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Xiao Y, Hu C, Hsiang T, Li J. Amino acid permease RcAAP1 increases the uptake and phloem translocation of an L-valine-phenazine-1-carboxylic acid conjugate. FRONTIERS IN PLANT SCIENCE 2023; 14:1191250. [PMID: 37332709 PMCID: PMC10272580 DOI: 10.3389/fpls.2023.1191250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Amino acid conjugates of pesticides can promote the phloem translocation of parent ingredients, allowing for the reduction of usage, and decreased environmental pollution. Plant transporters play important roles in the uptake and phloem translocation of such amino acid-pesticide conjugates such as L-Val-PCA (L-valine-phenazine-1-carboxylic acid conjugate). However, the effects of an amino acid permease, RcAAP1, on the uptake and phloem mobility of L-Val-PCA are still unclear. Here, the relative expression levels of RcAAP1 were found to be up-regulated 2.7-fold and 2.2-fold by the qRT-PCR after L-Val-PCA treatments of Ricinus cotyledons for 1 h and 3 h, respectively. Subsequently, expression of RcAAP1 in yeast cells increased the L-Val-PCA uptake (0.36 μmol/107 cells), which was 2.1-fold higher than the control (0.17 μmol/107 cells). Pfam analysis suggested RcAAP1 with its 11 transmembrane domains belongs to the amino acid transporter family. Phylogenetic analysis found RcAAP1 to be strongly similar to AAP3 in nine other species. Subcellular localization showed that fusion RcAAP1-eGFP proteins were observed in the plasma membrane of mesophyll cells and phloem cells. Furthermore, overexpression of RcAAP1 for 72 h significantly increased the phloem mobility of L-Val-PCA in Ricinus seedlings, and phloem sap concentration of the conjugate was 1.8-fold higher than the control. Our study suggested that RcAAP1 as carrier was involved in the uptake and phloem translocation of L-Val-PCA, which could lay foundation for the utilization of amino acids and further development of vectorized agrochemicals.
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Affiliation(s)
- Yongxin Xiao
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, Jingzhou, China
| | - Ciyin Hu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, Jingzhou, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Junkai Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, Jingzhou, China
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González-Lozano KJ, Aréchiga-Carvajal ET, Jiménez-Salas Z, Valdez-Rodríguez DM, León-Ramírez CG, Ruiz-Herrera J, Adame-Rodríguez JM, López-Cabanillas-Lomelí M, Campos-Góngora E. Identification and Characterization of Dmct: A Cation Transporter in Yarrowia lipolytica Involved in Metal Tolerance. J Fungi (Basel) 2023; 9:600. [PMID: 37367535 DOI: 10.3390/jof9060600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
Yarrowia lipolytica is a dimorphic fungus used as a model organism to investigate diverse biotechnological and biological processes, such as cell differentiation, heterologous protein production, and bioremediation strategies. However, little is known about the biological processes responsible for cation concentration homeostasis. Metals play pivotal roles in critical biochemical processes, and some are toxic at unbalanced intracellular concentrations. Membrane transport proteins control intracellular cation concentrations. Analysis of the Y. lipolytica genome revealed a characteristic functional domain of the cation efflux protein family, i.e., YALI0F19734g, which encodes YALI0F19734p (a putative Yl-Dmct protein), which is related to divalent metal cation tolerance. We report the in silico analysis of the putative Yl-Dmct protein's characteristics and the phenotypic response to divalent cations (Ca2+, Cu2+, Fe2+, and Zn2+) in the presence of mutant strains, Δdmct and Rdmct, constructed by deletion and reinsertion of the DMCT gene, respectively. The absence of the Yl-Dmct protein induces cellular and growth rate changes, as well as dimorphism differences, when calcium, copper, iron, and zinc are added to the cultured medium. Interestingly, the parental and mutant strains were able to internalize the ions. Our results suggest that the protein encoded by the DMCT gene is involved in cell development and cation homeostasis in Y. lipolytica.
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Affiliation(s)
- Katia Jamileth González-Lozano
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología, LMYF, Unidad de Manipulación Genética, Monterrey CP 66455, Nuevo León, Mexico
| | - Elva Teresa Aréchiga-Carvajal
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología, LMYF, Unidad de Manipulación Genética, Monterrey CP 66455, Nuevo León, Mexico
| | - Zacarías Jiménez-Salas
- Universidad Autónoma de Nuevo León, Centro de Investigación en Nutrición y Salud Pública, Monterrey CP 64460, Nuevo León, Mexico
| | - Debany Marlen Valdez-Rodríguez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología, LMYF, Unidad de Manipulación Genética, Monterrey CP 66455, Nuevo León, Mexico
| | - Claudia Geraldine León-Ramírez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Departamento de Ingeniería Genética, Irapuato CP 36824, Guanajuato, Mexico
| | - José Ruiz-Herrera
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Departamento de Ingeniería Genética, Irapuato CP 36824, Guanajuato, Mexico
| | - Juan Manuel Adame-Rodríguez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología, LMYF, Unidad de Manipulación Genética, Monterrey CP 66455, Nuevo León, Mexico
| | - Manuel López-Cabanillas-Lomelí
- Universidad Autónoma de Nuevo León, Centro de Investigación en Nutrición y Salud Pública, Monterrey CP 64460, Nuevo León, Mexico
| | - Eduardo Campos-Góngora
- Universidad Autónoma de Nuevo León, Centro de Investigación en Nutrición y Salud Pública, Monterrey CP 64460, Nuevo León, Mexico
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Hays M, Schwartz K, Schmidtke DT, Aggeli D, Sherlock G. Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination. PLoS Genet 2023; 19:e1010747. [PMID: 37192196 PMCID: PMC10218751 DOI: 10.1371/journal.pgen.1010747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/26/2023] [Accepted: 04/14/2023] [Indexed: 05/18/2023] Open
Abstract
There are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in chromosome structure, DNA copy number, and novel transposon insertions all create large genomic changes, which can have correspondingly large impacts on phenotypes and fitness. In this study we investigate the spectrum of adaptive mutations that arise in a population under consistently fluctuating nitrogen conditions. We specifically contrast these adaptive alleles and the mutational mechanisms that create them, with mechanisms of adaptation under batch glucose limitation and constant selection in low, non-fluctuating nitrogen conditions to address if and how selection dynamics influence the molecular mechanisms of evolutionary adaptation. We observe that retrotransposon activity accounts for a substantial number of adaptive events, along with microhomology-mediated mechanisms of insertion, deletion, and gene conversion. In addition to loss of function alleles, which are often exploited in genetic screens, we identify putative gain of function alleles and alleles acting through as-of-yet unclear mechanisms. Taken together, our findings emphasize that how selection (fluctuating vs. non-fluctuating) is applied also shapes adaptation, just as the selective pressure (nitrogen vs. glucose) does itself. Fluctuating environments can activate different mutational mechanisms, shaping adaptive events accordingly. Experimental evolution, which allows a wider array of adaptive events to be assessed, is thus a complementary approach to both classical genetic screens and natural variation studies to characterize the genotype-to-phenotype-to-fitness map.
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Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Katja Schwartz
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Danica T. Schmidtke
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Dimitra Aggeli
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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de Valk SC, Bouwmeester SE, de Hulster E, Mans R. Engineering proton-coupled hexose uptake in Saccharomyces cerevisiae for improved ethanol yield. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:47. [PMID: 35524322 PMCID: PMC9077909 DOI: 10.1186/s13068-022-02145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/16/2022] [Indexed: 11/28/2022]
Abstract
Background In the yeast Saccharomyces cerevisiae, which is widely applied for industrial bioethanol production, uptake of hexoses is mediated by transporters with a facilitated diffusion mechanism. In anaerobic cultures, a higher ethanol yield can be achieved when transport of hexoses is proton-coupled, because of the lower net ATP yield of sugar dissimilation. In this study, the facilitated diffusion transport system for hexose sugars of S. cerevisiae was replaced by hexose–proton symport. Results Introduction of heterologous glucose– or fructose–proton symporters in an hxt0 yeast background strain (derived from CEN.PK2-1C) restored growth on the corresponding sugar under aerobic conditions. After applying an evolutionary engineering strategy to enable anaerobic growth, the hexose–proton symporter-expressing strains were grown in anaerobic, hexose-limited chemostats on synthetic defined medium, which showed that the biomass yield of the resulting strains was decreased by 44.0-47.6%, whereas the ethanol yield had increased by up to 17.2% (from 1.51 to 1.77 mol mol hexose−1) compared to an isogenic strain expressing the hexose uniporter HXT5. To apply this strategy to increase the ethanol yield on sucrose, we constructed a platform strain in which all genes encoding hexose transporters, disaccharide transporters and disaccharide hydrolases were deleted, after which a combination of a glucose–proton symporter, fructose–proton symporter and extracellular invertase (SUC2) were introduced. After evolution, the resulting strain exhibited a 16.6% increased anaerobic ethanol yield (from 1.51 to 1.76 mol mol hexose equivalent−1) and 46.6% decreased biomass yield on sucrose. Conclusions This study provides a proof-of-concept for the replacement of the endogenous hexose transporters of S. cerevisiae by hexose-proton symport, and the concomitant decrease in ATP yield, to greatly improve the anaerobic yield of ethanol on sugar. Moreover, the sugar-negative platform strain constructed in this study acts as a valuable starting point for future studies on sugar transport or development of cell factories requiring specific sugar transport mechanisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02145-7.
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Pacheco A, Donzella L, Hernandez-Lopez MJ, Almeida MJ, Prieto JA, Randez-Gil F, Morrissey JP, Sousa MJ. Hexose transport in Torulaspora delbrueckii: identification of Igt1, a new dual-affinity transporter. FEMS Yeast Res 2021; 20:5715911. [PMID: 31981362 DOI: 10.1093/femsyr/foaa004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 01/24/2020] [Indexed: 01/23/2023] Open
Abstract
Torulaspora delbrueckii is a yeast species receiving increasing attention from the biotechnology industry, with particular relevance in the wine, beer and baking sectors. However, little is known about its sugar transporters and sugar transport capacity, frequently a rate-limiting step of sugar metabolism and efficient fermentation. Actually, only one glucose transporter, Lgt1, has been characterized so far. Here we report the identification and characterization of a second glucose transporter gene, IGT1, located in a cluster, upstream of LGT1 and downstream of two other putative hexose transporters. Functional characterization of IGT1 in a Saccharomyces cerevisiae hxt-null strain revealed that it encodes a transporter able to mediate uptake of glucose, fructose and mannose and established that its affinity, as measured by Km, could be modulated by glucose concentration in the medium. In fact, IGT1-transformed S. cerevisiae hxt-null cells, grown in 0.1% glucose displayed biphasic glucose uptake kinetics with an intermediate- (Km = 6.5 ± 2.0 mM) and a high-affinity (Km = 0.10 ± 0.01 mM) component, whereas cells grown in 2% glucose displayed monophasic kinetics with an intermediate-affinity (Km of 11.5 ± 1.5 mM). This work contributes to a better characterization of glucose transport in T. delbrueckii, with relevant implications for its exploitation in the food industry.
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Affiliation(s)
- Andreia Pacheco
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Lorena Donzella
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria Jose Hernandez-Lopez
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Maria Judite Almeida
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Jose Antonio Prieto
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria João Sousa
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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Identification of an Acidic Amino Acid Permease Involved in d-Aspartate Uptake in the Yeast Cryptococcus humicola. Microorganisms 2021; 9:microorganisms9010192. [PMID: 33477545 PMCID: PMC7831105 DOI: 10.3390/microorganisms9010192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 11/22/2022] Open
Abstract
d-aspartate oxidase (DDO) catalyzes the oxidative deamination of acidic d-amino acids, and its production is induced by d-Asp in several eukaryotes. The yeast Cryptococcus humicola strain UJ1 produces large amounts of DDO (ChDDO) only in the presence of d-Asp. In this study, we analyzed the relationship between d-Asp uptake by an amino acid permease (Aap) and the inducible expression of ChDDO. We identified two acidic Aap homologs, named “ChAap4 and ChAap5,” in the yeast genome sequence. ChAAP4 deletion resulted in partial growth defects on d-Asp as well as l-Asp, l-Glu, and l-Phe at pH 7, whereas ChAAP5 deletion caused partial growth defects on l-Phe and l-Lys, suggesting that ChAap4 might participate in d-Asp uptake as an acidic Aap. Interestingly, the growth of the Chaap4 strain on d- or l-Asp was completely abolished at pH 10, suggesting that ChAap4 is the only Aap responsible for d- and l-Asp uptake under high alkaline conditions. In addition, ChAAP4 deletion significantly decreased the induction of DDO activity and ChDDO transcription in the presence of d-Asp. This study revealed that d-Asp uptake by ChAap4 might be involved in the induction of ChDDO expression by d-Asp.
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7
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Hou J, Daniels PN, Burke MD. Small Molecule Channels Harness Membrane Potential to Concentrate Potassium in trk1Δtrk2Δ Yeast. ACS Chem Biol 2020; 15:1575-1580. [PMID: 32427463 DOI: 10.1021/acschembio.0c00180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many protein ion channels harness membrane potential to move ions in opposition to their chemical gradient. Deficiencies of such proteins cause several human diseases, including cystic fibrosis, Bartter Syndrome, and proximal renal tubular acidosis. Using yeast as a eukaryotic model system, we asked whether, in the context of a protein ion channel deficiency in vivo, small molecule channels could similarly harness membrane potential to concentrate ions. Trk potassium transporters use membrane potential to move potassium from a relatively low concentration outside cells (∼15 mM) to one of >10× higher inside (150-500 mM); trk1Δtrk2Δ are unable to concentrate potassium or grow in standard media. Here we show that potassium-permeable, but not potassium-selective, small-molecule ion channels formed by amphotericin B can harness membrane potential to concentrate potassium and thereby restore trk1Δtrk2Δ growth. This finding expands the list of potential human channelopathies that might be addressed by a molecular prosthetics approach.
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Affiliation(s)
- Jennifer Hou
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Page N. Daniels
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Martin D. Burke
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, 807 South Wright Street, Champaign, Illinois 61820, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Dr., Urbana, Illinois 61801, United States
- Arnold and Mabel Beckman Institute, University of Illinois at Urbana−Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
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8
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Designing yeast as plant-like hyperaccumulators for heavy metals. Nat Commun 2019; 10:5080. [PMID: 31704944 PMCID: PMC6841955 DOI: 10.1038/s41467-019-13093-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/14/2019] [Indexed: 02/01/2023] Open
Abstract
Hyperaccumulators typically refer to plants that absorb and tolerate elevated amounts of heavy metals. Due to their unique metal trafficking abilities, hyperaccumulators are promising candidates for bioremediation applications. However, compared to bacteria-based bioremediation systems, plant life cycle is long and growing conditions are difficult to maintain hindering their adoption. Herein, we combine the robust growth and engineerability of bacteria with the unique waste management mechanisms of plants by using a more tractable platform-the common baker’s yeast-to create plant-like hyperaccumulators. Through overexpression of metal transporters and engineering metal trafficking pathways, engineered yeast strains are able to sequester metals at concentrations 10–100 times more than established hyperaccumulator thresholds for chromium, arsenic, and cadmium. Strains are further engineered to be selective for either cadmium or strontium removal, specifically for radioactive Sr90. Overall, this work presents a systematic approach for transforming yeast into metal hyperaccumulators that are as effective as their plant counterparts. Existing heavy metal bioremediation systems are mainly based on plants, which require long growing time in specific conditions. Here, the authors mimic the characteristics of plant hyperaccumulators to engineer more tractable baker’s yeast and achieve 10–100-fold higher accumulation of chromium, arsenic, or cadmium.
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9
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Bezerra-Neto JP, de Araújo FC, Ferreira-Neto JRC, da Silva MD, Pandolfi V, Aburjaile FF, Sakamoto T, de Oliveira Silva RL, Kido EA, Barbosa Amorim LL, Ortega JM, Benko-Iseppon AM. Plant Aquaporins: Diversity, Evolution and Biotechnological Applications. Curr Protein Pept Sci 2019; 20:368-395. [PMID: 30387391 DOI: 10.2174/1389203720666181102095910] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
Abstract
The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.
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Affiliation(s)
- João P Bezerra-Neto
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - José R C Ferreira-Neto
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Manassés D da Silva
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Valesca Pandolfi
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Flavia F Aburjaile
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Tetsu Sakamoto
- Universidade Federal de Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Brazil
| | - Roberta L de Oliveira Silva
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Ederson A Kido
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Lidiane L Barbosa Amorim
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Piauí, Campus Oeiras, Avenida Projetada, s/n, 64.500-000, Oeiras, Piauí, Brazil
| | - José M Ortega
- Universidade Federal de Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Brazil
| | - Ana M Benko-Iseppon
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
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10
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Wang Y, Wang Y, Du X, Yan S, Zhang P, Chen HY, Huang S. Electrode-free nanopore sensing by DiffusiOptoPhysiology. SCIENCE ADVANCES 2019; 5:eaar3309. [PMID: 31523706 PMCID: PMC6731070 DOI: 10.1126/sciadv.aar3309] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/02/2019] [Indexed: 05/24/2023]
Abstract
A wide variety of single molecules can be identified by nanopore sensing. However, all reported nanopore sensing applications result from the same measurement configuration adapted from electrophysiology. Although urgently needed in commercial nanopore sequencing, parallel electrophysiology recording is limited in its cost and its throughput due to the introduced complexities from electronic integration. We present the first electrode-free nanopore sensing method defined as DiffusiOptoPhysiology (DOP), in which single-molecule events are monitored optically without any electrical connections. Single-molecule sensing of small molecules, macromolecules, and biomacromolecules was subsequently demonstrated. As a further extension, a fingertip-sized, multiplexed chip with single-molecule sensing capabilities has been introduced, which suggests a new concept of clinical diagnosis using disposable nanopore sensors. DOP, which is universally compatible with all types of channels and a variety of fluorescence imaging platforms, may benefit diverse areas such as nanopore sequencing, drug screening, and channel protein investigations.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
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12
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da Silveira FA, Diniz RHS, Sampaio GMS, Brandão RL, da Silveira WB, Castro IM. Sugar transport systems in Kluyveromyces marxianus CCT 7735. Antonie van Leeuwenhoek 2018; 112:211-223. [DOI: 10.1007/s10482-018-1143-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/11/2018] [Indexed: 11/30/2022]
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13
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de Lima LA, Diniz RHS, de Queiroz MV, Fietto LG, da Silveira WB. Screening of Yeasts Isolated from Brazilian Environments for the 2-Phenylethanol (2-PE) Production. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0119-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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The Role of Yeast-Surface-Display Techniques in Creating Biocatalysts for Consolidated BioProcessing. Catalysts 2018. [DOI: 10.3390/catal8030094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Climate change is directly linked to the rapid depletion of our non-renewable fossil resources and has posed concerns on sustainability. Thus, imploring the need for us to shift from our fossil based economy to a sustainable bioeconomy centered on biomass utilization. The efficient bioconversion of lignocellulosic biomass (an ideal feedstock) to a platform chemical, such as bioethanol, can be achieved via the consolidated bioprocessing technology, termed yeast surface engineering, to produce yeasts that are capable of this feat. This approach has various strategies that involve the display of enzymes on the surface of yeast to degrade the lignocellulosic biomass, then metabolically convert the degraded sugars directly into ethanol, thus elevating the status of yeast from an immobilization material to a whole-cell biocatalyst. The performance of the engineered strains developed from these strategies are presented, visualized, and compared in this article to highlight the role of this technology in moving forward to our quest against climate change. Furthermore, the qualitative assessment synthesized in this work can serve as a reference material on addressing the areas of improvement of the field and on assessing the capability and potential of the different yeast surface display strategies on the efficient degradation, utilization, and ethanol production from lignocellulosic biomass.
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Perpète P, Santos G, Bodart E, Collin S. Uptake of Amino Acids during Beer Production: The Concept of a Critical Time Value. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-63-0023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Philippe Perpète
- Unité de Brasserie et des Industries Alimentaires, Université catholique de Louvain, Croix du Sud, 2/7, B-1348 Louvain-la-Neuve, Belgium
| | - Gumer Santos
- Unité de Brasserie et des Industries Alimentaires, Université catholique de Louvain, Croix du Sud, 2/7, B-1348 Louvain-la-Neuve, Belgium
| | - Etienne Bodart
- Unité de Brasserie et des Industries Alimentaires, Université catholique de Louvain, Croix du Sud, 2/7, B-1348 Louvain-la-Neuve, Belgium
| | - Sonia Collin
- Unité de Brasserie et des Industries Alimentaires, Université catholique de Louvain, Croix du Sud, 2/7, B-1348 Louvain-la-Neuve, Belgium
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16
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Tani T, Taguchi H, Akamatsu T. Analysis of metabolisms and transports of xylitol using xylose- and xylitol-assimilating Saccharomyces cerevisiae. J Biosci Bioeng 2017; 123:613-620. [PMID: 28126230 DOI: 10.1016/j.jbiosc.2016.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 01/16/2023]
Abstract
To clarify the relationship between NAD(P)+/NAD(P)H redox balances and the metabolisms of xylose or xylitol as carbon sources, we analyzed aerobic and anaerobic batch cultures of recombinant Saccharomyces cerevisiae in a complex medium containing 20 g/L xylose or 20 g/L xylitol at pH 5.0 and 30°C. The TDH3p-GAL2 or gal80Δ strain completely consumed the xylose within 24 h and aerobically consumed 92-100% of the xylitol within 96 h, but anaerobically consumed only 20% of the xylitol within 96 h. Cells of both strains grew well in aerobic culture. The addition of acetaldehyde (an effective oxidizer of NADH) increased the xylitol consumption by the anaerobically cultured strain. These results indicate that in anaerobic culture, NAD+ generated in the NAD(P)H-dependent xylose reductase reaction was likely needed in the NAD+-dependent xylitol dehydrogenase reaction, whereas in aerobic culture, the NAD+ generated by oxidation of NADH in the mitochondria is required in the xylitol dehydrogenase reaction. The role of Gal2 and Fps1 in importing xylitol into the cytosol and exporting it from the cells was analyzed by examining the xylitol consumption in aerobic culture and the export of xylitol metabolized from xylose in anaerobic culture, respectively. The xylitol consumptions of gal80Δ gal2Δ and gal80Δ gal2Δ fps1Δ strains were reduced by 81% and 88% respectively, relative to the gal80Δ strain. The maximum xylitol concentration accumulated by the gal80Δ, gal80Δ gal2Δ, and gal80Δ gal2Δ fps1Δ strains was 7.25 g/L, 5.30 g/L, and 4.27 g/L respectively, indicating that Gal2 and Fps1 transport xylitol both inward and outward.
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Affiliation(s)
- Tatsunori Tani
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Hisataka Taguchi
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Takashi Akamatsu
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.
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17
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Chen X, Wang Z, Guo X, Liu S, He X. Regulation of general amino acid permeases Gap1p, GATA transcription factors Gln3p and Gat1p on 2-phenylethanol biosynthesis via Ehrlich pathway. J Biotechnol 2017; 242:83-91. [DOI: 10.1016/j.jbiotec.2016.11.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022]
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18
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Isolation and characterization of xylitol-assimilating mutants of recombinant Saccharomyces cerevisiae. J Biosci Bioeng 2016; 122:446-55. [DOI: 10.1016/j.jbiosc.2016.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/22/2016] [Accepted: 03/12/2016] [Indexed: 11/22/2022]
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19
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Solis-Escalante D, van den Broek M, Kuijpers NGA, Pronk JT, Boles E, Daran JM, Daran-Lapujade P. The genome sequence of the popular hexose-transport-deficient Saccharomyces cerevisiae strain EBY.VW4000 reveals LoxP/Cre-induced translocations and gene loss. FEMS Yeast Res 2015; 15:fou004. [PMID: 25673752 DOI: 10.1093/femsyr/fou004] [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] [Indexed: 11/12/2022] Open
Abstract
Saccharomyces cerevisiae harbours a large group of tightly controlled hexose transporters with different characteristics. Construction and characterization of S. cerevisiae EBY.VW4000, a strain devoid of glucose import, was a milestone in hexose-transporter research. This strain has become a widely used platform for discovery and characterization of transporters from a wide range of organisms. To abolish glucose uptake, 21 genes were knocked out, involving 16 successive deletion rounds with the LoxP/Cre system. Although such intensive modifications are known to increase the risk of genome alterations, the genome of EBY.VW4000 has hitherto not been characterized. Based on a combination of whole genome sequencing, karyotyping and molecular confirmation, the present study reveals that construction of EBY.VW4000 resulted in gene losses and chromosomal rearrangements. Recombinations between the LoxP scars have led to the assembly of four neo-chromosomes, truncation of two chromosomes and loss of two subtelomeric regions. Furthermore, sporulation and spore germination are severely impaired in EBY.VW4000. Karyotyping of the EBY.VW4000 lineage retraced its current chromosomal architecture to four translocations events occurred between the 6th and the 12th rounds of deletion. The presented data facilitate further studies on EBY.VW4000 and highlight the risks of genome alterations associated with repeated use of the LoxP/Cre system.
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Affiliation(s)
- Daniel Solis-Escalante
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Niels G A Kuijpers
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands Platform Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Eckhard Boles
- Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands Platform Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
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21
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Determinants of tolerance to inhibitors in hardwood spent sulfite liquor in genome shuffled Pachysolen tannophilus strains. Antonie van Leeuwenhoek 2015; 108:811-34. [PMID: 26231071 DOI: 10.1007/s10482-015-0537-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Genome shuffling was used to obtain Pachysolen tannophilus mutants with improved tolerance to inhibitors in hardwood spent sulfite liquor (HW SSL). Genome shuffled strains (GHW301, GHW302 and GHW303) grew at higher concentrations of HW SSL (80 % v/v) compared to the HW SSL UV mutant (70 % v/v) and the wild-type (WT) strain (50 % v/v). In defined media containing acetic acid (0.70-0.90 % w/v), GHW301, GHW302 and GHW303 exhibited a shorter lag compared to the acetic acid UV mutant, while the WT did not grow. Genome shuffled strains produced more ethanol than the WT at higher concentrations of HW SSL and an aspen hydrolysate. To identify the genetic basis of inhibitor tolerance, whole genome sequencing was carried out on GHW301, GHW302 and GHW303 and compared to the WT strain. Sixty single nucleotide variations were identified that were common to all three genome shuffled strains. Of these, 40 were in gene sequences and 20 were within 5 bp-1 kb either up or downstream of protein encoding genes. Based on the mutated gene products, mutations were grouped into functional categories and affected a variety of cellular functions, demonstrating the complexity of inhibitor tolerance in yeast. Sequence analysis of UV mutants (UAA302 and UHW303) from which GHW301, GHW302 and GHW303 were derived, confirmed the success of our cross-mating based genome shuffling strategy. Whole-genome sequencing analysis allowed identification of potential gene targets for tolerance to inhibitors in lignocellulosic hydrolysates.
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22
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Gournas C, Evangelidis T, Athanasopoulos A, Mikros E, Sophianopoulou V. The Aspergillus nidulans proline permease as a model for understanding the factors determining substrate binding and specificity of fungal amino acid transporters. J Biol Chem 2015; 290:6141-55. [PMID: 25572393 DOI: 10.1074/jbc.m114.612069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amino acid uptake in fungi is mediated by general and specialized members of the yeast amino acid transporter (YAT) family, a branch of the amino acid polyamine organocation (APC) transporter superfamily. PrnB, a highly specific l-proline transporter, only weakly recognizes other Put4p substrates, its Saccharomyces cerevisiae orthologue. Taking advantage of the high sequence similarity between the two transporters, we combined molecular modeling, induced fit docking, genetic, and biochemical approaches to investigate the molecular basis of this difference and identify residues governing substrate binding and specificity. We demonstrate that l-proline is recognized by PrnB via interactions with residues within TMS1 (Gly(56), Thr(57)), TMS3 (Glu(138)), and TMS6 (Phe(248)), which are evolutionary conserved in YATs, whereas specificity is achieved by subtle amino acid substitutions in variable residues. Put4p-mimicking substitutions in TMS3 (S130C), TMS6 (F252L, S253G), TMS8 (W351F), and TMS10 (T414S) broadened the specificity of PrnB, enabling it to recognize more efficiently l-alanine, l-azetidine-2-carboxylic acid, and glycine without significantly affecting the apparent Km for l-proline. S253G and W351F could transport l-alanine, whereas T414S, despite displaying reduced proline uptake, could transport l-alanine and glycine, a phenotype suppressed by the S130C mutation. A combination of all five Put4p-ressembling substitutions resulted in a functional allele that could also transport l-alanine and glycine, displaying a specificity profile impressively similar to that of Put4p. Our results support a model where residues in these positions determine specificity by interacting with the substrates, acting as gating elements, altering the flexibility of the substrate binding core, or affecting conformational changes of the transport cycle.
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Affiliation(s)
- Christos Gournas
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
| | - Thomas Evangelidis
- the School of Pharmacy, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Alexandros Athanasopoulos
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
| | - Emmanuel Mikros
- the School of Pharmacy, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Vicky Sophianopoulou
- From the Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, NCSR "Demokritos," Agia Paraskevi, 15310 Athens and
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23
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Bak JS. Lignocellulose depolymerization occurs via an environmentally adapted metabolic cascades in the wood-rotting basidiomycete Phanerochaete chrysosporium. Microbiologyopen 2014; 4:151-66. [PMID: 25470354 PMCID: PMC4335982 DOI: 10.1002/mbo3.228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 01/06/2023] Open
Abstract
Plant biomass can be utilized by a lignocellulose-degrading fungus, Phanerochaete chrysosporium, but the metabolic and regulatory mechanisms involved are not well understood. A polyomics-based analysis (metabolomics, proteomics, and transcriptomics) of P. chrysosporium has been carried out using statistically optimized conditions for lignocellulolytic reaction. Thirty-nine metabolites and 123 genes (14 encoded proteins) that consistently exhibited altered regulation patterns were identified. These factors were then integrated into a comprehensive map that fully depicts all signaling cascades involved in P. chrysosporium. Despite the diversity of these cascades, they showed complementary interconnection among themselves, ensuring the efficiency of passive biosystem and thereby yielding energy expenditure for the cells. Particularly, many factors related to intracellular regulatory networks showed compensating activity in homeostatic lignocellulolysis. In the main platform of proactive biosystem, although several deconstruction-related targets (e.g., glycoside hydrolase, ureidoglycolate hydrolase, transporters, and peroxidases) were systematically utilized, well-known supporters (e.g., cellobiose dehydrogenase and ferroxidase) were rarely generated.
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Affiliation(s)
- Jin Seop Bak
- Department of Chemical and Biomolecular Engineering, Advanced Biomass R&D Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Republic of Korea
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24
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Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM. Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2014; 38:254-99. [PMID: 24483210 PMCID: PMC4238866 DOI: 10.1111/1574-6976.12065] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights include the central role of the Snf1 protein kinase in the glucose repression pathway, galactose induction, the discovery of a G-protein-coupled receptor system, and role of Ras in glucose-induced cAMP signaling, the role of the protein synthesis initiation machinery in general control of nitrogen metabolism, the cyclin-controlled protein kinase Pho85 in phosphate regulation, nitrogen catabolite repression and the nitrogen-sensing target of rapamycin pathway, and the discovery of transporter-like proteins acting as nutrient sensors. In addition, a number of cellular targets, like carbohydrate stores, stress tolerance, and ribosomal gene expression, are controlled by the presence of multiple nutrients. The protein kinase A signaling pathway plays a major role in this general nutrient response. It has led to the discovery of nutrient transceptors (transporter receptors) as nutrient sensors. Major shortcomings in our knowledge are the relationship between rapid and steady-state nutrient signaling, the role of metabolic intermediates in intracellular nutrient sensing, and the identity of the nutrient sensors controlling cellular growth.
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Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Marta Rubio-Texeira
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
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25
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L-Phenylalanine Transport in Saccharomyces cerevisiae: Participation of GAP1, BAP2, and AGP1. JOURNAL OF AMINO ACIDS 2014; 2014:283962. [PMID: 24701347 PMCID: PMC3950631 DOI: 10.1155/2014/283962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/01/2013] [Accepted: 12/30/2013] [Indexed: 01/13/2023]
Abstract
We focused on the participation of GAP1, BAP2, and AGP1 in L-phenylalanine transport in yeast. In order to study the physiological functions of GAP1, BAP2, and AGP1 in L-phenylalanine transport, we examined the kinetics, substrate specificity, and regulation of these systems, employing isogenic haploid strains with the respective genes disrupted individually and in combination. During the characterization of phenylalanine transport, we noted important regulatory phenomena associated with these systems. Our results show that Agp1p is the major transporter of the phenylalanine in a gap1 strain growing in synthetic media with leucine present as an inducer. In a wild type strain grown in the presence of leucine, when ammonium ion was the nitrogen source, Bap2p is the principal phenylalanine carrier.
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26
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Ghaddar K, Krammer EM, Mihajlovic N, Brohée S, André B, Prévost M. Converting the yeast arginine can1 permease to a lysine permease. J Biol Chem 2014; 289:7232-7246. [PMID: 24448798 DOI: 10.1074/jbc.m113.525915] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Amino acid uptake in yeast cells is mediated by about 16 plasma membrane permeases, most of which belong to the amino acid-polyamine-organocation (APC) transporter family. These proteins display various substrate specificity ranges. For instance, the general amino acid permease Gap1 transports all amino acids, whereas Can1 and Lyp1 catalyze specific uptake of arginine and lysine, respectively. Although Can1 and Lyp1 have different narrow substrate specificities, they are close homologs. Here we investigated the molecular rules determining the substrate specificity of the H(+)-driven arginine-specific permease Can1. Using a Can1-Lyp1 sequence alignment as a guideline and a three-dimensional Can1 structural model based on the crystal structure of the bacterial APC family arginine/agmatine antiporter, we introduced amino acid substitutions liable to alter Can1 substrate specificity. We show that the single substitution T456S results in a Can1 variant transporting lysine in addition to arginine and that the combined substitutions T456S and S176N convert Can1 to a Lyp1-like permease. Replacement of a highly conserved glutamate in the Can1 binding site leads to variants (E184Q and E184A) incapable of any amino acid transport, pointing to a potential role for this glutamate in H(+) coupling. Measurements of the kinetic parameters of arginine and lysine uptake by the wild-type and mutant Can1 permeases, together with docking calculations for each amino acid in their binding site, suggest a model in which residues at positions 176 and 456 confer substrate selectivity at the ligand-binding stage and/or in the course of conformational changes required for transport.
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Affiliation(s)
- Kassem Ghaddar
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld. du Triomphe, 1050 Brussels, Belgium
| | - Natalija Mihajlovic
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Sylvain Brohée
- Machine Learning Group, Computer Science Department, Faculté des Sciences, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Bruno André
- Laboratoire de Physiologie Moléculaire de la Cellule CP300, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), 11 Rue des Pr. Jeener et Brachet, 6041 Gosselies, Belgium.
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Bld. du Triomphe, 1050 Brussels, Belgium.
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27
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Levi CE, Cardillo SB, Bertotti S, Ríos C, Correa García S, Moretti MB. GABA induction of the Saccharomyces cerevisiae UGA4 gene depends on the quality of the carbon source: role of the key transcription factors acting in this process. Biochem Biophys Res Commun 2012; 421:572-7. [PMID: 22525679 DOI: 10.1016/j.bbrc.2012.04.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 04/10/2012] [Indexed: 12/01/2022]
Abstract
Yeast cells are able to adapt their metabolism according to the quality of both carbon and nitrogen sources available in the environment. Saccharomyces cerevisiae UGA4 gene encodes a permease capable of transporting γ-aminobutyric acid (GABA) into the cells. Yeast uses this amino acid as a nitrogen source or as a carbon skeleton that enters the tricarboxylic acid cycle. The quality of the carbon source modulates UGA4 expression through two parallel pathways, each one acting on different regulatory elements, the UAS(GATA) and the UAS(GABA). In the presence of a fermentable carbon source, UGA4 expression is induced by GABA while in the presence of a non-fermentable carbon source this expression is GABA-independent. The aim of this work was to study the mechanisms responsible for the differences in the profiles of UGA4 expression in both growth conditions. We found that although the subcellular localization of Gln3 depends on the carbon source and UGA4 expression depends on Tor1 and Snf1, Gln3 localization does not depend on these kinases. We also found that the phosphorylation of Gln3 is mediated by two systems activated by a non-fermentable carbon source, involving the Snf1 kinase and an unidentified TORC1-regulated kinase. We also found that the activity of the main transcription factors responsible for UGA4 induction by GABA varies depending on the quality of the carbon source. In a fermentable carbon source such as glucose, the negative GATA factor Dal80 binds to UGA4 promoter; only after the addition of the inducer, the positive factors Uga3, Dal81 and Gln3 interact with the promoter removing Dal80 and leading to gene induction. In contrast, in the non-fermentable carbon source acetate the negative GATA factor remains bound to UGA4 promoter in the presence or absence of GABA, the positive factors are not detected bound in any of these conditions and in consequence, UGA4 is not induced.
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Affiliation(s)
- Carolina E Levi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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Apostolaki A, Harispe L, Calcagno-Pizarelli AM, Vangelatos I, Sophianopoulou V, Arst HN, Peñalva MA, Amillis S, Scazzocchio C. Aspergillus nidulans CkiA is an essential casein kinase I required for delivery of amino acid transporters to the plasma membrane. Mol Microbiol 2012; 84:530-49. [PMID: 22489878 PMCID: PMC3491690 DOI: 10.1111/j.1365-2958.2012.08042.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Type I casein kinases are highly conserved among Eukaryotes. Of the two Aspergillus nidulans casein kinases I, CkiA is related to the δ/ε mammalian kinases and to Saccharomyces cerevisiæ Hrr25p. CkiA is essential. Three recessive ckiA mutations leading to single residue substitutions, and downregulation using a repressible promoter, result in partial loss-of-function, which leads to a pleiotropic defect in amino acid utilization and resistance to toxic amino acid analogues. These phenotypes correlate with miss-routing of the YAT plasma membrane transporters AgtA (glutamate) and PrnB (proline) to the vacuole under conditions that, in the wild type, result in their delivery to the plasma membrane. Miss-routing to the vacuole and subsequent transporter degradation results in a major deficiency in the uptake of the corresponding amino acids that underlies the inability of the mutant strains to catabolize them. Our findings may have important implications for understanding how CkiA, Hrr25p and other fungal orthologues regulate the directionality of transport at the ER-Golgi interface.
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Affiliation(s)
- Angeliki Apostolaki
- Institut de Génétique et Microbiologie, Université Paris-Sud (XI), UMR 8621 CNRS 91450 Orsay, France
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29
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Mourad GS, Tippmann-Crosby J, Hunt KA, Gicheru Y, Bade K, Mansfield TA, Schultes NP. Genetic and molecular characterization reveals a unique nucleobase cation symporter 1 in Arabidopsis. FEBS Lett 2012; 586:1370-8. [PMID: 22616996 DOI: 10.1016/j.febslet.2012.03.058] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/25/2012] [Accepted: 03/26/2012] [Indexed: 11/13/2022]
Abstract
Locus At5g03555 encodes a nucleobase cation symporter 1 (AtNCS1) in the Arabidopsis genome. Arabidopsis insertion mutants, AtNcs1-1 and AtNcs1-3, were used for in planta toxic nucleobase analog growth studies and radio-labeled nucleobase uptake assays to characterize solute transport specificities. These results correlate with similar growth and uptake studies of AtNCS1 expressed in Saccharomyces cerevisiae. Both in planta and heterologous expression studies in yeast revealed a unique solute transport profile for AtNCS1 in moving adenine, guanine and uracil. This is in stark contrast to the canonical transport profiles determined for the well-characterized S. cerevisiae NCS1 proteins FUR4 (uracil transport) or FCY2 (adenine, guanine, and cytosine transport).
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Affiliation(s)
- George S Mourad
- Department of Biology, Indiana University-Purdue University Fort Wayne, Fort Wayne, IN 46805, USA.
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30
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Hartmann T, Cairns TC, Olbermann P, Morschhäuser J, Bignell EM, Krappmann S. Oligopeptide transport and regulation of extracellular proteolysis are required for growth of Aspergillus fumigatus on complex substrates but not for virulence. Mol Microbiol 2011; 82:917-35. [DOI: 10.1111/j.1365-2958.2011.07868.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Function and regulation of yeast genes involved in higher alcohol and ester metabolism during beverage fermentation. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1567-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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The Candida albicans GAP gene family encodes permeases involved in general and specific amino acid uptake and sensing. EUKARYOTIC CELL 2011; 10:1219-29. [PMID: 21764911 DOI: 10.1128/ec.05026-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Saccharomyces cerevisiae general amino acid permease Gap1 (ScGap1) not only mediates the uptake of most amino acids but also functions as a receptor for the activation of protein kinase A (PKA). Fungal pathogens can colonize different niches in the host, each containing various levels of different amino acids and sugars. The Candida albicans genome contains six genes homologous to the S. cerevisiae GAP1. The expression of these six genes in S. cerevisiae showed that the products of all six C. albicans genes differ in their transport capacities. C. albicans Gap2 (CaGap2) is the true orthologue of ScGap1 as it transports all tested amino acids. The other CaGap proteins have narrower substrate specificities though CaGap1 and CaGap6 transport several structurally unrelated amino acids. CaGap1, CaGap2, and CaGap6 also function as sensors. Upon detecting some amino acids, e.g., methionine, they are involved in a rapid activation of trehalase, a downstream target of PKA. Our data show that CaGAP genes can be functionally expressed in S. cerevisiae and that CaGap permeases communicate to the intracellular signal transduction pathway similarly to ScGap1.
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Orij R, Brul S, Smits GJ. Intracellular pH is a tightly controlled signal in yeast. Biochim Biophys Acta Gen Subj 2011; 1810:933-44. [PMID: 21421024 DOI: 10.1016/j.bbagen.2011.03.011] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 11/25/2022]
Abstract
BACKGROUND Nearly all processes in living cells are pH dependent, which is why intracellular pH (pH(i)) is a tightly regulated physiological parameter in all cellular systems. However, in microbes such as yeast, pH(i) responds to extracellular conditions such as the availability of nutrients. This raises the question of how pH(i) dynamics affect cellular function. SCOPE OF REVIEW We discuss the control of pH(i,) and the regulation of processes by pH(i), focusing on the model organism Saccharomyces cerevisiae. We aim to dissect the effects of pH(i) on various aspects of cell physiology, which are often intertwined. Our goal is to provide a broad overview of how pH(i) is controlled in yeast, and how pH(i) in turn controls physiology, in the context of both general cellular functioning as well as of cellular decision making upon changes in the cell's environment. MAJOR CONCLUSIONS Besides a better understanding of the regulation of pH(i), evidence for a signaling role of pH(i) is accumulating. We conclude that pH(i) responds to nutritional cues and relays this information to alter cellular make-up and physiology. The physicochemical properties of pH allow the signal to be fast, and affect multiple regulatory levels simultaneously. GENERAL SIGNIFICANCE The mechanisms for regulation of processes by pH(i) are tightly linked to the molecules that are part of all living cells, and the biophysical properties of the signal are universal amongst all living organisms, and similar types of regulation are suggested in mammals. Therefore, dynamic control of cellular decision making by pH(i) is therefore likely a general trait. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
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Affiliation(s)
- Rick Orij
- Swammerdam Institute for Life Sciences, University of Amsterdam, the Netherlands.
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Ethanol induces calcium influx via the Cch1-Mid1 transporter in Saccharomyces cerevisiae. Arch Microbiol 2011; 193:323-34. [PMID: 21259000 DOI: 10.1007/s00203-010-0673-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 12/02/2010] [Accepted: 12/24/2010] [Indexed: 10/18/2022]
Abstract
Yeast suffers from a variety of environmental stresses, such as osmotic pressure and ethanol produced during fermentation. Since calcium ions are protective for high concentrations of ethanol, we investigated whether Ca(2+) flux occurs in response to ethanol stress. We find that exposure of yeast to ethanol induces a rise in the cytoplasmic concentration of Ca(2+). The response is enhanced in cells shifted to high-osmotic media containing proline, galactose, sorbitol, or mannitol. Suspension of cells in proline and galactose-containing media increases the Ca(2+) levels in the cytoplasm independent of ethanol exposure. The enhanced ability for ethanol to induce Ca(2+) flux after the hypertonic shift is transient, decreasing rapidly over a period of seconds to minutes. There is partial recovery of the response after zymolyase treatment, suggesting that cell wall integrity affects the ethanol-induced Ca(2+) flux. Acetate inhibits the Ca(2+) accumulation elicited by the ethanol/osmotic stress. The Ca(2+) flux is primarily via the Cch1 Ca(2+) influx channel because strains carrying deletions of the cch1 and mid1 genes show greater than 90% reduction in Ca(2+) flux. Furthermore, a functional Cch1 channel reduced growth inhibition by ethanol.
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35
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Jones DL, Petty J, Hoyle DC, Hayes A, Oliver SG, Riba-Garcia I, Gaskell SJ, Stateva L. Genome-wide analysis of the effects of heat shock on a Saccharomyces cerevisiae mutant with a constitutively activated cAMP-dependent pathway. Comp Funct Genomics 2010; 5:419-31. [PMID: 18629174 PMCID: PMC2447466 DOI: 10.1002/cfg.415] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2004] [Revised: 06/07/2004] [Accepted: 06/17/2004] [Indexed: 11/06/2022] Open
Abstract
We have used DNA microarray technology and 2-D gel electrophoresis combined with
mass spectrometry to investigate the effects of a drastic heat shock from 30℃ to 50℃
on a genome-wide scale. This experimental condition is used to differentiate between
wild-type cells and those with a constitutively active cAMP-dependent pathway in
Saccharomyces cerevisiae. Whilst more than 50% of the former survive this shock,
almost all of the latter lose viability. We compared the transcriptomes of the wildtype
and a mutant strain deleted for the gene PDE2, encoding the high-affinity cAMP
phosphodiesterase before and after heat shock treatment. We also compared the two
heat-shocked samples with one another, allowing us to determine the changes that
occur in the pde2Δ mutant which cause such a dramatic loss of viability after heat
shock. Several genes involved in ergosterol biosynthesis and carbon source utilization
had altered expression levels, suggesting that these processes might be potential
factors in heat shock survival. These predictions and also the effect of the different
phases of the cell cycle were confirmed by biochemical and phenotypic analyses. 146
genes of previously unknown function were identified amongst the genes with altered
expression levels and deletion mutants in 13 of these genes were found to be highly
sensitive to heat shock. Differences in response to heat shock were also observed at
the level of the proteome, with a higher level of protein degradation in the mutant, as
revealed by comparing 2-D gels of wild-type and mutant heat-shocked samples and
mass spectrometry analysis of the differentially produced proteins.
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Affiliation(s)
- Dawn L Jones
- Department of Biomolecular Sciences, UMIST, Manchester M60 1QD, UK
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36
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Rubio-Texeira M, Van Zeebroeck G, Voordeckers K, Thevelein JM. Saccharomyces cerevisiae plasma membrane nutrient sensors and their role in PKA signaling. FEMS Yeast Res 2010; 10:134-49. [DOI: 10.1111/j.1567-1364.2009.00587.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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de Marañón IM, Gervais P, Molin P. Determination of cells' water membrane permeability: unexpected high osmotic permeability of Saccharomyces cerevisiae. Biotechnol Bioeng 2009; 56:62-70. [PMID: 18636610 DOI: 10.1002/(sici)1097-0290(19971005)56:1<62::aid-bit7>3.0.co;2-t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Water permeability (Lp), calculated from the volume variations of cells subjected to an osmotic shock, is classically used to characterize cell membrane properties. In this work, we have shown the importance of the kind of mixing reactor used to measure the Lp parameter. A mathematical model including the mixing time constant has been proposed allowing an accurate Lp estimation even though the mixing time constant is higher than the cell time constant obtained in response to a perfect shock. The estimated Lp values of human leukemia K562 cells were found to be the same whatever the mixing time constant. The Lp value of Saccharomyces cerevisiae could not be exactly estimated. However, S. cerevisiae has unexpectedly high water permeability, implying that this yeast may contain water channels in the membrane.
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Affiliation(s)
- I M de Marañón
- Laboratoire de Génie des Procédés Alimentaires et Biotechnologiques, ENSBANA, 1 Esplanade Erasme, 21000 Dijon, France
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Identification of Saccharomyces cerevisiae Genes Involved in the Resistance to Phenolic Fermentation Inhibitors. Appl Biochem Biotechnol 2009; 161:106-15. [DOI: 10.1007/s12010-009-8811-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
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Courchesne WE, Tunc M, Liao S. Amiodarone induces stress responses and calcium flux mediated by the cell wall in Saccharomyces cerevisiae. Can J Microbiol 2009; 55:288-303. [PMID: 19370072 DOI: 10.1139/w08-132] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used a proteomic approach to study effects of amiodarone on cells of the yeast Saccharomyces cerevisiae. Amiodarone has been shown to have antifungal activity in vitro and causes a massive increase in cytoplasmic calcium levels ([Ca2+]cyt). Proteomic analysis of cells exposed to amiodarone show that this drug elicits stress responses and points to involvement of proteins associated with the cell wall. We tested several of those proteins for involvement in the Ca2+ flux. In particular, the amiodarone-induced Ca2+ flux was decreased in bgl2Delta cells, which have altered levels of beta-glucan and chitin. The involvement of the cell wall in the Ca2+ flux induced by amiodarone treatment was tested by addition of yeast cell-wall components. While mannan inhibited the rise in [Ca2+]cyt, beta-glucan potentiated the Ca2+ flux by 4.5-fold, providing evidence that the cell wall is directly involved in controlling this Ca2+ flux. This conclusion is corroborated by the inhibition of the Ca2+ flux by calcofluor, which is known to bind to cell-wall chitin and inhibit cell growth. Zymolyase treatment altered the kinetics of amiodarone-induced calcium flux and uncoupled the inhibitory effect of calcofluor. These effects demonstrate that the cell-wall beta-glucan regulates calcium flux elicited by amiodarone.
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Affiliation(s)
- William E Courchesne
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
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40
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Aquaporins are multifunctional water and solute transporters highly divergent in living organisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1213-28. [DOI: 10.1016/j.bbamem.2009.03.009] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 03/09/2009] [Accepted: 03/11/2009] [Indexed: 01/09/2023]
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41
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AgtA, the dicarboxylic amino acid transporter of Aspergillus nidulans, is concertedly down-regulated by exquisite sensitivity to nitrogen metabolite repression and ammonium-elicited endocytosis. EUKARYOTIC CELL 2009; 8:339-52. [PMID: 19168757 DOI: 10.1128/ec.00270-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We identified agtA, a gene that encodes the specific dicarboxylic amino acid transporter of Aspergillus nidulans. The deletion of the gene resulted in loss of utilization of aspartate as a nitrogen source and of aspartate uptake, while not completely abolishing glutamate utilization. Kinetic constants showed that AgtA is a high-affinity dicarboxylic amino acid transporter and are in agreement with those determined for a cognate transporter activity identified previously. The gene is extremely sensitive to nitrogen metabolite repression, depends on AreA for its expression, and is seemingly independent from specific induction. We showed that the localization of AgtA in the plasma membrane necessitates the ShrA protein and that an active process elicited by ammonium results in internalization and targeting of AgtA to the vacuole, followed by degradation. Thus, nitrogen metabolite repression and ammonium-promoted vacuolar degradation act in concert to downregulate dicarboxylic amino acid transport activity.
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42
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Transport and signaling via the amino acid binding site of the yeast Gap1 amino acid transceptor. Nat Chem Biol 2008; 5:45-52. [DOI: 10.1038/nchembio.132] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 11/12/2008] [Indexed: 11/08/2022]
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43
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Gander S, Bonenfant D, Altermatt P, Martin DE, Hauri S, Moes S, Hall MN, Jenoe P. Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3743-3753. [PMID: 18980262 DOI: 10.1002/rcm.3790] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The Saccharomyces cerevisae nitrogen permease reactivator Npr1 is a hyperphosphorylated protein that belongs to a fungus-specific family of Ser/Thr protein kinases dedicated to the regulation of plasma membrane transporters. Its activity is regulated by the TOR (target of rapamycin) signalling pathway. Inhibition of the TOR proteins by treating yeast cells with the immunosuppressant drug rapamycin promotes rapid dephosphorylation of Npr1. To identify the rapamycin-sensitive phosphorylation sites in yeast Npr1, glutathione-S-transferase (GST)-tagged Npr1 was isolated from untreated or rapamycin-treated cells, and analyzed by mass spectrometry. Here, we report for the first time 22 phosphorylation sites that are clustered in two regions of the N-terminal serine-rich domain. All phosphorylation sites, except two, were found to be rapamycin-sensitive. Some phosphorylation sites are contained in motifs that closely resemble those in mammalian S6K (serines followed by a tyrosine or a phenylalanine) and 4E-BP1 (serines followed by a proline). Other sites, such as serines followed by Ala, Asn, Gln, His, Ile, Leu, or Val, appear to define new motifs. Thus, TOR controls an unusually broad array of phosphorylation sites in Npr1. In addition to phosphorylation by upstream kinases, Npr1 undergoes autophosphorylation that was mapped to three distinct serines in the N-terminal domain of which Ser257 appears to be the main autophosphorylation site. Site-directed mutagenesis confirmed the mass spectral assignments of the autophosphorylation sites and shows that Ser257 is specifically involved in forming an in vitro substrate-binding site.
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Affiliation(s)
- Stefan Gander
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
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Lucic E, Fourrey C, Kohler A, Martin F, Chalot M, Brun-Jacob A. A gene repertoire for nitrogen transporters in Laccaria bicolor. THE NEW PHYTOLOGIST 2008; 180:343-364. [PMID: 18665901 DOI: 10.1111/j.1469-8137.2008.02580.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ectomycorrhizal interactions established between the root systems of terrestrial plants and hyphae from soil-borne fungi are the most ecologically widespread plant symbioses. The efficient uptake of a broad range of nitrogen (N) compounds by the fungal symbiont and their further transfer to the host plant is a major feature of this symbiosis. Nevertheless, we far from understand which N form is preferentially transferred and what are the key molecular determinants required for this transfer. Exhaustive in silico analysis of N-compound transporter families were performed within the genome of the ectomycorrhizal model fungus Laccaria bicolor. A broad phylogenetic approach was undertaken for all families and gene regulation was investigated using whole-genome expression arrays. A repertoire of proteins involved in the transport of N compounds in L. bicolor was established that revealed the presence of at least 128 gene models in the genome of L. bicolor. Phylogenetic comparisons with other basidiomycete genomes highlighted the remarkable expansion of some families. Whole-genome expression arrays indicate that 92% of these gene models showed detectable transcript levels. This work represents a major advance in the establishment of a transportome blueprint at a symbiotic interface, which will guide future experiments.
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Affiliation(s)
- Eva Lucic
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
| | - Claire Fourrey
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
| | - Annegret Kohler
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
| | - Francis Martin
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
| | - Michel Chalot
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
| | - Annick Brun-Jacob
- Research Unit INRA/UHP 1136 'Tree-microbe Interactions', Nancy-University, BP 239, F-54506 Vandoeuvre-les-Nancy Cedex, France
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45
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Abstract
Early genetic and physiological work in bacteria and fungi has suggested the presence of highly specific nucleobase transport systems. Similar transport systems are now known to exist in algae, plants, protozoa and metazoa. Within the last 15 years, a small number of microbial genes encoding nucleobase transporters have been cloned and studied in great detail. The sequences of several other putative proteins submitted to databases are homologous to the microbial nucleobase transporters but their physiological functions remain largely undetermined. In this review, genetic, biochemical and molecular data are described concerning mostly the nucleobase transporters of Aspergillus nidulans and Saccharomyces cerevisiae, the two model ascomycetes from which the great majority of data come from. It is also discussed as to what is known on the nucleobase transporters of the two most significant pathogenic fungi: Candida albicans and Aspergillus fumigatus. Apart from highlighting how a basic process such as nucleobase recognition and transport operates, this review intends to highlight features that might be applicable to antifungal pharmacology.
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Affiliation(s)
- Areti Pantazopoulou
- Faculty of Biology, Department of Botany, University of Athens, Panepistimioupolis, Athens, Greece
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46
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Garrett JM. Amino acid transport through the Saccharomyces cerevisiae Gap1 permease is controlled by the Ras/cAMP pathway. Int J Biochem Cell Biol 2007; 40:496-502. [PMID: 17919965 PMCID: PMC2292834 DOI: 10.1016/j.biocel.2007.08.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 08/21/2007] [Indexed: 11/20/2022]
Abstract
The general amino acid permease (Gap1p) of Saccharomyces cerevisiae is a broad range, low affinity permease that imports amino acids in cells growing on poor nitrogen sources. This permease also signals the presence of amino acids through the fermentable growth medium pathway allowing the cell to respond to new sources of nitrogen in the surrounding medium. Yeast with an activated Ras2/cAMP pathway show many phenotypes indicative of altered nitrogen uptake and metabolism; sensitivity to nitrogen starvation, low amino acid pools. We have shown that Gap1p activity is lowered in cells with an activated RAS2(val19) allele or elevated cAMP levels whereas cells with inactive ras2 allele lose ammonia repression of Gap1p-mediated transport. This regulation is through a post-transcriptional mechanism; transcription of GAP1 is not affected by cAMP level. A mechanism by which the Ras2/cAMP/PKA pathway controls the ubiquitin-dependent degradation of Gap1p is most consistent with the data.
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Affiliation(s)
- Jinnie M Garrett
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA.
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47
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Eddy AA, Barnett JA. A history of research on yeasts 11. The study of solute transport: the first 90 years, simple and facilitated diffusion1. Yeast 2007; 24:1023-59. [DOI: 10.1002/yea.1572] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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48
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Menant A, Barbey R, Thomas D. Substrate-mediated remodeling of methionine transport by multiple ubiquitin-dependent mechanisms in yeast cells. EMBO J 2006; 25:4436-47. [PMID: 16977312 PMCID: PMC1589980 DOI: 10.1038/sj.emboj.7601330] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 08/16/2006] [Indexed: 11/09/2022] Open
Abstract
Plasma membrane transport of single amino-acid methionine in yeast is shown to be mediated by at least seven different permeases whose activities are transcriptionaly and post-transcriptionaly regulated by different ubiquitin-dependent mechanisms. Upon high extracellular methionine exposure, three methionine-permease genes are repressed while four others are induced. SCF(Met30), SCF(Grr1) and Rsp5 ubiquitin ligases are the key actors of the ubiquitin-dependent remodeling of methionine transport. In addition to regulating the activity of Met4, the SCF(Met30) ubiquitin ligase is shown to convey an intracellular signal to a membrane initiated signaling pathway by controlling the nuclear concentration of the Stp1 transcription factor. By coupling intra- and extracellular metabolite sensing, SCF(Met30) thus allows yeast cells to accurately adjust the intermediary sulfur metabolism to the growth conditions. The multiple ubiquitin-dependent mechanisms that function in methionine transport regulation further exemplify the pervasive role of ubiquitin in the adaptation of single-cell organisms to environmental modifications.
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Affiliation(s)
- Alexandra Menant
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvettte, France
| | - Régine Barbey
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvettte, France
| | - Dominique Thomas
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvettte, France
- Cytomics Systems SA, Gif sur Yvette, France
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Avenue de la Terrasse, Gif-sur-Yvette 91190, France. Tel.: +33 1 6982 3233; Fax: +33 1 6982 4372; E-mail:
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49
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Pribylová L, Papousková K, Zavrel M, Souciet JL, Sychrová H. Exploration of yeast alkali metal cation/H+ antiporters: Sequence and structure comparison. Folia Microbiol (Praha) 2006; 51:413-24. [PMID: 17176761 DOI: 10.1007/bf02931585] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Saccharomyces cerevisiae genome contains three genes encoding alkali metal cation/H+ antiporters (Nha1p, Nhx1p, Kha1p) that differ in cell localization, substrate specificity and physiological function. Systematic genome sequencing of other yeast species revealed highly conserved homologous ORFs in all of them. We compared the yeast sequences both at DNA and protein levels. The subfamily of yeast endosomal/prevacuolar Nhx1 antiporters is closely related to mammalian plasma membrane NHE proteins and to both plasma membrane and vacuolar plant antiporters. The high sequence conservation within this subfamily of yeast antiporters suggests that Nhx1p is of great importance in cell physiology. Yeast Kha1 proteins probably belong to the same subfamily as bacterial antiporters, whereas Nhal proteins form a distinct subfamily.
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Affiliation(s)
- L Pribylová
- Department of Membrane Transport, Institute of Physiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia
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Abstract
Ubiquitylation of membrane proteins has gained considerable interest in recent years. It has been recognized as a signal that negatively regulates the cell surface expression of many plasma membrane proteins both in yeast and in mammalian cells. Moreover, it is also involved in endoplasmic reticulum-associated degradation of membrane proteins, and it acts as a sorting signal both in the secretory pathway and in endosomes, where it targets proteins into multivesicular bodies in the lumen of vacuoles/lysosomes. In this review we discuss the progress in understanding these processes, achieved during the past several years.
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Affiliation(s)
- Olivier Staub
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland.
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