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Pirkmajer S, Chibalin AV. Exit, O Sodium! FUNCTION 2024; 5:zqae018. [PMID: 38711930 PMCID: PMC11070877 DOI: 10.1093/function/zqae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024] Open
Affiliation(s)
- Sergej Pirkmajer
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Alexander V Chibalin
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Integrative Physiology, Stockholm 17177, Sweden
- National Research Tomsk State University, Tomsk 634050, Russia
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2
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Saeki N, Yamamoto C, Eguchi Y, Sekito T, Shigenobu S, Yoshimura M, Yashiroda Y, Boone C, Moriya H. Overexpression profiling reveals cellular requirements in the context of genetic backgrounds and environments. PLoS Genet 2023; 19:e1010732. [PMID: 37115757 PMCID: PMC10171610 DOI: 10.1371/journal.pgen.1010732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/10/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Overexpression can help life adapt to stressful environments, making an examination of overexpressed genes valuable for understanding stress tolerance mechanisms. However, a systematic study of genes whose overexpression is functionally adaptive (GOFAs) under stress has yet to be conducted. We developed a new overexpression profiling method and systematically identified GOFAs in Saccharomyces cerevisiae under stress (heat, salt, and oxidative). Our results show that adaptive overexpression compensates for deficiencies and increases fitness under stress, like calcium under salt stress. We also investigated the impact of different genetic backgrounds on GOFAs, which varied among three S. cerevisiae strains reflecting differing calcium and potassium requirements for salt stress tolerance. Our study of a knockout collection also suggested that calcium prevents mitochondrial outbursts under salt stress. Mitochondria-enhancing GOFAs were only adaptive when adequate calcium was available and non-adaptive when calcium was deficient, supporting this idea. Our findings indicate that adaptive overexpression meets the cell's needs for maximizing the organism's adaptive capacity in the given environment and genetic context.
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Affiliation(s)
- Nozomu Saeki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Chie Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yuichi Eguchi
- Biomedical Business Center, RICOH Futures BU, Kanagawa, Japan
| | - Takayuki Sekito
- Graduate School of Agriculture, Ehime University, Matsuyama, Japan
| | | | - Mami Yoshimura
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Japan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hisao Moriya
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan
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3
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Camponeschi I, Montanari A, Mazzoni C, Bianchi MM. Light Stress in Yeasts: Signaling and Responses in Creatures of the Night. Int J Mol Sci 2023; 24:ijms24086929. [PMID: 37108091 PMCID: PMC10139380 DOI: 10.3390/ijms24086929] [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: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Living organisms on the surface biosphere are periodically yet consistently exposed to light. The adaptive or protective evolution caused by this source of energy has led to the biological systems present in a large variety of organisms, including fungi. Among fungi, yeasts have developed essential protective responses against the deleterious effects of light. Stress generated by light exposure is propagated through the synthesis of hydrogen peroxide and mediated by regulatory factors that are also involved in the response to other stressors. These have included Msn2/4, Crz1, Yap1, and Mga2, thus suggesting that light stress is a common factor in the yeast environmental response.
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Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michele Maria Bianchi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
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4
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The Trisubstituted Isoxazole MMV688766 Exerts Broad-Spectrum Activity against Drug-Resistant Fungal Pathogens through Inhibition of Lipid Homeostasis. mBio 2022; 13:e0273022. [PMID: 36300931 PMCID: PMC9765174 DOI: 10.1128/mbio.02730-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida species are among the most prevalent causes of systemic fungal infection, posing a growing threat to public health. While Candida albicans is the most common etiological agent of systemic candidiasis, the frequency of infections caused by non-albicans Candida species is rising. Among these is Candida auris, which has emerged as a particular concern. Since its initial discovery in 2009, it has been identified worldwide and exhibits resistance to all three principal antifungal classes. Here, we endeavored to identify compounds with novel bioactivity against C. auris from the Medicines for Malaria Venture's Pathogen Box library. Of the five hits identified, the trisubstituted isoxazole MMV688766 emerged as the only compound displaying potent fungicidal activity against C. auris, as well as other evolutionarily divergent fungal pathogens. Chemogenomic profiling, as well as subsequent metabolomic and phenotypic analyses, revealed that MMV688766 disrupts cellular lipid homeostasis, driving a decrease in levels of early sphingolipid intermediates and fatty acids and a concomitant increase in lysophospholipids. Experimental evolution to further probe MMV688766's mode of action in the model fungus Saccharomyces cerevisiae revealed that loss of function of the transcriptional regulator HAL9 confers resistance to MMV688766, in part through the upregulation of the lipid-binding chaperone HSP12, a response that appears to assist in tolerating MMV688766-induced stress. The novel mode of action we have uncovered for MMV688766 against drug-resistant fungal pathogens highlights the broad utility of targeting lipid homeostasis to disrupt fungal growth and how screening structurally-diverse chemical libraries can provide new insights into resistance-conferring stress responses of fungi. IMPORTANCE As widespread antimicrobial resistance threatens to propel the world into a postantibiotic era, there is a pressing need to identify mechanistically distinct antimicrobial agents. This is of particular concern when considering the limited arsenal of drugs available to treat fungal infections, coupled with the emergence of highly drug-resistant fungal pathogens, including Candida auris. In this work, we demonstrate that existing libraries of drug-like chemical matter can be rich resources for antifungal molecular scaffolds. We discovered that the small molecule MMV688766, from the Pathogen Box library, displays previously undescribed broad-spectrum fungicidal activity through perturbation of lipid homeostasis. Characterization of the mode of action of MMV688766 provided new insight into the protective mechanisms fungi use to cope with the disruption of lipid homeostasis. Our findings highlight that elucidating the genetic circuitry required to survive in the presence of cellular stress offers powerful insights into the biological pathways that govern this important phenotype.
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5
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Romero AM, Maciaszczyk-Dziubinska E, Mombeinipour M, Lorentzon E, Aspholm E, Wysocki R, Tamás MJ. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6551893. [PMID: 35323907 PMCID: PMC9041338 DOI: 10.1093/femsyr/foac018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
In a high-throughput yeast two-hybrid screen of predicted coiled-coil motif interactions in the Saccharomyces cerevisiae proteome, the protein Etp1 was found to interact with the yeast AP-1-like transcription factors Yap8, Yap1 and Yap6. Yap8 plays a crucial role during arsenic stress since it regulates expression of the resistance genes ACR2 and ACR3. The function of Etp1 is not well understood but the protein has been implicated in transcription and protein turnover during ethanol stress, and the etp1∆ mutant is sensitive to ethanol. In this current study, we investigated whether Etp1 is implicated in Yap8-dependent functions. We show that Etp1 is required for optimal growth in the presence of trivalent arsenite and for optimal expression of the arsenite export protein encoded by ACR3. Since Yap8 is the only known transcription factor that regulates ACR3 expression, we investigated whether Etp1 regulates Yap8. Yap8 ubiquitination, stability, nuclear localization and ACR3 promoter association were unaffected in etp1∆ cells, indicating that Etp1 affects ACR3 expression independently of Yap8. Thus, Etp1 impacts gene expression under arsenic and other stress conditions but the mechanistic details remain to be elucidated.
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Affiliation(s)
| | | | - Mandana Mombeinipour
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emma Lorentzon
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emelie Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Robert Wysocki
- Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Markus J Tamás
- Corresponding author: Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, S-405 30 Göteborg, Sweden. Tel: +46-31-786-2548; E-mail:
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6
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Menon AM, Dakal TC. Genomic scanning of the promoter sequence in osmo/halo-tolerance related QTLs in Zygosaccharomyces rouxii. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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7
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Stojiljkovic M, Foulquié-Moreno MR, Thevelein JM. Polygenic analysis of very high acetic acid tolerance in the yeast Saccharomyces cerevisiae reveals a complex genetic background and several new causative alleles. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:126. [PMID: 32695222 PMCID: PMC7364526 DOI: 10.1186/s13068-020-01761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND High acetic acid tolerance is of major importance in industrial yeast strains used for second-generation bioethanol production, because of the high acetic acid content of lignocellulose hydrolysates. It is also important in first-generation starch hydrolysates and in sourdoughs containing significant acetic acid levels. We have previously identified snf4 E269* as a causative allele in strain MS164 obtained after whole-genome (WG) transformation and selection for improved acetic acid tolerance. RESULTS We have now performed polygenic analysis with the same WG transformant MS164 to identify novel causative alleles interacting with snf4 E269* to further enhance acetic acid tolerance, from a range of 0.8-1.2% acetic acid at pH 4.7, to previously unmatched levels for Saccharomyces cerevisiae. For that purpose, we crossed the WG transformant with strain 16D, a previously identified strain displaying very high acetic acid tolerance. Quantitative trait locus (QTL) mapping with pooled-segregant whole-genome sequence analysis identified four major and two minor QTLs. In addition to confirmation of snf4 E269* in QTL1, we identified six other genes linked to very high acetic acid tolerance, TRT2, MET4, IRA2 and RTG1 and a combination of MSH2 and HAL9, some of which have never been connected previously to acetic acid tolerance. Several of these genes appear to be wild-type alleles that complement defective alleles present in the other parent strain. CONCLUSIONS The presence of several novel causative genes highlights the distinct genetic basis and the strong genetic background dependency of very high acetic acid tolerance. Our results suggest that elimination of inferior mutant alleles might be equally important for reaching very high acetic acid tolerance as introduction of rare superior alleles. The superior alleles of MET4 and RTG1 might be useful for further improvement of acetic acid tolerance in specific industrial yeast strains.
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Affiliation(s)
- Marija Stojiljkovic
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - María R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
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8
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Nguéa P A, Robertson J, Herrera MC, Chymkowitch P, Enserink JM. Desumoylation of RNA polymerase III lies at the core of the Sumo stress response in yeast. J Biol Chem 2019; 294:18784-18795. [PMID: 31676685 DOI: 10.1074/jbc.ra119.009721] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/30/2019] [Indexed: 12/14/2022] Open
Abstract
Post-translational modification by small ubiquitin-like modifier (Sumo) regulates many cellular processes, including the adaptive response to various types of stress, referred to as the Sumo stress response (SSR). However, it remains unclear whether the SSR involves a common set of core proteins regardless of the type of stress or whether each particular type of stress induces a stress-specific SSR that targets a unique, largely nonoverlapping set of Sumo substrates. In this study, we used MS and a Gene Ontology approach to identify differentially sumoylated proteins during heat stress, hyperosmotic stress, oxidative stress, nitrogen starvation, and DNA alkylation in Saccharomyces cerevisiae cells. Our results indicate that each stress triggers a specific SSR signature centered on proteins involved in transcription, translation, and chromatin regulation. Strikingly, whereas the various stress-specific SSRs were largely nonoverlapping, all types of stress tested here resulted in desumoylation of subunits of RNA polymerase III, which correlated with a decrease in tRNA synthesis. We conclude that desumoylation and subsequent inhibition of RNA polymerase III constitutes the core of all stress-specific SSRs in yeast.
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Affiliation(s)
- Aurélie Nguéa P
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Joseph Robertson
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway
| | - Maria Carmen Herrera
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Pierre Chymkowitch
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0371 Oslo, Norway; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway.
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9
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Gier S, Simon M, Nordström K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F. Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1. Front Microbiol 2019; 10:1102. [PMID: 31156606 PMCID: PMC6531845 DOI: 10.3389/fmicb.2019.01102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/30/2019] [Indexed: 11/29/2022] Open
Abstract
The K1 A/B toxin secreted by virus-infected Saccharomyces cerevisiae strains kills sensitive cells via disturbance of cytoplasmic membrane functions. Despite decades of research, the mechanisms underlying K1 toxicity and immunity have not been elucidated yet. In a novel approach, this study aimed to characterize transcriptome changes in K1-treated sensitive yeast cells in a time-dependent manner. Global transcriptional profiling revealed substantial cellular adaptations in target cells resulting in 1,189 differentially expressed genes in total. Killer toxin K1 induced oxidative, cell wall and hyperosmotic stress responses as well as rapid down-regulation of transcription and translation. Essential pathways regulating energy metabolism were also significantly affected by the toxin. Remarkably, a futile cycle of the osmolytes trehalose and glycogen was identified probably representing a critical feature of K1 intoxication. In silico analysis suggested several transcription factors involved in toxin-triggered signal transduction. The identified transcriptome changes provide valuable hints to illuminate the still unknown molecular events leading to K1 toxicity and immunity implicating an evolutionarily conserved response at least initially counteracting ionophoric toxin action.
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Affiliation(s)
- Stefanie Gier
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Martin Simon
- Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, Wuppertal, Germany.,Molecular Cell Dynamics, Saarland University, Saarbrücken, Germany
| | - Karl Nordström
- Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany.,Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Salem Khalifa
- Cluster of Excellence "Multimodal Computing and Interaction", Max Planck Institute for Informatics, Saarland University, Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence "Multimodal Computing and Interaction", Max Planck Institute for Informatics, Saarland University, Saarbrücken, Germany
| | - Manfred J Schmitt
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Frank Breinig
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
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10
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Locascio A, Andrés-Colás N, Mulet JM, Yenush L. Saccharomyces cerevisiae as a Tool to Investigate Plant Potassium and Sodium Transporters. Int J Mol Sci 2019; 20:E2133. [PMID: 31052176 PMCID: PMC6539216 DOI: 10.3390/ijms20092133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Sodium and potassium are two alkali cations abundant in the biosphere. Potassium is essential for plants and its concentration must be maintained at approximately 150 mM in the plant cell cytoplasm including under circumstances where its concentration is much lower in soil. On the other hand, sodium must be extruded from the plant or accumulated either in the vacuole or in specific plant structures. Maintaining a high intracellular K+/Na+ ratio under adverse environmental conditions or in the presence of salt is essential to maintain cellular homeostasis and to avoid toxicity. The baker's yeast, Saccharomyces cerevisiae, has been used to identify and characterize participants in potassium and sodium homeostasis in plants for many years. Its utility resides in the fact that the electric gradient across the membrane and the vacuoles is similar to plants. Most plant proteins can be expressed in yeast and are functional in this unicellular model system, which allows for productive structure-function studies for ion transporting proteins. Moreover, yeast can also be used as a high-throughput platform for the identification of genes that confer stress tolerance and for the study of protein-protein interactions. In this review, we summarize advances regarding potassium and sodium transport that have been discovered using the yeast model system, the state-of-the-art of the available techniques and the future directions and opportunities in this field.
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Affiliation(s)
- Antonella Locascio
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain.
| | - Nuria Andrés-Colás
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain.
| | - José Miguel Mulet
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain.
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain.
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11
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Alonso-Del-Real J, Pérez-Torrado R, Querol A, Barrio E. Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization. Environ Microbiol 2019; 21:1627-1644. [PMID: 30672093 DOI: 10.1111/1462-2920.14536] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 01/01/2023]
Abstract
Grape must is a sugar-rich habitat for a complex microbiota which is replaced by Saccharomyces cerevisiae strains during the first fermentation stages. Interest on yeast competitive interactions has recently been propelled due to the use of alternative yeasts in the wine industry to respond to new market demands. The main issue resides in the persistence of these yeasts due to the specific competitive activity of S. cerevisiae. To gather deeper knowledge of the molecular mechanisms involved, we performed a comparative transcriptomic analysis during fermentation carried out by a wine S. cerevisiae strain and a strain representative of the cryophilic S. kudriavzevii, which exhibits high genetic and physiological similarities to S. cerevisiae, but also differences of biotechnological interest. In this study, we report that transcriptomic response to the presence of a competitor is stronger in S. cerevisiae than in S. kudriavzevii. Our results demonstrate that a wine S. cerevisiae industrial strain accelerates nutrient uptake and utilization to outcompete the co-inoculated yeast, and that this process requires cell-to-cell contact to occur. Finally, we propose that this competitive phenotype evolved recently, during the adaptation of S. cerevisiae to man-manipulated fermentative environments, since a non-wine S. cerevisiae strain, isolated from a North American oak, showed a remarkable low response to competition.
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Affiliation(s)
- Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de los Alimentos (IATA)-CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, València, Spain
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12
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Wu G, Xu Z, Jönsson LJ. Profiling of Saccharomyces cerevisiae transcription factors for engineering the resistance of yeast to lignocellulose-derived inhibitors in biomass conversion. Microb Cell Fact 2017; 16:199. [PMID: 29137634 PMCID: PMC5686817 DOI: 10.1186/s12934-017-0811-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/04/2017] [Indexed: 11/24/2022] Open
Abstract
Background Yeast transcription factors (TFs) involved in the regulation of multidrug resistance (MDR) were investigated in experiments with deletion mutants, transformants overexpressing synthetic genes encoding TFs, and toxic concentrations of lignocellulose-derived substances added to cultures as complex mixtures or as specific compounds, viz. coniferyl aldehyde, 5-hydroxymethylfurfural, and furfural. Results In the presence of complex mixtures of toxic substances from spruce wood, transformants overexpressing YAP1 and STB5, TFs involved in oxidative stress response, exhibited enhanced relative growth rates amounting to 4.589 ± 0.261 and 1.455 ± 0.185, respectively. Other TFs identified as important for resistance included DAL81, GZF3, LEU3, PUT3, and WAR1. Potential overlapping functions of YAP1 and STB5 were investigated in experiments with permutations of deletions and overexpression of the two genes. YAP1 complemented STB5 with respect to resistance to 5-hydroxymethylfurfural, but had a distinct role with regard to resistance to coniferyl aldehyde as deletion of YAP1 rendered the cell incapable of resisting coniferyl aldehyde even if STB5 was overexpressed. Conclusions We have investigated 30 deletion mutants and eight transformants overexpressing MDR transcription factors with regard to the roles the transcription factors play in the resistance to toxic concentrations of lignocellulose-derived substances. This work provides an overview of the involvement of thirty transcription factors in the resistance to lignocellulose-derived substances, shows distinct and complementary roles played by YAP1 and STB5, and offers directions for the engineering of robust yeast strains for fermentation processes based on lignocellulosic feedstocks.![]() Electronic supplementary material The online version of this article (10.1186/s12934-017-0811-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guochao Wu
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.
| | - Zixiang Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
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13
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Crz1p Regulates pH Homeostasis in Candida glabrata by Altering Membrane Lipid Composition. Appl Environ Microbiol 2016; 82:6920-6929. [PMID: 27663025 DOI: 10.1128/aem.02186-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022] Open
Abstract
The asexual facultative aerobic haploid yeast Candida glabrata is widely used in the industrial production of various organic acids. To elucidate the physiological function of the C. glabrata transcription factor Crz1p (CgCrz1p) and its role in tolerance to acid stress, we deleted or overexpressed the corresponding gene, CgCRZ1 Deletion of CgCRZ1 resulted in a 60% decrease in the dry weight of cells (DCW) and a 50% drop in cell viability compared with those of the wild type at pH 2.0. Expression of lipid metabolism-associated genes was also significantly downregulated. Consequently, the proportion of C18:1 fatty acids, the ratio of unsaturated to saturated fatty acids, and the ergosterol content decreased by 30%, 46%, and 30%, respectively. Additionally, membrane integrity, fluidity, and H+-ATPase activity were reduced by 45%, 9%, and 50%, respectively. In contrast, overexpression of CgCrz1p increased C18:1 and ergosterol contents by 16% and 40%, respectively. Overexpression also enhanced membrane integrity, fluidity, and H+-ATPase activity by 31%, 6%, and 20%, respectively. Moreover, in the absence of pH buffering, the DCW and pyruvate titers increased by 48% and 60%, respectively, compared to that of the wild type. Together, these results suggest that CgCrz1p regulates tolerance to acidic conditions by altering membrane lipid composition in C. glabrataIMPORTANCE This study provides insight into the metabolism of Candida glabrata under acidic conditions, such as those encountered during the industrial production of organic acids. We found that overexpression of the transcription factor CgCrz1p improved viability, biomass, and pyruvate yields at a low pH. Analysis of plasma membrane lipid composition indicated that CgCrz1p might play an important role in its integrity and fluidity and that it enhanced the pumping of protons in acidic environments. We propose that altering the structure of the cell membrane may provide a successful strategy for increasing C. glabrata productivity at a low pH.
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Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress. BMC Genomics 2016; 17:662. [PMID: 27544903 PMCID: PMC4992276 DOI: 10.1186/s12864-016-3006-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
Background Exposure of the budding Saccharomyces cerevisiae to an alkaline environment produces a robust transcriptional response involving hundreds of genes. Part of this response is triggered by an almost immediate burst of calcium that activates the Ser/Thr protein phosphatase calcineurin. Activated calcineurin dephosphorylates the transcription factor (TF) Crz1, which moves to the nucleus and binds to calcineurin/Crz1 responsive gene promoters. In this work we present a genome-wide study of the binding of Crz1 to gene promoters in response to high pH stress. Results Environmental alkalinization promoted a time-dependent recruitment of Crz1 to 152 intergenic regions, the vast majority between 1 and 5 min upon stress onset. Positional evaluation of the genomic coordinates combined with existing transcriptional studies allowed identifying 140 genes likely responsive to Crz1 regulation. Gene Ontology analysis confirmed the relevant impact of calcineurin/Crz1 on a set of genes involved in glucose utilization, and uncovered novel targets, such as genes responsible for trehalose metabolism. We also identified over a dozen of genes encoding TFs that are likely under the control of Crz1, suggesting a possible mechanism for amplification of the signal at the transcription level. Further analysis of the binding sites allowed refining the consensus sequence for Crz1 binding to gene promoters and the effect of chromatin accessibility in the timing of Crz1 recruitment to promoters. Conclusions The present work defines at the genomic-wide level the kinetics of binding of Crz1 to gene promoters in response to alkaline stress, confirms diverse previously known Crz1 targets and identifies many putative novel ones. Because of the relevance of calcineurin/Crz1 in signaling diverse stress conditions, our data will contribute to understand the transcriptional response in other circumstances that also involve calcium signaling, such as exposition to sexual pheromones or saline stress. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3006-6) contains supplementary material, which is available to authorized users.
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Petrezsélyová S, López-Malo M, Canadell D, Roque A, Serra-Cardona A, Marqués MC, Vilaprinyó E, Alves R, Yenush L, Ariño J. Regulation of the Na+/K+-ATPase Ena1 Expression by Calcineurin/Crz1 under High pH Stress: A Quantitative Study. PLoS One 2016; 11:e0158424. [PMID: 27362362 PMCID: PMC4928930 DOI: 10.1371/journal.pone.0158424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/15/2016] [Indexed: 11/18/2022] Open
Abstract
Regulated expression of the Ena1 Na+-ATPase is a crucial event for adaptation to high salt and/or alkaline pH stress in the budding yeast Saccharomyces cerevisiae. ENA1 expression is under the control of diverse signaling pathways, including that mediated by the calcium-regulatable protein phosphatase calcineurin and its downstream transcription factor Crz1. We present here a quantitative study of the expression of Ena1 in response to alkalinization of the environment and we analyze the contribution of Crz1 to this response. Experimental data and mathematical models substantiate the existence of two stress-responsive Crz1-binding sites in the ENA1 promoter and estimate that the contribution of Crz1 to the early response of the ENA1 promoter is about 60%. The models suggest the existence of a second input with similar kinetics, which would be likely mediated by high pH-induced activation of the Snf1 kinase.
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Affiliation(s)
- Silvia Petrezsélyová
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - María López-Malo
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - David Canadell
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Alicia Roque
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Albert Serra-Cardona
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - M. Carmen Marqués
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, 46022, Spain
| | - Ester Vilaprinyó
- IRB Lleida, Universitat de Lleida, Lleida 25198, Spain
- Universitat de Lleida, Lleida 25198, Spain
| | - Rui Alves
- IRB Lleida, Universitat de Lleida, Lleida 25198, Spain
- Universitat de Lleida, Lleida 25198, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, 46022, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
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Tatjer L, González A, Serra-Cardona A, Barceló A, Casamayor A, Ariño J. The Saccharomyces cerevisiae Ptc1 protein phosphatase attenuates G2-M cell cycle blockage caused by activation of the cell wall integrity pathway. Mol Microbiol 2016; 101:671-87. [PMID: 27169355 DOI: 10.1111/mmi.13416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 01/24/2023]
Abstract
Lack of the yeast Ptc1 Ser/Thr protein phosphatase results in numerous phenotypic defects. A parallel search for high-copy number suppressors of three of these phenotypes (sensitivity to Calcofluor White, rapamycin and alkaline pH), allowed the isolation of 25 suppressor genes, which could be assigned to three main functional categories: maintenance of cell wall integrity (CWI), vacuolar function and protein sorting, and cell cycle regulation. The characterization of these genetic interactions strengthens the relevant role of Ptc1 in downregulating the Slt2-mediated CWI pathway. We show that under stress conditions activating the CWI pathway the ptc1 mutant displays hyperphosphorylated Cdc28 kinase and that these cells accumulate with duplicated DNA content, indicative of a G2-M arrest. Clb2-associated Cdc28 activity was also reduced in ptc1 cells. These alterations are attenuated by mutation of the MKK1 gene, encoding a MAP kinase kinase upstream Slt2. Therefore, our data show that Ptc1 is required for proper G2-M cell cycle transition after activation of the CWI pathway.
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Affiliation(s)
- Laura Tatjer
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Asier González
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Albert Serra-Cardona
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Anna Barceló
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
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Merhej J, Thiebaut A, Blugeon C, Pouch J, Ali Chaouche MEA, Camadro JM, Le Crom S, Lelandais G, Devaux F. A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata. Front Microbiol 2016; 7:645. [PMID: 27242683 PMCID: PMC4860858 DOI: 10.3389/fmicb.2016.00645] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/18/2016] [Indexed: 01/15/2023] Open
Abstract
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption, and iron metabolism.
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Affiliation(s)
- Jawad Merhej
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Antonin Thiebaut
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Corinne Blugeon
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Juliette Pouch
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Mohammed El Amine Ali Chaouche
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Jean-Michel Camadro
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Stéphane Le Crom
- Évolution, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7138, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Gaëlle Lelandais
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Frédéric Devaux
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
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Satomura A, Miura N, Kuroda K, Ueda M. Reconstruction of thermotolerant yeast by one-point mutation identified through whole-genome analyses of adaptively-evolved strains. Sci Rep 2016; 6:23157. [PMID: 26984760 DOI: 10.1038/srep23157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/01/2016] [Indexed: 01/26/2023] Open
Abstract
Saccharomyces cerevisiae is used as a host strain in bioproduction, because of its rapid growth, ease of genetic manipulation, and high reducing capacity. However, the heat produced during the fermentation processes inhibits the biological activities and growth of the yeast cells. We performed whole-genome sequencing of 19 intermediate strains previously obtained during adaptation experiments under heat stress; 49 mutations were found in the adaptation steps. Phylogenetic tree revealed at least five events in which these strains had acquired mutations in the CDC25 gene. Reconstructed CDC25 point mutants based on a parental strain had acquired thermotolerance without any growth defects. These mutations led to the downregulation of the cAMP-dependent protein kinase (PKA) signaling pathway, which controls a variety of processes such as cell-cycle progression and stress tolerance. The one-point mutations in CDC25 were involved in the global transcriptional regulation through the cAMP/PKA pathway. Additionally, the mutations enabled efficient ethanol fermentation at 39 °C, suggesting that the one-point mutations in CDC25 may contribute to bioproduction.
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Affiliation(s)
- Atsushi Satomura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Natsuko Miura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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Wu J, Chen X, Cai L, Tang L, Liu L. Transcription factors Asg1p and Hal9p regulate pH homeostasis in Candida glabrata. Front Microbiol 2015; 6:843. [PMID: 26347728 PMCID: PMC4539521 DOI: 10.3389/fmicb.2015.00843] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/03/2015] [Indexed: 12/27/2022] Open
Abstract
Candida glabrata is an important microorganism used in commercial fermentation to produce pyruvate, but very little is known about its mechanisms for surviving acid stress in culture. In this study, it was shown that transcription factors Asg1p and Hal9p play essential roles in C. glabrata in the tolerance of acid stress, as the deletion of CgASG1 or CgHAL9 resulted in the inability to survive in an acidic environment. Cgasg1Δ and Cghal9Δ mutant strains are unable to maintain pH homeostasis, as evidenced by a decrease in intracellular pH and an increase in reactive oxygen species production, which results in metabolic disorders. The results showed that intracellular acidification was partly due to the diminished activity of the plasma membrane proton pump, CgPma1p. In addition, transcriptome sequencing revealed that Cgasg1Δ and Cghal9Δ mutant strains displayed a variety of changes in gene expression under acidic conditions, including genes in the MAPK signaling pathway, plasma membrane, or cell wall organization, trehalose accumulation, and the RIM101 signaling pathway. Lastly, quantitative reverse-transcribed PCR and cellular localization showed that CgAsg1p and CgHal9p played independent roles in response to acid stress.
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Affiliation(s)
- Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University Wuxi, China ; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University Wuxi, China ; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University Wuxi, China
| | - Lijun Cai
- State Key Laboratory of Food Science and Technology, Jiangnan University Wuxi, China ; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University Wuxi, China
| | - Lei Tang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University Wuxi, China ; The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University Wuxi, China
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Serra-Cardona A, Canadell D, Ariño J. Coordinate responses to alkaline pH stress in budding yeast. MICROBIAL CELL 2015; 2:182-196. [PMID: 28357292 PMCID: PMC5349140 DOI: 10.15698/mic2015.06.205] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alkalinization of the medium represents a stress condition for the budding yeast Saccharomyces cerevisiae to which this organism responds with profound remodeling of gene expression. This is the result of the modulation of a substantial number of signaling pathways whose participation in the alkaline response has been elucidated within the last ten years. These regulatory inputs involve not only the conserved Rim101/PacC pathway, but also the calcium-activated phosphatase calcineurin, the Wsc1-Pkc1-Slt2 MAP kinase, the Snf1 and PKA kinases and oxidative stress-response pathways. The uptake of many nutrients is perturbed by alkalinization of the environment and, consequently, an impact on phosphate, iron/copper and glucose homeostatic mechanisms can also be observed. The analysis of available data highlights cases in which diverse signaling pathways are integrated in the gene promoter to shape the appropriate response pattern. Thus, the expression of different genes sharing the same signaling network can be coordinated, allowing functional coupling of their gene products.
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Affiliation(s)
- Albert Serra-Cardona
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - David Canadell
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
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Son H, Park AR, Lim JY, Lee YW. Fss1 is involved in the regulation of anENA5homologue for sodium and lithium tolerance inFusarium graminearum. Environ Microbiol 2015; 17:2048-63. [DOI: 10.1111/1462-2920.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Hokyoung Son
- Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 Korea
- Center for Fungal Pathogenesis; Seoul National University; Seoul 151-921 Korea
| | - Ae Ran Park
- Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 Korea
- Center for Fungal Pathogenesis; Seoul National University; Seoul 151-921 Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 Korea
- Center for Fungal Pathogenesis; Seoul National University; Seoul 151-921 Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 Korea
- Center for Fungal Pathogenesis; Seoul National University; Seoul 151-921 Korea
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Vicent I, Navarro A, Mulet JM, Sharma S, Serrano R. Uptake of inorganic phosphate is a limiting factor for Saccharomyces cerevisiae during growth at low temperatures. FEMS Yeast Res 2015; 15:fov008. [DOI: 10.1093/femsyr/fov008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 11/14/2022] Open
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Kemmeren P, Sameith K, van de Pasch L, Benschop J, Lenstra T, Margaritis T, O’Duibhir E, Apweiler E, van Wageningen S, Ko C, van Heesch S, Kashani M, Ampatziadis-Michailidis G, Brok M, Brabers N, Miles A, Bouwmeester D, van Hooff S, van Bakel H, Sluiters E, Bakker L, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp M, Holstege F. Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors. Cell 2014; 157:740-52. [DOI: 10.1016/j.cell.2014.02.054] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/30/2013] [Accepted: 02/25/2014] [Indexed: 11/17/2022]
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Abstract
SIGNIFICANCE Postharvest pathogens can start its attack process immediately after spores land on wounded tissue, whereas other pathogens can forcibly breach the unripe fruit cuticle and then remain quiescent for months until fruit ripens and then cause major losses. RECENT ADVANCES Postharvest fungal pathogens activate their development by secreting organic acids or ammonia that acidify or alkalinize the host ambient surroundings. CRITICAL ISSUES These fungal pH modulations of host environment regulate an arsenal of enzymes to increase fungal pathogenicity. This arsenal includes genes and processes that compromise host defenses, contribute to intracellular signaling, produce cell wall-degrading enzymes, regulate specific transporters, induce redox protectant systems, and generate factors needed by the pathogen to effectively cope with the hostile environment found within the host. Further, evidence is accumulating that the secreted molecules (organic acids and ammonia) are multifunctional and together with effect of the ambient pH, they activate virulence factors and simultaneously hijack the plant defense response and induce program cell death to further enhance their necrotrophic attack. FUTURE DIRECTIONS Global studies of the effect of secreted molecules on fruit pathogen interaction, will determine the importance of these molecules on quiescence release and the initiation of fungal colonization leading to fruit and vegetable losses.
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Affiliation(s)
- Noam Alkan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
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Bastajian N, Friesen H, Andrews BJ. Bck2 acts through the MADS box protein Mcm1 to activate cell-cycle-regulated genes in budding yeast. PLoS Genet 2013; 9:e1003507. [PMID: 23675312 PMCID: PMC3649975 DOI: 10.1371/journal.pgen.1003507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 03/27/2013] [Indexed: 11/19/2022] Open
Abstract
The Bck2 protein is a potent genetic regulator of cell-cycle-dependent gene expression in budding yeast. To date, most experiments have focused on assessing a potential role for Bck2 in activation of the G1/S-specific transcription factors SBF (Swi4, Swi6) and MBF (Mbp1, Swi6), yet the mechanism of gene activation by Bck2 has remained obscure. We performed a yeast two-hybrid screen using a truncated version of Bck2 and discovered six novel Bck2-binding partners including Mcm1, an essential protein that binds to and activates M/G1 promoters through Early Cell cycle Box (ECB) elements as well as to G2/M promoters. At M/G1 promoters Mcm1 is inhibited by association with two repressors, Yox1 or Yhp1, and gene activation ensues once repression is relieved by an unknown activating signal. Here, we show that Bck2 interacts physically with Mcm1 to activate genes during G1 phase. We used chromatin immunoprecipitation (ChIP) experiments to show that Bck2 localizes to the promoters of M/G1-specific genes, in a manner dependent on functional ECB elements, as well as to the promoters of G1/S and G2/M genes. The Bck2-Mcm1 interaction requires valine 69 on Mcm1, a residue known to be required for interaction with Yox1. Overexpression of BCK2 decreases Yox1 localization to the early G1-specific CLN3 promoter and rescues the lethality caused by overexpression of YOX1. Our data suggest that Yox1 and Bck2 may compete for access to the Mcm1-ECB scaffold to ensure appropriate activation of the initial suite of genes required for cell cycle commitment.
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Affiliation(s)
- Nazareth Bastajian
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Helena Friesen
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brenda J. Andrews
- The Donnelly Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Ríos G, Cabedo M, Rull B, Yenush L, Serrano R, Mulet JM. Role of the yeast multidrug transporter Qdr2 in cation homeostasis and the oxidative stress response. FEMS Yeast Res 2012; 13:97-106. [PMID: 23106982 DOI: 10.1111/1567-1364.12013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/05/2012] [Accepted: 10/21/2012] [Indexed: 11/30/2022] Open
Abstract
We have identified QDR2 in a screening for genes able to confer tolerance to sodium and/or lithium stress upon overexpression. Qdr2 is a multidrug transporter of the major facilitator superfamily, originally described for its ability to transport the antimalarial drug quinidine and the herbicide barban. To identify its physiological substrate, we have screened for phenotypes dependent on QDR2 and found that Qdr2 is able to transport monovalent and divalent cations with poor selectivity, as shown by growth tests and the determination of internal cation content. Moreover, strains overexpressing or lacking QDR2 also exhibit phenotypes when reactive oxygen species- producing agents, such as hydrogen peroxide or menadione were added to the growth medium. We have also found that the presence of copper and hydrogen peroxide repress the expression of QDR2. In addition, the copper uptake of a qdr2 mutant strain is similar to a wild type, but the extrusion is clearly impaired. Based on our results, we propose that free divalent copper is the main physiological substrate of Qdr2. As copper is a substrate for several redox reactions that occur within the cytoplasm, its function in copper homeostasis explains its role in the oxidative stress response.
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Affiliation(s)
- Gabino Ríos
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-CSIC, Valencia, Spain
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Chen G, Lu D, Chiang H, Leszczynski D, Xu Z. Using model organism Saccharomyces cerevisiae to evaluate the effects of ELF-MF and RF-EMF exposure on global gene expression. Bioelectromagnetics 2012; 33:550-60. [DOI: 10.1002/bem.21724] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 03/07/2012] [Indexed: 11/07/2022]
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Antifungal resistance and new strategies to control fungal infections. Int J Microbiol 2011; 2012:713687. [PMID: 22187560 PMCID: PMC3236459 DOI: 10.1155/2012/713687] [Citation(s) in RCA: 260] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/06/2011] [Indexed: 11/28/2022] Open
Abstract
Despite improvement of antifungal therapies over the last 30 years, the phenomenon of antifungal resistance is still of major concern in clinical practice. In the last 10 years the molecular mechanisms underlying this phenomenon were extensively unraveled. In this paper, after a brief overview of currently available antifungals, molecular mechanisms of antifungal resistance will be detailed. It appears that major mechanisms of resistance are essential due to the deregulation of antifungal resistance effector genes. This deregulation is a consequence of point mutations occurring in transcriptional regulators of these effector genes. Resistance can also follow the emergence of point mutations directly in the genes coding antifungal targets. In addition we further describe new strategies currently undertaken to discover alternative therapy targets and antifungals. Identification of new antifungals is essentially achieved by the screening of natural or synthetic chemical compound collections. Discovery of new putative antifungal targets is performed through genome-wide approaches for a better understanding of the human pathogenic fungi biology.
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Morin N, Cescut J, Beopoulos A, Lelandais G, Le Berre V, Uribelarrea JL, Molina-Jouve C, Nicaud JM. Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica. PLoS One 2011; 6:e27966. [PMID: 22132183 PMCID: PMC3222671 DOI: 10.1371/journal.pone.0027966] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/28/2011] [Indexed: 12/12/2022] Open
Abstract
We previously developed a fermentation protocol for lipid accumulation in the oleaginous yeast Y. lipolytica. This process was used to perform transcriptomic time-course analyses to explore gene expression in Y. lipolytica during the transition from biomass production to lipid accumulation. In this experiment, a biomass concentration of 54.6 g(CDW)/l, with 0.18 g/g(CDW) lipid was obtained in ca. 32 h, with low citric acid production. A transcriptomic profiling was performed on 11 samples throughout the fermentation. Through statistical analyses, 569 genes were highlighted as differentially expressed at one point during the time course of the experiment. These genes were classified into 9 clusters, according to their expression profiles. The combination of macroscopic and transcriptomic profiles highlighted 4 major steps in the culture: (i) a growth phase, (ii) a transition phase, (iii) an early lipid accumulation phase, characterized by an increase in nitrogen metabolism, together with strong repression of protein production and activity; (iv) a late lipid accumulation phase, characterized by the rerouting of carbon fluxes within cells. This study explores the potential of Y. lipolytica as an alternative oil producer, by identifying, at the transcriptomic level, the genes potentially involved in the metabolism of oleaginous species.
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Affiliation(s)
| | - Julien Cescut
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | | | - Gaëlle Lelandais
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR-S 665 - Université Paris 7, INTS, Paris, France
| | - Veronique Le Berre
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
- Plateforme Biopuces de la Génopole de Toulouse Midi Pyrénées, INSA/DGBA 135, Toulouse, France
| | - Jean-Louis Uribelarrea
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Carole Molina-Jouve
- Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Jean-Marc Nicaud
- INRA, UMR1319 Micalis, Jouy-en-Josas, France
- CNRS, Micalis, Jouy-en-Josas, France
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Bozdag GO, Uluisik I, Gulculer GS, Karakaya HC, Koc A. Roles of ATR1 paralogs YMR279c and YOR378w in boron stress tolerance. Biochem Biophys Res Commun 2011; 409:748-51. [DOI: 10.1016/j.bbrc.2011.05.080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 05/15/2011] [Indexed: 10/18/2022]
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Saint-Auret G, Danan JL, Hiron M, Blache C, Sulpice E, Tendil S, Daveau M, Gidrol X, Salier JP. Characterization of the transcriptional signature of C/EBPbeta isoforms (LAP/LIP) in Hep3B cells: implication of LIP in pro-survival functions. J Hepatol 2011; 54:1185-94. [PMID: 21145827 DOI: 10.1016/j.jhep.2010.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 09/24/2010] [Accepted: 09/27/2010] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS C/EBPbeta is an important mediator of several cellular processes, such as differentiation, proliferation, and survival of hepatic cells. However, a complete catalog of the targets of C/EBPbeta or the mechanism by which this transcription factor regulates certain liver-dependent pathways has not been clearly determined. Two major natural isoforms of this transcription factor exist: the liver-enriched activating protein (LAP) and the liver-enriched inhibitory protein (LIP), a functional LAP antagonist. In this study, we used the opposing transcriptional effects driven by LAP and LIP to determine the genuine C/EBPbeta molecular signature in the Hep3B human hepatoma cell line. We subsequently investigated the role of each of the LAP and LIP isoforms in drug-induced Hep3B cell death. METHODS We engineered Hep3B cells with regulated LAP or LIP expression using the Tet-off expression system. The genes that showed inverse regulation by LAP and LIP were identified by cDNA array analysis. The cohort of direct-C/EBPbeta-targets was distinguished from indirect-targets by ChIP-on-chip analysis. RESULTS We characterized 676 genes by this approach. Among these genes, 39 are novel direct targets of C/EBPbeta. Eleven of these new direct targets are involved in cell survival, suggesting critical roles for LAP/LIP isoforms in this cellular process. Therefore, we examined the effects of LAP and LIP over-expression on cell survival. We show that LIP promotes survival in staurosporine- or taxol-induced Hep3B cell death. CONCLUSIONS Our study provides new molecular and cellular insights into the role of C/EBPbeta in cells of hepatic origin.
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Diagnosis of Antifungal Drug Resistance Mechanisms in Fungal Pathogens: Transcriptional Gene Regulation. CURRENT FUNGAL INFECTION REPORTS 2011. [DOI: 10.1007/s12281-011-0055-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Shah AN, Cadinu D, Henke RM, Xin X, Dastidar RG, Zhang L. Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance. Physiol Genomics 2011; 43:855-72. [PMID: 21586670 DOI: 10.1152/physiolgenomics.00232.2010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae. Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans.
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Affiliation(s)
- Ajit N Shah
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA
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Hanlon SE, Rizzo JM, Tatomer DC, Lieb JD, Buck MJ. The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. PLoS One 2011; 6:e19060. [PMID: 21552514 PMCID: PMC3084262 DOI: 10.1371/journal.pone.0019060] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/23/2011] [Indexed: 11/19/2022] Open
Abstract
Maintaining the proper expression of the transcriptome during development or in response to a changing environment requires a delicate balance between transcriptional regulators with activating and repressing functions. The budding yeast transcriptional co-repressor Tup1-Ssn6 is a model for studying similar repressor complexes in multicellular eukaryotes. Tup1-Ssn6 does not bind DNA directly, but is directed to individual promoters by one or more DNA-binding proteins, referred to as Tup1 recruiters. This functional architecture allows the Tup1-Ssn6 to modulate the expression of genes required for the response to a variety of cellular stresses. To understand the targeting or the Tup1-Ssn6 complex, we determined the genomic distribution of Tup1 and Ssn6 by ChIP-chip. We found that most loci bound by Tup1-Ssn6 could not be explained by co-occupancy with a known recruiting cofactor and that deletion of individual known Tup1 recruiters did not significantly alter the Tup1 binding profile. These observations suggest that new Tup1 recruiting proteins remain to be discovered and that Tup1 recruitment typically depends on multiple recruiting cofactors. To identify new recruiting proteins, we computationally screened for factors with binding patterns similar to the observed Tup1-Ssn6 genomic distribution. Four top candidates, Cin5, Skn7, Phd1, and Yap6, all known to be associated with stress response gene regulation, were experimentally confirmed to physically interact with Tup1 and/or Ssn6. Incorporating these new recruitment cofactors with previously characterized cofactors now explains the majority of Tup1 targeting across the genome, and expands our understanding of the mechanism by which Tup1-Ssn6 is directed to its targets.
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Affiliation(s)
- Sean E. Hanlon
- Department of Biology, Carolina Center for Genome Sciences and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jason M. Rizzo
- Department of Biochemistry and the Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Deirdre C. Tatomer
- Department of Biology, Carolina Center for Genome Sciences and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jason D. Lieb
- Department of Biology, Carolina Center for Genome Sciences and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (JDL); (MJB)
| | - Michael J. Buck
- Department of Biochemistry and the Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- * E-mail: (JDL); (MJB)
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Dhar R, Sägesser R, Weikert C, Yuan J, Wagner A. Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J Evol Biol 2011; 24:1135-53. [PMID: 21375649 DOI: 10.1111/j.1420-9101.2011.02249.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.
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Affiliation(s)
- R Dhar
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
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Biver S, Portetelle D, Vandenbol M. Multicopy suppression screen in a Saccharomyces cerevisiae strain lacking the Rab GTPase-activating protein Msb3p. Biotechnol Lett 2010; 33:123-9. [PMID: 20872164 DOI: 10.1007/s10529-010-0407-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 08/31/2010] [Indexed: 11/30/2022]
Abstract
The yeast proteins, Msb3p and Msb4p, are two Ypt/Rab-specific GTPase-activating proteins sharing redundant functions in exocytosis, organization of the actin cytoskeleton, and budding site selection. To see if Msb3p might play an additional, specific role, we first tested the sensitivities of msb3 and msb4 mutant strains to different drugs and then screened a genomic library for multicopy suppressors of msb3 sensitivity to CdCl(2) or to the calcium channel blocker diltiazem hydrochloride. Three genes (ADH1, RNT1, and SUI1) were found to suppress the CdCl(2) sensitivity of the msb3 strain and three others (YAP6, ZEO1, and SLM1) its diltiazem-HCl sensitivity. The results suggest a possible involvement of Msb3p in calcineurin-mediated signalling.
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Affiliation(s)
- Sophie Biver
- Unité de Biologie Animale et Microbienne, Gembloux Agro-Bio Tech, Université de Liège, Avenue Maréchal Juin 6, 5030, Gembloux, Belgium.
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Martínez-Montañés F, Pascual-Ahuir A, Proft M. Toward a genomic view of the gene expression program regulated by osmostress in yeast. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:619-27. [PMID: 20726780 DOI: 10.1089/omi.2010.0046] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Osmostress triggers profound adaptive changes in the physiology of the cell with a great impact on gene expression. Saccharomyces cerevisiae has served as an instructive model system to unravel the complexity of the stress response at the transcriptional level. The main signal transduction pathways like the HOG (high osmolarity glycerol) MAP kinase cascade or the protein kinase A pathway regulate multiple specific transcription factors to accomplish large changes in the expression pattern of the genome. Transcription profiling and proteomic studies give us an idea about the impact of osmostress on gene expression and the overall protein composition. Recent genome wide location studies for several transcription factors and signaling kinases involved in the transcriptional stress response shed light on the genomic organization of the osmostress response at the level of the dynamic association of regulators with chromatin. Finally, global surveys of mRNA stability complete our picture of the mechanisms underlying the massive reprogramming of global gene expression, which leads to efficient adaptation to osmotic stress.
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Affiliation(s)
- Fernando Martínez-Montañés
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación, Ingeniero Fausto Elio s/n, Valencia, Spain
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Ariño J. Integrative responses to high pH stress in S. cerevisiae. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:517-23. [PMID: 20726779 DOI: 10.1089/omi.2010.0044] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae grows far better at acidic than at neutral or alkaline pH. Consequently, even a modest alkalinization of the medium represents a stressful situation for this yeast. In the past few years, data generated by a combination of genome-wide techniques has demonstrated that adaptive responses of S. cerevisiae to high pH stress involves extensive gene remodeling as a result of the fast activation of a number of stress-related signaling pathways, such as the Rim101, the Wsc1-Pkc1-Slt2 MAP kinase, and the calcium-activated calcineurin pathways. Alkalinization of the environment also disturbs nutrient homeostasis, as deduced from its impact on iron/copper, phosphate, and glucose uptake/utilization pathways. In this review we will examine these responses, their possible interactions, and the role that they play in tolerance to high pH stress.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular & Institut de Biotecnologia i Biomedicina, Universitat Autónoma de Barcelona, Barcelona, Spain.
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Abstract
The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K(+) and Na(+), is of utmost importance for living cells, since they determine cell volume, intracellular pH, and potential across the plasma membrane, among other important cellular parameters. Yeasts have developed a number of strategies to adapt to large variations in the concentrations of these cations in the environment, basically by controlling transport processes. Plasma membrane high-affinity K(+) transporters allow intracellular accumulation of this cation even when it is scarce in the environment. Exposure to high concentrations of Na(+) can be tolerated due to the existence of an Na(+), K(+)-ATPase and an Na(+), K(+)/H(+)-antiporter, which contribute to the potassium balance as well. Cations can also be sequestered through various antiporters into intracellular organelles, such as the vacuole. Although some uncertainties still persist, the nature of the major structural components responsible for alkali metal cation fluxes across yeast membranes has been defined within the last 20 years. In contrast, the regulatory components and their interactions are, in many cases, still unclear. Conserved signaling pathways (e.g., calcineurin and HOG) are known to participate in the regulation of influx and efflux processes at the plasma membrane level, even though the molecular details are obscure. Similarly, very little is known about the regulation of organellar transport and homeostasis of alkali metal cations. The aim of this review is to provide a comprehensive and up-to-date vision of the mechanisms responsible for alkali metal cation transport and their regulation in the model yeast Saccharomyces cerevisiae and to establish, when possible, comparisons with other yeasts and higher plants.
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Rodrigues-Pousada C, Menezes RA, Pimentel C. The Yap family and its role in stress response. Yeast 2010; 27:245-58. [DOI: 10.1002/yea.1752] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Regulation of Trk-dependent potassium transport by the calcineurin pathway involves the Hal5 kinase. FEBS Lett 2010; 584:2415-20. [DOI: 10.1016/j.febslet.2010.04.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 04/14/2010] [Accepted: 04/16/2010] [Indexed: 11/17/2022]
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Ref2, a regulatory subunit of the yeast protein phosphatase 1, is a novel component of cation homoeostasis. Biochem J 2010; 426:355-64. [DOI: 10.1042/bj20091909] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Maintenance of cation homoeostasis is a key process for any living organism. Specific mutations in Glc7, the essential catalytic subunit of yeast protein phosphatase 1, result in salt and alkaline pH sensitivity, suggesting a role for this protein in cation homoeostasis. We screened a collection of Glc7 regulatory subunit mutants for altered tolerance to diverse cations (sodium, lithium and calcium) and alkaline pH. Among 18 candidates, only deletion of REF2 (RNA end formation 2) yielded increased sensitivity to these conditions, as well as to diverse organic toxic cations. The Ref2F374A mutation, which renders it unable to bind Glc7, did not rescue the salt-related phenotypes of the ref2 strain, suggesting that Ref2 function in cation homoeostasis is mediated by Glc7. The ref2 deletion mutant displays a marked decrease in lithium efflux, which can be explained by the inability of these cells to fully induce the Na+-ATPase ENA1 gene. The effect of lack of Ref2 is additive to that of blockage of the calcineurin pathway and might disrupt multiple mechanisms controlling ENA1 expression. ref2 cells display a striking defect in vacuolar morphogenesis, which probably accounts for the increased calcium levels observed under standard growth conditions and the strong calcium sensitivity of this mutant. Remarkably, the evidence collected indicates that the role of Ref2 in cation homoeostasis may be unrelated to its previously identified function in the formation of mRNA via the APT (for associated with Pta1) complex.
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The TEA transcription factor Tec1 confers promoter-specific gene regulation by Ste12-dependent and -independent mechanisms. EUKARYOTIC CELL 2010; 9:514-31. [PMID: 20118212 DOI: 10.1128/ec.00251-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, the TEA transcription factor Tec1 is known to regulate target genes together with a second transcription factor, Ste12. Tec1-Ste12 complexes can activate transcription through Tec1 binding sites (TCSs), which can be further combined with Ste12 binding sites (PREs) for cooperative DNA binding. However, previous studies have hinted that Tec1 might regulate transcription also without Ste12. Here, we show that in vivo, physiological amounts of Tec1 are sufficient to stimulate TCS-mediated gene expression and transcription of the FLO11 gene in the absence of Ste12. In vitro, Tec1 is able to bind TCS elements with high affinity and specificity without Ste12. Furthermore, Tec1 contains a C-terminal transcriptional activation domain that confers Ste12-independent activation of TCS-regulated gene expression. On a genome-wide scale, we identified 302 Tec1 target genes that constitute two distinct classes. A first class of 254 genes is regulated by Tec1 in a Ste12-dependent manner and is enriched for genes that are bound by Tec1 and Ste12 in vivo. In contrast, a second class of 48 genes can be regulated by Tec1 independently of Ste12 and is enriched for genes that are bound by the stress transcription factors Yap6, Nrg1, Cin5, Skn7, Hsf1, and Msn4. Finally, we find that combinatorial control by Tec1-Ste12 complexes stabilizes Tec1 against degradation. Our study suggests that Tec1 is able to regulate TCS-mediated gene expression by Ste12-dependent and Ste12-independent mechanisms that enable promoter-specific transcriptional control.
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Sanglard D, Coste A, Ferrari S. Antifungal drug resistance mechanisms in fungal pathogens from the perspective of transcriptional gene regulation. FEMS Yeast Res 2009; 9:1029-50. [PMID: 19799636 DOI: 10.1111/j.1567-1364.2009.00578.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fungi are primitive eukaryotes and have adapted to a variety of niches during evolution. Some fungal species may interact with other life forms (plants, insects, mammals), but are considered as pathogens when they cause mild to severe diseases. Chemical control strategies have emerged with the development of several drugs with antifungal activity against pathogenic fungi. Antifungal agents have demonstrated their efficacy by improving patient health in medicine. However, fungi have counteracted antifungal agents in several cases by developing resistance mechanisms. These mechanisms rely on drug resistance genes including multidrug transporters and drug targets. Their regulation is crucial for the development of antifungal drug resistance and therefore transcriptional factors critical for their regulation are being characterized. Recent genome-wide studies have revealed complex regulatory circuits involving these genetic and transcriptional regulators. Here, we review the current understanding of the transcriptional regulation of drug resistance genes from several fungal pathogens including Candida and Aspergillus species.
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Affiliation(s)
- Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital Center, 1011 Lausanne, Switzerland.
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Sollner S, Macheroux P. New roles of flavoproteins in molecular cell biology: An unexpected role for quinone reductases as regulators of proteasomal degradation. FEBS J 2009; 276:4313-24. [DOI: 10.1111/j.1742-4658.2009.07143.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gilbert A, Sangurdekar DP, Srienc F. Rapid strain improvement through optimized evolution in the cytostat. Biotechnol Bioeng 2009; 103:500-12. [DOI: 10.1002/bit.22272] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev 2009; 23:1351-63. [PMID: 19487574 DOI: 10.1101/gad.1781909] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed, and thus the temporal order of events and mechanisms by which this occurs are poorly understood. We globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes. Analysis of Yap4 and Sko1 binding to their target genes revealed multiple temporal classes of binding patterns: (1) constant binding, (2) rapid induction, (3) slow induction, and (4) transient induction. These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7, and Yap6, and found significant coassociation among the different factors at their gene targets. Moreover, the binding of several key factors was correlated with distinct classes of Yap4- and Sko1-binding patterns and with distinct types of genes. Gene expression studies revealed association of Yap4, Sko1, and other transcription factor-binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response.
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Affiliation(s)
- Li Ni
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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Jain D, Roy N, Chattopadhyay D. CaZF, a plant transcription factor functions through and parallel to HOG and calcineurin pathways in Saccharomyces cerevisiae to provide osmotolerance. PLoS One 2009; 4:e5154. [PMID: 19365545 PMCID: PMC2664467 DOI: 10.1371/journal.pone.0005154] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/13/2009] [Indexed: 01/19/2023] Open
Abstract
Salt-sensitive yeast mutants were deployed to characterize a gene encoding a C2H2 zinc finger protein (CaZF) that is differentially expressed in a drought-tolerant variety of chickpea (Cicer arietinum) and provides salinity-tolerance in transgenic tobacco. In Saccharomyces cerevisiae most of the cellular responses to hyper-osmotic stress is regulated by two interconnected pathways involving high osmolarity glycerol mitogen-activated protein kinase (Hog1p) and Calcineurin (CAN), a Ca(2+)/calmodulin-regulated protein phosphatase 2B. In this study, we report that heterologous expression of CaZF provides osmotolerance in S. cerevisiae through Hog1p and Calcineurin dependent as well as independent pathways. CaZF partially suppresses salt-hypersensitive phenotypes of hog1, can and hog1can mutants and in conjunction, stimulates HOG and CAN pathway genes with subsequent accumulation of glycerol in absence of Hog1p and CAN. CaZF directly binds to stress response element (STRE) to activate STRE-containing promoter in yeast. Transactivation and salt tolerance assays of CaZF deletion mutants showed that other than the transactivation domain a C-terminal domain composed of acidic and basic amino acids is also required for its function. Altogether, results from this study suggests that CaZF is a potential plant salt-tolerance determinant and also provide evidence that in budding yeast expression of HOG and CAN pathway genes can be stimulated in absence of their regulatory enzymes to provide osmotolerance.
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Affiliation(s)
- Deepti Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Nilanjan Roy
- National Institute for Pharmaceutical Education and Research, SAS Nagar, Punjab, India
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Shahi P, Moye-Rowley WS. Coordinate control of lipid composition and drug transport activities is required for normal multidrug resistance in fungi. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:852-9. [PMID: 19150512 DOI: 10.1016/j.bbapap.2008.12.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 12/12/2008] [Accepted: 12/15/2008] [Indexed: 10/21/2022]
Abstract
Pathogenic fungi present a special problem in the clinic as the range of drugs that can be used to treat these types of infections is limited. This situation is further complicated by the presence of robust inducible gene networks encoding different proteins that confer tolerance to many available antifungal drugs. The transcriptional control of these multidrug resistance systems in several key fungi will be discussed. Experiments in the non-pathogenic Saccharomyces cerevisiae have provided much of our current understanding of the molecular framework on which fungal multidrug resistance is built. More recent studies on the important pathogenic Candida species, Candida albicans and Candida glabrata, have provided new insights into the organization of the multidrug resistance systems in these organisms. We will compare the circuitry of multidrug resistance networks in these three organisms and suggest that, in addition to the well-accepted drug efflux activities, the regulation of membrane composition by multidrug resistance proteins provides an important contribution to the resistant phenotypes observed.
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Affiliation(s)
- Puja Shahi
- Department of Molecular Physiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Two zinc finger transcription factors, CrzA and SltA, are involved in cation homoeostasis and detoxification in Aspergillus nidulans. Biochem J 2008; 414:419-29. [PMID: 18471095 DOI: 10.1042/bj20080344] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To investigate cation adaptation and homoeostasis in Aspergillus nidulans, two transcription-factor-encoding genes have been characterized. The A. nidulans orthologue crzA of the Saccharomyces cerevisiae CRZ1 gene, encoding a transcription factor mediating gene regulation by Ca(2+), has been identified and deleted. The crzA deletion phenotype includes extreme sensitivity to alkaline pH, Ca(2+) toxicity and aberrant morphology connected with alterations of cell-wall-related phenotypes such as reduced expression of a chitin synthase gene, chsB. A fully functional C-terminally GFP (green fluorescent protein)-tagged form of the CrzA protein is apparently excluded from nuclei in the absence of added Ca(2+), but rapidly accumulates in nuclei upon exposure to Ca(2+). In addition, the previously identified sltA gene, which has no identifiable homologues in yeasts, was deleted, and the resulting phenotype includes considerably enhanced toxicity by a number of cations other than Ca(2+) and also by alkaline pH. Reduced expression of a homologue of the S. cerevisiae P-type ATPase Na(+) pump gene ENA1 might partly explain the cation sensitivity of sltA-null strains. Up-regulation of the homologue of the S. cerevisiae vacuolar Ca(2+)/H(+) exchanger gene VCX1 might explain the lack of Ca(2+) toxicity to null-sltA mutants, whereas down-regulation of this gene might be responsible for Ca(2+) toxicity to crzA-null mutants. Both crzA and sltA encode DNA-binding proteins, and the latter exerts both positive and negative gene regulation.
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