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Sinha A, Pick E. Fluorescence Detection of Increased Reactive Oxygen Species Levels in Saccharomyces cerevisiae at the Diauxic Shift. Methods Mol Biol 2021; 2202:81-91. [PMID: 32857348 DOI: 10.1007/978-1-0716-0896-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The budding yeast Saccharomyces cerevisiae is a facultative organism that is able to utilize both anaerobic and aerobic metabolism, depending on the composition of carbon source in the growth medium. When glucose is abundant, yeast catabolizes it to ethanol and other by-products by anaerobic fermentation through the glycolysis pathway. Following glucose exhaustion, cells switch to oxygenic respiration (a.k.a. "diauxic shift"), which allows catabolizing ethanol and the other carbon compounds via the TCA cycle and oxidative phosphorylation in the mitochondria. The diauxic shift is accompanied by elevated reactive oxygen species (ROS) levels and is characterized by activation of ROS defense mechanisms. Traditional measurement of the diauxic shift is done through measuring optical density of cultures grown in a batch at intermediate time points and generating a typical growth curve or by estimating the reduction of glucose and accumulation of ethanol in growth media over time. In this manuscript, we describe a method for determining changes in ROS levels upon yeast growth, using carboxy-H(2)-dichloro-dihydrofluorescein diacetate (carboxy-H(2)-DCFDA). H2-DCFDA is a widely used fluorescent dye for measuring intracellular ROS levels. H2-DCFDA enables a direct measurement of ROS in yeast cells at intermediate time points. The outcome of H2-DCFDA fluorescent readout measurements correlates with the growth curve information, hence providing a clear understanding of the diauxic shift.
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Affiliation(s)
- Abhishek Sinha
- Department of Biology and Environment, University of Haifa at Oranim, Tivon, Israel
- Department of Microbiology, Swami Vivekand University, Sagar, Madhya Pradesh, India
| | - Elah Pick
- Department of Biology and Environment, University of Haifa at Oranim, Tivon, Israel.
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2
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Cruz-Garcia D, Brouwers N, Malhotra V, Curwin AJ. Reactive oxygen species triggers unconventional secretion of antioxidants and Acb1. J Cell Biol 2020; 219:151570. [PMID: 32328640 PMCID: PMC7147093 DOI: 10.1083/jcb.201905028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 12/18/2019] [Accepted: 01/24/2020] [Indexed: 02/07/2023] Open
Abstract
Nutrient deprivation triggers the release of signal-sequence–lacking Acb1 and the antioxidant superoxide dismutase 1 (SOD1). We now report that secreted SOD1 is functionally active and accompanied by export of other antioxidant enzymes such as thioredoxins (Trx1 and Trx2) and peroxiredoxin Ahp1 in a Grh1-dependent manner. Our data reveal that starvation leads to production of nontoxic levels of reactive oxygen species (ROS). Treatment of cells with N-acetylcysteine (NAC), which sequesters ROS, prevents antioxidants and Acb1 secretion. Starved cells lacking Grh1 are metabolically active, but defective in their ability to regrow upon return to growth conditions. Treatment with NAC restored the Grh1-dependent effect of starvation on cell growth. In sum, starvation triggers ROS production and cells respond by secreting antioxidants and the lipogenic signaling protein Acb1. We suggest that starvation-specific unconventional secretion of antioxidants and Acb1-like activities maintain cells in a form necessary for growth upon their eventual return to normal conditions.
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Affiliation(s)
- David Cruz-Garcia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Nathalie Brouwers
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Vivek Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluis COmpanys 23, 08010 Barcelona, Spain
| | - Amy J Curwin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
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Ding H, Ali A, Cheng Z. An Allelopathic Role for Garlic Root Exudates in the Regulation of Carbohydrate Metabolism in Cucumber in a Hydroponic Co-Culture System. PLANTS (BASEL, SWITZERLAND) 2019; 9:E45. [PMID: 31892150 PMCID: PMC7020217 DOI: 10.3390/plants9010045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022]
Abstract
Garlic is considered to have a strong positive effect on the growth and yield of receptors under soil cultivation conditions. However, how this positive promotion is produced by changing the growth environment of the receptors or directly acting on the receptors is still not very clear. The direct influence of co-culturing with different quantities of garlic plants (the control 5, 10, 15, 20) on the growth and biochemical processes of cucumber plants was studied using a hydroponic co-culture system. Different numbers of garlic bulbs inhibited the growth of cucumber plants and increased the production and induction of reactive oxygen species, which accompanied the enhancement of lipid peroxidation and oxidative damage to cucumber. This allelopathic exposure further reduced the chlorophyll contents and photosynthesis rate, and consequently impaired the photosynthetic performance of photosystem II (PSII). Garlic root exudates increased the leaves' carbohydrates accumulation, such as soluble sugar contents and sucrose levels by regulating the activities of metabolismic enzymes; however, no such accumulation was observed in the roots. Our results suggested that garlic root exudates can mediate negative plant-plant interactions and its phytotoxic influence on cucumber plants may have occurred through the application of oxidative stress, which consequently imbalanced the source-to-sink photo-assimilate flow.
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Affiliation(s)
- Haiyan Ding
- School of public health, Dali University, Dali 671000, Yunnan, China;
| | - Ahmad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China;
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4
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Karaffa L, Kubicek CP. Citric acid and itaconic acid accumulation: variations of the same story? Appl Microbiol Biotechnol 2019; 103:2889-2902. [PMID: 30758523 PMCID: PMC6447509 DOI: 10.1007/s00253-018-09607-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 01/15/2023]
Abstract
Citric acid production by Aspergillus niger and itaconic acid production by Aspergillus terreus are two major examples of technical scale fungal fermentations based on metabolic overflow of primary metabolism. Both organic acids are formed by the same metabolic pathway, but whereas citric acid is the end product in A. niger, A. terreus performs two additional enzymatic steps leading to itaconic acid. Despite of this high similarity, the optimization of the production process and the mechanism and regulation of overflow of these two acids has mostly been investigated independently, thereby ignoring respective knowledge from the other. In this review, we will highlight where the similarities and the real differences of these two processes occur, which involves various aspects of medium composition, metabolic regulation and compartmentation, transcriptional regulation, and gene evolution. These comparative data may facilitate further investigations of citric acid and itaconic acid accumulation and may contribute to improvements in their industrial production.
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Affiliation(s)
- Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary.
| | - Christian P Kubicek
- Institute of Chemical, Environmental & Bioscience Engineering, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria.,, 1100, Vienna, Austria
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He RR, Wang ZC, Tong HF, Chen WX, Chen WJ, Chen HM, Zhong QP. Effects of Metal Ion Addition on Acetic Acid Removal by Saccharomyces cerevisiae during Lychee Wine Fermentation. INTERNATIONAL JOURNAL OF FOOD ENGINEERING 2019. [DOI: 10.1515/ijfe-2018-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractAcetic acid (AA) is the main component of the volatile acidity of lychee wine. It can be generated by yeast, contaminated lactic acid, and AA bacteria at any time during lychee wine fermentation. AA has a negative impact on yeast fermentative performance and affects the quality of lychee wine when present above a given concentration. Thus, excessive amounts of AA should be removed to control the quality of lychee wine. This study investigated the effects of supplementing lychee juice with different concentrations of metal (magnesium, potassium, and calcium) ions on AA removal during lychee wine fermentation at 20 °C. All treatments of metal ion addition negatively affected yeast growth. The addition of either magnesium or potassium ions decreased the AA content, and the lowest values were attained with the addition of 4 mM magnesium ions and 6 mM potassium ions. By contrast, the addition of calcium ions increased the AA content. The addition of metal ions significantly affected metabolites, because more succinic acid, more malic acid, more glycerol, and less acetaldehyde were produced with increasing activities of acetaldehyde dehydrogenase, acetyl-CoA synthetase, isocitrate lyase, and malate synthase. Moreover, the addition of metal ions significantly modified the aroma components of deacidified lychee wine. These findings offer insight into the mechanism of yeast utilization of AA and suggest that selectively adding metal ions may be used a tool to modulate the AA content of lychee wine.
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Affiliation(s)
- Rong-Rong He
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Zhen-Chang Wang
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Hai-Feng Tong
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Wen-Xue Chen
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Wei-Jun Chen
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Hai-Ming Chen
- College of Food Science and Technology, Hainan University, Haikou570228, China
| | - Qiu-Ping Zhong
- College of Food Science and Technology, Hainan University, Haikou570228, China
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Functional analysis of Mig1 and Rag5 as expressional regulators in thermotolerant yeast Kluyveromyces marxianus. Appl Microbiol Biotechnol 2018; 103:395-410. [DOI: 10.1007/s00253-018-9462-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/30/2018] [Accepted: 10/09/2018] [Indexed: 11/30/2022]
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Lopandic K. Saccharomyces interspecies hybrids as model organisms for studying yeast adaptation to stressful environments. Yeast 2018; 35:21-38. [PMID: 29131388 DOI: 10.1002/yea.3294] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/02/2017] [Accepted: 10/25/2017] [Indexed: 01/05/2023] Open
Abstract
The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes. Such fusing usually results in a wide variety of alterations at the genetic and chromosomal levels. The observed changes have suggested a high genome plasticity and a significant role of interspecies hybridization in the adaptation of yeasts to environmental stresses and industrial processes. There is a high probability that harsh wine and beer fermentation environments, from which the majority of interspecies hybrids have been isolated so far, influence their selection and stabilization as well as their genomic and phenotypic heterogeneity. The lessons we have learned about geno- and phenotype plasticity and the diversity of natural and commercial yeast hybrids have already had a strong impact on the development of artificial hybrids that can be successfully used in the fermentation-based food and beverage industry. The creation of artificial hybrids through the crossing of strains with desired attributes is a possibility to obtain a vast variety of new, but not genetically modified yeasts with a range of improved and beneficial traits. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Ksenija Lopandic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11/3, A-1190, Vienna, Austria
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Wang Z, Zhang H, Liu C, Xing J, Chen XL. A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae. Front Microbiol 2018; 9:769. [PMID: 29720973 PMCID: PMC5915541 DOI: 10.3389/fmicb.2018.00769] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/04/2018] [Indexed: 02/02/2023] Open
Abstract
Ubiquitination is an essential protein modification in eukaryotic cells, which is reversible. Deubiquitinating enzymes (DUBs) catalyze deubiquitination process to reverse ubiquitination, maintain ubiquitin homeostasis or promote protein degradation by recycling ubiquitins. In order to investigate effects of deubiquitination process in plant pathogenic fungus Magnaporthe oryzae, we generated deletion mutants of MoUBP14. Ortholog of MoUbp14 was reported to play general roles in ubiquitin-mediated protein degradation in Saccharomyces cerevisiae. The ΔMoubp14 mutant lost its pathogenicity and was severely reduced in mycelial growth, sporulation, carbon source utilization, and increased in sensitivity to distinct stresses. The mutant was blocked in penetration, which could due to defect in turgor generation. It is also blocked in invasive growth, which could due to reduction in stress tolerance and nutrient utilization. Deletion of UBP14 also led to accumulation of free polyubiquitin chains. Pulldown assay identified some proteins related to carbohydrate metabolism and stress response may putatively interact with MoUbp14, including two key rate-limiting enzymes of gluconeogenesis, MoFbp1 and MoPck1. These two proteins were degraded when the glucose was supplied to M. oryzae grown in low glucose media for a short period of time (∼12 h), and this process required MoUbp14. In summary, pleiotropic phenotypes of the deletion mutants indicated that MoUbp14 is required for different developments and pathogenicity of M. oryzae.
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Affiliation(s)
- Zhao Wang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong Zhang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caiyun Liu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Xiao-Lin Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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Wang D, Sun J, Zhang W, Jia F, Yang Y, Lin Z, Feng J, Pavlovic M. Disruption of Brewer's Yeast Alcohol Dehydrogenase II Gene and Reduction of Acetaldehyde Content during Brewery Fermentation. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-64-0195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Deliang Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China, 100083
- China National Research Institute of Food and Fermentation Industries, Beijing, China, 100027
| | - Junshe Sun
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China, 100083
| | - Wujiu Zhang
- China National Research Institute of Food and Fermentation Industries, Beijing, China, 100027
| | - Fengchao Jia
- Beijing Yanjing Brewery Group Corporation Research Center, Beijing, China, 101300
| | - Yi Yang
- Beijing Yanjing Brewery Group Corporation Research Center, Beijing, China, 101300
| | - Zhiping Lin
- Beijing Yanjing Brewery Group Corporation Research Center, Beijing, China, 101300
| | - Jingzhang Feng
- Beijing Yanjing Brewery Group Corporation Research Center, Beijing, China, 101300
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10
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Pérez-González A, Kniewel R, Veldhuizen M, Verma HK, Navarro-Rodríguez M, Rubio LM, Caro E. Adaptation of the GoldenBraid modular cloning system and creation of a toolkit for the expression of heterologous proteins in yeast mitochondria. BMC Biotechnol 2017; 17:80. [PMID: 29132331 PMCID: PMC5683533 DOI: 10.1186/s12896-017-0393-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions. Another advantage is that mitochondria are suitable organelles to host oxygen sensitive proteins as a low oxygen environment is created within the matrix during cellular respiration. RESULTS Here we describe the adaptation of a modular cloning system, GoldenBraid2.0, for the integration of assembled transcriptional units into two different sites of the yeast genome, yielding a high expression level. We have also generated a toolkit comprising various promoters, terminators and selection markers that facilitate the generation of multigenic constructs and allow the reconstruction of biosynthetic pathways within Saccharomyces cerevisiae. To facilitate the specific expression of recombinant proteins within the mitochondrial matrix, we have also included in the toolkit an array of mitochondrial targeting signals and tested their efficiency at different growth conditions. As a proof of concept, we show here the integration and expression of 14 bacterial nitrogen fixation (nif) genes, some of which are known to require specific metallocluster cofactors that contribute to their stability yet make these proteins highly sensitive to oxygen. For one of these genes, nifU, we show that optimal production of this protein is achieved through the use of the Su9 mitochondrial targeting pre-sequence and glycerol as a carbon source to sustain aerobic respiration. CONCLUSIONS We present here an adapted GoldenBraid2.0 system for modular cloning, genome integration and expression of recombinant proteins in yeast. We have produced a toolkit that includes inducible and constitutive promoters, mitochondrial targeting signals, terminators and selection markers to guarantee versatility in the design of recombinant transcriptional units. By testing the efficiency of the system with nitrogenase Nif proteins and different mitochondrial targeting pre-sequences and growth conditions, we have paved the way for future studies addressing the expression of heterologous proteins in yeast mitochondria.
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Affiliation(s)
- Ana Pérez-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Ryan Kniewel
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), 28040, Madrid, Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Hemant K Verma
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Mankind Research Centre, IMT Manesar, Gurgaon, Haryana, 122050, India
| | - Mónica Navarro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
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11
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The proteome of baker's yeast mitochondria. Mitochondrion 2017; 33:15-21. [DOI: 10.1016/j.mito.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/12/2016] [Accepted: 08/13/2016] [Indexed: 01/29/2023]
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12
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Miyata N, Watanabe Y, Tamura Y, Endo T, Kuge O. Phosphatidylserine transport by Ups2-Mdm35 in respiration-active mitochondria. J Cell Biol 2016; 214:77-88. [PMID: 27354379 PMCID: PMC4932372 DOI: 10.1083/jcb.201601082] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Phosphatidylethanolamine, an essential phospholipid for mitochondrial functions, is synthesized at the mitochondrial inner membrane. Miyata et al. demonstrate that Ups2–Mdm35, a protein complex in the mitochondrial intermembrane space, mediates phosphatidylserine transport for phosphatidylethanolamine synthesis in respiration-active mitochondria of Saccharomyces cerevisiae. Phosphatidylethanolamine (PE) is an essential phospholipid for mitochondrial functions and is synthesized mainly by phosphatidylserine (PS) decarboxylase at the mitochondrial inner membrane. In Saccharomyces cerevisiae, PS is synthesized in the endoplasmic reticulum (ER), such that mitochondrial PE synthesis requires PS transport from the ER to the mitochondrial inner membrane. Here, we provide evidence that Ups2–Mdm35, a protein complex localized at the mitochondrial intermembrane space, mediates PS transport for PE synthesis in respiration-active mitochondria. UPS2- and MDM35-null mutations greatly attenuated conversion of PS to PE in yeast cells growing logarithmically under nonfermentable conditions, but not fermentable conditions. A recombinant Ups2–Mdm35 fusion protein exhibited phospholipid-transfer activity between liposomes in vitro. Furthermore, UPS2 expression was elevated under nonfermentable conditions and at the diauxic shift, the metabolic transition from glycolysis to oxidative phosphorylation. These results demonstrate that Ups2–Mdm35 functions as a PS transfer protein and enhances mitochondrial PE synthesis in response to the cellular metabolic state.
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Affiliation(s)
- Non Miyata
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yasunori Watanabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Osamu Kuge
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
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Shang YH, Zeng YJ, Zhu P, Zhong QP. Acetate metabolism of Saccharomyces cerevisiae at different temperatures during lychee wine fermentation. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1142831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Yu-hui Shang
- Food Department, College of Food Science and Technology, Hainan University, Haikou, China
| | - Ying-jie Zeng
- Food Department, College of Food Science and Technology, Hainan University, Haikou, China
| | - Ping Zhu
- Horticulture Department, College of Horticulture and Landscape Architecture, Hainan University, Haikou, China
| | - Qiu-ping Zhong
- Food Department, College of Food Science and Technology, Hainan University, Haikou, China
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14
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Kobayashi Y, Iwata H, Mizushima D, Ogihara J, Kasumi T. Erythritol production by Moniliella megachiliensis using nonrefined glycerol waste as carbon source. Lett Appl Microbiol 2015; 60:475-80. [PMID: 25645520 DOI: 10.1111/lam.12391] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 01/09/2015] [Indexed: 11/27/2022]
Abstract
UNLABELLED The number of naphtha plants is being reduced due to a worldwide shift in energy sources. Consequently, a shortage of chemical materials heavily dependent on naphtha-oil, especially C4 compounds such as butene and butane-diol, is an urgent issue in chemical manufacturing. Erythritol is a rare C4 compound produced by fermentation processes using glucose as the carbon source. Since erythritol is considerably more expensive than hydrocarbons derived from naphtha-oil, a reduction in its cost is critical. We found that Moniliella megachiliensis, a highly osmotolerant yeast strain, can utilize nonrefined glycerol waste derived from palm oil or beef tallow and convert it to erythritol. Cell growth on glycerol was almost the same as on glucose, and the cells could grow in up to 300 mg ml(-1) glycerol. When 200 mg ml(-1) nonrefined glycerol was supplied, the yield of erythritol from the glycerol was approx. 60%, which is slightly higher than that obtained using glucose. The cost of glycerol waste is considerably lower than that of glucose. Thus, the conversion of glycerol waste into valuable erythritol, proposed here, is attractive and promising from the viewpoint of ensuring a supply of C4 hydrocarbons and utilizing a waste natural resource. SIGNIFICANCE AND IMPACT OF THE STUDY A shortage of C4 hydrocarbon depending much on naptha-oil has become urgent problem due to rapid reduction of naphtha plants together with global energy revolution. Erythritol, obtained by fermentation, is a rare C4 polyol that can be converted to C4 hydrocarbons. Erythritol is considerably expensive than hydrocarbons, a reduction in cost is critical issue. To meet this, we proposed to utilize low-cost glycerol waste from bio-diesel fuel as a carbon source. Moniliella megachiliensis successfully converted glycerol waste to erythritol. This proposal is promising to obtain C4 hydrocarbon substitute, and concomitantly to dispose a large amount of glycerol waste discharged.
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Affiliation(s)
- Y Kobayashi
- Applied Microbiology and Biotechnology Laboratory, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
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15
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Venturelli OS, Zuleta I, Murray RM, El-Samad H. Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS Biol 2015; 13:e1002042. [PMID: 25626086 PMCID: PMC4307983 DOI: 10.1371/journal.pbio.1002042] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/03/2014] [Indexed: 01/28/2023] Open
Abstract
Detailed study of the dynamic response of yeast to combinations of sugars reveals an anticipatory population diversification strategy that allows rapid adaptation to shifts in environmental carbon source availability. To survive in resource-limited and dynamic environments, microbial populations implement a diverse repertoire of regulatory strategies. These strategies often rely on anticipating impending environmental shifts, enabling the population to be prepared for a future change in conditions. It has long been known that cells optimize nutritional value from mixtures of carbon sources, for example glucose and galactose, by sequential activation of regulatory programs that allow for metabolizing the preferred carbon source first before metabolizing the secondary carbon source. Using automated flow-cytometry, we mapped the dynamical behavior of populations simultaneously presented with a large panel of different glucose and galactose concentrations. We show that, counter to expectations, in populations presented with glucose and galactose simultaneously, the galactose regulatory pathway is activated in a fraction of the cell population hours before glucose is fully consumed. We demonstrate that the size of this fraction of cells is tuned by the concentration of the two sugars. This population diversification may constitute a tradeoff between the benefit of rapid galactose consumption once glucose is depleted and the cost of expressing the galactose pathway. Delineating the strategies by which cells contend with combinatorial changing environments is crucial for understanding cellular regulatory organization. When presented with two carbon sources, microorganisms first consume the carbon substrate that supports the highest growth rate (e.g., glucose) and then switch to the secondary carbon source (e.g., galactose), a paradigm known as the Monod model. Sequential sugar utilization has been attributed to transcriptional repression of the secondary metabolic pathway, followed by activation of this pathway upon depletion of the preferred carbon source. In this work, we demonstrate that although Saccharomyces cerevisiae cells consume glucose before galactose, the galactose regulatory pathway is activated in a fraction of the cell population hours before glucose is fully consumed. This early activation reduces the time required for the population to transition between the two metabolic programs and provides a fitness advantage that might be crucial in competitive environments.
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Affiliation(s)
- Ophelia S. Venturelli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- The California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Ignacio Zuleta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- The California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Richard M. Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- The California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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16
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López-Malo M, García-Rios E, Chiva R, Guillamon JM, Martí-Raga M. Effect of deletion and overexpression of tryptophan metabolism genes on growth and fermentation capacity at low temperature in wine yeast. Biotechnol Prog 2014; 30:776-83. [DOI: 10.1002/btpr.1915] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/01/2014] [Indexed: 11/11/2022]
Affiliation(s)
- María López-Malo
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
- Dept. de Bioquímica i Biotecnologia, Biotecnologia Enològica, Facultat d'Enologia; Universitat Rovira i Virgili; Marcel·li Domingo s/n, 43007 Tarragona Spain
| | - Estefani García-Rios
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - Rosana Chiva
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - José Manuel Guillamon
- Dept. de Biotecnología de los alimentos; Inst. de Agroquímica y Tecnología de los Alimentos (CSIC); Avda, Agustín Escardino, 7, E-46980-Paterna Valencia Spain
| | - María Martí-Raga
- Dept. de Bioquímica i Biotecnologia, Biotecnologia Enològica, Facultat d'Enologia; Universitat Rovira i Virgili; Marcel·li Domingo s/n, 43007 Tarragona Spain
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17
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Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, Li WH. Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. Genome Biol Evol 2013; 5:1065-78. [PMID: 23650209 PMCID: PMC3698916 DOI: 10.1093/gbe/evt067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as aerobic fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of aerobic fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of aerobic fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution.
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Affiliation(s)
- Zhenguo Lin
- Department of Ecology and Evolution, University of Chicago, USA
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18
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Han BK, Emr SD. The phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)-dependent Tup1 conversion (PIPTC) regulates metabolic reprogramming from glycolysis to gluconeogenesis. J Biol Chem 2013; 288:20633-45. [PMID: 23733183 DOI: 10.1074/jbc.m113.452813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Glucose/carbon metabolism is a fundamental cellular process in living cells. In response to varying environments, eukaryotic cells reprogram their glucose/carbon metabolism between aerobic or anaerobic glycolysis, oxidative phosphorylation, and/or gluconeogenesis. The distinct type of glucose/carbon metabolism that a cell carries out has significant effects on the cell's proliferation and differentiation. However, it is poorly understood how the reprogramming of glucose/carbon metabolism is regulated. Here, we report a novel endosomal PI(3,5)P2 lipid-dependent regulatory mechanism that is required for metabolic reprogramming from glycolysis to gluconeogenesis in Saccharomyces cerevisiae. Certain gluconeogenesis genes, such as FBP1 (encoding fructose-1,6-bisphosphatase 1) and ICL1 (encoding isocitrate lyase 1) are under control of the Mig1 repressor and Cyc8-Tup1 corepressor complex. We previously identified the PI(3,5)P2-dependent Tup1 conversion (PIPTC), a mechanism to convert Cyc8-Tup1 corepressor to Cti6-Cyc8-Tup1 coactivator. We demonstrate that the PIPTC plays a critical role for transcriptional activation of FBP1 and ICL1. Furthermore, without the PIPTC, the Cat8 and Sip4 transcriptional activators cannot be efficiently recruited to the promoters of FBP1 and ICL1, suggesting a key role for the PIPTC in remodulating the chromatin architecture at the promoters. Our findings expand our understanding of the regulatory mechanisms for metabolic reprogramming in eukaryotes to include key regulation steps outside the nucleus. Given that Tup1 and the metabolic enzymes that control PI(3,5)P2 are highly conserved among eukaryotes, our findings may provide important insights toward understanding glucose/carbon metabolic reprogramming in other eukaryotes, including humans.
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Affiliation(s)
- Bong-Kwan Han
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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19
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Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD. Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics 2013; 12:1421-35. [PMID: 23349476 DOI: 10.1074/mcp.o112.019166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187.
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Affiliation(s)
- Sunhee Jung
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
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20
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Ancín-Azpilicueta C, Barriuso-Esteban B, Nieto-Rojo R, Aristizábal-López N. SO(2) protects the amino nitrogen metabolism of Saccharomyces cerevisiae under thermal stress. Microb Biotechnol 2012; 5:654-62. [PMID: 22452834 PMCID: PMC3815877 DOI: 10.1111/j.1751-7915.2012.00343.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermal stress conditions during alcoholic fermentation modify yeasts' plasma membrane since they become more hyperfluid, which results in a loss of bilayer integrity. In this study, the influence of elevated temperatures on nitrogen metabolism of a Saccharomyces cerevisiae strain was studied, as well as the effect of different concentrations of SO2 on nitrogen metabolism under thermal stress conditions. The results obtained revealed that amino nitrogen consumption was lower in the fermentation sample subjected to thermal stress than in the control, and differences in amino acid consumption preferences were also detected, especially at the beginning of the fermentation. Under thermal stress conditions, among the three doses of SO2 studied (0, 35, 70 mg l−1 SO2), the highest dose was observed to favour amino acid utilization during the fermentative process, whereas sugar consumption presented higher rates at medium doses.
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Affiliation(s)
- Carmen Ancín-Azpilicueta
- Departamento de Química Aplicada, Universidad Pública de Navarra, Campus Arrosadía s/n, 31006 Pamplona, Spain.
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21
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Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2011; 12:104-17. [DOI: 10.1111/j.1567-1364.2011.00765.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ana Paula Oliveira
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
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22
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Differences in the glucose and fructose consumption profiles in diverse Saccharomyces wine species and their hybrids during grape juice fermentation. Int J Food Microbiol 2009; 134:237-43. [PMID: 19632733 DOI: 10.1016/j.ijfoodmicro.2009.07.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/23/2009] [Accepted: 07/04/2009] [Indexed: 11/24/2022]
Abstract
Yeasts with a high fructose consumption capability are very important for winemakers to solve problems associated with sluggish or stuck fermentations causing undesirable sweetness in wines. In the present study, we analyze the kinetics of glucose and fructose consumption during wine fermentations performed at low (12 degrees C) and high (28 degrees C) temperatures by twelve different yeast strains belonging to the species Saccharomyces cerevisiae, S. bayanus var. uvarum, S. kudriavzevii as well as interspecific Saccharomyces hybrids. Different mathematical equations (sigmoid, exponential and linear decay functions) were used to fit, by means of linear and nonlinear regressions, the sugar degradation along the fermentative process. Temperature had an important influence on glucose and fructose consumption, and clearly different degradation profiles were observed at 12 and 28 degrees C. From the obtained equations, times to consume half and total of the initial glucose and fructose concentrations present in the must were calculated, allowing a quantitative comparison among yeasts in order to select the fastest fermentative yeast according to the fermentation temperature. In general, all yeasts assayed showed a slightly higher preference for glucose than fructose at both temperatures, confirming the glucophilic character of Saccharomyces wine yeasts. However, at low temperatures, some Saccharomyces yeasts showed a fructophilic character at the beginning of fermentation. This kind of studies can be very useful for the wine industry to select yeast strains with different glucose/fructose preferences.
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23
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Arroyo-López FN, Querol A, Barrio E. Application of a substrate inhibition model to estimate the effect of fructose concentration on the growth of diverse Saccharomyces cerevisiae strains. J Ind Microbiol Biotechnol 2009; 36:663-9. [DOI: 10.1007/s10295-009-0535-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
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24
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Correlation between glucose/fructose discrepancy and hexokinase kinetic properties in different Saccharomyces cerevisiae wine yeast strains. Appl Microbiol Biotechnol 2007; 77:1083-91. [PMID: 17955190 DOI: 10.1007/s00253-007-1231-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 08/16/2007] [Accepted: 09/29/2007] [Indexed: 10/22/2022]
Abstract
Grape juice contains about equal amounts of glucose and fructose, but wine strains of Saccharomyces cerevisiae ferment glucose slightly faster than fructose, leading to fructose concentrations that exceed glucose concentrations in the fermenting must. A high fructose/glucose ratio may contribute to sluggish and stuck fermentations, a major problem in the global wine industry. We evaluated wine yeast strains with different glucose and fructose consumption rates to show that a lower glucose preference correlates with a higher fructose/glucose phosphorylation ratio in cell extracts and a lower K (m) for both sugars. Hxk1 has a threefold higher V (max) with fructose than with glucose, whereas Hxk2 has only a slightly higher V (max) with glucose than with fructose. Overexpression of HXK1 in a laboratory strain of S. cerevisiae (W303-1A) accelerated fructose consumption more than glucose consumption, but overexpression in a wine yeast strain (VIN13) reduced fructose consumption less than glucose consumption. Results with laboratory strains expressing a single kinase showed that total hexokinase activity is inversely correlated with the glucose/fructose (G/F) discrepancy. The latter has been defined as the difference between the rate of glucose and fructose fermentation. We conclude that the G/F discrepancy in wine yeast strains correlates with the kinetic properties of hexokinase-mediated sugar phosphorylation. A higher fructose/glucose phosphorylation ratio and a lower K (m) might serve as markers in selection and breeding of wine yeast strains with a lower tendency for sluggish fructose fermentation.
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25
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Smart KA. Brewing yeast genomes and genome-wide expression and proteome profiling during fermentation. Yeast 2007; 24:993-1013. [PMID: 17879324 DOI: 10.1002/yea.1553] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The genome structure, ancestry and instability of the brewing yeast strains have received considerable attention. The hybrid nature of brewing lager yeast strains provides adaptive potential but yields genome instability which can adversely affect fermentation performance. The requirement to differentiate between production strains and assess master cultures for genomic instability has led to significant adoption of specialized molecular tool kits by the industry. Furthermore, the development of genome-wide transcriptional and protein expression technologies has generated significant interest from brewers. The opportunity presented to explore, and the concurrent requirement to understand both, the constraints and potential of their strains to generate existing and new products during fermentation is discussed.
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Affiliation(s)
- Katherine A Smart
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK.
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26
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27
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Abstract
Eukaryotic cells possess an exquisitely interwoven and fine-tuned series of signal transduction mechanisms with which to sense and respond to the ubiquitous fermentable carbon source glucose. The budding yeast Saccharomyces cerevisiae has proven to be a fertile model system with which to identify glucose signaling factors, determine the relevant functional and physical interrelationships, and characterize the corresponding metabolic, transcriptomic, and proteomic readouts. The early events in glucose signaling appear to require both extracellular sensing by transmembrane proteins and intracellular sensing by G proteins. Intermediate steps involve cAMP-dependent stimulation of protein kinase A (PKA) as well as one or more redundant PKA-independent pathways. The final steps are mediated by a relatively small collection of transcriptional regulators that collaborate closely to maximize the cellular rates of energy generation and growth. Understanding the nuclear events in this process may necessitate the further elaboration of a new model for eukaryotic gene regulation, called "reverse recruitment." An essential feature of this idea is that fine-structure mapping of nuclear architecture will be required to understand the reception of regulatory signals that emanate from the plasma membrane and cytoplasm. Completion of this task should result in a much improved understanding of eukaryotic growth, differentiation, and carcinogenesis.
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Affiliation(s)
- George M Santangelo
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406-5018, USA.
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28
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Barnett JA, Entian KD. A history of research on yeasts 9: regulation of sugar metabolism. Yeast 2005; 22:835-94. [PMID: 16134093 DOI: 10.1002/yea.1249] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- James A Barnett
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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29
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Ohlmeier S, Kastaniotis AJ, Hiltunen JK, Bergmann U. The Yeast Mitochondrial Proteome, a Study of Fermentative and Respiratory Growth. J Biol Chem 2004; 279:3956-79. [PMID: 14597615 DOI: 10.1074/jbc.m310160200] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Saccharomyces cerevisiae is able to switch from fermentation to respiration (diauxic shift) with major changes in metabolic activity. This phenomenon has been previously studied on the transcriptional level. Here we present a parallel analysis of the yeast mitochondrial proteome and the corresponding transcriptional activity in cells grown on glucose (fermentation) and glycerol (respiration). A two-dimensional reference gel for this organelle proteome was established (available at www.biochem.oulu.fi/proteomics/), which contains about 800 intense spots. From 459 spots 253 individual proteins were identified, among them low abundant and hydrophobic proteins, and 37 proteins previously deemed hypothetical, with partially unknown cellular localization. After the diauxic shift, mitochondrial levels of only 18 proteins were changed (17 increased, with 1 decreased), among them proteins involved in the tricarboxylic acid cycle (Sdh1p, Sdh2p, and Sdh4p) and the respiratory chain (Cox4p, Cyb2p, and Qcr7p), proteins contributing to other respiratory pathways (Ach1p, Adh2p, Ald4p, Cat2p, Icl2p, and Pdh1p), and two proteins with unknown function (Om45p and Ybr230p). Apart from an overall increase in mitochondrial protein mass, the mitochondrial proteome remains remarkably constant, even in a major metabolic adaptation. This seemingly disagrees with results of the DNA microarray analyses, where a rather heterogenous up- or down-regulation of genes encoding mitochondrial proteins implies large changes in the proteome. We propose that the discrepancy between proteome and transcriptional regulation, apart from different translation efficiency, indicates a changed turnover rate of proteins in different physiological conditions.
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Affiliation(s)
- Steffen Ohlmeier
- Biocenter Oulu and Department of Biochemistry, P. O. Box 3000, University of Oulu, Oulu FIN-90014, Finland.
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30
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Ahuatzi D, Herrero P, de la Cera T, Moreno F. The glucose-regulated nuclear localization of hexokinase 2 in Saccharomyces cerevisiae is Mig1-dependent. J Biol Chem 2004; 279:14440-6. [PMID: 14715653 DOI: 10.1074/jbc.m313431200] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two major mediators of glucose repression in Saccharomyces cerevisiae are the proteins Mig1 and Hxk2. The mechanism of Hxk2-dependent glucose repression pathway is not well understood, but the Mig1-dependent part of the pathway has been elucidated in great detail. Here we report that Hxk2 has a glucose-regulated nuclear localization and that Mig1, a transcriptional repressor responsible for glucose repression of many genes, is required to sequester Hxk2 into the nucleus. Mig1 and Hxk2 interacted in vivo in a yeast two-hybrid assay and in vitro in immunoprecipitation and glutathione S-transferase pull-down experiments. We found that the Lys(6)-Met(15) decapeptide of Hxk2, which is necessary for nuclear localization of the protein, is also essential for interaction with the Mig1 protein. Our results also show that the Hxk2-Mig1 interaction is of physiological significance because both proteins have been found interacting together in a cluster with DNA fragments containing the MIG1 site of SUC2 promoter. We conclude that Hxk2 operates by interacting with Mig1 to generate a repressor complex located in the nucleus of S. cerevisiae during growth in glucose medium.
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Affiliation(s)
- Deifilia Ahuatzi
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Campus del Cristo, 33006 Oviedo, Spain
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31
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Malherbe S, Fromion V, Hilgert N, Sablayrolles JM. Modeling the effects of assimilable nitrogen and temperature on fermentation kinetics in enological conditions. Biotechnol Bioeng 2004; 86:261-72. [PMID: 15083506 DOI: 10.1002/bit.20075] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We propose a dynamic model of alcoholic fermentation in wine-making conditions. In this model, the speed at which CO(2) is released is related to the effects of the main factors involved in fermentation in wine-making conditions: temperature (which can vary within a predefined range) and nitrogen additions (which must not exceed the maximal authorized level). The resulting model consists of ordinary differential equations including numerous parameters that need to be identified and important interactions between explicative variables. These parameters were identified by uncoupling the effects of variables during specific experiments. The results were validated on another series of experiments in different conditions.
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Affiliation(s)
- S Malherbe
- Equipe de Microbiologie et Technologies des Fermentations, INRA, UMR Sciences pour l'oenologie, 2 Place Viala, 34060 Montpellier cedex 1, France
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32
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James TC, Campbell S, Donnelly D, Bond U. Transcription profile of brewery yeast under fermentation conditions. J Appl Microbiol 2003; 94:432-48. [PMID: 12588552 DOI: 10.1046/j.1365-2672.2003.01849.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS Yeast strains, used in the brewing industry, experience distinctive physiological conditions. During a brewing fermentation, yeast are exposed to anaerobic conditions, high pressure, high specific gravity and low temperatures. The purpose of this study was to examine the global gene expression profile of yeast subjected to brewing stress. METHODS AND RESULTS We have carried out a microarray analysis of a typical brewer's yeast during the course of an 8-day fermentation in 15 degrees P wort. We used the probes derived from Saccharomyces cerevisiae genomic DNA on the chip and RNA isolated from three stages of brewing. This analysis shows a high level of expression of genes involved in fatty acid and ergosterol biosynthesis early in fermentation. Furthermore, genes involved in respiration and mitochondrial protein synthesis also show higher levels of expression. CONCLUSIONS Surprisingly, we observed a complete repression of many stress response genes and genes involved in protein synthesis throughout the 8-day period compared with that at the start of fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY This microarray data set provides an analysis of gene expression under brewing fermentation conditions. The data provide an insight into the various metabolic processes altered or activated by brewing conditions of growth. This study leads to future experiments whereby selective alterations in brewing conditions could be introduced to take advantage of the changing transcript profile to improve the quality of the brew.
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Affiliation(s)
- T C James
- Moyne Institute for Preventive Medicine, Microbiology Department, Trinity College, University of Dublin, Dublin 2, Ireland
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33
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Winderickx J, Holsbeeks I, Lagatie O, Giots F, Thevelein J, de Winde H. From feast to famine; adaptation to nutrient availability in yeast. ACTA ACUST UNITED AC 2002. [DOI: 10.1007/3-540-45611-2_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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34
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Portela P, Howell S, Moreno S, Rossi S. In vivo and in vitro phosphorylation of two isoforms of yeast pyruvate kinase by protein kinase A. J Biol Chem 2002; 277:30477-87. [PMID: 12063246 DOI: 10.1074/jbc.m201094200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Saccharomyces cerevisiae pyruvate kinase 1 (Pyk1) was demonstrated to be associated to an immunoprecipitate of yeast protein kinase A holoenzyme (HA-Tpk1.Bcy1) and to be phosphorylated in a cAMP-dependent process. Both glutathione S-transferase (GST)-Pyk1 and GST-Pyk2 were phosphorylated in vitro by the bovine heart protein kinase A (PKA) catalytic subunit and by immobilized yeast HA-Tpk1. The specificity constant for the phosphorylation of GST-Pyk1 and GST-Pyk2 by bovine catalytic subunit was in the range of the value for Leu-Arg-Arg-Ala-Ser-Leu-Gly (Kemptide). Both fusion proteins were phosphorylated in vivo, in intact cells overexpressing the protein, or in vitro using crude extracts, as source of protein kinase A, when a wild type strain was used but were not phosphorylated when using a strain with only one TPK gene with an attenuated mutation (tpk1(w1)). The effect of phosphorylation on Pyk activity was assayed in partially purified preparations from three strains, containing different endogenous protein kinase A activity levels. Pyk1 activity was measured at different phosphoenolpyruvate concentrations in the absence or in the presence of the activator fructose 1,6-bisphosphate at 1.5 mm. Preliminary kinetic results derived from the comparison of Pyk1 obtained from extracts with the highest versus those from the lowest protein kinase A activity indicate that the enzyme is more active upon phosphorylation conditions; in the absence of the activator it shows a shift in the titration curve for phosphoenolpyruvate to the left and an increase in the Hill coefficient, whereas in the presence of fructose 1,6-bisphosphate it shows an n(H) value of 1.4, as compared with an n(H) of 2 for the Pyk1 obtained from extracts with almost null protein kinase A activity.
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Affiliation(s)
- Paula Portela
- Laboratory of Protein Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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Agostini D, Polidori E, Palma F, Ceccaroli P, Saltarelli R, Tonelli D, Stocchi V. Cloning, expression, and characterization of the hxk-1 Gene from the white truffle Tuber borchii vittad.: A first step toward understanding sugar metabolism. Fungal Genet Biol 2001; 33:15-23. [PMID: 11407882 DOI: 10.1006/fgbi.2001.1268] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent biochemical investigations of Tuber borchii Vittad. mycelium have demonstrated the presence of three distinct forms of hexokinase (HK(M1), HK(M2), and HKM3). In the investigation described here, a gene coding for hexokinase (hxk-1) from T. borchii was isolated and characterized. The hxk-1 gene is characterized by an ORF of 1494 nucleotides and codes for a polypeptide of 497 aa. The gene was overexpressed in Escherichia coli, and the recombinant protein was kinetically characterized. The K(cat) value for fructose is in agreement with the data reported for the hexokinase of Yarrowia lipolytica, the Km for ATP is not dependent on the sugar used, and the enzyme is not inhibited by trehalose 6-phosphate or glucose 6-phosphate. The biochemical characteristics confirm that this enzyme is a hexokinase, as suggested by the Pileup results, and it corresponds to the HKM1 isoform. This work represents the first characterization of the key enzyme of the glycolytic pathway and the related gene in a Tuber species.
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Affiliation(s)
- D Agostini
- Istituto di Chimica Biologica Giorgio Fornaini, Università degli Studi di Urbino, Via A. Saffi 2, Urbino, (PU), 61029, Italy
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Ho S, Chao Y, Tong W, Yu S. Sugar coordinately and differentially regulates growth- and stress-related gene expression via a complex signal transduction network and multiple control mechanisms. PLANT PHYSIOLOGY 2001; 125:877-90. [PMID: 11161045 PMCID: PMC64889 DOI: 10.1104/pp.125.2.877] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2000] [Revised: 08/25/2000] [Accepted: 10/07/2000] [Indexed: 05/18/2023]
Abstract
In plants, sugars are required to sustain growth and regulate gene expression. A large set of genes are either up- or down-regulated by sugars; however, whether there is a common mechanism and signal transduction pathway for differential and coordinated sugar regulation remain unclear. In the present study, the rice (Oryza sativa cv Tainan 5) cell culture was used as a model system to address this question. Sucrose and glucose both played dual functions in gene regulation as exemplified by the up-regulation of growth-related genes and down-regulation of stress-related genes. Sugar coordinately but differentially activated or repressed gene expression, and nuclear run-on transcription and mRNA half-life analyses revealed regulation of both the transcription rate and mRNA stability. Although coordinately regulated by sugars, these growth- and stress-related genes were up-regulated or down-regulated through hexokinase-dependent and/or hexokinase-independent pathways. We also found that the sugar signal transduction pathway may overlap the glycolytic pathway for gene repression. alpha-Amylase and the stress-related genes identified in this study were coordinately expressed under sugar starvation, suggesting a convergence of the nutritional and environmental stress signal transduction pathways. Together, our studies provide a new insight into the complex signal transduction network and mechanisms of sugar regulation of growth and stress-related genes in plants.
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Affiliation(s)
- S Ho
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 11529, Republic of China
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Ceccaroli P, Saltarelli R, Cesari P, Zambonelli A, Stocchi V. Effects of different carbohydrate sources on the growth of Tuber borchii Vittad. mycelium strains in pure culture. Mol Cell Biochem 2001; 218:65-70. [PMID: 11330839 DOI: 10.1023/a:1007265423786] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The influence of carbohydrate utilisation on the growth of three strains of Tuber borchii Vittad. mycelium (1BO, 17BO and 10RA) in culture was assessed using culture media containing glucose (control), mannose or mannitol. Mannose was the best substrate for growth of the strains and this was particularly evident for strain 17BO. Mannitol instead was metabolized only by 10RA and 1BO. In order to explain the different growth trends, analyses of enzyme levels, kinetic parameters, protein patterns and the morphology of the three strains were carried out. Our results show that these strains of T. borchii mycelium were affected by the substrates used in the media. The aim of the present work was to optimise the in vitro production of T. borchii mycelium for use in experiments which require the fungus in precise and reproducible conditions, such as mycorrhizal synthesis or protein and nucleic acid extractions.
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Affiliation(s)
- P Ceccaroli
- Istituto di Chimica Biologica Giorgio Fornaini, Università degli Studi di Urbino, PU, Italy
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Menu T, Rothan C, Dai N, Petreikov M, Etienne C, Destrac-Irvine A, Schaffer A, Granot D, Ricard B. Cloning and characterization of a cDNA encoding hexokinase from tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:209-218. [PMID: 11164592 DOI: 10.1016/s0168-9452(00)00332-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two different partial sequences encoding putative hexokinase (HXK, ATP: hexose-6-phosphotransferase, EC 2.7.1.1) were isolated from tomato (Lycopersicon esculentum) by RT-PCR using degenerate primers. Southern blot analysis suggested the existence of two divergent HXK genes. A complete cDNA of one HXK was isolated by screening a cDNA library prepared from young cherry tomato fruit. The 1770 bp cDNA of LeHXK2 contained an open reading frame encoding a 496 amino acid protein that has 69% identity with the two Arabidopsis HXKs, 83 and 85% identity with potato StHXK1 and tobacco NtHXK, respectively. However, this clone had 97% amino acid identity with potato StHXK2 and, therefore, was named LeHXK2. LeHXK2 cDNA was expressed in a triple mutant yeast (Saccharomyces cerevisiae) strain which lacked the ability to phosphorylate glucose and fructose and, therefore, was unable to grow on these sugars as carbon sources. Mutant cells expressing LeHXK2 grew on both glucose and fructose with shorter doubling time on glucose. The kinetic properties of LeHXK2 expressed in yeast were determined after the purification of LeHXK2 by HPLC-ion exchange chromatography, confirming the identity of LeHXK2 as hexokinase with higher affinity to glucose. LeHXK2 mRNA was detected by RT-PCR expression analysis in all organs and tissues and at all stages of fruit development. However, semi-quantitative RT-PCR analysis showed that LeHXK2 was most highly expressed in flowers.
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Affiliation(s)
- T Menu
- Unité de Physiologie Végétale, Institut National de la Recherche Agronomique, B.P. 81, 33883, Villenave d'Ornon, France
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Affiliation(s)
- J A Barnett
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Jault JM, Fieulaine S, Nessler S, Gonzalo P, Di Pietro A, Deutscher J, Galinier A. The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding. J Biol Chem 2000; 275:1773-80. [PMID: 10636874 DOI: 10.1074/jbc.275.3.1773] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbon catabolite repression allows bacteria to rapidly alter the expression of catabolic genes in response to the availability of metabolizable carbon sources. In Bacillus subtilis, this phenomenon is controlled by the HPr kinase (HprK) that catalyzes ATP-dependent phosphorylation of either HPr (histidine containing protein) or Crh (catabolite repression HPr) on residue Ser-46. We report here that B. subtilis HprK forms homo-oligomers constituted most likely of eight subunits. Related to this complex structure, the enzyme displays strong positive cooperativity for the binding of its allosteric activator, fructose 1,6-bisphosphate, as evidenced by either kinetics of its phosphorylation activity or the intrinsic fluorescence properties of its unique tryptophan residue, Trp-235. It is further shown that activation of HPr phosphorylation by fructose 1,6-bisphosphate essentially occurs at low ATP and enzyme concentrations. A positive cooperativity was also detected for the binding of natural nucleotides or their 2'(3')-N-methylanthraniloyl derivatives, in either phosphorylation or fluorescence experiments. Most interestingly, quenching of the HprK tryptophan fluorescence by using either iodide or acrylamide revealed a heterogeneity of tryptophan residues within the population of oligomers, suggesting that the enzyme exists in two different conformations. This result suggests a concerted-symmetry model for the catalytic mechanism of positive cooperativity displayed by HprK.
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Affiliation(s)
- J M Jault
- Institut de Biologie et Chimie des Protéines, UPR 412 CNRS, 69367 Lyon Cedex 07, France
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Abstract
We have cloned the gene HXK1 from the dimorphic yeast Yarrowia lipolytica that encodes the unique hexokinase of this yeast. The gene has an intron located 39 base pairs after the A of the first ATG. The putative protein contains a sequence of 40 amino acids which is absent from other known hexokinase sequences. Y. lipolytica strains devoid of hexokinase grew in glucose slower than wild-type. This growth was due to the existence of a glucokinase. The hexokinase from Y. lipolytica substituted effectively for hexokinase II from S. cerevisiae in catabolite repression of invertase. The hexokinases from Schizosaccharomyces pombe or Kluyveromyces lactis were much less effective in this role. The K(m) for glucose and fructose of hexokinase was 0.38 mM and 3.56 mM, respectively. The K(m) of glucokinase for glucose was 0.17 mM. While the hexokinase was strongly inhibited by trehalose-6-phosphate (K(i)=3.6 microM), glucokinase was not affected by this compound.
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Affiliation(s)
- T Petit
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C.-UAM, 28029 Madrid, Spain
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Ceccaroli P, Saltarelli R, Buffalini M, Piccoli G, Stocchi V. Three different forms of hexokinase are identified during Tuber borchii mycelium growth. Mol Cell Biochem 1999; 194:71-7. [PMID: 10391126 DOI: 10.1023/a:1006908501788] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Truffles are ectomycorrhizal fungi which have a great dependence on carbohydrates supplied by their host plants. The catabolism of hexoses in the mycobiont is important for the production of energy, and the first enzyme in the hexose assimilation pathways is hexokinase. This study reports differences in the expression of this enzyme during the growth of Tuber borchii Vittad. mycelium (strain ATCC 96540). Three hexokinase activities (HKM1, HKM2 and HKM3) were isolated by anion-exchange chromatography and partially purified. HKM1 and HKM2 were present in the linear phase at 15-50 days of growth. Two remarkable differences were found in the sugar-phosphorylating activity and stability of HKM1 and HKM2. HKM2 did not phosphorylate the fructose and it was present in the chromatographic profile only when substrates such as glucose, glucosamine or mannose were added to the extraction buffer. On the contrary, HKM1 utilized also fructose and was detected under all the experimental conditions used. HKM3 was the only molecular form observed after 70 days, when the fungus growth had reached a plateau. To our knowledge these results represent the first evidence for the presence in T. borchii mycelium of three distinct enzymatic forms of hexokinase which are differently expressed during growth of the fungus.
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Affiliation(s)
- P Ceccaroli
- Istituto di Chimica Biologica Giorgio Fornaini, Università degli Studi di Urbino, Italy
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Heinisch JJ, Valdés E, Alvarez J, Rodicio R. Molecular genetics of ICL2, encoding a non-functional isocitrate lyase in saccharomyces cerevisiae. Yeast 1998. [DOI: 10.1002/(sici)1097-0061(199610)12:13<1285::aid-yea5>3.0.co;2-b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Smits HP, Cohen A, Buttler T, Nielsen J, Olsson L. Cleanup and analysis of sugar phosphates in biological extracts by using solid-phase extraction and anion-exchange chromatography with pulsed amperometric detection. Anal Biochem 1998; 261:36-42. [PMID: 9683509 DOI: 10.1006/abio.1998.2714] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A cleanup method based on anion-exchange solid-phase extraction (SPE) was developed to render biological extracts suitable for the analysis of hexose phosphates with a modified anion-exchange chromatography method and pulsed amperometric detection. The method was applied to cell extracts of Saccharomyces cerevisiae obtained by using cold methanol as quenching agent and chloroform as extraction solvent. It was shown that pretreatment of the cell extract with SPE markedly improved the quality of the liquid chromatography analysis with recoveries of the sugar phosphates close to 100%. Furthermore, the method allowed for sample enrichment and the original extraction procedure could be simplified by implementing SPE early in the extraction protocol.
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Affiliation(s)
- H P Smits
- Department of Biotechnology, Technical University of Denmark, Building 223, Lyngby DK-2800, Denmark
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Klein CJ, Olsson L, Nielsen J. Nitrogen-limited continuous cultivations as a tool to quantify glucose control in Saccharomyces cerevisiae. Enzyme Microb Technol 1998. [DOI: 10.1016/s0141-0229(98)00019-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Scheffler IE. Molecular genetics of succinate:quinone oxidoreductase in eukaryotes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 60:267-315. [PMID: 9594577 DOI: 10.1016/s0079-6603(08)60895-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Succinate:quinone oxidoreductase is a membrane-associated complex in mitochondria, often referred to as complex II, based on the fractionation scheme developed by Y. Hatefi and colleagues. It consists of four peptides, two of which are integral membrane proteins (15 and 12-13 kDa, respectively) and two others that are peripheral membrane proteins, i.e., a flavoprotein (Fp, 70 kDa) and an iron-protein (Ip, 27 kDa). The mature, functional complex contains a cytochrome in association with the membrane proteins, a flavin linked covalently to the largest peptide, and three iron-sulfur clusters in the 27-kDa subunit. The present review touches only briefly on the biochemical and biophysical properties of this complex. Instead, the focus is on the molecular-genetic studies that have become possible since the first genes from eukaryotes were cloned in 1989. The evolutionary conservation of the amino acid sequence of both the Fp and the Ip peptides has facilitated the cloning of these genes from a large variety of eukaryotic organisms by PCR-based methods. The review addresses questions related to the regulation of the expression of these genes, with an emphasis on mammals and yeast, for which most of the information is available. Four different genes have to be co-ordinately regulated. Transcriptional as well as posttranscriptional regulatory mechanisms have been observed in diverse organisms. Intriguing observations have been made in studies of this enzyme during the life cycle of organisms existing alternately under aerobic and anaerobic conditions. Naturally occurring or induced mutations in these genes have shed light on several questions related to the assembly of this complex, and on the relationship between structure and function. Four different peptides are imported into the mitochondria. They have to be modified, folded, and assembled. The stage is set for the exploration of highly specific changes introduced by site-directed mutagenesis. Until recently the genes were believed to be exclusively nuclear in all eukaryotes, but exceptions have since been found. This finding has relevance in the discussion of the evolution of mitochondria from prokaryotes. A highly conserved set of genes is found in prokaryotes, and some informative comparisons on gene organization and expression in prokaryotes and eukaryotes have been included.
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Affiliation(s)
- I E Scheffler
- Department of Biology, University of California, San Diego 92093, USA
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Lu CA, Lim EK, Yu SM. Sugar response sequence in the promoter of a rice alpha-amylase gene serves as a transcriptional enhancer. J Biol Chem 1998; 273:10120-31. [PMID: 9553059 DOI: 10.1074/jbc.273.17.10120] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of alpha-amylase genes in both rice suspension cells and germinating embryos is repressed by sugars and the mechanism involves transcriptional regulation. The promoter of a rice alpha-amylase gene alphaAmy3 was analyzed by both loss- and gain-of-function studies and the major sugar response sequence (SRS) was located between 186 and 82 base pairs upstream of the transcription start site. The SRS conferred sugar responsiveness to a minimal promoter in an orientation-independent manner. It also converted a sugar-insensitive rice actin gene promoter into a sugar-sensitive promoter in a dose-dependent manner. Linker-scan mutation studies identified three essential motifs: the GC box, the G box, and the TATCCA element, within the SRS. Sequences containing either the GC box plus G box or the TATCCA element each mediated sugar response, however, they acted synergistically to give a high level glucose starvation-induced expression. Nuclear proteins from rice suspension cells binding to the TATCCA element in a sequence-specific and sugar-dependent manner were identified. The TATCCA element is also an important component of the gibberellin response complex of the alpha-amylase genes in germinating cereal grains, suggesting that the regulation of alpha-amylase gene expression by sugar and hormone signals may share common regulatory machinery.
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Affiliation(s)
- C A Lu
- Graduate Institute of Life Sciences, National Defense Medical Center, and Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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Jonassen T, Proft M, Randez-Gil F, Schultz JR, Marbois BN, Entian KD, Clarke CF. Yeast Clk-1 homologue (Coq7/Cat5) is a mitochondrial protein in coenzyme Q synthesis. J Biol Chem 1998; 273:3351-7. [PMID: 9452453 DOI: 10.1074/jbc.273.6.3351] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mutations in the clk-1 gene result in slower development and increased life span in Caenorhabditis elegans. The Saccharomyces cerevisiae homologue COQ7/CAT5 is essential for several metabolic pathways including ubiquinone biosynthesis, respiration, and gluconeogenic gene activation. We show here that Coq7p/Cat5p is a mitochondrial inner membrane protein directly involved in ubiquinone biosynthesis, and that the defect in gluconeogenic gene activation in coq7/cat5 null mutants is a general consequence of a defect in respiration. These results obtained in the yeast model suggest that the effects on development and life span in C. elegans clk-1 mutants may relate to changes in the amount of ubiquinone, an essential electron transport component and a lipid soluble antioxidant.
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Affiliation(s)
- T Jonassen
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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