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Rosa S, Tagliani A, Bertaso C, Tadini L, Visentin C, Gourlay LJ, Pricl S, Feni L, Pellegrino S, Pesaresi P, Masiero S. The cyclic peptide G4CP2 enables the modulation of galactose metabolism in yeast by interfering with GAL4 transcriptional activity. Front Mol Biosci 2023; 10:1017757. [PMID: 36936986 PMCID: PMC10014601 DOI: 10.3389/fmolb.2023.1017757] [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: 08/12/2022] [Accepted: 01/23/2023] [Indexed: 03/04/2023] Open
Abstract
Genetically-encoded combinatorial peptide libraries are convenient tools to identify peptides to be used as therapeutics, antimicrobials and functional synthetic biology modules. Here, we report the identification and characterization of a cyclic peptide, G4CP2, that interferes with the GAL4 protein, a transcription factor responsible for the activation of galactose catabolism in yeast and widely exploited in molecular biology. G4CP2 was identified by screening CYCLIC, a Yeast Two-Hybrid-based combinatorial library of cyclic peptides developed in our laboratory. G4CP2 interferes with GAL4-mediated activation of galactose metabolic enzymes both when expressed intracellularly, as a recombinant peptide, and when provided exogenously, as a chemically-synthesized cyclic peptide. Our results support the application of G4CP2 in microbial biotechnology and, additionally, demonstrate that CYCLIC can be used as a tool for the rapid identification of peptides, virtually without any limitations with respect to the target protein. The possible biotechnological applications of cyclic peptides are also discussed.
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Affiliation(s)
- Stefano Rosa
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Andrea Tagliani
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Bertaso
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Luca Tadini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Cristina Visentin
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | | | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@Units), DEA, University of Trieste, Trieste, Italy
- Department of General Biophysics, University of Łódź, Łódź, Poland
| | - Lucia Feni
- DISFARM-Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Sara Pellegrino
- DISFARM-Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Paolo Pesaresi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Simona Masiero
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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2
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Pimentel FSA, Machado CM, De-Souza EA, Fernandes CM, De-Queiroz ALFV, Silva GFS, Del Poeta M, Montero-Lomeli M, Masuda CA. Sphingolipid depletion suppresses UPR activation and promotes galactose hypersensitivity in yeast models of classic galactosemia. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166389. [PMID: 35301088 DOI: 10.1016/j.bbadis.2022.166389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022]
Abstract
Classic galactosemia is an inborn error of metabolism caused by deleterious mutations on the GALT gene, which encodes the Leloir pathway enzyme galactose-1-phosphate uridyltransferase. Previous studies have shown that the endoplasmic reticulum unfolded protein response (UPR) is relevant to galactosemia, but the molecular mechanism behind the endoplasmic reticulum stress that triggers this response remains elusive. In the present work, we show that the activation of the UPR in yeast models of galactosemia does not depend on the binding of unfolded proteins to the ER stress sensor protein Ire1p since the protein domain responsible for unfolded protein binding to Ire1p is not necessary for UPR activation. Interestingly, myriocin - an inhibitor of the de novo sphingolipid synthesis pathway - inhibits UPR activation and causes galactose hypersensitivity in these models, indicating that myriocin-mediated sphingolipid depletion impairs yeast adaptation to galactose toxicity. Supporting the interpretation that the effects observed after myriocin treatment were due to a reduction in sphingolipid levels, the addition of phytosphingosine to the culture medium reverses all myriocin effects tested. Surprisingly, constitutively active UPR signaling did not prevent myriocin-induced galactose hypersensitivity suggesting multiple roles for sphingolipids in the adaptation of yeast cells to galactose toxicity. Therefore, we conclude that sphingolipid homeostasis has an important role in UPR activation and cellular adaptation in yeast models of galactosemia, highlighting the possible role of lipid metabolism in the pathophysiology of this disease.
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Affiliation(s)
- Felipe S A Pimentel
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caio M Machado
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evandro A De-Souza
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Ana Luiza F V De-Queiroz
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme F S Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA; Division of Infectious Diseases, Stony Brook, NY, USA; Veteran Administration Medical Center, Northport, New York, USA
| | - Monica Montero-Lomeli
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudio A Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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3
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Fan J, Zhang Z, Long C, He B, Hu Z, Jiang C, Zeng B. Identification and functional characterization of glycerol dehydrogenase reveal the role in kojic acid synthesis in Aspergillus oryzae. World J Microbiol Biotechnol 2020; 36:136. [PMID: 32783085 DOI: 10.1007/s11274-020-02912-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/06/2020] [Indexed: 02/02/2023]
Abstract
Glycerol dehydrogenase has been identified and characterized functionally in many species. However, little is known about glycerol dehydrogenase genes and their functions in Aspergillus oryzae. Here, a total of 45 glycerol dehydrogenase genes in Aspergillus oryzae were identified and renamed from AoGld1 to AoGld45 according to their chromosome distribution. They were classified into three groups based on phylogenetic analysis. Synteny analysis revealed that thirteen AoGld genes are conserved among Aspergillus species. Promoter analysis displayed that AoGld3 and AoGld13 harbored multiple binding elements of GATA-type transcription factors and zinc-finger protein msnA that were involved in nitrogen and kojic acid metabolism, respectively. Moreover, the AoGld3 deletion strain Δgld3 was generated by the CRISPR/Cas9 system, which had no visible growth defects compared with the control wild-type strain under the control and osmotic stress treatments. However, disruption of AoGld3 led to the inhibition of kojic acid production, and the expression of kojA, kojR was down-regulated in the Δgld3 strain. Furthermore, when kojA or kojR was overexpressed in the Δgld3 strain, the yield of kojic acid was restored, suggesting that AoGld3 is involved in kojic acid production through affecting the expression of kojR and kojA. Taken together, these findings provide new insights into our understanding of glycerol dehydrogenase and establish foundation for further study of their roles in Aspergillus oryzae.
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Affiliation(s)
- Junxia Fan
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhe Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
| | - Chuannan Long
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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De-Souza EA, Pimentel FSA, De-Queiroz ALFV, Camara H, Felix-Formiga ML, Machado CM, Pinto S, Galina A, Mori MA, Montero-Lomeli M, Masuda CA. The yeast protein Ubx4p contributes to mitochondrial respiration and lithium-galactose-mediated activation of the unfolded protein response. J Biol Chem 2020; 295:3773-3782. [PMID: 31996377 PMCID: PMC7086034 DOI: 10.1074/jbc.ra119.011271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
In the presence of galactose, lithium ions activate the unfolded protein response (UPR) by inhibiting phosphoglucomutase activity and causing the accumulation of galactose-related metabolites, including galactose-1-phosphate. These metabolites also accumulate in humans who have the disease classic galactosemia. Here, we demonstrate that Saccharomyces cerevisiae yeast strains harboring a deletion of UBX4, a gene encoding a partner of Cdc48p in the endoplasmic reticulum-associated degradation (ERAD) pathway, exhibit delayed UPR activation after lithium and galactose exposure because the deletion decreases galactose-1-phosphate levels. The delay in UPR activation did not occur in yeast strains in which key ERAD or proteasomal pathway genes had been disrupted, indicating that the ubx4Δ phenotype is ERAD-independent. We also observed that the ubx4Δ strain displays decreased oxygen consumption. The inhibition of mitochondrial respiration was sufficient to diminish galactose-1-phosphate levels and, consequently, affects UPR activation. Finally, we show that the deletion of the AMP-activated protein kinase ortholog-encoding gene SNF1 can restore the oxygen consumption rate in ubx4Δ strain, thereby reestablishing galactose metabolism, UPR activation, and cellular adaption to lithium-galactose challenge. Our results indicate a role for Ubx4p in yeast mitochondrial function and highlight that mitochondrial and endoplasmic reticulum functions are intertwined through galactose metabolism. These findings also shed new light on the mechanisms of lithium action and on the pathophysiology of galactosemia.
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Affiliation(s)
- Evandro A De-Souza
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Felipe S A Pimentel
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Ana Luiza F V De-Queiroz
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Henrique Camara
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Mikaella L Felix-Formiga
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Caio M Machado
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Antonio Galina
- Programa de Bioquímica e Biofísica Celular, Instituto de Bioquímica M[c33c]zpi;●dica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Monica Montero-Lomeli
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Claudio A Masuda
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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5
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Jagtap SS, Bedekar AA, Liu JJ, Jin YS, Rao CV. Production of galactitol from galactose by the oleaginous yeast Rhodosporidium toruloides IFO0880. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:250. [PMID: 31636709 PMCID: PMC6798376 DOI: 10.1186/s13068-019-1586-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/04/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Sugar alcohols are commonly used as low-calorie sweeteners and can serve as potential building blocks for bio-based chemicals. Previous work has shown that the oleaginous yeast Rhodosporidium toruloides IFO0880 can natively produce arabitol from xylose at relatively high titers, suggesting that it may be a useful host for sugar alcohol production. In this work, we explored whether R. toruloides can produce additional sugar alcohols. RESULTS Rhodosporidium toruloides is able to produce galactitol from galactose. During growth in nitrogen-rich medium, R. toruloides produced 3.2 ± 0.6 g/L, and 8.4 ± 0.8 g/L galactitol from 20 to 40 g/L galactose, respectively. In addition, R. toruloides was able to produce galactitol from galactose at reduced titers during growth in nitrogen-poor medium, which also induces lipid production. These results suggest that R. toruloides can potentially be used for the co-production of lipids and galactitol from galactose. We further characterized the mechanism for galactitol production, including identifying and biochemically characterizing the critical aldose reductase. Intracellular metabolite analysis was also performed to further understand galactose metabolism. CONCLUSIONS Rhodosporidium toruloides has traditionally been used for the production of lipids and lipid-based chemicals. Our work demonstrates that R. toruloides can also produce galactitol, which can be used to produce polymers with applications in medicine and as a precursor for anti-cancer drugs. Collectively, our results further establish that R. toruloides can produce multiple value-added chemicals from a wide range of sugars.
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Affiliation(s)
- Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Ashwini Ashok Bedekar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Jing-Jing Liu
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Yong-Su Jin
- Department of Food Science and Nutrition, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801 USA
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6
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Kobayashi J, Sasaki D, Bamba T, Hasunuma T, Kondo A. Sustainable production of glutathione from lignocellulose-derived sugars using engineered Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2018; 103:1243-1254. [DOI: 10.1007/s00253-018-9493-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
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7
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A Mutation in PGM2 Causing Inefficient Galactose Metabolism in the Probiotic Yeast Saccharomyces boulardii. Appl Environ Microbiol 2018. [PMID: 29523547 DOI: 10.1128/aem.02858-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The probiotic yeast Saccharomyces boulardii has been extensively studied for the prevention and treatment of diarrheal diseases, and it is now commercially available in some countries. S. boulardii displays notable phenotypic characteristics, such as a high optimal growth temperature, high tolerance against acidic conditions, and the inability to form ascospores, which differentiate S. boulardii from Saccharomyces cerevisiae The majority of prior studies stated that S. boulardii exhibits sluggish or halted galactose utilization. Nonetheless, the molecular mechanisms underlying inefficient galactose uptake have yet to be elucidated. When the galactose utilization of a widely used S. boulardii strain, ATCC MYA-796, was examined under various culture conditions, the S. boulardii strain could consume galactose, but at a much lower rate than that of S. cerevisiae While all GAL genes were present in the S. boulardii genome, according to analysis of genomic sequencing data in a previous study, a point mutation (G1278A) in PGM2, which codes for phosphoglucomutase, was identified in the genome of the S. boulardii strain. As the point mutation resulted in the truncation of the Pgm2 protein, which is known to play a pivotal role in galactose utilization, we hypothesized that the truncated Pgm2 might be associated with inefficient galactose metabolism. Indeed, complementation of S. cerevisiaePGM2 in S. boulardii restored galactose utilization. After reverting the point mutation to a full-length PGM2 in S. boulardii by Cas9-based genome editing, the growth rates of wild-type (with a truncated PGM2 gene) and mutant (with a full-length PGM2) strains with glucose or galactose as the carbon source were examined. As expected, the mutant (with a full-length PGM2) was able to ferment galactose faster than the wild-type strain. Interestingly, the mutant showed a lower growth rate than that of the wild-type strain on glucose at 37°C. Also, the wild-type strain was enriched in the mixed culture of wild-type and mutant strains on glucose at 37°C, suggesting that the truncated PGM2 might offer better growth on glucose at a higher temperature in return for inefficient galactose utilization. Our results suggest that the point mutation in PGM2 might be involved in multiple phenotypes with different effects.IMPORTANCESaccharomyces boulardii is a probiotic yeast strain capable of preventing and treating diarrheal diseases. However, the genetics and metabolism of this yeast are largely unexplored. In particular, molecular mechanisms underlying the inefficient galactose metabolism of S. boulardii remain unknown. Our study reports that a point mutation in PGM2, which codes for phosphoglucomutase, is responsible for inferior galactose utilization by S. boulardii After correction of the mutated PGM2 via genome editing, the resulting strain was able to use galactose faster than a parental strain. While the PGM2 mutation made the yeast use galactose slowly, investigation of the genomic sequencing data of other S. boulardii strains revealed that the PGM2 mutation is evolutionarily conserved. Interestingly, the PGM2 mutation was beneficial for growth at a higher temperature on glucose. We speculate that the PGM2 mutation was enriched due to selection of S. boulardii in the natural habitat (sugar-rich fruits in tropical areas).
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8
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Gibney PA, Schieler A, Chen JC, Bacha-Hummel JM, Botstein M, Volpe M, Silverman SJ, Xu Y, Bennett BD, Rabinowitz JD, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell 2018; 29:897-910. [PMID: 29444955 PMCID: PMC5896929 DOI: 10.1091/mbc.e17-11-0666] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Metabolic dysregulation leading to sugar-phosphate accumulation is toxic in organisms ranging from bacteria to humans. By comparing two models of sugar-phosphate toxicity in Saccharomyces cerevisiae, we demonstrate that toxicity occurs, at least in part, through multiple, isomer-specific mechanisms, rather than a single general mechanism.
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Affiliation(s)
- Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Ariel Schieler
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jonathan C Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Maxim Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew Volpe
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Sanford J Silverman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Yifan Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Calico Life Sciences LLC, South San Francisco, CA 94080.,Department of Food Science, Cornell University, Ithaca, NY 14853
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9
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Schuler D, Höll C, Grün N, Ulrich J, Dillner B, Klebl F, Ammon A, Voll LM, Kämper J. Galactose metabolism and toxicity in Ustilago maydis. Fungal Genet Biol 2018; 114:42-52. [PMID: 29580862 DOI: 10.1016/j.fgb.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/07/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
In most organisms, galactose is metabolized via the Leloir pathway, which is conserved from bacteria to mammals. Utilization of galactose requires a close interplay of the metabolic enzymes, as misregulation or malfunction of individual components can lead to the accumulation of toxic intermediate compounds. For the phytopathogenic basidiomycete Ustilago maydis, galactose is toxic for wildtype strains, i.e. leads to growth repression despite the presence of favorable carbon sources as sucrose. The galactose sensitivity can be relieved by two independent modifications: (1) by disruption of Hxt1, which we identify as the major transporter for galactose, and (2) by a point mutation in the gene encoding the galactokinase Gal1, the first enzyme of the Leloir pathway. The mutation in gal1(Y67F) leads to reduced enzymatic activity of Gal1 and thus may limit the formation of putatively toxic galactose-1-phosphate. However, systematic deletions and double deletions of different genes involved in galactose metabolism point to a minor role of galactose-1-phosphate in galactose toxicity. Our results show that molecular triggers for galactose toxicity in U. maydis differ from yeast and mammals.
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Affiliation(s)
- David Schuler
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Christina Höll
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Nathalie Grün
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Jonas Ulrich
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Bastian Dillner
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Franz Klebl
- FAU Erlangen-Nuremberg, Department of Biology, Molecular Plant Physiology, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alexandra Ammon
- Philips-University of Marburg, Department of Biology, Plant Physiology and Photo Biology, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Lars M Voll
- Philips-University of Marburg, Department of Biology, Plant Physiology and Photo Biology, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Jörg Kämper
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany.
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10
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Machado CM, De-Souza EA, De-Queiroz ALFV, Pimentel FSA, Silva GFS, Gomes FM, Montero-Lomelí M, Masuda CA. The galactose-induced decrease in phosphate levels leads to toxicity in yeast models of galactosemia. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1403-1409. [PMID: 28213126 DOI: 10.1016/j.bbadis.2017.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/05/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
Abstract
Classic galactosemia is an inborn error of metabolism caused by deleterious mutations in the GALT gene. A number of evidences indicate that the galactose-1-phosphate accumulation observed in patient cells is a cause of toxicity in this disease. Nevertheless, the consequent molecular events caused by the galactose-1-phosphate accumulation remain elusive. Here we show that intracellular inorganic phosphate levels decreased when yeast models of classic galactosemia were exposed to galactose. The decrease in phosphate levels is probably due to the trapping of phosphate in the accumulated galactose-1-phosphate since the deletion of the galactokinase encoding gene GAL1 suppressed this phenotype. Galactose-induced phosphate depletion caused an increase in glycogen content, an expected result since glycogen breakdown by the enzyme glycogen phosphorylase is dependent on inorganic phosphate. Accordingly, an increase in intracellular phosphate levels suppressed the galactose effect on glycogen content and conferred galactose tolerance to yeast models of galactosemia. These results support the hypothesis that the galactose-induced decrease in phosphate levels leads to toxicity in galactosemia and opens new possibilities for the development of better treatments for this disease.
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Affiliation(s)
- Caio M Machado
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Evandro A De-Souza
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Ana Luiza F V De-Queiroz
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Felipe S A Pimentel
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Guilherme F S Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Fabio M Gomes
- Laboratório de Entomologia Médica, Programa de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | - Mónica Montero-Lomelí
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Claudio A Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
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Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C. Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun 2015; 6:8882. [PMID: 26582123 PMCID: PMC4673486 DOI: 10.1038/ncomms9882] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/13/2015] [Indexed: 11/14/2022] Open
Abstract
Although many factors required for the formation of export-competent mRNPs have been described, an integrative view of the spatiotemporal coordinated cascade leading mRNPs from their site of transcription to their site of nuclear exit, at a single cell level, is still partially missing due to technological limitations. Here we report that the RNA Spinach aptamer is a powerful tool for mRNA imaging in live S. cerevisiae with high spatial-temporal resolution and no perturbation of the mRNA biogenesis properties. Dedicated image processing workflows are developed to allow detection of very low abundance of transcripts, accurate quantitative dynamic studies, as well as to provide a localization precision close to 100 nm at consistent time scales. Combining these approaches has provided a state-of-the-art analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts. Measuring single-cell mRNA dynamics is critical to understand gene expression. Here, using RNA Spinach technique to detect very low abundant mRNAs, Guet et al. report an analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts.
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Affiliation(s)
- David Guet
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Laura T Burns
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Suman Maji
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Jérôme Boulanger
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Pascal Hersen
- Univ Paris Diderot, Sorbonne Paris Cité, CNRS UMR7057, Laboratoire Matière et Systèmes Complexes, 10 rue Alice Domon et Léonie Duquet, Paris 75013, France
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Jean Salamero
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France.,PICT-IBiSA Imaging Core Facility, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Catherine Dargemont
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
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12
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De-Souza EA, Pimentel FSA, Machado CM, Martins LS, da-Silva WS, Montero-Lomelí M, Masuda CA. The unfolded protein response has a protective role in yeast models of classic galactosemia. Dis Model Mech 2013; 7:55-61. [PMID: 24077966 PMCID: PMC3882048 DOI: 10.1242/dmm.012641] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast), which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.
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Affiliation(s)
- Evandro A De-Souza
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
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13
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Abstract
For most eukaryotic organisms, including Saccharomyces cerevisiae, the rapid inhibition of protein synthesis forms part of a response to stress. In order to balance the changing conditions, precise stress-specific alterations to the cell's proteome are required. Therefore, in the background of a global down-regulation in protein synthesis, specific proteins are induced. Given the level of plasticity required to enable stress-specific alterations of this kind, it is surprising that the mechanisms of translational regulation are not more diverse. In the present review, we summarize the impact of stress on translation initiation, highlighting both the similarities and distinctions between various stress responses. Finally, we speculate as to how yeast cells generate stress-responsive programmes of protein production when regulation is focused on the same steps in the translation pathway.
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Zaidi I, González A, Touzri M, Alvarez MC, Ramos J, Masmoudi K, Ariño J, Hanin M. The wheat MAP kinase phosphatase 1 confers higher lithium tolerance in yeast. FEMS Yeast Res 2012; 12:774-84. [PMID: 22741610 DOI: 10.1111/j.1567-1364.2012.00827.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 05/17/2012] [Accepted: 06/25/2012] [Indexed: 11/27/2022] Open
Abstract
The durum wheat TMKP1 gene encodes a MAP kinase phosphatase. When overexpressed in Saccharomyces cerevisiae, TMKP1 leads to salt stress tolerance (especially LiCl ), which is dependent on the phosphatase activity of the protein. The TMKP1-associated Li(+) resistance is restricted to a galactose-containing medium. Interestingly, this salt tolerance is abolished in the absence of one member of the yeast type 2C Ser/Thr protein phosphatase family (Ptc1) but not when other members such as Ptc2 or Ptc3 are lacking. Increased Li(+) tolerance is not mediated by regulation of the P-type ATPase Ena1, a major determinant for salt tolerance. In contrast, the effect of TMKP1 depends on Hal3 (a negative regulator of Ppz phosphatases) and on the presence of the high-affinity potassium transporters Trk1/Trk2. Tolerance to Li(+) is also abolished in cells lacking the aldose reductase Gre3, previously shown to be involved in the resistance to this cation. This study provides evidence that the wheat TMKP1 phosphatase is contributing to reduce the exacerbated lithium toxicity in galactose-grown cells, in a way that depends on the presence of the potassium Trk transporters.
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Affiliation(s)
- Ikram Zaidi
- Laboratory of Plant Protection and Improvement, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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