1
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Barlit H, Romero AM, Gülhan A, Patnaik PK, Tyshkovskiy A, Martínez-Pastor MT, Gladyshev VN, Puig S, Labunskyy VM. Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation. iScience 2024; 27:109868. [PMID: 38779483 PMCID: PMC11109004 DOI: 10.1016/j.isci.2024.109868] [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: 09/28/2023] [Revised: 03/12/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.
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Affiliation(s)
- Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Antonia M. Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Praveen K. Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - María T. Martínez-Pastor
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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2
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Puig-Segui MS, Decker CJ, Barlit H, Labunskyy VM, Parker R, Puig S. Regulation of translation in response to iron deficiency in human cells. Sci Rep 2024; 14:8451. [PMID: 38605136 PMCID: PMC11009288 DOI: 10.1038/s41598-024-59003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Protein synthesis is a highly energy-consuming process that is downregulated in response to many environmental stresses or adverse conditions. Studies in the yeast Saccharomyces cerevisiae have shown that bulk translation is inhibited during adaptation to iron deficiency, which is consistent with its requirement for ribosome biogenesis and recycling. Although iron deficiency anemia is the most common human nutritional disorder, how iron modulates translation in mammals is poorly understood. Studies during erythropoiesis have shown that iron bioavailability is coordinated with globin synthesis via bulk translation regulation. However, little is known about the control of translation during iron limitation in other tissues. Here, we investigated how iron depletion affects protein synthesis in human osteosarcoma U-2 OS cells. By adding an extracellular iron chelator, we observed that iron deficiency limits cell proliferation, induces autophagy, and decreases the global rate of protein synthesis. Analysis of specific molecular markers indicates that the inhibition of bulk translation upon iron limitation occurs through the eukaryotic initiation factor eIF2α and mechanistic target of rapamycin (mTOR) pathways. In contrast to other environmental and nutritional stresses, iron depletion does not trigger the assembly of messenger ribonucleoprotein stress granules, which typically form upon polysome disassembly.
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Affiliation(s)
- Mireia S Puig-Segui
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Hanna Barlit
- Department of Dermatology, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Calle Catedrático Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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3
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Shapiro JS, Chang HC, Tatekoshi Y, Zhao Z, Waxali ZS, Hong BJ, Chen H, Geier JA, Bartom ET, De Jesus A, Nejad FK, Mahmoodzadeh A, Sato T, Ramos-Alonso L, Romero AM, Martinez-Pastor MT, Jiang SC, Sah-Teli SK, Li L, Bentrem D, Lopaschuk G, Ben-Sahra I, O'Halloran TV, Shilatifard A, Puig S, Bergelson J, Koivunen P, Ardehali H. Iron drives anabolic metabolism through active histone demethylation and mTORC1. Nat Cell Biol 2023; 25:1478-1494. [PMID: 37749225 DOI: 10.1038/s41556-023-01225-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 08/08/2023] [Indexed: 09/27/2023]
Abstract
All eukaryotic cells require a minimal iron threshold to sustain anabolic metabolism. However, the mechanisms by which cells sense iron to regulate anabolic processes are unclear. Here we report a previously undescribed eukaryotic pathway for iron sensing in which molecular iron is required to sustain active histone demethylation and maintain the expression of critical components of the pro-anabolic mTORC1 pathway. Specifically, we identify the iron-binding histone-demethylase KDM3B as an intrinsic iron sensor that regulates mTORC1 activity by demethylating H3K9me2 at enhancers of a high-affinity leucine transporter, LAT3, and RPTOR. By directly suppressing leucine availability and RAPTOR levels, iron deficiency supersedes other nutrient inputs into mTORC1. This process occurs in vivo and is not an indirect effect by canonical iron-utilizing pathways. Because ancestral eukaryotes share homologues of KDMs and mTORC1 core components, this pathway probably pre-dated the emergence of the other kingdom-specific nutrient sensors for mTORC1.
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Affiliation(s)
- Jason S Shapiro
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Hsiang-Chun Chang
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yuki Tatekoshi
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Zohra Sattar Waxali
- The Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Bong Jin Hong
- The Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Haimei Chen
- The Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Justin A Geier
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Adam De Jesus
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Farnaz K Nejad
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Amir Mahmoodzadeh
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA
| | - Tatsuya Sato
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Lucia Ramos-Alonso
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Antonia Maria Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Shang-Chuan Jiang
- Plant Production and Protection Division (NSP), Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, Rome, Italy
| | - Shiv K Sah-Teli
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Liming Li
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Bentrem
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Gary Lopaschuk
- Cardiovascular Research Centre, Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Thomas V O'Halloran
- The Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Joy Bergelson
- Center of Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Hossein Ardehali
- Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL, USA.
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4
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Jordá T, Rozès N, Martínez-Pastor MT, Puig S. The yeast mRNA-binding protein Cth2 post-transcriptionally modulates ergosterol biosynthesis in response to iron deficiency. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194959. [PMID: 37453649 DOI: 10.1016/j.bbagrm.2023.194959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Sterol synthesis is an iron-dependent metabolic pathway in eukaryotes. Consequently, fungal ergosterol biosynthesis (ERG) is down-regulated in response to iron deficiency. In this report, we show that, upon iron limitation or overexpression of the iron-regulated mRNA-binding protein Cth2, the yeast Saccharomyces cerevisiae down-regulates the three initial enzymatic steps of ergosterol synthesis (ERG1, ERG7 and ERG11). Mechanistically, we show that Cth2 protein limits the translation and promotes the decrease in the mRNA levels of these specific ERG genes, which contain consensus Cth2-binding sites defined as AU-rich elements (AREs). Thus, expression of CTH2 leads to the accumulation of initial sterol intermediates, such as squalene, and to the drop of ergosterol levels. Changes in CTH2 expression levels disturb the response of yeast cells to stresses related to membrane integrity such as high ethanol and sorbitol concentrations. Therefore, CTH2 should be considered as a critical regulatory factor of ergosterol biosynthesis during iron deficiency.
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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.
| | - Nicolas Rozès
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - María Teresa Martínez-Pastor
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain; Departament de Bioquímica i Biologia Molecular, Facultat de Ciències Biològiques, 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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5
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Nicco C, Thomas M, Guillermet J, Havard M, Laurent-Tchenio F, Doridot L, Dautry F, Batteux F, Tchenio T. Mechanistic target of rapamycin (mTOR) regulates self-sustained quiescence, tumor indolence, and late clinical metastasis in a Beclin-1-dependent manner. Cell Cycle 2023; 22:542-564. [PMID: 36123968 PMCID: PMC9928463 DOI: 10.1080/15384101.2022.2123187] [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: 01/10/2023] Open
Abstract
Self-sustained quiescence (SSQ) has been characterized as a stable but reversible non-proliferative cellular state that limits the cloning of cultured cancer cells. By developing refined clonogenic assays, we showed here that cancer cells in SSQ can be selected with anticancer agents and that culture at low cell density induced SSQ in pancreas and prostate adenocarcinoma cells. Pre-culture of cells in 3D or their pretreatment with pharmacological inhibitors of mechanistic target of rapamycin (mTOR) synergize with low cell density for induction of SSQ in a Beclin-1-dependent manner. Dissociated pancreatic adenocarcinoma (PAAD) cells rendered defective for SSQ by down-regulating Beclin-1 expression exhibit higher tumor growth rate when injected subcutaneously into mice. Conversely, dissociated PAAD cells in SSQ promote the formation of small indolent tumors that eventually transitioned to a rapid growth phase. Ex vivo clonogenic assays showed that up to 40% of clonogenic cancer cells enzymatically dissociated from resected fast-growing tumors could enter SSQ, suggesting that SSQ could significantly impact the proliferation of cancer cells that are naturally dispersed from tumors. Remarkably, the kinetics of clinical metastatic recurrence in 124 patients with pancreatic adenocarcinoma included in the TGCA-PAAD project could be predicted from Beclin-1 and Cyclin-A2 mRNA levels in their primary tumor, Cyclin A2 mRNA being a marker of both cell proliferation and mTOR complex 1 activity. Overall, our data show that SSQ is likely to promote the late development of clinical metastases and suggest that identifying new agents targeting cancer cells in SSQ could help improve patient survival.
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Affiliation(s)
- Carole Nicco
- Institut Cochin, INSERM U1016/CNRS UMR 8104, Université de Paris, Paris, France
| | - Marine Thomas
- Institut Cochin, INSERM U1016/CNRS UMR 8104, Université de Paris, Paris, France
| | - Julie Guillermet
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Inserm U1037, CNRS U5071, Université Toulouse III, Toulouse, France
| | - Maryline Havard
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Fanny Laurent-Tchenio
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ludivine Doridot
- Institut Cochin, INSERM U1016/CNRS UMR 8104, Université de Paris, Paris, France
| | - François Dautry
- Laboratory of Biology and Applied Pharmacology (LBPA), CNRS UMR8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Frédéric Batteux
- Institut Cochin, INSERM U1016/CNRS UMR 8104, Université de Paris, Paris, France
| | - Thierry Tchenio
- Institut Cochin, INSERM U1016/CNRS UMR 8104, Université de Paris, Paris, France
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6
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Fan C, Ge X, Hao J, Wu T, Liu R, Sui W, Geng J, Zhang M. Identification of high iron–chelating peptides with unusual antioxidant effect from sea cucumbers and the possible binding mode. Food Chem 2023; 399:133912. [DOI: 10.1016/j.foodchem.2022.133912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/11/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022]
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7
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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] [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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8
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Jordá T, Martínez-Martín A, Martínez-Pastor MT, Puig S. Modulation of yeast Erg1 expression and terbinafine susceptibility by iron bioavailability. Microb Biotechnol 2022; 15:2705-2716. [PMID: 35837730 PMCID: PMC9618313 DOI: 10.1111/1751-7915.14102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022] Open
Abstract
Ergosterol is a specific sterol component of yeast and fungal membranes. Its biosynthesis is one of the most effective targets for antifungal treatments. However, the emergent resistance to multiple sterol‐based antifungal drugs emphasizes the need for new therapeutic approaches. The allylamine terbinafine, which selectively inhibits squalene epoxidase Erg1 within the ergosterol biosynthetic pathway, is mainly used to treat dermatomycoses, whereas its effectiveness in other fungal infections is limited. Given that ergosterol biosynthesis depends on iron as an essential cofactor, in this report, we used the yeast Saccharomyces cerevisiae to investigate how iron bioavailability influences Erg1 expression and terbinafine susceptibility. We observed that both chemical and genetic depletion of iron decrease ERG1 expression, leading to an increase in terbinafine susceptibility. Deletion of either ROX1 transcriptional repressor or CTH1 and CTH2 post‐transcriptional repressors of ERG1 expression led to an increase in Erg1 protein levels and terbinafine resistance. On the contrary, overexpression of CTH2 led to the opposite effect, lowering Erg1 levels and increasing terbinafine susceptibility. Although strain‐specific particularities exist, opportunistic pathogenic strains of S. cerevisiae displayed a response similar to the laboratory strain. These data indicate that iron bioavailability and particular regulatory factors could be used to modulate susceptibility to terbinafine.
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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
| | - Ana Martínez-Martín
- 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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9
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Genetic suppressors of Δgrx3 Δgrx4, lacking redundant multidomain monothiol yeast glutaredoxins, rescue growth and iron homeostasis. Biosci Rep 2022; 42:231328. [PMID: 35593209 PMCID: PMC9202360 DOI: 10.1042/bsr20212665] [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: 11/25/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Saccharomyces cerevisiae Grx3 and Grx4 are multidomain monothiol glutaredoxins that are redundant with each other. They can be efficiently complemented by heterologous expression of their mammalian ortholog, PICOT, which has been linked to tumor development and embryogenesis. PICOT is now believed to act as a chaperone distributing Fe-S clusters, although the first link to iron metabolism was observed with its yeast counterparts. Like PICOT, yeast Grx3 and Grx4 reside in the cytosol and nucleus where they form unusual Fe-S clusters coordinated by two glutaredoxins with CGFS motifs and two molecules of glutathione. Depletion or deletion of Grx3/Grx4 leads to functional impairment of virtually all cellular iron-dependent processes and loss of cell viability, thus making these genes the most upstream components of the iron utilization system. Nevertheless, the Δgrx3/4 double mutant in the BY4741 genetic background is viable and exhibits slow but stable growth under hypoxic conditions. Upon exposure to air, growth of the double deletion strain ceases, and suppressor mutants appear. Adopting a high copy-number library screen approach, we discovered novel genetic interactions: overexpression of ESL1, ESL2, SOK1, SFP1 or BDF2 partially rescues growth and iron utilization defects of Δgrx3/4. This genetic escape from the requirement for Grx3/Grx4 has not been previously described. Our study shows that even a far-upstream component of the iron regulatory machinery (Grx3/4) can be bypassed, and cellular networks involving RIM101 pH sensing, cAMP signaling, mTOR nutritional signaling, or bromodomain acetylation, may confer the bypassing activities.
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10
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Iron in Translation: From the Beginning to the End. Microorganisms 2021; 9:microorganisms9051058. [PMID: 34068342 PMCID: PMC8153317 DOI: 10.3390/microorganisms9051058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is an essential element for all eukaryotes, since it acts as a cofactor for many enzymes involved in basic cellular functions, including translation. While the mammalian iron-regulatory protein/iron-responsive element (IRP/IRE) system arose as one of the first examples of translational regulation in higher eukaryotes, little is known about the contribution of iron itself to the different stages of eukaryotic translation. In the yeast Saccharomyces cerevisiae, iron deficiency provokes a global impairment of translation at the initiation step, which is mediated by the Gcn2-eIF2α pathway, while the post-transcriptional regulator Cth2 specifically represses the translation of a subgroup of iron-related transcripts. In addition, several steps of the translation process depend on iron-containing enzymes, including particular modifications of translation elongation factors and transfer RNAs (tRNAs), and translation termination by the ATP-binding cassette family member Rli1 (ABCE1 in humans) and the prolyl hydroxylase Tpa1. The influence of these modifications and their correlation with codon bias in the dynamic control of protein biosynthesis, mainly in response to stress, is emerging as an interesting focus of research. Taking S. cerevisiae as a model, we hereby discuss the relevance of iron in the control of global and specific translation steps.
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11
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Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae. Biochem J 2021; 478:811-837. [DOI: 10.1042/bcj20200849] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/21/2023]
Abstract
We have investigated the effects that iron limitation provokes in Saccharomyces cerevisiae exponential cultures. We have demonstrated that one primary response is the induction of bulk autophagy mediated by TORC1. Coherently, Atg13 became dephosphorylated whereas Atg1 appeared phosphorylated. The signal of iron deprivation requires Tor2/Ypk1 activity and the inactivation of Tor1 leading to Atg13 dephosphorylation, thus triggering the autophagy process. Iron replenishment in its turn, reduces autophagy flux through the AMPK Snf1 and the subsequent activity of the iron-responsive transcription factor, Aft1. This signalling converges in Atg13 phosphorylation mediated by Tor1. Iron limitation promotes accumulation of trehalose and the increase in stress resistance leading to a quiescent state in cells. All these effects contribute to the extension of the chronological life, in a manner totally dependent on autophagy activation.
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Zhang Y, Ding X, Li M. Preparation, characterization and in vitro stability of iron-chelating peptides from mung beans. Food Chem 2021; 349:129101. [PMID: 33540219 DOI: 10.1016/j.foodchem.2021.129101] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/24/2020] [Accepted: 01/10/2021] [Indexed: 01/20/2023]
Abstract
Mung bean protein was enzymatically hydrolyzed with either alcalase, neutral protease, or papain. The mung bean protein hydrolysates (MPH) showed good ability to chelate ferrous ions, and the chelates had high stability in vitro. The hydrolysates prepared by alcalase showed the highest degree of hydrolysis and the highest ferrous chelating rate. Single factor tests showed that the pH and the material ratio had significant effects on ferrous chelating rates. The optimal MPH to FeCl2·4H2O material ratio was 8:1 (w/w) and the optimal pH of the reaction was 7.0, which yielded a chelating rate of 96.19 ± 0.94%. The fraction 3 with the highest ferrous chelating activity up to 61.25 ± 1.02 μg/mg was obtained from MPH by affinity chromatography. Meanwhile, the MPH-Fe complex had higher digestive stability than just MPH in both in vitro and acid-alkali tolerance assays. The characterization results showed that ferrous ions mainly combined with the amino, carboxyl, imidazole and other chelating active groups in mung bean peptides to form peptide-iron chelates. Scanning electron microscopy (SEM) analysis showed that mung bean peptide chelated ferrous ions to form polymer particles. These results provided insight into ways to develop functional foods such as iron-fortified cereals.
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Affiliation(s)
- Yijun Zhang
- Anhui Engineering Laboratory for Agro-products Processing, Anhui Agricultural University, Hefei 230036, China; Anhui Engineering Research Center of Functional Food for Plant Active Peptides, Hefei 230036, Anhui, China
| | - Xiangjun Ding
- Anhui Engineering Laboratory for Agro-products Processing, Anhui Agricultural University, Hefei 230036, China; Anhui Engineering Research Center of Functional Food for Plant Active Peptides, Hefei 230036, Anhui, China; College of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Meiqing Li
- Anhui Engineering Laboratory for Agro-products Processing, Anhui Agricultural University, Hefei 230036, China; Anhui Engineering Research Center of Functional Food for Plant Active Peptides, Hefei 230036, Anhui, China; College of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, Anhui, China.
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13
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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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14
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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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Laguna-Teno F, Suarez-Diez M, Tamayo-Ramos JA. Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials. Front Microbiol 2020; 11:1943. [PMID: 32849484 PMCID: PMC7431627 DOI: 10.3389/fmicb.2020.01943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
Graphene oxide has become a very appealing nanomaterial during the last years for many different applications, but its possible impact in different biological systems remains unclear. Here, an assessment to understand the toxicity of different commercial graphene oxide nanomaterials on the unicellular fungal model organism Saccharomyces cerevisiae was performed. For this task, an RNA purification protocol was optimized to avoid the high nucleic acid absorption capacity of graphene oxide. The developed protocol is based on a sorbitol gradient separation process for the isolation of adequate ribonucleic acid levels (in concentration and purity) from yeast cultures exposed to the carbon derived nanomaterial. To pinpoint potential toxicity mechanisms and pathways, the transcriptome of S. cerevisiae exposed to 160 mg L–1 of monolayer graphene oxide (GO) and graphene oxide nanocolloids (GOC) was studied and compared. Both graphene oxide products induced expression changes in a common group of genes (104), many of them related to iron homeostasis, starvation and stress response, amino acid metabolism and formate catabolism. Also, a high number of genes were only differentially expressed in either GO (236) or GOC (1077) exposures, indicating that different commercial products can induce specific changes in the physiological state of the fungus.
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Affiliation(s)
- Felix Laguna-Teno
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Burgos, Spain
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
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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: 175] [Impact Index Per Article: 43.8] [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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Martínez-Pastor MT, Puig S. Adaptation to iron deficiency in human pathogenic fungi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118797. [PMID: 32663505 DOI: 10.1016/j.bbamcr.2020.118797] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/13/2020] [Accepted: 07/05/2020] [Indexed: 02/08/2023]
Abstract
Iron is an essential micronutrient for virtually all eukaryotic organisms and plays a central role during microbial infections. Invasive fungal diseases are associated with strikingly high rates of mortality, but their impact on human health is usually underestimated. Upon a fungal infection, hosts restrict iron availability in order to limit the growth and virulence of the pathogen. Here, we use two model yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, to delve into the response to iron deficiency of human fungal pathogens, such as Candida glabrata, Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans. Fungi possess common and species-specific mechanisms to acquire iron and to control the response to iron limitation. Upon iron scarcity, fungi activate a wide range of elegant strategies to capture and import exogenous iron, mobilize iron from intracellular stores, and modulate their metabolism to economize and prioritize iron utilization. Hence, iron homeostasis genes represent remarkable virulence factors that can be used as targets for the development of novel antifungal treatments.
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Affiliation(s)
| | - 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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18
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The yeast Aft1 transcription factor activates ribonucleotide reductase catalytic subunit RNR1 in response to iron deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194522. [PMID: 32147528 DOI: 10.1016/j.bbagrm.2020.194522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/25/2020] [Accepted: 03/01/2020] [Indexed: 12/18/2022]
Abstract
Eukaryotic ribonucleotide reductases are iron-dependent enzymes that catalyze the rate-limiting step in the de novo synthesis of deoxyribonucleotides. Multiple mechanisms regulate the activity of ribonucleotide reductases in response to genotoxic stresses and iron deficiency. Upon iron starvation, the Saccharomyces cerevisiae Aft1 transcription factor specifically binds to iron-responsive cis elements within the promoter of a group of genes, known as the iron regulon, activating their transcription. Members of the iron regulon participate in iron acquisition, mobilization and recycling, and trigger a genome-wide metabolic remodeling of iron-dependent pathways. Here, we describe a mechanism that optimizes the activity of yeast ribonucleotide reductase when iron is scarce. We demonstrate that Aft1 and the DNA-binding protein Ixr1 enhance the expression of the gene encoding for its catalytic subunit, RNR1, in response to iron limitation, leading to an increase in both mRNA and protein levels. By mutagenesis of the Aft1-binding sites within RNR1 promoter, we conclude that RNR1 activation by iron depletion is important for Rnr1 protein and deoxyribonucleotide synthesis. Remarkably, Aft1 also activates the expression of IXR1 upon iron scarcity through an iron-responsive element located within its promoter. These results provide a novel mechanism for the direct activation of ribonucleotide reductase function by the iron-regulated Aft1 transcription factor.
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