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Song J, Wang J, Wang X, Zhao H, Hu T, Feng Z, Lei Z, Li W, Zheng Y, Wang M. Improving the Acetic Acid Fermentation of Acetobacter pasteurianus by Enhancing the Energy Metabolism. Front Bioeng Biotechnol 2022; 10:815614. [PMID: 35350179 PMCID: PMC8957916 DOI: 10.3389/fbioe.2022.815614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Energy metabolism is important for cell growth and tolerance against environment stress. In acetic acid fermentation by Acetobacter pasteurianus, the correlation coefficients of acid production rate with energy charge and ATP content were 0.9981 and 0.9826, respectively. The main energy metabolism pathway, including glycolysis pathway, TCA cycle, ethanol oxidation, pentose phosphate pathway, and ATP production, was constructed by transcriptome analysis. The effects of fermentation conditions, including dissolved oxygen, initial acetic acid concentration, and total concentration, on acetic acid fermentation and energy metabolism of A. pasteurianus were analyzed by using the RT-PCR method. The results showed the high energy charge inhibited glucose catabolism, and associated with the high ethanol oxidation rate. Consequently, a virtuous circle of increased ethanol oxidation, increased energy generation, and acetic acid tolerance was important for improving acetic acid fermentation.
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Affiliation(s)
- Jia Song
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xinyu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tao Hu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhiwei Feng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhi Lei
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Weizhao Li
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
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Maestri S, Merelli E, Pettini M. Agent-based models for detecting the driving forces of biomolecular interactions. Sci Rep 2022; 12:1878. [PMID: 35115584 PMCID: PMC8814177 DOI: 10.1038/s41598-021-04205-8] [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: 09/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Agent-based modelling and simulation have been effectively applied to the study of complex biological systems, especially when composed of many interacting entities. Representing biomolecules as autonomous agents allows this approach to bring out the global behaviour of biochemical processes as resulting from local molecular interactions. In this paper, we leverage the capabilities of the agent paradigm to construct an in silico replica of the glycolytic pathway; the aim is to detect the role that long-range electrodynamic forces might have on the rate of glucose oxidation. Experimental evidences have shown that random encounters and short-range potentials might not be sufficient to explain the high efficiency of biochemical reactions in living cells. However, while the latest in vitro studies are limited by present-day technology, agent-based simulations provide an in silico support to the outcomes hitherto obtained and shed light on behaviours not yet well understood. Our results grasp properties hard to uncover through other computational methods, such as the effect of electromagnetic potentials on glycolytic oscillations.
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Affiliation(s)
- Stefano Maestri
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.,Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
| | - Emanuela Merelli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
| | - Marco Pettini
- Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France
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Jung S, Koo KM, Ryu J, Baek I, Kwon SJ, Kim JB, Ahn JW. Overexpression of Phosphoribosyl Pyrophosphate Synthase Enhances Resistance of Chlamydomonas to Ionizing Radiation. FRONTIERS IN PLANT SCIENCE 2021; 12:719846. [PMID: 34512699 PMCID: PMC8427504 DOI: 10.3389/fpls.2021.719846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The enzyme phosphoribosyl pyrophosphate synthase (PRPS) catalyzes the conversion of ribose 5-phosphate into phosphoribosyl diphosphate; the latter is a precursor of purine and pyrimidine nucleotides. Here, we investigated the function of PRPS from the single-celled green alga Chlamydomonas reinhardtii in its response to DNA damage from gamma radiation or the alkylating agent LiCl. CrPRPS transcripts were upregulated in cells treated with these agents. We generated CrPRPS-overexpressing transgenic lines to study the function of CrPRPS. When grown in culture with LiCl or exposed to gamma radiation, the transgenic cells grew faster and had a greater survival rate than wild-type cells. CrPRPS overexpression enhanced expression of genes associated with DNA damage response, namely RAD51, RAD1, and LIG1. We observed, from transcriptome analysis, upregulation of genes that code for key enzymes in purine metabolism, namely ribonucleoside-diphosphate pyrophosphokinase subunit M1, adenylate kinase, and nucleoside-diphosphate kinase. We conclude that CrPRPS may affect DNA repair process via regulation of de novo nucleotide synthesis.
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Affiliation(s)
- Sera Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Advanced Process Technology and Fermentation Research Group, Research and Development Division, World Institute of Kimchi, Jeongeup-si, South Korea
| | - Kwang Min Koo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Inwoo Baek
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
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Zhang X, Wang L, Li Q, den Haan R, Li F, Liu CG, Bai FW. Omics analysis reveals mechanism underlying metabolic oscillation during continuous very-high-gravity ethanol fermentation by Saccharomyces cerevisiae. Biotechnol Bioeng 2021; 118:2990-3001. [PMID: 33934328 DOI: 10.1002/bit.27809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 11/10/2022]
Abstract
During continuous very-high-gravity (VHG) ethanol fermentation with Saccharomyces cerevisiae, the process exhibits sustained oscillation in residual glucose, ethanol, and biomass, raising a question: how do yeast cells respond to this phenomenon? In this study, the oscillatory behavior of yeast cells was characterized through transcriptome and metabolome analysis for one complete oscillatory period. By analyzing the accumulation of 26 intracellular metabolites and the expression of 90 genes related to central carbon metabolism and stress response, we confirmed that the process oscillation was attributed to intracellular metabolic oscillation with phase difference, and the expression of HXK1, HXT1,2,4, and PFK1 was significantly different from other genes in the Embden-Meyerhof-Parnas pathway, indicating that glucose transport and phosphorylation could be key nodes for regulating the intracellular metabolism under oscillatory conditions. Moreover, the expression of stress response genes was triggered and affected predominately by ethanol inhibition in yeast cells. This progress not only contributes to the understanding of mechanisms underlying the process oscillation observed for continuous VHG ethanol fermentation, but also provides insights for understanding unsteady state that might develop in other continuous fermentation processes operated under VHG conditions to increase product titers for robust production.
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Affiliation(s)
- Xue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Qian Li
- School of Life Science and Biotechnology, Dalian University, Dalian, Liaoning, China
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Fan Li
- COFCO Nutrition & Health Research Institute, Beijing, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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5
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Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast. Metab Eng 2020; 65:243-254. [PMID: 33279674 DOI: 10.1016/j.ymben.2020.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/04/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022]
Abstract
Proton coupled transport of α-glucosides via Mal11 into Saccharomyces cerevisiae costs one ATP per imported molecule. Targeted mutation of all three acidic residues in the active site resulted in sugar uniport, but expression of these mutant transporters in yeast did not enable growth on sucrose. We then isolated six unique transporter variants of these mutants by directed evolution of yeast for growth on sucrose. In three variants, new acidic residues emerged near the active site that restored proton-coupled sucrose transport, whereas the other evolved transporters still catalysed sucrose uniport. The localization of mutations and transport properties of the mutants enabled us to propose a mechanistic model of proton-coupled sugar transport by Mal11. Cultivation of yeast strains expressing one of the sucrose uniporters in anaerobic, sucrose-limited chemostat cultures indicated an increase in the efficiency of sucrose dissimilation by 21% when additional changes in strain physiology were taken into account. We thus show that a combination of directed and evolutionary engineering results in more energy efficient sucrose transport, as a starting point to engineer yeast strains with increased yields for industrially relevant products.
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Salgar-Chaparro SJ, Lepkova K, Pojtanabuntoeng T, Darwin A, Machuca LL. Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness. Appl Environ Microbiol 2020; 86:e02885-19. [PMID: 31980429 PMCID: PMC7082584 DOI: 10.1128/aem.02885-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/18/2020] [Indexed: 01/04/2023] Open
Abstract
The impact that nutrient level has on biofilm characteristics, biocide effectiveness, and the associated risk of microbiologically influenced corrosion (MIC) was assessed using multispecies biofilms from two different oilfield consortia. A range of microbiological, microscopy, and corrosion methods demonstrated that the continuous flow of nutrients for the microbial growth resulted in higher activity, thickness, and robustness of the biofilms formed on carbon steel, which induced greater localized corrosion compared to biofilms formed under batch, nutrient-depleted conditions. Despite of the differences in biofilm characteristics, biofilms displayed comparable susceptibilities to glutaraldehyde biocide, with similar log10 reductions and percent reductions of microorganisms under both nutrient conditions. Nevertheless, nutrient replenishment impacted the effectiveness of the biocide in controlling microbial populations; a higher concentration of cells survived the biocide treatment in biofilms formed under a continuous flow of nutrients. Complementary DNA-/RNA-based amplicon sequencing and bioinformatics analysis were used to discriminate the active within the total populations in biofilms established at the different nutrient conditions and allowed the identification of the microbial species that remained active despite nutrient depletion and biocide treatment. Detection of persistent active microorganisms after exposure to glutaraldehyde, regardless of biofilm structure, suggested the presence of microorganisms less susceptible to this biocide and highlighted the importance of monitoring active microbial species for the early detection of biocide resistance in oil production facilities.IMPORTANCE Microbiologically influenced corrosion (MIC) is a complex process that generates economic losses to the industry every year. Corrosion must be managed to prevent a loss of containment of produced fluids to the external environment. MIC management includes the identification of assets with higher MIC risk, which could be influenced by nutrient levels in the system. Assessing biofilms under different nutrient conditions is essential for understanding the impact of flow regime on microbial communities and the subsequent impact on microbial corrosion and on the effectiveness of biocide treatment. This investigation simulates closely oil production systems, which contain piping sections exposed to continuous flow and sections that remain stagnant for long periods. Therefore, the results reported here are useful for MIC management and prevention. Moreover, the complementary methodological approach applied in this investigation highlighted the importance of implementing RNA-based methods for better identification of active microorganisms that survive stress conditions in oil systems.
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Affiliation(s)
- Silvia J Salgar-Chaparro
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy, and Chemical Engineering, Curtin University, Bentley, WA, Australia
| | - Katerina Lepkova
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy, and Chemical Engineering, Curtin University, Bentley, WA, Australia
| | - Thunyaluk Pojtanabuntoeng
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy, and Chemical Engineering, Curtin University, Bentley, WA, Australia
| | | | - Laura L Machuca
- Curtin Corrosion Centre, WA School of Mines: Minerals, Energy, and Chemical Engineering, Curtin University, Bentley, WA, Australia
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Hayakawa K, Matsuda F, Shimizu H. Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production. AMB Express 2016; 6:38. [PMID: 27277079 PMCID: PMC4899347 DOI: 10.1186/s13568-016-0210-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/30/2016] [Indexed: 11/10/2022] Open
Abstract
S-Adenosyl-l-methionine (SAM) is a fine chemical used as a nutritional supplement and a prescription drug. It is industrially produced using Saccharomyces cerevisiae owing to its high SAM content. To investigate the optimization of culture medium components for higher SAM production, metabolome analysis was conducted to compare the intracellular metabolite concentrations between Kyokai no. 6 (high SAM-producing) and laboratory yeast S288C (control) under different SAM production conditions. Metabolome analysis and the result of principal component analysis showed that the rate-limiting step for SAM production was ATP supply and the levels of degradation products of adenosine nucleotides were higher in Kyokai 6 strain than in the S288C strain under the l-methionine supplemented condition. Analysis of ATP accumulation showed that the levels of intracellular ATP in the Kyokai 6 strain were also higher compared to those in the S288C strain. Furthermore, as expected from metabolome analysis, the SAM content of Kyokai 6 strain cultivated in the medium without yeast extract increased by 2.5-fold compared to that in the additional condition, by increasing intracellular ATP level with inhibited cell growth. These results suggest that high SAM production is attributed to the enhanced ATP supply with l-methionine condition and high efficiency of intracellular ATP consumption.
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8
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Busti S, Mapelli V, Tripodi F, Sanvito R, Magni F, Coccetti P, Rocchetti M, Nielsen J, Alberghina L, Vanoni M. Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast. Sci Rep 2016; 6:27942. [PMID: 27305947 PMCID: PMC4910072 DOI: 10.1038/srep27942] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/27/2016] [Indexed: 11/26/2022] Open
Abstract
Calcium homeostasis is crucial to eukaryotic cell survival. By acting as an enzyme cofactor and a second messenger in several signal transduction pathways, the calcium ion controls many essential biological processes. Inside the endoplasmic reticulum (ER) calcium concentration is carefully regulated to safeguard the correct folding and processing of secretory proteins. By using the model organism Saccharomyces cerevisiae we show that calcium shortage leads to a slowdown of cell growth and metabolism. Accumulation of unfolded proteins within the calcium-depleted lumen of the endoplasmic reticulum (ER stress) triggers the unfolded protein response (UPR) and generates a state of oxidative stress that decreases cell viability. These effects are severe during growth on rapidly fermentable carbon sources and can be mitigated by decreasing the protein synthesis rate or by inducing cellular respiration. Calcium homeostasis, protein biosynthesis and the unfolded protein response are tightly intertwined and the consequences of facing calcium starvation are determined by whether cellular energy production is balanced with demands for anabolic functions. Our findings confirm that the connections linking disturbance of ER calcium equilibrium to ER stress and UPR signaling are evolutionary conserved and highlight the crucial role of metabolism in modulating the effects induced by calcium shortage.
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Affiliation(s)
- Stefano Busti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Valeria Mapelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Rossella Sanvito
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Fulvio Magni
- Department of Health Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marcella Rocchetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lilia Alberghina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- SYSBIO, Centre of Systems Biology, Milan, Italy
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Quantifying intracellular metabolites in yeast using a matrix with minimal interference from naturally occurring analytes. Anal Biochem 2015; 487:17-26. [PMID: 26142219 DOI: 10.1016/j.ab.2015.06.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 12/13/2022]
Abstract
For quantification of intracellular metabolites, mass spectrometry combined with liquid chromatography, capillary electrophoresis, or gas chromatography is currently the method of choice, especially when combined with stable isotope-labeled internal standards (SIL-ISs). Due to the difficulties in finding a biological matrix free of intracellular metabolites, a standard addition based validation is needed. Here, we present an alternative by producing a matrix with minimal signal interferences on both the analytes and their SIL-ISs. The matrix was obtained by cultivating Saccharomyces cerevisiae in [(13)C6]glucose/nonlabeled glucose (50:50, w/w) growth medium. The areas of both (12)C6 and (13)C6 fractions of ATP in the matrix were measured to be 2% of the sum of the areas of all ATP isotopes detected. The matrix allowed for spiking of both the nonlabeled and SIL-ISs and more straightforward validation. The intra- and inter-day accuracy and precision were ⩾80% and ⩽20%, respectively. The methodology was used for quantification of nucleotides, coenzymes, and redox compounds from Saccharomyces cerevisiae. The determined energy charge ratio was 0.9, whereas the Mal-CoA/Ac-CoA ratio was 0.04. The analysis of the redox compounds was challenging due to the oxidation of NADH and NADPH, when dissolved in water or tributylamine. The oxidation was reduced by dissolving them in ammonium acetate solution (pH 8.0).
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De la Fuente IM, Cortés JM, Valero E, Desroches M, Rodrigues S, Malaina I, Martínez L. On the dynamics of the adenylate energy system: homeorhesis vs homeostasis. PLoS One 2014; 9:e108676. [PMID: 25303477 PMCID: PMC4193753 DOI: 10.1371/journal.pone.0108676] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Unit of Biophysics (CSIC, UPV/EHU), and Department of Biochemistry and Molecular Biology University of the Basque Country, Bilbao, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Jesús M. Cortés
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Ikerbasque: The Basque Foundation for Science, Bilbao, Basque Country, Spain
| | - Edelmira Valero
- Department of Physical Chemistry, School of Industrial Engineering, University of Castilla-La Mancha, Albacete, Spain
| | | | - Serafim Rodrigues
- School of Computing and Mathematics, University of Plymouth, Plymouth, United Kingdom
| | - Iker Malaina
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Department of Physiology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
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11
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Ekberg J, Rautio J, Mattinen L, Vidgren V, Londesborough J, Gibson BR. Adaptive evolution of the lager brewing yeastSaccharomyces pastorianusfor improved growth under hyperosmotic conditions and its influence on fermentation performance. FEMS Yeast Res 2013; 13:335-49. [DOI: 10.1111/1567-1364.12038] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/08/2013] [Accepted: 02/08/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
| | | | | | - Virve Vidgren
- VTT Technical Research Centre of Finland; Espoo; Finland
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12
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Peifer S, Barduhn T, Zimmet S, Volmer DA, Heinzle E, Schneider K. Metabolic engineering of the purine biosynthetic pathway in Corynebacterium glutamicum results in increased intracellular pool sizes of IMP and hypoxanthine. Microb Cell Fact 2012; 11:138. [PMID: 23092390 PMCID: PMC3538647 DOI: 10.1186/1475-2859-11-138] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background Purine nucleotides exhibit various functions in cellular metabolism. Besides serving as building blocks for nucleic acid synthesis, they participate in signaling pathways and energy metabolism. Further, IMP and GMP represent industrially relevant biotechnological products used as flavor enhancing additives in food industry. Therefore, this work aimed towards the accumulation of IMP applying targeted genetic engineering of Corynebacterium glutamicum. Results Blocking of the degrading reactions towards AMP and GMP lead to a 45-fold increased intracellular IMP pool of 22 μmol gCDW-1. Deletion of the pgi gene encoding glucose 6-phosphate isomerase in combination with the deactivated AMP and GMP generating reactions, however, resulted in significantly decreased IMP pools (13 μmol gCDW-1). Targeted metabolite profiling of the purine biosynthetic pathway further revealed a metabolite shift towards the formation of the corresponding nucleobase hypoxanthine (102 μmol gCDW-1) derived from IMP degradation. Conclusions The purine biosynthetic pathway is strongly interconnected with various parts of the central metabolism and therefore tightly controlled. However, deleting degrading reactions from IMP to AMP and GMP significantly increased intracellular IMP levels. Due to the complexity of this pathway further degradation from IMP to the corresponding nucleobase drastically increased suggesting additional targets for future strain optimization.
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Affiliation(s)
- Susanne Peifer
- Biochemical Engineering Institute, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
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13
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Metabolic Flux and Nodes Control Analysis of Brewer’s Yeasts Under Different Fermentation Temperature During Beer Brewing. Appl Biochem Biotechnol 2012; 168:1938-52. [PMID: 23065402 DOI: 10.1007/s12010-012-9909-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 10/03/2012] [Indexed: 11/25/2022]
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14
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A comparative study on physiological activities of lager and ale brewing yeasts under different gravity conditions. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0658-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Yu Z, Zhao H, Wan C, Sun G, Zhao M. The Dynamic Changes of Proton Efflux Rate in Saccharomyces pastorianus Strains During High Gravity or Very High Gravity Brewing. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2011.tb00457.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Szijgyarto Z, Garedew A, Azevedo C, Saiardi A. Influence of inositol pyrophosphates on cellular energy dynamics. Science 2011; 334:802-5. [PMID: 22076377 DOI: 10.1126/science.1211908] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
With its high-energy phosphate bonds, adenosine triphosphate (ATP) is the main intracellular energy carrier. It also functions in most signaling pathways, as a phosphate donor or a precursor for cyclic adenosine monophosphate. We show here that inositol pyrophosphates participate in the control of intracellular ATP concentration. Yeasts devoid of inositol pyrophosphates have dysfunctional mitochondria but, paradoxically, contain four times as much ATP because of increased glycolysis. We demonstrate that inositol pyrophosphates control the activity of the major glycolytic transcription factor GCR1. Thus, inositol pyrophosphates regulate ATP concentration by altering the glycolytic/mitochondrial metabolic ratio. Metabolic reprogramming through inositol pyrophosphates is an evolutionary conserved mechanism that is also preserved in mammalian systems.
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Affiliation(s)
- Zsolt Szijgyarto
- Cell Biology Unit, Medical Research Council Laboratory for Molecular Cell Biology, and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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Robust industrial Saccharomyces cerevisiae strains for very high gravity bio-ethanol fermentations. J Biosci Bioeng 2011; 112:130-6. [DOI: 10.1016/j.jbiosc.2011.03.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 11/18/2022]
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18
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Puligundla P, Smogrovicova D, Obulam VSR, Ko S. Very high gravity (VHG) ethanolic brewing and fermentation: a research update. J Ind Microbiol Biotechnol 2011; 38:1133-44. [DOI: 10.1007/s10295-011-0999-3] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/07/2011] [Indexed: 11/30/2022]
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Dynamic analysis of cytosolic glucose and ATP levels in yeast using optical sensors. Biochem J 2010; 432:399-406. [PMID: 20854260 DOI: 10.1042/bj20100946] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Precise and dynamic measurement of intracellular metabolite levels has been hampered by difficulties in differentiating between adsorbed and imported fractions and the subcellular distribution between cytosol, endomembrane compartments and mitochondria. In the present study, genetically encoded FRET (Förster resonance energy transfer)-based sensors were deployed for dynamic measurements of free cytosolic glucose and ATP with varying external supply and in glucose-transport mutants. Moreover, by using the FRET sensors in a microfluidic platform, we were able to monitor in vivo changes of intracellular free glucose in individual yeast cells. We demonstrate the suitability of the FRET sensors for gaining physiological insight by demonstrating that free intracellular glucose and ATP levels are reduced in a hxt5Δ hexose-transporter mutant compared with wild-type and other hxtΔ strains.
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Mussatto SI, Dragone G, Guimarães PM, Silva JPA, Carneiro LM, Roberto IC, Vicente A, Domingues L, Teixeira JA. Technological trends, global market, and challenges of bio-ethanol production. Biotechnol Adv 2010; 28:817-30. [DOI: 10.1016/j.biotechadv.2010.07.001] [Citation(s) in RCA: 479] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 07/02/2010] [Indexed: 11/27/2022]
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Xue C, Zhao X, Bai F. Effect of the size of yeast flocs and zinc supplementation on continuous ethanol fermentation performance and metabolic flux distribution under very high concentration conditions. Biotechnol Bioeng 2010; 105:935-44. [DOI: 10.1002/bit.22610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhao XQ, Bai FW. Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production. J Biotechnol 2009; 144:23-30. [PMID: 19446584 DOI: 10.1016/j.jbiotec.2009.05.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 04/28/2009] [Accepted: 05/06/2009] [Indexed: 11/17/2022]
Abstract
Yeast strains of Saccharomyces cerevisiae have been extensively studied in recent years for fuel ethanol production, in which yeast cells are exposed to various stresses such as high temperature, ethanol inhibition, and osmotic pressure from product and substrate sugars as well as the inhibitory substances released from the pretreatment of lignocellulosic biomass. An in-depth understanding of the mechanism of yeast stress tolerance contributes to breeding more robust strains for ethanol production, especially under very high gravity conditions. Taking advantage of the "omics" technology, the stress response and defense mechanism of yeast cells during ethanol fermentation were further explored, and the newly emerged tools such as genome shuffling and global transcription machinery engineering have been applied to breed stress resistant yeast strains for ethanol production. In this review, the latest development of stress tolerance mechanisms was focused, and improvement of yeast stress tolerance by both random and rational tools was presented.
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Affiliation(s)
- X Q Zhao
- Department of Bioscience and Bioengineering, Dalian University of Technology, China
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23
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Stimulation of zero-trans rates of lactose and maltose uptake into yeasts by preincubation with hexose to increase the adenylate energy charge. Appl Environ Microbiol 2008; 74:3076-84. [PMID: 18378647 DOI: 10.1128/aem.00188-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Initial rates of sugar uptake (zero-trans rates) are often measured by incubating yeast cells with radiolabeled sugars for 5 to 30 s and determining the radioactivity entering the cells. The yeast cells used are usually harvested from growth medium, washed, suspended in nutrient-free buffer, and stored on ice before they are assayed. With this method, the specific rates of zero-trans lactose uptake by Kluyveromyces lactis or recombinant Saccharomyces cerevisiae strains harvested from lactose fermentations were three- to eightfold lower than the specific rates of lactose consumption during fermentation. No significant extracellular beta-galactosidase activity was detected. The ATP content and adenylate energy charge (EC) of the yeasts were relatively low before the [(14)C]lactose uptake reactions were started. A short (1- to 7-min) preincubation of the yeasts with 10 to 30 mM glucose caused 1.5- to 5-fold increases in the specific rates of lactose uptake. These increases correlated with increases in EC (from 0.6 to 0.9) and ATP (from 4 to 8 micromol x g dry yeast(-1)). Stimulation by glucose affected the transport V(max) values, with smaller increases in K(m) values. Similar observations were made for maltose transport, using a brewer's yeast. These findings suggest that the electrochemical proton potential that drives transport through sugar/H(+) symports is significantly lower in the starved yeast suspensions used for zero-trans assays than in actively metabolizing cells. Zero-trans assays with such starved yeast preparations can produce results that seriously underestimate the capacity of sugar/H(+) symports. A short exposure to glucose allows a closer approach to the sugar/H(+) symport capacity of actively metabolizing cells.
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