1
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Deitert A, Fees J, Mertens A, Nguyen Van D, Maares M, Haase H, Blank LM, Keil C. Rapid Fluorescence Assay for Polyphosphate in Yeast Extracts Using JC-D7. Yeast 2024. [PMID: 39262085 DOI: 10.1002/yea.3979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 08/07/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
Polyphosphate (polyP) is an intriguing molecule that is found in almost any organism, covering a multitude of cellular functions. In industry, polyP is used due to its unique physiochemical properties, including pH buffering, water binding, and bacteriostatic activities. Despite the importance of polyP, its analytics is still challenging, with the gold standard being 31P NMR. Here, we present a simple staining method using the fluorescent dye JC-D7 for the semi-quantitative polyP evaluation in yeast extracts. Notably, fluorescence response was affected by polyP concentration and polymer chain length in the 0.5-500 µg/mL polyP concentration range. Hence, for polyP samples of unknown chain compositions, JC-D7 cannot be used for absolute quantification. Fluorescence of JC-D7 was unaffected by inorganic phosphate up to 50 mM. Trace elements (FeSO4 > CuSO4 > CoCl2 > ZnSO4) and toxic mineral salts (PbNO3 and HgCl2) diminished polyP-induced JC-D7 fluorescence, affecting its applicability to samples containing polyP-metal complexes. The fluorescence was only marginally affected by other parameters, such as pH and temperature. After validation, this simple assay was used to elucidate the degree of polyP production by yeast strains carrying gene deletions in (poly)phosphate homeostasis. The results suggest that staining with JC-D7 provides a robust and sensitive method for detecting polyP in yeast extracts and likely in extracts of other microbes. The simplicity of the assay enables high-throughput screening of microbes to fully elucidate and potentially enhance biotechnological polyP production, ultimately contributing to a sustainable phosphorus utilization.
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Affiliation(s)
- Alexander Deitert
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Jana Fees
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Anna Mertens
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Duc Nguyen Van
- Department of Food Chemistry and Toxicology, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Maria Maares
- Department of Food Chemistry and Toxicology, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Hajo Haase
- Department of Food Chemistry and Toxicology, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Lars Mathias Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Aachen, Germany
| | - Claudia Keil
- Department of Food Chemistry and Toxicology, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, Berlin, Germany
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2
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Gogianu LI, Ruta LL, Farcasanu IC. Kcs1 and Vip1: The Key Enzymes behind Inositol Pyrophosphate Signaling in Saccharomyces cerevisiae. Biomolecules 2024; 14:152. [PMID: 38397389 PMCID: PMC10886477 DOI: 10.3390/biom14020152] [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: 12/12/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
The inositol pyrophosphate pathway, a complex cell signaling network, plays a pivotal role in orchestrating vital cellular processes in the budding yeast, where it regulates cell cycle progression, growth, endocytosis, exocytosis, apoptosis, telomere elongation, ribosome biogenesis, and stress responses. This pathway has gained significant attention in pharmacology and medicine due to its role in generating inositol pyrophosphates, which serve as crucial signaling molecules not only in yeast, but also in higher eukaryotes. As targets for therapeutic development, genetic modifications within this pathway hold promise for disease treatment strategies, offering practical applications in biotechnology. The model organism Saccharomyces cerevisiae, renowned for its genetic tractability, has been instrumental in various studies related to the inositol pyrophosphate pathway. This review is focused on the Kcs1 and Vip1, the two enzymes involved in the biosynthesis of inositol pyrophosphate in S. cerevisiae, highlighting their roles in various cell processes, and providing an up-to-date overview of their relationship with phosphate homeostasis. Moreover, the review underscores the potential applications of these findings in the realms of medicine and biotechnology, highlighting the profound implications of comprehending this intricate signaling network.
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Affiliation(s)
- Larisa Ioana Gogianu
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania;
- National Institute for Research and Development in Microtechnologies, Erou Iancu Nicolae Str. 126A, 077190 Voluntari, Romania
| | - Lavinia Liliana Ruta
- Faculty of Chemistry, University of Bucharest, Panduri Road 90-92, 050663 Bucharest, Romania;
| | - Ileana Cornelia Farcasanu
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, 050095 Bucharest, Romania;
- Faculty of Chemistry, University of Bucharest, Panduri Road 90-92, 050663 Bucharest, Romania;
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3
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Takado M, Komamura T, Nishimura T, Ohkubo I, Ohuchi K, Matsumoto T, Takeda K. Phosphate uptake restriction, phosphate export, and polyphosphate synthesis contribute synergistically to cellular proliferation and survival. J Biol Chem 2023; 299:105454. [PMID: 37949217 PMCID: PMC10704438 DOI: 10.1016/j.jbc.2023.105454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Phosphate (Pi) is a macronutrient, and Pi homeostasis is essential for life. Pi homeostasis has been intensively studied; however, many questions remain, even at the cellular level. Using Schizosaccharomyces pombe, we sought to better understand cellular Pi homeostasis and showed that three Pi regulators with SPX domains, Xpr1/Spx2, Pqr1, and the VTC complex synergistically contribute to Pi homeostasis to support cell proliferation and survival. SPX domains bind to inositol pyrophosphate and modulate activities of Pi-related proteins. Xpr1 is a plasma membrane protein and its Pi-exporting activity has been demonstrated in metazoan orthologs, but not in fungi. We first found that S. pombe Xpr1 is a Pi exporter, activity of which is regulated and accelerated in the mutants of Pqr1 and the VTC complex. Pqr1 is the ubiquitin ligase downregulating the Pi importers, Pho84 and Pho842. The VTC complex synthesizes polyphosphate in vacuoles. Triple deletion of Xpr1, Pqr1, and Vtc4, the catalytic core of the VTC complex, was nearly lethal in normal medium but survivable at lower [Pi]. All double-deletion mutants of the three genes were viable at normal Pi, but Δpqr1Δxpr1 showed severe viability loss at high [Pi], accompanied by hyper-elevation of cellular total Pi and free Pi. This study suggests that the three cellular processes, restriction of Pi uptake, Pi export, and polyP synthesis, contribute synergistically to cell proliferation through maintenance of Pi homeostasis, leading to the hypothesis that cooperation between Pqr1, Xpr1, and the VTC complex protects the cytoplasm and/or the nucleus from lethal elevation of free Pi.
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Affiliation(s)
- Masahiro Takado
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tochi Komamura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomoki Nishimura
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Ikkei Ohkubo
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Keita Ohuchi
- Graduate School of Natural Science, Konan University, Kobe, Japan
| | - Tomohiro Matsumoto
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kojiro Takeda
- Graduate School of Natural Science, Konan University, Kobe, Japan; Institute of Integrative Neurobiology, Konan University, Kobe, Japan.
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4
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Chabert V, Kim GD, Qiu D, Liu G, Michaillat Mayer L, Jamsheer K M, Jessen HJ, Mayer A. Inositol pyrophosphate dynamics reveals control of the yeast phosphate starvation program through 1,5-IP 8 and the SPX domain of Pho81. eLife 2023; 12:RP87956. [PMID: 37728314 PMCID: PMC10511240 DOI: 10.7554/elife.87956] [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] [Indexed: 09/21/2023] Open
Abstract
Eukaryotic cells control inorganic phosphate to balance its role as essential macronutrient with its negative bioenergetic impact on reactions liberating phosphate. Phosphate homeostasis depends on the conserved INPHORS signaling pathway that utilizes inositol pyrophosphates and SPX receptor domains. Since cells synthesize various inositol pyrophosphates and SPX domains bind them promiscuously, it is unclear whether a specific inositol pyrophosphate regulates SPX domains in vivo, or whether multiple inositol pyrophosphates act as a pool. In contrast to previous models, which postulated that phosphate starvation is signaled by increased production of the inositol pyrophosphate 1-IP7, we now show that the levels of all detectable inositol pyrophosphates of yeast, 1-IP7, 5-IP7, and 1,5-IP8, strongly decline upon phosphate starvation. Among these, specifically the decline of 1,5-IP8 triggers the transcriptional phosphate starvation response, the PHO pathway. 1,5-IP8 inactivates the cyclin-dependent kinase inhibitor Pho81 through its SPX domain. This stimulates the cyclin-dependent kinase Pho85-Pho80 to phosphorylate the transcription factor Pho4 and repress the PHO pathway. Combining our results with observations from other systems, we propose a unified model where 1,5-IP8 signals cytosolic phosphate abundance to SPX proteins in fungi, plants, and mammals. Its absence triggers starvation responses.
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Affiliation(s)
- Valentin Chabert
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Geun-Don Kim
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
| | - Danye Qiu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Guizhen Liu
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | | | | | - Henning J Jessen
- Institute of Organic Chemistry, Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Andreas Mayer
- Département d'immunobiologie, Université de LausanneEpalingesSwitzerland
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5
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Ojima Y, Naoi K, Akiyoshi R, Azuma M. Quantitative analysis of phosphate accumulation in PHO regulatory system-mutant strains of Saccharomyces cerevisiae. Arch Microbiol 2023; 205:138. [PMID: 36961589 DOI: 10.1007/s00203-023-03488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023]
Abstract
PHO-mutant strains of Saccharomyces cerevisiae, NOF-1 and NBD82-1, which constitutively express PHO81 and PHO4, respectively, have been reported to accumulate phosphate in high-phosphate conditions. However, detailed analysis, including a quantitative evaluation of the accumulated phosphate, has not been performed for these mutants. In this study, NOF-1 and NBD82-1 mutant and double mutant strains were cultured in a high-phosphate medium to quantitatively analyze the amount, accumulation form, and physiological use of the accumulated phosphate in the cells. In control strains (BY4741 and NBW7), the percentage of phosphorus in total dry weight of cell was approximately 2%TDW; for the NBD82-1 mutant and double mutant strains, it was approximately 6%TDW; and for strain NOF-1, it was 8.5%TDW. When cells of the mutant strains were stained with 4',6-diamidino-2-phenylindole (DAPI), they showed a fluorescence peak at 540 nm, suggesting that phosphate accumulated as polyphosphoric acid (polyP). Quantitative evaluation revealed that for strain NOF-1, the percentage of phosphorus exiting as polyP in total dry weight of cell was approximately 5.0%TDW, equivalent to 60% of the total phosphorus in the cells. We also demonstrated that the mutant strains could grow well in phosphate-free medium, suggesting that phosphate accumulated in the cells was used as a phosphorus source. This is the first report concerning the quantitative analysis of phosphate accumulation and utilization of PHO regulatory system-mutant strains of Saccharomyces cerevisiae.
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Affiliation(s)
- Yoshihiro Ojima
- Department of Chemistry and Bioengineering, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan.
| | - Kyohei Naoi
- Department of Chemistry and Bioengineering, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Riho Akiyoshi
- Department of Chemistry and Bioengineering, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Masayuki Azuma
- Department of Chemistry and Bioengineering, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
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6
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Satheesh V, Tahir A, Li J, Lei M. Plant phosphate nutrition: sensing the stress. STRESS BIOLOGY 2022; 2:16. [PMID: 37676547 PMCID: PMC10441931 DOI: 10.1007/s44154-022-00039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 09/08/2023]
Abstract
Phosphorus (P) is obtained by plants as phosphate (Pi) from the soil and low Pi levels affects plant growth and development. Adaptation to low Pi condition entails sensing internal and external Pi levels and translating those signals to molecular and morphophysiological changes in the plant. In this review, we present findings related to local and systemin Pi sensing with focus the molecular mechanisms behind root system architectural changes and the impact of hormones and epigenetic mechanisms affecting those changes. We also present some of the recent advances in the Pi sensing and signaling mechanisms focusing on inositol pyrophosphate InsP8 and its interaction with SPX domain proteins to regulate the activity of the central regulator of the Pi starvation response, PHR.
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Affiliation(s)
- Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602 China
| | - Ayesha Tahir
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, Pakistan
| | - Jinkai Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602 China
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7
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Kerdsomboon K, Techo T, Limcharoensuk T, Tatip S, Auesukaree C. Low phosphate mitigates cadmium-induced oxidative stress in Saccharomyces cerevisiae by enhancing endogenous antioxidant defence system. Environ Microbiol 2021; 24:707-720. [PMID: 34927334 DOI: 10.1111/1462-2920.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/30/2022]
Abstract
Cadmium is a highly toxic heavy metal that causes many harmful effects on human health and ecosystems. Metal chelation-based techniques have become a common approach for the treatment of metal poisoning and also for the remediation of metal contamination. Phosphate, an essential nutrient required for key cellular functions, has been supposed to be effective in reducing cadmium bioavailability, possibly through its chelating potential. In this study, we explored the effects of phosphate on cadmium toxicity and cellular response to cadmium stress in the eukaryotic model Saccharomyces cerevisiae. Our results reveal that cadmium toxicity is unexpectedly enhanced during phosphate repletion and optimal phosphate levels for yeast growth under cadmium stress conditions decline with increasing cadmium concentrations. The profound cadmium toxicity during phosphate repletion is unlikely to result from either elevated cadmium accumulation or dysregulated homeostasis of essential metals, but rather due to increased production of intracellular reactive oxygen species. We show that, under phosphate-depleted conditions, the activities of antioxidant enzymes, especially Mn-superoxide dismutase and catalase, are significantly promoted through transcriptional upregulation. Our findings highlight the important role of cellular response to phosphate limitation in mitigating cadmium toxicity and endogenous oxidative stress through the enhancement of antioxidant enzyme activity.
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Affiliation(s)
- Kittikhun Kerdsomboon
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Todsapol Techo
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Tossapol Limcharoensuk
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Supinda Tatip
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Choowong Auesukaree
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, 10400, Thailand.,Mahidol University-Osaka University Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
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8
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Austin S, Mayer A. Phosphate Homeostasis - A Vital Metabolic Equilibrium Maintained Through the INPHORS Signaling Pathway. Front Microbiol 2020; 11:1367. [PMID: 32765429 PMCID: PMC7381174 DOI: 10.3389/fmicb.2020.01367] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cells face major changes in demand for and supply of inorganic phosphate (Pi). Pi is often a limiting nutrient in the environment, particularly for plants and microorganisms. At the same time, the need for phosphate varies, establishing conflicts of goals. Cells experience strong peaks of Pi demand, e.g., during the S-phase, when DNA, a highly abundant and phosphate-rich compound, is duplicated. While cells must satisfy these Pi demands, they must safeguard themselves against an excess of Pi in the cytosol. This is necessary because Pi is a product of all nucleotide-hydrolyzing reactions. An accumulation of Pi shifts the equilibria of these reactions and reduces the free energy that they can provide to drive endergonic metabolic reactions. Thus, while Pi starvation may simply retard growth and division, an elevated cytosolic Pi concentration is potentially dangerous for cells because it might stall metabolism. Accordingly, the consequences of perturbed cellular Pi homeostasis are severe. In eukaryotes, they range from lethality in microorganisms such as yeast (Sethuraman et al., 2001; Hürlimann, 2009), severe growth retardation and dwarfism in plants (Puga et al., 2014; Liu et al., 2015; Wild et al., 2016) to neurodegeneration or renal Fanconi syndrome in humans (Legati et al., 2015; Ansermet et al., 2017). Intracellular Pi homeostasis is thus not only a fundamental topic of cell biology but also of growing interest for medicine and agriculture.
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Affiliation(s)
- Sisley Austin
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Lausanne, Switzerland
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9
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Gupta R, Walvekar AS, Liang S, Rashida Z, Shah P, Laxman S. A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis. eLife 2019; 8:e44795. [PMID: 31259691 PMCID: PMC6688859 DOI: 10.7554/elife.44795] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/30/2019] [Indexed: 12/21/2022] Open
Abstract
Cells must appropriately sense and integrate multiple metabolic resources to commit to proliferation. Here, we report that S. cerevisiae cells regulate carbon and nitrogen metabolic homeostasis through tRNA U34-thiolation. Despite amino acid sufficiency, tRNA-thiolation deficient cells appear amino acid starved. In these cells, carbon flux towards nucleotide synthesis decreases, and trehalose synthesis increases, resulting in a starvation-like metabolic signature. Thiolation mutants have only minor translation defects. However, in these cells phosphate homeostasis genes are strongly down-regulated, resulting in an effectively phosphate-limited state. Reduced phosphate enforces a metabolic switch, where glucose-6-phosphate is routed towards storage carbohydrates. Notably, trehalose synthesis, which releases phosphate and thereby restores phosphate availability, is central to this metabolic rewiring. Thus, cells use thiolated tRNAs to perceive amino acid sufficiency, balance carbon and amino acid metabolic flux and grow optimally, by controlling phosphate availability. These results further biochemically explain how phosphate availability determines a switch to a 'starvation-state'.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Adhish S Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Shun Liang
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Premal Shah
- Department of GeneticsRutgers UniversityPiscatawayUnited States
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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10
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Karginov AV, Fokina AV, Kang HA, Kalebina TS, Sabirzyanova TA, Ter-Avanesyan MD, Agaphonov MO. Dissection of differential vanadate sensitivity in two Ogataea species links protein glycosylation and phosphate transport regulation. Sci Rep 2018; 8:16428. [PMID: 30401924 PMCID: PMC6219546 DOI: 10.1038/s41598-018-34888-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/24/2018] [Indexed: 11/08/2022] Open
Abstract
The closely related yeasts Ogataea polymorpha and O. parapolymorpha differ drastically from each other by sensitivity to the toxic phosphate analog vanadate. Search for genes underlying this difference revealed two genes, one designated as ABV1 (Alcian Blue staining, Vanadate resistance), which encodes a homologue of Saccharomyces cerevisiae Mnn4 responsible for attachment of mannosylphosphate to glycoside chains of secretory proteins, and the other designated as its S. cerevisiae homologue PHO87, encoding the plasma membrane low affinity phosphate sensor/transporter. The effect of Pho87 on vanadate resistance was bidirectional, since it decreased the resistance on phosphate-depleted medium, but was required for pronounced protection against vanadate by external phosphate. This highlights the dual function of this protein as a low affinity phosphate transporter and an external phosphate sensor. Involvement of Pho87 in phosphate sensing was confirmed by its effects on regulation of the promoter of the PHO84 gene, encoding a high affinity phosphate transporter. The effect of Abv1 was also complex, since it influenced Pho87 level and enhanced repression of the PHO84 promoter via a Pho87-independent pathway. Role of the identified genes in the difference in vanadate resistance between O. polymorpha and O. parapolymorpha is discussed.
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Affiliation(s)
- Azamat V Karginov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Anastasia V Fokina
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Tatyana S Kalebina
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Tatyana A Sabirzyanova
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Michael O Agaphonov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation.
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11
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Wild R, Gerasimaite R, Jung JY, Truffault V, Pavlovic I, Schmidt A, Saiardi A, Jessen HJ, Poirier Y, Hothorn M, Mayer A. Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Science 2016; 352:986-90. [DOI: 10.1126/science.aad9858] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/31/2016] [Indexed: 12/23/2022]
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12
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Zhou Y, Yuikawa N, Nakatsuka H, Maekawa H, Harashima S, Nakanishi Y, Kaneko Y. Core regulatory components of the PHO pathway are conserved in the methylotrophic yeast Hansenula polymorpha. Curr Genet 2016; 62:595-605. [PMID: 26794724 PMCID: PMC4929164 DOI: 10.1007/s00294-016-0565-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
To gain better understanding of the diversity and evolution of the gene regulation system in eukaryotes, the phosphate signal transduction (PHO) pathway in non-conventional yeasts has been studied in recent years. Here we characterized the PHO pathway of Hansenula polymorpha, which is genetically tractable and distantly related to Saccharomyces cerevisiae and Schizosaccharomyces pombe, in order to get more information for the diversity and evolution of the PHO pathway in yeasts. We generated several pho gene-deficient mutants based on the annotated draft genome of H. polymorpha BY4329. Except for the Hppho2-deficient mutant, these mutants exhibited the same phenotype of repressible acid phosphatase (APase) production as their S. cerevisiae counterparts. Subsequently, Hppho80 and Hppho85 mutants were isolated as suppressors of the Hppho81 mutation and Hppho4 was isolated from Hppho80 and Hppho85 mutants as the sole suppressor of the Hppho80 and Hppho85 mutations. To gain more complete delineation of the PHO pathway in H. polymorpha, we screened for UV-irradiated mutants that expressed APase constitutively. As a result, three classes of recessive constitutive mutations and one dominant constitutive mutation were isolated. Genetic analysis showed that one group of recessive constitutive mutations was allelic to HpPHO80 and that the dominant mutation occurred in the HpPHO81 gene. Epistasis analysis between Hppho81 and the other two classes of recessive constitutive mutations suggested that the corresponding new genes, named PHO51 and PHO53, function upstream of HpPHO81 in the PHO pathway. Taking these findings together, we conclude that the main components of the PHO pathway identified in S. cerevisiae are conserved in the methylotrophic yeast H. polymorpha, even though these organisms separated from each other before duplication of the whole genome. This finding is useful information for the study of evolution of the PHO regulatory system in yeasts.
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Affiliation(s)
- Ying Zhou
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Naoya Yuikawa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Hiroki Nakatsuka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Hiromi Maekawa
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.,Division of Applied Microbial Technology, Graduate School of Engineering, Sojo University, Kumamoto, 860-0082, Japan
| | - Yoichi Nakanishi
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshinobu Kaneko
- Yeast Genetic Resources Laboratory, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.
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Samyn DR, Persson BL. Inorganic Phosphate and Sulfate Transport in S. cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:253-269. [PMID: 26721277 DOI: 10.1007/978-3-319-25304-6_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Inorganic ions such as phosphate and sulfate are essential macronutrients required for a broad spectrum of cellular functions and their regulation. In a constantly fluctuating environment microorganisms have for their survival developed specific nutrient sensing and transport systems ensuring that the cellular nutrient needs are met. This chapter focuses on the S. cerevisiae plasma membrane localized transporters, of which some are strongly induced under conditions of nutrient scarcity and facilitate the active uptake of inorganic phosphate and sulfate. Recent advances in studying the properties of the high-affinity phosphate and sulfate transporters by means of site-directed mutagenesis have provided further insight into the molecular mechanisms contributing to substrate selectivity and transporter functionality of this important class of membrane transporters.
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Affiliation(s)
- D R Samyn
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden.
| | - B L Persson
- Department of Chemistry and Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden
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14
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Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
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15
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Phosphate homeostasis in the yeast Saccharomyces cerevisiae, the key role of the SPX domain-containing proteins. FEBS Lett 2012; 586:289-95. [PMID: 22285489 DOI: 10.1016/j.febslet.2012.01.036] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/11/2012] [Accepted: 01/16/2012] [Indexed: 12/27/2022]
Abstract
In the yeast Saccharomyces cerevisiae, a working model for nutrient homeostasis in eukaryotes, inorganic phosphate (Pi) homeostasis is regulated by the PHO pathway, a set of phosphate starvation induced genes, acting to optimize Pi uptake and utilization. Among these, a subset of proteins containing the SPX domain has been shown to be key regulators of Pi homeostasis. In this review, we summarize the recent progresses in elucidating the mechanisms controlling Pi homeostasis in yeast, focusing on the key roles of the SPX domain-containing proteins in these processes, as well as describing the future challenges and opportunities in this fast-moving field.
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16
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Sambuk EV, Fizikova AY, Savinov VA, Padkina MV. Acid phosphatases of budding yeast as a model of choice for transcription regulation research. Enzyme Res 2011; 2011:356093. [PMID: 21785706 PMCID: PMC3137970 DOI: 10.4061/2011/356093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Acid phosphatases of budding yeast have been studied for more than forty years. This paper covers biochemical characteristics of acid phosphatases and different aspects in expression regulation of eukaryotic genes, which were researched using acid phosphatases model. A special focus is devoted to cyclin-dependent kinase Pho85p, a negative transcriptional regulator, and its role in maintaining mitochondrial genome stability and to pleiotropic effects of pho85 mutations.
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Affiliation(s)
- Elena V Sambuk
- Genetics and Breeding Department, Biology and Soil Sciences Faculty, Saint Petersburg State University, Universitetskaya emb. 7-9, Saint Petersburg 199034, Russia
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17
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Dick CF, Dos-Santos ALA, Meyer-Fernandes JR. Inorganic phosphate as an important regulator of phosphatases. Enzyme Res 2011; 2011:103980. [PMID: 21755037 PMCID: PMC3132463 DOI: 10.4061/2011/103980] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/03/2011] [Indexed: 11/20/2022] Open
Abstract
Cellular metabolism depends on the appropriate concentration of intracellular inorganic phosphate (Pi). Pi starvation-responsive genes appear to be involved in multiple metabolic pathways, implying a complex Pi regulation system in microorganisms and plants. A group of enzymes is required for absorption and maintenance of adequate phosphate levels, which is released from phosphate esters and anhydrides. The phosphatase system is particularly suited for the study of regulatory mechanisms because phosphatase activity is easily measured using specific methods and the difference between the repressed and derepressed levels of phosphatase activity is easily detected. This paper analyzes the protein phosphatase system induced during phosphate starvation in different organisms.
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Affiliation(s)
- Claudia Fernanda Dick
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Medica, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
| | - André Luiz Araújo Dos-Santos
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Medica, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
| | - José Roberto Meyer-Fernandes
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Medica, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-590 Rio de Janeiro, RJ, Brazil
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18
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Chung SC, Kim TI, Ahn CH, Shin J, Oh KB. Candida albicans PHO81 is required for the inhibition of hyphal development by farnesoic acid. FEBS Lett 2010; 584:4639-45. [PMID: 20965180 DOI: 10.1016/j.febslet.2010.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/12/2010] [Accepted: 10/12/2010] [Indexed: 11/18/2022]
Abstract
Farnesoic acid is a signaling molecule that inhibits the transition from budding yeast to filament formation in Candida albicans, but the molecular mechanism regulated by this substance is unknown. In this study, we analyzed the function of CaPHO81, which is induced by farnesoic acid. The pho81Δ mutant cells existed exclusively as filaments under favorable yeast growth conditions. Furthermore, the inhibition of hyphal growth and repression of CPH1, EFG1, HWP1, and GAP1 mRNA expression in response to farnesoic acid were defective in pho81Δ mutant cells. These data suggest a role for CaPHO81 in the inhibition of hyphal development by farnesoic acid.
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Affiliation(s)
- Soon-Chun Chung
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Republic of Korea
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19
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Monserrate JP, York JD. Inositol phosphate synthesis and the nuclear processes they affect. Curr Opin Cell Biol 2010; 22:365-73. [DOI: 10.1016/j.ceb.2010.03.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 01/30/2023]
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20
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Liu F, Wang Z, Ren H, Shen C, Li Y, Ling HQ, Wu C, Lian X, Wu P. OsSPX1 suppresses the function of OsPHR2 in the regulation of expression of OsPT2 and phosphate homeostasis in shoots of rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:508-17. [PMID: 20149131 DOI: 10.1111/j.1365-313x.2010.04170.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Phosphate (Pi) homeostasis in plants is required for plant growth and development, and is achieved by the coordination of Pi acquisition, translocation from roots to shoots, and remobilization within plants. Previous reports have demonstrated that over-expression of OsPHR2 (the homolog of AtPHR1) and knockdown of OsSPX1 result in accumulation of excessive shoot Pi in rice. Here we report that OsPHR2 positively regulates the low-affinity Pi transporter gene OsPT2 by physical interaction and upstream regulation of OsPHO2 in roots. OsPT2 is responsible for most of the OsPHR2-mediated accumulation of excess shoot Pi. OsSPX1 suppresses the regulation on expression of OsPT2 by OsPHR2 and the accumulation of excess shoot Pi, but it does not suppress induction of OsPT2 or the accumulation of excessive shoot Pi in the Ospho2 mutant. Our data also show that OsSPX1 is a negative regulator of OsPHR2 and is involved in the feedback of Pi-signaling network in roots that is defined by OsPHR2 and OsPHO2. This finding provides new insight into the regulatory mechanism of Pi uptake, translocation, allocation and homeostasis in plants.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China
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21
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Rouached H, Arpat AB, Poirier Y. Regulation of phosphate starvation responses in plants: signaling players and cross-talks. MOLECULAR PLANT 2010; 3:288-99. [PMID: 20142416 DOI: 10.1093/mp/ssp120] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.
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Affiliation(s)
- Hatem Rouached
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
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22
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Degradation of Saccharomyces cerevisiae transcription factor Gcn4 requires a C-terminal nuclear localization signal in the cyclin Pcl5. EUKARYOTIC CELL 2009; 8:496-510. [PMID: 19218424 DOI: 10.1128/ec.00324-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pcl5 is a Saccharomyces cerevisiae cyclin that directs the phosphorylation of the general amino acid control transcriptional activator Gcn4 by the cyclin-dependent kinase (CDK) Pho85. Phosphorylation of Gcn4 by Pho85/Pcl5 initiates its degradation via the ubiquitin/proteasome system and is regulated by the availability of amino acids. In this study, we show that Pcl5 is a nuclear protein and that artificial dislocation of Pcl5 into the cytoplasm prevents the degradation of Gcn4. Nuclear localization of Pcl5 depends on the beta-importin Kap95 and does not require Pho85, Gcn4, or the CDK inhibitor Pho81. Pcl5 nuclear import is independent on the availability of amino acids and is mediated by sequences in its C-terminal domain. The nuclear localization signal is distinct from other functional domains of Pcl5. This is corroborated by a C-terminally truncated Pcl5 variant, which carries the N-terminal nuclear domain of Pho80. This hybrid is still able to fulfill Pcl5 function, whereas Pho80, which is another Pho85 interacting cyclin, does not mediate Gcn4 degradation.
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23
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Breeding of wastewater treatment yeasts that accumulate high concentrations of phosphorus. Appl Microbiol Biotechnol 2008; 80:331-8. [PMID: 18604532 PMCID: PMC2491421 DOI: 10.1007/s00253-008-1529-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 05/01/2008] [Accepted: 05/03/2008] [Indexed: 11/02/2022]
Abstract
Inorganic phosphate is an essential nutrient. In general, microorganisms take up phosphorus when the extracellular phosphorus concentration is low, but not when it is high. In Saccharomyces cerevisiae, the major phosphate transporters, such as Pho84p, and acid phosphatases (APases), such as Pho5p, are regulated in parallel by the phosphate signal transduction pathway (PHO pathway). We found that PHO mutants expressing PHO84 and PHO5, even under high-P conditions, could take up phosphorus at twice the rate of the wild-type strain. The regulatory pathway for phosphorus accumulation in two wastewater treatment yeasts, Hansenula fabianii J640 and Hansenula anomala J224-1, was found to be similar to that in S. cerevisiae. We screened for mutants of these yeasts that constitutively expressed APase. Such mutants formed blue colonies on high phosphorus concentration agar plates containing 5-bromo-4-chloro-3-indolylphosphate (X-phosphate). We found four mutants of H. fabianii J640 and one mutant of H. anomala J224-1 that accumulated from 2.2 to 3.5 times more phosphorus than the parent strains. The growth rates and abilities to remove dissolved total nitrogen and dissolved organic carbon of the mutants were similar to those of the parent strains. In addition, the mutants removed 95% of dissolved total phosphorus from shochu wastewater, while the parent strain removed only 50%.
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24
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de Gouvêa PF, Soriani FM, Malavazi I, Savoldi M, Goldman MHDS, Loss O, Bignell E, da Silva Ferreira ME, Goldman GH. Functional characterization of the Aspergillus fumigatus PHO80 homologue. Fungal Genet Biol 2008; 45:1135-46. [DOI: 10.1016/j.fgb.2008.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
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25
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Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol 2008; 68:1583-94. [PMID: 18433446 DOI: 10.1111/j.1365-2958.2008.06261.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenylate kinase (Adk1p) is a pivotal enzyme in both energetic and adenylic nucleotide metabolisms. In this paper, using a transcriptomic analysis, we show that the lack of Adk1p strongly induced expression of the PHO and ADE genes involved in phosphate utilization and AMP de novo biosynthesis respectively. Isolation and characterization of adk1 point mutants affecting PHO5 expression revealed that all these mutations also severely affected Adk1p catalytic activity, as well as PHO84 and ADE1 transcription. Furthermore, overexpression of distantly related enzymes such as human adenylate kinase or yeast UMP kinase was sufficient to restore regulation. These results demonstrate that adenylate kinase catalytic activity is critical for proper regulation of the PHO and ADE pathways. We also establish that adk1 deletion and purine limitation have similar effects on both adenylic nucleotide pool and PHO84 or ADE17 expression. Finally, we show that, in the adk1 mutant, upregulation of ADE1 depends on synthesis of the previously described effector(s) (S)AICAR ((N-succinyl)-5-aminoimidazol-4-carboxamide ribotide), while upregulation of PHO84 necessitates the Spl2p positive regulator. This work reveals that adenylic nucleotide availability is a key signal used by yeast to co-ordinate phosphate utilization and purine synthesis.
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Affiliation(s)
- Sébastien Gauthier
- Université Victor Segalen/Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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26
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Structure of the Pho85-Pho80 CDK-cyclin complex of the phosphate-responsive signal transduction pathway. Mol Cell 2008; 28:614-23. [PMID: 18042456 DOI: 10.1016/j.molcel.2007.09.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 08/06/2007] [Accepted: 09/25/2007] [Indexed: 11/20/2022]
Abstract
The ability to sense and respond appropriately to environmental changes is a primary requirement of all living organisms. In response to phosphate limitation, Saccharomyces cerevisiae induces transcription of a set of genes involved in the regulation of phosphate acquisition from the ambient environment. A signal transduction pathway (the PHO pathway) mediates this response, with Pho85-Pho80 playing a vital role. Here we report the X-ray structure of Pho85-Pho80, a prototypic structure of a CDK-cyclin complex functioning in transcriptional regulation in response to environmental changes. The structure revealed a specific salt link between a Pho85 arginine and a Pho80 aspartate that makes phosphorylation of the Pho85 activation loop dispensable and that maintains a Pho80 loop conformation for possible substrate recognition. It further showed two sites on the Pho80 cyclin for high-affinity binding of the transcription factor substrate (Pho4) and the CDK inhibitor (Pho81) that are markedly distant to each other and the active site.
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27
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Lee YS, Huang K, Quiocho FA, O'Shea EK. Molecular basis of cyclin-CDK-CKI regulation by reversible binding of an inositol pyrophosphate. Nat Chem Biol 2007; 4:25-32. [PMID: 18059263 DOI: 10.1038/nchembio.2007.52] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 10/11/2007] [Indexed: 12/22/2022]
Abstract
When Saccharomyces cerevisiae cells are starved of inorganic phosphate, the Pho80-Pho85 cyclin-cyclin-dependent kinase (CDK) is inactivated by the Pho81 CDK inhibitor (CKI). The regulation of Pho80-Pho85 is distinct from previously characterized mechanisms of CDK regulation: the Pho81 CKI is constitutively associated with Pho80-Pho85, and a small-molecule ligand, inositol heptakisphosphate (IP7), is required for kinase inactivation. We investigated the molecular basis of the IP7- and Pho81-dependent Pho80-Pho85 inactivation using electrophoretic mobility shift assays, enzyme kinetics and fluorescence spectroscopy. We found that IP7 interacts noncovalently with Pho80-Pho85-Pho81 and induces additional interactions between Pho81 and Pho80-Pho85 that prevent substrates from accessing the kinase active site. Using synthetic peptides corresponding to Pho81, we define regions of Pho81 responsible for constitutive Pho80-Pho85 binding and IP7-regulated interaction and inhibition. These findings expand our understanding of the mechanisms of cyclin-CDK regulation and of the biochemical mechanisms of IP7 action.
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Affiliation(s)
- Young-Sam Lee
- Howard Hughes Medical Institute, Harvard University, Department of Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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28
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Auesukaree C, Fuchigami I, Homma T, Kaneko Y, Harashima S. Ddi1p and Rad23p play a cooperative role as negative regulators in the PHO pathway in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2007; 365:821-5. [PMID: 18035052 DOI: 10.1016/j.bbrc.2007.11.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Accepted: 11/13/2007] [Indexed: 11/27/2022]
Abstract
In Saccharomyces cerevisiae, the PHO pathway regulates expression of phosphate-responsive genes such as PHO5, which encodes repressible acid phosphatase (rAPase). In this pathway, Pho81p functions as an inhibitor of the cyclin-cyclin-dependent kinase (CDK) complex Pho80p-Pho85p. However, the mechanism regulating the inhibitory activity of Pho81p is poorly understood. Through use of the yeast two-hybrid system, we identified the UbL-UbA protein Ddi1p as a Pho81p-binding protein. Further, Pho81p levels were found to be low under high-phosphate condition and high during phosphate starvation, indicating that Pho81p is regulated by phosphate concentration. However, our results revealed that Ddi1p and its associated protein Rad23p are not involved in the decrease in Pho81p level under high-phosphate condition. Significantly, the Deltaddi1Deltarad23 strain exhibited a remarkable increase in rAPase activity at an intermediate-phosphate concentration of 0.4mM, suggesting that Ddi1p and Rad23p play a cooperative role as negative regulators in the PHO pathway.
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Affiliation(s)
- Choowong Auesukaree
- Department of Biology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
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29
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Adkins MW, Williams SK, Linger J, Tyler JK. Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol Cell Biol 2007; 27:6372-82. [PMID: 17620413 PMCID: PMC2099613 DOI: 10.1128/mcb.00981-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The disassembly of promoter nucleosomes appears to be a general property of highly transcribed eukaryotic genes. We have previously shown that the disassembly of chromatin from the promoters of the Saccharomyces cerevisiae PHO5 and PHO8 genes, mediated by the histone chaperone anti-silencing function 1 (Asf1), is essential for transcriptional activation upon phosphate depletion. This mechanism of transcriptional regulation is shared with the ADY2 and ADH2 genes upon glucose removal. Promoter chromatin disassembly by Asf1 is required for recruitment of TBP and RNA polymerase II, but not the Pho4 and Pho2 activators. Furthermore, accumulation of SWI/SNF and SAGA at the PHO5 promoter requires promoter chromatin disassembly. By contrast, the requirement for SWI/SNF and SAGA to facilitate Pho4 activator recruitment to the nucleosome-buried binding site in the PHO5 promoter occurs prior to chromatin disassembly and is distinct from the stable recruitment of SWI/SNF and SAGA that occurs after chromatin disassembly.
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Affiliation(s)
- Melissa W Adkins
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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30
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Yu H, Xia Y, Trifonov V, Gerstein M. Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol 2007; 7:R55. [PMID: 16859507 PMCID: PMC1779570 DOI: 10.1186/gb-2006-7-7-r55] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 05/19/2006] [Accepted: 06/20/2006] [Indexed: 02/01/2023] Open
Abstract
A global comparison of the four basic molecular networks in yeast - regulatory, co-expression, interaction and metabolic - reveals general design principles. Background Molecular networks are of current interest, particularly with the publication of many large-scale datasets. Previous analyses have focused on topologic structures of individual networks. Results Here, we present a global comparison of four basic molecular networks: regulatory, co-expression, interaction, and metabolic. In terms of overall topologic correlation - whether nearby proteins in one network are close in another - we find that the four are quite similar. However, focusing on the occurrence of local features, we introduce the concept of composite hubs, namely hubs shared by more than one network. We find that the three 'action' networks (metabolic, co-expression, and interaction) share the same scaffolding of hubs, whereas the regulatory network uses distinctly different regulator hubs. Finally, we examine the inter-relationship between the regulatory network and the three action networks, focusing on three composite motifs - triangles, trusses, and bridges - involving different degrees of regulation of gene pairs. Our analysis shows that interaction and co-expression networks have short-range relationships, with directly interacting and co-expressed proteins sharing regulators. However, the metabolic network contains many long-distance relationships: far-away enzymes in a pathway often have time-delayed expression relationships, which are well coordinated by bridges connecting their regulators. Conclusion We demonstrate how basic molecular networks are distinct yet connected and well coordinated. Many of our conclusions can be mapped onto structured social networks, providing intuitive comparisons. In particular, the long-distance regulation in metabolic networks agrees with its counterpart in social networks (namely, assembly lines). Conversely, the segregation of regulator hubs from other hubs diverges from social intuitions (as managers often are centers of interactions).
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Affiliation(s)
- Haiyuan Yu
- Department of Molecular Biophysics and Biochemistry, Whitney Avenue, Yale University, New Haven, CT 06520, USA
| | - Yu Xia
- Department of Molecular Biophysics and Biochemistry, Whitney Avenue, Yale University, New Haven, CT 06520, USA
| | - Valery Trifonov
- Department of Molecular Biophysics and Biochemistry, Whitney Avenue, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Whitney Avenue, Yale University, New Haven, CT 06520, USA
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31
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Bömeke K, Pries R, Korte V, Scholz E, Herzog B, Schulze F, Braus GH. Yeast Gcn4p stabilization is initiated by the dissociation of the nuclear Pho85p/Pcl5p complex. Mol Biol Cell 2006; 17:2952-62. [PMID: 16611745 PMCID: PMC1483032 DOI: 10.1091/mbc.e05-10-0975] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 04/04/2006] [Accepted: 04/05/2006] [Indexed: 11/11/2022] Open
Abstract
Protein stability of the c-jun-like yeast bZIP transcriptional activator Gcn4p is exclusively controlled in the yeast nucleus. Phosphorylation by the nuclear Pho85p cyclin-dependent protein kinase, a functional homolog of mammalian Cdk5, initiates the Gcn4p degradation pathway in complex with the cyclin Pcl5p. We show that the initial step in Gcn4p stabilization is the dissociation of the Pho85p/Pcl5p complex. Pcl7p, another nuclear and constantly present cyclin, is required for Gcn4p stabilization and is able to associate to Pho85p independently of the activity of the Gcn4p degradation pathway. In addition, the nuclear cyclin-dependent Pho85p kinase inhibitor Pho81p is required for Gcn4p stabilization. Pho81p only interacts with Pcl5p when Gcn4p is rapidly degraded but constitutively interacts with Pcl7p. Our data suggest that Pcl7p and Pho81p are antagonists of the Pho85p/Pcl5p complex formation in a yet unknown way, which are specifically required for Gcn4p stabilization. We suggest that dissociation of the Pho85p/Pcl5p complex as initial step in Gcn4p stabilization is a prerequisite for a shift of equilibrium to an increased amount of the Pho85p/Pcl7p complexes and subsequently results in decreased Gcn4p phosphorylation and therefore increased stability of the transcription factor.
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Affiliation(s)
- Katrin Bömeke
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Ralph Pries
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Virginia Korte
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Eva Scholz
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Britta Herzog
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Florian Schulze
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
| | - Gerhard H. Braus
- Institute of Microbiology and Genetics, Georg August University, D-37077 Göttingen, Germany
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Wongwisansri S, Laybourn PJ. Disruption of histone deacetylase gene RPD3 accelerates PHO5 activation kinetics through inappropriate Pho84p recycling. EUKARYOTIC CELL 2005; 4:1387-95. [PMID: 16087743 PMCID: PMC1214523 DOI: 10.1128/ec.4.8.1387-1395.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The histone deacetylase Rpd3p functions as a transcriptional repressor of a diverse set of genes, including PHO5. Here we describe a novel role for RPD3 in the regulation of phosphate transporter Pho84p retention in the cytoplasmic membrane. We show that under repressing conditions (with P(i)), PHO5 expression is increased in a pho4Delta rpd3Delta strain, demonstrating PHO regulatory pathway independence. However, the effect of RPD3 disruption on PHO5 activation kinetics is dependent on the PHO regulatory pathway. Upon switching to activating conditions (without P(i)), PHO5 transcripts accumulated more rapidly in rpd3Delta cells. This more rapid response correlates with a defect in phosphate uptake due to premature recycling of Pho84p, the high-affinity H+/PO4(3-) symporter. Thus, RPD3 also participates in PHO5 regulation through a previously unidentified effect on maintenance of high-affinity phosphate uptake during phosphate starvation. We propose that Rpd3p has a negative role in the regulation of Pho84p endocytosis.
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Affiliation(s)
- Sriwan Wongwisansri
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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Swinnen E, Rosseels J, Winderickx J. The minimum domain of Pho81 is not sufficient to control the Pho85-Rim15 effector branch involved in phosphate starvation-induced stress responses. Curr Genet 2005; 48:18-33. [PMID: 15926040 DOI: 10.1007/s00294-005-0583-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 04/14/2005] [Accepted: 04/19/2005] [Indexed: 10/25/2022]
Abstract
The phosphate regulatory mechanism in yeast, known as the PHO pathway, is regulated by inorganic phosphate to control the expression of genes involved in the acquisition of phosphate from the medium. This pathway is also reported to contribute to other nutritional responses and as such it affects several phenotypic characteristics known also to be regulated by protein kinase A, including the transcription of genes involved in the general stress response and trehalose metabolism. We now demonstrate that transcription of post-diauxic shift (PDS)-controlled stress-responsive genes is solely regulated by the Pho85-Pho80 complex, whereas regulation of trehalose metabolism apparently involves several Pho85 cyclins. Interestingly, both read-outs depend on Pho81 but, while the previously described minimum domain of Pho81 is sufficient to sustain phosphate-regulated transcription of PHO genes, full-length Pho81 is required to control trehalose metabolism and the PDS targets. Consistently, neither the expression control of stress-regulated genes nor the trehalose metabolism relies directly on Pho4. Finally, we present data supporting that the PHO pathway functions in parallel to the fermentable growth medium- or Sch9-controlled pathway and that both pathways may share the protein kinase Rim15, which was previously reported to play a central role in the integration of glucose, nitrogen and amino acid availability.
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Affiliation(s)
- Erwin Swinnen
- Functional Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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Auesukaree C, Tochio H, Shirakawa M, Kaneko Y, Harashima S. Plc1p, Arg82p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae. J Biol Chem 2005; 280:25127-33. [PMID: 15866881 DOI: 10.1074/jbc.m414579200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, the phosphate signal transduction PHO pathway is involved in regulating several phosphate-responsive genes such as PHO5, which encodes repressible acid phosphatase. In this pathway, a cyclin-dependent kinase inhibitor (Pho81p) regulates the kinase activity of the cyclin-cyclin-dependent kinase complex Pho80p-Pho85p, which phosphorylates the transcription factor Pho4p in response to intracellular phosphate levels. However, how cells sense phosphate availability and transduce the phosphate signal to Pho81p remains unknown. To identify additional components of the PHO pathway, we have screened a collection of yeast deletion strains. We found that disruptants of PLC1, ARG82, and KCS1, which are involved in the synthesis of inositol polyphosphate, and ADK1, which encodes adenylate kinase, constitutively express PHO5. Each of these factors functions upstream of Pho81p and negatively regulates the PHO pathway independently of intracellular orthophosphate levels. Overexpression of KCS1, but not of the other genes, suppressed PHO5 expression in the wild-type strain under low phosphate conditions. These results raise the possibility that diphosphoinositol tetrakisphosphate and/or bisdiphosphoinositol triphosphate may be essential for regulation of the PHO pathway. Furthermore, the Deltaplc1, Deltaarg82, and Deltakcs1 deletion strains, but not the Deltaipk1 deletion strain, had significantly reduced intracellular polyphosphate levels, suggesting that enzymes involved in inositol pyrophosphate synthesis are also required for polyphosphate accumulation.
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Affiliation(s)
- Choowong Auesukaree
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Huang S, O'Shea EK. A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation. Genetics 2005; 169:1859-71. [PMID: 15695358 PMCID: PMC1360160 DOI: 10.1534/genetics.104.038695] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In response to phosphate limitation, Saccharomyces cerevisiae induces transcription of a set of genes important for survival. One of these genes is PHO5, which encodes a secreted acid phosphatase. A phosphate-responsive signal transduction pathway (the PHO pathway) mediates this response through three central components: a cyclin-dependent kinase (CDK), Pho85; a cyclin, Pho80; and a CDK inhibitor (CKI), Pho81. While signaling downstream of the Pho81/Pho80/Pho85 complex to PHO5 expression has been well characterized, little is known about factors acting upstream of these components. To identify missing factors involved in the PHO pathway, we carried out a high-throughput, quantitative enzymatic screen of a yeast deletion collection, searching for novel mutants defective in expression of PHO5. As a result of this study, we have identified at least nine genes that were previously not known to regulate PHO5 expression. The functional diversity of these genes suggests that the PHO pathway is networked with other important cellular signaling pathways. Among these genes, ADK1 and ADO1, encoding an adenylate kinase and an adenosine kinase, respectively, negatively regulate PHO5 expression and appear to function upstream of PHO81.
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Affiliation(s)
- Sidong Huang
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, 94143-2240, USA
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36
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Pinson B, Merle M, Franconi JM, Daignan-Fornier B. Low affinity orthophosphate carriers regulate PHO gene expression independently of internal orthophosphate concentration in Saccharomyces cerevisiae. J Biol Chem 2004; 279:35273-80. [PMID: 15194704 DOI: 10.1074/jbc.m405398200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphate is an essential nutrient that must be taken up from the growth medium through specific transporters. In Saccharomyces cerevisiae, both high and low affinity orthophosphate carriers allow this micro-organism to cope with environmental variations. Intriguingly, in this study we found a tight correlation between selenite resistance and expression of the high affinity orthophosphate carrier Pho84p. Our work further revealed that mutations in the low affinity orthophosphate carrier genes (PHO87, PHO90, and PHO91) cause deregulation of phosphate-repressed genes. Strikingly, the deregulation due to pho87Delta, pho90Delta, or pho91Delta mutations was neither correlated to impaired orthophosphate uptake capacity nor to a decrease of the intracellular orthophosphate or polyphosphate pools, as shown by (31)P NMR spectroscopy. Thus, our data clearly establish that the low affinity orthophosphate carriers affect phosphate regulation independently of intracellular orthophosphate concentration through a new signaling pathway that was found to strictly require the cyclin-dependent kinase inhibitor Pho81p. We propose that phosphate-regulated gene expression is under the control of two different regulatory signals as follows: the sensing of internal orthophosphate by a yet unidentified protein and the sensing of external orthophosphate by low affinity orthophosphate transporters; the former would be required to maintain phosphate homeostasis, and the latter would keep the cell informed on the medium phosphate richness.
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Affiliation(s)
- Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS-Université Victor Segalen Bordeaux 2, 33077 Bordeaux Cedex, France.
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37
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Auesukaree C, Homma T, Tochio H, Shirakawa M, Kaneko Y, Harashima S. Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae. J Biol Chem 2004; 279:17289-94. [PMID: 14966138 DOI: 10.1074/jbc.m312202200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, the phosphate signal transduction pathway (PHO pathway) is known to regulate the expression of several phosphate-responsive genes, such as PHO5 and PHO84. However, the fundamental issue of whether cells sense intracellular or extracellular phosphate remains unresolved. To address this issue, we have directly measured intracellular phosphate concentrations by (31)P NMR spectroscopy. We find that PHO5 expression is strongly correlated with the levels of both intracellular orthophosphate and intracellular polyphosphate and that the signaling defect in the Deltapho84 strain is likely to result from insufficient intracellular phosphate caused by a defect in phosphate uptake. Furthermore, the Deltaphm1Deltaphm2, Deltaphm3, and Deltaphm4 strains, which lack intracellular polyphosphate, have higher intracellular orthophosphate levels and lower expression of PHO5 than the wild-type strain. By contrast, the Deltaphm5 strain, which has lower intracellular orthophosphate and higher polyphosphate levels than the wild-type strain, shows repressed expression of PHO5, similar to the wild-type strain. These observations suggest that PHO5 expression is under the regulation of intracellular orthophosphate, although orthophosphate is not the sole signaling molecule. Moreover, the disruption of PHM3, PHM4, or of both PHM1 and PHM2 in the Deltapho84 strain suppresses, although not completely, the PHO5 constitutive phenotype by increasing intracellular orthophosphate, suggesting that Pho84p affects phosphate signaling largely by functioning as a transporter.
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Affiliation(s)
- Choowong Auesukaree
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871
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38
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Persson BL, Lagerstedt JO, Pratt JR, Pattison-Granberg J, Lundh K, Shokrollahzadeh S, Lundh F. Regulation of phosphate acquisition in Saccharomyces cerevisiae. Curr Genet 2003; 43:225-44. [PMID: 12740714 DOI: 10.1007/s00294-003-0400-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2003] [Revised: 04/05/2003] [Accepted: 04/08/2003] [Indexed: 01/08/2023]
Abstract
Membrane transport systems active in cellular inorganic phosphate (P(i)) acquisition play a key role in maintaining cellular P(i) homeostasis, independent of whether the cell is a unicellular microorganism or is contained in the tissue of a higher eukaryotic organism. Since unicellular eukaryotes such as yeast interact directly with the nutritious environment, regulation of P(i) transport is maintained solely by transduction of nutrient signals across the plasma membrane. The individual yeast cell thus recognizes nutrients that can act as both signals and sustenance. The present review provides an overview of P(i) acquisition via the plasma membrane P(i) transporters of Saccharomyces cerevisiae and the regulation of internal P(i) stores under the prevailing P(i) status.
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Affiliation(s)
- Bengt L Persson
- Department of Chemistry and Biomedical Science, Kalmar University, P.O. Box 905, 39182, Kalmar, Sweden.
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39
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Winderickx J, Holsbeeks I, Lagatie O, Giots F, Thevelein J, de Winde H. From feast to famine; adaptation to nutrient availability in yeast. ACTA ACUST UNITED AC 2002. [DOI: 10.1007/3-540-45611-2_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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40
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Abstract
Cellular metabolism depends on the appropriate concentration of intracellular inorganic phosphate; however, little is known about how phosphate concentrations are sensed. The similarity of Pho84p, a high-affinity phosphate transporter in Saccharomyces cerevisiae, to the glucose sensors Snf3p and Rgt2p has led to the hypothesis that Pho84p is an inorganic phosphate sensor. Furthermore, pho84Delta strains have defects in phosphate signaling; they constitutively express PHO5, a phosphate starvation-inducible gene. We began these studies to determine the role of phosphate transporters in signaling phosphate starvation. Previous experiments demonstrated a defect in phosphate uptake in phosphate-starved pho84Delta cells; however, the pho84Delta strain expresses PHO5 constitutively when grown in phosphate-replete media. We determined that pho84Delta cells have a significant defect in phosphate uptake even when grown in high phosphate media. Overexpression of unrelated phosphate transporters or a glycerophosphoinositol transporter in the pho84Delta strain suppresses the PHO5 constitutive phenotype. These data suggest that PHO84 is not required for sensing phosphate. We further characterized putative phosphate transporters, identifying two new phosphate transporters, PHO90 and PHO91. A synthetic lethal phenotype was observed when five phosphate transporters were inactivated, and the contribution of each transporter to uptake in high phosphate conditions was determined. Finally, a PHO84-dependent compensation response was identified; the abundance of Pho84p at the plasma membrane increases in cells that are defective in other phosphate transporters.
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Affiliation(s)
- D D Wykoff
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143-0448, USA
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41
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Huang S, Jeffery DA, Anthony MD, O'Shea EK. Functional analysis of the cyclin-dependent kinase inhibitor Pho81 identifies a novel inhibitory domain. Mol Cell Biol 2001; 21:6695-705. [PMID: 11533256 PMCID: PMC99814 DOI: 10.1128/mcb.21.19.6695-6705.2001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2001] [Accepted: 07/07/2001] [Indexed: 11/20/2022] Open
Abstract
In response to phosphate limitation, Saccharomyces cerevisiae induces transcription of a set of genes important for survival. A phosphate-responsive signal transduction pathway mediates this response by controlling the activity of the transcription factor Pho4. Three components of this signal transduction pathway resemble those used to regulate the eukaryotic cell cycle: a cyclin-dependent kinase (CDK), Pho85; a cyclin, Pho80; and a CDK inhibitor (CKI), Pho81. Pho81 forms a stable complex with Pho80-Pho85 under both high- and low-phosphate conditions, but it only inhibits the kinase when cells are starved for phosphate. Pho81 contains six tandem repeats of the ankyrin consensus domain homologous to the INK4 family of mammalian CKIs. INK4 proteins inhibit kinase activity through an interaction of the ankyrin repeats and the CDK subunits. Surprisingly, we find that a region of Pho81 containing 80 amino acids C terminal to the ankyrin repeats is necessary and sufficient for Pho81's CKI function. The ankyrin repeats of Pho81 appear to have no significant role in Pho81 inhibition. Our results suggest that Pho81 inhibits Pho80-Pho85 with a novel motif.
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Affiliation(s)
- S Huang
- Department of Biochemistry & Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94143-0448, USA
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42
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Lamb TM, Xu W, Diamond A, Mitchell AP. Alkaline response genes of Saccharomyces cerevisiae and their relationship to the RIM101 pathway. J Biol Chem 2001; 276:1850-6. [PMID: 11050096 DOI: 10.1074/jbc.m008381200] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Environmental pH exerts broad control over growth and differentiation, but the molecular responses to external pH changes are poorly understood. Here we have used open reading frame macroarray hybridization to identify alkaline response genes in Saccharomyces cerevisiae. Northern or lacZ fusion assays confirmed the alkaline induction of two ion pump genes (ENA1 and VMA4), several ion limitation genes (CTR3, FRE1, PHO11/12, and PHO84), a siderophore-iron transporter gene (ARN4/ENB1), two transcription factor genes (NRG2 and TIS11), and two predicted membrane protein genes (YAR068W/YHR214W and YOL154W). Unlike ENA1 and SHC1, these new alkaline response genes are not induced by high salinity. The known pH-responsive genes in other fungi depend on the conserved PacC/Rim101p transcription factor, but induction of several of these new genes relied upon Rim101p-independent pH signaling mechanisms. Rim101p-dependent genes were also dependent on Rim13p, a protease required for Rim101p processing. The Rim101p-dependent gene VMA4 is required for growth in alkaline conditions, illustrating how Rim101p may control adaptation. Because Rim101p activates ion pump genes, we tested the role of RIM101 in ion homeostasis and found that RIM101 promotes resistance to elevated cation concentrations. Thus, gene expression surveys can reveal new functions for characterized transcription factors in addition to uncovering physiological responses to environmental conditions.
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Affiliation(s)
- T M Lamb
- Department of Microbiology, the Institute of Cancer Research, Columbia University, New York, New York 10032, USA
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43
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Ogawa N, DeRisi J, Brown PO. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 2000; 11:4309-21. [PMID: 11102525 PMCID: PMC15074 DOI: 10.1091/mbc.11.12.4309] [Citation(s) in RCA: 363] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The PHO regulatory pathway is involved in the acquisition of phosphate (P(i)) in the yeast Saccharomyces cerevisiae. When extracellular P(i) concentrations are low, several genes are transcriptionally induced by this pathway, which includes the Pho4 transcriptional activator, the Pho80-Pho85 cyclin-CDK pair, and the Pho81 CDK inhibitor. In an attempt to identify all the components regulated by this system, a whole-genome DNA microarray analysis was employed, and 22 PHO-regulated genes were identified. The promoter regions of 21 of these genes contained at least one copy of a sequence that matched the Pho4 recognition site. Eight of these genes, PHM1-PHM8, had no previously defined function in phosphate metabolism. The amino acid sequences of PHM1 (YFL004w), PHM2 (YPL019c), PHM3 (YJL012c), and PHM4 (YER072w) are 32-56% identical. The phm3 and phm4 single mutants and the phm1 phm2 double mutant were each severely deficient in accumulation of inorganic polyphosphate (polyP) and P(i). The phenotype of the phm5 mutant suggests that PHM5 (YDR452w) is essential for normal catabolism of polyP in the yeast vacuole. Taken together, the results reveal important new features of a genetic system that plays a critical role in P(i) acquisition and polyP metabolism in yeast.
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Affiliation(s)
- N Ogawa
- Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5307, USA
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Robinson KA, Lopes JM. SURVEY AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes. Nucleic Acids Res 2000; 28:1499-505. [PMID: 10710415 PMCID: PMC102793 DOI: 10.1093/nar/28.7.1499] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/1999] [Revised: 02/14/2000] [Accepted: 02/14/2000] [Indexed: 01/07/2023] Open
Abstract
Basic helix-loop-helix (bHLH) proteins are among the most well studied and functionally important regulatory proteins in all eukaryotes. The HLH domain dictates dimerization to create homo- and heterodimers. Dimerization juxtaposes the basic regions of the two monomers to create a DNA interaction surface that recognizes the consensus sequence called the E-box, 5'-CANNTG-3'. Several bHLH proteins have been identified in the yeast Saccharomyces cerevisiae using traditional genetic methodologies. These proteins regulate diverse biological pathways. The completed sequence of the yeast genome, combined with novel methodologies allowing whole-genome expression studies, now offers a unique opportunity to study the function of these bHLH proteins. It is the purpose of this review to summarize the current knowledge of bHLH protein function in yeast.
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Affiliation(s)
- K A Robinson
- Department of Molecular and Cellular Biochemistry, Loyola University of Chicago, Maywood, IL 60153, USA
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45
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Persson BL, Petersson J, Fristedt U, Weinander R, Berhe A, Pattison J. Phosphate permeases of Saccharomyces cerevisiae: structure, function and regulation. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1422:255-72. [PMID: 10548719 DOI: 10.1016/s0304-4157(99)00010-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- B L Persson
- Department of Engineering, Växjö University, S-351 95, Växjö, Sweden.
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46
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Nishizawa M, Suzuki K, Fujino M, Oguchi T, Toh-e A. The Pho85 kinase, a member of the yeast cyclin-dependent kinase (Cdk) family, has a regulation mechanism different from Cdks functioning throughout the cell cycle. Genes Cells 1999; 4:627-42. [PMID: 10620010 DOI: 10.1046/j.1365-2443.1999.00290.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The PHO85 gene is a negative regulator of the PHO system in the yeast Saccharomyces cerevisiae and encodes a protein kinase (Pho85p) which is highly homologous to the Cdc28 kinase (Cdc28p). Although the two kinases share a 51% identity and their functional domains are well conserved, PHO85 fails to replace CDC28. Pho85p forms complexes with G1-cyclin homologues, including Pcl1p, Pcl2p and Pcl9p, and is thought to be involved in the cell-cycle regulation at G1 and the end of M. By analysing the genetic and biochemical properties of Pho85p, we studied whether the regulation of Pho85p activity is similar to other cyclin-dependent kinases (Cdks) directly involved in cell cycle regulation. RESULTS A functional analysis of various Pho85 mutants revealed that E53 in the PSTAIRE sequence was important for Pho85p function. On the other hand, residues in the T-loop including S166, S167 and E168, appeared dispensable for Pho85p function, suggesting that the phosphorylation of S166, corresponding to T161 of Cdc2p and T169 of Cdc28p, was not required for the kinase activity of Pho85p. Instead, we found that phosphorylation of Y18, corresponding to Y15 of Cdc2p and Y19 of Cdc28p, may be important for the binding of Pho80p but not of Pcl1p, suggesting that tyrosine phosphorylation may function as a signal which discriminates various Pho85-cyclins. CONCLUSION In Cdks functioning throughout the cell cycle, tyrosine phosphorylation is inhibitory to the activation of kinase, whereas the phosphorylation of threonine in the T-loop is essential for activation. Our finding indicates that the regulation mechanism of Pho85p activation appears to be distinct from these Cdks.
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Affiliation(s)
- M Nishizawa
- Department of Microbiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
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47
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Wilson WA, Mahrenholz AM, Roach PJ. Substrate targeting of the yeast cyclin-dependent kinase Pho85p by the cyclin Pcl10p. Mol Cell Biol 1999; 19:7020-30. [PMID: 10490639 PMCID: PMC84697 DOI: 10.1128/mcb.19.10.7020] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/1999] [Accepted: 07/26/1999] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, PHO85 encodes a cyclin-dependent protein kinase (Cdk) catalytic subunit with multiple regulatory roles thought to be specified by association with different cyclin partners (Pcls). Pcl10p is one of four Pcls with little sequence similarity to cyclins involved in cell cycle control. It has been implicated in specifying the phosphorylation of glycogen synthase (Gsy2p). We report that recombinant Pho85p and Pcl10p produced in Escherichia coli reconstitute an active Gsy2p kinase in vitro. Gsy2p phosphorylation required Pcl10p, occurred at physiologically relevant sites, and resulted in inactivation of Gsy2p. The activity of the reconstituted enzyme was even greater than Pho85p-Pcl10p isolated from yeast, and we conclude that, unlike many Cdks, Pho85p does not require phosphorylation for activity. Pcl10p formed complexes with Gsy2p, as judged by (i) gel filtration of recombinant Pcl10p and Gsy2p, (ii) coimmunoprecipitation from yeast cell lysates, and (iii) enzyme kinetic behavior consistent with Pcl10p binding the substrate. Synthetic peptides modeled on the sequences of known Pho85p sites were poor substrates with high K(m) values, and we propose that Pcl10p-Gsy2p interaction is important for substrate selection. Gel filtration of yeast cell lysates demonstrated that most Pho85p was present as a monomer, although a portion coeluted in high-molecular-weight fractions with Pcl10p and Gsy2p. Overexpression of Pcl10p sequestered most of the Pho85p into association with Pcl10p. We suggest a model for Pho85p function in the cell whereby cyclins like Pcl10p recruit Pho85p from a pool of monomers, both activating the kinase and targeting it to substrate.
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Affiliation(s)
- W A Wilson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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48
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Cohen A, Perzov N, Nelson H, Nelson N. A novel family of yeast chaperons involved in the distribution of V-ATPase and other membrane proteins. J Biol Chem 1999; 274:26885-93. [PMID: 10480897 DOI: 10.1074/jbc.274.38.26885] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Null mutations in genes encoding V-ATPase subunits in Saccharomyces cerevisiae result in a phenotype that is unable to grow at high pH and is sensitive to high and low metal-ion concentrations. Treatment of these null mutants with ethylmethanesulfonate causes mutations that suppress the V-ATPase null phenotype, and the mutant cells are able to grow at pH 7.5. The suppressor mutants were denoted as svf (suppressor of V-ATPase function). The frequency of svf is relatively high, suggesting a large target containing several genes for the ethylmethanesulfonate mutagenesis. The suppressors' frequency is dependent on the individual genes that were inactivated to manifest the V-ATPase null mutation. The svf mutations are recessive, because crossing the svf mutants with their corresponding V-ATPase null mutants resulted in diploid strains that are unable to grow at pH 7.5. A novel gene family in which null mutations cause pleiotropic effects on metal-ion resistance or sensitivity and distribution of membrane proteins in different targets was discovered. The family was defined as VTC (Vacuolar Transporter Chaperon) and it contains four genes in the S. cerevisiae genome. Inactivation of one of them, VTC1, in the background of V-ATPase null mutations resulted in svf phenotype manifested by growth at pH 7.5. Deletion of the VTC1 gene (DeltaVTC1) results in a reduced amount of V-ATPase in the vacuolar membrane. These mutant cells fail to accumulate quinacrine into their vacuoles, but they are able to grow at pH 7.5. The VTC1 null mutant also results in a reduced amount of the plasma membrane H(+)-ATPase (Pma1p) in membrane preparations and possibly mis-targeting. This observation may provide an explanation for the svf phenotype in the double disruptant mutants of DeltaVTC1 and DeltaVMA subunits.
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Affiliation(s)
- A Cohen
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Sedgwick SG, Smerdon SJ. The ankyrin repeat: a diversity of interactions on a common structural framework. Trends Biochem Sci 1999; 24:311-6. [PMID: 10431175 DOI: 10.1016/s0968-0004(99)01426-7] [Citation(s) in RCA: 582] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The ankyrin repeat is one of the most common protein sequence motifs. Recent X-ray and NMR structures of ankyrin-repeat proteins and their complexes have provided invaluable insights into the molecular basis of the extraordinary variety of biological activities of these molecules. In particular, they have begun to reveal how a large family of structurally related proteins can interact specifically with such a diverse array of macromolecular targets.
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Affiliation(s)
- S G Sedgwick
- Division of Yeast Genetics, National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK NW7 1AA.
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50
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Esser K, Scholle B, Michaelis G. Disruption of six open reading frames on chromosome X of Saccharomyces cerevisiae reveals a cluster of four essential genes. Yeast 1999; 15:921-33. [PMID: 10407272 DOI: 10.1002/(sici)1097-0061(199907)15:10b<921::aid-yea389>3.0.co;2-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In this study we report the construction and basic phenotypic analysis of six Saccharomyces cerevisiae deletion mutants. The open reading frames (ORFs) YJL008C (gene symbol CCT8), YJL010C, YJL011C, YJL012C, YJL017W, and YJL020C from chromosome X have been disrupted by integration of deletion cassettes, comprising the bacterial KanMX4 marker gene and terminal long (LFH) or short (SFH) flanking sequences that are homologous to the 5' and 3' untranslated regions of the respective ORFs. For correct disruption of ORF YJL008C, it was necessary to construct a deletion cassette flanked by 300-350 bp long target guide sequences by LFH-PCR. Transformations using ORF YJL008C gene disruption cassettes synthesized by standard SFH-PCR exclusively resulted in false-positive or multiple integration events, probably because seven additional genes homologous to CCT8 exist in the yeast genome. The other five ORFs have been disrupted using cassettes generated by SFH-PCR, comprising terminal homologous regions of approximately 50 bp to each target site. Correct genomic integration of the reporter modules was verified by analytical PCR and Southern hybridization. Deletion of YJL008C, YJL010C, YJL011C, and YJL012C was found to be lethal, as shown by sporulation and tetrad analysis. This result is in contrast to the finding that only 16-20% of the genes in S. cerevisiae are estimated to be essential. The four essential genes described in this work are clustered, while the two other non-essential ORFs are separated by further ORFs. Although the two viable deletion mutants were tested against 60 different inhibitors, heavy metal ions and salts, no phenotype could be detected that co-segregated with the deletion during meiosis.
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Affiliation(s)
- K Esser
- Botanisches Institut, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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