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Cruz-Leite VRM, Moreira ALE, Silva LOS, Inácio MM, Parente-Rocha JA, Ruiz OH, Weber SS, Soares CMDA, Borges CL. Proteomics of Paracoccidioides lutzii: Overview of Changes Triggered by Nitrogen Catabolite Repression. J Fungi (Basel) 2023; 9:1102. [PMID: 37998907 PMCID: PMC10672198 DOI: 10.3390/jof9111102] [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: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Members of the Paracoccidioides complex are the causative agents of Paracoccidioidomycosis (PCM), a human systemic mycosis endemic in Latin America. Upon initial contact with the host, the pathogen needs to uptake micronutrients. Nitrogen is an essential source for biosynthetic pathways. Adaptation to nutritional stress is a key feature of fungi in host tissues. Fungi utilize nitrogen sources through Nitrogen Catabolite Repression (NCR). NCR ensures the scavenging, uptake and catabolism of alternative nitrogen sources, when preferential ones, such as glutamine or ammonium, are unavailable. The NanoUPLC-MSE proteomic approach was used to investigate the NCR response of Paracoccidioides lutzii after growth on proline or glutamine as a nitrogen source. A total of 338 differentially expressed proteins were identified. P. lutzii demonstrated that gluconeogenesis, β-oxidation, glyoxylate cycle, adhesin-like proteins, stress response and cell wall remodeling were triggered in NCR-proline conditions. In addition, within macrophages, yeast cells trained under NCR-proline conditions showed an increased ability to survive. In general, this study allows a comprehensive understanding of the NCR response employed by the fungus to overcome nutritional starvation, which in the human host is represented by nutritional immunity. In turn, the pathogen requires rapid adaptation to the changing microenvironment induced by macrophages to achieve successful infection.
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Affiliation(s)
- Vanessa Rafaela Milhomem Cruz-Leite
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - André Luís Elias Moreira
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Lana O’Hara Souza Silva
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Moises Morais Inácio
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
- Estácio de Goiás University Center—FESGO, Goiânia 74063-010, GO, Brazil
| | - Juliana Alves Parente-Rocha
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Orville Hernandez Ruiz
- MICROBA Research Group, Cellular and Molecular Biology Unit, Department of Microbiology, School of Microbiology, University of Antioquia, Medellín 050010, Colombia;
| | - Simone Schneider Weber
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79304-902, MS, Brazil;
| | - Célia Maria de Almeida Soares
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
| | - Clayton Luiz Borges
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences II, Federal University of Goiás, Goiânia 74690-900, GO, Brazil; (A.L.E.M.); (L.O.S.S.); (M.M.I.); (J.A.P.-R.); (C.M.d.A.S.)
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Spealman P, De T, Chuong JN, Gresham D. Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution. J Mol Evol 2023; 91:356-368. [PMID: 37012421 PMCID: PMC10275804 DOI: 10.1007/s00239-023-10102-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Copy number variants (CNVs), comprising gene amplifications and deletions, are a pervasive class of heritable variation. CNVs play a key role in rapid adaptation in both natural, and experimental, evolution. However, despite the advent of new DNA sequencing technologies, detection and quantification of CNVs in heterogeneous populations has remained challenging. Here, we summarize recent advances in the use of CNV reporters that provide a facile means of quantifying de novo CNVs at a specific locus in the genome, and nanopore sequencing, for resolving the often complex structures of CNVs. We provide guidance for the engineering and analysis of CNV reporters and practical guidelines for single-cell analysis of CNVs using flow cytometry. We summarize recent advances in nanopore sequencing, discuss the utility of this technology, and provide guidance for the bioinformatic analysis of these data to define the molecular structure of CNVs. The combination of reporter systems for tracking and isolating CNV lineages and long-read DNA sequencing for characterizing CNV structures enables unprecedented resolution of the mechanisms by which CNVs are generated and their evolutionary dynamics.
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Affiliation(s)
- Pieter Spealman
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Titir De
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Julie N Chuong
- Department of Biology, New York University, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, 10003, USA.
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
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3
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Kahlhofer J, Leon S, Teis D, Schmidt O. The α-arrestin family of ubiquitin ligase adaptors links metabolism with selective endocytosis. Biol Cell 2021; 113:183-219. [PMID: 33314196 DOI: 10.1111/boc.202000137] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
The regulation of nutrient uptake into cells is important, as it allows to either increase biomass for cell growth or to preserve homoeostasis. A key strategy to adjust cellular nutrient uptake is the reconfiguration of the nutrient transporter repertoire at the plasma membrane by the addition of nutrient transporters through the secretory pathway and by their endocytic removal. In this review, we focus on the mechanisms that regulate selective nutrient transporter endocytosis, which is mediated by the α-arrestin protein family. In the budding yeast Saccharomyces cerevisiae, 14 different α-arrestins (also named arrestin-related trafficking adaptors, ARTs) function as adaptors for the ubiquitin ligase Rsp5. They instruct Rsp5 to ubiquitinate subsets of nutrient transporters to orchestrate their endocytosis. The ART proteins are under multilevel control of the major nutrient sensing systems, including amino acid sensing by the general amino acid control and target of rapamycin pathways, and energy sensing by 5'-adenosine-monophosphate-dependent kinase. The function of the six human α-arrestins is comparably under-characterised. Here, we summarise the current knowledge about the function, regulation and substrates of yeast ARTs and human α-arrestins, and highlight emerging communalities and general principles.
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Affiliation(s)
- Jennifer Kahlhofer
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Oliver Schmidt
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
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4
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The effect of two antifungal commercial formulations on the metabolism of a commercial Saccharomyces cerevisiae strain and their repercussion on fermentation evolution and phenylalanine catabolism. Food Microbiol 2020; 92:103554. [DOI: 10.1016/j.fm.2020.103554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/10/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
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5
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Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. eLife 2020; 9:e51254. [PMID: 31985403 PMCID: PMC7004572 DOI: 10.7554/elife.51254] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. To leverage these advantages, we developed a method for scRNAseq in budding yeast (Saccharomyces cerevisiae). We pooled diverse transcriptionally barcoded gene deletion mutants in 11 different environmental conditions and determined their expression state by sequencing 38,285 individual cells. We benchmarked a framework for learning gene regulatory networks from scRNAseq data that incorporates multitask learning and constructed a global gene regulatory network comprising 12,228 interactions.
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Affiliation(s)
- Christopher A Jackson
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
| | | | | | - Richard Bonneau
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, Computer Science DepartmentNew York UniversityNew YorkUnited States
- Center For Data ScienceNew York UniversityNew YorkUnited States
- Flatiron Institute, Center for Computational BiologySimons FoundationNew YorkUnited States
| | - David Gresham
- Center For Genomics and Systems BiologyNew York UniversityNew YorkUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
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6
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Zahumensky J, Malinsky J. Role of MCC/Eisosome in Fungal Lipid Homeostasis. Biomolecules 2019; 9:E305. [PMID: 31349700 PMCID: PMC6723945 DOI: 10.3390/biom9080305] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
One of the best characterized fungal membrane microdomains is the MCC/eisosome. The MCC (membrane compartment of Can1) is an evolutionarily conserved ergosterol-rich plasma membrane domain. It is stabilized on its cytosolic face by the eisosome, a hemitubular protein complex composed of Bin/Amphiphysin/Rvs (BAR) domain-containing Pil1 and Lsp1. These two proteins bind directly to phosphatidylinositol 4,5-bisphosphate and promote the typical furrow-like shape of the microdomain, with highly curved edges and bottom. While some proteins display stable localization in the MCC/eisosome, others enter or leave it under particular conditions, such as misbalance in membrane lipid composition, changes in membrane tension, or availability of specific nutrients. These findings reveal that the MCC/eisosome, a plasma membrane microdomain with distinct morphology and lipid composition, acts as a multifaceted regulator of various cellular processes including metabolic pathways, cellular morphogenesis, signalling cascades, and mRNA decay. In this minireview, we focus on the MCC/eisosome's proposed role in the regulation of lipid metabolism. While the molecular mechanisms of the MCC/eisosome function are not completely understood, the idea of intracellular processes being regulated at the plasma membrane, the foremost barrier exposed to environmental challenges, is truly exciting.
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Affiliation(s)
- Jakub Zahumensky
- Department of Microscopy, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Jan Malinsky
- Department of Microscopy, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic.
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7
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Gobert A, Tourdot-Maréchal R, Sparrow C, Morge C, Alexandre H. Influence of nitrogen status in wine alcoholic fermentation. Food Microbiol 2019; 83:71-85. [PMID: 31202421 DOI: 10.1016/j.fm.2019.04.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022]
Abstract
Nitrogen is an essential nutrient for yeast during alcoholic fermentation. Nitrogen is involved in the biosynthesis of protein, amino acids, nucleotides, and other metabolites, including volatile compounds. However, recent studies have called several mechanisms that regulate its role in biosynthesis into question. An initial focus on S. cerevisiae has highlighted that the concept of "preferred" versus "non-preferred" nitrogen sources is extremely variable and strain-dependent. Then, the direct involvement of amino acids consumed in the formation of proteins and volatile compounds has recently been reevaluated. Indeed, studies have highlighted the key role of lipids in nitrogen regulation in S. cerevisiae and their involvement in the mechanism of cell death. New winemaking strategies using non-Saccharomyces yeast strains in co- or sequential fermentation improve nitrogen management. Indeed, recent studies show that non-Saccharomyces yeasts have significant and specific needs for nitrogen. Moreover, sluggish fermentation can occur when they are associated with S. cerevisiae, necessitating nitrogen addition. In this context, we will present the consequences of nitrogen addition, discussing the sources, time of addition, transcriptome changes, and effect on volatile compound composition.
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Affiliation(s)
- Antoine Gobert
- UMR Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/ AgroSup Dijon - Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France.
| | - Raphaëlle Tourdot-Maréchal
- UMR Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/ AgroSup Dijon - Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
| | - Céline Sparrow
- SAS Sofralab, 79, Av. A.A. Thévenet, BP 1031, Magenta, France
| | | | - Hervé Alexandre
- UMR Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/ AgroSup Dijon - Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
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Lauer S, Avecilla G, Spealman P, Sethia G, Brandt N, Levy SF, Gresham D. Single-cell copy number variant detection reveals the dynamics and diversity of adaptation. PLoS Biol 2018; 16:e3000069. [PMID: 30562346 PMCID: PMC6298651 DOI: 10.1371/journal.pbio.3000069] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Copy number variants (CNVs) are a pervasive source of genetic variation and evolutionary potential, but the dynamics and diversity of CNVs within evolving populations remain unclear. Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation and the temporal dynamics with which they are generated, selected, and maintained. Here, we developed a fluorescent CNV reporter to detect de novo gene amplifications and deletions in individual cells. We used the CNV reporter in Saccharomyces cerevisiae to study CNV formation at the GAP1 locus, which encodes the general amino acid permease, in different nutrient-limited chemostat conditions. We find that under strong selection, GAP1 CNVs are repeatedly generated and selected during the early stages of adaptive evolution, resulting in predictable dynamics. Molecular characterization of CNV-containing lineages shows that the CNV reporter detects different classes of CNVs, including aneuploidies, nonreciprocal translocations, tandem duplications, and complex CNVs. Despite GAP1's proximity to repeat sequences that facilitate intrachromosomal recombination, breakpoint analysis revealed that short inverted repeat sequences mediate formation of at least 50% of GAP1 CNVs. Inverted repeat sequences are also found at breakpoints at the DUR3 locus, where CNVs are selected in urea-limited chemostats. Analysis of 28 CNV breakpoints indicates that inverted repeats are typically 8 nucleotides in length and separated by 40 bases. The features of these CNVs are consistent with origin-dependent inverted-repeat amplification (ODIRA), suggesting that replication-based mechanisms of CNV formation may be a common source of gene amplification. We combined the CNV reporter with barcode lineage tracking and found that 102-104 independent CNV-containing lineages initially compete within populations, resulting in extreme clonal interference. However, only a small number (18-21) of CNV lineages ever constitute more than 1% of the CNV subpopulation, and as selection progresses, the diversity of CNV lineages declines. Our study introduces a novel means of studying CNVs in heterogeneous cell populations and provides insight into their dynamics, diversity, and formation mechanisms in the context of adaptive evolution.
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Affiliation(s)
- Stephanie Lauer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Grace Avecilla
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Gunjan Sethia
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Sasha F. Levy
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford University, Stanford, California, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
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Miller D, Brandt N, Gresham D. Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen. PLoS Genet 2018; 14:e1007406. [PMID: 29782489 PMCID: PMC5983874 DOI: 10.1371/journal.pgen.1007406] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 01/20/2023] Open
Abstract
Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen the pooled deletion collection library for trans factors that mediate rapid GAP1 mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for GAP1 mRNA clearance. We also find that the decapping modulators EDC3 and SCD6, translation factor eIF4G2, and the 5' UTR of GAP1 are factors that mediate rapid repression of GAP1 mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.
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Affiliation(s)
- Darach Miller
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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10
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Wang Z, Jiang M, Guo X, Liu Z, He X. Reconstruction of metabolic module with improved promoter strength increases the productivity of 2-phenylethanol in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:60. [PMID: 29642888 PMCID: PMC5896102 DOI: 10.1186/s12934-018-0907-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/03/2018] [Indexed: 11/12/2022] Open
Abstract
Background 2-phenylethanol (2-PE) is an important aromatic compound with a lovely rose-like scent. Saccharomyces cerevisiae is a desirable microbe for 2-PE production but its natural yield is not high, and one or two crucial genes’ over-expression in S. cerevisiae did not improve 2-PE greatly. Results A new metabolic module was established here, in which, permease Gap1p for l-phenylalanine transportation, catalytic enzymes Aro8p, Aro10p and Adh2p in Ehrlich pathway respectively responsible for transamination, decarboxylation and reduction were assembled, besides, glutamate dehydrogenase Gdh2p was harbored for re-supplying another substrate 2-oxoglutarate, relieving product glutamate repression and regenerating cofactor NADH. Due to different promoter strengths, GAP1, ARO8, ARO9, ARO10, ADH2 and GDH2 in the new modularized YS58(G1-A8-A10-A2)-GDH strain enhanced 11.6-, 15.4-, 3.6-, 17.7-, 12.4- and 7.5-folds respectively, and crucial enzyme activities of aromatic aminotransferases and phenylpyruvate decarboxylase were 4.8- and 7-folds respectively higher than that of the control. Conclusions Under the optimum medium and cell density, YS58(G1-A8-A10-A2)-GDH presented efficient 2-PE synthesis ability with ~ 6.3 g L−1 of 2-PE titer in 5-L fermenter reaching 95% of conversation ratio. Under fed-batch fermentation, 2-PE productivity at 24 h increased 29% than that of single-batch fermentation. Metabolic modularization with promoter strategy provides a new prospective for efficient 2-PE production.
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Affiliation(s)
- Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingyue Jiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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11
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Petersen EE, Margaritis A, Stewart RJ, Pilkington PH, Mensour NA. The Effects of Wort Valine Concentration on the Total Diacetyl Profile and Levels Late in Batch Fermentations with Brewing YeastSaccharomyces Carlsbergensis. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-62-0131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Erin E. Petersen
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London N6A 5B9, Ontario, Canada
| | - Argyrios Margaritis
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London N6A 5B9, Ontario, Canada
| | - Robert J. Stewart
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
| | - P. Heather Pilkington
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
| | - Normand A. Mensour
- Interbrew, Science and Technology Development, 197 Richmond Street, London N6A 4M3, Ontario, Canada
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12
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Kodama Y, Omura F, Miyajima K, Ashikari T. Control of Higher Alcohol Production by Manipulation of theBAP2Gene in Brewing Yeast. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-59-0157] [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)
- Yukiko Kodama
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Fumihiko Omura
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Keiji Miyajima
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Toshihiko Ashikari
- Institute for Fundamental Research, Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
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13
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Chen Y, Nielsen J. Flux control through protein phosphorylation in yeast. FEMS Yeast Res 2017; 16:fow096. [PMID: 27797916 DOI: 10.1093/femsyr/fow096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 01/26/2023] Open
Abstract
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
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14
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Besnard J, Pratelli R, Zhao C, Sonawala U, Collakova E, Pilot G, Okumoto S. UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6385-6397. [PMID: 27856708 PMCID: PMC5181585 DOI: 10.1093/jxb/erw412] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Amino acids are the main form of nitrogen transported between the plant organs. Transport of amino acids across membranes is mediated by specialized proteins: importers, exporters, and facilitators. Unlike amino acid importers, amino acid exporters have not been thoroughly studied, partly due to a lack of high-throughput techniques enabling their isolation. Usually Multiple Acids Move In and out Transporters 14 (UMAMIT14) from Arabidopsis shares sequence similarity to the amino acid facilitator Silique Are Red1 (UMAMIT18), and has been shown to be involved in amino acid transfer to the seeds. We show here that UMAMIT14 is also expressed in root pericycle and phloem cells and mediates export of a broad range of amino acids in yeast. Loss-of-function of UMAMIT14 leads to a reduced shoot-to-root and root-to-medium transfer of amino acids originating from the leaves. These fluxes were further reduced in an umamti14 umamit18 double loss-of-function mutant. This study suggests that UMAMIT14 is involved in phloem unloading of amino acids in roots, and that UMAMIT14 and UMAMIT18 are involved in the radial transport of amino acids in roots, which is essential for maintaining amino acid secretion to the soil.
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Affiliation(s)
- Julien Besnard
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Réjane Pratelli
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Chengsong Zhao
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Unnati Sonawala
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Eva Collakova
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Guillaume Pilot
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
| | - Sakiko Okumoto
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061, VA, USA
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15
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Kasavi C, Eraslan S, Oner ET, Kirdar B. An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae. MOLECULAR BIOSYSTEMS 2016; 12:464-76. [PMID: 26661334 DOI: 10.1039/c5mb00622h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The accumulation of ethanol is one of the main environmental stresses that Saccharomyces cerevisiae cells are exposed to in industrial alcoholic beverage and bioethanol production processes. Despite the known impacts of ethanol, the molecular mechanisms underlying ethanol tolerance are still not fully understood. Novel gene targets leading to ethanol tolerance were previously identified via a network approach and the investigations of the deletions of these genes resulted in the improved ethanol tolerance of pmt7Δ/pmt7Δ and yhl042wΔ/yhl042wΔ strains. In the present study, an integrative system based approach was used to investigate the global transcriptional changes in these two ethanol tolerant strains in response to ethanol and hence to elucidate the mechanisms leading to the observed tolerant phenotypes. In addition to strain specific biological processes, a number of common and already reported biological processes were found to be affected in the reference and both ethanol tolerant strains. However, the integrative analysis of the transcriptome with the transcriptional regulatory network and the ethanol tolerance network revealed that each ethanol tolerant strain had a specific organization of the transcriptomic response. Transcription factors around which most important changes occur were determined and active subnetworks in response to ethanol and functional clusters were identified in all strains.
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Affiliation(s)
- Ceyda Kasavi
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
| | - Serpil Eraslan
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
| | - Ebru Toksoy Oner
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Betul Kirdar
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
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16
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Function and Regulation of Fungal Amino Acid Transporters: Insights from Predicted Structure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:69-106. [PMID: 26721271 DOI: 10.1007/978-3-319-25304-6_4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amino acids constitute a major nutritional source for probably all fungi. Studies of model species such as the yeast Saccharomyces cerevisiae and the filamentous fungus Aspergillus nidulans have shown that they possess multiple amino acid transporters. These proteins belong to a limited number of superfamilies, now defined according to protein fold in addition to sequence criteria, and differ in subcellular location, substrate specificity range, and regulation. Structural models of several of these transporters have recently been built, and the detailed molecular mechanisms of amino acid recognition and translocation are now being unveiled. Furthermore, the particular conformations adopted by some of these transporters in response to amino acid binding appear crucial to promoting their ubiquitin-dependent endocytosis and/or to triggering signaling responses. We here summarize current knowledge, derived mainly from studies on S. cerevisiae and A. nidulans, about the transport activities, regulation, and sensing role of fungal amino acid transporters, in relation to predicted structure.
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17
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Fayyad-Kazan M, Feller A, Bodo E, Boeckstaens M, Marini AM, Dubois E, Georis I. Yeast nitrogen catabolite repression is sustained by signals distinct from glutamine and glutamate reservoirs. Mol Microbiol 2015; 99:360-79. [DOI: 10.1111/mmi.13236] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Mohammad Fayyad-Kazan
- Institut de Recherches Microbiologiques J.-M. Wiame; 1070 Brussels Belgium
- Laboratoire de Biologie du Transport Membranaire; Institut de Biologie et de Médecine Moléculaires; Université Libre de Bruxelles; 6041 Gosselies Belgium
| | - A. Feller
- Institut de Recherches Microbiologiques J.-M. Wiame; 1070 Brussels Belgium
- Laboratoire de Microbiologie; Institut de Biologie et de Médecine Moléculaires; Université Libre de Bruxelles; 6041 Gosselies Belgium
| | - E. Bodo
- Unité de Biotechnologie; 1070 Brussels Belgium
| | - M. Boeckstaens
- Laboratoire de Biologie du Transport Membranaire; Institut de Biologie et de Médecine Moléculaires; Université Libre de Bruxelles; 6041 Gosselies Belgium
| | - A. M. Marini
- Laboratoire de Biologie du Transport Membranaire; Institut de Biologie et de Médecine Moléculaires; Université Libre de Bruxelles; 6041 Gosselies Belgium
| | - E. Dubois
- Institut de Recherches Microbiologiques J.-M. Wiame; 1070 Brussels Belgium
- Laboratoire de Microbiologie; Institut de Biologie et de Médecine Moléculaires; Université Libre de Bruxelles; 6041 Gosselies Belgium
| | - I. Georis
- Institut de Recherches Microbiologiques J.-M. Wiame; 1070 Brussels Belgium
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18
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Kankipati HN, Rubio-Texeira M, Castermans D, Diallinas G, Thevelein JM. Sul1 and Sul2 sulfate transceptors signal to protein kinase A upon exit of sulfur starvation. J Biol Chem 2015; 290:10430-46. [PMID: 25724649 PMCID: PMC4400352 DOI: 10.1074/jbc.m114.629022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Indexed: 11/24/2022] Open
Abstract
Sulfate is an essential nutrient with pronounced regulatory effects on cellular metabolism and proliferation. Little is known, however, about how sulfate is sensed by cells. Sul1 and Sul2 are sulfate transporters in the yeast Saccharomyces cerevisiae, strongly induced upon sulfur starvation and endocytosed upon the addition of sulfate. We reveal Sul1,2-dependent activation of PKA targets upon sulfate-induced exit from growth arrest after sulfur starvation. We provide two major arguments in favor of Sul1 and Sul2 acting as transceptors for signaling to PKA. First, the sulfate analogue, d-glucosamine 2-sulfate, acted as a non-transported agonist of signaling by Sul1 and Sul2. Second, mutagenesis to Gln of putative H+-binding residues, Glu-427 in Sul1 or Glu-443 in Sul2, abolished transport without affecting signaling. Hence, Sul1,2 can function as pure sulfate sensors. Sul1E427Q and Sul2E443Q are also deficient in sulfate-induced endocytosis, which can therefore be uncoupled from signaling. Overall, our data suggest that transceptors can undergo independent conformational changes, each responsible for triggering different downstream processes. The Sul1 and Sul2 transceptors are the first identified plasma membrane sensors for extracellular sulfate. High affinity transporters induced upon starvation for their substrate may generally act as transceptors during exit from starvation.
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Affiliation(s)
- Harish Nag Kankipati
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Marta Rubio-Texeira
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - Dries Castermans
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
| | - George Diallinas
- the Faculty of Biology, University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - Johan M Thevelein
- From the Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, the Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium, and
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19
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Substrate-induced ubiquitylation and endocytosis of yeast amino acid permeases. Mol Cell Biol 2014; 34:4447-63. [PMID: 25266656 DOI: 10.1128/mcb.00699-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many plasma membrane transporters are downregulated by ubiquitylation, endocytosis, and delivery to the lysosome in response to various stimuli. We report here that two amino acid transporters of Saccharomyces cerevisiae, the general amino acid permease (Gap1) and the arginine-specific permease (Can1), undergo ubiquitin-dependent downregulation in response to their substrates and that this downregulation is not due to intracellular accumulation of the transported amino acids but to transport catalysis itself. Following an approach based on permease structural modeling, mutagenesis, and kinetic parameter analysis, we obtained evidence that substrate-induced endocytosis requires transition of the permease to a conformational state preceding substrate release into the cell. Furthermore, this transient conformation must be stable enough, and thus sufficiently populated, for the permease to undergo efficient downregulation. Additional observations, including the constitutive downregulation of two active Gap1 mutants altered in cytosolic regions, support the model that the substrate-induced conformational transition inducing endocytosis involves remodeling of cytosolic regions of the permeases, thereby promoting their recognition by arrestin-like adaptors of the Rsp5 ubiquitin ligase. Similar mechanisms might control many other plasma membrane transporters according to the external concentrations of their substrates.
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20
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Sekito T, Nakamura K, Manabe K, Tone J, Sato Y, Murao N, Kawano-Kawada M, Kakinuma Y. Loss of ATP-dependent lysine uptake in the vacuolar membrane vesicles of Saccharomyces cerevisiae ypq1∆ mutant. Biosci Biotechnol Biochem 2014; 78:1199-202. [PMID: 25229858 DOI: 10.1080/09168451.2014.918489] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Saccharomyces cerevisiae Ypq1p is a vacuolar membrane protein of the PQ-loop protein family. We found that ATP-dependent uptake activities of amino acids by vacuolar membrane vesicles were impaired by ypq1∆ mutation. Loss of lysine uptake was most remarkable, and the uptake was recovered by overproduction of Ypq1p. Ypq1p is thus involved in transport of amino acids into vacuoles.
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Affiliation(s)
- Takayuki Sekito
- a Faculty of Agriculture, Department of Applied Bioresource Science , Ehime University , Matsuyama , Japan
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21
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Rødkaer SV, Faergeman NJ. Glucose- and nitrogen sensing and regulatory mechanisms inSaccharomyces cerevisiae. FEMS Yeast Res 2014; 14:683-96. [DOI: 10.1111/1567-1364.12157] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/11/2014] [Accepted: 04/13/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Steven V. Rødkaer
- Villum Center for Bioanalytical Sciences; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense M Denmark
| | - Nils J. Faergeman
- Villum Center for Bioanalytical Sciences; Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense M Denmark
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22
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VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol 2014; 15:R64. [PMID: 24721214 PMCID: PMC4053978 DOI: 10.1186/gb-2014-15-4-r64] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 04/10/2014] [Indexed: 01/15/2023] Open
Abstract
Background Genome-wide sensitivity screens in yeast have been immensely popular following the construction of a collection of deletion mutants of non-essential genes. However, the auxotrophic markers in this collection preclude experiments on minimal growth medium, one of the most informative metabolic environments. Here we present quantitative growth analysis for mutants in all 4,772 non-essential genes from our prototrophic deletion collection across a large set of metabolic conditions. Results The complete collection was grown in environments consisting of one of four possible carbon sources paired with one of seven nitrogen sources, for a total of 28 different well-defined metabolic environments. The relative contributions to mutants' fitness of each carbon and nitrogen source were determined using multivariate statistical methods. The mutant profiling recovered known and novel genes specific to the processing of nutrients and accurately predicted functional relationships, especially for metabolic functions. A benchmark of genome-scale metabolic network modeling is also given to demonstrate the level of agreement between current in silico predictions and hitherto unavailable experimental data. Conclusions These data address a fundamental deficiency in our understanding of the model eukaryote Saccharomyces cerevisiae and its response to the most basic of environments. While choice of carbon source has the greatest impact on cell growth, specific effects due to nitrogen source and interactions between the nutrients are frequent. We demonstrate utility in characterizing genes of unknown function and illustrate how these data can be integrated with other whole-genome screens to interpret similarities between seemingly diverse perturbation types.
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23
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Rai R, Tate JJ, Georis I, Dubois E, Cooper TG. Constitutive and nitrogen catabolite repression-sensitive production of Gat1 isoforms. J Biol Chem 2013; 289:2918-33. [PMID: 24324255 DOI: 10.1074/jbc.m113.516740] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrogen catabolite repression (NCR)-sensitive transcription is activated by Gln3 and Gat1. In nitrogen excess, Gln3 and Gat1 are cytoplasmic, and transcription is minimal. In poor nitrogen, Gln3 and Gat1 become nuclear and activate transcription. A long standing paradox has surrounded Gat1 production. Gat1 was first reported as an NCR-regulated activity mediating NCR-sensitive transcription in gln3 deletion strains. Upon cloning, GAT1 transcription was, as predicted, NCR-sensitive and Gln3- and Gat1-activated. In contrast, Western blots of Gat1-Myc(13) exhibited two constitutively produced species. Investigating this paradox, we demonstrate that wild type Gat1 isoforms (IsoA and IsoB) are initiated at Gat1 methionines 40, 95, and/or 102, but not at methionine 1. Their low level production is the same in rich and poor nitrogen conditions. When the Myc(13) tag is placed after Gat1 Ser-233, four N-terminal Gat1 isoforms (IsoC-F) are also initiated at methionines 40, 95, and/or 102. However, their production is highly NCR-sensitive, being greater in proline than glutamine medium. Surprisingly, all Gat1 isoforms produced in sufficient quantities to be confidently analyzed (IsoA, IsoC, and IsoD) require Gln3 and UASGATA promoter elements, both requirements typical of NCR-sensitive transcription. These data demonstrate that regulated Gat1 production is more complex than previously recognized, with wild type versus truncated Gat1 proteins failing to be regulated in parallel. This is the first reported instance of Gln3 UASGATA-dependent protein production failing to derepress in nitrogen poor conditions. A Gat1-lacZ ORF swap experiment indicated sequence(s) responsible for the nonparallel production are downstream of Gat1 leucine 61.
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Affiliation(s)
- Rajendra Rai
- From the Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and
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24
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Krogerus K, Gibson BR. 125thAnniversary Review: Diacetyl and its control during brewery fermentation. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.84] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Brian R. Gibson
- VTT Technical Research Centre of Finland; Tietotie 2, PO Box 1000; FI-02044; VTT, Espoo; Finland
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25
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de Barros Pita W, Silva DC, Simões DA, Passoth V, de Morais MA. Physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability. Antonie van Leeuwenhoek 2013; 104:855-68. [DOI: 10.1007/s10482-013-9998-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/07/2013] [Indexed: 12/01/2022]
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26
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Lei H, Li H, Mo F, Zheng L, Zhao H, Zhao M. Effects of Lys and His supplementations on the regulation of nitrogen metabolism in lager yeast. Appl Microbiol Biotechnol 2013; 97:8913-21. [PMID: 23917636 DOI: 10.1007/s00253-013-5137-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/13/2013] [Accepted: 07/17/2013] [Indexed: 12/01/2022]
Abstract
Significant positive correlations between wort fermentability and the assimilation of Lys and His under normal-gravity and high-gravity conditions indicated that Lys and His were the key amino acids for lager yeast during beer brewing. In order to obtain insight into the roles of Lys and His in nitrogen regulation, the influences of Lys, His and their mixture supplementations on the fermentation performance and nitrogen metabolism in lager yeast during high-gravity fermentation were further investigated in the present study. Results showed that Lys and His supplementations improved yeast growth, wort fermentability, ethanol yield and the formation of flavor volatiles. Lys supplementation up-regulated Ssy1p-Ptr3p-Ssy5p (SPS)-regulated genes (LYP1, HIP1, BAP2 and AGP1) dramatically compared to nitrogen catabolite repression (NCR)-sensitive genes (GAP1 and MEP2), whereas His supplementation activated SPS-regulated genes slightly in exponential phase, and repressed NCR-sensitive genes significantly throughout the fermentation. Lys and His supplementations increased the consumption of Glu and Phe, and decreased the consumption of Ser, Trp and Arg. Moreover, Lys and His supplementations exhibited similar effects on the fermentation performance, and were more effective than their mixture supplementation when the same dose was kept. These results demonstrate that both Lys and His are important amino acids for yeast nitrogen metabolism and fermentation performance.
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Affiliation(s)
- Hongjie Lei
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China
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27
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Pallotta ML. L-Proline uptake in Saccharomyces cerevisiae mitochondria can contribute to bioenergetics during nutrient stress as alternative mitochondrial fuel. World J Microbiol Biotechnol 2013; 30:19-31. [PMID: 23824663 DOI: 10.1007/s11274-013-1415-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/23/2013] [Indexed: 11/28/2022]
Abstract
L-Proline (pyrrolidine-2-carboxylic acid) is a distinctive metabolite both biochemically and biotechnologically and is currently recognized to have a cardinal role in gene expression and cellular signaling pathways in stress response. Proline-fueled mitochondrial metabolism involves the oxidative conversion of L-Proline to L-Glutamate in two enzymatic steps by means of Put1p and Put2p that help Saccharomyces cerevisiae to respond to changes in the nutritional environment by initiating the breakdown of L-Proline as a source for nitrogen, carbon, and energy. Compartmentalization of L-Proline catabolic pathway implies that extensive L-Proline transport must take place between the cytosol where its biogenesis via Pro1p, Pro2p, Pro3p occurs and mitochondria. L-Proline uptake in S. cerevisiae purified and active mitochondria was investigated by swelling experiments, oxygen uptake and fluorimetric measurement of a membrane potential generation (ΔΨ). Our results strongly suggest that L-Proline uptake occurs via a carried-mediated process as demonstrated by saturation kinetics and experiments with N-ethylmaleimide, a pharmacological compound that is a cysteine-modifying reagent in hydrophobic protein domains and that inhibited mitochondrial transport. Plasticity of S. cerevisiae cell biochemistry according to background fluctuations is an important factor of adaptation to stress. Thus L-Proline → Glutamate route feeds Krebs cycle providing energy and anaplerotic carbon for yeast survival.
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Affiliation(s)
- Maria Luigia Pallotta
- Department of Medicine and Health Sciences, University of Molise, 86100, Campobasso, Italy,
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28
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Identification of metabolic pathways influenced by the G-protein coupled receptors GprB and GprD in Aspergillus nidulans. PLoS One 2013; 8:e62088. [PMID: 23658706 PMCID: PMC3641053 DOI: 10.1371/journal.pone.0062088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/16/2013] [Indexed: 11/19/2022] Open
Abstract
Heterotrimeric G-protein-mediated signaling pathways play a pivotal role in transmembrane signaling in eukaryotes. Our main aim was to identify signaling pathways regulated by A. nidulans GprB and GprD G-protein coupled receptors (GPCRs). When these two null mutant strains were compared to the wild-type strain, the ΔgprB mutant showed an increased protein kinase A (PKA) activity while growing in glucose 1% and during starvation. In contrast, the ΔgprD has a much lower PKA activity upon starvation. Transcriptomics and 1H NMR-based metabolomics were performed on two single null mutants grown on glucose. We noted modulation in the expression of 11 secondary metabolism gene clusters when the ΔgprB and ΔgprD mutant strains were grown in 1% glucose. Several members of the sterigmatocystin-aflatoxin gene cluster presented down-regulation in both mutant strains. The genes of the NR-PKS monodictyphenone biosynthesis cluster had overall increased mRNA accumulation in ΔgprB, while in the ΔgprD mutant strain the genes had decreased mRNA accumulation. Principal component analysis of the metabolomic data demonstrated that there was a significant metabolite shift in the ΔgprD strain. The 1H NMR analysis revealed significant expression of essential amino acids with elevated levels in the ΔgprD strain, compared to the wild-type and ΔgprB strains. With the results, we demonstrated the differential expression of a variety of genes related mainly to secondary metabolism, sexual development, stress signaling, and amino acid metabolism. We propose that the absence of GPCRs triggered stress responses at the genetic level. The data suggested an intimate relationship among different G-protein coupled receptors, fine-tune regulation of secondary and amino acid metabolisms, and fungal development.
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29
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Abstract
Ure2p, normally a regulator of nitrogen catabolism in Saccharomyces cerevisiae, can be a prion (infectious protein) by forming a folded in-register parallel amyloid called [URE3]. Using S. cerevisiae as a test bed, we previously showed that Ure2p of Candida albicans (CaUre2p) can also form a prion, but that Ure2p of C. glabrata (CgUre2p) cannot. Here, we constructed C. glabrata strains to test whether CgUre2p can form a prion in its native environment. We find that while CaUre2p can form a [URE3] in C. glabrata, CgUre2p cannot, although the latter has a prion domain sequence more similar to that of ScUre2p than that of CaUre2p. This supports the notion that prion formation is not a conserved property of Ure2p but is a pathology arising sporadically. We find that some [URE3albicans] variants are restricted in their transmissibility to certain recipient strains. In addition, we show that the C. glabrata HO can induce switching of the C. glabrata mating type locus.
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30
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Sequential use of nitrogen compounds by Saccharomyces cerevisiae during wine fermentation: a model based on kinetic and regulation characteristics of nitrogen permeases. Appl Environ Microbiol 2012; 78:8102-11. [PMID: 22983966 DOI: 10.1128/aem.02294-12] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The efficiency of nitrogen use is a key determinant of the completion of alcoholic fermentation. We analyzed the kinetics of consumption of 18 nitrogen compounds by 14 Saccharomyces cerevisiae strains of various origins in a synthetic medium that mimicked a grape must. The kinetic profiles of total nitrogen consumption were diverse, but the order of nitrogen source consumption was similar for all strains. The nitrogen compounds could be classified into three groups, according to their order of use: prematurely consumed (Lys), early consumed (Asp, Thr, Glu, Leu, His, Met, Ile, Ser, Gln, and Phe), and late consumed (ammonium, Val, Arg, Ala, Trp, and Tyr). The initial concentrations of these compounds did not alter the order in which they were consumed, except for arginine and ammonium. Early consumed amino acids are transported by specific permeases under Ssy1p-Ptr3p-Ssy5 (SPS)-mediated control that are expressed at the beginning of consumption. Most nitrogen compounds consumed late are transported by permeases under nitrogen catabolite repression (NCR), and others (Val, Trp, and Tyr) are transported by SPS-regulated low-affinity permeases. Therefore, the kinetic characteristics of transporters, as well as SPS and NCR, are likely key factors controlling the temporal sequence of consumption of nitrogen compounds and constitute a system highly conserved in S. cerevisiae species. This work sheds new light on the mechanistic basis of the sequential use of different nitrogen compounds in complex environments.
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31
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Nakase M, Nakase Y, Chardwiriyapreecha S, Kakinuma Y, Matsumoto T, Takegawa K. Intracellular trafficking and ubiquitination of the Schizosaccharomyces pombe amino acid permease Aat1p. Microbiology (Reading) 2012; 158:659-673. [DOI: 10.1099/mic.0.053389-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mai Nakase
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
| | - Yukiko Nakase
- Department of Biostudies, Kyoto University, Kyoto 6060-8501, Japan
| | - Soracom Chardwiriyapreecha
- Department of Applied Bioresource Science, Faculty of Agriculture, Ehime University, Ehime 790-8566, Japan
| | - Yoshimi Kakinuma
- Department of Applied Bioresource Science, Faculty of Agriculture, Ehime University, Ehime 790-8566, Japan
| | | | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
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32
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Jennings ML, Cui J. Inactivation of Saccharomyces cerevisiae sulfate transporter Sul2p: use it and lose it. Biophys J 2012; 102:768-76. [PMID: 22385847 DOI: 10.1016/j.bpj.2012.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 12/09/2011] [Accepted: 01/03/2012] [Indexed: 12/12/2022] Open
Abstract
Saccharomyces cerevisiae SO(4)(=) transport is regulated over a wide dynamic range. Sulfur starvation causes ∼10,000-fold increase in the (35)SO(4)(=) influx mediated by transporters Sul1p and Sul2p; >80% of the influx is via Sul2p. Adding methionine to S-starved cells causes a 50-fold decline (t(1/2) ∼5 min) in SUL1 and SUL2 mRNA but a slower decline (t(1/2) ∼1 h) in transport. In contrast, SO(4)(=) addition does not affect mRNA but causes a rapid (t(1/2) = 2-4 min) decrease in transport. In met3Δ cells (unable to metabolize SO(4)(=)), addition of SO(4)(=) to S-starved cells causes inactivation of (35)SO(4)(=) influx over times in which cellular SO(4)(=) contents are nearly constant. The relationship between cellular SO(4)(=) and transport inactivation shows that cellular SO(4)(=) is not the signal for Sul2p inactivation. Instead, the transport inactivation rate has the same dependence on extracellular SO(4)(=) as (35)SO(4)(=) influx, indicating that Sul2p exhibits use-dependent inactivation; the transport process itself increases the probability of Sul2p inactivation and degradation. In addition, there is a transient efflux of SO(4)(=) shortly after adding >0.02 mM SO(4)(=) to S-starved met3Δ cells. This transient efflux provides further protection against excessive SO(4)(=) influx and may represent an alternate transport mode of Sul2p.
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Affiliation(s)
- Michael L Jennings
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
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Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2011; 12:104-17. [DOI: 10.1111/j.1567-1364.2011.00765.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ana Paula Oliveira
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology; Department of Biology; ETH Zurich; Zurich; Switzerland
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34
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Kriel J, Haesendonckx S, Rubio-Texeira M, Van Zeebroeck G, Thevelein JM. From transporter to transceptor: signaling from transporters provokes re-evaluation of complex trafficking and regulatory controls: endocytic internalization and intracellular trafficking of nutrient transceptors may, at least in part, be governed by their signaling function. Bioessays 2011; 33:870-9. [PMID: 21913212 PMCID: PMC3258547 DOI: 10.1002/bies.201100100] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
When cells are starved of their substrate, many nutrient transporters are induced. These undergo rapid endocytosis and redirection of their intracellular trafficking when their substrate becomes available again. The discovery that some of these transporters also act as receptors, or transceptors, suggests that at least part of the sophisticated controls governing the trafficking of these proteins has to do with their signaling function rather than with control of transport. In yeast, the general amino acid permease Gap1 mediates signaling to the protein kinase A pathway. Its endocytic internalization and intracellular trafficking are subject to amino acid control. Other nutrient transceptors controlling this signal transduction pathway appear to be subject to similar trafficking regulation. Transporters with complex regulatory control have also been suggested to function as transceptors in other organisms. Hence, precise regulation of intracellular trafficking in nutrient transporters may be related to the need for tight control of nutrient-induced signaling.
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Affiliation(s)
- Johan Kriel
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, K. U. Leuven, Leuven, Belgium
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35
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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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36
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Cain NE, Kaiser CA. Transport activity-dependent intracellular sorting of the yeast general amino acid permease. Mol Biol Cell 2011; 22:1919-29. [PMID: 21471002 PMCID: PMC3103407 DOI: 10.1091/mbc.e10-10-0800] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Intracellular trafficking of the general amino acid permease, Gap1p, is regulated by amino acid abundance. Through the use of mutants that alter the set of amino acids that can be transported by Gap1p, we show that only those amino acids that can be transported by Gap1p can act as a signal to affect Gap1p sorting. Intracellular trafficking of the general amino acid permease, Gap1p, of Saccharomyces cerevisiae is regulated by amino acid abundance. When amino acids are scarce Gap1p is sorted to the plasma membrane, whereas when amino acids are abundant Gap1p is sorted from the trans-Golgi through the multivesicular endosome (MVE) and to the vacuole. Here we test the hypothesis that Gap1p itself is the sensor of amino acid abundance by examining the trafficking of Gap1p mutants with altered substrate specificity and transport activity. We show that trafficking of mutant Gap1pA297V, which does not transport basic amino acids, is also not regulated by these amino acids. Furthermore, we have identified a catalytically inactive mutant that does not respond to complex amino acid mixtures and constitutively sorts Gap1p to the plasma membrane. Previously we showed that amino acids govern the propensity of Gap1p to recycle from the MVE to the plasma membrane. Here we propose that in the presence of substrate the steady-state conformation of Gap1p shifts to a state that is unable to be recycled from the MVE. These results indicate a parsimonious regulatory mechanism by which Gap1p senses its transport substrates to set an appropriate level of transporter activity at the cell surface.
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Affiliation(s)
- Natalie E Cain
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Poole K, E Walker M, Warren T, Gardner J, McBryde C, de Barros Lopes M, Jiranek V. Proline transport and stress tolerance of ammonia-insensitive mutants of the PUT4-encoded proline-specific permease in yeast. J GEN APPL MICROBIOL 2010; 55:427-39. [PMID: 20118607 DOI: 10.2323/jgam.55.427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The imino amino acid, proline, has roles in both cellular nutrition and response to stress. Proline uptake in Saccharomyces cerevisiae is largely mediated by a high affinity, specific permease, Put4p, and a low affinity general amino acid permease, Gap1p. Both are subject to nitrogen catabolite repression (NCR) and nitrogen catabolite inactivation (NCI). In order for proline to be fully exploited, its transport must be derepressed, as occurs upon depletion of preferred nitrogen sources, and molecular oxygen must be present to allow the first step of catabolism via proline oxidase. This study focuses on the isolation of variants of Put4p, which are insensitive to repression by a preferred nitrogen source (ammonia) and their subsequent effect on proline transport and stress tolerance. Specific amino acid residues in the carboxy-terminal region of Put4p were targeted by site-directed mutagenesis. Substitution at Serine(605), a potential phosphorylation target, led to the amelioration of ammonia-induced down-regulation of Put4p. When combined with a promoter mutation (-160), the S(605)A mutation resulted in increased proline uptake and accumulation. This increase in proline accumulation was associated with increased cell viability in conditions of high temperature and osmotic stress raising possible benefits in industrial fermentation applications.
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Affiliation(s)
- Kate Poole
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, Australia
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Gander S, Martin D, Hauri S, Moes S, Poletto G, Pagano MA, Marin O, Meggio F, Jenoe P. A Modified KESTREL Search Reveals a Basophilic Substrate Consensus for the Saccharomyces cerevisiae Npr1 Protein Kinase. J Proteome Res 2009; 8:5305-16. [DOI: 10.1021/pr9005469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefan Gander
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Dietmar Martin
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Simon Hauri
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Suzette Moes
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Giorgia Poletto
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Mario A. Pagano
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Oriano Marin
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Flavio Meggio
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Paul Jenoe
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
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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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40
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Barnett JA. A history of research on yeasts 13. Active transport and the uptake of various metabolites. Yeast 2008; 25:689-731. [PMID: 18951365 DOI: 10.1002/yea.1630] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- James A Barnett
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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41
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Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii. EUKARYOTIC CELL 2008; 8:170-80. [PMID: 19098129 DOI: 10.1128/ec.00330-08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Blastocladiella emersonii is an aquatic fungus of the Chytridiomycete class. During germination, the zoospore, a motile nongrowing cell, goes through a cascade of morphological changes that culminates with its differentiation into the germling cell, capable of coenocytic vegetative growth. Transcriptome analyses of B. emersonii cells were carried out during germination induced under various environmental conditions. Microarray data analyzing 3,563 distinct B. emersonii genes revealed that 26% of them are differentially expressed during germination in nutrient medium at at least one of the time points investigated. Over 500 genes are upregulated during the time course of germination under those conditions, most being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are downregulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport, and chromosome organization. In addition, germination induced in the presence of nutrients was compared with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth, induced during germination in nutrient medium, do not show increased expression when B. emersonii zoospores germinate in inorganic solution, suggesting that nutrients exert a positive effect on gene transcription. The transcriptome data also revealed that most genes involved in cell signaling show the same expression pattern irrespective of the initial germination stimulus.
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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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Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications. Appl Microbiol Biotechnol 2008; 81:211-23. [DOI: 10.1007/s00253-008-1698-5] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/29/2008] [Accepted: 09/01/2008] [Indexed: 10/21/2022]
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44
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Subileau M, Schneider RÃ, Salmon JM, Degryse E. Nitrogen catabolite repression modulates the production of aromatic thiols characteristic of Sauvignon Blanc at the level of precursor transport. FEMS Yeast Res 2008; 8:771-80. [DOI: 10.1111/j.1567-1364.2008.00400.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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45
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Rho5p is involved in mediating the osmotic stress response in Saccharomyces cerevisiae, and its activity is regulated via Msi1p and Npr1p by phosphorylation and ubiquitination. EUKARYOTIC CELL 2008; 7:1441-9. [PMID: 18621925 DOI: 10.1128/ec.00120-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small GTPases of the Rho family act as molecular switches, and modulation of the GTP-bound state of Rho proteins is a well-characterized means of regulating their signaling activity in vivo. In contrast, the regulation of Rho-type GTPases by posttranslational modifications is poorly understood. Here, we present evidence of the control of the Saccharomyces cerevisiae Rho-type GTPase Rho5p by phosphorylation and ubiquitination. Rho5p binds to Ste50p, and the expression of the activated RHO5(Q91H) allele in an Deltaste50 strain is lethal under conditions of osmotic stress. An overexpression screen identified RGD2 and MSI1 as being high-copy suppressors of the osmotic sensitivity of this lethality. Rgd2p had been identified as being a possible Rho5p GTPase-activating protein based on an in vitro assay; this result supports its function as a regulator of Rho5p activity in vivo. MSI1 was previously identified as being a suppressor of hyperactive Ras/cyclic AMP signaling, where it antagonizes Npr1p kinase activity and promotes ubiquitination. Here, we show that Msi1p also acts via Npr1p to suppress activated Rho5p signaling. Rho5p is ubiquitinated, and its expression is lethal in a strain that is compromised for proteasome activity. These data identify Rho5p as being a target of Msi1p/Npr1p regulation and describe a regulatory circuit involving phosphorylation and ubiquitination.
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46
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Recent advances in nitrogen regulation: a comparison between Saccharomyces cerevisiae and filamentous fungi. EUKARYOTIC CELL 2008; 7:917-25. [PMID: 18441120 DOI: 10.1128/ec.00076-08] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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47
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Smit A, Moses SG, Pretorius IS, Cordero Otero RR. The Thr505 and Ser557 residues of the AGT1-encoded alpha-glucoside transporter are critical for maltotriose transport in Saccharomyces cerevisiae. J Appl Microbiol 2008; 104:1103-11. [PMID: 18179544 DOI: 10.1111/j.1365-2672.2007.03671.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS The main objective of this study was to identify amino acid residues in the AGT1-encoded alpha-glucoside transporter (Agt1p) that are critical for efficient transport of maltotriose in the yeast Saccharomyces cerevisiae. METHODS AND RESULTS The sequences of two AGT1-encoded alpha-glucoside transporters with different efficiencies of maltotriose transport in two Saccharomyces strains (WH310 and WH314) were compared. The sequence variations and discrepancies between these two proteins (Agt1p(WH310) and Agt1p(WH314)) were investigated for potential effects on the functionality and maltotriose transport efficiency of these two AGT1-encoded alpha-glucoside transporters. A 23-amino-acid C-terminal truncation proved not to be critical for maltotriose affinity. The identification of three amino acid differences, which potentially could have been instrumental in the transportation of maltotriose, were further investigated. Single mutations were created to restore the point mutations I505T, V549A and T557S one by one. The single site mutant V549A showed a decrease in maltotriose transport ability, and the I505T and T557S mutants showed complete reduction in maltotriose transport. CONCLUSIONS The amino acids Thr(505) and Ser(557), which are respectively located in the transmembrane (TM) segment TM(11) and on the intracellular segment after TM(12) of the AGT1-encoded alpha-glucoside transporters, are critical for efficient transport of maltotriose in S. cerevisiae. SIGNIFICANCE AND IMPACT OF THE STUDY Improved fermentation of starch and its dextrin products, such as maltotriose and maltose, would benefit the brewing and whisky industries. This study could facilitate the development of engineered maltotriose transporters adapted to starch-efficient fermentation systems, and offers prospects for the development of yeast strains with improved maltose and maltotriose uptake capabilities that, in turn, could increase the overall fermentation efficiencies in the beer and whisky industries.
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Affiliation(s)
- A Smit
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Matieland, South Africa
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48
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Acetaldehyde addition throughout the growth phase alleviates the phenotypic effect of zinc deficiency in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2007; 77:1093-109. [PMID: 17938904 DOI: 10.1007/s00253-007-1234-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 09/12/2007] [Accepted: 09/28/2007] [Indexed: 10/22/2022]
Abstract
During experiments to determine the effects of exogenously added acetaldehyde on pure cultures of various yeast strains, we discovered that an early acetaldehyde perfusion during the growth phase allowed several yeasts to partially overcome the phenotypic effects of zinc depletion during alcoholic fermentation. We, therefore, performed genome-wide expression and proteomic analysis on an industrial Saccharomyces cerevisiae yeast strain (VL1) growing in zinc-replete or zinc-depleted conditions in the presence of perfused acetaldehyde to identify molecular markers of this effect. Zinc depletion severely affects ethanol production and therefore nicotinamide adenine dinucleotide (NAD) regeneration, although we observed partial compensation by the upregulation of the poorly efficient Fe-dependent Adh4p in our conditions. A coordinate metabolic response was indeed observed in response to the early acetaldehyde perfusion, and particularly of the lower part of glycolysis, leading to the cellular replenishment of NAD cofactor. These various findings suggest that acetaldehyde exchange between strains may inhibit the growth of some yeast strains while encouraging the growth of others. This phenomenon could be particularly important for understanding the ecology of colonization of complex fermentation media by S. cerevisiae after elimination of non-Saccharomyces yeasts.
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49
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Omura F, Hatanaka H, Nakao Y. Characterization of a novel tyrosine permease of lager brewing yeast shared by Saccharomyces cerevisiae strain RM11-1a. FEMS Yeast Res 2007; 7:1350-61. [PMID: 17825063 DOI: 10.1111/j.1567-1364.2007.00310.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In Saccharomyces cerevisiae yeast, the uptake of aromatic amino acids is mediated by the relatively specific permeases Tat1p, Tat2p, Bap2p, and Bap3p, as well as by two other permeases with broader specificities: Gap1p and Agp1p. Here, a novel permease gene TAT3 (Tyrosine Amino acid Transporter) identified in the S. cerevisiae-type subset genome of the lager brewing yeast strain Weihenstephan Nr.34 (34/70) is reported. The TAT3 sequence was also found in the genome of S. cerevisiae strain RM11-1a, but not in S. cerevisiae strain S288C. Tat3p showed a significant similarity to Penicillium chrysogenum ArlP permease, which has transport activity for aromatic amino acids and leucine. When overexpressed in ssy1Delta gap1Delta mutant cells, Tat3p exhibited a tyrosine transport activity with an apparent K(m) of 160 microM. TAT3 transcription in lager brewing yeast was subjected to nitrogen catabolite repression in a manner similar to that of GAP1. Furthermore, the subcellular localization of Tat3p-green fluorescent protein (GFP) fusion protein was dependent on the quality of the nitrogen source, indicating a post-translational control of Tat3p function.
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Affiliation(s)
- Fumihiko Omura
- Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka, Japan.
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50
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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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