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Aguirre-López B, Escalera-Fanjul X, Hersch-González J, Rojas-Ortega E, El-Hafidi M, Lezama M, González J, Bianchi MM, López G, Márquez D, Scazzocchio C, Riego-Ruiz L, González A. In Kluyveromyces lactis a Pair of Paralogous Isozymes Catalyze the First Committed Step of Leucine Biosynthesis in Either the Mitochondria or the Cytosol. Front Microbiol 2020; 11:1843. [PMID: 32849440 PMCID: PMC7418496 DOI: 10.3389/fmicb.2020.01843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/14/2020] [Indexed: 12/31/2022] Open
Abstract
Divergence of paralogous pairs, resulting from gene duplication, plays an important role in the evolution of specialized or novel gene functions. Analysis of selected duplicated pairs has elucidated some of the mechanisms underlying the functional diversification of Saccharomyces cerevisiae (S. cerevisiae) paralogous genes. Similar studies of the orthologous pairs extant in pre-whole genome duplication yeast species, such as Kluyveromyces lactis (K. lactis) remain to be addressed. The genome of K. lactis, an aerobic yeast, includes gene pairs generated by sporadic duplications. The genome of this organism comprises the KlLEU4 and KlLEU4BIS paralogous pair, annotated as putative α-isopropylmalate synthases (α-IPMSs), considered to be the orthologs of the S. cerevisiae ScLEU4/ScLEU9 paralogous genes. The enzymes encoded by the latter two genes are mitochondrially located, differing in their sensitivity to leucine allosteric inhibition resulting in ScLeu4-ScLeu4 and ScLeu4-ScLeu9 sensitive dimers and ScLeu9-ScLeu9 relatively resistant homodimers. Previous work has shown that, in a Scleu4Δ mutant, ScLEU9 expression is increased and assembly of ScLeu9-ScLeu9 leucine resistant homodimers results in loss of feedback regulation of leucine biosynthesis, leading to leucine accumulation and decreased growth rate. Here we report that: (i) K. lactis harbors a sporadic gene duplication, comprising the KlLEU4, syntenic with S. cerevisiae ScLEU4 and ScLEU9, and the non-syntenic KlLEU4BIS, arising from a pre-WGD event. (ii) That both, KlLEU4 and KlLEU4BIS encode leucine sensitive α-IPMSs isozymes, located in the mitochondria (KlLeu4) and the cytosol (KlLeu4BIS), respectively. (iii) That both, KlLEU4 or KlLEU4BIS complement the Scleu4Δ Scleu9Δ leucine auxotrophic phenotype and revert the enhanced ScLEU9 transcription observed in a Scleu4Δ ScLEU9 mutant. The Scleu4Δ ScLEU9 growth mutant phenotype is only fully complemented when transformed with the syntenic KlLEU4 mitochondrial isoform. KlLEU4 and KlLEU4BIS underwent a different diversification pathways than that leading to ScLEU4/ScLEU9. KlLEU4 could be considered as the functional ortholog of ScLEU4, since its encoded isozyme can complement both the Scleu4Δ Scleu9Δ leucine auxotrophy and the Scleu4Δ ScLEU9 complex phenotype.
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Affiliation(s)
- Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Jaqueline Hersch-González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eréndira Rojas-Ortega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mohammed El-Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Mijail Lezama
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - James González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Michele Maria Bianchi
- Dipartimento di Biologia e Biotecnologie Charles Darwin, Sapienza Università di Roma, Rome, Italy
| | - Geovani López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dariel Márquez
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College London, London, United Kingdom.,Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, San Luis Potosí, Mexico
| | - Alicia González
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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2
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Denecker T, Zhou Li Y, Fairhead C, Budin K, Camadro JM, Bolotin-Fukuhara M, Angoulvant A, Lelandais G. Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata. NAR Genom Bioinform 2020; 2:lqaa027. [PMID: 33575583 PMCID: PMC7671338 DOI: 10.1093/nargab/lqaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/27/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Candida glabrata is a cause of life-threatening invasive infections especially in elderly and immunocompromised patients. Part of human digestive and urogenital microbiota, C. glabrata faces varying iron availability, low during infection or high in digestive and urogenital tracts. To maintain its homeostasis, C. glabrata must get enough iron for essential cellular processes and resist toxic iron excess. The response of this pathogen to both depletion and lethal excess of iron at 30°C have been described in the literature using different strains and iron sources. However, adaptation to iron variations at 37°C, the human body temperature and to gentle overload, is poorly known. In this study, we performed transcriptomic experiments at 30°C and 37°C with low and high but sub-lethal ferrous concentrations. We identified iron responsive genes and clarified the potential effect of temperature on iron homeostasis. Our exploration of the datasets was facilitated by the inference of functional networks of co-expressed genes, which can be accessed through a web interface. Relying on stringent selection and independently of existing knowledge, we characterized a list of 214 genes as key elements of C. glabrata iron homeostasis and interesting candidates for medical applications.
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Affiliation(s)
- Thomas Denecker
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91198, Gif-sur-Yvette, France
| | - Youfang Zhou Li
- Université Paris-Saclay, INRAE, CNRS, Génétique Quantitative et Évolution Le Moulon, 91400, Orsay, France
| | - Cécile Fairhead
- Université Paris-Saclay, INRAE, CNRS, Génétique Quantitative et Évolution Le Moulon, 91400, Orsay, France
| | - Karine Budin
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Michel Camadro
- Université de Paris, CNRS, Institut Jacques Monod (IJM), 75013, Paris, France
| | - Monique Bolotin-Fukuhara
- Université Paris-Saclay, INRAE, CNRS, Génétique Quantitative et Évolution Le Moulon, 91400, Orsay, France
| | - Adela Angoulvant
- Université Paris-Saclay, INRAE, CNRS, Génétique Quantitative et Évolution Le Moulon, 91400, Orsay, France.,Parasitology and Mycology Department, Bicêtre University Hospital, Univ. Paris-Sud/Univ. Paris Saclay, Le Kremlin-Bicêtre, France
| | - Gaëlle Lelandais
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), 91198, Gif-sur-Yvette, France
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3
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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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4
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Benchouaia M, Ripoche H, Sissoko M, Thiébaut A, Merhej J, Delaveau T, Fasseu L, Benaissa S, Lorieux G, Jourdren L, Le Crom S, Lelandais G, Corel E, Devaux F. Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata. Front Microbiol 2018; 9:2689. [PMID: 30505294 PMCID: PMC6250833 DOI: 10.3389/fmicb.2018.02689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/22/2018] [Indexed: 11/21/2022] Open
Abstract
In this work, we used comparative transcriptomics to identify regulatory outliers (ROs) in the human pathogen Candida glabrata. ROs are genes that have very different expression patterns compared to their orthologs in other species. From comparative transcriptome analyses of the response of eight yeast species to toxic doses of selenite, a pleiotropic stress inducer, we identified 38 ROs in C. glabrata. Using transcriptome analyses of C. glabrata response to five different stresses, we pointed out five ROs which were more particularly responsive to iron starvation, a process which is very important for C. glabrata virulence. Global chromatin Immunoprecipitation and gene profiling analyses showed that four of these genes are actually new targets of the iron starvation responsive Aft2 transcription factor in C. glabrata. Two of them (HBS1 and DOM34b) are required for C. glabrata optimal growth in iron limited conditions. In S. cerevisiae, the orthologs of these two genes are involved in ribosome rescue by the NO GO decay (NGD) pathway. Hence, our results suggest a specific contribution of NGD co-factors to the C. glabrata adaptation to iron starvation.
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Affiliation(s)
- Médine Benchouaia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Hugues Ripoche
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Mariam Sissoko
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Antonin Thiébaut
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Jawad Merhej
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thierry Delaveau
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Laure Fasseu
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Sabrina Benaissa
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Geneviève Lorieux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Laurent Jourdren
- École Normale Supérieure, PSL Research University, CNRS, Inserm U1024, Institut de Biologie de l’École Normale Supérieure, Plateforme Génomique, Paris, France
| | - Stéphane Le Crom
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Évolution, Paris, France
| | - Gaëlle Lelandais
- UMR 9198, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, UPSay, Gif-sur-Yvette, France
| | - Eduardo Corel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7138, Évolution, Paris, France
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- *Correspondence: Frédéric Devaux,
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5
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Gerwien F, Skrahina V, Kasper L, Hube B, Brunke S. Metals in fungal virulence. FEMS Microbiol Rev 2018; 42:4562650. [PMID: 29069482 PMCID: PMC5812535 DOI: 10.1093/femsre/fux050] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/19/2017] [Indexed: 12/25/2022] Open
Abstract
Metals are essential for life, and they play a central role in the struggle between infecting microbes and their hosts. In fact, an important aspect of microbial pathogenesis is the 'nutritional immunity', in which metals are actively restricted (or, in an extended definition of the term, locally enriched) by the host to hinder microbial growth and virulence. Consequently, fungi have evolved often complex regulatory networks, uptake and detoxification systems for essential metals such as iron, zinc, copper, nickel and manganese. These systems often differ fundamentally from their bacterial counterparts, but even within the fungal pathogens we can find common and unique solutions to maintain metal homeostasis. Thus, we here compare the common and species-specific mechanisms used for different metals among different fungal species-focusing on important human pathogens such as Candida albicans, Aspergillus fumigatus or Cryptococcus neoformans, but also looking at model fungi such as Saccharomyces cerevisiae or A. nidulans as well-studied examples for the underlying principles. These direct comparisons of our current knowledge reveal that we have a good understanding how model fungal pathogens take up iron or zinc, but that much is still to learn about other metals and specific adaptations of individual species-not the least to exploit this knowledge for new antifungal strategies.
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Affiliation(s)
- Franziska Gerwien
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology– Hans Knoell Institute, 07745 Jena, Germany
| | - Volha Skrahina
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology– Hans Knoell Institute, 07745 Jena, Germany
| | - Lydia Kasper
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology– Hans Knoell Institute, 07745 Jena, Germany
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology– Hans Knoell Institute, 07745 Jena, Germany
| | - Sascha Brunke
- Department Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology– Hans Knoell Institute, 07745 Jena, Germany
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Dieryckx C, Gaudin V, Dupuy JW, Bonneu M, Girard V, Job D. Beyond plant defense: insights on the potential of salicylic and methylsalicylic acid to contain growth of the phytopathogen Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2015; 6:859. [PMID: 26528317 PMCID: PMC4607878 DOI: 10.3389/fpls.2015.00859] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/29/2015] [Indexed: 05/27/2023]
Abstract
Using Botrytis cinerea we confirmed in the present work several previous studies showing that salicylic acid, a main plant hormone, inhibits fungal growth in vitro. Such an inhibitory effect was also observed for the two salicylic acid derivatives, methylsalicylic and acetylsalicylic acid. In marked contrast, 5-sulfosalicylic acid was totally inactive. Comparative proteomics from treated vs. control mycelia showed that both the intracellular and extracellular proteomes were affected in the presence of salicylic acid or methylsalicylic acid. These data suggest several mechanisms that could potentially account for the observed fungal growth inhibition, notably pH regulation, metal homeostasis, mitochondrial respiration, ROS accumulation and cell wall remodeling. The present observations support a role played by the phytohormone SA and derivatives in directly containing the pathogen. Data are available via ProteomeXchange with identifier PXD002873.
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Affiliation(s)
- Cindy Dieryckx
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Vanessa Gaudin
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Jean-William Dupuy
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de BordeauxBordeaux, France
| | - Marc Bonneu
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de BordeauxBordeaux, France
| | - Vincent Girard
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Dominique Job
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
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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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8
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Ruth C, Buchetics M, Vidimce V, Kotz D, Naschberger S, Mattanovich D, Pichler H, Gasser B. Pichia pastoris Aft1--a novel transcription factor, enhancing recombinant protein secretion. Microb Cell Fact 2014; 13:120. [PMID: 25205197 PMCID: PMC4161868 DOI: 10.1186/s12934-014-0120-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/10/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The methylotrophic yeast Pichia pastoris is frequently used for the production of recombinant proteins. However, expression levels can vary depending on the target protein. Allowing for simultaneous regulation of many genes, which may elicit a desired phenotype like increased protein production, overexpression of transcription factors can be used to overcome expression bottlenecks. Here, we present a novel P. pastoris transcription factor currently annotated as Aft1, activator of ferrous transport. RESULTS The promoter regions of key secretory P. pastoris genes were screened for fungal transcription factor binding sites, revealing Aft1 as an interesting candidate for improving secretion. Genome wide analysis of transcription factor binding sites suggested Aft1 to be involved in the regulation of many secretory genes, but also indicated possible novel functions in carbohydrate metabolism. No Aft binding sites were found in promoters of characteristic iron homeostasis genes in P. pastoris. Microarrays were used to study the Aft1 regulon in detail, confirming Aft1 involvement in the regulation of carbon-responsive genes, and showing that iron regulation is dependent on FEP1, but not AFT1 expression levels. The positive effect of AFT1 overexpression on recombinant protein secretion was demonstrated for a carboxylesterase from Sphingopyxis sp. MTA144, for which secretion was improved 2.5-fold in fed batch bioreactor cultivations. CONCLUSION This study demonstrates that the transcription factor Aft1 can be used to improve recombinant protein secretion in P. pastoris. Furthermore, we discovered possible novel functions of Aft1 in carbohydrate metabolism and provide evidence arguing against a direct role of Aft1 in P. pastoris iron regulation.
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Novel role of the Candida albicans ferric reductase gene CFL1 in iron acquisition, oxidative stress tolerance, morphogenesis and virulence. Res Microbiol 2014; 165:252-61. [PMID: 24631590 DOI: 10.1016/j.resmic.2014.03.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 03/02/2014] [Indexed: 01/28/2023]
Abstract
Ferric reductase catalyzes the reduction of ferric iron into ferrous iron and plays an essential role in high-affinity iron acquisition. In this study, we found that the cfl1Δ/Δ (orf19.1263) mutant was not defective in iron acquisition. However, deletion of CFL1 increased cellular iron accumulation by elevating surface ferric reductase activity in Candida albicans, revealing that there existed functional redundancy and/or a compensatory upregulation mechanism among ferric reductase genes. The absence of CFL1 resulted in increased expression levels of other alternative ferric reductase genes, including FRP1, CFL2 and FRE10. In addition, CFL1 played an important role in the response to different oxidative stresses. Further research revealed that the cfl1Δ/Δ mutant exhibited higher levels of both ROS production and SOD activity under oxidative conditions. Moreover, deletion of CFL1 led to a profound defect in filamentous development in an iron-independent manner at both 30 and 37 °C. The cfl1Δ/Δ mutant exhibited highly attenuated virulence and reduced fungal burdens in the mouse systemic infection model, indicating that CFL1 might be a potential target for antifungal drug development. In summary, our results provide new insights into the roles of ferric reductase gene in C. albicans.
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Dias PJ, Sá-Correia I. The drug:H⁺ antiporters of family 2 (DHA2), siderophore transporters (ARN) and glutathione:H⁺ antiporters (GEX) have a common evolutionary origin in hemiascomycete yeasts. BMC Genomics 2013; 14:901. [PMID: 24345006 PMCID: PMC3890622 DOI: 10.1186/1471-2164-14-901] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 12/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Saccharomyces cerevisiae 14-spanner Drug:H+ Antiporter family 2 (DHA2) are transporters of the Major Facilitator Superfamily (MFS) involved in multidrug resistance (MDR). Although poorly characterized, DHA2 family members were found to participate in the export of structurally and functionally unrelated compounds or in the uptake of amino acids into the vacuole or the cell. In S. cerevisiae, the four ARN/SIT family members encode siderophore transporters and the two GEX family members encode glutathione extrusion pumps. The evolutionary history of DHA2, ARN and GEX genes, encoding 14-spanner MFS transporters, is reconstructed in this study. RESULTS The translated ORFs of 31 strains from 25 hemiascomycetous species, including 10 pathogenic Candida species, were compared using a local sequence similarity algorithm. The constraining and traversing of a network representing the pairwise similarity data gathered 355 full size proteins and retrieved ARN and GEX family members together with DHA2 transporters, suggesting the existence of a close phylogenetic relationship among these 14-spanner major facilitators. Gene neighbourhood analysis was combined with tree construction methodologies to reconstruct their evolutionary history and 7 DHA2 gene lineages, 5 ARN gene lineages, and 1 GEX gene lineage, were identified. The S. cerevisiae DHA2 proteins Sge1, Azr1, Vba3 and Vba5 co-clustered in a large phylogenetic branch, the ATR1 and YMR279C genes were proposed to be paralogs formed during the Whole Genome Duplication (WGD) whereas the closely related ORF YOR378W resides in its own lineage. Homologs of S. cerevisiae DHA2 vacuolar proteins Vba1, Vba2 and Vba4 occur widespread in the Hemiascomycetes. Arn1/Arn2 homologs were only found in species belonging to the Saccharomyces complex and are more abundant in the pre-WGD species. Arn4 homologs were only found in sub-telomeric regions of species belonging to the Sacharomyces sensu strictu group (SSSG). Arn3 type siderophore transporters are abundant in the Hemiascomycetes and form an ancient gene lineage extending to the filamentous fungi. CONCLUSIONS The evolutionary history of DHA2, ARN and GEX genes was reconstructed and a common evolutionary root shared by the encoded proteins is hypothesized. A new protein family, denominated DAG, is proposed to span these three phylogenetic subfamilies of 14-spanner MFS transporters.
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Affiliation(s)
| | - Isabel Sá-Correia
- IBB - Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av, Rovisco Pais, 1049-001, Lisboa, Portugal.
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The basis for evolution of DNA-binding specificity of the Aft1 transcription factor in yeasts. Genetics 2013; 196:149-60. [PMID: 24172132 DOI: 10.1534/genetics.113.157693] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Saccharomyces cerevisiae Aft1 and Kluyveromyces lactis KlAft are orthologous yeast transcription activators that regulate the expression of the same group of iron-uptake genes but bind to the different DNA sites: TGCACCC for Aft1 and PuCACCC for KlAft. To establish whether the DNA-binding mechanisms of Aft1 and KlAft have diverged during the evolution of the Aft-type transcription factor, we examined the function of a nonconserved region in their DNA-binding domains. A large part of this region is composed of a sequence predicted to be disordered in structure and potentially phosphorylated. We show with deletion mutant analyses that this sequence is essential for the binding of Aft1 to its DNA site and for the iron uptake and growth of S. cerevisiae under iron-limited conditions. We constructed hybrid proteins by exchanging the nonconserved regions of Aft1 and KlAft. We show that the Aft1 region is necessary and sufficient for KlAft to bind efficiently to the Aft1 DNA site in S. cerevisiae and to complement the iron-dependent phenotype of the aft1Δaft2Δ mutant. This demonstrates that the changes in the nonconserved region of the Aft-type DNA-binding domain have led to changes in the DNA-binding specificity and have major consequences for the regulation of iron homeostasis. The combination of bioinformatic and experimental analyses indicates that the sequence TGCACCC is the most probable ancestral Aft-type element. Our findings suggest that the changes in the nonconserved region of the DNA-binding domain are responsible for the evolution of the TGCACCC sequence toward PuCACCC in the K. lactis species.
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Xu N, Cheng X, Yu Q, Qian K, Ding X, Liu R, Zhang B, Xing L, Li M. Aft2, a novel transcription regulator, is required for iron metabolism, oxidative stress, surface adhesion and hyphal development in Candida albicans. PLoS One 2013; 8:e62367. [PMID: 23626810 PMCID: PMC3633901 DOI: 10.1371/journal.pone.0062367] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/20/2013] [Indexed: 12/11/2022] Open
Abstract
Morphological transition and iron metabolism are closely relevant to Candida albicans pathogenicity and virulence. In our previous study, we demonstrated that C. albicans Aft2 plays an important role in ferric reductase activity and virulence. Here, we further explored the roles of C. albicans Aft2 in numerous cellular processes. We found that C. albicans Aft2 exhibited an important role in iron metabolism through bi-directional regulation effects on iron-regulon expression. Deletion of AFT2 reduced cellular iron accumulation under iron-deficient conditions. Furthermore, both reactive oxygen species (ROS) generation and superoxide dismutase (SOD) activity were remarkably increased in the aft2Δ/Δ mutant, which were thought to be responsible for the defective responses to oxidative stress. However, we found that over-expression of C. albicans AFT2 under the regulation of the strong PGK1 promoter could not effectively rescue Saccharomyces cerevisiae aft1Δ mutant defects in some cellular processes, such as cell-wall assembly, ion homeostasis and alkaline resistance, suggesting a possibility that C. albicans Aft2 weakened its functional role of regulating some cellular metabolism during the evolutionary process. Interestingly, deletion of AFT2 in C. albicans increased cell surface hydrophobicity, cell flocculation and the ability of adhesion to polystyrene surfaces. In addition, our results also revealed that C. albicans Aft2 played a dual role in regulating hypha-specific genes under solid and liquid hyphal inducing conditions. Deletion of AFT2 caused an impaired invasive growth in solid medium, but an increased filamentous aggregation and growth in liquid conditions. Moreover, iron deficiency and environmental cues induced nuclear import of Aft2, providing additional evidence for the roles of Aft2 in transcriptional regulation.
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Affiliation(s)
- Ning Xu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinxin Cheng
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Qian
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaohui Ding
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Ruming Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Biao Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Laijun Xing
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- * E-mail:
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Lill R, Hoffmann B, Molik S, Pierik AJ, Rietzschel N, Stehling O, Uzarska MA, Webert H, Wilbrecht C, Mühlenhoff U. The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:1491-508. [PMID: 22609301 DOI: 10.1016/j.bbamcr.2012.05.009] [Citation(s) in RCA: 360] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 12/21/2022]
Abstract
Mitochondria play a key role in iron metabolism in that they synthesize heme, assemble iron-sulfur (Fe/S) proteins, and participate in cellular iron regulation. Here, we review the latter two topics and their intimate connection. The mitochondrial Fe/S cluster (ISC) assembly machinery consists of 17 proteins that operate in three major steps of the maturation process. First, the cysteine desulfurase complex Nfs1-Isd11 as the sulfur donor cooperates with ferredoxin-ferredoxin reductase acting as an electron transfer chain, and frataxin to synthesize an [2Fe-2S] cluster on the scaffold protein Isu1. Second, the cluster is released from Isu1 and transferred toward apoproteins with the help of a dedicated Hsp70 chaperone system and the glutaredoxin Grx5. Finally, various specialized ISC components assist in the generation of [4Fe-4S] clusters and cluster insertion into specific target apoproteins. Functional defects of the core ISC assembly machinery are signaled to cytosolic or nuclear iron regulatory systems resulting in increased cellular iron acquisition and mitochondrial iron accumulation. In fungi, regulation is achieved by iron-responsive transcription factors controlling the expression of genes involved in iron uptake and intracellular distribution. They are assisted by cytosolic multidomain glutaredoxins which use a bound Fe/S cluster as iron sensor and additionally perform an essential role in intracellular iron delivery to target metalloproteins. In mammalian cells, the iron regulatory proteins IRP1, an Fe/S protein, and IRP2 act in a post-transcriptional fashion to adjust the cellular needs for iron. Thus, Fe/S protein biogenesis and cellular iron metabolism are tightly linked to coordinate iron supply and utilization. This article is part of a Special Issue entitled: Cell Biology of Metals.
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Affiliation(s)
- Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Str. 6, 35033 Marburg, Germany.
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14
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Xu N, Cheng X, Yu Q, Zhang B, Ding X, Xing L, Li M. Identification and functional characterization of mitochondrial carrier Mrs4 in Candida albicans. FEMS Yeast Res 2012; 12:844-58. [PMID: 22846114 DOI: 10.1111/j.1567-1364.2012.00835.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 11/30/2022] Open
Abstract
Iron is an essential nutrient required for the growth and metabolism in Candida albicans. Here, we for the first time identified Mrs4 as a new member of mitochondrial carrier family in C. albicans. Our experiments revealed that C. albicans Mrs4 (CaMrs4) is localized to the mitochondria and required for mitochondrial morphology. We found that CaMrs4 is required for cell growth, and the mrs4Δ/Δ mutant showed a more severe growth defect in iron deficiency. Deletion of MRS4 affected cellular iron content by altering the expression of iron regulon genes in C. albicans, such as AFT2, SMF3, FTR1 and ISU1. Candida albicans Aft2 factor functions as a negative regulator of MRS4 expression through the CACCC Aft-type sequence in a gene dose-dependent fashion. In addition, the mrs4Δ/Δ mutant exhibited hypersensitivity to oxidants and most metal ions, but decreased sensitivity to cobalt. Exogenous iron could suppress the sensitivity of the mrs4Δ/Δ mutant to oxidants and most metal ions, suggesting that the role of CaMrs4 is partially mediated by iron availability. Furthermore, deletion of MRS4 resulted in delayed filamentation under tested conditions. Taken together, these findings characterize a new mitochondrial carrier and provide a novel insight into the role of CaMrs4 in mitochondrial function.
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Affiliation(s)
- Ning Xu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, Nankai University, Tianjin, China
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15
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Lai ACW, Nguyen Ba AN, Moses AM. Predicting kinase substrates using conservation of local motif density. ACTA ACUST UNITED AC 2012; 28:962-9. [PMID: 22302575 DOI: 10.1093/bioinformatics/bts060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
MOTIVATION Protein kinases represent critical links in cell signaling. A central problem in computational biology is to systematically identify their substrates. RESULTS This study introduces a new method to predict kinase substrates by extracting evolutionary information from multiple sequence alignments in a manner that is tolerant to degenerate motif positioning. Given a known consensus, the new method (ConDens) compares the observed density of matches to a null model of evolution and does not require labeled training data. We confirmed that ConDens has improved performance compared with several existing methods in the field. Further, we show that it is generalizable and can predict interesting substrates for several important eukaryotic kinases where training data is not available. AVAILABILITY AND IMPLEMENTATION ConDens can be found at http://www.moseslab.csb.utoronto.ca/andyl/. CONTACT alan.moses@utoronto.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andy C W Lai
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
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16
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Philpott CC, Leidgens S, Frey AG. Metabolic remodeling in iron-deficient fungi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1509-20. [PMID: 22306284 DOI: 10.1016/j.bbamcr.2012.01.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/13/2012] [Accepted: 01/18/2012] [Indexed: 01/12/2023]
Abstract
Eukaryotic cells contain dozens, perhaps hundreds, of iron-dependent proteins, which perform critical functions in nearly every major cellular process. Nutritional iron is frequently available to cells in only limited amounts; thus, unicellular and higher eukaryotes have evolved mechanisms to cope with iron scarcity. These mechanisms have been studied at the molecular level in the model eukaryotes Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as in some pathogenic fungi. Each of these fungal species exhibits metabolic adaptations to iron deficiency that serve to reduce the cell's reliance on iron. However, the regulatory mechanisms that accomplish these adaptations differ greatly between fungal species. This article is part of a Special Issue entitled: Cell Biology of Metals.
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Affiliation(s)
- Caroline C Philpott
- Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 10, Rm. 9B-16, 10 Center Drive, Bethesda, MD 20892, USA.
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17
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Cherrad S, Girard V, Dieryckx C, Gonçalves IR, Dupuy JW, Bonneu M, Rascle C, Job C, Job D, Vacher S, Poussereau N. Proteomic analysis of proteins secreted by Botrytis cinerea in response to heavy metal toxicity. Metallomics 2012; 4:835-46. [DOI: 10.1039/c2mt20041d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Candida albicans Hap43 is a repressor induced under low-iron conditions and is essential for iron-responsive transcriptional regulation and virulence. EUKARYOTIC CELL 2010; 10:207-25. [PMID: 21131439 DOI: 10.1128/ec.00158-10] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Candida albicans is an opportunistic fungal pathogen that exists as normal flora in healthy human bodies but causes life-threatening infections in immunocompromised patients. In addition to innate and adaptive immunities, hosts also resist microbial infections by developing a mechanism of "natural resistance" that maintains a low level of free iron to restrict the growth of invading pathogens. C. albicans must overcome this iron-deprived environment to cause infections. There are three types of iron-responsive transcriptional regulators in fungi; Aft1/Aft2 activators in yeast, GATA-type repressors in many fungi, and HapX/Php4 in Schizosaccharomyces pombe and Aspergillus species. In this study, we characterized the iron-responsive regulator Hap43, which is the C. albicans homolog of HapX/Php4 and is repressed by the GATA-type repressor Sfu1 under iron-sufficient conditions. We provide evidence that Hap43 is essential for the growth of C. albicans under low-iron conditions and for C. albicans virulence in a mouse model of infection. Hap43 was not required for iron acquisition under low-iron conditions. Instead, it was responsible for repression of genes that encode iron-dependent proteins involved in mitochondrial respiration and iron-sulfur cluster assembly. We also demonstrated that Hap43 executes its function by becoming a transcriptional repressor and accumulating in the nucleus in response to iron deprivation. Finally, we found a connection between Hap43 and the global corepressor Tup1 in low-iron-induced flavinogenesis. Taken together, our data suggest a complex interplay among Hap43, Sfu1, and Tup1 to coordinately regulate iron acquisition, iron utilization, and other iron-responsive metabolic activities.
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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