1
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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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2
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Lindahl PA. Iron Homeostatic Regulation in Saccharomyces cerevisiae: Introduction to a Computational Modeling Method. Methods Mol Biol 2024; 2839:3-29. [PMID: 39008245 DOI: 10.1007/978-1-0716-4043-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Over the past 30 years, much has been learned regarding iron homeostatic regulation in budding yeast, S. cerevisiae, including the identity of many of the proteins and molecular-level regulatory mechanisms involved. Most advances have involved inferring such mechanisms based on the analysis of iron-dysregulation phenotypes arising in various genetic mutant strains. Still lacking is a cellular- or system-level understanding of iron homeostasis. These experimental advances are summarized in this review, and a method for developing cellular-level regulatory mechanisms in yeast is presented. The method employs the results of Mössbauer spectroscopy of whole cells and organelles, iron quantification of the same, and ordinary differential equation-based mathematical models. Current models are simplistic when compared to the complexity of iron homeostasis in real cells, yet they hold promise as a useful, perhaps even required, complement to the popular genetics-based approach. The fundamental problem in comprehending cellular regulatory mechanisms is that, given the complexities involved, different molecular-level mechanisms can often give rise to virtually indistinguishable cellular phenotypes. Mathematical models cannot eliminate this problem, but they can minimize it.
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Affiliation(s)
- Paul A Lindahl
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
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3
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Pijuan J, Moreno DF, Yahya G, Moisa M, Ul Haq I, Krukiewicz K, Mosbah R, Metwally K, Cavalu S. Regulatory and pathogenic mechanisms in response to iron deficiency and excess in fungi. Microb Biotechnol 2023; 16:2053-2071. [PMID: 37804207 PMCID: PMC10616654 DOI: 10.1111/1751-7915.14346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023] Open
Abstract
Iron is an essential element for all eukaryote organisms because of its redox properties, which are important for many biological processes such as DNA synthesis, mitochondrial respiration, oxygen transport, lipid, and carbon metabolism. For this reason, living organisms have developed different strategies and mechanisms to optimally regulate iron acquisition, transport, storage, and uptake in different environmental responses. Moreover, iron plays an essential role during microbial infections. Saccharomyces cerevisiae has been of key importance for decrypting iron homeostasis and regulation mechanisms in eukaryotes. Specifically, the transcription factors Aft1/Aft2 and Yap5 regulate the expression of genes to control iron metabolism in response to its deficiency or excess, adapting to the cell's iron requirements and its availability in the environment. We also review which iron-related virulence factors have the most common fungal human pathogens (Aspergillus fumigatus, Cryptococcus neoformans, and Candida albicans). These factors are essential for adaptation in different host niches during pathogenesis, including different fungal-specific iron-uptake mechanisms. While being necessary for virulence, they provide hope for developing novel antifungal treatments, which are currently scarce and usually toxic for patients. In this review, we provide a compilation of the current knowledge about the metabolic response to iron deficiency and excess in fungi.
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Affiliation(s)
- Jordi Pijuan
- Laboratory of Neurogenetics and Molecular MedicineInstitut de Recerca Sant Joan de DéuBarcelonaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIIIMadridSpain
| | - David F. Moreno
- Department of Molecular Cellular and Developmental BiologyYale UniversityNew HavenConnecticutUSA
- Systems Biology InstituteYale UniversityWest HavenConnecticutUSA
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of PharmacyZagazig UniversityAl SharqiaEgypt
| | - Mihaela Moisa
- Faculty of Medicine and PharmacyUniversity of OradeaOradeaRomania
| | - Ihtisham Ul Haq
- Department of Physical Chemistry and Polymers TechnologySilesian University of TechnologyGliwicePoland
- Programa de Pós‐graduação em Inovação TecnológicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Polymers TechnologySilesian University of TechnologyGliwicePoland
- Centre for Organic and Nanohybrid ElectronicsSilesian University of TechnologyGliwicePoland
| | - Rasha Mosbah
- Infection Control UnitHospitals of Zagazig UniversityZagazigEgypt
| | - Kamel Metwally
- Department of Medicinal Chemistry, Faculty of PharmacyUniversity of TabukTabukSaudi Arabia
- Department of Pharmaceutical Medicinal Chemistry, Faculty of PharmacyZagazig UniversityZagazigEgypt
| | - Simona Cavalu
- Faculty of Medicine and PharmacyUniversity of OradeaOradeaRomania
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4
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Elias D, Tóth Hervay N, Bujdos M, Gbelska Y. Essential Role of CgErg6p in Maintaining Oxidative Stress Tolerance and Iron Homeostasis in Candida glabrata. J Fungi (Basel) 2023; 9:jof9050579. [PMID: 37233290 DOI: 10.3390/jof9050579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
The human pathogenic fungus Candida glabrata is the second leading cause of candidemia, a life-threatening invasive mycosis. Clinical outcomes are complicated by reduced susceptibility of C. glabrata to azoles together with its ability to evolve stable resistance to both azoles and echinocandins following drug exposure. Compared to other Candida spp., C. glabrata displays robust oxidative stress resistance. In this study, we investigated the impact of CgERG6 gene deletion on the oxidative stress response in C. glabrata. CgERG6 gene encodes sterol-24-C-methyltransferase, which is involved in the final steps of ergosterol biosynthesis. Our previous results showed that the Cgerg6Δ mutant has a lower ergosterol content in its membranes. Here, we show that the Cgerg6Δ mutant displays increased susceptibility to oxidative stress inducing agents, such as menadione, hydrogen peroxide and diamide, accompanied with increased intracellular ROS production. The Cgerg6Δ mutant is not able to tolerate higher concentrations of iron in the growth media. We observed increased expression of transcription factors, CgYap1p, CgMsn4p and CgYap5p, together with increased expression of catalase encoding the CgCTA1 gene and vacuolar iron transporter CgCCC1 in the Cgerg6Δ mutant cells. However, it seems that the CgERG6 gene deletion does not influence the function of mitochondria.
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Affiliation(s)
- Daniel Elias
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Nora Tóth Hervay
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Marek Bujdos
- Faculty of Natural Sciences, Institute of Laboratory Research on Geomaterials, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Yvetta Gbelska
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
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Adaptation of Saccharomyces Species to High-Iron Conditions. Int J Mol Sci 2022; 23:ijms232213965. [PMID: 36430442 PMCID: PMC9693265 DOI: 10.3390/ijms232213965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Iron is an indispensable element that participates as an essential cofactor in multiple biological processes. However, when present in excess, iron can engage in redox reactions that generate reactive oxygen species that damage cells at multiple levels. In this report, we characterized the response of budding yeast species from the Saccharomyces genus to elevated environmental iron concentrations. We have observed that S. cerevisiae strains are more resistant to high-iron concentrations than Saccharomyces non-cerevisiae species. Liquid growth assays showed that species evolutionarily closer to S. cerevisiae, such as S. paradoxus, S. jurei, S. mikatae, and S. arboricola, were more resistant to high-iron levels than the more distant species S. eubayanus and S. uvarum. Remarkably, S. kudriavzevii strains were especially iron sensitive. Growth assays in solid media suggested that S. cerevisiae and S. paradoxus were more resistant to the oxidative stress caused by elevated iron concentrations. When comparing iron accumulation and sensitivity, different patterns were observed. As previously described for S. cerevisiae, S. uvarum and particular strains of S. kudriavzevii and S. paradoxus became more sensitive to iron while accumulating more intracellular iron levels. However, no remarkable changes in intracellular iron accumulation were observed for the remainder of species. These results indicate that different mechanisms of response to elevated iron concentrations exist in the different species of the genus Saccharomyces.
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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7
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Sherry Wines: Worldwide Production, Chemical Composition and Screening Conception for Flor Yeasts. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The manufacturing of sherry wines is a unique, carefully regulated process, from harvesting to quality control of the finished product, involving dynamic biological aging in a “criadera-solera” system or some other techniques. Specialized “flor” strains of the yeast Saccharomyces cerevisiae play the central role in the sherry manufacturing process. As a result, sherry wines have a characteristic and unique chemical composition that determines their organoleptic properties (such as color, odor, and taste) and distinguishes them from all other types of wine. The use of modern methods of genetics and biotechnology contributes to a deep understanding of the microbiology of sherry production and allows us to define a new methodology for breeding valuable flor strains. This review discusses the main sherry-producing regions and the chemical composition of sherry wines, as well as genetic, oenological, and other selective markers for flor strains that can be used for screening novel candidates that are promising for sherry production among environmental isolates.
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Sorribes-Dauden R, Martínez-Pastor MT, Puig S. Expression of a Truncated Yeast Ccc1 Vacuolar Transporter Increases the Accumulation of Endogenous Iron. Genes (Basel) 2021; 12:genes12081120. [PMID: 34440294 PMCID: PMC8391176 DOI: 10.3390/genes12081120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023] Open
Abstract
Iron is an essential micronutrient for all eukaryotic organisms because it participates as a redox cofactor in multiple metabolic processes. Iron bioavailability is highly restricted due to the low solubility of its oxidized form, frequently leading to iron deficiency anemia. The baker’s yeast Saccharomyces cerevisiae is used as a model organism for iron homeostasis studies, but also as a food supplement and fermentative microorganism in the food industry. Yeast cells use the vacuolar Ccc1 transporter to detoxify and store excess iron in the vacuoles. Here, we modulate CCC1 expression and properties to increase iron extraction from the environment. We show that constitutive expression of full-length CCC1 is toxic, whereas deletion of its cytosolic amino-terminal (Nt) domain (NtΔCCC1) rescues this phenotype. Toxicity is exacerbated in cells lacking AFT1 transcription factor. Further characterization of NtΔCcc1 protein suggests that it is a partially functional protein. Western blot analyses indicate that deletion of Ccc1 Nt domain does not significantly alter GFP-Ccc1 protein stability. A functional full-length GFP-Ccc1 protein localized to particular regions of the vacuolar membrane, whereas GFP-NtΔCcc1 protein was evenly distributed throughout this endogenous membrane. Interestingly, expression of NtΔCCC1 increased the accumulation of endogenous iron in cells cultivated under iron-sufficient conditions, a strategy that could be used to extract iron from media that are not rich in iron.
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Affiliation(s)
- Raquel Sorribes-Dauden
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Doctor Moliner 50, 46100 Burjassot, Valencia, Spain;
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Doctor Moliner 50, 46100 Burjassot, Valencia, Spain;
- Correspondence: (M.T.M.-P.); (S.P.)
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Agustín Escardino 7, 46980 Paterna, Valencia, Spain
- Correspondence: (M.T.M.-P.); (S.P.)
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Robinson JR, Isikhuemhen OS, Anike FN. Fungal-Metal Interactions: A Review of Toxicity and Homeostasis. J Fungi (Basel) 2021; 7:225. [PMID: 33803838 PMCID: PMC8003315 DOI: 10.3390/jof7030225] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
Metal nanoparticles used as antifungals have increased the occurrence of fungal-metal interactions. However, there is a lack of knowledge about how these interactions cause genomic and physiological changes, which can produce fungal superbugs. Despite interest in these interactions, there is limited understanding of resistance mechanisms in most fungi studied until now. We highlight the current knowledge of fungal homeostasis of zinc, copper, iron, manganese, and silver to comprehensively examine associated mechanisms of resistance. Such mechanisms have been widely studied in Saccharomyces cerevisiae, but limited reports exist in filamentous fungi, though they are frequently the subject of nanoparticle biosynthesis and targets of antifungal metals. In most cases, microarray analyses uncovered resistance mechanisms as a response to metal exposure. In yeast, metal resistance is mainly due to the down-regulation of metal ion importers, utilization of metallothionein and metallothionein-like structures, and ion sequestration to the vacuole. In contrast, metal resistance in filamentous fungi heavily relies upon cellular ion export. However, there are instances of resistance that utilized vacuole sequestration, ion metallothionein, and chelator binding, deleting a metal ion importer, and ion storage in hyphal cell walls. In general, resistance to zinc, copper, iron, and manganese is extensively reported in yeast and partially known in filamentous fungi; and silver resistance lacks comprehensive understanding in both.
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Affiliation(s)
| | - Omoanghe S. Isikhuemhen
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, 1601 East Market Street, Greensboro, NC 27411, USA; (J.R.R.); (F.N.A.)
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Pujol-Carrion N, Pavón-Vergés M, Arroyo J, de la Torre-Ruiz MA. The MAPK Slt2/Mpk1 plays a role in iron homeostasis through direct regulation of the transcription factor Aft1. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118974. [PMID: 33549702 DOI: 10.1016/j.bbamcr.2021.118974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/14/2021] [Accepted: 01/28/2021] [Indexed: 01/18/2023]
Abstract
Iron is an essential element for life. Cells develop mechanisms to tightly regulate its homeostasis, in order to avoid abnormal accumulation and the consequent cell toxicity. In budding yeast, the high affinity iron regulon is under the control of the transcription factor Aft1. We present evidence demonstrating that the MAPK Slt2 of the cell wall integrity pathway (CWI), phosphorylates and negatively regulates Aft1 activity upon the iron depletion signal, both in fermentative or respiratory conditions. The lack of Slt2 provokes Aft1 dysfunction leading to a shorter chronological life span. The signal of iron scarcity is not transmitted to Slt2 through other signalling pathways such as TOR1, PKA, SNF1 or TOR2/YPK1. The observation that Slt2 physically binds Aft1 rather suggests a direct regulation.
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Affiliation(s)
- Nuria Pujol-Carrion
- Cell Signalling in Yeast Unit, Department of Basic Medical Sciences, Institut de Recerca Biomèdica de Lleida (IRBLleida), University of Lleida, 25198 Lleida, Spain
| | - Mónica Pavón-Vergés
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - Javier Arroyo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University Complutense de Madrid, IRYCIS, 28040 Madrid, Spain
| | - Maria Angeles de la Torre-Ruiz
- Cell Signalling in Yeast Unit, Department of Basic Medical Sciences, Institut de Recerca Biomèdica de Lleida (IRBLleida), University of Lleida, 25198 Lleida, Spain.
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Sorribes-Dauden R, Peris D, Martínez-Pastor MT, Puig S. Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi. Comput Struct Biotechnol J 2020; 18:3712-3722. [PMID: 33304466 PMCID: PMC7714665 DOI: 10.1016/j.csbj.2020.10.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/28/2020] [Accepted: 10/31/2020] [Indexed: 02/06/2023] Open
Abstract
Iron is an essential micronutrient for most living beings since it participates as a redox active cofactor in many biological processes including cellular respiration, lipid biosynthesis, DNA replication and repair, and ribosome biogenesis and recycling. However, when present in excess, iron can participate in Fenton reactions and generate reactive oxygen species that damage cells at the level of proteins, lipids and nucleic acids. Organisms have developed different molecular strategies to protect themselves against the harmful effects of high concentrations of iron. In the case of fungi and plants, detoxification mainly occurs by importing cytosolic iron into the vacuole through the Ccc1/VIT1 iron transporter. New sequenced genomes and bioinformatic tools are facilitating the functional characterization, evolution and ecological relevance of metabolic pathways and homeostatic networks across the Tree of Life. Sequence analysis shows that Ccc1/VIT1 homologs are widely distributed among organisms with the exception of animals. The recent elucidation of the crystal structure of a Ccc1/VIT1 plant ortholog has enabled the identification of both conserved and species-specific motifs required for its metal transport mechanism. Moreover, recent studies in the yeast Saccharomyces cerevisiae have also revealed that multiple transcription factors including Yap5 and Msn2/Msn4 contribute to the expression of CCC1 in high-iron conditions. Interestingly, Malaysian S. cerevisiae strains express a partially functional Ccc1 protein that renders them sensitive to iron. Different regulatory mechanisms have been described for non-Saccharomycetaceae Ccc1 homologs. The characterization of Ccc1/VIT1 proteins is of high interest in the development of biofortified crops and the protection against microbial-derived diseases.
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Key Words
- BLOSUM, BLOcks SUbstitution Matrix
- CBC, CCAAT-binding core complex
- CRD, Cysteine-rich domain
- CS, Consistency score
- Ccc1
- Cg, Candida glabrata
- Eg, Eucalyptus grandis
- Fe, Iron
- Fungi
- H, Helix
- Hap, Heme activator protein
- ISC, Iron-sulfur luster
- Iron detoxification
- Iron regulation
- Iron transport
- MAFFT, Multiple Alignment using Fast Fourier Transform
- MBD, Metal-binding domain
- ML, Maximum-likelihood
- NRAMP, Natural Resistance-Associated Macrophage Protein
- Plants
- ROS, Reactive oxygen species
- TMD, Transmembrane domain
- VIT, Vacuolar iron transporter
- VIT1
- VTL, Vacuolar iron transporter-like
- Vacuole
- YRE, Yap response elements
- Yeast
- bZIP, basic leucine-zipper
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Affiliation(s)
- Raquel Sorribes-Dauden
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - David Peris
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, 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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12
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Ramos-Alonso L, Romero AM, Martínez-Pastor MT, Puig S. Iron Regulatory Mechanisms in Saccharomyces cerevisiae. Front Microbiol 2020; 11:582830. [PMID: 33013818 PMCID: PMC7509046 DOI: 10.3389/fmicb.2020.582830] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
Iron is an essential micronutrient for all eukaryotic organisms because it participates as a redox cofactor in many cellular processes. However, excess iron can damage cells since it promotes the generation of reactive oxygen species. The budding yeast Saccharomyces cerevisiae has been used as a model organism to study the adaptation of eukaryotic cells to changes in iron availability. Upon iron deficiency, yeast utilizes two transcription factors, Aft1 and Aft2, to activate the expression of a set of genes known as the iron regulon, which are implicated in iron uptake, recycling and mobilization. Moreover, Aft1 and Aft2 activate the expression of Cth2, an mRNA-binding protein that limits the expression of genes encoding for iron-containing proteins or that participate in iron-using processes. Cth2 contributes to prioritize iron utilization in particular pathways over other highly iron-consuming and non-essential processes including mitochondrial respiration. Recent studies have revealed that iron deficiency also alters many other metabolic routes including amino acid and lipid synthesis, the mitochondrial retrograde response, transcription, translation and deoxyribonucleotide synthesis; and activates the DNA damage and general stress responses. At high iron levels, the yeast Yap5, Msn2, and Msn4 transcription factors activate the expression of a vacuolar iron importer called Ccc1, which is the most important high-iron protecting factor devoted to detoxify excess cytosolic iron that is stored into the vacuole for its mobilization upon scarcity. The complete sequencing and annotation of many yeast genomes is starting to unveil the diversity and evolution of the iron homeostasis network in this species.
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Affiliation(s)
- Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | | | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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Machinery for fungal heme acquisition. Curr Genet 2020; 66:703-711. [PMID: 32185489 DOI: 10.1007/s00294-020-01067-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023]
Abstract
Iron is essential for nearly all aerobic organisms. One source of iron in nature is in the form of heme. Due to its critical physiological importance as a cofactor for several enzymes, organisms have evolved various means to secure heme for their needs. In the case of heme prototrophs, these organisms possess a highly conserved eight-step biosynthetic pathway. Another means used by many organisms is to acquire heme from external sources. As opposed to the knowledge of enzymes responsible for heme biosynthesis, the nature of the players and mechanisms involved in the acquisition of exogenous heme is limited. This review focuses on a description of newly discovered proteins that have novel functions in heme assimilation in the model organism Schizosaccharomyces pombe. This tractable model allows the use of the power of genetics to selectively block heme biosynthesis, setting conditions to investigate the mechanisms by which external heme is taken up by the cells. Studies have revealed that S. pombe possesses two independent heme uptake systems that require Shu1 and Str3, respectively. Heme-bound iron is captured by Shu1 at the cell surface, triggering its internalization to the vacuole with the aid of ubiquitinated proteins and the ESCRT machinery. In the case of the plasma membrane transporter Str3, it promotes cellular heme import in cells lacking Shu1. The discovery of these two pathways may contribute to gain novel insights into the mechanisms whereby fungi assimilate heme, which is an essentially biological process for their ability to invade and colonize new niches.
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Simpson-Lavy K, Kupiec M. Carbon catabolite repression: not only for glucose. Curr Genet 2019; 65:1321-1323. [PMID: 31119370 DOI: 10.1007/s00294-019-00996-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 04/28/2019] [Accepted: 05/14/2019] [Indexed: 12/18/2022]
Abstract
Most organisms prefer to utilize glucose as a carbon source. Accordingly, the expression of genes involved in the catabolism of other carbon sources is repressed by the presence of glucose in a process known as (carbon) catabolite repression. However, much less is known about the relationships between "poor" carbon sources. We have recently shown that the enzyme alcohol dehydrogenase of the yeast Saccharomyces cerevisiae (ADH2), required for the utilization of ethanol, is not only inhibited by glucose, but by the acetate imported from the medium or produced by ethanol metabolism. Our study showed that sensing of acetate takes place within the cell, and not in the external medium, and that "poor" carbon sources are also utilized according to a pre-established hierarchy.
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Affiliation(s)
- Kobi Simpson-Lavy
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel
| | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel.
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El’darov MA, Avdanina DA, Shalamitskii MY, Ivanova EV, Tanashchuk TN, Kishkovskaya SA, Ravin NV, Mardanov AV. Polymorphism of the Iron Homeostasis Genes and Iron Sensitivity in Saccharomyces cerevisiae Flor and Wine Strains. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Ramos-Alonso L, Romero AM, Polaina J, Puig S, Martínez-Pastor MT. Dissecting mRNA decay and translation inhibition during iron deficiency. Curr Genet 2018; 65:139-145. [PMID: 30128746 DOI: 10.1007/s00294-018-0880-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 10/28/2022]
Abstract
Iron participates as a vital cofactor in multiple metabolic pathways. Despite its abundance, iron bioavailability is highly restricted in aerobic and alkaline environments. Therefore, living organisms have evolved multiple adaptive mechanisms to respond to iron scarcity. These strategies include a global remodeling of iron metabolism directed to optimize iron utilization. In the baker's yeast Saccharomyces cerevisiae, this metabolic reorganization is accomplished to a large extent by an mRNA-binding protein called Cth2. Yeast Cth2 belongs to a conserved family of tandem zinc finger containing proteins that specifically bind to transcripts with AU-rich elements and promote their turnover. A recent study has revealed that Cth2 also inhibits the translation of its target mRNAs (Ramos-Alonso et al., PLoS Genet 14:e1007476, https://doi.org/10.1371/journal.pgen.1007476 , 2018). Interestingly, the mammalian Cth2 ortholog known as tristetraprolin (aka TTP/TIS11/ZFP36), which is also implicated in controlling iron metabolism, promotes the decay and prevents the translation of its regulated transcripts. These observations open the possibility to study the relative contribution of altering mRNA stability and translation to the physiological adaptation to iron deficiency, the function played by the different domains within the mRNA-binding protein, and the potential factors implicated in coordinating both post-transcriptional events.
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Affiliation(s)
- Lucía Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Antonia María Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Julio Polaina
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), C/ Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Ave. Doctor Moliner 50, Burjassot, 46100, Valencia, Spain.
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