1
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Li L, Wang G. Enzymatic origin and various curvatures of metabolic scaling in microbes. Sci Rep 2019; 9:4082. [PMID: 30858543 PMCID: PMC6411939 DOI: 10.1038/s41598-019-40712-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/22/2019] [Indexed: 11/11/2022] Open
Abstract
The famous and controversial power law is a basal metabolic scaling model mainly derived from the “surface rule” or a fractal transport network. However, this law neglects biological mechanisms in the important active state. Here, we hypothesized that the relative metabolic rate and growth rate of actively growing microbes are driven by the changeable rate of their rate-limiting enzymes and concluded that natural logarithmic microbial metabolism (lnλ) and growth (or biomass) (lnM) are both dependent on limiting resources, and then developed novel models with interdependence between lnλ and lnM. We tested the models using the data obtained from the literature. We explain how and why the scaling is usually curved with the difference between microbial metabolic and growth (or biomass’s) half-saturation constants (KM, Kλ) in the active state and agree that the linear relationship of the power law is a particular case under the given condition: KM = Kλ, which means that the enzyme dynamics may drive active and basal metabolic scaling relationships. Our interdependent model is more general than the power law, which is important for integrating the ecology and biochemical processes.
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Affiliation(s)
- Liyan Li
- College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Genxuan Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China.
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2
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de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé JL. Mathematical modelling of microbes: metabolism, gene expression and growth. J R Soc Interface 2017; 14:20170502. [PMID: 29187637 PMCID: PMC5721159 DOI: 10.1098/rsif.2017.0502] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 11/12/2022] Open
Abstract
The growth of microorganisms involves the conversion of nutrients in the environment into biomass, mostly proteins and other macromolecules. This conversion is accomplished by networks of biochemical reactions cutting across cellular functions, such as metabolism, gene expression, transport and signalling. Mathematical modelling is a powerful tool for gaining an understanding of the functioning of this large and complex system and the role played by individual constituents and mechanisms. This requires models of microbial growth that provide an integrated view of the reaction networks and bridge the scale from individual reactions to the growth of a population. In this review, we derive a general framework for the kinetic modelling of microbial growth from basic hypotheses about the underlying reaction systems. Moreover, we show that several families of approximate models presented in the literature, notably flux balance models and coarse-grained whole-cell models, can be derived with the help of additional simplifying hypotheses. This perspective clearly brings out how apparently quite different modelling approaches are related on a deeper level, and suggests directions for further research.
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Affiliation(s)
| | - Stefano Casagranda
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
| | - Nils Giordano
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | | | | | - Johannes Geiselmann
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | - Jean-Luc Gouzé
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
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3
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He Y, Chen L, Zhou Y, Chen H, Zhou X, Cai F, Huang J, Wang M, Chen B, Guo Z. Analysis and model delineation of marine microalgae growth and lipid accumulation in flat-plate photobioreactor. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.03.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Costa R, Rocha I, Ferreira E, Machado D. Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Syst Biol 2011; 5:157-63. [DOI: 10.1049/iet-syb.2009.0058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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5
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Small GE, Helton AM, Kazanci C. Can consumer stoichiometric regulation control nutrient spiraling in streams? ACTA ACUST UNITED AC 2009. [DOI: 10.1899/08-099.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gaston E. Small
- Odum School of Ecology, University of Georgia, Athens, Georgia 30602 USA
| | - Ashley M. Helton
- Odum School of Ecology, University of Georgia, Athens, Georgia 30602 USA
| | - Caner Kazanci
- Department of Mathematics and Faculty of Engineering, University of Georgia, Athens, Georgia 30602 USA
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GENON G, GIANETTO A, SPECCHIA V. PRODUCTION OF ETHANOL WITH SACCHAROMYCES CEREVISIAE IN A CONTINUOUS REACTOR Note III: an experimental, kinetic study with suspended, recycled biomass. CHEM ENG COMMUN 2007. [DOI: 10.1080/00986448308940477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- G. GENON
- a Dipartimento di Scienza dei Materiali ed Ingegneria Chimica , Poltecnico di Torino
| | - A. GIANETTO
- a Dipartimento di Scienza dei Materiali ed Ingegneria Chimica , Poltecnico di Torino
| | - V. SPECCHIA
- a Dipartimento di Scienza dei Materiali ed Ingegneria Chimica , Poltecnico di Torino
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8
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Ishii N, Suga Y, Hagiya A, Watanabe H, Mori H, Yoshino M, Tomita M. Dynamic simulation of an in vitro multi-enzyme system. FEBS Lett 2007; 581:413-20. [PMID: 17239859 DOI: 10.1016/j.febslet.2006.12.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 11/23/2006] [Accepted: 12/25/2006] [Indexed: 11/16/2022]
Abstract
Parameters often are tuned with metabolite concentration time series data to build a dynamic model of metabolism. However, such tuning may reduce the extrapolation ability (generalization capability) of the model. In this study, we determined detailed kinetic parameters of three purified Escherichia coli glycolytic enzymes using the initial velocity method for individual enzymes; i.e., the parameters were determined independently from metabolite concentration time series data. The metabolite concentration time series calculated by the model using the parameters matched the experimental data obtained in an actual multi-enzyme system consisting of the three purified E. coli glycolytic enzymes. Thus, the results indicate that kinetic parameters can be determined without using an undesirable tuning process.
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Affiliation(s)
- Nobuyoshi Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan
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9
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Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. Toward large-scale modeling of the microbial cell for computer simulation. J Biotechnol 2004; 113:281-94. [PMID: 15380661 DOI: 10.1016/j.jbiotec.2004.04.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Revised: 03/30/2004] [Accepted: 04/01/2004] [Indexed: 11/26/2022]
Abstract
In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these "omics" methods are the focus of intensive research activities. As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective. Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry. In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging. Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system developed in our laboratory is introduced. Finally, our strategy for building a "whole cell metabolism model", including the experimental approach, is presented.
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Affiliation(s)
- Nobuyoshi Ishii
- Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan
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Gelmi C, Pérez-Correa R, Agosin E. Modelling Gibberella fujikuroi growth and GA3 production in solid-state fermentation. Process Biochem 2002. [DOI: 10.1016/s0032-9592(01)00314-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Boudreau BP. A kinetic model for microbic organic-matter decomposition in marine sediments. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05789.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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12
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Comby S, Flandrois JP, Carret G, Pichat C. Mathematical modelling of bacterial growth at subinhibitory levels of aminoglycosides. ANNALES DE L'INSTITUT PASTEUR. MICROBIOLOGY 1988; 139:613-29. [PMID: 3075502 DOI: 10.1016/0769-2609(88)90159-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The subinhibitory effect of antibiotics has often been studied without any clear theoretical framework; we have chosen to use mathematical bacterial growth modelling as a useful tool to analyse these biological states in a more rigorous manner. Since their mode of action and molecular target are relatively well known, aminoglycosides were well suited for this more sophisticated study of subinhibitory action. We have shown that two models (the Monod and the logistic models) regularly used in bacteriology, were adequate to describe these effects in a glucose-limited medium. A change of model, according to antibiotic concentration, revealed the existence of two separate actions. At lower concentrations, inhibition affected mainly glucose use, the substrate remained limiting and growth mode did not change. As soon as the concentration exceeded a threshold, growth was totally disturbed, probably through a physiological "catastrophe". This threshold can be used to estimate bacterial susceptibility to these antibiotics.
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Affiliation(s)
- S Comby
- Laboratoire de Biométrie (CNRS UA243), Villeurbanne, France
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13
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Coupling of microbial kinetics and oxygen transfer for analysis and optimization of gluconic acid production with Aspergillus niger. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00387499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Blanch HW. Cell growth and enzyme kinetics. Biotechnol Adv 1983; 1:193-204. [PMID: 14540891 DOI: 10.1016/0734-9750(83)90588-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- H W Blanch
- Department of Chemical Engineering, University of California, Berkeley 94720, USA
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