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Assalve G, Lunetti P, Zara V, Ferramosca A. Ctp1 and Yhm2: Two Mitochondrial Citrate Transporters to Support Metabolic Flexibility of Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:1870. [PMID: 38339147 PMCID: PMC10855732 DOI: 10.3390/ijms25031870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Differently from higher eukaryotic cells, in the yeast Saccharomyces cerevisiae there are two mitochondrial carrier proteins involved in the transport of citrate: Ctp1 and Yhm2. Very little is known about the physiological role of these proteins. Wild-type and mutant yeast strains deleted in CTP1 and YHM2 were grown in media supplemented with a fermentable (glucose) or a nonfermentable (ethanol) carbon source. To assess changes in Ctp1 and Yhm2 mRNA expression levels, real-time PCR was performed after total RNA extraction. In the wild-type strain, the metabolic switch from the exponential to the stationary phase is associated with an increase in the expression level of the two citrate transporters. In addition, the results obtained in the mutant strains suggest that the presence of a single citrate transporter can partially compensate for the absence of the other. Ctp1 and Yhm2 differently contribute to fermentative and respiratory metabolism. Moreover, the two mitochondrial carriers represent a link between the Krebs cycle and the glyoxylate cycle, which play a key role in the metabolic adaptation strategies of S. cerevisiae.
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Affiliation(s)
- Graziana Assalve
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Vincenzo Zara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Alessandra Ferramosca
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
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Montañés JC, Huertas M, Moro SG, Blevins WR, Carmona M, Ayté J, Hidalgo E, Albà MM. Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms. Genome Res 2022; 32:1215-1227. [PMID: 35618415 PMCID: PMC9248878 DOI: 10.1101/gr.276516.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/09/2022] [Indexed: 11/25/2022]
Abstract
The unicellular yeast Schizosaccharomyces pombe (fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here we leverage Oxford Nanopore Technologies native RNA sequencing (dRNA), as well as ribosome profiling data, to uncover the full range of polyadenylated transcripts and translated open reading frames. We identify 332 alternative isoforms affecting the coding sequences of 262 different genes, 97 of which occur at frequencies >20%, indicating that functional alternative splicing in S. pombe is more prevalent than previously suspected. Intron retention events make ∼80% of the cases; these events may be involved in the regulation of gene expression and, in some cases, generate novel protein isoforms, as supported by ribosome profiling data in 18 of the intron retention isoforms. One example is the rpl22 gene, in which intron retention is associated with the translation of a protein of only 13 amino acids. We also find that lowly expressed transcripts tend to have longer poly(A) tails than highly expressed transcripts, highlighting an interdependence between poly(A) tail length and transcript expression level. Finally, we discover 214 novel transcripts that are not annotated, including 158 antisense transcripts, some of which also show translation evidence. The methodologies described in this work open new opportunities to study the regulation of splicing in a simple eukaryotic model.
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Affiliation(s)
- José Carlos Montañés
- Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marta Huertas
- Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Simone G Moro
- Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - William R Blevins
- Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Mercè Carmona
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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Jiang Y, Zhuge B, Qin Y, Zong H, Lu X. Candida glycerinogenes Strains Overexpressing Transcription Factors have Improved Furfural Tolerance in Ethanol Production from Non-detoxified Cellulose Hydrolysate. Curr Microbiol 2022; 79:196. [PMID: 35595863 DOI: 10.1007/s00284-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/27/2022] [Indexed: 11/26/2022]
Abstract
Cellulose is one of the main raw materials for production of green ethanol, but the presence of the growth inhibitor furfural in non-detoxified lignocellulosic hydrolysates often seriously affects their utilization. In a previous study, we obtained strains of Candida glycerinogenes that were tolerant to furfural, but at concentrations above 2.5 g L-1 there was a significant increase in the growth lag phase. In this work, transcription factor genes (SEF1, STB5, CAS5, and ETP1) associated with furfural tolerance were identified and employed to obtain modified strains permitting ethanol fermentation of concentrated and non-detoxified cellulose hydrolysates containing more than 2.5 g L-1 furfural. Tolerance to furfural could be increased to 4.5 g L-1 by overexpression of either STB5 or ETP1, which have different regulation patterns. Moreover, in non-detoxified and concentrated cellulose hydrolysate, overexpression of ETP1 significantly shortened the growth lag phase and ethanol fermentation time was reduced by 17-20%. In batch fermentations fed with concentrated non-detoxified lignocellulose hydrolysate, ethanol productivity and maximum ethanol concentration reached 2.4 g L-1 h-1 and 72.5 g L-1, increases of 26.1% and 6.6%, respectively. The results provided a route for the economic use of lignocellulose for chemical production.
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Affiliation(s)
- Yudi Jiang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Research Center of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Research Center of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Yuyao Qin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Research Center of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Research Center of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Research Center of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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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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Wang X, Schlatter DC, Glawe DA, Edwards CG, Weller DM, Paulitz TC, Abatzoglou JT, Okubara PA. Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation. Int J Food Microbiol 2021; 350:109225. [PMID: 34023678 DOI: 10.1016/j.ijfoodmicro.2021.109225] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
To address a knowledge gap about the grape berry mycobiome from Washington State vineyards, next-generation sequencing of the internal transcribed spacer region (ITS1) was used to identify native yeast and fungal species on berries of cultivar 'Cabernet Sauvignon' from two vineyards at veraison and harvest in 2015 and 2016. Four hundred fifty-six different yeast amplicon sequence variants (ASV), representing 184 distinct taxa, and 2467 non-yeast fungal ASV (791 distinct taxa) were identified in this study. A set of 50 recurrent yeast taxa, including Phaeococcomyces, Vishniacozyma and Metschnikowia, were found at both locations and sampling years. These yeast species were monitored from the vineyard into laboratory-scale spontaneous fermentations. Taxa assignable to Metschnikowia and Saccharomyces persisted during fermentation, whereas Curvibasidium, which also has possible impact on biocontrol and wine quality, did not. Sulfite generally reduced yeast diversity and richness, but its effect on the abundance of specific yeasts during fermentation was negligible. Among the 106 recurring non-yeast fungal taxa, Alternaria, Cladosporium and Ulocladium were especially abundant in the vineyard. Vineyard location was the primary factor that accounted for the variation among both communities, followed by year and berry developmental stage. The Washington mycobiomes were compared to those from other parts of the world. Sixteen recurrent yeast species appeared to be unique to Washington State vineyards. This subset also contained a higher proportion of species associated with cold and extreme environments, relative to other localities. Certain yeast and non-yeast fungal species known to suppress diseases or modify wine sensory properties were present in Washington vineyards, and likely have consequences to vineyard health and wine quality.
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Affiliation(s)
- Xuefei Wang
- College of Enology, Northwest A&F University, Shaanxi 712100, China; Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Daniel C Schlatter
- USDA-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman 99163-6430, WA, USA.
| | - Dean A Glawe
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Charles G Edwards
- School of Food Science, Washington State University, Pullman, WA 99163-6376, USA.
| | - David M Weller
- USDA-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman 99163-6430, WA, USA.
| | - Timothy C Paulitz
- USDA-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman 99163-6430, WA, USA.
| | - John T Abatzoglou
- Management of Complex Systems, University of California, Merced, Merced, CA 95343, USA.
| | - Patricia A Okubara
- USDA-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman 99163-6430, WA, USA.
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Bagamery LE, Justman QA, Garner EC, Murray AW. A Putative Bet-Hedging Strategy Buffers Budding Yeast against Environmental Instability. Curr Biol 2020; 30:4563-4578.e4. [PMID: 32976801 DOI: 10.1016/j.cub.2020.08.092] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/20/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
To grow and divide, cells must extract resources from dynamic and unpredictable environments. Many organisms use different metabolic strategies for distinct contexts. Budding yeast can produce ATP from carbon sources by mechanisms that prioritize either speed (fermentation) or yield (respiration). Withdrawing glucose from exponentially growing cells reveals variability in their ability to switch from fermentation to respiration. We observe two subpopulations of glucose-starved cells: recoverers, which rapidly adapt and resume growth, and arresters, which enter a shock state characterized by deformation of many cellular structures, including mitochondria. These states are heritable, and on high glucose, arresters grow and divide faster than recoverers. Recoverers have a fitness advantage during a carbon source shift but are less fit in a constant, high-glucose environment, and we observe natural variation in the frequency of the two states across wild yeast strains. These experiments suggest that bet hedging has evolved in budding yeast.
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Affiliation(s)
- Laura E Bagamery
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Quincey A Justman
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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Mo W, Wang M, Zhan R, Yu Y, He Y, Lu H. Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:63. [PMID: 30949239 PMCID: PMC6429784 DOI: 10.1186/s13068-019-1393-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Kluyveromyces marxianus, the known fastest-growing eukaryote on the earth, has remarkable thermotolerance and capacity to utilize various agricultural residues to produce low-cost bioethanol, and hence is industrially important to resolve the imminent energy shortage crisis. Currently, the poor ethanol tolerance hinders its operable application in the industry, and it is necessary to improve K. marxianus' ethanol resistance and unravel the underlying systematical mechanisms. However, this has been seldom reported to date. RESULTS We carried out a wild-type haploid K. marxianus FIM1 in adaptive evolution in 6% (v/v) ethanol. After 100-day evolution, the KM-100d population was obtained; its ethanol tolerance increased up to 10% (v/v). Interestingly, DNA analysis and RNA-seq analysis showed that KM-100d yeasts' ethanol tolerance improvement was not due to ploidy change or meaningful mutations, but founded on transcriptional reprogramming in a genome-wide range. Even growth in an ethanol-free medium, many genes in KM-100d maintained their up-regulation. Especially, pathways of ethanol consumption, membrane lipid biosynthesis, anti-osmotic pressure, anti-oxidative stress, and protein folding were generally up-regulated in KM-100d to resist ethanol. Notably, enhancement of the secretory pathway may be the new strategy KM-100d developed to anti-osmotic pressure, instead of the traditional glycerol production way in S. cerevisiae. Inferred from the transcriptome data, besides ethanol tolerance, KM-100d may also develop the ability to resist osmotic, oxidative, and thermic stresses, and this was further confirmed by the cell viability test. Furthermore, under such environmental stresses, KM-100d greatly improved ethanol production than the original strain. In addition, we found that K. marxianus may adopt distinct routes to resist different ethanol concentrations. Trehalose biosynthesis was required for low ethanol, while sterol biosynthesis and the whole secretory pathway were activated for high ethanol. CONCLUSIONS This study reveals that ethanol-driven laboratory evolution could improve K. marxianus' ethanol tolerance via significant up-regulation of multiple pathways including anti-osmotic, anti-oxidative, and anti-thermic processes, and indeed consequently raised ethanol yield in industrial high-temperature and high-ethanol circumstance. Our findings give genetic clues for further rational optimization of K. marxianus' ethanol production, and also partly confirm the positively correlated relationship between yeast's ethanol tolerance and production.
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Affiliation(s)
- Wenjuan Mo
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Mengzhu Wang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Rongrong Zhan
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
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Takahashi H, Kusuya Y, Hagiwara D, Takahashi-Nakaguchi A, Sakai K, Gonoi T. Global gene expression reveals stress-responsive genes in Aspergillus fumigatus mycelia. BMC Genomics 2017; 18:942. [PMID: 29202712 PMCID: PMC5715996 DOI: 10.1186/s12864-017-4316-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus fumigatus is a human fungal pathogen that causes aspergillosis in immunocompromised hosts. A. fumigatus is believed to be exposed to diverse environmental stresses in the host cells. The adaptation mechanisms are critical for infections in human bodies. Transcriptional networks in response to diverse environmental challenges remain to be elucidated. To gain insights into the adaptation to environmental stresses in A. fumigatus mycelia, we conducted time series transcriptome analyses. Results With the aid of RNA-seq, we explored the global gene expression profiles of mycelia in A. fumigatus upon exposure to diverse environmental changes, including heat, superoxide, and osmotic stresses. From the perspective of global transcriptomes, transient responses to superoxide and osmotic stresses were observed while responses to heat stresses were gradual. We identified the stress-responsive genes for particular stresses, and the 266 genes whose expression levels drastically fluctuated upon exposure to all tested stresses. Among these, the 77 environmental stress response genes are conserved in S. cerevisiae, suggesting that these genes might be more general prerequisites for adaptation to environmental stresses. Finally, we revealed the strong correlations among expression profiles of genes related to ‘rRNA processing’. Conclusions The time series transcriptome analysis revealed the stress-responsive genes underlying the adaptation mechanisms in A. fumigatus mycelia. These results will shed light on the regulatory networks underpinning the adaptation of the filamentous fungi. Electronic supplementary material The online version of this article (10.1186/s12864-017-4316-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan. .,Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | | | - Kanae Sakai
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
| | - Tohru Gonoi
- Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan
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Hovsepian J, Defenouillère Q, Albanèse V, Váchová L, Garcia C, Palková Z, Léon S. Multilevel regulation of an α-arrestin by glucose depletion controls hexose transporter endocytosis. J Cell Biol 2017; 216:1811-1831. [PMID: 28468835 PMCID: PMC5461024 DOI: 10.1083/jcb.201610094] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 03/28/2017] [Indexed: 01/13/2023] Open
Abstract
Changes in nutrient availability trigger massive rearrangements of the yeast plasma membrane proteome. This work shows that the arrestin-related protein Csr2/Art8 is regulated by glucose signaling at multiple levels, allowing control of hexose transporter ubiquitylation and endocytosis upon glucose depletion. Nutrient availability controls the landscape of nutrient transporters present at the plasma membrane, notably by regulating their ubiquitylation and subsequent endocytosis. In yeast, this involves the Nedd4 ubiquitin ligase Rsp5 and arrestin-related trafficking adaptors (ARTs). ARTs are targeted by signaling pathways and warrant that cargo ubiquitylation and endocytosis appropriately respond to nutritional inputs. Here, we show that glucose deprivation regulates the ART protein Csr2/Art8 at multiple levels to trigger high-affinity glucose transporter endocytosis. Csr2 is transcriptionally induced in these conditions through the AMPK orthologue Snf1 and downstream transcriptional repressors. Upon synthesis, Csr2 becomes activated by ubiquitylation. In contrast, glucose replenishment induces CSR2 transcriptional shutdown and switches Csr2 to an inactive, deubiquitylated form. This glucose-induced deubiquitylation of Csr2 correlates with its phospho-dependent association with 14-3-3 proteins and involves protein kinase A. Thus, two glucose signaling pathways converge onto Csr2 to regulate hexose transporter endocytosis by glucose availability. These data illustrate novel mechanisms by which nutrients modulate ART activity and endocytosis.
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Affiliation(s)
- Junie Hovsepian
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Quentin Defenouillère
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Véronique Albanèse
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i. BIOCEV, 252 50 Vestec, Czech Republic.,Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Camille Garcia
- Proteomics Facility, Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
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Moreno-García J, Mauricio JC, Moreno J, García-Martínez T. Stress responsive proteins of a flor yeast strain during the early stages of biofilm formation. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Doğan A, Demirci S, Aytekin AÖ, Şahin F. Improvements of tolerance to stress conditions by genetic engineering in Saccharomyces cerevisiae during ethanol production. Appl Biochem Biotechnol 2014; 174:28-42. [PMID: 24908051 DOI: 10.1007/s12010-014-1006-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 05/29/2014] [Indexed: 02/07/2023]
Abstract
Saccharomyces cerevisiae, industrial yeast isolate, has been of great interest in recent years for fuel ethanol production. The ethanol yield and productivity depend on many inhibitory factors during the fermentation process such as temperature, ethanol, compounds released as the result of pretreatment procedures, and osmotic stress. An ideal strain should be able to grow under different stress conditions occurred at different fermentation steps. Development of tolerant yeast strains can be achieved by reprogramming pathways supporting the ethanol metabolism by regulating the energy balance and detoxicification processes. Complex gene interactions should be solved for an in-depth comprehension of the yeast stress tolerance mechanism. Genetic engineering as a powerful biotechnological tool is required to design new strategies for increasing the ethanol fermentation performance. Upregulation of stress tolerance genes by recombinant DNA technology can be a useful approach to overcome inhibitory situations. This review presents the application of several genetic engineering strategies to increase ethanol yield under different stress conditions including inhibitor tolerance, ethanol tolerance, thermotolerance, and osmotolerance.
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Affiliation(s)
- Ayşegül Doğan
- Department of Genetics and BioEngineering, Faculty of Engineering and Architecture, Yeditepe University, 26 Ağustos Campus, Kayisdagi cad., Kayisdagi, TR-34755, Istanbul, Turkey,
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Roy A, Kim YB, Cho KH, Kim JH. Glucose starvation-induced turnover of the yeast glucose transporter Hxt1. Biochim Biophys Acta Gen Subj 2014; 1840:2878-85. [PMID: 24821015 DOI: 10.1016/j.bbagen.2014.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND The budding yeast Saccharomyces cerevisiae possesses multiple glucose transporters with different affinities for glucose that enable it to respond to a wide range of glucose concentrations. The steady-state levels of glucose transporters are regulated in response to changes in the availability of glucose. This study investigates the glucose regulation of the low affinity, high capacity glucose transporter Hxt1. METHODS AND RESULTS Western blotting and confocal microscopy were performed to evaluate glucose regulation of the stability of Hxt1. Our results show that glucose starvation induces endocytosis and degradation of Hxt1 and that this event requires End3, a protein required for endocytosis, and the Doa4 deubiquitination enzyme. Mutational analysis of the lysine residues in the Hxt1 N-terminal domain demonstrates that the two lysine residues, K12 and K39, serve as the putative ubiquitin-acceptor sites by the Rsp5 ubiquitin ligase. We also demonstrate that inactivation of PKA (cAMP-dependent protein kinase A) is needed for Hxt1 turnover, implicating the role of the Ras/cAMP-PKA glucose signaling pathway in the stability of Hxt1. CONCLUSION AND GENERAL SIGNIFICANCE Hxt1, most useful when glucose is abundant, is internalized and degraded when glucose becomes depleted. Of note, the stability of Hxt1 is regulated by PKA, known as a positive regulator for glucose induction of HXT1 gene expression, demonstrating a dual role of PKA in regulation of Hxt1.
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Affiliation(s)
- Adhiraj Roy
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA
| | - Yong-Bae Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA
| | - Kyu Hong Cho
- Department of Microbiology, Southern Illinois University Carbondale, 1125 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical Center, 2300 Eye Street, Washington, DC 20037, USA.
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13
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A rapid, high-throughput method for quantitative determination of ethanol tolerance in Saccharomyces cerevisiae. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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14
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Regulations of sugar transporters: insights from yeast. Curr Genet 2013; 59:1-31. [PMID: 23455612 DOI: 10.1007/s00294-013-0388-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 02/02/2013] [Indexed: 12/24/2022]
Abstract
Transport across the plasma membrane is the first step at which nutrient supply is tightly regulated in response to intracellular needs and often also rapidly changing external environment. In this review, I describe primarily our current understanding of multiple interconnected glucose-sensing systems and signal-transduction pathways that ensure fast and optimum expression of genes encoding hexose transporters in three yeast species, Saccharomyces cerevisiae, Kluyveromyces lactis and Candida albicans. In addition, an overview of GAL- and MAL-specific regulatory networks, controlling galactose and maltose utilization, is provided. Finally, pathways generating signals inducing posttranslational degradation of sugar transporters will be highlighted.
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Chen Q, Fang Y, Zhao H, Zhang G, Jin Y. Transcriptional analysis of Saccharomyces cerevisiae during high-temperature fermentation. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0606-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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16
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Snowdon C, van der Merwe G. Regulation of Hxt3 and Hxt7 turnover converges on the Vid30 complex and requires inactivation of the Ras/cAMP/PKA pathway in Saccharomyces cerevisiae. PLoS One 2012; 7:e50458. [PMID: 23227176 PMCID: PMC3515616 DOI: 10.1371/journal.pone.0050458] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic cells adjust their intracellular protein complement as a mechanism to adapt to changing environmental signals. In Saccharomyces cerevisiae the hexose transporters Hxt3 and Hxt7 are expressed and function on the plasma membrane in high and low glucose abundance, respectively. By contrast, Hxt3 is endocytosed and degraded in the vacuole when cells are starved of glucose and Hxt7 in response to rapamycin treatment or when nitrogen is limiting. Yeast uses several signaling pathways, including the TORC1 and Ras/cAMP/Protein Kinase A (PKA) pathways, to adapt to nutrient changes in the environment. The multi-protein Vid30 complex (Vid30c), an E3 ubiquitin ligase required for the degradation of FBPase, assists in this adaptation process in a mechanism that is poorly understood. Here we show the endocytosis and the subsequent degradation of both Hxt3 and Hxt7, in response to different nutrient signals, is dependent on components of the Vid30c. Additionally, we define the signaling events required for the turnover of Hxt3 and Hxt7 by showing that Hxt3 turnover requires Ras2 and PKA inactivation, whereas Hxt7 turnover requires TORC1 and Ras2 inactivation. Further investigation led us to identify Rim15, a kinase that is inhibited by both the TORC1 and Ras/cAMP/PKA pathways, as a key downstream effector in signaling both turnover events. Finally, we show that the turnover of both Hxt3 and Hxt7 is dependent on the essential E3 ubiquitin ligase, Rsp5, indicating that the role of the Vid30c might be indirect of Hxt ubiquitylation.
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Affiliation(s)
- Chris Snowdon
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - George van der Merwe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Li H, Ma ML, Luo S, Zhang RM, Han P, Hu W. Metabolic responses to ethanol in Saccharomyces cerevisiae using a gas chromatography tandem mass spectrometry-based metabolomics approach. Int J Biochem Cell Biol 2012; 44:1087-96. [PMID: 22504284 DOI: 10.1016/j.biocel.2012.03.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/22/2012] [Accepted: 03/26/2012] [Indexed: 11/16/2022]
Abstract
During the fermentation process, Saccharomyces cerevisiae cells are often inhibited by the accumulated ethanol, and the mechanism of the S. cerevisiae response to ethanol is not fully understood. In the current study, a systematic analytical approach was used to investigate the changes in the S. cerevisiae cell metabolome that were elicited by treatment with various concentrations of ethanol. Gas chromatography-mass spectrometry and a multivariate analysis were employed to investigate the ethanol-associated intracellular biochemical changes in S. cerevisiae. The intracellular metabolite profiles that were found upon treatment of the cells with different concentrations of ethanol were unique and could be distinguished with the aid of principal component analysis. Furthermore, partial least-squares-discriminant analysis revealed a group classification and pairwise discrimination between the control without ethanol and ethanol treated groups, and 29 differential metabolites with variable importance in the projection value greater than 1 were identified, which was also confirmed by the subsequent hierarchical cluster analysis. The metabolic relevance of these compounds in the response of S. cerevisiae to ethanol stress was investigated. Under ethanol stress, the glycolysis was inhibited and the use of carbon sources for fermentation was diminished, which might account for the growth inhibition of S. cerevisiae cells. It was suggested that S. cerevisiae cells change the levels of fatty acids, e.g., hexadecanoic, octadecanoic and palmitelaidic acids, to maintain the integrity of their plasma membrane through decreasing membrane fluidity in the medium containing ethanol. Moreover, the increased levels of some amino acids idemtified in the cells of ethanol-treated experimental group might also confer ethanol tolerance to S. cerevisiae. These results reveal that the metabolomics strategy is a powerful tool to gain insight into the molecular mechanism of a microorganism's cellular response to environmental stress factors.
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Affiliation(s)
- Hao Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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18
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Laluce C, Schenberg ACG, Gallardo JCM, Coradello LFC, Pombeiro-Sponchiado SR. Advances and Developments in Strategies to Improve Strains of Saccharomyces cerevisiae and Processes to Obtain the Lignocellulosic Ethanol−A Review. Appl Biochem Biotechnol 2012; 166:1908-26. [DOI: 10.1007/s12010-012-9619-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
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19
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Ding MZ, Li BZ, Cheng JS, Yuan YJ. Metabolome analysis of differential responses of diploid and haploid yeast to ethanol stress. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 14:553-61. [PMID: 20955008 DOI: 10.1089/omi.2010.0015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Metabolomic analysis was carried out to investigate the metabolic differences of diploid (α/a) and homogenous haploid (α,a) yeasts, and further assess their response to ethanol stress. The dynamic metabolic variations of diploid and haploid caused by 3 and 7% (v/v) ethanol stress were evaluated by gas chromatography coupled to time-of-flight mass spectrometry combined with statistical analysis. Metabolite profiles originating from three strains in presence/absence of ethanol stress were distinctive and could be distinguished by principal components analysis. Results showed that the divergence among the strains with ethanol stress was smaller than without it. Furthermore, the levels of most glycolytic intermediates and amino acids in haploid were lower than these in diploid with/without ethanol stress, which was considered as species-specific behaviors. The increases of protective metabolites including polyols, amino acids, precursors of phospholipids, and unsaturated fatty acids under ethanol stress in three strains revealed the ethanol stress-specific responses. Higher fold change in most of these protectants in haploid indicated that haploid was more susceptible to ethanol stress than diploid. These findings provided underlying basis for better understanding diploid and haploid yeasts, and further breeding tolerant strains for efficient ethanol fermentation.
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Affiliation(s)
- Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education and Department of Pharmaceutical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
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The effect of trehalose on the fermentation performance of aged cells of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2011; 90:697-704. [DOI: 10.1007/s00253-010-3053-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/19/2010] [Accepted: 11/28/2010] [Indexed: 10/18/2022]
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21
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Jia K, Zhang Y, Li Y. Systematic engineering of microorganisms to improve alcohol tolerance. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000076] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Stanley D, Bandara A, Fraser S, Chambers P, Stanley G. The ethanol stress response and ethanol tolerance of
Saccharomyces cerevisiae. J Appl Microbiol 2010; 109:13-24. [PMID: 20070446 DOI: 10.1111/j.1365-2672.2009.04657.x] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Stanley
- School of Engineering and Science, Victoria University, Melbourne, Vic., Australia
| | - A. Bandara
- School of Engineering and Science, Victoria University, Melbourne, Vic., Australia
| | - S. Fraser
- School of Engineering and Science, Victoria University, Melbourne, Vic., Australia
| | - P.J. Chambers
- The Australian Wine Research Institute, Glen Osmond, SA, Australia
| | - G.A. Stanley
- School of Engineering and Science, Victoria University, Melbourne, Vic., Australia
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23
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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