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Murphy EJ, Rezoagli E, Collins C, Saha SK, Major I, Murray P. Sustainable production and pharmaceutical applications of β-glucan from microbial sources. Microbiol Res 2023; 274:127424. [PMID: 37301079 DOI: 10.1016/j.micres.2023.127424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/14/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
β-glucans are a large class of complex polysaccharides found in abundant sources. Our dietary sources of β-glucans are cereals that include oats and barley, and non-cereal sources can consist of mushrooms, microalgae, bacteria, and seaweeds. There is substantial clinical interest in β-glucans; as they can be used for a variety of diseases including cancer and cardiovascular conditions. Suitable sources of β-glucans for biopharmaceutical applications include bacteria, microalgae, mycelium, and yeast. Environmental factors including culture medium can influence the biomass and ultimately β-glucan content. Therefore, cultivation conditions for the above organisms can be controlled for sustainable enhanced production of β-glucans. This review discusses the various sources of β-glucans and their cultivation conditions that may be optimised to exploit sustainable production. Finally, this article discusses the immune-modulatory potential of β-glucans from these sources.
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Affiliation(s)
- Emma J Murphy
- LIFE - Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, Limerick V94EC5T, Ireland; PRISM Research Institute, Midlands Campus, Technological University of the Shannon, Athlone N37 HD68, Ireland.
| | - Emanuele Rezoagli
- Department of Emergency and Intensive Care, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy; School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Catherine Collins
- LIFE - Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, Limerick V94EC5T, Ireland
| | - Sushanta Kumar Saha
- LIFE - Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, Limerick V94EC5T, Ireland
| | - Ian Major
- PRISM Research Institute, Midlands Campus, Technological University of the Shannon, Athlone N37 HD68, Ireland
| | - Patrick Murray
- LIFE - Health and Biosciences Research Institute, Midwest Campus, Technological University of the Shannon, Limerick V94EC5T, Ireland
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2
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Jordá T, Barba-Aliaga M, Rozès N, Alepuz P, Martínez-Pastor MT, Puig S. Transcriptional regulation of ergosterol biosynthesis genes in response to iron deficiency. Environ Microbiol 2022; 24:5248-5260. [PMID: 36382795 DOI: 10.1111/1462-2920.16157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/01/2022] [Indexed: 01/07/2023]
Abstract
Iron participates as an essential cofactor in the biosynthesis of critical cellular components, including DNA, proteins and lipids. The ergosterol biosynthetic pathway, which is an important target of antifungal treatments, depends on iron in four enzymatic steps. Our results in the model yeast Saccharomyces cerevisiae show that the expression of ergosterol biosynthesis (ERG) genes is tightly modulated by iron availability probably through the iron-dependent variation of sterol and heme levels. Whereas the transcription factors Upc2 and Ecm22 are responsible for the activation of ERG genes upon iron deficiency, the heme-dependent factor Hap1 triggers their Tup1-mediated transcriptional repression. The combined regulation by both activating and repressing regulatory factors allows for the fine-tuning of ERG transcript levels along the progress of iron deficiency, avoiding the accumulation of toxic sterol intermediates and enabling efficient adaptation to rapidly changing conditions. The lack of these regulatory factors leads to changes in the yeast sterol profile upon iron-deficient conditions. Both environmental iron availability and specific regulatory factors should be considered in ergosterol antifungal treatments.
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Affiliation(s)
- Tania Jordá
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Nicolas Rozès
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | | | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
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3
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Rico-Díaz A, Barreiro-Alonso A, Rey-Souto C, Becerra M, Lamas-Maceiras M, Cerdán ME, Vizoso-Vázquez Á. The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis. Biomolecules 2021; 11:biom11091392. [PMID: 34572607 PMCID: PMC8465852 DOI: 10.3390/biom11091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
In the traditional fermentative model yeast Saccharomyces cerevisiae, ScIxr1 is an HMGB (High Mobility Group box B) protein that has been considered as an important regulator of gene transcription in response to external changes like oxygen, carbon source, or nutrient availability. Kluyveromyces lactis is also a useful eukaryotic model, more similar to many human cells due to its respiratory metabolism. We cloned and functionally characterized by different methodologies KlIXR1, which encodes a protein with only 34.4% amino acid sequence similarity to ScIxr1. Our data indicate that both proteins share common functions, including their involvement in the response to hypoxia or oxidative stress induced by hydrogen peroxide or metal treatments, as well as in the control of key regulators for maintenance of the dNTP (deoxyribonucleotide triphosphate) pool and ribosome synthesis. KlIxr1 is able to bind specific regulatory DNA sequences in the promoter of its target genes, which are well conserved between S. cerevisiae and K. lactis. Oppositely, we found important differences between ScIrx1 and KlIxr1 affecting cellular responses to cisplatin or cycloheximide in these yeasts, which could be dependent on specific and non-conserved domains present in these two proteins.
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4
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Shekhawat K, Bauer FF, Setati ME. The transcriptomic response of a wine strain of Lachancea thermotolerans to oxygen deprivation. FEMS Yeast Res 2020; 20:5909970. [PMID: 32960268 DOI: 10.1093/femsyr/foaa054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/20/2020] [Indexed: 11/14/2022] Open
Abstract
The yeast Lachancea thermotolerans is of significant biotechnological interest, and selected strains of this species have become commonly used starter cultures in wine fermentation. However, the impact of this species on wine is frequently limited by the rapid dominance of Saccharomyces cerevisiae strains which are better adapted to wine alcoholic fermentation conditions. Previous studies have shown that the major limiting factor for L. thermotolerans competitive performance in the wine ecosystem is oxygen availability, and not ethanol levels as had been previously suggested. Here we investigated the transcriptional response of L. thermotolerans to anaerobiosis in wine fermentation conditions. The data show that L. thermotolerans broadly redirects gene expression towards genes involved in central carbon metabolism, lipid metabolism, remodeling of the cell wall as well as autophagy. Furthermore, the induction of genes that are likely involved in the generation of lactate indicates a redirection of metabolic flux towards this metabolite. The data provide the first insight into the oxygen-dependent response of L. thermotolerans and suggest potential genetic targets to improve lactate production and/or anaerobic fermentation performance of this yeast.
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Affiliation(s)
- Kirti Shekhawat
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, P/Bag X1 Matieland, 7600, Western Cape, South Africa
| | - Florian F Bauer
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, P/Bag X1 Matieland, 7600, Western Cape, South Africa
| | - Mathabatha E Setati
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, P/Bag X1 Matieland, 7600, Western Cape, South Africa
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5
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Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020; 369:325-329. [PMID: 32675375 DOI: 10.1126/science.aax9552] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging. The structure of the landscape drives single-cell differentiation toward one of these states during aging, whereby the fate is determined quite early and is insensitive to intracellular noise. Guided by a quantitative model of the aging landscape, we genetically engineered a long-lived equilibrium state characterized by an extended life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julie Paxman
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuelian Zhu
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. .,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
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6
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Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae. Genes (Basel) 2020; 11:genes11070795. [PMID: 32679672 PMCID: PMC7397035 DOI: 10.3390/genes11070795] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Ergosterol is an essential component of fungal cell membranes that determines the fluidity, permeability and activity of membrane-associated proteins. Ergosterol biosynthesis is a complex and highly energy-consuming pathway that involves the participation of many enzymes. Deficiencies in sterol biosynthesis cause pleiotropic defects that limit cellular proliferation and adaptation to stress. Thereby, fungal ergosterol levels are tightly controlled by the bioavailability of particular metabolites (e.g., sterols, oxygen and iron) and environmental conditions. The regulation of ergosterol synthesis is achieved by overlapping mechanisms that include transcriptional expression, feedback inhibition of enzymes and changes in their subcellular localization. In the budding yeast Saccharomyces cerevisiae, the sterol regulatory element (SRE)-binding proteins Upc2 and Ecm22, the heme-binding protein Hap1 and the repressor factors Rox1 and Mot3 coordinate ergosterol biosynthesis (ERG) gene expression. Here, we summarize the sterol biosynthesis, transport and detoxification systems of S. cerevisiae, as well as its adaptive response to sterol depletion, low oxygen, hyperosmotic stress and iron deficiency. Because of the large number of ERG genes and the crosstalk between different environmental signals and pathways, many aspects of ergosterol regulation are still unknown. The study of sterol metabolism and its regulation is highly relevant due to its wide applications in antifungal treatments, as well as in food and pharmaceutical industries.
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7
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Fuller GG, Han T, Freeberg MA, Moresco JJ, Ghanbari Niaki A, Roach NP, Yates JR, Myong S, Kim JK. RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. eLife 2020; 9:e48480. [PMID: 32298230 PMCID: PMC7162659 DOI: 10.7554/elife.48480] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Targeting nonspecific endoribonucleases to G bodies reveals that RNA nucleates G body formation and maintains its structural integrity. Consistent with a phase separation mechanism of biogenesis, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies fuse in vivo and are largely insensitive to 1,6-hexanediol, consistent with a hydrogel-like composition. Taken together, our results elucidate the biophysical nature of G bodies and demonstrate that RNA nucleates phase separation of the glycolysis machinery in response to hypoxic stress.
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Affiliation(s)
- Gregory G Fuller
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Ting Han
- National Institute of Biological SciencesBeijingChina
| | | | - James J Moresco
- Department of Chemical Physiology, The Scripps Research InstituteLa JollaUnited States
| | | | - Nathan P Roach
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research InstituteLa JollaUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
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8
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Devaux F, Thiébaut A. The regulation of iron homeostasis in the fungal human pathogen Candida glabrata. MICROBIOLOGY-SGM 2019; 165:1041-1060. [PMID: 31050635 DOI: 10.1099/mic.0.000807] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron is an essential element to most microorganisms, yet an excess of iron is toxic. Hence, living cells have to maintain a tight balance between iron uptake and iron consumption and storage. The control of intracellular iron concentrations is particularly challenging for pathogens because mammalian organisms have evolved sophisticated high-affinity systems to sequester iron from microbes and because iron availability fluctuates among the different host niches. In this review, we present the current understanding of iron homeostasis and its regulation in the fungal pathogen Candida glabrata. This yeast is an emerging pathogen which has become the second leading cause of candidemia, a life-threatening invasive mycosis. C. glabrata is relatively poorly studied compared to the closely related model yeast Saccharomyces cerevisiae or to the pathogenic yeast Candida albicans. Still, several research groups have started to identify the actors of C. glabrata iron homeostasis and its transcriptional and post-transcriptional regulation. These studies have revealed interesting particularities of C. glabrata and have shed new light on the evolution of fungal iron homeostasis.
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Affiliation(s)
- Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Antonin Thiébaut
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
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9
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Barreiro-Alonso A, Lamas-Maceiras M, Cerdán EM, Vizoso-Vázquez Á. The HMGB protein Ixr1 interacts with Ssn8 and Tdh3 involved in transcriptional regulation. FEMS Yeast Res 2019; 18:4847888. [PMID: 29438513 DOI: 10.1093/femsyr/foy013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/07/2018] [Indexed: 12/18/2022] Open
Abstract
Ixr1 is a Saccharomyces cerevisiae transcriptional factor that extensively regulates the response to hypoxia and controls other important cellular functions and DNA repair. During aerobic growth, the Ixr1 repressor function is predominant on regulated promoters of hypoxic genes, although activator effects are also observed on other genes. During hypoxia, Ixr1 expression increases and the number of genes activated by Ixr1 also increase. In this work we demonstrate that the NH2-terminal region of Ixr1 is involved in transcriptional activation. We also present the first analysis about Ixr1 interactions with three factors that have been previously identified as important players in the yeast hypoxic response, Cyc8, Tup1 and Ssn8; results demonstrate that only Ssn8 binds to Ixr1. We have also looked for other Ixr1-binding proteins associated with transcriptional regulation, by co-purification and mass spectrometry identification. Tdh3, a protein involved in transcriptional silencing, is among the new identified Ixr1-binding proteins. Differential phosphorylation of Ixr1 is found when comparing aerobic and hypoxic yeast growth. Implication of these results in transcriptional regulation mediated by Ixr1 is discussed.
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Affiliation(s)
- Aida Barreiro-Alonso
- EXPRELA Group, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña 15001, Spain
| | - Mónica Lamas-Maceiras
- EXPRELA Group, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña 15001, Spain
| | - Esperanza M Cerdán
- EXPRELA Group, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña 15001, Spain
| | - Ángel Vizoso-Vázquez
- EXPRELA Group, Departamento de Bioloxía, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña 15001, Spain
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10
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Song J, Zhang S, Lu L. Fungal cytochrome P450 protein Cyp51: What we can learn from its evolution, regulons and Cyp51-based azole resistance. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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11
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A Novel Sterol-Signaling Pathway Governs Azole Antifungal Drug Resistance and Hypoxic Gene Repression in Saccharomyces cerevisiae. Genetics 2017; 208:1037-1055. [PMID: 29263028 DOI: 10.1534/genetics.117.300554] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/19/2017] [Indexed: 12/26/2022] Open
Abstract
During antifungal drug treatment and hypoxia, genetic and epigenetic changes occur to maintain sterol homeostasis and cellular function. In this study, we show that SET domain-containing epigenetic factors govern drug efficacy to the medically relevant azole class of antifungal drugs. Upon this discovery, we determined that Set4 is induced when Saccharomyces cerevisiae are treated with azole drugs or grown under hypoxic conditions; two conditions that deplete cellular ergosterol and increase sterol precursors. Interestingly, Set4 induction is controlled by the sterol-sensing transcription factors, Upc2 and Ecm22 To determine the role of Set4 on gene expression under hypoxic conditions, we performed RNA-sequencing analysis and showed that Set4 is required for global changes in gene expression. Specifically, loss of Set4 led to an upregulation of nearly all ergosterol genes, including ERG11 and ERG3, suggesting that Set4 functions in gene repression. Furthermore, mass spectrometry analysis revealed that Set4 interacts with the hypoxic-specific transcriptional repressor, Hap1, where this interaction is necessary for Set4 recruitment to ergosterol gene promoters under hypoxia. Finally, an erg3Δ strain, which produces precursor sterols but lacks ergosterol, expresses Set4 under untreated aerobic conditions. Together, our data suggest that sterol precursors are needed for Set4 induction through an Upc2-mediated mechanism. Overall, this new sterol-signaling pathway governs azole antifungal drug resistance and mediates repression of sterol genes under hypoxic conditions.
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12
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Burr R, Espenshade PJ. Oxygen-responsive transcriptional regulation of lipid homeostasis in fungi: Implications for anti-fungal drug development. Semin Cell Dev Biol 2017; 81:110-120. [PMID: 28851600 DOI: 10.1016/j.semcdb.2017.08.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/08/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023]
Abstract
Low oxygen adaptation is essential for aerobic fungi that must survive in varied oxygen environments. Pathogenic fungi in particular must adapt to the low oxygen host tissue environment in order to cause infection. Maintenance of lipid homeostasis is especially important for cell growth and proliferation, and is a highly oxygen-dependent process. In this review, we focus on recent advances in our understanding of the transcriptional regulation and coordination of the low oxygen response across fungal species, paying particular attention to pathogenic fungi. Comparison of lipid homeostasis pathways in these organisms suggests common mechanisms of transcriptional regulation and points toward untapped potential to target low oxygen adaptation in antifungal development.
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Affiliation(s)
- Risa Burr
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peter J Espenshade
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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13
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Zhang T, Bu P, Zeng J, Vancura A. Increased heme synthesis in yeast induces a metabolic switch from fermentation to respiration even under conditions of glucose repression. J Biol Chem 2017; 292:16942-16954. [PMID: 28830930 DOI: 10.1074/jbc.m117.790923] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/18/2017] [Indexed: 01/13/2023] Open
Abstract
Regulation of mitochondrial biogenesis and respiration is a complex process that involves several signaling pathways and transcription factors as well as communication between the nuclear and mitochondrial genomes. Under aerobic conditions, the budding yeast Saccharomyces cerevisiae metabolizes glucose predominantly by glycolysis and fermentation. We have recently shown that altered chromatin structure in yeast induces respiration by a mechanism that requires transport and metabolism of pyruvate in mitochondria. However, how pyruvate controls the transcriptional responses underlying the metabolic switch from fermentation to respiration is unknown. Here, we report that this pyruvate effect involves heme. We found that heme induces transcription of HAP4, the transcriptional activation subunit of the Hap2/3/4/5p complex, required for growth on nonfermentable carbon sources, in a Hap1p- and Hap2/3/4/5p-dependent manner. Increasing cellular heme levels by inactivating ROX1, which encodes a repressor of many hypoxic genes, or by overexpressing HEM3 or HEM12 induced respiration and elevated ATP levels. Increased heme synthesis, even under conditions of glucose repression, activated Hap1p and the Hap2/3/4/5p complex and induced transcription of HAP4 and genes required for the tricarboxylic acid (TCA) cycle, electron transport chain, and oxidative phosphorylation, leading to a switch from fermentation to respiration. Conversely, inhibiting metabolic flux into the TCA cycle reduced cellular heme levels and HAP4 transcription. Together, our results indicate that the glucose-mediated repression of respiration in budding yeast is at least partly due to the low cellular heme level.
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Affiliation(s)
- Tiantian Zhang
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Pengli Bu
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Joey Zeng
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
| | - Ales Vancura
- From the Department of Biological Sciences, St. John's University, Queens, New York 11439
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14
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Willis SD, Hossian AKMN, Evans N, Hickman MJ. Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response. J Vis Exp 2017:56226. [PMID: 28829420 PMCID: PMC5614221 DOI: 10.3791/56226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Complex changes in gene expression typically mediate a large portion of a cellular response. Each gene may change expression with unique kinetics as the gene is regulated by the particular timing of one of many stimuli, signaling pathways or secondary effects. In order to capture the entire gene expression response to hypoxia in the yeast S. cerevisiae, RNA-seq analysis was used to monitor the mRNA levels of all genes at specific times after exposure to hypoxia. Hypoxia was established by growing cells in ~100% N2 gas. Importantly, unlike other hypoxic studies, ergosterol and unsaturated fatty acids were not added to the media because these metabolites affect gene expression. Time points were chosen in the range of 0 - 4 h after hypoxia because that period captures the major changes in gene expression. At each time point, mid-log hypoxic cells were quickly filtered and frozen, limiting exposure to O2 and concomitant changes in gene expression. Total RNA was extracted from cells and used to enrich for mRNA, which was then converted to cDNA. From this cDNA, multiplex libraries were created and eight or more samples were sequenced in one lane of a next-generation sequencer. A post-sequencing pipeline is described, which includes quality base trimming, read mapping and determining the number of reads per gene. DESeq2 within the R statistical environment was used to identify genes that change significantly at any one of the hypoxic time points. Analysis of three biological replicates revealed high reproducibility, genes of differing kinetics and a large number of expected O2-regulated genes. These methods can be used to study how the cells of various organisms respond to hypoxia over time and adapted to study gene expression during other cellular responses.
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Affiliation(s)
- Stephen D Willis
- Department of Molecular Biology, Rowan School of Osteopathic Medicine
| | | | - Nathan Evans
- Department of Biological Sciences, Rowan University
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15
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Adelantado N, Tarazona P, Grillitsch K, García-Ortega X, Monforte S, Valero F, Feussner I, Daum G, Ferrer P. The effect of hypoxia on the lipidome of recombinant Pichia pastoris. Microb Cell Fact 2017; 16:86. [PMID: 28526017 PMCID: PMC5437588 DOI: 10.1186/s12934-017-0699-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/10/2017] [Indexed: 01/17/2023] Open
Abstract
Background Cultivation of recombinant Pichia pastoris (Komagataella sp.) under hypoxic conditions has a strong positive effect on specific productivity when the glycolytic GAP promoter is used for recombinant protein expression, mainly due to upregulation of glycolytic conditions. In addition, transcriptomic analyses of hypoxic P. pastoris pointed out important regulation of lipid metabolism and unfolded protein response (UPR). Notably, UPR that plays a role in the regulation of lipid metabolism, amino acid metabolism and protein secretion, was found to be upregulated under hypoxia. Results To improve our understanding of the interplay between lipid metabolism, UPR and protein secretion, the lipidome of a P. pastoris strain producing an antibody fragment was studied under hypoxic conditions. Furthermore, lipid composition analyses were combined with previously available transcriptomic datasets to further understand the impact of hypoxia on lipid metabolism. Chemostat cultures operated under glucose-limiting conditions under normoxic and hypoxic conditions were analyzed in terms of intra/extracellular product distribution and lipid composition. Integrated analysis of lipidome and transcriptome datasets allowed us to demonstrate an important remodeling of the lipid metabolism under limited oxygen availability. Additionally, cells with reduced amounts of ergosterol through fluconazole treatment were also included in the study to observe the impact on protein secretion and its lipid composition. Conclusions Our results show that cells adjust their membrane composition in response to oxygen limitation mainly by changing their sterol and sphingolipid composition. Although fluconazole treatment results a different lipidome profile than hypoxia, both conditions result in higher recombinant protein secretion levels. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0699-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Núria Adelantado
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain.,Evonik Nutrition & Care GmbH, Hanau, Germany
| | - Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Xavier García-Ortega
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Sergi Monforte
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria. .,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
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16
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Hypoxia and iron requirements are the main drivers in transcriptional adaptation of Kluyveromyces lactis during wine aerobic fermentation. Int J Food Microbiol 2017; 246:40-49. [DOI: 10.1016/j.ijfoodmicro.2017.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 01/06/2023]
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17
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Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. G3-GENES GENOMES GENETICS 2017; 7:221-231. [PMID: 27883312 PMCID: PMC5217111 DOI: 10.1534/g3.116.034991] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.
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18
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Vizoso-Vázquez A, Lamas-Maceiras M, Fernández-Leiro R, Rico-Díaz A, Becerra M, Cerdán ME. Dual function of Ixr1 in transcriptional regulation and recognition of cisplatin-DNA adducts is caused by differential binding through its two HMG-boxes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:256-269. [PMID: 27871851 DOI: 10.1016/j.bbagrm.2016.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/30/2022]
Abstract
Ixr1 is a transcriptional factor involved in the response to hypoxia, which is also related to DNA repair. It binds to DNA through its two in-tandem high mobility group box (HMG-box) domains. Each function depends on recognition of different DNA structures, B-form DNA at specific consensus sequences for transcriptional regulation, or distorted DNA, like cisplatin-DNA adducts, for DNA repair. However, the contribution of the HMG-box domains in the Ixr1 protein to the formation of different protein-DNA complexes is poorly understood. We have biophysically and biochemically characterized these interactions with specific DNA sequences from the promoters regulated by Ixr1, or with cisplatin-DNA adducts. Both HMG-boxes are necessary for transcriptional regulation, and they are not functionally interchangeable. The in-tandem arrangement of their HMG-boxes is necessary for functional folding and causes sequential cooperative binding to specific DNA sequences, with HMG-box A showing a higher contribution to DNA binding and bending than the HMG-box B. Binding of Ixr1 HMG boxes to specific DNA sequences is entropy driven, whereas binding to platinated DNA is enthalpy driven for HMG-box A and entropy driven for HMG-box B. This is the first proof that HMG-box binding to different DNA structures is associated with predictable thermodynamic differences. Based on our study, we present a model to explain the dual function of Ixr1 in the regulation of gene expression and recognition of distorted DNA structures caused by cisplatin treatment.
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Affiliation(s)
- A Vizoso-Vázquez
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain
| | - M Lamas-Maceiras
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain
| | - R Fernández-Leiro
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain
| | - A Rico-Díaz
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain
| | - M Becerra
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain
| | - M E Cerdán
- Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
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DuBois JC, Smulian AG. Sterol Regulatory Element Binding Protein (Srb1) Is Required for Hypoxic Adaptation and Virulence in the Dimorphic Fungus Histoplasma capsulatum. PLoS One 2016; 11:e0163849. [PMID: 27711233 PMCID: PMC5053422 DOI: 10.1371/journal.pone.0163849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 09/08/2016] [Indexed: 01/12/2023] Open
Abstract
The Histoplasma capsulatum sterol regulatory element binding protein (SREBP), Srb1 is a member of the basic helix-loop-helix (bHLH), leucine zipper DNA binding protein family of transcription factors that possess a unique tyrosine (Y) residue instead of an arginine (R) residue in the bHLH region. We have determined that Srb1 message levels increase in a time dependent manner during growth under oxygen deprivation (hypoxia). To further understand the role of Srb1 during infection and hypoxia, we silenced the gene encoding Srb1 using RNA interference (RNAi); characterized the resulting phenotype, determined its response to hypoxia, and its ability to cause disease within an infected host. Silencing of Srb1 resulted in a strain of H. capsulatum that is incapable of surviving in vitro hypoxia. We found that without complete Srb1 expression, H. capsulatum is killed by murine macrophages and avirulent in mice given a lethal dose of yeasts. Additionally, silencing Srb1 inhibited the hypoxic upregulation of other known H. capsulatum hypoxia-responsive genes (HRG), and genes that encode ergosterol biosynthetic enzymes. Consistent with these regulatory functions, Srb1 silenced H. capsulatum cells were hypersensitive to the antifungal azole drug itraconazole. These data support the theory that the H. capsulatum SREBP is critical for hypoxic adaptation and is required for H. capsulatum virulence.
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Affiliation(s)
- Juwen C. DuBois
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- Cincinnati VA Medical Center, Cincinnati, Ohio, United States of America
| | - A. George Smulian
- Cincinnati VA Medical Center, Cincinnati, Ohio, United States of America
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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20
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Compartmentalization of iron between mitochondria and the cytosol and its regulation. Eur J Cell Biol 2015; 94:292-308. [DOI: 10.1016/j.ejcb.2015.05.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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21
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Merhej J, Delaveau T, Guitard J, Palancade B, Hennequin C, Garcia M, Lelandais G, Devaux F. Yap7 is a transcriptional repressor of nitric oxide oxidase in yeasts, which arose from neofunctionalization after whole genome duplication. Mol Microbiol 2015; 96:951-72. [DOI: 10.1111/mmi.12983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Jawad Merhej
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Thierry Delaveau
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Juliette Guitard
- Sorbonne Universités, UPMC Univ Paris 06, CR7; Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris); 91 Bd de l'hôpital F-75013 Paris France
- Inserm; U1135; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
- Assistance Publique-Hôpitaux de Paris, Hôpital St Antoine; Service de Parasitologie-Mycologie; F-75012 Paris France
- CNRS; ERL 8255; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot; Sorbonne Paris Cité; F-75205 Paris France
| | - Christophe Hennequin
- Sorbonne Universités, UPMC Univ Paris 06, CR7; Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris); 91 Bd de l'hôpital F-75013 Paris France
- Inserm; U1135; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
- Assistance Publique-Hôpitaux de Paris, Hôpital St Antoine; Service de Parasitologie-Mycologie; F-75012 Paris France
- CNRS; ERL 8255; CIMI-Paris; 91 Bd de l'hôpital F-75013 Paris France
| | - Mathilde Garcia
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
| | - Gaëlle Lelandais
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot; Sorbonne Paris Cité; F-75205 Paris France
| | - Frédéric Devaux
- Sorbonne Universités, UPMC Univ. Paris 06, Institut de Biologie Paris Seine UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
- CNRS, UMR 7238; Laboratoire de biologie computationnelle et quantitative; F-75006 Paris France
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22
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Mates N, Kettner K, Heidenreich F, Pursche T, Migotti R, Kahlert G, Kuhlisch E, Breunig KD, Schellenberger W, Dittmar G, Hoflack B, Kriegel TM. Proteomic and functional consequences of hexokinase deficiency in glucose-repressible Kluyveromyces lactis. Mol Cell Proteomics 2014; 13:860-75. [PMID: 24434903 DOI: 10.1074/mcp.m113.032714] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The analysis of glucose signaling in the Crabtree-positive eukaryotic model organism Saccharomyces cerevisiae has disclosed a dual role of its hexokinase ScHxk2, which acts as a glycolytic enzyme and key signal transducer adapting central metabolism to glucose availability. In order to identify evolutionarily conserved characteristics of hexokinase structure and function, the cellular response of the Crabtree-negative yeast Kluyveromyces lactis to rag5 null mutation and concomitant deficiency of its unique hexokinase KlHxk1 was analyzed by means of difference gel electrophoresis. In total, 2,851 fluorescent spots containing different protein species were detected in the master gel representing all of the K. lactis proteins that were solubilized from glucose-grown KlHxk1 wild-type and mutant cells. Mass spectrometric peptide analysis identified 45 individual hexokinase-dependent proteins related to carbohydrate, short-chain fatty acid and tricarboxylic acid metabolism as well as to amino acid and protein turnover, but also to general stress response and chromatin remodeling, which occurred as a consequence of KlHxk1 deficiency at a minimum 3-fold enhanced or reduced level in the mutant proteome. In addition, three proteins exhibiting homology to 2-methylcitrate cycle enzymes of S. cerevisiae were detected at increased concentrations, suggesting a stimulation of pyruvate formation from amino acids and/or fatty acids. Experimental validation of the difference gel electrophoresis approach by post-lysis dimethyl labeling largely confirmed the abundance changes detected in the mutant proteome via the former method. Taking into consideration the high proportion of identified hexokinase-dependent proteins exhibiting increased proteomic levels, KlHxk1 is likely to have a repressive function in a multitude of metabolic pathways. The proteomic alterations detected in the mutant classify KlHxk1 as a multifunctional enzyme and support the view of evolutionary conservation of dual-role hexokinases even in organisms that are less specialized than S. cerevisiae in terms of glucose utilization.
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Affiliation(s)
- Nadia Mates
- Technische Universität Dresden, Medizinische Fakultät Carl Gustav Carus, Institute of Physiological Chemistry, D-01307 Dresden, Germany
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23
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Abstract
The response of eukaryotic microbes to low-oxygen (hypoxic) conditions is strongly regulated at the level of transcription. Comparative analysis shows that some of the transcriptional regulators (such as the sterol regulatory element-binding proteins, or SREBPs) are of ancient origin and probably regulate sterol synthesis in most eukaryotic microbes. However, in some fungi SREBPs have been replaced by a zinc-finger transcription factor (Upc2). Nuclear localization of fungal SREBPs is determined by regulated proteolysis, either by site-specific proteases or by an E3 ligase complex and the proteasome. The exact mechanisms of oxygen sensing are not fully characterized but involve responding to low levels of heme and/or sterols and possibly to levels of nitric oxide and reactive oxygen species. Changes in central carbon metabolism (glycolysis and respiration) are a core hypoxic response in some, but not all, fungal species. Adaptation to hypoxia is an important virulence characteristic of pathogenic fungi.
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Affiliation(s)
- Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;
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24
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Siso MIG, Becerra M, Maceiras ML, Vázquez ÁV, Cerdán ME. The yeast hypoxic responses, resources for new biotechnological opportunities. Biotechnol Lett 2012; 34:2161-73. [DOI: 10.1007/s10529-012-1039-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/14/2012] [Indexed: 10/27/2022]
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25
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Ding XF, Huang GM, Shi Y, Li JA, Fang XD. Med19 promotes gastric cancer progression and cellular growth. Gene 2012; 504:262-7. [DOI: 10.1016/j.gene.2012.04.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 03/25/2012] [Accepted: 04/11/2012] [Indexed: 01/19/2023]
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26
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Kluyveromyces lactis: a suitable yeast model to study cellular defense mechanisms against hypoxia-induced oxidative stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:634674. [PMID: 22928082 PMCID: PMC3425888 DOI: 10.1155/2012/634674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/22/2012] [Indexed: 11/17/2022]
Abstract
Studies about hypoxia-induced oxidative stress in human health disorders take advantage from the use of unicellular eukaryote models. A widely extended model is the fermentative yeast Saccharomyces cerevisiae. In this paper, we describe an overview of the molecular mechanisms induced by a decrease in oxygen availability and their interrelationship with the oxidative stress response in yeast. We focus on the differential characteristics between S. cerevisiae and the respiratory yeast Kluyveromyces lactis, a complementary emerging model, in reference to multicellular eukaryotes.
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27
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Micolonghi C, Ottaviano D, Di Silvio E, Damato G, Heipieper HJ, Bianchi MM. A dual signalling pathway for the hypoxic expression of lipid genes, dependent on the glucose sensor Rag4, is revealed by the analysis of the KlMGA2 gene in Kluyveromyces lactis. MICROBIOLOGY-SGM 2012; 158:1734-1744. [PMID: 22516223 DOI: 10.1099/mic.0.059402-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the respiratory yeast Kluyveromyces lactis, little is known about the factors regulating the metabolic response to oxygen shortage. After searching for homologues of characterized Saccharomyces cerevisiae regulators of the hypoxic response, we identified a gene that we named KlMGA2, which is homologous to MGA2. The deletion of KlMGA2 strongly reduced both the fermentative and respiratory growth rate and altered fatty acid composition and the unsaturation index of membranes. The reciprocal heterologous expression of MGA2 and KlMGA2 in the corresponding deletion mutant strains suggested that Mga2 and KlMga2 are functional homologues. KlMGA2 transcription was induced by hypoxia and the glucose sensor Rag4 mediated the hypoxic induction of KlMGA2. Transcription of lipid biosynthetic genes KlOLE1, KlERG1, KlFAS1 and KlATF1 was induced by hypoxia and was dependent on KlMga2, except for KlOLE1. Rag4 was required for hypoxic induction of transcription for both KlMga2-dependent (KlERG1) and KlMga2-independent (KlOLE1) structural genes.
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Affiliation(s)
- Chiara Micolonghi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Daniela Ottaviano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Eva Di Silvio
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe Damato
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hermann J Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Michele M Bianchi
- Pasteur Institut Cenci-Bolognetti Foundation, Sapienza University of Rome, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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Vizoso-Vázquez A, Lamas-Maceiras M, Becerra M, González-Siso MI, Rodríguez-Belmonte E, Cerdán ME. Ixr1p and the control of the Saccharomyces cerevisiae hypoxic response. Appl Microbiol Biotechnol 2011; 94:173-84. [PMID: 22189861 DOI: 10.1007/s00253-011-3785-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
Abstract
In Saccharomyces cerevisiae, adaptation to hypoxia/anaerobiosis requires the transcriptional induction or derepression of multiple genes organized in regulons controlled by specific transcriptional regulators. Ixr1p is a transcriptional regulatory factor that causes aerobic repression of several hypoxic genes (COX5B, TIR1, and HEM13) and also the activation of HEM13 during hypoxic growth. Analysis of the transcriptome of the wild-type strain BY4741 and its isogenic derivative Δixr1, grown in aerobic and hypoxic conditions, reveals differential regulation of genes related not only to the hypoxic and oxidative stress responses but also to the re-adaptation of catabolic and anabolic fluxes in response to oxygen limitation. The function of Ixr1p in the transcriptional regulation of genes from the sulfate assimilation pathway and other pathways producing α-keto acids is of biotechnological importance for industries based on yeast-derived fermentation products.
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Affiliation(s)
- Angel Vizoso-Vázquez
- Departamento de Biología Celular y Molecular, F. Ciencias, Universidad de A Coruña, Campus de A Zapateira s/n. A, Coruña 15071, Spain
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29
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Cui X, Xu D, Lv C, Qu F, He J, Chen M, Liu Y, Gao Y, Che J, Yao Y, Yu H. Suppression of MED19 expression by shRNA induces inhibition of cell proliferation and tumorigenesis in human prostate cancer cells. BMB Rep 2011; 44:547-52. [DOI: 10.5483/bmbrep.2011.44.8.547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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30
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Contador CA, Andrews BA, Liao JC, Asenjo JA. Identification of transcription factors perturbed by the synthesis of high levels of a foreign protein in yeast saccharomyces cerevisiae. Biotechnol Prog 2011; 27:925-36. [DOI: 10.1002/btpr.616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 11/25/2010] [Indexed: 11/10/2022]
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The Hog1 mitogen-activated protein kinase mediates a hypoxic response in Saccharomyces cerevisiae. Genetics 2011; 188:325-38. [PMID: 21467572 DOI: 10.1534/genetics.111.128322] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have studied hypoxic induction of transcription by studying the seripauperin (PAU) genes of Saccharomyces cerevisiae. Previous studies showed that PAU induction requires the depletion of heme and is dependent upon the transcription factor Upc2. We have now identified additional factors required for PAU induction during hypoxia, including Hog1, a mitogen-activated protein kinase (MAPK) whose signaling pathway originates at the membrane. Our results have led to a model in which heme and ergosterol depletion alters membrane fluidity, thereby activating Hog1 for hypoxic induction. Hypoxic activation of Hog1 is distinct from its previously characterized response to osmotic stress, as the two conditions cause different transcriptional consequences. Furthermore, Hog1-dependent hypoxic activation is independent of the S. cerevisiae general stress response. In addition to Hog1, specific components of the SAGA coactivator complex, including Spt20 and Sgf73, are also required for PAU induction. Interestingly, the mammalian ortholog of Spt20, p38IP, has been previously shown to interact with the mammalian ortholog of Hog1, p38. Taken together, our results have uncovered a previously unknown hypoxic-response pathway that may be conserved throughout eukaryotes.
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Rintala E, Jouhten P, Toivari M, Wiebe MG, Maaheimo H, Penttilä M, Ruohonen L. Transcriptional responses of Saccharomyces cerevisiae to shift from respiratory and respirofermentative to fully fermentative metabolism. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:461-76. [PMID: 21348598 DOI: 10.1089/omi.2010.0082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In industrial fermentations of Saccharomyces cerevisiae, transient changes in oxygen concentration commonly occur and it is important to understand the behavior of cells during these changes. Glucose-limited chemostat cultivations were used to study the time-dependent effect of sudden oxygen depletion on the transcriptome of S. cerevisiae cells initially in fully aerobic or oxygen-limited conditions. The overall responses to anaerobic conditions of cells initially in different conditions were very similar. Independent of initial culture conditions, transient downregulation of genes related to growth and cell proliferation, mitochondrial translation and protein import, and sulphate assimilation was seen. In addition, transient or permanent upregulation of genes related to protein degradation, and phosphate and amino acid uptake was observed in all cultures. However, only in the initially oxygen-limited cultures was a transient upregulation of genes related to fatty acid oxidation, peroxisomal biogenesis, oxidative phosphorylation, TCA cycle, response to oxidative stress, and pentose phosphate pathway observed. Furthermore, from the initially oxygen-limited conditions, a rapid response around the metabolites of upper glycolysis and the pentose phosphate pathway was seen, while from the initially fully aerobic conditions, a slower response around the pathways for utilization of respiratory carbon sources was observed.
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Affiliation(s)
- Eija Rintala
- VTT Technical Research Centre of Finland, Finland.
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Yang F, Wang ED. Heme regulates protein homeostasis at transcription, protein translation, and degradation levels. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11515-010-7700-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Abstract
The regulation of the response of Candida albicans to hypoxic (low-oxygen) conditions is poorly understood. We used microarray and other transcriptional analyses to investigate the role of the Upc2 and Bcr1 transcription factors in controlling expression of genes involved in cell wall metabolism, ergosterol synthesis, and glycolysis during adaptation to hypoxia. Hypoxic induction of the ergosterol pathway is mimicked by treatment with sterol-lowering drugs (ketoconazole) and requires UPC2. Expression of three members of the family CFEM (common in several fungal extracellular membranes) of cell wall genes (RBT5, PGA7, and PGA10) is also induced by hypoxia and ketoconazole and requires both UPC2 and BCR1. Expression of glycolytic genes is induced by hypoxia but not by treatment with sterol-lowering drugs, whereas expression of respiratory pathway genes is repressed. However, Upc2 does not play a major role in regulating expression of genes required for central carbon metabolism. Our results indicate that regulation of gene expression in response to hypoxia in C. albicans is complex and is signaled both via lowered sterol levels and other unstudied mechanisms. We also show that induction of filamentation under hypoxic conditions requires the Ras1- and Cdc35-dependent pathway.
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Grahl N, Cramer RA. Regulation of hypoxia adaptation: an overlooked virulence attribute of pathogenic fungi? Med Mycol 2010; 48:1-15. [PMID: 19462332 DOI: 10.3109/13693780902947342] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Over the past two decades, the incidence of fungal infections has dramatically increased. This is primarily due to increases in the population of immunocompromised individuals attributed to the HIV/AIDS pandemic and immunosuppression therapies associated with organ transplantation, cancer, and other diseases where new immunomodulatory therapies are utilized. Significant advances have been made in understanding how fungi cause disease, but clearly much remains to be learned about the pathophysiology of these often lethal infections. Fungal pathogens face numerous environmental challenges as they colonize and infect mammalian hosts. Regardless of a pathogen's complexity, its ability to adapt to environmental changes is critical for its survival and ability to cause disease. For example, at sites of fungal infections, the significant influx of immune effector cells and the necrosis of tissue by the invading pathogen generate hypoxic microenvironments to which both the pathogen and host cells must adapt in order to survive. However, our current knowledge of how pathogenic fungi adapt to and survive in hypoxic conditions during fungal pathogenesis is limited. Recent studies have begun to observe that the ability to adapt to various levels of hypoxia is an important component of the virulence arsenal of pathogenic fungi. In this review, we focus on known oxygen sensing mechanisms that non-pathogenic and pathogenic fungi utilize to adapt to hypoxic microenvironments and their possible relation to fungal virulence.
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Affiliation(s)
- Nora Grahl
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, USA
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Transcriptional response to hypoxia in the aquatic fungus Blastocladiella emersonii. EUKARYOTIC CELL 2010; 9:915-25. [PMID: 20418381 DOI: 10.1128/ec.00047-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Global gene expression analysis was carried out with Blastocladiella emersonii cells subjected to oxygen deprivation (hypoxia) using cDNA microarrays. In experiments of gradual hypoxia (gradual decrease in dissolved oxygen) and direct hypoxia (direct decrease in dissolved oxygen), about 650 differentially expressed genes were observed. A total of 534 genes were affected directly or indirectly by oxygen availability, as they showed recovery to normal expression levels or a tendency to recover when cells were reoxygenated. In addition to modulating many genes with no putative assigned function, B. emersonii cells respond to hypoxia by readjusting the expression levels of genes responsible for energy production and consumption. At least transcriptionally, this fungus seems to favor anaerobic metabolism through the upregulation of genes encoding glycolytic enzymes and lactate dehydrogenase and the downregulation of most genes coding for tricarboxylic acid (TCA) cycle enzymes. Furthermore, genes involved in energy-costly processes, like protein synthesis, amino acid biosynthesis, protein folding, and transport, had their expression profiles predominantly downregulated during oxygen deprivation, indicating an energy-saving effort. Data also revealed similarities between the transcriptional profiles of cells under hypoxia and under iron(II) deprivation, suggesting that Fe(2+) ion could have a role in oxygen sensing and/or response to hypoxia in B. emersonii. Additionally, treatment of fungal cells prior to hypoxia with the antibiotic geldanamycin, which negatively affects the stability of mammalian hypoxia transcription factor HIF-1alpha, caused a significant decrease in the levels of certain upregulated hypoxic genes.
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Regulatory factors controlling transcription of Saccharomyces cerevisiae IXR1 by oxygen levels: a model of transcriptional adaptation from aerobiosis to hypoxia implicating ROX1 and IXR1 cross-regulation. Biochem J 2009; 425:235-43. [PMID: 19807692 DOI: 10.1042/bj20091500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ixr1p from Saccharomyces cerevisiae has been previously studied because it binds to DNA containing intrastrand cross-links formed by the anticancer drug cisplatin. Ixr1p is also a transcriptional regulator of anaerobic/hypoxic genes, such as SRP1/TIR1, which encodes a stress-response cell wall manoprotein, and COX5B, which encodes the Vb subunit of the mitochondrial complex cytochrome c oxidase. However, factors controlling IXR1 expression remained unexplored. In the present study we show that IXR1 mRNA levels are controlled by oxygen availability and increase during hypoxia. In aerobiosis, low levels of IXR1 expression are maintained by Rox1p repression through the general co-repressor complex Tup1-Ssn6. Ixr1p itself is necessary for full IXR1 expression under hypoxic conditions. Deletion analyses have identified the region in the IXR1 promoter responsible for this positive auto-control (nucleotides -557 to -376). EMSA (electrophoretic mobility-shift assay) and ChIP (chromatin immunoprecipitation) assays show that Ixr1p binds to the IXR1 promoter both in vitro and in vivo. Ixr1p is also required for hypoxic repression of ROX1 and binds to its promoter. UPC2 deletion has opposite effects on IXR1 and ROX1 transcription during hypoxia. Ixr1p is also necessary for resistance to oxidative stress generated by H2O2. IXR1 expression is moderately activated by H2O2 and this induction is Yap1p-dependent. A model of IXR1 regulation as a relay for sensing different signals related to change in oxygen availability is proposed. In this model, transcriptional adaptation from aerobiosis to hypoxia depends on ROX1 and IXR1 cross-regulation.
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Iron regulation through the back door: iron-dependent metabolite levels contribute to transcriptional adaptation to iron deprivation in Saccharomyces cerevisiae. EUKARYOTIC CELL 2009; 9:460-71. [PMID: 20008079 DOI: 10.1128/ec.00213-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Budding yeast (Saccharomyces cerevisiae) responds to iron deprivation both by Aft1-Aft2-dependent transcriptional activation of genes involved in cellular iron uptake and by Cth1-Cth2-specific degradation of certain mRNAs coding for iron-dependent biosynthetic components. Here, we provide evidence for a novel principle of iron-responsive gene expression. This regulatory mechanism is based on the modulation of transcription through the iron-dependent variation of levels of regulatory metabolites. As an example, the LEU1 gene of branched-chain amino acid biosynthesis is downregulated under iron-limiting conditions through depletion of the metabolic intermediate alpha-isopropylmalate, which functions as a key transcriptional coactivator of the Leu3 transcription factor. Synthesis of alpha-isopropylmalate involves the iron-sulfur protein Ilv3, which is inactivated under iron deficiency. As another example, decreased mRNA levels of the cytochrome c-encoding CYC1 gene under iron-limiting conditions involve heme-dependent transcriptional regulation via the Hap1 transcription factor. Synthesis of the iron-containing heme is directly correlated with iron availability. Thus, the iron-responsive expression of genes that are downregulated under iron-limiting conditions is conferred by two independent regulatory mechanisms: transcriptional regulation through iron-responsive metabolites and posttranscriptional mRNA degradation. Only the combination of the two processes provides a quantitative description of the response to iron deprivation in yeast.
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Rintala E, Toivari M, Pitkänen JP, Wiebe MG, Ruohonen L, Penttilä M. Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae. BMC Genomics 2009; 10:461. [PMID: 19804647 PMCID: PMC2767370 DOI: 10.1186/1471-2164-10-461] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 10/05/2009] [Indexed: 12/19/2022] Open
Abstract
Background The industrially important yeast Saccharomyces cerevisiae is able to grow both in the presence and absence of oxygen. However, the regulation of its metabolism in conditions of intermediate oxygen availability is not well characterised. We assessed the effect of oxygen provision on the transcriptome and proteome of S. cerevisiae in glucose-limited chemostat cultivations in anaerobic and aerobic conditions, and with three intermediate (0.5, 1.0 and 2.8% oxygen) levels of oxygen in the feed gas. Results The main differences in the transcriptome were observed in the comparison of fully aerobic, intermediate oxygen and anaerobic conditions, while the transcriptome was generally unchanged in conditions receiving different intermediate levels (0.5, 1.0 or 2.8% O2) of oxygen in the feed gas. Comparison of the transcriptome and proteome data suggested post-transcriptional regulation was important, especially in 0.5% oxygen. In the conditions of intermediate oxygen, the genes encoding enzymes of the respiratory pathway were more highly expressed than in either aerobic or anaerobic conditions. A similar trend was also seen in the proteome and in enzyme activities of the TCA cycle. Further, genes encoding proteins of the mitochondrial translation machinery were present at higher levels in all oxygen-limited and anaerobic conditions, compared to fully aerobic conditions. Conclusion Global upregulation of genes encoding components of the respiratory pathway under conditions of intermediate oxygen suggested a regulatory mechanism to control these genes as a response to the need of more efficient energy production. Further, cells grown in three different intermediate oxygen levels were highly similar at the level of transcription, while they differed at the proteome level, suggesting post-transcriptional mechanisms leading to distinct physiological modes of respiro-fermentative metabolism.
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Affiliation(s)
- Eija Rintala
- VTT Technical Research Centre of Finland, P,O, Box 1000, FI-02044 VTT, Finland.
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González-Siso MI, García-Leiro A, Tarrío N, Cerdán ME. Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis. Microb Cell Fact 2009; 8:46. [PMID: 19715615 PMCID: PMC2754438 DOI: 10.1186/1475-2859-8-46] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/30/2009] [Indexed: 12/04/2022] Open
Abstract
A lot of studies have been carried out on Saccharomyces cerevisiae, an yeast with a predominant fermentative metabolism under aerobic conditions, which allows exploring the complex response induced by oxidative stress. S. cerevisiae is considered a eukaryote model for these studies. We propose Kluyveromyces lactis as a good alternative model to analyse variants in the oxidative stress response, since the respiratory metabolism in this yeast is predominant under aerobic conditions and it shows other important differences with S. cerevisiae in catabolic repression and carbohydrate utilization. The knowledge of oxidative stress response in K. lactis is still a developing field. In this article, we summarize the state of the art derived from experimental approaches and we provide a global vision on the characteristics of the putative K. lactis components of the oxidative stress response pathway, inferred from their sequence homology with the S. cerevisiae counterparts. Since K. lactis is also a well-established alternative host for industrial production of native enzymes and heterologous proteins, relevant differences in the oxidative stress response pathway and their potential in biotechnological uses of this yeast are also reviewed.
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Affiliation(s)
- M Isabel González-Siso
- Department of Molecular and Cell Biology, University of A Coruña, Campus da Zapateira s/n, 15071- A Coruña, Spain.
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41
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Stuart GR, Humble MM, Strand MK, Copeland WC. Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae. Mitochondrion 2009; 9:211-21. [PMID: 19254780 DOI: 10.1016/j.mito.2009.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 02/13/2009] [Accepted: 02/19/2009] [Indexed: 02/05/2023]
Abstract
Yeast cells lacking the mitochondrial NADH kinase encoded by POS5 display increased sensitivity to hydrogen peroxide, a slow-growth phenotype, reduced mitochondrial function and increased levels of mitochondrial protein oxidation and mtDNA mutations. Here we examined gene expression in pos5Delta cells, comparing these data to those from cells containing deletions of superoxide dismutase-encoding genes SOD1 or SOD2. Surprisingly, stress-response genes were down-regulated in pos5Delta, sod1Delta and sod2Delta cells, implying that cells infer stress levels from mitochondrial activity rather than sensing reactive oxygen species directly. Additionally, pos5Delta, but not sod1 or sod2, cells displayed an anaerobic expression profile, indicating a defect in oxygen sensing that is specific to pos5, and is not a general stress-response. Finally, the pos5Delta expression profile is quite similar to the hap1Delta expression profile previously reported, which may indicate a shared mechanism.
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Affiliation(s)
- Gregory R Stuart
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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42
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Young MJ, Court DA. Effects of the S288c genetic background and common auxotrophic markers on mitochondrial DNA function in Saccharomyces cerevisiae. Yeast 2009; 25:903-12. [PMID: 19160453 DOI: 10.1002/yea.1644] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Saccharomyces cerevisiae is a valuable model organism for the study of eukaryotic processes. Throughout its development as a research tool, several strain backgrounds have been utilized and different combinations of auxotrophic marker genes have been introduced into them, creating a useful but non-homogeneous set of strains. The ade2 allele was used as an auxotrophic marker, and for 'red-white' screening for respiratory competence. his3 alleles that influence the expression of MRM1 have been used as selectable markers, and the MIP1[S] allele, found in the commonly used S228c strain, is associated with mitochondrial DNA defects. The focus of the current work was to examine the effects of these alleles, singly and in combination, on the maintenance of mitochondrial function. The combination of the ade2 and MIP1[S] alleles is associated with a slight increase in point mutations in mitochondrial DNA. The deletion in the his3Delta200 allele, which removes the promoter for MRM1, is associated with loss of respiratory competence at 37 degrees C in the presence of either MIP1 allele. Thus, multiple factors can contribute to the maintenance of mitochondrial function, reinforcing the concept that strain background is an important consideration in both designing experiments and comparing results obtained by different research groups.
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Affiliation(s)
- M J Young
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Abstract
Hypoxia is typical for most battlefields of host-pathogen interactions in the human host. While adaptation of human cells to low levels of oxygen has been well established, little information exists on mechanisms of hypoxic adaptation in microbial pathogens. Importantly, the impact of hypoxia on microbial infection, virulence and pathogenesis is rarely investigated. Recent results on the human pathogens Candida albicans and Cryptococcus neoformans indicate that these fungi adapt to hypoxia specifically by altering several morphological phenotypes, metabolic and transcriptomal activities, as well as virulence traits. In this review, novel components and mechanisms involved in hypoxic adaptation of human fungals pathogens are summarized and discussed.
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Affiliation(s)
- Joachim F Ernst
- Institut für Mikrobiologie, Molekulare Mykologie, Heinrich-Heine-Universität Düsseldorf, Germany.
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Role of heme in the antifungal activity of the azaoxoaporphine alkaloid sampangine. EUKARYOTIC CELL 2007; 7:387-400. [PMID: 18156292 DOI: 10.1128/ec.00323-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sampangine, a plant-derived alkaloid found in the Annonaceae family, exhibits strong inhibitory activity against the opportunistic fungal pathogens Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. In the present study, transcriptional profiling experiments coupled with analyses of mutants were performed in an effort to elucidate its mechanism of action. Using Saccharomyces cerevisiae as a model organism, we show that sampangine produces a transcriptional response indicative of hypoxia, altering the expression of genes known to respond to low-oxygen conditions. Several additional lines of evidence obtained suggest that these responses could involve effects on heme. First, the hem1Delta mutant lacking the first enzyme in the heme biosynthetic pathway showed increased sensitivity to sampangine, and exogenously supplied hemin partially rescued the inhibitory activity of sampangine in wild-type cells. In addition, heterozygous mutants with deletions in genes involved in five out of eight steps in the heme biosynthetic pathway showed increased susceptibility to sampangine. Furthermore, spectral analyses of pyridine extracts indicated significant accumulation of free porphyrins in sampangine-treated cells. Transcriptional profiling experiments were also performed with C. albicans to investigate the response of a pathogenic fungal species to sampangine. Taking into account the known differences in the physiological responses of C. albicans and S. cerevisiae to low oxygen, significant correlations were observed between the two transcription profiles, suggestive of heme-related defects. Our results indicate that the antifungal activity of the plant alkaloid sampangine is due, at least in part, to perturbations in the biosynthesis or metabolism of heme.
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Hickman MJ, Winston F. Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor. Mol Cell Biol 2007; 27:7414-24. [PMID: 17785431 PMCID: PMC2169065 DOI: 10.1128/mcb.00887-07] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 06/25/2007] [Accepted: 08/27/2007] [Indexed: 12/17/2022] Open
Abstract
Changes in oxygen levels cause widespread changes in gene expression in organisms ranging from bacteria to humans. In Saccharomyces cerevisiae, this response is mediated in part by Hap1, originally identified as a heme-dependent transcriptional activator that functions during aerobic growth. We show here that Hap1 also plays a significant and direct role under hypoxic conditions, not as an activator, but as a repressor. The repressive activity of Hap1 controls several genes, including three ERG genes required for ergosterol biosynthesis. Chromatin immunoprecipitation experiments showed that Hap1 binds to the ERG gene promoters, while additional experiments showed that the corepressor Tup1/Ssn6 is recruited by Hap1 and is also required for repression. Furthermore, mutational analysis demonstrated that conserved Hap1 binding sites in the ERG5 5' regulatory region are required for repression. The switch of Hap1 from acting as a hypoxic repressor to an aerobic activator is determined by heme, which is synthesized only in the presence of oxygen. The ability of Hap1 to function as a ligand-dependent repressor and activator is a property shared with mammalian nuclear hormone receptors and likely allows greater transcriptional control by Hap1 in response to changing oxygen levels.
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Affiliation(s)
- Mark J Hickman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Abstract
The Ccr4-Not complex is a multifunctional regulatory platform composed of nine subunits that controls diverse cellular events including mRNA degradation, protein ubiquitination, and transcription. In this study, we identified the yeast Saccharomyces cerevisiae osmotic and oxidative stress transcription factor Skn7 as a new target for regulation by the Ccr4-Not complex. Skn7 interacts with Not1 in a two-hybrid assay and coimmunoprecipitates with Not5 in a Not4-dependent manner. Skn7-dependent expression of OCH1 and Skn7 binding to the OCH1 promoter are increased in not4Delta or not5Delta mutants. Skn7 purified from wild-type cells but not from not4Delta cells is associated with the Srb10 kinase. This kinase plays a central role in the regulation of Skn7 by Not4, since increased OCH1 expression in not4Delta cells requires Srb10. These results reveal a critical role for the Ccr4-Not complex in the mechanism of activation of Skn7 that is dependent upon the Srb10 kinase.
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Lamas-Maceiras M, Núñez L, Rodríguez-Belmonte E, González-Siso MI, Cerdán ME. Functional characterization of KlHAP1: a model to foresee different mechanisms of transcriptional regulation by Hap1p in yeasts. Gene 2007; 405:96-107. [PMID: 17942245 DOI: 10.1016/j.gene.2007.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 09/04/2007] [Accepted: 09/10/2007] [Indexed: 01/10/2023]
Abstract
In this work we have cloned and characterized the Kluyveromyces lactis HAP1 gene and we have found that, contrary to data previously described for the homologous gene of Saccharomyces cerevisiae, i.) the function of this gene does not affect growth in media with carbon sources used by fermentative or respiratory pathways ii) in aerobiosis, KlHap1p is not a transcriptional activator of the expression of genes related to respiration, cholesterol biosynthesis or oxidative stress defence analyzed in this study. The comparison of homology between specific regions of ScHap1p and KlHap1p reveals that the dimerization domain is poorly conserved and we have verified that this domain, cloned in the two plasmids of the two hybrid system, does not reconstitute S. cerevisiae Gal4p activity. Since the COOH-terminal transcriptional activation domain of KlHap1p is active when fused to the Gal4p-DNA binding domain, we hypothesize that differences in the capacity to form dimers could contribute to allow different functions of the protein in K. lactis and S. cerevisiae. Transcriptional expression of KlHAP1 is dependent on oxygen availability, increasing its expression in hypoxia. Deletion of KlHAP1 increases the resistance to oxidative stress or cadmium and the induction of KlYAP1 and KlTSA1 by the addition of 0.5 mM H(2)O(2) is repressed by KlHap1p. These data are discussed in reference to the evolution of respiro-fermentative metabolism in yeasts.
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Affiliation(s)
- Mónica Lamas-Maceiras
- Dpto. Biología Celular y Molecular. Universidad de A Coruña, F. Ciencias, Campus de A Zapateira s/n 15075, A Coruña, Spain
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Núñez L, González-Siso MI, Becerra M, Cerdán ME. Functional motifs outside the kinase domain of yeast Srb10p. Their role in transcriptional regulation and protein-interactions with Tup1p and Srb11p. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1227-35. [PMID: 17689156 DOI: 10.1016/j.bbapap.2007.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 06/21/2007] [Accepted: 06/26/2007] [Indexed: 11/16/2022]
Abstract
Several derivatives of the native Srb10 proteins from Saccharomyces cerevisiae and Kluyveromyces lactis, with removed selected motifs, have been constructed in order to test their role in Srb10p function. It has been demonstrated that the ATP binding site is necessary for repression of FLO11, CYC7 and SPI1. Yeast Srb10p specific motifs CM-I and CM-II, outside the kinase domain, are also necessary to complement two mutant phenotypes in S. cerevisiae Deltasrb10 strains, the failure to growth in galactose at 37 degrees C and flocculation. They are also required to keep transcriptional repression of FLO11 in non-flocculants, and for aerobic repression of CYC7 and SPI1. Two-hybrid analyses revealed that, in Srb10p derivatives, the absence of these motifs decreases the interaction of Srb10p with its cyclin partner Srb11p and with the component Tup1p of the general co-repressor complex Tup1p-Ssn6p.
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Affiliation(s)
- Laura Núñez
- Departamento de Biología Celular y Molecular. Facultad de Ciencias, Universidad de A Coruña, 15071, Spain
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Pagani MA, Casamayor A, Serrano R, Atrian S, Ariño J. Disruption of iron homeostasis in Saccharomyces cerevisiae by high zinc levels: a genome-wide study. Mol Microbiol 2007; 65:521-37. [PMID: 17630978 DOI: 10.1111/j.1365-2958.2007.05807.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Zinc is an essential metal that, when in excess, can be deleterious to the cell. Therefore, homeostatic mechanisms for this cation must be finely tuned. To better understand the response of yeast in front of an excess of zinc, we screened a systematic deletion mutant library for altered growth in the presence of 6 mM zinc. Eighty-nine mutants exhibited increased zinc sensitivity, including many genes involved in vacuolar assembling and biogenesis. Interestingly, a mutant lacking the Aft1 transcription factor, required for the transcriptional response to iron starvation, was found to be highly sensitive to zinc. Genome-wide transcriptional profiling revealed that exposure to 5 mM ZnCl(2) results in rapid increase in the expression of numerous chaperones required for proper protein folding or targeting to vacuole and mitochondria, as well as genes involved in stress response (mainly oxidative), sulphur metabolism and some components of the iron regulon. The effect of the lack of Aft1 both in the absence and in the presence of zinc overload was also investigated. Exposure to high zinc generated reactive oxygen species and markedly decreased glutathione content. Interestingly, zinc excess results in decreased intracellular iron content and aconitase and cytochrome c activities in stationary-phase cultures. These findings suggest that high zinc levels may alter the assembly and/or function of iron-sulphur-containing proteins, as well as the biosynthesis of haem groups, thus establishing a link between zinc, iron and sulphur metabolism.
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Affiliation(s)
- M Ayelen Pagani
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
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50
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Baidoobonso SM, Guidi BW, Myers LC. Med19(Rox3) Regulates Intermodule Interactions in the Saccharomyces cerevisiae Mediator Complex. J Biol Chem 2007; 282:5551-9. [PMID: 17192271 DOI: 10.1074/jbc.m609484200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Saccharomyces cerevisiae Mediator is a 25-subunit complex that facilitates both transcriptional activation and repression. Structural and functional studies have divided Mediator subunits into four distinct modules. The Head, Middle, and Tail modules form the core functional Mediator complex, whereas a fourth, the Cyc-C module, is variably associated with the core. By purifying Mediator from a strain lacking the Med19(Rox3) subunit, we have found that a complex missing only the Med19(Rox3) subunit can be isolated under mild conditions. Additionally, we have established that the entire Middle module is released when the Deltamed19(rox3) Mediator is purified under more stringent conditions. In contrast to most models of the modular structure of Mediator, we show that release of the Middle module in the Deltamed19(rox3) Mediator leaves a stable complex made up solely of Head and Tail subunits. Both the intact and Head-Tail Deltamed19(rox3) Mediator complexes have defects in enhanced basal transcription, enhanced TFIIH phosphorylation of the CTD, as well as binding of RNA Pol II and the CTD. The largely intact Deltamed19(rox3) complex facilitates activated transcription at levels similar to the wild type Mediator. In the absence of the Middle module, however, the Deltamed19(rox3) Mediator is unable to facilitate activated transcription. Although the Middle module is unnecessary for holding the Head and Tail modules together, it is required for the complex to function as a conduit between activators and the core transcription machinery.
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Affiliation(s)
- Shamara M Baidoobonso
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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