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Albacar M, Casamayor A, Ariño J. Harnessing alkaline-pH regulatable promoters for efficient methanol-free expression of enzymes of industrial interest in Komagataella Phaffii. Microb Cell Fact 2024; 23:99. [PMID: 38566096 PMCID: PMC10985989 DOI: 10.1186/s12934-024-02362-9] [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: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The yeast Komagataella phaffii has become a very popular host for heterologous protein expression, very often based on the use of the AOX1 promoter, which becomes activated when cells are grown with methanol as a carbon source. However, the use of methanol in industrial settings is not devoid of problems, and therefore, the search for alternative expression methods has become a priority in the last few years. RESULTS We recently reported that moderate alkalinization of the medium triggers a fast and wide transcriptional response in K. phaffii. Here, we present the utilization of three alkaline pH-responsive promoters (pTSA1, pHSP12 and pPHO89) to drive the expression of a secreted phytase enzyme by simply shifting the pH of the medium to 8.0. These promoters offer a wide range of strengths, and the production of phytase could be modulated by adjusting the pH to specific values. The TSA1 and PHO89 promoters offered exquisite regulation, with virtually no enzyme production at acidic pH, while limitation of Pi in the medium further potentiated alkaline pH-driven phytase expression from the PHO89 promoter. An evolved strain based on this promoter was able to produce twice as much phytase as the reference pAOX1-based strain. Functional mapping of the TSA1 and HSP12 promoters suggests that both contain at least two alkaline pH-sensitive regulatory regions. CONCLUSIONS Our work shows that the use of alkaline pH-regulatable promoters could be a useful alternative to methanol-based expression systems, offering advantages in terms of simplicity, safety and economy.
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Affiliation(s)
- Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain.
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2
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Baruah D, Tamuli R. The cell functions of phospholipase C-1, Ca 2+/H + exchanger-1, and secretory phospholipase A 2 in tolerance to stress conditions and cellulose degradation in Neurospora crassa. Arch Microbiol 2023; 205:327. [PMID: 37676310 DOI: 10.1007/s00203-023-03662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023]
Abstract
We investigated the cell functions of the Ca2+ signaling genes phospholipase C-1 (plc-1), Ca2+/H+ exchanger (cpe-1), and secretory phospholipase A2 (splA2) for stress responses and cellulose utilization in Neurospora crassa. The Δplc-1, Δcpe-1, and ΔsplA2 mutants displayed increased sensitivity to the alkaline pH and reduced survival during induced thermotolerance. The ΔsplA2 mutant also exhibited hypersensitivity to the DTT-induced endoplasmic reticulum (ER) stress, increased microcrystalline cellulose utilization, increased protein secretion, and glucose accumulation in the culture supernatants. Moreover, the ΔsplA2 mutant could not grow on microcrystalline cellulose during ER stress. Furthermore, plc-1, cpe-1, and splA2 synthetically regulate the acquisition of thermotolerance induced by heat shock, responses to alkaline pH and ER stress, and utilization of cellulose and other alternate carbon sources in N. crassa. In addition, expression of the alkaline pH regulator, pac-3, and heat shock proteins, hsp60, and hsp80 was reduced in the Δplc-1, Δcpe-1, and ΔsplA2 single and double mutants. The expression of the unfolded protein response (UPR) markers grp-78 and pdi-1 was also significantly reduced in the mutants showing growth defect during ER stress. The increased cellulolytic activities of the ΔsplA2 and Δcpe-1; ΔsplA2 mutants were due to increased cbh-1, cbh-2, and endo-2 expression in N. crassa. Therefore, plc-1, cpe-1, and splA2 are involved in stress responses and cellulose utilization in N. crassa.
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Affiliation(s)
- Darshana Baruah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India.
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3
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Farhadi Cheshmeh Morvari S, McCann BL, Bignell EM. Conserved and Divergent Features of pH Sensing in Major Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:120-130. [PMID: 37577059 PMCID: PMC10421798 DOI: 10.1007/s40588-023-00195-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2023] [Indexed: 08/15/2023]
Abstract
Purpose of Review For human fungal pathogens, sensory perception of extracellular pH is essential for colonisation of mammalian tissues and immune evasion. The molecular complexes that perceive and transmit the fungal pH signal are membrane-proximal and essential for virulence and are therefore of interest as novel antifungal drug targets. Intriguingly, the sensory machinery has evolved divergently in different fungal pathogens, yet spatial co-ordination of cellular components is conserved. Recent Findings The recent discovery of a novel pH sensor in the basidiomycete pathogen Cryptococcus neformans highlights that, although the molecular conservation of fungal pH sensors is evolutionarily restricted, their subcellular localisation and coupling to essential components of the cellular ESCRT machinery are consistent features of the cellular pH sensing and adaptation mechanism. In both basidiomycetes and ascomycetes, the lipid composition of the plasma membrane to which pH sensing complexes are localised appears to have pivotal functional importance. Endocytosis of pH-sensing complexes occurs in multiple fungal species, but its relevance for signal transduction appears not to be universal. Summary Our overview of current understanding highlights conserved and divergent mechanisms of the pH sensing machinery in model and pathogenic fungal species, as well as important unanswered questions that must be addressed to inform the future study of such sensing mechanisms and to devise therapeutic strategies for manipulating them.
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Affiliation(s)
| | - Bethany L. McCann
- Medical Research Council Centre for Medical Mycology at The University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Elaine M. Bignell
- Medical Research Council Centre for Medical Mycology at The University of Exeter, Stocker Road, Exeter, EX4 4QD UK
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4
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Albacar M, Zekhnini A, Pérez-Valle J, Martínez JL, Casamayor A, Ariño J. Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization. Microb Cell Fact 2023; 22:63. [PMID: 37013612 PMCID: PMC10071690 DOI: 10.1186/s12934-023-02074-6] [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: 02/08/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast, in search of suitable novel promoters able to drive transcription in response to the pH signal. RESULTS In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. CONCLUSIONS This work defines in K. phaffii a subset of genes and diverse cellular pathways that are altered in response to moderate alkalinization of the medium, thus setting the basis for developing novel pH-controlled systems for heterologous protein expression in this fungus.
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Affiliation(s)
- Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Abdelghani Zekhnini
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Jorge Pérez-Valle
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - José L Martínez
- Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain.
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5
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Shimasawa M, Sakamaki JI, Maeda T, Mizushima N. The pH-sensing Rim101 pathway regulates cell size in budding yeast. J Biol Chem 2023; 299:102973. [PMID: 36738789 PMCID: PMC10011510 DOI: 10.1016/j.jbc.2023.102973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Although cell size regulation is crucial for cellular functions in a variety of organisms from bacteria to humans, the underlying mechanisms remain elusive. Here, we identify Rim21, a component of the pH-sensing Rim101 pathway, as a positive regulator of cell size through a flow cytometry-based genome-wide screen of Saccharomyces cerevisiae deletion mutants. We found that mutants defective in the Rim101 pathway were consistently smaller than wildtype cells in the log and stationary phases. We show that the expression of the active form of Rim101 increased the size of wildtype cells. Furthermore, the size of wildtype cells increased in response to external alkalization. Microscopic observation revealed that this cell size increase was associated with changes in both vacuolar and cytoplasmic volume. We also found that these volume changes were dependent on Rim21 and Rim101. In addition, a mutant lacking Vph1, a component of V-ATPase that is transcriptionally regulated by Rim101, was also smaller than wildtype cells, with no increase in size in response to alkalization. We demonstrate that the loss of Vph1 suppressed the Rim101-induced increase in cell size under physiological pH conditions. Taken together, our results suggest that the cell size of budding yeast is regulated by the Rim101-V-ATPase axis under physiological conditions as well as in response to alkaline stresses.
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Affiliation(s)
- Masaru Shimasawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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6
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Piccirillo S, Morgan AP, Leon AY, Smith AL, Honigberg SM. Investigating cell autonomy in microorganisms. Curr Genet 2022; 68:305-318. [PMID: 35119506 PMCID: PMC9101301 DOI: 10.1007/s00294-022-01231-5] [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: 11/08/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.
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Affiliation(s)
- Sarah Piccirillo
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andrew P. Morgan
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Andy Y. Leon
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Annika L. Smith
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
| | - Saul M. Honigberg
- Department of Genetics, Developmental and Evolutionary Biology, School of Biological and Chemical Sciences, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110, USA
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7
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Chaudhary A, Singh D. In-silico analysis of the regulatory region of effector protein genes in Verticillium dahliae. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Kiel Reese B, Sobol MS, Bowles MW, Hinrichs KU. Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:727543. [PMID: 37744089 PMCID: PMC10512353 DOI: 10.3389/ffunb.2021.727543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 09/26/2023]
Abstract
The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.
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Affiliation(s)
- Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, AL, United States
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, United States
- Hanse-Wissenschaftskolleg Institute for Advanced Study, Delmenhorst, Germany
| | - Morgan S. Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, United States
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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9
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Zhou X, Suo J, Liu C, Niu C, Zheng F, Li Q, Wang J. Genome comparison of three lager yeasts reveals key genes affecting yeast flocculation during beer fermentation. FEMS Yeast Res 2021; 21:6284804. [PMID: 34037755 DOI: 10.1093/femsyr/foab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/24/2021] [Indexed: 11/14/2022] Open
Abstract
Yeast flocculation plays an essential role in industrial application. Appropriate flocculation of yeast cells at the end of fermentation benefits the cell separation in production, which is an important characteristic of lager yeast for beer production. Due to the complex fermentation environment and diverse genetic background of yeast strains, it is difficult to explain the flocculation mechanism and find key genes that affect yeast flocculation during beer brewing. By analyzing the genomic mutation of two natural mutant yeasts with stronger flocculation ability compared to the parental strain, it was found that the mutated genes common in both mutants were enriched in protein processing in endoplasmic reticulum, membrane lipid metabolism and other pathways or biological processes involved in stress responses. Further functional verification of genes revealed that regulation of RIM101 and VPS36 played a role in lager yeast flocculation under the brewing condition. This work provided new clues for improving yeast flocculation in beer brewing.
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Affiliation(s)
- Xuefei Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Jingyi Suo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China.,Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Ave, Binhu District, Wuxi 214122, Jiangsu, China
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10
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Garza NM, Griffin AT, Zulkifli M, Qiu C, Kaplan CD, Gohil VM. A genome-wide copper-sensitized screen identifies novel regulators of mitochondrial cytochrome c oxidase activity. J Biol Chem 2021; 296:100485. [PMID: 33662401 PMCID: PMC8027276 DOI: 10.1016/j.jbc.2021.100485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022] Open
Abstract
Copper is essential for the activity and stability of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Loss-of-function mutations in genes required for copper transport to CcO result in fatal human disorders. Despite the fundamental importance of copper in mitochondrial and organismal physiology, systematic identification of genes that regulate mitochondrial copper homeostasis is lacking. To discover these genes, we performed a genome-wide screen using a library of DNA-barcoded yeast deletion mutants grown in copper-supplemented media. Our screen recovered a number of genes known to be involved in cellular copper homeostasis as well as genes previously not linked to mitochondrial copper biology. These newly identified genes include the subunits of the adaptor protein 3 complex (AP-3) and components of the cellular pH-sensing pathway Rim20 and Rim21, both of which are known to affect vacuolar function. We find that AP-3 and Rim mutants exhibit decreased vacuolar acidity, which in turn perturbs mitochondrial copper homeostasis and CcO function. CcO activity of these mutants could be rescued by either restoring vacuolar pH or supplementing growth media with additional copper. Consistent with these genetic data, pharmacological inhibition of the vacuolar proton pump leads to decreased mitochondrial copper content and a concomitant decrease in CcO abundance and activity. Taken together, our study uncovered novel genetic regulators of mitochondrial copper homeostasis and provided a mechanism by which vacuolar pH impacts mitochondrial respiration through copper homeostasis.
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Affiliation(s)
- Natalie M Garza
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Aaron T Griffin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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11
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The pH-sensing Rim101 pathway positively regulates the transcriptional expression of the calcium pump gene PMR1 to affect calcium sensitivity in budding yeast. Biochem Biophys Res Commun 2020; 532:453-458. [PMID: 32891431 DOI: 10.1016/j.bbrc.2020.08.083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 08/22/2020] [Indexed: 11/20/2022]
Abstract
In Saccharomyces cerevisiae, the Rim101 pathway senses extracellular pH changes through a complex consisted of Rim8, Rim9 and Rim21 at the plasma membrane. Activation of this sensor complex induces a proteolytical complex composed of Rim13 and Rim20 and leads to the C-terminal processing and activation of the transcription factor Rim101. Deletion mutants for RIM8, RIM9, RIM13, RIM20, RIM21 and RIM101 causes yeast cells to be sensitive to calcium stress, but how they regulate calcium sensitivity remain unknown. Here we show that deletion mutations of these six Rim101 pathway components elevate the activation level of the calcium/calcineurin signaling and the transcriptional expression level of the vacuolar calcium pump gene PMC1, but lead to a reduction in transcriptional expression level of the ER/Golgi calcium pump gene PMR1 in yeast cells. Deletion of NRG1, encoding one of the repression targets of Rim101, rescues the transcriptional expression of PMR1 in all these mutants. Furthermore, ectopic expression of a constitutively active form of Rim101 or further deletion of NRG1 suppresses the calcium sensitivity of these six deletion mutants. Therefore, the pH-sensing Rim101 pathway positively regulates the transcriptional expression of PMR through its downstream target Nrg1 to affect the calcium sensitivity of yeast cells.
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12
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Athanasopoulos A, André B, Sophianopoulou V, Gournas C. Fungal plasma membrane domains. FEMS Microbiol Rev 2020; 43:642-673. [PMID: 31504467 DOI: 10.1093/femsre/fuz022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/25/2019] [Indexed: 12/11/2022] Open
Abstract
The plasma membrane (PM) performs a plethora of physiological processes, the coordination of which requires spatial and temporal organization into specialized domains of different sizes, stability, protein/lipid composition and overall architecture. Compartmentalization of the PM has been particularly well studied in the yeast Saccharomyces cerevisiae, where five non-overlapping domains have been described: The Membrane Compartments containing the arginine permease Can1 (MCC), the H+-ATPase Pma1 (MCP), the TORC2 kinase (MCT), the sterol transporters Ltc3/4 (MCL), and the cell wall stress mechanosensor Wsc1 (MCW). Additional cortical foci at the fungal PM are the sites where clathrin-dependent endocytosis occurs, the sites where the external pH sensing complex PAL/Rim localizes, and sterol-rich domains found in apically grown regions of fungal membranes. In this review, we summarize knowledge from several fungal species regarding the organization of the lateral PM segregation. We discuss the mechanisms of formation of these domains, and the mechanisms of partitioning of proteins there. Finally, we discuss the physiological roles of the best-known membrane compartments, including the regulation of membrane and cell wall homeostasis, apical growth of fungal cells and the newly emerging role of MCCs as starvation-protective membrane domains.
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Affiliation(s)
- Alexandros Athanasopoulos
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
| | - Bruno André
- Molecular Physiology of the Cell laboratory, Université Libre de Bruxelles (ULB), Institut de Biologie et de Médecine Moléculaires, rue des Pr Jeener et Brachet 12, 6041, Gosselies, Belgium
| | - Vicky Sophianopoulou
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
| | - Christos Gournas
- Microbial Molecular Genetics Laboratory, Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos,' Patr. Grigoriou E & 27 Neapoleos St. 15341, Agia Paraskevi, Greece
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13
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Maki M. Structures and functions of penta-EF-hand calcium-binding proteins and their interacting partners: enigmatic relationships between ALG-2 and calpain-7. Biosci Biotechnol Biochem 2019; 84:651-660. [PMID: 31814542 DOI: 10.1080/09168451.2019.1700099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The penta-EF-hand (PEF) protein family includes ALG-2 (gene name, PDCD6) and its paralogs as well as classical calpain family members. ALG-2 is a prototypic PEF protein that is widely distributed in eukaryotes and interacts with a variety of proteins in a Ca2+-dependent manner. Mammalian ALG-2 and its interacting partners have various modulatory roles including roles in cell death, signal transduction, membrane repair, ER-to-Golgi vesicular transport, and RNA processing. Some ALG-2-interacting proteins are key factors that function in the endosomal sorting complex required for transport (ESCRT) system. On the other hand, mammalian calpain-7 (CAPN7) lacks the PEF domain but contains two microtubule-interacting and trafficking (MIT) domains in tandem. CAPN7 interacts with a subset of ESCRT-III proteins through the MIT domains and regulates EGF receptor downregulation. Structures and functions of ALG-2 and those of its interacting partners as well as relationships with the calpain family are reviewed in this article.
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Affiliation(s)
- Masatoshi Maki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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14
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Piccirillo S, McCune AH, Dedert SR, Kempf CG, Jimenez B, Solst SR, Tiede-Lewis LM, Honigberg SM. How Boundaries Form: Linked Nonautonomous Feedback Loops Regulate Pattern Formation in Yeast Colonies. Genetics 2019; 213:1373-1386. [PMID: 31619446 PMCID: PMC6893387 DOI: 10.1534/genetics.119.302700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/15/2019] [Indexed: 12/28/2022] Open
Abstract
Under conditions in which budding yeast form colonies and then undergo meiosis/sporulation, the resulting colonies are organized such that a sharply defined layer of meiotic cells overlays a layer of unsporulated cells termed "feeder cells." This differentiation pattern requires activation of both the Rlm1/cell-wall integrity pathway and the Rim101/alkaline-response pathway. In the current study, we analyzed the connection between these two signaling pathways in regulating colony development by determining expression patterns and cell-autonomy relationships. We present evidence that two parallel cell-nonautonomous positive-feedback loops are active in colony patterning, an Rlm1-Slt2 loop active in feeder cells and an Rim101-Ime1 loop active in meiotic cells. The Rlm1-Slt2 loop is expressed first and subsequently activates the Rim101-Ime1 loop through a cell-nonautonomous mechanism. Once activated, each feedback loop activates the cell fate specific to its colony region. At the same time, cell-autonomous mechanisms inhibit ectopic fates within these regions. In addition, once the second loop is active, it represses the first loop through a cell-nonautonomous mechanism. Linked cell-nonautonomous positive-feedback loops, by amplifying small differences in microenvironments, may be a general mechanism for pattern formation in yeast and other organisms.
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Affiliation(s)
- Sarah Piccirillo
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Abbigail H McCune
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Samuel R Dedert
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Cassandra G Kempf
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Brian Jimenez
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Shane R Solst
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
| | - LeAnn M Tiede-Lewis
- UMKC Department of Oral and Craniofacial Sciences, University of Missouri-Kansas City, Missouri 64108
| | - Saul M Honigberg
- Division of Cell Biology and Biophysics, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Missouri 64110
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15
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Kim MS, Cho KH, Park KH, Jang J, Hahn JS. Activation of Haa1 and War1 transcription factors by differential binding of weak acid anions in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 47:1211-1224. [PMID: 30476185 PMCID: PMC6379682 DOI: 10.1093/nar/gky1188] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 01/03/2023] Open
Abstract
In Saccharomyces cerevisiae, Haa1 and War1 transcription factors are involved in cellular adaptation against hydrophilic weak acids and lipophilic weak acids, respectively. However, it is unclear how these transcription factors are differentially activated depending on the identity of the weak acid. Using a field-effect transistor (FET)-type biosensor based on carbon nanofibers, in the present study we demonstrate that Haa1 and War1 directly bind to various weak acid anions with different affinities. Haa1 is most sensitive to acetate, followed by lactate, whereas War1 is most sensitive to benzoate, followed by sorbate, reflecting their differential activation during weak acid stresses. We show that DNA binding by Haa1 is induced in the presence of acetic acid and that the N-terminal Zn-binding domain is essential for this activity. Acetate binds to the N-terminal 150-residue region, and the transcriptional activation domain is located between amino acid residues 230 and 483. Our data suggest that acetate binding converts an inactive Haa1 to the active form, which is capable of DNA binding and transcriptional activation.
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Affiliation(s)
- Myung Sup Kim
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kyung Hee Cho
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kwang Hyun Park
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jyongsik Jang
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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16
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Rockenfeller P, Gourlay CW. Lipotoxicty in yeast: a focus on plasma membrane signalling and membrane contact sites. FEMS Yeast Res 2019; 18:4953420. [PMID: 29718175 PMCID: PMC5905628 DOI: 10.1093/femsyr/foy034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/23/2018] [Indexed: 12/23/2022] Open
Abstract
Lipotoxicity is a pathophysiological process triggered by lipid overload. In metazoans, lipotoxicity is characterised by the ectopic deposition of lipids on organs other than adipose tissue. This leads to organ dysfunction, cell death, and is intimately linked to lipid-associated diseases such as cardiac dysfunction, atherosclerosis, stroke, hepatosteatosis, cancer and the metabolic syndrome. The molecules involved in eliciting lipotoxicity include FAs and their acyl-CoA derivatives, triacylglycerol (TG), diacylglycerol (DG), ceramides, acyl-carnitines and phospholipids. However, the cellular transport of toxic lipids through membrane contact sites (MCS) and vesicular mechanisms as well as lipid metabolism that progress lipotoxicity to the onset of disease are not entirely understood. Yeast has proven a useful model organism to study the molecular mechanisms of lipotoxicity. Recently, the Rim101 pathway, which senses alkaline pH and the lipid status at the plasmamembrane, has been connected to lipotoxicity. In this review article, we summarise recent research advances on the Rim101 pathway and MCS in the context of lipotoxicity in yeast and present a perspective for future research directions.
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Affiliation(s)
- Patrick Rockenfeller
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ Kent, UK.,Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstr. 50, 8010 Graz, Austria
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ Kent, UK
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17
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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18
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Silva R, de Almeida DM, Cabral BCA, Dias VHG, Mello ICDTE, Ürményi TP, Woerner AE, Neto RSDM, Budowle B, Nassar CAG. Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant. PLoS One 2018; 13:e0205228. [PMID: 30286173 PMCID: PMC6171911 DOI: 10.1371/journal.pone.0205228] [Citation(s) in RCA: 3] [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: 08/22/2017] [Accepted: 09/21/2018] [Indexed: 11/28/2022] Open
Abstract
Microorganisms developing in the liner of the spent fuel pool (SFP) and the fuel transfer channel (FTC) of a Nuclear Power Plant (NPP) can form high radiation resistant biofilms and cause corrosion. Due to difficulties and limitations to obtain large samples from SFP and FTC, cotton swabs were used to collect the biofilm from the wall of these installations. Molecular characterization was performed using massively parallel sequencing to obtain a taxonomic and functional gene classification. Also, samples from the drainage system were evaluated because microorganisms may travel over the 12-meter column of the pool water of the Brazilian Nuclear Power Plant (Angra1), which has been functioning since 1985. Regardless of the treatment of the pool water, our data reveal the unexpected presence of Fungi (Basidiomycota and Ascomycota) as the main contaminators of the SFP and FTC. Ustilaginomycetes (Basidiomycota) was the major class contributor (70%) in the SFP and FTC reflecting the little diversity in these sites; nevertheless, Proteobacteria, Actinobacteria, Firmicutes (Bacilli) were present in small proportions. Mapping total reads against six fungal reference genomes indicate that there is, in fact, a high abundance of fungal sequences in samples collected from SFP and FTC. Analysis of the ribosomal internal transcribed spacer (ITS) 1 and 2 regions and the protein found in the mitochondria of eukaryotic cells, cytochrome b (cytb) grouped our sample fungi in the clade 7 as Ustilago and Pseudozyma. In contrast, in the drainage system, Alphaproteobacteria were present in high abundances (55%). The presence of Sphingopyxis, Mesorhizobium, Erythrobacter, Sphingomonas, Novosphingobium, Sphingobium, Chelativorans, Oceanicaulis, Acidovorax, and Cyanobacteria was observed. Based on genomic annotation data, the assessment of the biological function found a higher proportion of protein-coding sequences related to respiration and protein metabolism in SFP and FTC samples. The knowledge of this biological inventory present in the system may contribute to further studies of potential microorganisms that might be useful for bioremediation of nuclear waste.
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Affiliation(s)
- Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
| | - Darcy Muniz de Almeida
- Escola Politécnica & Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Victor Hugo Giordano Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Turán Péter Ürményi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, United States of America
| | | | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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19
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Sánchez-Rangel D, Hernández-Domínguez EE, Pérez-Torres CA, Ortiz-Castro R, Villafán E, Rodríguez-Haas B, Alonso-Sánchez A, López-Buenfil A, Carrillo-Ortiz N, Hernández-Ramos L, Ibarra-Laclette E. Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. BMC Genomics 2018; 19:721. [PMID: 30285612 PMCID: PMC6167834 DOI: 10.1186/s12864-018-5083-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Ambrosia Fusarium Clade phytopathogenic Fusarium fungi species have a symbiotic relationship with ambrosia beetles in the genus Euwallacea (Coleoptera: Curculionidae). Related beetle species referred to as Euwallacea sp. near fornicatus have been spread in California, USA and are recognized as the causal agents of Fusarium dieback, a disease that causes mortality of many plant species. Despite the importance of this fungi, no transcriptomic resources have been generated. The datasets described here represent the first ever transcripts available for these species. We focused our study on the isolated species of Fusarium that is associated with one of the cryptic species referred to as Kuroshio Shot Hole Borer (KSHB) Euwallacea sp. near fornicatus. RESULTS Hydrogen concentration is a critical signal in fungi for growth and host colonization, the aim of this study was to evaluate the effect of different pH conditions on growth and gene expression of the fungus Fusarium sp. associated with KSHB. An RNA-seq approach was used to compare the gene expression of the fungus grown for 2 weeks in liquid medium at three different pH levels (5.0, 6.0, and 7.0). An unbuffered treatment was included to evaluate the capability of the fungus to change the pH of its environment and the impact in gene expression. The results showed that the fungus can grow and modulate its genetic expression at different pH conditions; however, growth was stunted in acidic pH in comparison with neutral pH. The results showed a differential expression pattern in each pH condition even when acidic conditions prevailed at the end of the experiment. After comparing transcriptomics data from the three treatments, we found a total of 4,943 unique transcripts that were differentially expressed. CONCLUSIONS We identified transcripts related to pH signaling such as the conserved PAL/RIM pathway, some transcripts related to secondary metabolism and other transcripts that were differentially expressed. Our analysis suggests possible mechanisms involved in pathogenicity in this novel Fusarium species. This is the first report that shows transcriptomic data of this pathogen as well as the first report of genes and proteins involved in their metabolism identifying potential virulence factors.
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Affiliation(s)
- Diana Sánchez-Rangel
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
- Cátedra CONACYT en el Instituto de Ecología A.C, Xalapa, Veracruz Mexico
| | - Eric-Edmundo Hernández-Domínguez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
- Cátedra CONACYT en el Instituto de Ecología A.C, Xalapa, Veracruz Mexico
| | - Claudia-Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
- Cátedra CONACYT en el Instituto de Ecología A.C, Xalapa, Veracruz Mexico
| | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
- Cátedra CONACYT en el Instituto de Ecología A.C, Xalapa, Veracruz Mexico
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
| | - Benjamín Rodríguez-Haas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
| | | | - Abel López-Buenfil
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, 55740 Tecámac, Estado de México Mexico
| | - Nayeli Carrillo-Ortiz
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, 55740 Tecámac, Estado de México Mexico
| | - Lervin Hernández-Ramos
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Unidad Integral de Diagnóstico, Servicios y Constatación, 55740 Tecámac, Estado de México Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, 91070 Xalapa, Veracruz Mexico
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20
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Rockenfeller P, Smolnig M, Diessl J, Bashir M, Schmiedhofer V, Knittelfelder O, Ring J, Franz J, Foessl I, Khan MJ, Rost R, Graier WF, Kroemer G, Zimmermann A, Carmona-Gutierrez D, Eisenberg T, Büttner S, Sigrist SJ, Kühnlein RP, Kohlwein SD, Gourlay CW, Madeo F. Diacylglycerol triggers Rim101 pathway-dependent necrosis in yeast: a model for lipotoxicity. Cell Death Differ 2018; 25:767-783. [PMID: 29230001 PMCID: PMC5864183 DOI: 10.1038/s41418-017-0014-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/18/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023] Open
Abstract
The loss of lipid homeostasis can lead to lipid overload and is associated with a variety of disease states. However, little is known as to how the disruption of lipid regulation or lipid overload affects cell survival. In this study we investigated how excess diacylglycerol (DG), a cardinal metabolite suspected to mediate lipotoxicity, compromises the survival of yeast cells. We reveal that increased DG achieved by either genetic manipulation or pharmacological administration of 1,2-dioctanoyl-sn-glycerol (DOG) triggers necrotic cell death. The toxic effects of DG are linked to glucose metabolism and require a functional Rim101 signaling cascade involving the Rim21-dependent sensing complex and the activation of a calpain-like protease. The Rim101 cascade is an established pathway that triggers a transcriptional response to alkaline or lipid stress. We propose that the Rim101 pathway senses DG-induced lipid perturbation and conducts a signaling response that either facilitates cellular adaptation or triggers lipotoxic cell death. Using established models of lipotoxicity, i.e., high-fat diet in Drosophila and palmitic acid administration in cultured human endothelial cells, we present evidence that the core mechanism underlying this calpain-dependent lipotoxic cell death pathway is phylogenetically conserved.
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Affiliation(s)
- Patrick Rockenfeller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria.
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Martin Smolnig
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Jutta Diessl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Mina Bashir
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Division of Endocrinology and Diabetology, Medical University of Graz, Graz, 8010, Austria
| | - Vera Schmiedhofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Oskar Knittelfelder
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Julia Ring
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Joakim Franz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Ines Foessl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Division of Endocrinology and Diabetology, Medical University of Graz, Graz, 8010, Austria
| | - Muhammad J Khan
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Islamabad, 44000, Pakistan
| | - René Rost
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
| | - Wolfgang F Graier
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, 8010, Austria
| | - Guido Kroemer
- INSERM U848, Villejuif, 94805, France
- Metabolomics Platform, Institut Gustave Roussy, Paris, 94805, France
- Centre de Recherche des Cordeliers, Paris, 75006, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, 75015, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, 75270, France
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | | | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden
| | - Stephan J Sigrist
- Institute for Biology, Freie Universität Berlin, Berlin, 14195, Germany
- NeuroCure Charité, Berlin, 10117, Germany
| | - Ronald P Kühnlein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
- Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Sepp D Kohlwein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed-Graz, Graz, 8010, Austria
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, 8010, Austria.
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21
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Yeast Cells Exposed to Exogenous Palmitoleic Acid Either Adapt to Stress and Survive or Commit to Regulated Liponecrosis and Die. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:3074769. [PMID: 29636840 PMCID: PMC5831759 DOI: 10.1155/2018/3074769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/27/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
Abstract
A disturbed homeostasis of cellular lipids and the resulting lipotoxicity are considered to be key contributors to many human pathologies, including obesity, metabolic syndrome, type 2 diabetes, cardiovascular diseases, and cancer. The yeast Saccharomyces cerevisiae has been successfully used for uncovering molecular mechanisms through which impaired lipid metabolism causes lipotoxicity and elicits different forms of regulated cell death. Here, we discuss mechanisms of the “liponecrotic” mode of regulated cell death in S. cerevisiae. This mode of regulated cell death can be initiated in response to a brief treatment of yeast with exogenous palmitoleic acid. Such treatment prompts the incorporation of exogenously added palmitoleic acid into phospholipids and neutral lipids. This orchestrates a global remodeling of lipid metabolism and transfer in the endoplasmic reticulum, mitochondria, lipid droplets, and the plasma membrane. Certain features of such remodeling play essential roles either in committing yeast to liponecrosis or in executing this mode of regulated cell death. We also outline four processes through which yeast cells actively resist liponecrosis by adapting to the cellular stress imposed by palmitoleic acid and maintaining viability. These prosurvival cellular processes are confined in the endoplasmic reticulum, lipid droplets, peroxisomes, autophagosomes, vacuoles, and the cytosol.
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22
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Compensatory Internalization of Pma1 in V-ATPase Mutants in Saccharomyces cerevisiae Requires Calcium- and Glucose-Sensitive Phosphatases. Genetics 2017; 208:655-672. [PMID: 29254995 PMCID: PMC5788529 DOI: 10.1534/genetics.117.300594] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/09/2017] [Indexed: 11/23/2022] Open
Abstract
Loss of V-ATPase activity in organelles triggers compensatory endocytic downregulation of the plasma membrane proton pump Pma1. Here, Velivela and Kane... Loss of V-ATPase activity in organelles, whether through V-ATPase inhibition or V-ATPase (vma) mutations, triggers a compensatory downregulation of the essential plasma membrane proton pump Pma1 in Saccharomyces cerevisiae. We have previously determined that the α-arrestin Rim8 and ubiquitin ligase Rsp5 are essential for Pma1 ubiquination and endocytosis in response to loss of V-ATPase activity. Here, we show that Pma1 endocytosis in V-ATPase mutants does not require Rim101 pathway components upstream and downstream of Rim8, indicating that Rim8 is acting independently in Pma1 internalization. We find that two phosphatases, the calcium-responsive phosphatase calcineurin and the glucose-sensitive phosphatase Glc7 (PP1), and one of the Glc7 regulatory subunits Reg1, exhibit negative synthetic genetic interactions with vma mutants, and demonstrate that both phosphatases are essential for ubiquitination and endocytic downregulation of Pma1 in these mutants. Although both acute and chronic loss of V-ATPase activity trigger the internalization of ∼50% of surface Pma1, a comparable reduction in Pma1 expression in a pma1-007 mutant neither compensates for loss of V-ATPase activity nor stops further Pma1 endocytosis. The results indicate that the cell surface level of Pma1 is not directly sensed and that internalized Pma1 may play a role in compensating for loss of V-ATPase-dependent acidification. Taken together, these results provide new insights into cross talk between two major proton pumps central to cellular pH control.
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Virgilio S, Bertolini MC. Functional diversity in the pH signaling pathway: an overview of the pathway regulation in Neurospora crassa. Curr Genet 2017; 64:529-534. [DOI: 10.1007/s00294-017-0772-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 10/18/2022]
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24
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Affiliation(s)
- Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
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25
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Arlia-Ciommo A, Svistkova V, Mohtashami S, Titorenko VI. A novel approach to the discovery of anti-tumor pharmaceuticals: searching for activators of liponecrosis. Oncotarget 2017; 7:5204-25. [PMID: 26636650 PMCID: PMC4868681 DOI: 10.18632/oncotarget.6440] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/21/2015] [Indexed: 02/04/2023] Open
Abstract
A recently conducted chemical genetic screen for pharmaceuticals that can extend longevity of the yeast Saccharomyces cerevisiae has identified lithocholic acid as a potent anti-aging molecule. It was found that this hydrophobic bile acid is also a selective anti-tumor chemical compound; it kills different types of cultured cancer cells if used at concentrations that do not compromise the viability of non-cancerous cells. These studies have revealed that yeast can be successfully used as a model organism for high-throughput screens aimed at the discovery of selectively acting anti-tumor small molecules. Two metabolic traits of rapidly proliferating fermenting yeast, namely aerobic glycolysis and lipogenesis, are known to be similar to those of cancer cells. The mechanisms underlying these key metabolic features of cancer cells and fermenting yeast have been established; such mechanisms are discussed in this review. We also suggest how a yeast-based chemical genetic screen can be used for the high-throughput development of selective anti-tumor pharmaceuticals that kill only cancer cells. This screen consists of searching for chemical compounds capable of increasing the abundance of membrane lipids enriched in unsaturated fatty acids that would therefore be toxic only to rapidly proliferating cells, such as cancer cells and fermenting yeast.
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Affiliation(s)
| | | | - Sadaf Mohtashami
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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26
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Ono Y, Saido TC, Sorimachi H. Calpain research for drug discovery: challenges and potential. Nat Rev Drug Discov 2016; 15:854-876. [PMID: 27833121 DOI: 10.1038/nrd.2016.212] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calpains are a family of proteases that were scientifically recognized earlier than proteasomes and caspases, but remain enigmatic. However, they are known to participate in a multitude of physiological and pathological processes, performing 'limited proteolysis' whereby they do not destroy but rather modulate the functions of their substrates. Calpains are therefore referred to as 'modulator proteases'. Multidisciplinary research on calpains has begun to elucidate their involvement in pathophysiological mechanisms. Therapeutic strategies targeting malfunctions of calpains have been developed, driven primarily by improvements in the specificity and bioavailability of calpain inhibitors. Here, we review the calpain superfamily and calpain-related disorders, and discuss emerging calpain-targeted therapeutic strategies.
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Affiliation(s)
- Yasuko Ono
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science (IGAKUKEN), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Sorimachi
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science (IGAKUKEN), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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27
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Maki M, Takahara T, Shibata H. Multifaceted Roles of ALG-2 in Ca(2+)-Regulated Membrane Trafficking. Int J Mol Sci 2016; 17:ijms17091401. [PMID: 27571067 PMCID: PMC5037681 DOI: 10.3390/ijms17091401] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/15/2022] Open
Abstract
ALG-2 (gene name: PDCD6) is a penta-EF-hand Ca2+-binding protein and interacts with a variety of proteins in a Ca2+-dependent fashion. ALG-2 recognizes different types of identified motifs in Pro-rich regions by using different hydrophobic pockets, but other unknown modes of binding are also used for non-Pro-rich proteins. Most ALG-2-interacting proteins associate directly or indirectly with the plasma membrane or organelle membranes involving the endosomal sorting complex required for transport (ESCRT) system, coat protein complex II (COPII)-dependent ER-to-Golgi vesicular transport, and signal transduction from membrane receptors to downstream players. Binding of ALG-2 to targets may induce conformational change of the proteins. The ALG-2 dimer may also function as a Ca2+-dependent adaptor to bridge different partners and connect the subnetwork of interacting proteins.
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Affiliation(s)
- Masatoshi Maki
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Terunao Takahara
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hideki Shibata
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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28
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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29
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Du H, Huang G. Environmental pH adaption and morphological transitions in Candida albicans. Curr Genet 2015; 62:283-6. [PMID: 26581628 DOI: 10.1007/s00294-015-0540-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/26/2022]
Abstract
The human fungal pathogen Candida albicans encounters a wide range of pH stresses during its commensal and pathogenic lifestyles. It has been well studied that environmental pH regulates the yeast-filamentous growth transition in this fungus. White-opaque switching is another type of phenotypic transitions in C. albicans. White and opaque cells are two morphologically and functionally distinct cell types, which differ in many aspects including global gene expression profiles, virulence, mating competency, and susceptibility to antifungals. The switch between white and opaque cell types is heritable and epigenetically regulated. In a recently study, Sun et al. (Eukaryot Cell 14:1127-1134, 2015) reported that pH plays a critical role in the regulation of the white-opaque phenotypic switch and sexual mating in C. albicans via both the conserved Rim101-mediated pH sensing and cAMP signaling pathways. The effect of pH on the two biological processes may represent a balancing act between host environmental adaptation and sexual reproduction in this pathogenic fungus.
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Affiliation(s)
- Han Du
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanghua Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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30
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Richard VR, Beach A, Piano A, Leonov A, Feldman R, Burstein MT, Kyryakov P, Gomez-Perez A, Arlia-Ciommo A, Baptista S, Campbell C, Goncharov D, Pannu S, Patrinos D, Sadri B, Svistkova V, Victor A, Titorenko VI. Mechanism of liponecrosis, a distinct mode of programmed cell death. Cell Cycle 2015; 13:3707-26. [PMID: 25483081 DOI: 10.4161/15384101.2014.965003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An exposure of the yeast Saccharomyces cerevisiae to exogenous palmitoleic acid (POA) elicits "liponecrosis," a mode of programmed cell death (PCD) which differs from the currently known PCD subroutines. Here, we report the following mechanism for liponecrotic PCD. Exogenously added POA is incorporated into POA-containing phospholipids that then amass in the endoplasmic reticulum membrane, mitochondrial membranes and the plasma membrane. The buildup of the POA-containing phospholipids in the plasma membrane reduces the level of phosphatidylethanolamine in its extracellular leaflet, thereby increasing plasma membrane permeability for small molecules and committing yeast to liponecrotic PCD. The excessive accumulation of POA-containing phospholipids in mitochondrial membranes impairs mitochondrial functionality and causes the excessive production of reactive oxygen species in mitochondria. The resulting rise in cellular reactive oxygen species above a critical level contributes to the commitment of yeast to liponecrotic PCD by: (1) oxidatively damaging numerous cellular organelles, thereby triggering their massive macroautophagic degradation; and (2) oxidatively damaging various cellular proteins, thus impairing cellular proteostasis. Several cellular processes in yeast exposed to POA can protect cells from liponecrosis. They include: (1) POA oxidation in peroxisomes, which reduces the flow of POA into phospholipid synthesis pathways; (2) POA incorporation into neutral lipids, which prevents the excessive accumulation of POA-containing phospholipids in cellular membranes; (3) mitophagy, a selective macroautophagic degradation of dysfunctional mitochondria, which sustains a population of functional mitochondria needed for POA incorporation into neutral lipids; and (4) a degradation of damaged, dysfunctional and aggregated cytosolic proteins, which enables the maintenance of cellular proteostasis.
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Key Words
- CFU, colony forming units
- CL, cardiolipin
- Cvt, cytoplasm-to-vacuole pathway
- ER, endoplasmic reticulum
- IMM, inner mitochondrial membrane
- LD, lipid droplets
- NL, neutral lipids
- PA, phosphatidic acid
- PC, phosphatidylcholine
- PCD, programmed cell death
- PE, phosphatidylethanolamine
- PI, phosphatidylinositol
- PL, phospholipids
- PM, plasma membrane
- POA, palmitoleic acid
- PS, phosphatidylserine
- ROS, reactive oxygen species
- TAG, triacylglycerols
- WT, wild-type
- apoptosis
- autophagy
- cellular proteostasis
- lipid metabolism in cellular organelles
- mechanisms of programmed cell death
- mitochondria,
- mitophagy
- plasma membrane
- signal transduction
- yeast
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Affiliation(s)
- Vincent R Richard
- a Department of Biology ; Concordia University ; Montreal , QC Canada
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pH Regulates White-Opaque Switching and Sexual Mating in Candida albicans. EUKARYOTIC CELL 2015; 14:1127-34. [PMID: 26342021 DOI: 10.1128/ec.00123-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 08/31/2015] [Indexed: 11/20/2022]
Abstract
As a successful commensal and pathogen of humans, Candida albicans encounters a wide range of environmental conditions. Among them, ambient pH, which changes frequently and affects many biological processes in this species, is an important factor, and the ability to adapt to pH changes is tightly linked with pathogenesis and morphogenesis. In this study, we report that pH has a profound effect on white-opaque switching and sexual mating in C. albicans. Acidic pH promotes white-to-opaque switching under certain culture conditions but represses sexual mating. The Rim101-mediated pH-sensing pathway is involved in the control of pH-regulated white-opaque switching and the mating response. Phr2 and Rim101 could play a major role in acidic pH-induced opaque cell formation. Despite the fact that the cyclic AMP (cAMP) signaling pathway does not play a major role in pH-regulated white-opaque switching and mating, white and opaque cells of the cyr1/cyr1 mutant, which is defective in the production of cAMP, showed distinct growth defects under acidic and alkaline conditions. We further discovered that acidic pH conditions repressed sexual mating due to the failure of activation of the Ste2-mediated α-pheromone response pathway in opaque A: cells. The effects of pH changes on phenotypic switching and sexual mating could involve a balance of host adaptation and sexual reproduction in C. albicans.
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32
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Conserved Mode of Interaction between Yeast Bro1 Family V Domains and YP(X)nL Motif-Containing Target Proteins. EUKARYOTIC CELL 2015; 14:976-82. [PMID: 26150415 DOI: 10.1128/ec.00091-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/02/2015] [Indexed: 11/20/2022]
Abstract
Yeast Bro1 and Rim20 belong to a family of proteins which possess a common architecture of Bro1 and V domains. Alix and His domain protein tyrosine phosphatase (HD-PTP), mammalian Bro1 family proteins, bind YP(X)nL (n = 1 to 3) motifs in their target proteins through their V domains. In Alix, the Phe residue, which is located in the hydrophobic groove of the V domain, is critical for binding to the YP(X)nL motif. Although the overall sequences are not highly conserved between mammalian and yeast V domains, we show that the conserved Phe residue in the yeast Bro1 V domain is important for binding to its YP(X)nL-containing target protein, Rfu1. Furthermore, we show that Rim20 binds to its target protein Rim101 through the interaction between the V domain of Rim20 and the YPIKL motif of Rim101. The mutation of either the critical Phe residue in the Rim20 V domain or the YPIKL motif of Rim101 affected the Rim20-mediated processing of Rim101. These results suggest that the interactions between V domains and YP(X)nL motif-containing proteins are conserved from yeast to mammalian cells. Moreover, the specificities of each V domain to their target protein suggest that unidentified elements determine the binding specificity.
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33
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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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34
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Marqués MC, Zamarbide-Forés S, Pedelini L, Llopis-Torregrosa V, Yenush L. A functional Rim101 complex is required for proper accumulation of the Ena1 Na+-ATPase protein in response to salt stress in Saccharomyces cerevisiae. FEMS Yeast Res 2015; 15:fov017. [PMID: 25934176 DOI: 10.1093/femsyr/fov017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2015] [Indexed: 12/14/2022] Open
Abstract
The maintenance of ionic homeostasis is essential for cell viability, thus the activity of plasma membrane ion transporters must be tightly controlled. Previous studies in Saccharomyces cerevisiae revealed that the proper trafficking of several nutrient permeases requires the E3 ubiquitin ligase Rsp5 and, in many cases, the presence of specific adaptor proteins needed for Rsp5 substrate recognition. Among these adaptor proteins are nine members of the arrestin-related trafficking adaptor (ART) family. We studied the possible role of the ART family in the regulation of monovalent cation transporters. We show here that the salt sensitivity phenotype of the rim8/art9 mutant is due to severe defects in Ena1 protein accumulation, which is not attributable to transcriptional defects. Many components of the Rim pathway are required for correct Ena1 accumulation, but not for the accumulation of other nutrient permeases. Moreover, we observe that strains lacking components of the endosomal sorting complexes required for transport (ESCRT) pathway previously described to play a role in Rim complex formation present similar defects in Ena1 accumulation. Our results show that, in response to salt stress, a functional Rim complex via specific ESCRT interactions is required for the proper accumulation of the Ena1 protein, but not induction of the ENA1 gene.
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Affiliation(s)
- M Carmen Marqués
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia 46022, Spain
| | - Sara Zamarbide-Forés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia 46022, Spain
| | - Leda Pedelini
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia 46022, Spain
| | - Vicent Llopis-Torregrosa
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia 46022, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Avd. de los Naranjos s/n, Valencia 46022, Spain
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35
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Herrero E, Wellinger RE. Yeast as a model system to study metabolic impact of selenium compounds. MICROBIAL CELL 2015; 2:139-149. [PMID: 28357286 PMCID: PMC5349236 DOI: 10.15698/mic2015.05.200] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Inorganic Se forms such as selenate or selenite (the two more abundant forms in nature) can be toxic in Saccharomyces cerevisiae cells, which constitute an adequate model to study such toxicity at the molecular level and the functions participating in protection against Se compounds. Those Se forms enter the yeast cell through other oxyanion transporters. Once inside the cell, inorganic Se forms may be converted into selenide through a reductive pathway that in physiological conditions involves reduced glutathione with its consequent oxidation into diglutathione and alteration of the cellular redox buffering capacity. Selenide can subsequently be converted by molecular oxygen into elemental Se, with production of superoxide anions and other reactive oxygen species. Overall, these events result in DNA damage and dose-dependent reversible or irreversible protein oxidation, although additional oxidation of other cellular macromolecules cannot be discarded. Stress-adaptation pathways are essential for efficient Se detoxification, while activation of DNA damage checkpoint and repair pathways protects against Se-mediated genotoxicity. We propose that yeast may be used to improve our knowledge on the impact of Se on metal homeostasis, the identification of Se-targets at the DNA and protein levels, and to gain more insights into the mechanism of Se-mediated apoptosis.
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Affiliation(s)
- Enrique Herrero
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Rovira Roure 80, 25198 Lleida, Spain
| | - Ralf E Wellinger
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, 41092 Sevilla, Spain
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36
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Herrador A, Livas D, Soletto L, Becuwe M, Léon S, Vincent O. Casein kinase 1 controls the activation threshold of an α-arrestin by multisite phosphorylation of the interdomain hinge. Mol Biol Cell 2015; 26:2128-38. [PMID: 25851600 PMCID: PMC4472021 DOI: 10.1091/mbc.e14-11-1552] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/30/2015] [Indexed: 12/16/2022] Open
Abstract
The yeast Rim8/Art9 α-arrestin, involved in ambient pH signaling, is regulated through multisite phosphorylation of the hinge region by the plasma membrane–associated casein kinase 1. This modification prevents its stable association with the pH sensor protein Rim21 at the plasma membrane and thereby inhibits signal transduction at acidic pH. α-Arrestins play a key role as trafficking adaptors in both yeast and mammals. The yeast Rim8/Art9 α-arrestin mediates the recruitment of endosomal sorting complex required for transport (ESCRT) to the seven-transmembrane protein Rim21 in the ambient pH signaling RIM pathway. ESCRT is believed to function as a signaling platform that enables the proteolytic activation of the Rim101 transcription factor upon external alkalization. Here we provide evidence that the pH signal promotes the stable association of Rim8 with Rim21 at the plasma membrane. We show that Rim8 is phosphorylated in a pH-independent but Rim21-dependent manner by the plasma membrane–associated casein kinase 1 (CK1). We further show that this process involves a cascade of phosphorylation events within the hinge region connecting the arrestin domains. Strikingly, loss of casein kinase 1 activity causes constitutive activation of the RIM pathway, and, accordingly, pH signaling is activated in a phosphodeficient Rim8 mutant and impaired in the corresponding phosphomimetic mutant. Our results indicate that Rim8 phosphorylation prevents its accumulation at the plasma membrane at acidic pH and thereby inhibits RIM signaling. These findings support a model in which CK1-mediated phosphorylation of Rim8 contributes to setting a signaling threshold required to inhibit the RIM pathway at acidic pH.
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Affiliation(s)
- Antonio Herrador
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Daniela Livas
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Lucía Soletto
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Michel Becuwe
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Sébastien Léon
- Institut Jacques Monod, Centre National de la Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid, Spain
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37
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Smardon AM, Kane PM. Loss of vacuolar H+-ATPase activity in organelles signals ubiquitination and endocytosis of the yeast plasma membrane proton pump Pma1p. J Biol Chem 2014; 289:32316-32326. [PMID: 25271159 DOI: 10.1074/jbc.m114.574442] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Yeast mutants lacking the intracellular V-ATPase proton pump (vma mutants) have reduced levels of the Pma1p proton pump at the plasma membrane and increased levels in organelles including the vacuolar lumen. We examined the mechanism and physiological consequences of Pma1p mislocalization. Pma1p is ubiquitinated in vma mutants, and ubiquitination depends on the ubiquitin ligase Rsp5p and the arrestin-related adaptor protein Rim8p. vma mutant strains containing rsp5 or rim8 mutations maintain Pma1p at the plasma membrane, suggesting that ubiquitination is required for Pma1p internalization. Acute inhibition of V-ATPase activity with concanamycin A triggers Pma1p ubiquitination and internalization. In an endocytosis-deficient mutant (end4Δ) Pma1p is ubiquitinated but retained at the plasma membrane during concanamycin A treatment. Consistent with specificity in signaling loss of V-ATPase activity to Pma1p, another plasma membrane transporter, Mup1p, is not internalized in a vma mutant, and loss of the Mup1p adaptor Art1p does not prevent Pma1p internalization in a vma mutant. Very poor growth of vma2 rsp5-1 and vma2 rim8Δ double mutants suggests that Pma1p internalization benefits the vma mutants. We hypothesize that loss of V-ATPase-mediated organelle acidification signals ubiquitination, internalization, and degradation of a portion of Pma1p as a means of balancing overall pH homeostasis.
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Affiliation(s)
- Anne M Smardon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210.
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Pérez-Sampietro M, Herrero E. The PacC-family protein Rim101 prevents selenite toxicity in Saccharomyces cerevisiae by controlling vacuolar acidification. Fungal Genet Biol 2014; 71:76-85. [PMID: 25239548 DOI: 10.1016/j.fgb.2014.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/02/2014] [Accepted: 09/06/2014] [Indexed: 01/10/2023]
Abstract
Saccharomyces cerevisiae Rim101 is a member of the fungal PacC family of transcription factors involved in the response to alkaline pH stress. Further studies have also implicated Rim101 in the responses to other stresses, and have shown its genetic interaction with the iron deprivation-responsive factor Aft1. The present study shows that the absence of Rim101 leads to hypersensitivity to oxidants such as t-butyl hydroperoxide and diamide, and also to the prooxidant agent selenite. The protective role of Rim101 against selenite requires the sensing complex component Rim8, the ESCRT-I/II/III complexes and the Rim13 protease involved in proteolytic activation of Rim101. The Nrg1 transcriptional repressor is a downstream effector of Rim101 in this response to selenite, as occurs in the responses to alkaline pH, Na(+) and Li(+) stresses. Deletion of RIM101 causes downregulation of the vacuolar ATPase genes VMA2 and VMA4, which becomes accentuated compared to wild type cells upon selenite stress, and activation of the Rim101 protein prevents inhibition of vacuolar acidification caused by selenite. These observations therefore support a role of Rim101 in modulation of vacuolar acidity necessary for selenite detoxification. In addition, a parallel Rim101-independent pathway requiring the complete ESCRT machinery (including the ESCRT-0 complex) also participates in protection against selenite.
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Affiliation(s)
- Maria Pérez-Sampietro
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Edifici Biomedicina I, Rovira Roure 198, 25198-Lleida, Spain
| | - Enrique Herrero
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, IRBLleida, Edifici Biomedicina I, Rovira Roure 198, 25198-Lleida, Spain.
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39
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The vacuolar-sorting protein Snf7 is required for export of virulence determinants in members of the Cryptococcus neoformans complex. Sci Rep 2014; 4:6198. [PMID: 25178636 PMCID: PMC4151102 DOI: 10.1038/srep06198] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/04/2014] [Indexed: 02/06/2023] Open
Abstract
Fungal pathogenesis requires a number of extracellularly released virulence factors. Recent studies demonstrating that most fungal extracellular molecules lack secretory tags suggest that unconventional secretion mechanisms and fungal virulence are strictly connected. Proteins of the endosomal sorting complex required for transport (ESCRT) have been recently associated with polysaccharide export in the yeast-like human pathogen Cryptococcus neoformans. Snf7 is a key ESCRT operator required for unconventional secretion in Eukaryotes. In this study we generated snf7Δ mutant strains of C. neoformans and its sibling species C. gattii. Lack of Snf7 resulted in important alterations in polysaccharide secretion, capsular formation and pigmentation. This phenotype culminated with loss of virulence in an intranasal model of murine infection in both species. Our data support the notion that Snf7 expression regulates virulence in C. neoformans and C. gattii by ablating polysaccharide and melanin traffic. These results are in agreement with the observation that unconventional secretion is essential for cryptococcal pathogenesis and strongly suggest the occurrence of still obscure mechanisms of exportation of non-protein molecules in Eukaryotes.
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40
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Maemoto Y, Ono Y, Kiso S, Shibata H, Takahara T, Sorimachi H, Maki M. Involvement of calpain-7 in epidermal growth factor receptor degradation via the endosomal sorting pathway. FEBS J 2014; 281:3642-55. [PMID: 24953135 DOI: 10.1111/febs.12886] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/19/2014] [Accepted: 06/18/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Calpain-7 (CAPN7) is a unique intracellular cysteine protease that has a tandem repeat of microtubule interacting and trafficking (MIT) domains and lacks a penta-EF-hand domain. Although the MIT domains of CAPN7 were previously shown to interact with a subset of endosomal sorting complex required for transport (ESCRT)-III and ESCRT-III-related proteins, including charged multivesicular body protein 1 and increased sodium tolerance (IST)1, knowledge of the involvement of the protease in membrane trafficking has been limited. In the present study, compared with control cells, we found that epidermal growth factor receptor (EGFR) degradation was mildly delayed in CAPN7-knockdown HeLa cells and mouse embryonic fibroblast cells established from CAPN7 knockout (Capn7(-/-) ) mice. Re-expression of wild-type CAPN7 but not a protease-inactive mutant of CAPN7 (CAPN7(C290S) ) resulted in a recovery of the rate of EGFR degradation. We found, by immunofluorescence microscopic analysis, that monomeric GFP fused with the protease-inactive mutant of CAPN7 [monomeric green fluorescent protein (mGFP)-CAPN7(C290S) ] was mobilized to EGFR-positive endosomes upon epidermal growth factor stimulation in HeLa cells. Although mGFP-CAPN7(C290S) exhibited dominant-negative effects on EGFR degradation, a deletion mutant of MIT domains in mGFP-CAPN7(C290S) did not have such properties, suggesting that the interaction between the MIT domains and ESCRT proteins is important for the function of CAPN7. Moreover, we found that epidermal growth factor stimulation induces translocation of IST1 from the cytosol to endosomes positive in both EGFR and mGFP-CAPN7(C290S) . When IST1 was knocked down, mGFP-CAPN7(C290S) lost its co-localization with EGFR. These results demonstrate for the first time that the proteolytic activity of CAPN7 is important for the acceleration of EGFR degradation via the endosomal sorting pathway utilizing a part of the ESCRT system. STRUCTURED DIGITAL ABSTRACT EGFR and CAPN7 colocalize by fluorescence microscopy (View interaction) EGFR, CAPN7 and IST1 colocalize by fluorescence microscopy (View interaction) EEA1 and CAPN7 colocalize by fluorescence microscopy (View interaction) CAPN7 and LAMP1 colocalize by fluorescence microscopy (View interaction).
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Affiliation(s)
- Yuki Maemoto
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Japan
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Toulmay A, Prinz WA. Direct imaging reveals stable, micrometer-scale lipid domains that segregate proteins in live cells. ACTA ACUST UNITED AC 2013; 202:35-44. [PMID: 23836928 PMCID: PMC3704982 DOI: 10.1083/jcb.201301039] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Stable raftlike lipid domains form and segregate membrane proteins in the yeast vacuole in response to various stresses. It has been proposed that membrane rafts, which are sterol- and sphingolipid-enriched liquid-ordered (Lo) domains, segregate proteins in membranes and play critical roles in numerous processes in cells. However, rafts remain controversial because they are difficult to observe in cells without invasive methods and seem to be very small (nanoscale) and short lived, leading many to question whether they exist or are physiologically relevant. In this paper, we show that micrometer-scale, stable lipid domains formed in the yeast vacuole membrane in response to nutrient deprivation, changes in the pH of the growth medium, and other stresses. All vacuolar membrane proteins tested segregated to one of two domains. These domains formed quasi-symmetrical patterns strikingly similar to those found in liposomes containing coexisting Lo and liquid-disordered regions. Indeed, we found that one of these domains is probably sterol enriched and Lo. Domain formation was shown to be regulated by the pH-responsive Rim101 signaling pathway and may also require vesicular trafficking to vacuoles.
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Affiliation(s)
- Alexandre Toulmay
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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43
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Maemoto Y, Kiso S, Shibata H, Maki M. Analysis of limited proteolytic activity of calpain-7 using non-physiological substrates in mammalian cells. FEBS J 2013; 280:2594-607. [DOI: 10.1111/febs.12243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/27/2013] [Accepted: 03/11/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Maemoto
- Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Chikusa-ku; Japan
| | - Satomi Kiso
- Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Chikusa-ku; Japan
| | - Hideki Shibata
- Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Chikusa-ku; Japan
| | - Masatoshi Maki
- Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Chikusa-ku; Japan
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cis- and trans-acting localization determinants of pH response regulator Rim13 in Saccharomyces cerevisiae. EUKARYOTIC CELL 2012; 11:1201-9. [PMID: 22865500 DOI: 10.1128/ec.00158-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Rim101/PacC pathway governs adaptation to alkaline pH in many fungi. Output of the pathway is mediated by transcription factors of the Rim101/PacC family, which are activated by proteolytic cleavage. The proteolytic complex includes scaffold protein Rim20 and endosome-associated subunits of the endosomal sorting complex required for transport (ESCRT). We provide here evidence that Saccharomyces cerevisiae Rim13, the protease that is implicated in Rim101 cleavage, is associated with the Rim20-ESCRT complex, and we investigate its regulation. Rim13-GFP is dispersed in cells grown in acidic medium but forms punctate foci when cells encounter alkaline conditions. A vps4Δ mutant, which accumulates elevated levels of endosomal ESCRT, also accumulates elevated levels of Rim13-GFP foci, independently of external pH. In the vps4Δ background, mutation of ESCRT subunit Snf7 or of Rim20 blocks the formation of Rim13 foci, and we found that Rim13 and Rim20 are colocalized. The Rim13 ortholog PalB of Aspergillus nidulans has been shown to undergo ESCRT and membrane association through an N-terminal MIT domain, but Rim13 orthologs in the Saccharomyces clade lack homology to this N-terminal region. Instead, there is a clade-limited C-terminal region, and we show that point mutations in this region prevent punctate localization and impair Rim13 function. We suggest that RIM13 arose from its ancestral gene through two genome rearrangements. The ancestor lost the coding region for its MIT domain through a 5' rearrangement and acquired the coding region for the Saccharomyces-specific functional equivalent through a 3' rearrangement.
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Maki M, Maemoto Y, Osako Y, Shibata H. Evolutionary and physical linkage between calpains and penta-EF-hand Ca2+-binding proteins. FEBS J 2012; 279:1414-21. [PMID: 22404899 DOI: 10.1111/j.1742-4658.2012.08560.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The name calpain was historically given to a protease that is activated by Ca(2+) and whose primary structure contains a Ca(2+)-binding penta-EF-hand (PEF) as well as a calpain cysteine protease (CysPc) domain and a C2-domain-like (C2L) domain. In the human genome, CysPc domains are found in 15 genes, but only nine of them encode PEF domains. Fungi and budding yeasts have calpain-like sequences that lack the PEF domain, and each protein (designated PalB and Rim13, respectively) is orthologous to human calpain-7, indicating that the calpain-7 orthologs are evolutionarily more conserved than classical calpains possessing PEF domains. An N-terminal region of calpain-7 has a tandem repeat of microtubule-interacting and transport domains that interact with a subset of endosomal sorting complex required for transport (ESCRT) III proteins. In addition to calpains, PEF domains are found in other Ca(2+)-binding proteins including ALG-2 that associates with ALIX (an ESCRT-III accessory protein) and TSG101 (an ESCRT-I subunit). Phylogenetic comparison of dissected domain structures of calpains and experimentally confirmed protein-protein interaction networks imply that there is an evolutionary and physical linkage between mammalian calpains and PEF proteins involving the ESCRT system.
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Affiliation(s)
- Masatoshi Maki
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan.
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Morita E. Differential requirements of mammalian ESCRTs in multivesicular body formation, virus budding and cell division. FEBS J 2012; 279:1399-406. [DOI: 10.1111/j.1742-4658.2012.08534.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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