1
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van Niekerk DD, van Wyk M, Kouril T, Snoep JL. Kinetic modelling of glycolytic oscillations. Essays Biochem 2024; 68:15-25. [PMID: 38206647 DOI: 10.1042/ebc20230037] [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: 11/06/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Glycolytic oscillations have been studied for well over 60 years, but aspects of their function, and mechanisms of regulation and synchronisation remain unclear. Glycolysis is amenable to mechanistic mathematical modelling, as its components have been well characterised, and the system can be studied at many organisational levels: in vitro reconstituted enzymes, cell free extracts, individual cells, and cell populations. In recent years, the emergence of individual cell analysis has opened new ways of studying this intriguing system.
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Affiliation(s)
- David D van Niekerk
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Morne van Wyk
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Theresa Kouril
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
- Molecular Cell Biology, Vrije Universiteit, Amsterdam, The Netherlands
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2
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Hario S, Le GNT, Sugimoto H, Takahashi-Yamashiro K, Nishinami S, Toda H, Li S, Marvin JS, Kuroda S, Drobizhev M, Terai T, Nasu Y, Campbell RE. High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l-Lactate. ACS CENTRAL SCIENCE 2024; 10:402-416. [PMID: 38435524 PMCID: PMC10906044 DOI: 10.1021/acscentsci.3c01250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024]
Abstract
l-Lactate is a monocarboxylate produced during the process of cellular glycolysis and has long generally been considered a waste product. However, studies in recent decades have provided new perspectives on the physiological roles of l-lactate as a major energy substrate and a signaling molecule. To enable further investigations of the physiological roles of l-lactate, we have developed a series of high-performance (ΔF/F = 15 to 30 in vitro), intensiometric, genetically encoded green fluorescent protein (GFP)-based intracellular l-lactate biosensors with a range of affinities. We evaluated these biosensors in cultured cells and demonstrated their application in an ex vivo preparation of Drosophila brain tissue. Using these biosensors, we were able to detect glycolytic oscillations, which we analyzed and mathematically modeled.
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Affiliation(s)
- Saaya Hario
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Giang N. T. Le
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Hikaru Sugimoto
- Department
of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kei Takahashi-Yamashiro
- Department
of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, Faculty of Science, University
of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Suguru Nishinami
- International
Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hirofumi Toda
- International
Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Selene Li
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jonathan S. Marvin
- Howard
Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, United States
| | - Shinya Kuroda
- Department
of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mikhail Drobizhev
- Department
of Microbiology and Cell Biology, Montana
State University, Bozeman, Montana 59717, United States
| | - Takuya Terai
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Nasu
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO,
Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Robert E. Campbell
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, Faculty of Science, University
of Alberta, Edmonton, Alberta T6G 2G2, Canada
- CERVO
Brain Research Center and Department of Biochemistry, Microbiology,
and Bioinformatics, Université Laval, Québec, Québec G1 V 0A6, Canada
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3
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Leathard AS, Beales PA, Taylor AF. Design of oscillatory dynamics in numerical simulations of compartment-based enzyme systems. CHAOS (WOODBURY, N.Y.) 2023; 33:123128. [PMID: 38149992 DOI: 10.1063/5.0180256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
Enzymatic reactions that yield non-neutral products are known to involve feedback due to the bell-shaped pH-rate curve of the enzyme. Compartmentalizing the reaction has been shown to lead to transport-driven oscillations in theory; however, there have been few reproducible experimental examples. Our objective was to determine how the conditions could be optimized to achieve pH oscillations. We employed numerical simulations to investigate the hydrolysis of ethyl acetate in a confined esterase enzyme system, examining the influence of key factors on its behavior. Specific parameter ranges that lead to bistability and self-sustained pH oscillations and the importance of fast base transport for oscillations in this acid-producing system are highlighted. Suggestions are made to expand the parameter space for the occurrence of oscillations, including modifying the maximum of the enzyme pH-rate curve and increasing the negative feedback rate. This research not only sheds light on the programmable nature of enzyme-driven pH regulation but also furthers knowledge on the optimal design of such feedback systems for experimentalists.
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Affiliation(s)
- Anna S Leathard
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annette F Taylor
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
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4
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Venegas-Pineda LG, Jardón-Kojakhmetov H, Cao M. Stable chimera states: A geometric singular perturbation approach. CHAOS (WOODBURY, N.Y.) 2023; 33:113123. [PMID: 37972302 DOI: 10.1063/5.0142122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023]
Abstract
Over the past decades, chimera states have attracted considerable attention given their unexpected symmetry-breaking spatiotemporal nature and simultaneously exhibiting synchronous and incoherent behaviors under specific conditions. Despite relevant precursory results of such unforeseen states for diverse physical and topological configurations, there remain structures and mechanisms yet to be unveiled. In this work, using mean-field techniques, we analyze a multilayer network composed of two populations of heterogeneous Kuramoto phase oscillators with coevolutive coupling strengths. Moreover, we employ the geometric singular perturbation theory through the inclusion of a time-scale separation between the dynamics of the network elements and the adaptive coupling strength connecting them, gaining a better insight into the behavior of the system from a fast-slow dynamics perspective. Consequently, we derive the necessary and sufficient condition to produce stable chimera states when considering a coevolutionary intercoupling strength. Additionally, under the aforementioned constraint and with a suitable adaptive law election, it is possible to generate intriguing patterns, such as persistent breathing chimera states. Thereafter, we analyze the geometric properties of the mean-field system with a coevolutionary intracoupling strength and demonstrate the production of stable chimera states. Next, we give arguments for the presence of such patterns in the associated network under specific conditions. Finally, relaxation oscillations and canard cycles, seemingly related to breathing chimeras, are numerically produced under identified conditions due to the geometry of our system.
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Affiliation(s)
- Luis Guillermo Venegas-Pineda
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Nijenborgh 9, 9700 AK Groningen, The Netherlands
| | - Hildeberto Jardón-Kojakhmetov
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Nijenborgh 9, 9700 AK Groningen, The Netherlands
| | - Ming Cao
- Engineering and Technology Institute Groningen, University of Groningen, Nijenborgh 4, 9700 AE Groningen, The Netherlands
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5
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Bendig T, Ulmer A, Luzia L, Müller S, Sahle S, Bergmann FT, Lösch M, Erdemann F, Zeidan AA, Mendoza SN, Teusink B, Takors R, Kummer U, Figueiredo AS. The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. J Biotechnol 2023; 374:90-100. [PMID: 37572793 DOI: 10.1016/j.jbiotec.2023.08.001] [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: 02/09/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is hallmarked by the breakdown of lactose to organic acids such as lactate. This leads to a substantial decrease in pH - both in the medium, as well as cytosolic. The latter impairs metabolic activities due to the pH-dependence of enzymes, which compromises microbial growth. To quantitatively elucidate the impact of the acidification on metabolism of L. bulgaricus in an integrated way, we have developed a proton-dependent computational model of lactose metabolism and casein degradation based on experimental data. The model accounts for the influence of pH on enzyme activities as well as cellular growth and proliferation of the bacterial population. We used a machine learning approach to quantify the cell volume throughout fermentation. Simulation results show a decrease in metabolic flux with acidification of the cytosol. Additionally, the validated model predicts a similar metabolic behaviour within a wide range of non-limiting substrate concentrations. This computational model provides a deeper understanding of the intricate relationships between metabolic activity and acidification and paves the way for further optimization of yoghurt production under industrial settings.
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Affiliation(s)
- Tamara Bendig
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Laura Luzia
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Susanne Müller
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Sven Sahle
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Frank T Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Maren Lösch
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Florian Erdemann
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ahmad A Zeidan
- Systems Biology, R&D Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | | | - Bas Teusink
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
| | - Ana Sofia Figueiredo
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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6
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Efremenko E, Senko O, Stepanov N, Aslanli A, Maslova O, Lyagin I. Quorum Sensing as a Trigger That Improves Characteristics of Microbial Biocatalysts. Microorganisms 2023; 11:1395. [PMID: 37374897 DOI: 10.3390/microorganisms11061395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Quorum sensing (QS) of various microorganisms (bacteria, fungi, microalgae) today attracts the attention of researchers mainly from the point of view of clarifying the biochemical basics of this general biological phenomenon, establishing chemical compounds that regulate it, and studying the mechanisms of its realization. Such information is primarily aimed at its use in solving environmental problems and the development of effective antimicrobial agents. This review is oriented on other aspects of the application of such knowledge; in particular, it discusses the role of QS in the elaboration of various prospective biocatalytic systems for different biotechnological processes carried out under aerobic and anaerobic conditions (synthesis of enzymes, polysaccharides, organic acids, etc.). Particular attention is paid to the biotechnological aspects of QS application and the use of biocatalysts, which have a heterogeneous microbial composition. The priorities of how to trigger a quorum response in immobilized cells to maintain their long-term productive and stable metabolic functioning are also discussed. There are several approaches that can be realized: increase in cell concentration, introduction of inductors for synthesis of QS-molecules, addition of QS-molecules, and provoking competition between the participants of heterogeneous biocatalysts, etc.).
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Affiliation(s)
- Elena Efremenko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Olga Senko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Nikolay Stepanov
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Aysel Aslanli
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Olga Maslova
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
| | - Ilya Lyagin
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia
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7
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Bi S, Kargeti M, Colin R, Farke N, Link H, Sourjik V. Dynamic fluctuations in a bacterial metabolic network. Nat Commun 2023; 14:2173. [PMID: 37061520 PMCID: PMC10105761 DOI: 10.1038/s41467-023-37957-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Manika Kargeti
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Niklas Farke
- University of Tübingen, D-72076, Tübingen, Germany
| | - Hannes Link
- University of Tübingen, D-72076, Tübingen, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany.
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