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Ghiaci P, Jouhten P, Martyushenko N, Roca-Mesa H, Vázquez J, Konstantinidis D, Stenberg S, Andrejev S, Grkovska K, Mas A, Beltran G, Almaas E, Patil KR, Warringer J. Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes. Mol Syst Biol 2024:10.1038/s44320-024-00059-0. [PMID: 39174863 DOI: 10.1038/s44320-024-00059-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/17/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
Adaptive Laboratory Evolution (ALE) of microorganisms can improve the efficiency of sustainable industrial processes important to the global economy. However, stochasticity and genetic background effects often lead to suboptimal outcomes during laboratory evolution. Here we report an ALE platform to circumvent these shortcomings through parallelized clonal evolution at an unprecedented scale. Using this platform, we evolved 104 yeast populations in parallel from many strains for eight desired wine fermentation-related traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum leading to improved wine yeasts unencumbered by unwanted side effects. At the genomic level, evolutionary gains in metabolic characteristics often coincided with distinct chromosome amplifications and the emergence of side-effect syndromes that were characteristic of each selection niche. Several high-performing ALE strains exhibited desired wine fermentation kinetics when tested in larger liquid cultures, supporting their suitability for application. More broadly, our high-throughput ALE platform opens opportunities for rapid optimization of microbes which otherwise could take many years to accomplish.
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Affiliation(s)
- Payam Ghiaci
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, Gothenburg, 40530, Sweden
- Department of Biorefinery and Energy, High-throughput Centre, Research Institutes of Sweden, Örnsköldsvik, 89250, Sweden
- European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | - Paula Jouhten
- European Molecular Biology Laboratory, Heidelberg, 69117, Germany
- VTT Technical Research Centre of Finland Ltd, Espoo, 02044 VTT, Finland
- Aalto University, Department of Bioproducts and Biosystems, Espoo, 02150, Finland
| | - Nikolay Martyushenko
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Helena Roca-Mesa
- Universitat Rovira i Virgili, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Tarragona, 43007, Spain
| | - Jennifer Vázquez
- Universitat Rovira i Virgili, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Tarragona, 43007, Spain
- Centro Tecnológico del Vino-VITEC, Carretera de Porrera Km. 1, Falset, 43730, Spain
| | | | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, Gothenburg, 40530, Sweden
| | - Sergej Andrejev
- European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | | | - Albert Mas
- Universitat Rovira i Virgili, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Tarragona, 43007, Spain
| | - Gemma Beltran
- Universitat Rovira i Virgili, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Tarragona, 43007, Spain
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.
| | - Kiran R Patil
- European Molecular Biology Laboratory, Heidelberg, 69117, Germany.
- Medical Research Council (MRC) Toxicology Unit, University of Cambridge, Cambridge, CB2 1QR, UK.
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, Gothenburg, 40530, Sweden.
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Grigaitis P, Teusink B. An excess of glycolytic enzymes under glucose-limited conditions may enable Saccharomyces cerevisiae to adapt to nutrient availability. FEBS Lett 2022; 596:3203-3210. [PMID: 36008883 DOI: 10.1002/1873-3468.14484] [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: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 01/14/2023]
Abstract
Microorganisms, including the budding yeast Saccharomyces cerevisiae, express glycolytic proteins to a maximal capacity that (largely) exceeds the actual flux through the enzymes, especially at low growth rates. An open question is if this apparent expression level is really an overcapacity, or maintains the (optimal) enzyme capacity needed to carry flux at (very) low substrate availability. Here, we use computational modelling to suggest that yeast maintains a genuine excess of glycolytic enzymes at low specific growth rates. During fast fermentative growth at high glucose levels, the observed expression of the glycolytic enzymes matched the predicted optimal levels. We suggest that the excess glycolytic capacity at low glucose levels is a preparatory strategy in the adaptation to sugar fluctuations in the environment.
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Affiliation(s)
- Pranas Grigaitis
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, The Netherlands
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3
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In-vivo correlations between skin metabolic oscillations and vasomotion in wild-type mice and in a model of oxidative stress. Sci Rep 2019; 9:186. [PMID: 30655574 PMCID: PMC6336806 DOI: 10.1038/s41598-018-36970-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/27/2018] [Indexed: 12/17/2022] Open
Abstract
Arterioles in the cutaneous microcirculation frequently display an oscillatory phenomenon defined vasomotion, consistent with periodic diameter variations in the micro-vessels associated with particular physiological or abnormal conditions. The cellular mechanisms underlying vasomotion and its physiological role have not been completely elucidated. Various mechanisms were demonstrated, based on cell Ca2+ oscillations determined by the activity of channels in the plasma membrane or sarcoplasmic reticulum of vascular cells. However, the possible engagement in vasomotion of cell metabolic oscillations of mitochondrial or glycolytic origin has been poorly explored. Metabolic oscillations associated with the production of ATP energy were previously described in cells, while limited studies have investigated these fluctuations in-vivo. Here, we characterised a low-frequency metabolic oscillator (MO-1) in skin from live wild-type and Nrf2−/− mice, by combination of fluorescence spectroscopy and wavelet transform processing technique. Furthermore, the relationships between metabolic and microvascular oscillators were examined during phenylephrine-induced vasoconstriction. We found a significant interaction between MO-1 and the endothelial EDHF vasomotor mechanism that was reduced in the presence of oxidative stress (Nrf2−/− mice). Our findings suggest indirectly that metabolic oscillations may be involved in the mechanisms underlying endothelium-mediated skin vasomotion, which might be altered in the presence of metabolic disturbance.
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Lancaster G, Suprunenko YF, Jenkins K, Stefanovska A. Modelling chronotaxicity of cellular energy metabolism to facilitate the identification of altered metabolic states. Sci Rep 2016; 6:29584. [PMID: 27483987 PMCID: PMC4971499 DOI: 10.1038/srep29584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/22/2016] [Indexed: 12/22/2022] Open
Abstract
Altered cellular energy metabolism is a hallmark of many diseases, one notable example being cancer. Here, we focus on the identification of the transition from healthy to abnormal metabolic states. To do this, we study the dynamics of energy production in a cell. Due to the thermodynamic openness of a living cell, the inability to instantaneously match fluctuating supply and demand in energy metabolism results in nonautonomous time-varying oscillatory dynamics. However, such oscillatory dynamics is often neglected and treated as stochastic. Based on experimental evidence of metabolic oscillations, we show that changes in metabolic state can be described robustly by alterations in the chronotaxicity of the corresponding metabolic oscillations, i.e. the ability of an oscillator to resist external perturbations. We also present a method for the identification of chronotaxicity, applicable to general oscillatory signals and, importantly, apply this to real experimental data. Evidence of chronotaxicity was found in glycolytic oscillations in real yeast cells, verifying that chronotaxicity could be used to study transitions between metabolic states.
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Affiliation(s)
- Gemma Lancaster
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK
| | - Yevhen F Suprunenko
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Kirsten Jenkins
- Randall Division of Cell &Molecular Biophysics, King's College London, London, WC2R 2LS, UK
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Meier K, Carstensen F, Wessling M, Regestein L, Büchs J. Quasi-continuous fermentation in a reverse-flow diafiltration bioreactor. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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Bioperformance interpretation of a two-stage membrane bioreactor with cell recycling for intensive microbial production using residence time and internal age distributions. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Rehman S, Day PJR, Bayat A, Westerhoff HV. Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism. Front Physiol 2012; 3:316. [PMID: 22934066 PMCID: PMC3429086 DOI: 10.3389/fphys.2012.00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/18/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Samrina Rehman
- Manchester Centre for Integrative Systems Biology, University of Manchester Manchester, UK
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Lejeune A, Delvigne F, Thonart P. Influence of bioreactor hydraulic characteristics on a Saccharomyces cerevisiae fed-batch culture: hydrodynamic modelling and scale-down investigations. J Ind Microbiol Biotechnol 2009; 37:225-36. [DOI: 10.1007/s10295-009-0564-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 03/16/2009] [Indexed: 11/27/2022]
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Abstract
Biological functions governed by the circadian clock are the evident result of the entrainment operated by the earth's day and night cycle on living organisms. However, the circadian clock is not unique, and cells and organisms possess many other cyclic activities. These activities are difficult to observe if carried out by single cells and the cells are not coordinated but, if they can be detected, cell-to-cell cross-talk and synchronization among cells must exist. Some of these cycles are metabolic and cell synchronization is due to small molecules acting as metabolic messengers. We propose a short survey of cellular cycles, paying special attention to metabolic cycles and cellular cross-talking, particularly when the synchronization of metabolism or, more generally, cellular functions are concerned. Questions arising from the observation of phenomena based on cell communication and from basic cellular cycles are also proposed.
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Affiliation(s)
- Michele M Bianchi
- Department of Cell and Developmental Biology, University of Rome La Sapienza, Rome, Italy.
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Elaboration of a biased random walk model with a high spatial resolution for the simulation of the microorganisms exposure to gradient stress in scale-down reactors. Biochem Eng J 2008. [DOI: 10.1016/j.bej.2007.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Rossell S, Lindenbergh A, van der Weijden CC, Kruckeberg AL, van Eunen K, Westerhoff HV, Bakker BM. Mixed and diverse metabolic and gene-expression regulation of the glycolytic and fermentative pathways in response to a HXK2 deletion in Saccharomyces cerevisiae. FEMS Yeast Res 2007; 8:155-64. [PMID: 17662056 DOI: 10.1111/j.1567-1364.2007.00282.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
In Saccharomyces cerevisiae the HXK2 gene, which encodes the glycolytic enzyme hexokinase II, is involved in the regulatory mechanism known as 'glucose repression'. Its deletion leads to fully respiratory growth at high glucose concentrations where the wild type ferments profusely. Here we describe that deletion of the HXK2 gene resulted in a 75% reduction in fermentative capacity. Using regulation analysis we found that the fluxes through most glycolytic and fermentative enzymes were regulated cooperatively by changes in their capacities (Vmax) and by changes in the way they interacted with the rest of the metabolism. Glucose transport and phosphofructokinase were regulated purely at the metabolic level. The reduction of fermentative capacity in the mutant was accompanied by a remarkable resilience of the remaining capacity to nutrient starvation. After starvation, the fermentative capacity of the hxk2Delta mutant was similar to that of the wild type. Based on our results and previous reports, we suggest an inverse correlation between glucose repression and the resilience of fermentative capacity towards nutrient starvation. Only a limited number of glycolytic enzyme activities changed upon starvation of the hxk2Delta mutant and we discuss to what extent this could explain the stability of the fermentative capacity.
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Affiliation(s)
- Sergio Rossell
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam, The Netherlands
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Current awareness on yeast. Yeast 2005. [DOI: 10.1002/yea.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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