2024; 151:dev202937. [PMID: 38912552 PMCID: PMC11299503 DOI: 10.1242/dev.202937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
The field of developmental metabolism is experiencing a technological revolution that is opening entirely new fields of inquiry. Advances in metabolomics, small-molecule sensors, single-cell RNA sequencing and computational modeling present new opportunities for exploring cell-specific and tissue-specific metabolic networks, interorgan metabolic communication, and gene-by-metabolite interactions in time and space. Together, these advances not only present a means by which developmental biologists can tackle questions that have challenged the field for centuries, but also present young scientists with opportunities to define new areas of inquiry. These emerging frontiers of developmental metabolism were at the center of a highly interactive 2023 EMBO workshop 'Developmental metabolism: flows of energy, matter, and information'. Here, we summarize key discussions from this forum, emphasizing modern developmental biology's challenges and opportunities.
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Affiliation(s)
- Alexandra M. Garfinkel
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
| | - Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Kathrin Schmeisser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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3
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Mizohata T, Kobayashi TJ, Bouchard LS, Miyahara H. Information geometric bound on general chemical reaction networks. Phys Rev E 2024; 109:044308. [PMID: 38755923 DOI: 10.1103/physreve.109.044308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
We investigate the convergence of chemical reaction networks (CRNs), aiming to establish an upper bound on their reaction rates. The nonlinear characteristics and discrete composition of CRNs pose significant challenges in this endeavor. To circumvent these complexities, we adopt an information geometric perspective, utilizing the natural gradient to formulate a nonlinear system. This system effectively determines an upper bound for the dynamics of CRNs. We corroborate our methodology through numerical simulations, which reveal that our constructed system converges more rapidly than CRNs within a particular class of reactions. This class is defined by the count of chemicals, the highest stoichiometric coefficients in the reactions, and the total number of reactions involved. Further, we juxtapose our approach with traditional methods, illustrating that the latter falls short in providing an upper bound for CRN reaction rates. Although our investigation centers on CRNs, the widespread presence of hypergraphs across various disciplines, ranging from natural sciences to engineering, indicates potential wider applications of our method, including in the realm of information science.
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Affiliation(s)
- Tsuyoshi Mizohata
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8505 Japan
| | - Louis-S Bouchard
- Center for Quantum Science and Engineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Hideyuki Miyahara
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
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4
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Hishida A, Okada T, Mochizuki A. Patterns of change in regulatory modules of chemical reaction systems induced by network modification. PNAS NEXUS 2024; 3:pgad441. [PMID: 38292559 PMCID: PMC10825507 DOI: 10.1093/pnasnexus/pgad441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024]
Abstract
Cellular functions are realized through the dynamics of chemical reaction networks formed by thousands of chemical reactions. Numerical studies have empirically demonstrated that small differences in network structures among species or tissues can cause substantial changes in dynamics. However, a general principle for behavior changes in response to network structure modifications is not known. The chemical reaction system possesses substructures called buffering structures, which are characterized by a certain topological index being zero. It was proven that the steady-state response to modulation of reaction parameters inside a buffering structure is localized in the buffering structure. In this study, we developed a method to systematically identify the loss or creation of buffering structures induced by the addition of a single degradation reaction from network structure alone. This makes it possible to predict the qualitative and macroscopic changes in regulation that will be caused by the network modification. This method was applied to two reaction systems: the central metabolic system and the mitogen-activated protein kinases signal transduction system. Our method enables identification of reactions that are important for biological functions in living systems.
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Affiliation(s)
- Atsuki Hishida
- Graduate School of Science, Kyoto University, Kyoto, 6068502, Japan
| | - Takashi Okada
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 6068507, Japan
| | - Atsushi Mochizuki
- Graduate School of Science, Kyoto University, Kyoto, 6068502, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 6068507, Japan
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5
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Fajiculay E, Hsu C. Noise response in monomolecular closed systems. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Affiliation(s)
- Erickson Fajiculay
- Institute of Chemistry Academia Sinica Taipei Taiwan
- Bioinformatics Program, Institute of Statistical Science, Taiwan International Graduate Program Academia Sinica Taipei Taiwan
- Institute of Bioinformatics and Structure Biology National Tsinghua University Hsinchu City Taiwan
| | - Chao‐Ping Hsu
- Institute of Chemistry Academia Sinica Taipei Taiwan
- Bioinformatics Program, Institute of Statistical Science, Taiwan International Graduate Program Academia Sinica Taipei Taiwan
- Physics Division National Center for Theoretical Sciences Taipei Taiwan
- Genome and Systems Biology Degree Program National Taiwan University Taipei Taiwan
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6
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Fajiculay E, Hsu CP. Localization of Noise in Biochemical Networks. ACS OMEGA 2023; 8:3043-3056. [PMID: 36713703 PMCID: PMC9878546 DOI: 10.1021/acsomega.2c06113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
Noise, or uncertainty in biochemical networks, has become an important aspect of many biological problems. Noise can arise and propagate from external factors and probabilistic chemical reactions occurring in small cellular compartments. For species survival, it is important to regulate such uncertainties in executing vital cell functions. Regulated noise can improve adaptability, whereas uncontrolled noise can cause diseases. Simulation can provide a detailed analysis of uncertainties, but parameters such as rate constants and initial conditions are usually unknown. A general understanding of noise dynamics from the perspective of network structure is highly desirable. In this study, we extended the previously developed law of localization for characterizing noise in terms of (co)variances and developed noise localization theory. With linear noise approximation, we can expand a biochemical network into an extended set of differential equations representing a fictitious network for pseudo-components consisting of variances and covariances, together with chemical species. Through localization analysis, perturbation responses at the steady state of pseudo-components can be summarized into a sensitivity matrix that only requires knowledge of network topology. Our work allows identification of buffering structures at the level of species, variances, and covariances and can provide insights into noise flow under non-steady-state conditions in the form of a pseudo-chemical reaction. We tested noise localization in various systems, and here we discuss its implications and potential applications. Results show that this theory is potentially applicable in discriminating models, scanning network topologies with interesting noise behavior, and designing and perturbing networks with the desired response.
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Affiliation(s)
- Erickson Fajiculay
- Institute
of Chemistry, Academia Sinica, Taipei115201, Taiwan
- Bioinformatics
Program, Institute of Information Science, Taiwan International Graduate
Program, Academia Sinica, Taipei115201, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu300044, Taiwan
| | - Chao-Ping Hsu
- Institute
of Chemistry, Academia Sinica, Taipei115201, Taiwan
- Bioinformatics
Program, Institute of Information Science, Taiwan International Graduate
Program, Academia Sinica, Taipei115201, Taiwan
- Physics
Division, National Center for Theoretical
Sciences, Taipei106319, Taiwan
- Genome
and Systems Biology Degree Program, National
Taiwan University, Taipei106319, Taiwan
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7
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Grziwotz F, Chang CW, Dakos V, van Nes EH, Schwarzländer M, Kamps O, Heßler M, Tokuda IT, Telschow A, Hsieh CH. Anticipating the occurrence and type of critical transitions. SCIENCE ADVANCES 2023; 9:eabq4558. [PMID: 36608135 PMCID: PMC9821862 DOI: 10.1126/sciadv.abq4558] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Critical transition can occur in many real-world systems. The ability to forecast the occurrence of transition is of major interest in a range of contexts. Various early warning signals (EWSs) have been developed to anticipate the coming critical transition or distinguish types of transition. However, no effective method allows to establish practical threshold indicating the condition when the critical transition is most likely to occur. Here, we introduce a powerful EWS, named dynamical eigenvalue (DEV), that is rooted in bifurcation theory of dynamical systems to estimate the dominant eigenvalue of the system. Theoretically, the absolute value of DEV approaches 1 when the system approaches bifurcation, while its position in the complex plane indicates the type of transition. We demonstrate the efficacy of the DEV approach in model systems with known bifurcation types and also test the DEV approach on various critical transitions in real-world systems.
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Affiliation(s)
- Florian Grziwotz
- Institute for Evolution and Biodiversity, Westphalian Wilhelms-University Münster, Münster 48149, Germany
| | - Chun-Wei Chang
- Institute of Fisheries Science, Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- National Center for Theoretical Sciences, Taipei 10617, Taiwan
| | - Vasilis Dakos
- ISEM, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | - Egbert H. van Nes
- Department of Environmental Science, Wageningen University, Wageningen P.O. Box 47, 6700 AA, Netherlands
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Münster 48143, Germany
| | - Oliver Kamps
- Center for Nonlinear Science, Westphalian Wilhelms-University Münster, Münster 48149, Germany
| | - Martin Heßler
- Center for Nonlinear Science, Westphalian Wilhelms-University Münster, Münster 48149, Germany
- Institute for Theoretical Physics, Westphalian Wilhelms-University Münster, Münster 48149, Germany
| | - Isao T. Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Arndt Telschow
- Institute for Evolution and Biodiversity, Westphalian Wilhelms-University Münster, Münster 48149, Germany
- Institute for Environmental Systems Science, University of Osnabrück, Osnabrück 49076, Germany
| | - Chih-hao Hsieh
- National Center for Theoretical Sciences, Taipei 10617, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
- Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Research Center for Environmental Changes, Academia Sinica, Taipei 11529, Taiwan
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8
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Mochizuki A. A structural approach to understanding enzymatic regulation of chemical reaction networks. Biochem J 2022; 479:1265-1283. [PMID: 35713414 PMCID: PMC9246345 DOI: 10.1042/bcj20210545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/02/2022]
Abstract
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex systems, i.e. chemical reaction network. One of the largest missions in modern biology is to understand behaviors of such systems logically based on information of network structures. However, there are series of obstacles to study dynamical behaviors of complex network systems in biology. For example, network structure does not provide sufficient information to determine details of the dynamical behaviors. In this review, I will introduce a novel mathematical theory, structural sensitivity analysis, by which the responses of reaction systems upon the changes in enzyme activities/amounts are determined from network structure alone. The patterns of responses exhibit characteristic features, localization and hierarchy, depending on the topology of the network. The theory also shows that ranges of enzymatic regulations are governed by a mathematical law characterized by local topology of substructures. These findings imply that the network topology is one of the origins of biological robustness.
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Affiliation(s)
- Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
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9
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Fajiculay E, Hsu CP. BioSANS: A software package for symbolic and numeric biological simulation. PLoS One 2022; 17:e0256409. [PMID: 35436294 PMCID: PMC9015124 DOI: 10.1371/journal.pone.0256409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.
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Affiliation(s)
- Erickson Fajiculay
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structure Biology, National Tsinghua University, Hsinchu, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Physics Division, National Center for Theoretical Sciences, Taipei, Hsinchu, Taiwan
- Genome and Systems Biology Degree program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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10
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Okada T, Mochizuki A, Furuta M, Tsai JC. Flux-augmented bifurcation analysis in chemical reaction network systems. Phys Rev E 2021; 103:062212. [PMID: 34271769 DOI: 10.1103/physreve.103.062212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 05/28/2021] [Indexed: 11/07/2022]
Abstract
The dynamics of biochemical reaction networks are considered to be responsible for biological functions in living systems. Since real networks are immense and complicated, it is difficult to determine which reactions can cause a significant change of dynamical behaviors, namely, bifurcations. Also to what extent numerical results of network systems depend on the chosen kinetic rate parameters is not known. In this paper, an analytical setting that splits the information of the dynamics into the network structure and reaction kinetics is introduced. This setting possesses a factorization structure for some class of network systems which allows one to determine which subnetworks are responsible for the occurrence of a bifurcation. Subsequently, the bifurcation criteria are reformulated in a manner that allows the efficient determination of relevant reactions for bifurcations.
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Affiliation(s)
- Takashi Okada
- RIKEN iTHEMS, Wako, Saitama 351-0198, Japan and Department of Physics and Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Mikio Furuta
- Graduate School of Mathematical Sciences, University of Tokyo, Tokyo 153-8914, Japan
| | - Je-Chiang Tsai
- Department of Mathematics, National Tsing Hua University, Hsinchu 300, Taiwan and National Center for Theoretical Sciences, Number 1, Section 4, Roosevelt Road, National Taiwan University, Taipei 106, Taiwan
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11
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Wang Y, Liu C, Liu P, Eisenberg B. Field theory of reaction-diffusion: Law of mass action with an energetic variational approach. Phys Rev E 2020; 102:062147. [PMID: 33465972 DOI: 10.1103/physreve.102.062147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
We extend the energetic variational approach so it can be applied to a chemical reaction system with general mass action kinetics. Our approach starts with an energy-dissipation law. We show that the chemical equilibrium is determined by the choice of the free energy and the dynamics of the chemical reaction is determined by the choice of the dissipation. This approach enables us to couple chemical reactions with other effects, such as diffusion and drift in an electric field. As an illustration, we apply our approach to a nonequilibrium reaction-diffusion system in a specific but canonical setup. We show by numerical simulations that the input-output relation of such a system depends on the choice of the dissipation.
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Affiliation(s)
- Yiwei Wang
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - Chun Liu
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - Pei Liu
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Bob Eisenberg
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA and Department of Physiology and Biophysics, Rush University, 1750 W. Harrison, Chicago, Illinois 60612, USA
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12
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Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo. Sci Rep 2018; 8:14696. [PMID: 30279540 PMCID: PMC6168488 DOI: 10.1038/s41598-018-32894-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/18/2018] [Indexed: 12/02/2022] Open
Abstract
Pyrophosphate (PPi) is produced by anabolic reactions and serves as an energy donor in the cytosol of plant cells; however, its accumulation to toxic levels disrupts several common biosynthetic pathways and is lethal. Before acquiring photosynthetic capacity, young seedlings must endure a short but critical heterotrophic period, during which they are nourished solely by sugar produced from seed reserves by the anabolic process of gluconeogenesis. Previously, we reported that excess PPi in H+-PPase-knockout fugu5 mutants of Arabidopsis thaliana severely compromised gluconeogenesis. However, the precise metabolic target of PPi inhibition in vivo remained elusive. Here, CE-TOF MS analyses of major metabolites characteristic of gluconeogenesis from seed lipids showed that the Glc6P;Fru6P level significantly increased and that Glc1P level was consistently somewhat higher in fugu5 compared to wild type. In contrast, the UDP-Glc level decreased significantly in the mutants. Importantly, specific removal of PPi in fugu5, and thus in AVP1pro:IPP1 transgenic lines, restored the Glc1P and the Glc6P;Fru6P levels, increased the UDP-Glc level ~2.0-fold, and subsequently increased sucrose synthesis. Given the reversible nature of the Glc1P/UDP-Glc reaction, our results indicate that UGP-Glc pyrophosphorylase is the major target when excess PPi exerts inhibitory effects in vivo. To validate our findings, we analyzed metabolite responses using a mathematical theory called structural sensitivity analysis (SSA), in which the responses of concentrations in reaction systems to perturbations in enzyme activity are determined from the structure of the network alone. A comparison of our experimental data with the results of pure structural theory predicted the existence of unknown reactions as the necessary condition for the above metabolic profiles, and confirmed the above results. Our data support the notion that H+-PPase plays a pivotal role in cytosolic PPi homeostasis in plant cells. We propose that the combination of metabolomics and SSA is powerful when seeking to identify and predict metabolic targets in living cells.
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13
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Okada T, Tsai JC, Mochizuki A. Structural bifurcation analysis in chemical reaction networks. Phys Rev E 2018; 98:012417. [PMID: 30110840 DOI: 10.1103/physreve.98.012417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 06/08/2023]
Abstract
In living cells, chemical reactions form complex networks. Dynamics arising from such networks are the origins of biological functions. We propose a mathematical method to analyze bifurcation behaviors of network systems using their structures alone. Specifically, a whole network is decomposed into subnetworks, and for each of them the bifurcation condition can be studied independently. Further, parameters inducing bifurcations and chemicals exhibiting bifurcations can be determined on the network. We illustrate our theory using hypothetical and real networks.
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Affiliation(s)
- Takashi Okada
- iTHEMS Program, RIKEN, Wako 351-0198, Japan
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | - Je-Chiang Tsai
- Department of Mathematics, National Tsing Hua University, Hsinchu 300, Taiwan
- National Center for Theoretical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Atsushi Mochizuki
- iTHEMS Program, RIKEN, Wako 351-0198, Japan
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- CREST, JST, Kawaguchi 332-0012, Japan
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14
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Okada T, Mochizuki A. Sensitivity and network topology in chemical reaction systems. Phys Rev E 2017; 96:022322. [PMID: 28950505 DOI: 10.1103/physreve.96.022322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 06/07/2023]
Abstract
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses to enzyme perturbations only from network topology, and then proved a theorem, called the law of localization, explaining response patterns in terms of network topology. In this paper, we generalize these results to reaction networks with conserved concentrations, which allows us to study any reaction system. We also propose network characteristics quantifying robustness. We compare E. coli metabolic network with randomly rewired networks, and find that the robustness of the E. coli network is significantly higher than that of the random networks.
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Affiliation(s)
- Takashi Okada
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
- CREST, JST 4-1-8 Honcho, Kawaguchi 332-0012, Japan
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