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Kar M, Vogel LT, Chauhan G, Felekyan S, Ausserwöger H, Welsh TJ, Dar F, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Solutes unmask differences in clustering versus phase separation of FET proteins. Nat Commun 2024; 15:4408. [PMID: 38782886 PMCID: PMC11116469 DOI: 10.1038/s41467-024-48775-3] [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] [Received: 08/22/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Phase separation and percolation contribute to phase transitions of multivalent macromolecules. Contributions of percolation are evident through the viscoelasticity of condensates and through the formation of heterogeneous distributions of nano- and mesoscale pre-percolation clusters in sub-saturated solutions. Here, we show that clusters formed in sub-saturated solutions of FET (FUS-EWSR1-TAF15) proteins are affected differently by glutamate versus chloride. These differences on the nanoscale, gleaned using a suite of methods deployed across a wide range of protein concentrations, are prevalent and can be unmasked even though the driving forces for phase separation remain unchanged in glutamate versus chloride. Strikingly, differences in anion-mediated interactions that drive clustering saturate on the micron-scale. Beyond this length scale the system separates into coexisting phases. Overall, we find that sequence-encoded interactions, mediated by solution components, make synergistic and distinct contributions to the formation of pre-percolation clusters in sub-saturated solutions, and to the driving forces for phase separation.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anjana R Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany.
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany.
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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2
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Narvaez-Ortiz HY, Lynch MJ, Liu SL, Fries A, Nolen BJ. Both Las17-binding sites on Arp2/3 complex are important for branching nucleation and assembly of functional endocytic actin networks in S. cerevisiae. J Biol Chem 2024; 300:105766. [PMID: 38367669 PMCID: PMC10944109 DOI: 10.1016/j.jbc.2024.105766] [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] [Received: 09/27/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
Arp2/3 complex nucleates branched actin filaments that drive membrane invagination during endocytosis and leading-edge protrusion in lamellipodia. Arp2/3 complex is maximally activated in vitro by binding of a WASP family protein to two sites-one on the Arp3 subunit and one spanning Arp2 and ARPC1-but the importance of each site in the regulation of force-producing actin networks is unclear. Here, we identify mutations in budding yeast Arp2/3 complex that decrease or block engagement of Las17, the budding yeast WASP, at each site. As in the mammalian system, both sites are required for maximal activation in vitro. Dimerization of Las17 partially restores activity of mutations at both CA-binding sites. Arp2/3 complexes defective at either site assemble force-producing actin networks in a bead motility assay, but their reduced activity hinders motility by decreasing actin assembly near the bead surface and by failing to suppress actin filament bundling within the networks. While even the most defective Las17-binding site mutants assembled actin filaments at endocytic sites, they showed significant internalization defects, potentially because they lack the proper architecture to drive plasma membrane remodeling. Together, our data indicate that both Las17-binding sites are important to assemble functional endocytic actin networks in budding yeast, but Arp2/3 complex retains some activity in vitro and in vivo even with a severe defect at either Las17-binding site.
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Affiliation(s)
- Heidy Y Narvaez-Ortiz
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Michael J Lynch
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Su-Ling Liu
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Adam Fries
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Brad J Nolen
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
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3
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Tolleter D, Smith EN, Dupont-Thibert C, Uwizeye C, Vile D, Gloaguen P, Falconet D, Finazzi G, Vandenbrouck Y, Curien G. The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration. QUANTITATIVE PLANT BIOLOGY 2024; 5:e2. [PMID: 38572078 PMCID: PMC10988163 DOI: 10.1017/qpb.2024.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 01/17/2024] [Indexed: 04/05/2024]
Abstract
Quantitative analyses and models are required to connect a plant's cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is time-consuming. Consequently, there is a need to centralise the available data and to highlight the remaining knowledge gaps. Here, we present a step-by-step approach to manually extract quantitative data from various information sources, and to unify the data format. First, data from Arabidopsis leaf were collated, checked for consistency and correctness and curated by cross-checking sources. Second, quantitative data were combined by applying calculation rules. They were then integrated into a unique comprehensive, referenced, modifiable and reusable data compendium representing an Arabidopsis reference leaf. This atlas contains the metrics of the 15 cell types found in leaves at the cellular and subcellular levels.
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Affiliation(s)
- Dimitri Tolleter
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Edward N. Smith
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Clémence Dupont-Thibert
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Clarisse Uwizeye
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Denis Vile
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), UMR 759, Université de Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Pauline Gloaguen
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | | | - Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
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4
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Kouril T, October C, Hollocks S, Odendaal C, van Niekerk DD, Snoep JL. Inhibitor titrations reveal low control of glyceraldehyde 3-phosphate dehydrogenase and high control of hexokinase on glycolytic flux in an aggressive triple-negative breast cancer cell line. Biosystems 2023; 231:104969. [PMID: 37423593 DOI: 10.1016/j.biosystems.2023.104969] [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: 05/08/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023]
Abstract
The glycolytic flux, and in particular lactate production, is strongly increased in cancer cells compared to normal cells, a characteristic often referred to as aerobic glycolysis or the Warburg effect. This makes the glycolytic pathway a potential drug target, in particular if the flux control distribution in the pathway has shifted due to the metabolic reprogramming in cancer cells. The flux response of a drug is dependent on both the sensitivity of the target to the drug and the flux control of the target, and both these characteristics can be exploited to obtain selectivity for cancer cells. Traditionally drug development programs have focused on selective sensitivity of the drug, not necessarily focussing on the flux control of the target. We determined the flux control of two steps that have been suggested to have high control in cancer cells, using two inhibitors, iodoacetic acid and 3-bromopyruvate, and measured a flux control of the glyceraldehyde 3-phosphate dehydrogenase close to zero, while the hexokinase holds 50% of all flux control in glycolysis in an invasive cancer cell line MDA-mb-231.
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Affiliation(s)
- Theresa Kouril
- Department of Biochemistry, Stellenbosch University, South Africa
| | - Craig October
- Department of Biochemistry, Stellenbosch University, South Africa
| | | | | | | | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, South Africa; Molecular Cell Biology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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5
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Marín-Hernández Á, Saavedra E. Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis. Biosystems 2023; 231:104986. [PMID: 37506818 DOI: 10.1016/j.biosystems.2023.104986] [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: 03/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The use of kinetic modeling and metabolic control analysis (MCA) to identify possible therapeutic targets and to investigate the controlling and regulatory mechanisms in cancer glycolysis is here reviewed. The glycolytic pathway has been considered a target to decrease cancer cell growth; however, its occurrence in normal cells makes it difficult to design therapeutic strategies that target this pathway in pathological cells. Notwithstanding, the over-expression of all enzymes and transporters, as well as the expression of isoenzymes with different kinetic and regulatory properties in cancer cells, suggested a different distribution of the control of glycolytic flux than that observed in normal cells. Kinetic models of glycolysis are constructed with enzyme kinetics experimental data, validated with the steady-state metabolite concentrations and glycolytic fluxes; applying MCA, permitted us to identify the steps with the highest control of glycolysis in cancer cells, but low control in normal cells. The cancer glycolysis main controlling steps under several metabolic conditions were: glucose transport, hexokinase and hexose-6-phosphate isomerase (HPI); whereas in normal cells were: the first two and phosphofructokinase-1. HPI is the best therapeutic target because it exerts high control in cancer glycolytic flux, but not in normal cells. Furthermore, kinetic modeling also contributed to identifying new feed-back and feed-forward regulatory loops in cancer cells glycolysis, and to understanding the mode of metabolic action of glycolytic inhibitors. Thus, MCA and metabolic modeling allowed to propose new strategies for inhibiting glycolysis in cancer cells.
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Affiliation(s)
- Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
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6
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Hall AG, King JC. The Molecular Basis for Zinc Bioavailability. Int J Mol Sci 2023; 24:ijms24076561. [PMID: 37047530 PMCID: PMC10095312 DOI: 10.3390/ijms24076561] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
Zinc is an essential micronutrient, and its deficiency is perhaps the most prevalent and least understood worldwide. Recent advances have expanded the understanding of zinc’s unique chemistry and molecular roles in a vast array of critical functions. However, beyond the concept of zinc absorption, few studies have explored the molecular basis of zinc bioavailability that determines the proportion of dietary zinc utilized in zinc-dependent processes in the body. The purpose of this review is to merge the concepts of zinc molecular biology and bioavailability with a focus on the molecular determinants of zinc luminal availability, absorption, transport, and utilization.
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7
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Jaramillo-Martinez V, Dominguez MJ, Bell GM, Souness ME, Carhart AH, Cuibus MA, Masoumzadeh E, Lantz BJ, Adkins AJ, Latham MP, Ball KA, Stollar EJ. How a highly acidic SH3 domain folds in the absence of its charged peptide target. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.532811. [PMID: 36993259 PMCID: PMC10055188 DOI: 10.1101/2023.03.21.532811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years. Statement for broader audience Some protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the protein’s high charge. Supplementary material Supplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. ( Supplementary_Material.docx ), 15 pages Supplemental excel file containing covariation data across AbpSH3 orthologs ( FileS1.xlsx ).
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8
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Lao-Martil D, Schmitz JPJ, Teusink B, van Riel NAW. Elucidating yeast glycolytic dynamics at steady state growth and glucose pulses through kinetic metabolic modeling. Metab Eng 2023; 77:128-142. [PMID: 36963461 DOI: 10.1016/j.ymben.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/12/2023] [Accepted: 03/05/2023] [Indexed: 03/26/2023]
Abstract
Microbial cell factories face changing environments during industrial fermentations. Kinetic metabolic models enable the simulation of the dynamic metabolic response to these perturbations, but their development is challenging due to model complexity and experimental data requirements. An example of this is the well-established microbial cell factory Saccharomyces cerevisiae, for which no consensus kinetic model of central metabolism has been developed and implemented in industry. Here, we aim to bring the academic and industrial communities closer to this consensus model. We developed a physiology informed kinetic model of yeast glycolysis connected to central carbon metabolism by including the effect of anabolic reactions precursors, mitochondria and the trehalose cycle. To parametrize such a large model, a parameter estimation pipeline was developed, consisting of a divide and conquer approach, supplemented with regularization and global optimization. Additionally, we show how this first mechanistic description of a growing yeast cell captures experimental dynamics at different growth rates and under a strong glucose perturbation, is robust to parametric uncertainty and explains the contribution of the different pathways in the network. Such a comprehensive model could not have been developed without using steady state and glucose perturbation data sets. The resulting metabolic reconstruction and parameter estimation pipeline can be applied in the future to study other industrially-relevant scenarios. We show this by generating a hybrid CFD-metabolic model to explore intracellular glycolytic dynamics for the first time. The model suggests that all intracellular metabolites oscillate within a physiological range, except carbon storage metabolism, which is sensitive to the extracellular environment.
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Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Noord-Brabant, 5612AE, the Netherlands
| | - Joep P J Schmitz
- DSM Biotechnology Center, Delft, Zuid-Holland, 2613AX, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Noord-Holland, 1081HZ, the Netherlands
| | - Natal A W van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Noord-Brabant, 5612AE, the Netherlands; Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Noord-Holland, 1105AZ, the Netherlands.
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9
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Guo W, Ji D, Kinghorn AB, Chen F, Pan Y, Li X, Li Q, Huck WTS, Kwok CK, Shum HC. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates. J Am Chem Soc 2023; 145:2375-2385. [PMID: 36689740 DOI: 10.1021/jacs.2c11362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Feipeng Chen
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yi Pan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Qingchuan Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
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10
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Goldberg RN, Giessmann RT, Halling PJ, Kettner C, Westerhoff HV. Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements. Beilstein J Org Chem 2023; 19:303-316. [PMID: 36960304 PMCID: PMC10028569 DOI: 10.3762/bjoc.19.26] [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: 11/23/2022] [Accepted: 02/15/2023] [Indexed: 03/17/2023] Open
Abstract
The measurement of values of apparent equilibrium constants K' for enzyme-catalyzed reactions involve a substantial number of critical details, neglect of which could lead to systematic errors. Here, interferences, impurities in the substances used, and failure to achieve equilibrium are matters of substantial consequence. Careful reporting of results is of great importance if the results are to have archival value. Thus, attention must be paid to the identification of the substances, specification of the reaction(s), the conditions of reaction, the definition of the equilibrium constant(s) and standard states, the use of standard nomenclature, symbols, and units, and uncertainties. This document contains a general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results.
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Affiliation(s)
- Robert N Goldberg
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, USA
| | - Robert T Giessmann
- Institute for Globally Distributed Open Research and Education (IGDORE), Berlin, Germany
| | | | - Carsten Kettner
- Beilstein-Institut, Trakehner Straße 7–9, 60487 Frankfurt am Main, Germany
| | - Hans V Westerhoff
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Molecular Cell Biology, Faculty of Science, Free University Amsterdam, The Netherlands
- School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK
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11
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Wang Y, Xu F, Nichols CB, Shi Y, Hellinga HW, Alspaugh JA, Distefano MD, Beese LS. Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase. J Med Chem 2022; 65:13753-13770. [PMID: 36218371 PMCID: PMC10755971 DOI: 10.1021/acs.jmedchem.2c00902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infections by fungal pathogens are difficult to treat due to a paucity of antifungals and emerging resistances. Next-generation antifungals therefore are needed urgently. We have developed compounds that prevent farnesylation of Cryptoccoccus neoformans Ras protein by inhibiting protein farnesyltransferase with 3-4 nanomolar affinities. Farnesylation directs Ras to the cell membrane and is required for infectivity of this lethal pathogenic fungus. Our high-affinity compounds inhibit fungal growth with 3-6 micromolar minimum inhibitory concentrations (MICs), 4- to 8-fold better than Fluconazole, an antifungal commonly used in the clinic. Compounds bound with distinct inhibition mechanisms at two alternative, partially overlapping binding sites, accessed via different inhibitor conformations. We showed that antifungal potency depends critically on the selected inhibition mechanism because this determines the efficacy of an inhibitor at low in vivo levels of enzyme and farnesyl substrate. We elucidated how chemical modifications of the antifungals encode desired inhibitor conformation and concomitant inhibitory mechanism.
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Affiliation(s)
- You Wang
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - Feng Xu
- Department of Chemistry, University of Minnesota,
Minneapolis, Minnesota, USA 55455
| | - Connie B. Nichols
- Department of Medicine, Duke University School of
Medicine, Durham, North Carolina, USA 27710
- Department of Molecular Genetics and Microbiology,
Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Yuqian Shi
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - Homme W. Hellinga
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - J. Andrew Alspaugh
- Department of Medicine, Duke University School of
Medicine, Durham, North Carolina, USA 27710
- Department of Molecular Genetics and Microbiology,
Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota,
Minneapolis, Minnesota, USA 55455
| | - Lorena S. Beese
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
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12
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Luzia L, Lao‐Martil D, Savakis P, van Heerden J, van Riel N, Teusink B. pH dependencies of glycolytic enzymes of yeast under in vivo-like assay conditions. FEBS J 2022; 289:6021-6037. [PMID: 35429225 PMCID: PMC9790636 DOI: 10.1111/febs.16459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
Under carbon source transitions, the intracellular pH of Saccharomyces cerevisiae is subject to change. Dynamics in pH modulate the activity of the glycolytic enzymes, resulting in a change in glycolytic flux and ultimately cell growth. To understand how pH affects the global behavior of glycolysis and ethanol fermentation, we measured the activity of the glycolytic and fermentative enzymes in S. cerevisiae under in vivo-like conditions at different pH. We demonstrate that glycolytic enzymes exhibit differential pH dependencies, and optima, in the pH range observed during carbon source transitions. The forward reaction of GAPDH shows the highest decrease in activity, 83%, during a simulated feast/famine regime upon glucose removal (cytosolic pH drop from 7.1 to 6.4). We complement our biochemical characterization of the glycolytic enzymes by fitting the Vmax to the progression curves of product formation or decay over time. The fitting analysis shows that the observed changes in enzyme activities require changes in Vmax , but changes in Km cannot be excluded. Our study highlights the relevance of pH as a key player in metabolic regulation and provides a large set of quantitative data that can be explored to improve our understanding of metabolism in dynamic environments.
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Affiliation(s)
| | | | | | | | - Natal van Riel
- Department of Biomedical EngineeringTU EindhovenNetherlands
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13
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Nicastro R, Gaillard H, Zarzuela L, Péli-Gulli MP, Fernández-García E, Tomé M, García-Rodríguez N, Durán RV, De Virgilio C, Wellinger RE. Manganese is a physiologically relevant TORC1 activator in yeast and mammals. eLife 2022; 11:80497. [PMID: 35904415 PMCID: PMC9337852 DOI: 10.7554/elife.80497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/18/2022] [Indexed: 12/09/2022] Open
Abstract
The essential biometal manganese (Mn) serves as a cofactor for several enzymes that are crucial for the prevention of human diseases. Whether intracellular Mn levels may be sensed and modulate intracellular signaling events has so far remained largely unexplored. The highly conserved target of rapamycin complex 1 (TORC1, mTORC1 in mammals) protein kinase requires divalent metal cofactors such as magnesium (Mg2+) to phosphorylate effectors as part of a homeostatic process that coordinates cell growth and metabolism with nutrient and/or growth factor availability. Here, our genetic approaches reveal that TORC1 activity is stimulated in vivo by elevated cytoplasmic Mn levels, which can be induced by loss of the Golgi-resident Mn2+ transporter Pmr1 and which depend on the natural resistance-associated macrophage protein (NRAMP) metal ion transporters Smf1 and Smf2. Accordingly, genetic interventions that increase cytoplasmic Mn2+ levels antagonize the effects of rapamycin in triggering autophagy, mitophagy, and Rtg1-Rtg3-dependent mitochondrion-to-nucleus retrograde signaling. Surprisingly, our in vitro protein kinase assays uncovered that Mn2+ activates TORC1 substantially better than Mg2+, which is primarily due to its ability to lower the Km for ATP, thereby allowing more efficient ATP coordination in the catalytic cleft of TORC1. These findings, therefore, provide both a mechanism to explain our genetic observations in yeast and a rationale for how fluctuations in trace amounts of Mn can become physiologically relevant. Supporting this notion, TORC1 is also wired to feedback control mechanisms that impinge on Smf1 and Smf2. Finally, we also show that Mn2+-mediated control of TORC1 is evolutionarily conserved in mammals, which may prove relevant for our understanding of the role of Mn in human diseases.
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Affiliation(s)
- Raffaele Nicastro
- University of Fribourg, Department of Biology, Fribourg, Switzerland
| | - Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Laura Zarzuela
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | | | - Elisabet Fernández-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | - Néstor García-Rodríguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | | | - Ralf Erik Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa - CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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14
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Abstract
Eukaryotic cells contain branched actin networks that are essential for endocytosis, motility, and other key cellular processes. These networks, which are formed by filamentous actin and the Arp2/3 complex, must subsequently be debranched to allow network remodeling and to recycle the Arp2/3 complex. Debranching appears to be catalyzed by two different members of the actin depolymerizing factor homology protein family: cofilin and glial maturation factor (GMF). However, their mechanisms of debranching are only partially understood. Here, we used single-molecule fluorescence imaging of Arp2/3 complex and actin filaments under physiological ionic conditions to observe debranching by GMF and cofilin. We demonstrate that cofilin, like GMF, is an authentic debrancher independent of its filament-severing activity and that the debranching activities of the two proteins are additive. While GMF binds directly to the Arp2/3 complex, cofilin selectively accumulates on branch-junction daughter filaments in tropomyosin-decorated networks just prior to debranching events. Quantitative comparison of debranching rates with the known kinetics of cofilin-actin binding suggests that cofilin occupancy of a particular single actin site at the branch junction is sufficient to trigger debranching. In rare cases in which the order of departure could be resolved during GMF- or cofilin-induced debranching, the Arp2/3 complex left the branch junction bound to the pointed end of the daughter filament, suggesting that both GMF and cofilin can work by destabilizing the mother filament-Arp2/3 complex interface. Taken together, these observations suggest that GMF and cofilin promote debranching by distinct yet complementary mechanisms.
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15
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Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder MD, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran JM, Bakker BM, Daran-Lapujade P. Full humanization of the glycolytic pathway in Saccharomyces cerevisiae. Cell Rep 2022; 39:111010. [PMID: 35767960 DOI: 10.1016/j.celrep.2022.111010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light context-dependent responses. Human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, whereas hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire essential pathway paves the way for establishment of species-, tissue-, and disease-specific metazoan models.
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Affiliation(s)
- Francine J Boonekamp
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Ewout Knibbe
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marcel A Vieira-Lara
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Karen van Eunen
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Reinier Bron
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ana Maria Almonacid Suarez
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Patrick van Rijn
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Justina C Wolters
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands.
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16
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Kerkhoven EJ. Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints. Curr Opin Microbiol 2022; 68:102168. [PMID: 35691074 DOI: 10.1016/j.mib.2022.102168] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022]
Abstract
The concept of metabolic models with resource allocation constraints has been around for over a decade and has clear advantages even when implementation is relatively rudimentary. Nonetheless, the number of organisms for which such a model is reconstructed is low. Various approaches exist, from coarse-grained consideration of enzyme usage to fine-grained description of protein translation. These approaches are reviewed here, with a particular focus on user-friendly solutions that can introduce resource allocation constraints to metabolic models of any organism. The availability of kcat data is a major hurdle, where recent advances might help to fill in the numerous gaps that exist for this data, especially for nonmodel organisms.
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Affiliation(s)
- Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden.
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17
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Genetically encoded tools for measuring and manipulating metabolism. Nat Chem Biol 2022; 18:451-460. [PMID: 35484256 DOI: 10.1038/s41589-022-01012-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
Over the past few years, we have seen an explosion of novel genetically encoded tools for measuring and manipulating metabolism in live cells and animals. Here, we will review the genetically encoded tools that are available, describe how these tools can be used and outline areas where future development is needed in this fast-paced field. We will focus on tools for direct measurement and manipulation of metabolites. Metabolites are master regulators of metabolism and physiology through their action on metabolic enzymes, signaling enzymes, ion channels and transcription factors, among others. We hope that this Perspective will encourage more people to use these novel reagents or even join this exciting new field to develop novel tools for measuring and manipulating metabolism.
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18
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Li Z, Zhang C, Wang Z, Yan H, Li C, Yang Z, Li Z, Zhang L, Wang W. High-throughput and reliable acquisition of in vivo turnover number fuels precise metabolic engineering. Synth Syst Biotechnol 2022; 7:541-543. [PMID: 35059513 PMCID: PMC8749077 DOI: 10.1016/j.synbio.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
As synthetic biology enters the era of quantitative biology, mathematical information such as kinetic parameters of enzymes can offer us an accurate knowledge of metabolism and growth of cells, and further guidance on precision metabolic engineering. kcat, termed the turnover number, is a basic parameter of enzymes that describes the maximum number of substrates converted to products each active site per unit time. It reflects enzyme activity and is essential for quantitative understanding of biosystems. Usually, the kcat values are measured in vitro, thus may not be able to reflect the enzyme activity in vivo. In this case, Davidi et al. defined a surrogate kmaxvivo (kapp) for kcat and developed a high throughput method to acquire kmaxvivo from omics data. Heckmann et al. and Chen et al. proved that the surrogate parameter can be a good embodiment of the physiological state of enzymes and exhibit superior performance for enzyme-constrained metabolic model to the default one. These breakthroughs will fuel the development of system and synthetic biology.
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19
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol 2022; 18:161-170. [PMID: 34931064 PMCID: PMC8810680 DOI: 10.1038/s41589-021-00919-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.
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20
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Lao-Martil D, Verhagen KJA, Schmitz JPJ, Teusink B, Wahl SA, van Riel NAW. Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities. Metabolites 2022; 12:74. [PMID: 35050196 PMCID: PMC8779790 DOI: 10.3390/metabo12010074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement.
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Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
| | - Koen J. A. Verhagen
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Joep P. J. Schmitz
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands;
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands;
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Natal A. W. van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
- Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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21
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McDonald AG, Tipton KF. Parameter Reliability and Understanding Enzyme Function. Molecules 2022; 27:263. [PMID: 35011495 PMCID: PMC8746786 DOI: 10.3390/molecules27010263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge of the Michaelis-Menten parameters and their meaning in different circumstances is an essential prerequisite to understanding enzyme function and behaviour. The published literature contains an abundance of values reported for many enzymes. The problem concerns assessing the appropriateness and validity of such material for the purpose to which it is to be applied. This review considers the evaluation of such data with particular emphasis on the assessment of its fitness for purpose.
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Affiliation(s)
- Andrew G. McDonald
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland;
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22
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Marquardt J, Chen X, Bi E. Septin Assembly and Remodeling at the Cell Division Site During the Cell Cycle. Front Cell Dev Biol 2021; 9:793920. [PMID: 34901034 PMCID: PMC8656427 DOI: 10.3389/fcell.2021.793920] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
The septin family of proteins can assemble into filaments that further organize into different higher order structures to perform a variety of different functions in different cell types and organisms. In the budding yeast Saccharomyces cerevisiae, the septins localize to the presumptive bud site as a cortical ring prior to bud emergence, expand into an hourglass at the bud neck (cell division site) during bud growth, and finally “split” into a double ring sandwiching the cell division machinery during cytokinesis. While much work has been done to understand the functions and molecular makeups of these structures, the mechanisms underlying the transitions from one structure to another have largely remained elusive. Recent studies involving advanced imaging and in vitro reconstitution have begun to reveal the vast complexity involved in the regulation of these structural transitions, which defines the focus of discussion in this mini-review.
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Affiliation(s)
- Joseph Marquardt
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xi Chen
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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23
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Yamagami R, Sieg JP, Bevilacqua PC. Functional Roles of Chelated Magnesium Ions in RNA Folding and Function. Biochemistry 2021; 60:2374-2386. [PMID: 34319696 DOI: 10.1021/acs.biochem.1c00012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA regulates myriad cellular events such as transcription, translation, and splicing. To perform these essential functions, RNA often folds into complex tertiary structures in which its negatively charged ribose-phosphate backbone interacts with metal ions. Magnesium, the most abundant divalent metal ion in cells, neutralizes the backbone, thereby playing essential roles in RNA folding and function. This has been known for more than 50 years, and there are now thousands of in vitro studies, most of which have used ≥10 mM free Mg2+ ions to achieve optimal RNA folding and function. In the cell, however, concentrations of free Mg2+ ions are much lower, with most Mg2+ ions chelated by metabolites. In this Perspective, we curate data from a number of sources to provide extensive summaries of cellular concentrations of metabolites that bind Mg2+ and to estimate cellular concentrations of metabolite-chelated Mg2+ species, in the representative prokaryotic and eukaryotic systems Escherichia coli, Saccharomyces cerevisiae, and iBMK cells. Recent research from our lab and others has uncovered the fact that such weakly chelated Mg2+ ions can enhance RNA function, including its thermodynamic stability, chemical stability, and catalysis. We also discuss how metabolite-chelated Mg2+ complexes may have played roles in the origins of life. It is clear from this analysis that bound Mg2+ should not be simply considered non-RNA-interacting and that future RNA research, as well as protein research, could benefit from considering chelated magnesium.
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Affiliation(s)
- Ryota Yamagami
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jacob P Sieg
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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24
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Dekker WJC, Ortiz-Merino RA, Kaljouw A, Battjes J, Wiering FW, Mooiman C, Torre PDL, Pronk JT. Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth. Metab Eng 2021; 67:347-364. [PMID: 34303845 DOI: 10.1016/j.ymben.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Julius Battjes
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Frank W Wiering
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Pilar de la Torre
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands.
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25
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Mooiman C, Bouwknegt J, Dekker WJC, Wiersma SJ, Ortiz-Merino RA, de Hulster E, Pronk JT. Critical parameters and procedures for anaerobic cultivation of yeasts in bioreactors and anaerobic chambers. FEMS Yeast Res 2021; 21:foab035. [PMID: 34100921 PMCID: PMC8216787 DOI: 10.1093/femsyr/foab035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/06/2021] [Indexed: 12/11/2022] Open
Abstract
All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and, unless extensive precautions are taken to minimize inadvertent entry of trace amounts of oxygen, easily go unnoticed in small-scale laboratory cultivation systems. This paper discusses critical points in the design of anaerobic yeast cultivation experiments in anaerobic chambers and laboratory bioreactors. Serial transfer or continuous cultivation to dilute growth factors present in anaerobically pre-grown inocula, systematic inclusion of control strains and minimizing the impact of oxygen diffusion through tubing are identified as key elements in experimental design. Basic protocols are presented for anaerobic-chamber and bioreactor experiments.
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Affiliation(s)
- Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wijb J C Dekker
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sanne J Wiersma
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Erik de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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26
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Ortega AD, Takhaveev V, Vedelaar SR, Long Y, Mestre-Farràs N, Incarnato D, Ersoy F, Olsen LF, Mayer G, Heinemann M. A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux. Cell Chem Biol 2021; 28:1554-1568.e8. [PMID: 33915105 DOI: 10.1016/j.chembiol.2021.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
RNA-based sensors for intracellular metabolites are a promising solution to the emerging issue of metabolic heterogeneity. However, their development, i.e., the conversion of an aptamer into an in vivo-functional intracellular metabolite sensor, still harbors challenges. Here, we accomplished this for the glycolytic flux-signaling metabolite, fructose-1,6-bisphosphate (FBP). Starting from in vitro selection of an aptamer, we constructed device libraries with a hammerhead ribozyme as actuator. Using high-throughput screening in yeast with fluorescence-activated cell sorting (FACS), next-generation sequencing, and genetic-environmental perturbations to modulate the intracellular FBP levels, we identified a sensor that generates ratiometric fluorescent readout. An abrogated response in sensor mutants and occurrence of two sensor conformations-revealed by RNA structural probing-indicated in vivo riboswitching activity. Microscopy showed that the sensor can differentiate cells with different glycolytic fluxes within yeast populations, opening research avenues into metabolic heterogeneity. We demonstrate the possibility to generate RNA-based sensors for intracellular metabolites for which no natural metabolite-binding RNA element exits.
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Affiliation(s)
- Alvaro Darío Ortega
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Silke Roelie Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Yi Long
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Neus Mestre-Farràs
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Danny Incarnato
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | | | - Lars Folke Olsen
- Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Günter Mayer
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands.
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27
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Eakins BB, Patel SD, Kalra AP, Rezania V, Shankar K, Tuszynski JA. Modeling Microtubule Counterion Distributions and Conductivity Using the Poisson-Boltzmann Equation. Front Mol Biosci 2021; 8:650757. [PMID: 33842549 PMCID: PMC8027483 DOI: 10.3389/fmolb.2021.650757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Microtubules are highly negatively charged proteins which have been shown to behave as bio-nanowires capable of conducting ionic currents. The electrical characteristics of microtubules are highly complicated and have been the subject of previous work; however, the impact of the ionic concentration of the buffer solution on microtubule electrical properties has often been overlooked. In this work we use the non-linear Poisson Boltzmann equation, modified to account for a variable permittivity and a Stern Layer, to calculate counterion concentration profiles as a function of the ionic concentration of the buffer. We find that for low-concentration buffers ([KCl] from 10 μM to 10 mM) the counterion concentration is largely independent of the buffer's ionic concentration, but for physiological-concentration buffers ([KCl] from 100 to 500 mM) the counterion concentration varies dramatically with changes in the buffer's ionic concentration. We then calculate the conductivity of microtubule-counterion complexes, which are found to be more conductive than the buffer when the buffer's ionic concentrations is less than ≈100 mM and less conductive otherwise. These results demonstrate the importance of accounting for the ionic concentration of the buffer when analyzing microtubule electrical properties both under laboratory and physiological conditions. We conclude by calculating the basic electrical parameters of microtubules over a range of ionic buffer concentrations applicable to nanodevice and medical applications.
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Affiliation(s)
- Boden B Eakins
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Sahil D Patel
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Aarat P Kalra
- Department of Chemistry, Princeton University, Princeton, NJ, United States
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, AB, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB, Canada.,Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
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28
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Population-Based Parameter Identification for Dynamical Models of Biological Networks with an Application to Saccharomyces cerevisiae. Processes (Basel) 2021. [DOI: 10.3390/pr9010098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
One of the central elements in systems biology is the interaction between mathematical modeling and measured quantities. Typically, biological phenomena are represented as dynamical systems, and they are further analyzed and comprehended by identifying model parameters using experimental data. However, all model parameters cannot be found by gradient-based optimization methods by fitting the model to the experimental data due to the non-differentiable character of the problem. Here, we present POPI4SB, a Python-based framework for population-based parameter identification of dynamic models in systems biology. The code is built on top of PySCeS that provides an engine to run dynamic simulations. The idea behind the methodology is to provide a set of derivative-free optimization methods that utilize a population of candidate solutions to find a better solution iteratively. Additionally, we propose two surrogate-assisted population-based methods, namely, a combination of a k-nearest-neighbor regressor with the Reversible Differential Evolution and the Evolution of Distribution Algorithm, that speeds up convergence. We present the optimization framework on the example of the well-studied glycolytic pathway in Saccharomyces cerevisiae.
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29
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Kalra AP, Eakins BB, Patel SD, Ciniero G, Rezania V, Shankar K, Tuszynski JA. All Wired Up: An Exploration of the Electrical Properties of Microtubules and Tubulin. ACS NANO 2020; 14:16301-16320. [PMID: 33213135 DOI: 10.1021/acsnano.0c06945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microtubules are hollow, cylindrical polymers of the protein α, β tubulin, that interact mechanochemically with a variety of macromolecules. Due to their mechanically robust nature, microtubules have gained attention as tracks for precisely directed transport of nanomaterials within lab-on-a-chip devices. Primarily due to the unusually negative tail-like C-termini of tubulin, recent work demonstrates that these biopolymers are also involved in a broad spectrum of intracellular electrical signaling. Microtubules and their electrostatic properties are discussed in this Review, followed by an evaluation of how these biopolymers respond mechanically to electrical stimuli, through microtubule migration, electrorotation and C-termini conformation changes. Literature focusing on how microtubules act as nanowires capable of intracellular ionic transport, charge storage, and ionic signal amplification is reviewed, illustrating how these biopolymers attenuate ionic movement in response to electrical stimuli. The Review ends with a discussion on the important questions, challenges, and future opportunities for intracellular microtubule-based electrical signaling.
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Affiliation(s)
- Aarat P Kalra
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2M9, Canada
| | - Boden B Eakins
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Sahil D Patel
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Gloria Ciniero
- Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino 10129, Italy
| | - Vahid Rezania
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta T5J 4S2, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, University of Alberta, 9107-116 St, Edmonton, Alberta T6G 2 V4, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, Alberta T6G 2M9, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Politecnico di Torino, Torino 10129, Italy
- Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
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30
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Hong MS, Velez-Suberbie ML, Maloney AJ, Biedermann A, Love KR, Love JC, Mukhopadhyay TK, Braatz RD. Macroscopic modeling of bioreactors for recombinant protein producing Pichia pastoris in defined medium. Biotechnol Bioeng 2020; 118:1199-1212. [PMID: 33274756 DOI: 10.1002/bit.27643] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/26/2020] [Accepted: 11/28/2020] [Indexed: 11/06/2022]
Abstract
The methylotrophic yeast Pichia pastoris is widely used as a microbial host for recombinant protein production. Bioreactor models for P. pastoris can inform understanding of cellular metabolism and can be used to optimize bioreactor operation. This article constructs an extensive macroscopic bioreactor model for P. pastoris which describes substrates, biomass, total protein, other medium components, and off-gas components. Species and elemental balances are introduced to describe uptake and evolution rates for medium components and off-gas components. Additionally, a pH model is constructed using an overall charge balance, acid/base equilibria, and activity coefficients to describe production of recombinant protein and precipitation of medium components. The extent of run-to-run variability is modeled by distributions of a subset of the model parameters, which are estimated using the maximum likelihood method. Model prediction from the extensive macroscopic bioreactor model well describes experimental data with different operating conditions. The probability distributions of the model predictions quantified from the parameter distribution are quantifiably consistent with the run-to-run variability observed in the experimental data. The uncertainty description in this macroscopic bioreactor model identifies the model parameters that have large variability and provides guidance as to which aspects of cellular metabolism should be the focus of additional experimental studies. The model for medium components with pH and precipitation can be used for improving chemically defined medium by minimizing the amount of components needed while meeting cellular requirements.
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Affiliation(s)
- Moo Sun Hong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Andrew J Maloney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew Biedermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kerry R Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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31
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Gnügge R, Symington LS. Efficient DNA double-strand break formation at single or multiple defined sites in the Saccharomyces cerevisiae genome. Nucleic Acids Res 2020; 48:e115. [PMID: 33053188 PMCID: PMC7672422 DOI: 10.1093/nar/gkaa833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are common genome lesions that threaten genome stability and cell survival. Cells use sophisticated repair machineries to detect and heal DSBs. To study DSB repair pathways and associated factors, inducible site-specific endonucleases have proven to be fundamental tools. In Saccharomyces cerevisiae, galactose-inducible rare-cutting endonucleases are commonly used to create a single DSB at a unique cleavage site. Galactose induction requires cell cultivation in suboptimal growth media, which is tedious especially when working with slow growing DSB repair mutants. Moreover, endonucleases that simultaneously create DSBs in multiple defined and unique loci of the yeast genome are not available, hindering studies of DSB repair in different genomic regions and chromatin contexts. Here, we present new tools to overcome these limitations. We employ a heterologous media-independent induction system to express the yeast HO endonuclease or bacterial restriction enzymes for single or multiple DSB formation, respectively. The systems facilitate tightly controlled and efficient DSB formation at defined genomic sites and will be valuable tools to study DSB repair at a local and genome-wide scale.
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Affiliation(s)
- Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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32
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Smith-Cortinez N, van Eunen K, Heegsma J, Serna-Salas SA, Sydor S, Bechmann LP, Moshage H, Bakker BM, Faber KN. Simultaneous Induction of Glycolysis and Oxidative Phosphorylation during Activation of Hepatic Stellate Cells Reveals Novel Mitochondrial Targets to Treat Liver Fibrosis. Cells 2020; 9:cells9112456. [PMID: 33187083 PMCID: PMC7697161 DOI: 10.3390/cells9112456] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/09/2023] Open
Abstract
Upon liver injury, hepatic stellate cells (HSCs) transdifferentiate to migratory, proliferative and extracellular matrix-producing myofibroblasts (e.g., activated HSCs; aHSCs) causing liver fibrosis. HSC activation is associated with increased glycolysis and glutaminolysis. Here, we compared the contribution of glycolysis, glutaminolysis and mitochondrial oxidative phosphorylation (OXPHOS) in rat and human HSC activation. Basal levels of glycolysis (extracellular acidification rate ~3-fold higher) and particularly mitochondrial respiration (oxygen consumption rate ~5-fold higher) were significantly increased in rat aHSCs, when compared to quiescent rat HSC. This was accompanied by extensive mitochondrial fusion in rat and human aHSCs, which occurred without increasing mitochondrial DNA content and electron transport chain (ETC) components. Inhibition of glycolysis (by 2-deoxy-D-glucose) and glutaminolysis (by CB-839) did not inhibit rat aHSC proliferation, but did reduce Acta2 (encoding α-SMA) expression slightly. In contrast, inhibiting mitochondrial OXPHOS (by rotenone) significantly suppressed rat aHSC proliferation, as well as Col1a1 and Acta2 expression. Other than that observed for rat aHSCs, human aHSC proliferation and expression of fibrosis markers were significantly suppressed by inhibiting either glycolysis, glutaminolysis or mitochondrial OXPHOS (by metformin). Activation of HSCs is marked by simultaneous induction of glycolysis and mitochondrial metabolism, extending the possibilities to suppress hepatic fibrogenesis by interfering with HSC metabolism.
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Affiliation(s)
- Natalia Smith-Cortinez
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (N.S.-C.); (J.H.); (S.A.S.-S.); (H.M.)
| | - Karen van Eunen
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (K.v.E.); (B.M.B.)
| | - Janette Heegsma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (N.S.-C.); (J.H.); (S.A.S.-S.); (H.M.)
| | - Sandra Alejandra Serna-Salas
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (N.S.-C.); (J.H.); (S.A.S.-S.); (H.M.)
| | - Svenja Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University, 44892 Bochum, Germany; (S.S.); (L.P.B.)
| | - Lars P. Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Ruhr-University, 44892 Bochum, Germany; (S.S.); (L.P.B.)
| | - Han Moshage
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (N.S.-C.); (J.H.); (S.A.S.-S.); (H.M.)
| | - Barbara M. Bakker
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (K.v.E.); (B.M.B.)
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands; (N.S.-C.); (J.H.); (S.A.S.-S.); (H.M.)
- Correspondence: ; Tel.: +31-(0)-50-361-2364
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33
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Pylkkänen R, Mohammadi P, Arola S, de Ruijter JC, Sunagawa N, Igarashi K, Penttilä M. In Vitro Synthesis and Self-Assembly of Cellulose II Nanofibrils Catalyzed by the Reverse Reaction of Clostridium thermocellum Cellodextrin Phosphorylase. Biomacromolecules 2020; 21:4355-4364. [PMID: 32960595 DOI: 10.1021/acs.biomac.0c01162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, various organisms produce cellulose as microfibrils, which are processed into their nano- and microfibrillar and/or crystalline components by humans in order to obtain desired material properties. Interestingly, the natural synthesis machinery can be circumvented by enzymatically synthesizing cellulose from precursor molecules in vitro. This approach is appealing for producing tailor-made cellulosic particles and materials because it enables optimization of the reaction conditions for cellulose synthesis in order to generate particles with a desired morphology in their pure form. Here, we present enzymatic cellulose synthesis catalyzed by the reverse reaction of Clostridium thermocellum cellodextrin phosphorylase in vitro. We were able to produce cellulose II nanofibril networks in all conditions tested, using varying concentrations of the glycosyl acceptors d-glucose or d-cellobiose (0.5, 5, and 50 mM). We show that shorter cellulose chains assemble into flat ribbon-like fibrils with greater diameter, while longer chains assemble into cylindrical fibrils with smaller diameter.
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Affiliation(s)
- Robert Pylkkänen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Suvi Arola
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Kiyohiko Igarashi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland.,Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Merja Penttilä
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
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34
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Investigation of the Electrical Properties of Microtubule Ensembles under Cell-Like Conditions. NANOMATERIALS 2020; 10:nano10020265. [PMID: 32033331 PMCID: PMC7075204 DOI: 10.3390/nano10020265] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
Microtubules are hollow cylindrical polymers composed of the highly negatively-charged (~23e), high dipole moment (1750 D) protein α, β- tubulin. While the roles of microtubules in chromosomal segregation, macromolecular transport, and cell migration are relatively well-understood, studies on the electrical properties of microtubules have only recently gained strong interest. Here, we show that while microtubules at physiological concentrations increase solution capacitance, free tubulin has no appreciable effect. Further, we observed a decrease in electrical resistance of solution, with charge transport peaking between 20-60 Hz in the presence of microtubules, consistent with recent findings that microtubules exhibit electric oscillations at such low frequencies. We were able to quantify the capacitance and resistance of the microtubules (MT) network at physiological tubulin concentrations to be 1.27 × 10-5 F and 9.74 × 104 Ω. Our results show that in addition to macromolecular transport, microtubules also act as charge storage devices through counterionic condensation across a broad frequency spectrum. We conclude with a hypothesis of an electrically tunable cytoskeleton where the dielectric properties of tubulin are polymerisation-state dependent.
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35
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Gabba M, Frallicciardi J, van 't Klooster J, Henderson R, Syga Ł, Mans R, van Maris AJA, Poolman B. Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane. Biophys J 2019; 118:422-434. [PMID: 31843263 PMCID: PMC6976801 DOI: 10.1016/j.bpj.2019.11.3384] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022] Open
Abstract
We present a fluorescence-based approach for determination of the permeability of small molecules across the membranes of lipid vesicles and living cells. With properly designed experiments, the method allows us to assess the membrane physical properties both in vitro and in vivo. We find that the permeability of weak acids increases in the order of benzoic > acetic > formic > lactic, both in synthetic lipid vesicles and the plasma membrane of Saccharomyces cerevisiae, but the permeability is much lower in yeast (one to two orders of magnitude). We observe a relation between the molecule permeability and the saturation of the lipid acyl chain (i.e., lipid packing) in the synthetic lipid vesicles. By analyzing wild-type yeast and a manifold knockout strain lacking all putative lactic acid transporters, we conclude that the yeast plasma membrane is impermeable to lactic acid on timescales up to ∼2.5 h.
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Affiliation(s)
- Matteo Gabba
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jacopo Frallicciardi
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Joury van 't Klooster
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Ryan Henderson
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Łukasz Syga
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Robert Mans
- Department of Industrial Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, Delft University of Technology, Delft, the Netherlands; Industrial Biotechnology Division, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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36
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Thomas A, Cutlan R, Finnigan W, van der Giezen M, Harmer N. Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction. Commun Biol 2019; 2:429. [PMID: 31799431 PMCID: PMC6874671 DOI: 10.1038/s42003-019-0677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022] Open
Abstract
Carboxylic acid reductases (CARs) are biocatalysts of industrial importance. Their properties, especially their poor stability, render them sub-optimal for use in a bioindustrial pipeline. Here, we employed ancestral sequence reconstruction (ASR) - a burgeoning engineering tool that can identify stabilizing but enzymatically neutral mutations throughout a protein. We used a three-algorithm approach to reconstruct functional ancestors of the Mycobacterial and Nocardial CAR1 orthologues. Ancestral CARs (AncCARs) were confirmed to be CAR enzymes with a preference for aromatic carboxylic acids. Ancestors also showed varied tolerances to solvents, pH and in vivo-like salt concentrations. Compared to well-studied extant CARs, AncCARs had a Tm up to 35 °C higher, with half-lives up to nine times longer than the greatest previously observed. Using ancestral reconstruction we have expanded the existing CAR toolbox with three new thermostable CAR enzymes, providing access to the high temperature biosynthesis of aldehydes to drive new applications in biocatalysis.
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Affiliation(s)
- Adam Thomas
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Rhys Cutlan
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - William Finnigan
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Mark van der Giezen
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
- Centre for Organelle Research, University of Stavanger, Richard Johnsens gate 4, Stavanger, 4021 Norway
| | - Nicholas Harmer
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD UK
- Present Address: Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
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37
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Mendoza-Cózatl DG, Gokul A, Carelse MF, Jobe TO, Long TA, Keyster M. Keep talking: crosstalk between iron and sulfur networks fine-tunes growth and development to promote survival under iron limitation. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4197-4210. [PMID: 31231775 DOI: 10.1093/jxb/erz290] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/08/2019] [Indexed: 05/21/2023]
Abstract
Plants are capable of synthesizing all the molecules necessary to complete their life cycle from minerals, water, and light. This plasticity, however, comes at a high energetic cost and therefore plants need to regulate their economy and allocate resources accordingly. Iron-sulfur (Fe-S) clusters are at the center of photosynthesis, respiration, amino acid, and DNA metabolism. Fe-S clusters are extraordinary catalysts, but their main components (Fe2+ and S2-) are highly reactive and potentially toxic. To prevent toxicity, plants have evolved mechanisms to regulate the uptake, storage, and assimilation of Fe and S. Recent advances have been made in understanding the cellular economy of Fe and S metabolism individually, and growing evidence suggests that there is dynamic crosstalk between Fe and S networks. In this review, we summarize and discuss recent literature on Fe sensing, allocation, use efficiency, and, when pertinent, its relationship to S metabolism. Our future perspectives include a discussion about the open questions and challenges ahead and how the plant nutrition field can come together to approach these questions in a cohesive and more efficient way.
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Affiliation(s)
- David G Mendoza-Cózatl
- Division of Plant Sciences, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Arun Gokul
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Mogamat F Carelse
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Timothy O Jobe
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Terri A Long
- Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DST-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
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38
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Workflow for Data Analysis in Experimental and Computational Systems Biology: Using Python as ‘Glue’. Processes (Basel) 2019. [DOI: 10.3390/pr7070460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bottom-up systems biology entails the construction of kinetic models of cellular pathways by collecting kinetic information on the pathway components (e.g., enzymes) and collating this into a kinetic model, based for example on ordinary differential equations. This requires integration and data transfer between a variety of tools, ranging from data acquisition in kinetics experiments, to fitting and parameter estimation, to model construction, evaluation and validation. Here, we present a workflow that uses the Python programming language, specifically the modules from the SciPy stack, to facilitate this task. Starting from raw kinetics data, acquired either from spectrophotometric assays with microtitre plates or from Nuclear Magnetic Resonance (NMR) spectroscopy time-courses, we demonstrate the fitting and construction of a kinetic model using scientific Python tools. The analysis takes place in a Jupyter notebook, which keeps all information related to a particular experiment together in one place and thus serves as an e-labbook, enhancing reproducibility and traceability. The Python programming language serves as an ideal foundation for this framework because it is powerful yet relatively easy to learn for the non-programmer, has a large library of scientific routines and active user community, is open-source and extensible, and many computational systems biology software tools are written in Python or have a Python Application Programming Interface (API). Our workflow thus enables investigators to focus on the scientific problem at hand rather than worrying about data integration between disparate platforms.
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39
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Nilsson A, Nielsen J, Palsson BO. Metabolic Models of Protein Allocation Call for the Kinetome. Cell Syst 2019; 5:538-541. [PMID: 29284126 DOI: 10.1016/j.cels.2017.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 10/09/2017] [Accepted: 11/20/2017] [Indexed: 11/26/2022]
Abstract
The flux of metabolites in the living cell depend on enzyme activities. Recently, many metabolic phenotypes have been explained by computer models that incorporate enzyme activity data. To move further, the scientific community needs to measure the kinetics of all enzymes in a systematic way.
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Affiliation(s)
- Avlant Nilsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm DK2970, Denmark.
| | - Bernhard O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm DK2970, Denmark; Departments of Bioengineering and Pediatrics, Mail Code 412, University of California, San Diego, La Jolla, CA 92093, USA
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40
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Boer H, Andberg M, Pylkkänen R, Maaheimo H, Koivula A. In vitro reconstitution and characterisation of the oxidative D-xylose pathway for production of organic acids and alcohols. AMB Express 2019; 9:48. [PMID: 30972503 PMCID: PMC6458216 DOI: 10.1186/s13568-019-0768-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/25/2019] [Indexed: 01/01/2023] Open
Abstract
The oxidative d-xylose pathway, i.e. Dahms pathway, can be utilised to produce from cheap biomass raw material useful chemical intermediates. In vitro metabolic pathways offer a fast way to study the rate-limiting steps and find the most suitable enzymes for each reaction. We have constructed here in vitro multi-enzyme cascades leading from d-xylose or d-xylonolactone to ethylene glycol, glycolic acid and lactic acid, and use simple spectrophotometric assays for the read-out of the efficiency of these pathways. Based on our earlier results, we focussed particularly on the less studied xylonolactone ring opening (hydrolysis) reaction. The bacterial Caulobacter crescentus lactonase (Cc XylC), was shown to be a metal-dependent enzyme clearly improving the formation of d-xylonic acid at pH range from 6 to 8. The following dehydration reaction by the ILVD/EDD family d-xylonate dehydratase is a rate-limiting step in the pathway, and an effort was made to screen for novel enolase family d-xylonate dehydratases, however, no suitable replacing enzymes were found for this reaction. Concerning the oxidation of glycolaldehyde to glycolic acid, several enzyme candidates were also tested. Both Escherichia coli aldehyde dehydrogenase (Ec AldA) and Azospirillum brasilense α-ketoglutarate semialdehyde dehydrogenase (Ab AraE) proved to be suitable enzymes for this reaction.
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41
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Jensen PR, Matos MRA, Sonnenschein N, Meier S. Combined In-Cell NMR and Simulation Approach to Probe Redox-Dependent Pathway Control. Anal Chem 2019; 91:5395-5402. [PMID: 30896922 DOI: 10.1021/acs.analchem.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic response of intracellular reaction cascades to changing environments is a hallmark of living systems. As metabolism is complex, mechanistic models have gained popularity for describing the dynamic response of cellular metabolism and for identifying target genes for engineering. At the same time, the detailed tracking of transient metabolism in living cells on the subminute time scale has become amenable using dynamic nuclear polarization-enhanced 13C NMR. Here, we suggest an approach combining in-cell NMR spectroscopy with perturbation experiments and modeling to obtain evidence that the bottlenecks of yeast glycolysis depend on intracellular redox state. In pre-steady-state glycolysis, pathway bottlenecks shift from downstream to upstream reactions within a few seconds, consistent with a rapid decline in the NAD+/NADH ratio. Simulations using mechanistic models reproduce the experimentally observed response and help identify unforeseen biochemical events. Remaining inaccuracies in the computational models can be identified experimentally. The combined use of rapid injection NMR spectroscopy and in silico simulations provides a promising method for characterizing cellular reactions with increasing mechanistic detail.
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Affiliation(s)
- Pernille R Jensen
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Marta R A Matos
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Nikolaus Sonnenschein
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Sebastian Meier
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
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42
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Wilson ZN, Scott AL, Dowell RD, Odorizzi G. PI(3,5)P 2 controls vacuole potassium transport to support cellular osmoregulation. Mol Biol Cell 2018; 29:1718-1731. [PMID: 29791245 PMCID: PMC6080712 DOI: 10.1091/mbc.e18-01-0015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Lysosomes are dynamic organelles with critical roles in cellular physiology. The lysosomal signaling lipid phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is a key regulator that has been implicated to control lysosome ion homeostasis, but the scope of ion transporters targeted by PI(3,5)P2 and the purpose of this regulation is not well understood. Through an unbiased screen in Saccharomyces cerevisiae, we identified loss-of-function mutations in the vacuolar H+-ATPase (V-ATPase) and in Vnx1, a vacuolar monovalent cation/proton antiporter, as suppressor mutations that relieve the growth defects and osmotic swelling of vacuoles (lysosomes) in yeast lacking PI(3,5)P2. We observed that depletion of PI(3,5)P2 synthesis in yeast causes a robust accumulation of multiple cations, most notably an ∼85 mM increase in the cellular concentration of potassium, a critical ion used by cells to regulate osmolarity. The accumulation of potassium and other cations in PI(3,5)P2-deficient yeast is relieved by mutations that inactivate Vnx1 or inactivate the V-ATPase and by mutations that increase the activity of a vacuolar cation export channel, Yvc1. Collectively, our data demonstrate that PI(3,5)P2 signaling orchestrates vacuole/lysosome cation transport to aid cellular osmoregulation.
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Affiliation(s)
- Zachary N Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
| | - Amber L Scott
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
| | - Robin D Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
| | - Greg Odorizzi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
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43
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44
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Picosecond orientational dynamics of water in living cells. Nat Commun 2017; 8:904. [PMID: 29026086 PMCID: PMC5714959 DOI: 10.1038/s41467-017-00858-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
Cells are extremely crowded, and a central question in biology is how this affects the intracellular water. Here, we use ultrafast vibrational spectroscopy and dielectric-relaxation spectroscopy to observe the random orientational motion of water molecules inside living cells of three prototypical organisms: Escherichia coli, Saccharomyces cerevisiae (yeast), and spores of Bacillus subtilis. In all three organisms, most of the intracellular water exhibits the same random orientational motion as neat water (characteristic time constants ~9 and ~2 ps for the first-order and second-order orientational correlation functions), whereas a smaller fraction exhibits slower orientational dynamics. The fraction of slow intracellular water varies between organisms, ranging from ~20% in E. coli to ~45% in B. subtilis spores. Comparison with the water dynamics observed in solutions mimicking the chemical composition of (parts of) the cytosol shows that the slow water is bound mostly to proteins, and to a lesser extent to other biomolecules and ions. The cytoplasm’s crowdedness leads one to expect that cell water is different from bulk water. By measuring the rotational motion of water molecules in living cells, Tros et al. find that apart from a small fraction of water solvating biomolecules, cell water has the same dynamics as bulk water.
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45
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Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks. Biotechnol Adv 2017; 35:981-1003. [PMID: 28916392 DOI: 10.1016/j.biotechadv.2017.09.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/30/2017] [Accepted: 09/10/2017] [Indexed: 12/13/2022]
Abstract
Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction and analysis of kinetic models. Finally, we discuss opportunities and limitations hindering the development of larger kinetic reconstructions.
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46
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Zotter A, Bäuerle F, Dey D, Kiss V, Schreiber G. Quantifying enzyme activity in living cells. J Biol Chem 2017; 292:15838-15848. [PMID: 28784664 DOI: 10.1074/jbc.m117.792119] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/20/2017] [Indexed: 11/06/2022] Open
Abstract
For over a century, enzymatic activity has been studied in vitro, assuming similar activity in the crowded cellular milieu. Here, we determined in real time the catalytic activity of TEM1-β-lactamase inside living cells and compared the values to those obtained in vitro We found the apparent in vivo catalytic efficiency, kcat/Km , to be lower than in vitro, with significant cell-to-cell variability. Surprisingly, the results show that inside the cell the apparent catalytic efficiency decreases, and Km increases with increasing enzyme concentration. To rationalize these findings, we measured enzyme and substrate diffusion rates in the cell and found the latter to be slower than expected. Simulations showed that for attenuated diffusion the substrate flux becomes rate-limiting, explaining why reaction rates in vivo can be independent on enzyme concentrations. The octanol/water partition of the substrate is 4.5, which is in the range of Food and Drug Administration-approved drugs. This suggests substrate-limited reaction rates to be common. These findings indicate that in vitro data cannot be simply extrapolated to the crowded in vivo environment.
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Affiliation(s)
- Agnes Zotter
- From the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel and
| | - Felix Bäuerle
- From the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel and.,the Max Planck Institute for Dynamics and Self-Organization, D-37077 Goettingen, Germany
| | - Debabrata Dey
- From the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel and
| | - Vladimir Kiss
- From the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel and
| | - Gideon Schreiber
- From the Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel and
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47
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Lessons on enzyme kinetics from quantitative proteomics. Curr Opin Biotechnol 2017; 46:81-89. [DOI: 10.1016/j.copbio.2017.02.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 02/15/2017] [Indexed: 11/24/2022]
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48
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Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. Int J Mol Sci 2017; 18:ijms18040876. [PMID: 28425930 PMCID: PMC5412457 DOI: 10.3390/ijms18040876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 11/25/2022] Open
Abstract
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5′-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.
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Affiliation(s)
- Yanfei Zhang
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
| | - Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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49
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Etzel M, Mörl M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017; 56:1181-1198. [PMID: 28206750 DOI: 10.1021/acs.biochem.6b01218] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches. Riboswitches are especially well suited, as they show a modular composition of sensor and response elements, allowing a free combination of different modules in a plug-and-play-like mode. The sensor or aptamer domain specifically interacts with a trigger molecule as a ligand, modulating the activity of the adjacent response domain that controls the expression of the genes located downstream, in most cases at the level of transcription or translation. In this review, we discuss the recent advances and strategies for designing such synthetic riboswitches based on natural or artificial components and readout systems, from trial-and-error approaches to rational design strategies. As the past several years have shown dramatic development in this fascinating field of research, we can give only a limited overview of the basic riboswitch design principles that is far from complete, and we apologize for not being able to consider every successful and interesting approach described in the literature.
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Affiliation(s)
- Maja Etzel
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
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50
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Noor E, Flamholz A, Bar-Even A, Davidi D, Milo R, Liebermeister W. The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. PLoS Comput Biol 2016; 12:e1005167. [PMID: 27812109 PMCID: PMC5094713 DOI: 10.1371/journal.pcbi.1005167] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/27/2016] [Indexed: 02/03/2023] Open
Abstract
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell’s capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major determinant of metabolic strategies both in evolution and bioengineering. It depends on enzyme parameters (such as kcat and KM constants), but also on metabolite concentrations. Moreover, similar amounts of different enzymes might incur different costs for the cell, depending on enzyme-specific properties such as protein size and half-life. Here, we developed enzyme cost minimization (ECM), a scalable method for computing enzyme amounts that support a given metabolic flux at a minimal protein cost. The complex interplay of enzyme and metabolite concentrations, e.g. through thermodynamic driving forces and enzyme saturation, would make it hard to solve this optimization problem directly. By treating enzyme cost as a function of metabolite levels, we formulated ECM as a numerically tractable, convex optimization problem. Its tiered approach allows for building models at different levels of detail, depending on the amount of available data. Validating our method with measured metabolite and protein levels in E. coli central metabolism, we found typical prediction fold errors of 4.1 and 2.6, respectively, for the two kinds of data. This result from the cost-optimized metabolic state is significantly better than randomly sampled metabolite profiles, supporting the hypothesis that enzyme cost is important for the fitness of E. coli. ECM can be used to predict enzyme levels and protein cost in natural and engineered pathways, and could be a valuable computational tool to assist metabolic engineering projects. Furthermore, it establishes a direct connection between protein cost and thermodynamics, and provides a physically plausible and computationally tractable way to include enzyme kinetics into constraint-based metabolic models, where kinetics have usually been ignored or oversimplified. “Enzyme cost”, the amount of protein needed for a given metabolic flux, is crucial for the metabolic choices cells have to make. However, due to the technical limitations of linear optimization methods, this cost has traditionally been ignored by constraint-based metabolic models such as Flux Balance Analysis. On the other hand, more detailed kinetic models which use ordinary differential equations to simulate fluxes for different choices of enzyme allocation, are computationally demanding and not scalable enough. In this work, we developed a method which utilizes the full kinetic model to predict steady-state enzyme costs, using a scalable and robust algorithm based on convex optimization. We show that the minimization of enzyme cost is a meaningful optimality principle by comparing our predictions to measured enzyme and metabolite levels in exponentially growing E. coli. This method could be used to quantify the enzyme cost of many other pathways and explain why evolution has selected some low-yield metabolic strategies, including aerobic fermentation in yeast and cancer cells. Furthermore, future metabolic engineering projects could benefit from our method by choosing pathways that reduce the total amount of enzyme required for the synthesis of a value-added product.
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Affiliation(s)
- Elad Noor
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Avi Flamholz
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Arren Bar-Even
- Max Planck Institute for Molecular Plant Physiology, Golm, Germany
| | - Dan Davidi
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ron Milo
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Wolfram Liebermeister
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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