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MacDiarmid CW, Taggart J, Kubisiak M, Eide DJ. Restricted glycolysis is a primary cause of the reduced growth rate of zinc-deficient yeast cells. J Biol Chem 2024; 300:107147. [PMID: 38460940 PMCID: PMC11001634 DOI: 10.1016/j.jbc.2024.107147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024] Open
Abstract
Zinc is required for many critical processes, including intermediary metabolism. In Saccharomyces cerevisiae, the Zap1 activator regulates the transcription of ∼80 genes in response to Zn supply. Some Zap1-regulated genes are Zn transporters that maintain Zn homeostasis, while others mediate adaptive responses that enhance fitness. One adaptive response gene encodes the 2-cysteine peroxiredoxin Tsa1, which is critical to Zn-deficient (ZnD) growth. Depending on its redox state, Tsa1 can function as a peroxidase, a protein chaperone, or a regulatory redox sensor. In a screen for possible Tsa1 regulatory targets, we identified a mutation (cdc19S492A) that partially suppressed the tsa1Δ growth defect. The cdc19S492A mutation reduced activity of its protein product, pyruvate kinase isozyme 1 (Pyk1), implicating Tsa1 in adapting glycolysis to ZnD conditions. Glycolysis requires activity of the Zn-dependent enzyme fructose-bisphosphate aldolase 1, which was substantially decreased in ZnD cells. We hypothesized that in ZnD tsa1Δ cells, the loss of a compensatory Tsa1 regulatory function causes depletion of glycolytic intermediates and restricts dependent amino acid synthesis pathways, and that the decreased activity of Pyk1S492A counteracted this depletion by slowing the irreversible conversion of phosphoenolpyruvate to pyruvate. In support of this model, supplementing ZnD tsa1Δ cells with aromatic amino acids improved their growth. Phosphoenolpyruvate supplementation, in contrast, had a much greater effect on growth rate of WT and tsa1Δ ZnD cells, indicating that inefficient glycolysis is a major factor limiting yeast growth. Surprisingly however, this restriction was not primarily due to low fructose-bisphosphate aldolase 1 activity, but instead occurs earlier in glycolysis.
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Affiliation(s)
- Colin W MacDiarmid
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael Kubisiak
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Global Molecular Response of Paracoccidioides brasiliensis to Zinc Deprivation: Analyses at Transcript, Protein and MicroRNA Levels. J Fungi (Basel) 2023; 9:jof9030281. [PMID: 36983449 PMCID: PMC10056003 DOI: 10.3390/jof9030281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Zinc is one of the main micronutrients for all organisms. One of the defense mechanisms used by the host includes the sequestration of metals used in fungal metabolism, such as iron and zinc. There are several mechanisms that maintain the balance in the intracellular zinc supply. MicroRNAs are effector molecules of responses between the pathogen and host, favoring or preventing infection in many microorganisms. Fungi of the Paracoccidioides genus are thermodimorphic and the etiological agents of paracoccidioidomycosis (PCM). In the current pandemic scenario world mycosis studies continue to be highly important since a significant number of patients with COVID-19 developed systemic mycoses, co-infections that complicated their clinical condition. The objective was to identify transcriptomic and proteomic adaptations in Paracoccidioides brasiliensis during zinc deprivation. Nineteen microRNAs were identified, three of which were differentially regulated. Target genes regulated by those microRNAs are elements of zinc homeostasis such as ZRT1, ZRT3 and COT1 transporters. Transcription factors that have zinc in their structure are also targets of those miRNAs. Transcriptional and proteomic data suggest that P. brasiliensis undergoes metabolic remodeling to survive zinc deprivation and that miRNAs may be part of the regulatory process.
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3
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Fungal Zinc Homeostasis and Its Potential as an Antifungal Target: A Focus on the Human Pathogen Aspergillus fumigatus. Microorganisms 2022; 10:microorganisms10122469. [PMID: 36557722 PMCID: PMC9785309 DOI: 10.3390/microorganisms10122469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic airborne fungus that causes severe invasive aspergillosis in immunocompromised patients. Zinc is an essential micronutrient for the growth of A. fumigatus and even for all microorganisms. An increasing number of studies have reported that fungal zinc acquisition ability plays a key role in fungal survival in hosts with an extremely zinc-limited microenvironment. The ability to fight scarcity and excess of zinc are tightly related to fungal virulence and may be used as new potential targets. Because the regulation of zinc homeostasis is important, a thorough understanding of the functional genes involved in the regulatory network for zinc homeostasis is required for fungal pathogens. The current mini-review summarized potential zinc homeostasis regulators in A. fumigatus and classified these regulators according to localization and function, which were identified or predicted based on A. fumigatus or deduced from homologs in model yeasts. Future perspectives for zinc homeostasis regulators as potential antifungal targets to treat invasive aspergillosis are also discussed.
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4
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Chen HQ, Xing Q, Cheng C, Zhang MM, Liu CG, Champreda V, Zhao XQ. Identification of Kic1p and Cdc42p as Novel Targets to Engineer Yeast Acetic Acid Stress Tolerance. Front Bioeng Biotechnol 2022; 10:837813. [PMID: 35402407 PMCID: PMC8992792 DOI: 10.3389/fbioe.2022.837813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Robust yeast strains that are tolerant to multiple stress environments are desired for an efficient biorefinery. Our previous studies revealed that zinc sulfate serves as an important nutrient for stress tolerance of budding yeast Saccharomyces cerevisiae. Acetic acid is a common inhibitor in cellulosic hydrolysate, and the development of acetic acid-tolerant strains is beneficial for lignocellulosic biorefineries. In this study, comparative proteomic studies were performed using S. cerevisiae cultured under acetic acid stress with or without zinc sulfate addition, and novel zinc-responsive proteins were identified. Among the differentially expressed proteins, the protein kinase Kic1p and the small rho-like GTPase Cdc42p, which is required for cell integrity and regulation of cell polarity, respectively, were selected for further studies. Overexpression of KIC1 and CDC42 endowed S. cerevisiae with faster growth and ethanol fermentation under the stresses of acetic acid and mixed inhibitors, as well as in corncob hydrolysate. Notably, the engineered yeast strains showed a 12 h shorter lag phase under the three tested conditions, leading to up to 52.99% higher ethanol productivity than that of the control strain. Further studies showed that the transcription of genes related to stress response was significantly upregulated in the engineered strains under the stress condition. Our results in this study provide novel insights in exploring zinc-responsive proteins for applications of synthetic biology in developing a robust industrial yeast.
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Affiliation(s)
- Hong-Qi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Xing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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5
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Gaspar-Cordeiro A, Afonso G, Amaral C, da Silva SM, Pimentel C. Zap1 is required for Candida glabrata response to fluconazole. FEMS Yeast Res 2022; 22:6510815. [PMID: 35040997 DOI: 10.1093/femsyr/foab068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing prevalence of fluconazole-resistant clinical isolates of Candida spp. strongly hinders the widespread use of the drug. To tackle this problem, great efforts have been made to fully understand the fungal response to fluconazole. In this work, we show that the role of Zap1 in Candida glabrata goes beyond regulating yeast adaptation to zinc deficiency. In line with our previous observation that deletion of ZAP1 makes yeast cells more sensitive to fluconazole, we found that the mutant CgΔzap1 accumulates higher levels of the drug, which correlates well with its lower levels of ergosterol. Surprisingly, Zap1 is a negative regulator of the drug efflux transporter gene CDR1 and of its regulator, PDR1. The apparent paradox of drug accumulation in cells where genes encoding transporters relevant for drug extrusion are being overexpressed led us to postulate that their activity could be impaired. In agreement, Zap1-depleted cells present, in addition to decreased ergosterol levels, an altered composition of membrane phospholipids, which together should impact membrane function and impair the detoxification of fluconazole. Overall, our study brings to light Zap1 as an important hub in Candida glabrata response to fluconazole.
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Affiliation(s)
- A Gaspar-Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157 Oeiras, Portugal
| | - G Afonso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157 Oeiras, Portugal
| | - C Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157 Oeiras, Portugal
| | - S M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157 Oeiras, Portugal
| | - C Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157 Oeiras, Portugal
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6
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Haidara N, Giannini M, Porrua O. Modulated termination of non-coding transcription partakes in the regulation of gene expression. Nucleic Acids Res 2022; 50:1430-1448. [PMID: 35037029 PMCID: PMC8860598 DOI: 10.1093/nar/gkab1304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/17/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022] Open
Abstract
Pervasive transcription is a universal phenomenon leading to the production of a plethora of non-coding RNAs. If left uncontrolled, pervasive transcription can be harmful for genome expression and stability. However, non-coding transcription can also play important regulatory roles, for instance by promoting the repression of specific genes by a mechanism of transcriptional interference. The efficiency of transcription termination can strongly influence the regulatory capacity of non-coding transcription events, yet very little is known about the mechanisms modulating the termination of non-coding transcription in response to environmental cues. Here, we address this question by investigating the mechanisms that regulate the activity of the main actor in termination of non-coding transcription in budding yeast, the helicase Sen1. We identify a phosphorylation at a conserved threonine of the catalytic domain of Sen1 and we provide evidence that phosphorylation at this site reduces the efficiency of Sen1-mediated termination. Interestingly, we find that this phosphorylation impairs termination at an unannotated non-coding gene, thus repressing the expression of a downstream gene encoding the master regulator of Zn homeostasis, Zap1. Consequently, many additional genes exhibit an expression pattern mimicking conditions of Zn excess, where ZAP1 is naturally repressed. Our findings provide a novel paradigm of gene regulatory mechanism relying on the direct modulation of non-coding transcription termination.
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Affiliation(s)
- Nouhou Haidara
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France.,Université Paris-Saclay, Gif sur Yvette, France
| | - Marta Giannini
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, F-75013 Paris, France
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7
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Alamir OF, Oladele RO, Ibe C. Nutritional immunity: targeting fungal zinc homeostasis. Heliyon 2021; 7:e07805. [PMID: 34466697 PMCID: PMC8384899 DOI: 10.1016/j.heliyon.2021.e07805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/22/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
Transition metals, such as Zn2+, are essential dietary constituents of all biological life, including mammalian hosts and the pathogens that infect them. Therefore, to thrive and cause infection, pathogens must successfully assimilate these elements from the host milieu. Consequently, mammalian immunity has evolved to actively restrict and/or pool metals to toxic concentrations in an effort to attenuate microbial pathogenicity - a process termed nutritional immunity. Despite host-induced Zn2+ nutritional immunity, pathogens such as Candida albicans, are still capable of causing disease and thus must be equipped with robust Zn2+ sensory, uptake and detoxification machinery. This review will discuss the strategies employed by mammalian hosts to limit Zn2+ during infection, and the subsequent fungal interventions that counteract Zn2+ nutritional immunity.
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Affiliation(s)
- Omran F Alamir
- Department of Natural Sciences, College of Health Sciences, The Public Authority for Applied Education and Training, Al Asimah, Kuwait
| | - Rita O Oladele
- Department of Medical Microbiology & Parasitology, College of Medicine, University of Lagos, Lagos State, Nigeria
| | - C Ibe
- Department of Microbiology, Abia State University, PMB 2000, Uturu, Abia State, Nigeria
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8
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Shire DM, Kustka AB. Proteomic responses of the coccolithophore Emiliania huxleyi to zinc limitation and trace metal substitution. Environ Microbiol 2021; 24:819-834. [PMID: 34139058 DOI: 10.1111/1462-2920.15644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 11/30/2022]
Abstract
Zinc concentrations in pelagic surface waters are within the range that limits growth in marine phytoplankton cultures. However, the influence of zinc on marine primary production and phytoplankton communities is not straightforward due to largely uncharacterized abilities for some phytoplankton to access zinc species that may not be universally bioavailable and substitute zinc with cobalt or cadmium. We used a quantitative proteomic approach to investigate these strategies and other responses to zinc limitation in the coccolithophore Emiliania huxleyi, a dominant species in low zinc waters. Zinc limitation resulted in the upregulation of metal transport proteins (ZIP, TroA-like) and COG0523 metallochaperones. Some proteins were uniquely sensitive to growth under replete zinc, substitution of zinc with cobalt, or enhancement of growth with cadmium, and may be useful as biomarkers of zinc stress or substitution in situ. Several proteins specifically upregulated under cobalt-supported or cadmium-enhanced growth appear to reflect stress responses, despite titration of these metals to optimal nutritive levels. Relief from zinc limitation by zinc or cadmium resulted in increased expression of a δ-carbonic anhydrase. Our inability to detect metal binding enzymes that are specifically induced under cobalt- or cadmium-supported growth suggests cambialism is important for zinc substitution in E. huxleyi.
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Affiliation(s)
- David M Shire
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, USA
| | - Adam B Kustka
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, USA
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9
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Zlobin IE. Current understanding of plant zinc homeostasis regulation mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:327-335. [PMID: 33714765 DOI: 10.1016/j.plaphy.2021.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/02/2021] [Indexed: 05/27/2023]
Abstract
The essential nature of Zn and widespread Zn deficiency in plants under field conditions underlie the great interest of researchers in the regulation of plant Zn homeostasis. Here, the current knowledge of plant Zn homeostasis regulation, mainly in A. thaliana, is reviewed. The plant Zn homeostasis machinery is regulated largely at the transcriptional level. Local regulation in response to changes in cellular Zn status is based on the transcription factors bZIP19 and bZIP23, which sense changes in free Zn2+ concentrations in the cell. However, there are likely other unidentified ways to sense cellular free Zn2+ concentrations in addition to the well-known bZIP19 and bZIP23 factors. In recent years, the existence of a shoot-derived systemic Zn deficiency signal, which is involved in the upregulation of Zn transport from roots to shoots, was demonstrated. Additionally, rates of mRNA degradation of Zn homeostasis genes are likely regulated by changes in cellular Zn status. In addition to the regulation of Zn transport, other mechanisms for the regulation of plant Zn homeostasis exist. "Zn sparing" mechanisms could be involved in the decrease in plant Zn requirements under Zn deficiency. Additionally, autophagy is probably regulated by local Zn status and involved in Zn reutilization at the cellular level. Current issues related to studying Zn homeostasis regulation are discussed.
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Affiliation(s)
- Ilya E Zlobin
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya St., Moscow, 127276, Russia.
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10
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Soares LW, Bailão AM, Soares CMDA, Bailão MGS. Zinc at the Host-Fungus Interface: How to Uptake the Metal? J Fungi (Basel) 2020; 6:jof6040305. [PMID: 33233335 PMCID: PMC7711662 DOI: 10.3390/jof6040305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/31/2022] Open
Abstract
Zinc is an essential nutrient for all living organisms. However, firm regulation must be maintained since micronutrients also can be toxic in high concentrations. This notion is reinforced when we look at mechanisms deployed by our immune system, such as the use of chelators or membrane transporters that capture zinc, when threatened with pathogens, like fungi. Pathogenic fungi, on the other hand, also make use of a variety of transporters and specialized zinc captors to survive these changes. In this review, we sought to explain the mechanisms, grounded in experimental analysis and described to date, utilized by pathogenic fungi to maintain optimal zinc levels.
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11
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Ruta LL, Farcasanu IC. Interaction between Polyphenolic Antioxidants and Saccharomyces cerevisiae Cells Defective in Heavy Metal Transport across the Plasma Membrane. Biomolecules 2020; 10:biom10111512. [PMID: 33158278 PMCID: PMC7694260 DOI: 10.3390/biom10111512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/24/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022] Open
Abstract
Natural polyphenols are compounds with important biological implications which include antioxidant and metal-chelating characteristics relevant for their antimicrobial, antitumor, or antiaging potential. The mechanisms linking polyphenols and heavy metals in their concerted actions on cells are not completely elucidated. In this study, we used the model eukaryotic microorganism Saccharomyces cerevisiae to detect the action of widely prevalent natural polyphenols on yeast cells defective in the main components involved in essential heavy metal transport across the plasma membrane. We found that caffeic and gallic acids interfered with Zn accumulation, causing delays in cell growth that were alleviated by Zn supplementation. The flavones morin and quercetin interfered with both Mn and Zn accumulation, which resulted in growth improvement, but supplemental Mn and especially Zn turned the initially benefic action of morin and quercetin into potential toxicity. Our results imply that caution is needed when administering food supplements or nutraceuticals which contain both natural polyphenols and essential elements, especially zinc.
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12
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Alugoju P, Periyasamy L, Dyavaiah M. Protective effect of quercetin in combination with caloric restriction against oxidative stress-induced cell death of Saccharomyces cerevisiae cells. Lett Appl Microbiol 2020; 71:272-279. [PMID: 32394448 DOI: 10.1111/lam.13313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/18/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
Impairment of antioxidant enzymes activities has been well reported in several human diseases. Effective anti-ageing strategies involving antioxidant supplementation and/or caloric restriction (CR) are receiving a great attention to mitigate free radical-mediated oxidative damage in several disease conditions to improve active longevity. Therefore, in this work, we have evaluated the protective effect of quercetin under non restriction (NR) and CR conditions on the sensitivity of Saccharomyces cerevisiae mutant strains (sod1∆, sod2∆, cta1∆, ctt1∆, tsa1∆ and glr1∆) deficient in antioxidant defence systems (superoxide dismutase, catalase, thioredoxin peroxidase and glutathione reductase) against H2 O2 -induced oxidative stress. Our results demonstrate that quercetin in combination with CR has strongly reduced the H2 O2 -mediated stress in the yeast mutant cells compared to NR conditions. Furthermore, we show that quercetin in combination with CR enhanced the percentage viability of yeast cells during chronological ageing. Our research findings suggest that antioxidant supplementation in combination with CR might have potent beneficial effects than individual therapies against free radical-mediated oxidative stress. SIGNIFICANCE AND IMPACT OF THE STUDY: Oxidative stress results from an imbalance between free radicals and antioxidant defense systems in our body. Supplementation with exogenous antioxidants is necessary to neutralize the free radical mediated damage. Polyphenols are a group of naturally occurring plant compounds with strong free radical-scavenging activity and exhibits potent anti-aging property by mitigating oxidative stress. On the other hand, caloric restriction (CR) has been reported to be a popular leading anti-aging approach to ameliorate age-associate macromolecular damages in various chronic human diseases. Evaluation of protective effects of antioxidant supplementation in combination with CR against free radical mediated oxidative stress is pivotal for the development of novel anti-aging strategies to improve active longevity.
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Affiliation(s)
- P Alugoju
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
| | - L Periyasamy
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
| | - M Dyavaiah
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
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13
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Eide DJ. Transcription factors and transporters in zinc homeostasis: lessons learned from fungi. Crit Rev Biochem Mol Biol 2020; 55:88-110. [PMID: 32192376 DOI: 10.1080/10409238.2020.1742092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Zinc is an essential nutrient for all organisms because this metal serves as a critical structural or catalytic cofactor for many proteins. These zinc-dependent proteins are abundant in the cytosol as well as within organelles of eukaryotic cells such as the nucleus, mitochondria, endoplasmic reticulum, Golgi, and storage compartments such as the fungal vacuole. Therefore, cells need zinc transporters so that they can efficiently take up the metal and move it around within cells. In addition, because zinc levels in the environment can vary drastically, the activity of many of these transporters and other components of zinc homeostasis is regulated at the level of transcription by zinc-responsive transcription factors. Mechanisms of post-transcriptional control are also important for zinc homeostasis. In this review, the focus will be on our current knowledge of zinc transporters and their regulation by zinc-responsive transcription factors and other mechanisms in fungi because these organisms have served as useful paradigms of zinc homeostasis in all organisms. With this foundation, extension to other organisms will be made where warranted.
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Affiliation(s)
- David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
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14
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Identification of the Genetic Requirements for Zinc Tolerance and Toxicity in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:479-488. [PMID: 31836620 PMCID: PMC7003084 DOI: 10.1534/g3.119.400933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Zinc is essential for almost all living organisms, since it serves as a crucial cofactor for transcription factors and enzymes. However, it is toxic to cell growth when present in excess. The present work aims to investigate the toxicity mechanisms induced by zinc stress in yeast cells. To this end, 108 yeast single-gene deletion mutants were identified sensitive to 6 mM ZnCl2 through a genome-wide screen. These genes were predominantly related to the biological processes of vacuolar acidification and transport, polyphosphate metabolic process, cytosolic transport, the process utilizing autophagic mechanism. A result from the measurement of intracellular zinc content showed that 64 mutants accumulated higher intracellular zinc under zinc stress than the wild-type cells. We further measured the intracellular ROS (reactive oxygen species) levels of 108 zinc-sensitive mutants treated with 3 mM ZnCl2. We showed that the intracellular ROS levels in 51 mutants were increased by high zinc stress, suggesting their possible involvement in regulating ROS homeostasis in response to high zinc. The results also revealed that excess zinc could generate oxidative damage and then activate the expression of several antioxidant defenses genes. Taken together, the data obtained indicated that excess zinc toxicity might be mainly due to the high intracellular zinc levels and ROS levels induced by zinc stress in yeast cells. Our current findings would provide a basis to understand the molecular mechanisms of zinc toxicity in yeast cells.
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15
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Traynor AM, Sheridan KJ, Jones GW, Calera JA, Doyle S. Involvement of Sulfur in the Biosynthesis of Essential Metabolites in Pathogenic Fungi of Animals, Particularly Aspergillus spp.: Molecular and Therapeutic Implications. Front Microbiol 2019; 10:2859. [PMID: 31921039 PMCID: PMC6923255 DOI: 10.3389/fmicb.2019.02859] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Fungal sulfur uptake is required for incorporation into the sidechains of the amino acids cysteine and methionine, and is also essential for the biosynthesis of the antioxidant glutathione (GSH), S-adenosylmethionine (SAM), the key source of methyl groups in cellular transmethylation reactions, and S-adenosylhomocysteine (SAH). Biosynthesis of redox-active gliotoxin in the opportunistic fungal pathogen Aspergillus fumigatus has been elucidated over the past 10 years. Some fungi which produce gliotoxin-like molecular species have undergone unexpected molecular rewiring to accommodate this high-risk biosynthetic process. Specific disruption of gliotoxin biosynthesis, via deletion of gliK, which encodes a γ-glutamyl cyclotransferase, leads to elevated intracellular antioxidant, ergothioneine (EGT), levels, and confirms crosstalk between the biosynthesis of both sulfur-containing moieties. Gliotoxin is ultimately formed by gliotoxin oxidoreductase GliT-mediated oxidation of dithiol gliotoxin (DTG). In fact, DTG is a substrate for both GliT and a bis-thiomethyltransferase, GtmA. GtmA converts DTG to bisdethiobis(methylthio)gliotoxin (BmGT), using 2 mol SAM and resultant SAH must be re-converted to SAM via the action of the Methyl/Met cycle. In the absence of GliT, DTG fluxes via GtmA to BmGT, which results in both SAM depletion and SAH overproduction. Thus, the negative regulation of gliotoxin biosynthesis via GtmA must be counter-balanced by GliT activity to avoid Methyl/Met cycle dysregulation, SAM depletion and trans consequences on global cellular biochemistry in A. fumigatus. DTG also possesses potent Zn2+ chelation properties which positions this sulfur-containing metabolite as a putative component of the Zn2+ homeostasis system within fungi. EGT plays an essential role in high-level redox homeostasis and its presence requires significant consideration in future oxidative stress studies in pathogenic filamentous fungi. In certain filamentous fungi, sulfur is additionally indirectly required for the formation of EGT and the disulfide-bridge containing non-ribosomal peptide, gliotoxin, and related epipolythiodioxopiperazines. Ultimately, interference with emerging sulfur metabolite functionality may represent a new strategy for antifungal drug development.
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Affiliation(s)
- Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Ireland
| | | | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, United Kingdom
| | - José A Calera
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Salamanca, Spain.,Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
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16
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Wilson S, Liu YH, Cardona-Soto C, Wadhwa V, Foster MP, Bird AJ. The Loz1 transcription factor from Schizosaccharomyces pombe binds to Loz1 response elements and represses gene expression when zinc is in excess. Mol Microbiol 2019; 112:1701-1717. [PMID: 31515876 PMCID: PMC6904500 DOI: 10.1111/mmi.14384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2019] [Indexed: 12/14/2022]
Abstract
In Schizosaccharomyces pombe, the expression of the zrt1 zinc uptake gene is tightly regulated by zinc status. When intracellular zinc levels are low, zrt1 is highly expressed. However, when zinc levels are high, transcription of zrt1 is blocked in a manner that is dependent upon the transcription factor Loz1. To gain additional insight into the mechanism by which Loz1 inhibits gene expression in high zinc, we used RNA-seq to identify Loz1-regulated genes, and ChIP-seq to analyze the recruitment of Loz1 to target gene promoters. We find that Loz1 is recruited to the promoters of 27 genes that are also repressed in high zinc in a Loz1-dependent manner. We also find that the recruitment of Loz1 to the majority of target gene promoters is dependent upon zinc and the motif 5'-CGN(A/C)GATCNTY-3', which we have named the Loz1 response element (LRE). Using reporter assays, we show that LREs are both required and sufficient for Loz1-mediated gene repression, and that the level of gene repression is dependent upon the number and sequence of LREs. Our results elucidate the Loz1 regulon in fission yeast and provide new insight into how eukaryotic cells are able to respond to changes in zinc availability in the environment.
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Affiliation(s)
- Stevin Wilson
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210
| | - Yi-Hsuan Liu
- Department of Human Nutrition, The Ohio State University, Columbus, OH, 43210
| | - Carlos Cardona-Soto
- Department of Human Nutrition, The Ohio State University, Columbus, OH, 43210
| | - Vibhuti Wadhwa
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Mark P. Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| | - Amanda J. Bird
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210
- Department of Human Nutrition, The Ohio State University, Columbus, OH, 43210
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
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17
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Francis M, Cheng H, Ma P, Grider A. Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658. Biol Trace Elem Res 2019; 192:83-90. [PMID: 30734197 PMCID: PMC6685770 DOI: 10.1007/s12011-019-1650-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022]
Abstract
The zinc transcriptional regulatory element (ZTRE) is a newly reported binding motif for human zinc finger protein ZNF658, which alters gene expression in response to cellular zinc. The ZTRE has two nucleotide components-the palindromic flanking pairs and the bridging "N" bases between these flanks that range in number from 0 to 100. There are 12 pairs of ZTRE flanks (designated A-L). Three thousand five hundred twenty-five genes contain one or more ZTREs - 1000 to + 200 bp from their transcriptional start site (TSS). ZTRE-E is observed at a greater frequency, and ZTRE containing 25 bridging bases are less frequent, within - 200 bp from the TSS. The genes with ZTREs in this range are enriched in processes that may compensate zinc deficiency, while other genes with ZTREs outside this range are enriched in transcriptional activation processes. The division of ZTREs into two groups may imply a dual role of ZNF658, similar to the homologous yeast protein Zap1, via binding to low or high affinity sequences dependent upon cellular zinc. The KLF/Sp1-family binding motif is prevalent within the ZTRE "N" bridging bases, suggesting ZNF658 may compete with Sp1-like transactivators to suppress transcription.
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Affiliation(s)
- Michael Francis
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Huimin Cheng
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA, USA
| | - Arthur Grider
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
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18
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Tatip S, Taggart J, Wang Y, MacDiarmid CW, Eide DJ. Changes in transcription start sites of Zap1-regulated genes during zinc deficiency: Implications for HNT1 gene regulation. Mol Microbiol 2019; 113:285-296. [PMID: 31692084 DOI: 10.1111/mmi.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2019] [Indexed: 12/01/2022]
Abstract
Changes in RNA are often poor predictors of protein accumulation. One factor disrupting this relationship are changes in transcription start sites (TSSs). Therefore, we explored how alterations in TSS affected expression of genes regulated by the Zap1 transcriptional activator of Saccharomyces cerevisiae. Zap1 controls their response to zinc deficiency. Among over 80 known Zap1-regulated genes, several produced long leader transcripts (LLTs) in one zinc status condition and short leader transcripts (SLTs) in the other. Fusing LLT and SLT transcript leaders to green fluorescent protein indicated that for five genes, the start site shift likely has little effect on protein synthesis. For four genes, however, the different transcript leaders greatly affected translation. We focused on the HNT1 gene. Zap1 caused a shift from SLT HNT1 RNA in zinc-replete cells to LLT HNT1 RNA in deficient cells. This shift correlated with decreased protein production despite increased RNA. The LLT RNA contains multiple upstream open reading frames that can inhibit translation. Expression of the LLT HNT1 RNA was dependent on Zap1. However, expression of the long transcript was not required to decrease SLT HNT1 mRNA. Our results suggest that the Zap1-activated LLT RNA is a "fail-safe" mechanism to ensure decreased Hnt1 protein in zinc deficiency.
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Affiliation(s)
- Supinda Tatip
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin W MacDiarmid
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
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19
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Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics 2019; 212:667-690. [PMID: 31053593 DOI: 10.1534/genetics.119.302004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/18/2019] [Indexed: 01/07/2023] Open
Abstract
Signaling pathways can regulate biological responses by the transcriptional regulation of target genes. In yeast, multiple signaling pathways control filamentous growth, a morphogenetic response that occurs in many species including fungal pathogens. Here, we examine the role of signaling pathways that control filamentous growth in regulating adhesion-dependent surface responses, including mat formation and colony patterning. Expression profiling and mutant phenotype analysis showed that the major pathways that regulate filamentous growth [filamentous growth MAPK (fMAPK), RAS, retrograde (RTG), RIM101, RPD3, ELP, SNF1, and PHO85] also regulated mat formation and colony patterning. The chromatin remodeling complex, SAGA, also regulated these responses. We also show that the RAS and RTG pathways coregulated a common set of target genes, and that SAGA regulated target genes known to be controlled by the fMAPK, RAS, and RTG pathways. Analysis of surface growth-specific targets identified genes that respond to low oxygen, high temperature, and desiccation stresses. We also explore the question of why cells make adhesive contacts in colonies. Cell adhesion contacts mediated by the coregulated target and adhesion molecule, Flo11p, deterred entry into colonies by macroscopic predators and impacted colony temperature regulation. The identification of new regulators (e.g., SAGA), and targets of surface growth in yeast may provide insights into fungal pathogenesis in settings where surface growth and adhesion contributes to virulence.
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20
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Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics 2018; 10:1755-1776. [PMID: 30358795 PMCID: PMC6291366 DOI: 10.1039/c8mt00269j] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is an essential cofactor for many proteins. A key mechanism of zinc homeostasis during deficiency is "zinc sparing" in which specific zinc-binding proteins are repressed to reduce the cellular requirement. In this report, we evaluated zinc sparing across the zinc proteome of Saccharomyces cerevisiae. The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. Protein abundance was determined by mass spectrometry. In zinc-replete cells, we detected over 2500 proteins among which 229 were zinc proteins. Based on copy number estimates and binding stoichiometries, a replete cell contains ∼9 million zinc-binding sites on proteins. During zinc deficiency, many zinc proteins decreased in abundance and the zinc-binding requirement decreased to ∼5 million zinc atoms per cell. Many of these effects were due at least in part to changes in mRNA levels rather than simply protein degradation. Measurements of cellular zinc content showed that the level of zinc atoms per cell dropped from over 20 million in replete cells to only 1.7 million in deficient cells. These results confirmed the ability of replete cells to store excess zinc and suggested that the majority of zinc-binding sites on proteins in deficient cells are either unmetalated or mismetalated. Our analysis of two abundant zinc proteins, Fba1 aldolase and Met6 methionine synthetase, supported that hypothesis. Thus, we have discovered widespread zinc sparing mechanisms and obtained evidence of a high accumulation of zinc proteins that lack their cofactor during deficiency.
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Affiliation(s)
- Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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21
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Migocka M, Małas K, Maciaszczyk-Dziubinska E, Posyniak E, Migdal I, Szczech P. Cucumber Golgi protein CsMTP5 forms a Zn-transporting heterodimer with high molecular mass protein CsMTP12. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:196-206. [PMID: 30466585 DOI: 10.1016/j.plantsci.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/07/2018] [Accepted: 09/15/2018] [Indexed: 06/09/2023]
Abstract
Heterodimeric complexes formed by members of the cation facilitator (CDF) family catalyse the import of Zn into the secretory pathway of yeast and vertebrate cells. Orthologous proteins AtMTP5 and AtMTP12 from Arabidopsis have also been shown to form a heterodimeric complex at the Golgi compartment of plant cells that possibly transport Zn. In this study we show that cucumber proteins CsMTP5 and CsMTP12 form a functional heterodimer that is involved in the loading of Zn into the ER lumen under low Zn, and not in the detoxification of yeast from Zn excess through vesicle-mediated exocytosis. Using specific antibodies, we demonstrate that CsMTP5 is localized at the Golgi compartment of cucumber cells and is markedly up-regulated upon Zn deficiency. The level of CsMTP5 transcript in cucumber is also significantly elevated in Zn-limiting conditions, whereas the expression of CsMTP12 is independent of the availability of Zn. Therefore we propose that the cucumber heterodimeric complex CsMTP5-CsMTP12 functions to deliver Zn to Zn-dependent proteins of the Golgi compartment and is regulated by zinc at the level of CsMTP5 transcription.
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Affiliation(s)
- Magdalena Migocka
- University of Wroclaw, Institute of Experimental Biology, Department of Plant Molecular Physiology, Kanonia 6/8, 50-328 Wroclaw, Poland.
| | - Karolina Małas
- University of Wroclaw, Institute of Experimental Biology, Department of Plant Molecular Physiology, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- University of Wroclaw, Institute of Experimental Biology, Department of Genetics and Cell Physiology, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Ewelina Posyniak
- University of Wroclaw, Institute of Experimental Biology, Department of Animal Developmental Biology, Sienkiewicza 21, 50-335 Wroclaw, Poland
| | - Iwona Migdal
- University of Wroclaw, Institute of Experimental Biology, Department of Genetics and Cell Physiology, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Patryk Szczech
- University of Wroclaw, Institute of Experimental Biology, Department of Plant Molecular Physiology, Kanonia 6/8, 50-328 Wroclaw, Poland
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22
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Li Y, Sun L, Lu C, Gong Y, Li M, Sun S. Promising Antifungal Targets Against Candida albicans Based on Ion Homeostasis. Front Cell Infect Microbiol 2018; 8:286. [PMID: 30234023 PMCID: PMC6131588 DOI: 10.3389/fcimb.2018.00286] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
In recent decades, invasive fungal infections have been increasing significantly, contributing to high incidences and mortality in immunosuppressed patients. Candida albicans (C. albicans) is the most prevalent opportunistic fungal pathogen in humans that can cause severe and often fatal bloodstream infections. Current antifungal agents have several limitations, including that only a small number of classes of antifungals are available, certain of which have severe toxicity and high cost. Moreover, the emergence of drug resistance is a new limitation to successful patient outcomes. Therefore, the development of antifungals with novel targets is an essential strategy for the efficient management of C. albicans infections. It is widely recognized that ion homeostasis is crucial for all living cells. Many studies have identified that ion-signaling and transduction networks are central to fungal survival by regulating gene expression, morphological transition, host invasion, stress response, and drug resistance. Dysregulation of ion homeostasis rapidly mediates cell death, forming the mechanistic basis of a growing number of compounds that elicit antifungal activity. Most of the potent antifungals have been widely used in the clinic, and certain of them have low toxicity, meaning that they may be expected to be used as antifungal drugs in the future. Hence, we briefly summarize the homeostasis regulation of several important ions, potential antifungal targets based on these ion-signaling networks, and antifungal compounds based on the disruption of ion homeostasis. This summary will help in designing effective drugs and identifying new targets for combating fungal diseases.
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Affiliation(s)
- Yiman Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Licui Sun
- Department of Pharmacy, Feicheng Mining Central Hospital, Feicheng, China
| | - Chunyan Lu
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
| | - Ying Gong
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Min Li
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
| | - Shujuan Sun
- Department of Pharmacy, Qianfoshan Hospital Affiliated to Shandong University, Jinan, China
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23
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The Transcription Factor ZafA Regulates the Homeostatic and Adaptive Response to Zinc Starvation in Aspergillus fumigatus. Genes (Basel) 2018; 9:genes9070318. [PMID: 29949939 PMCID: PMC6070888 DOI: 10.3390/genes9070318] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 12/20/2022] Open
Abstract
One of the most important features that enables Aspergillus fumigatus to grow within a susceptible individual and to cause disease is its ability to obtain Zn2+ ions from the extremely zinc-limited environment provided by host tissues. Zinc uptake from this source in A. fumigatus relies on ZIP transporters encoded by the zrfA, zrfB and zrfC genes. The expression of these genes is tightly regulated by the ZafA transcription factor that regulates zinc homeostasis and is essential for A. fumigatus virulence. We combined the use of microarrays, Electrophoretic Mobility Shift Assays (EMSA) analyses, DNase I footprinting assays and in silico tools to better understand the regulation of the homeostatic and adaptive response of A. fumigatus to zinc starvation. We found that under zinc-limiting conditions, ZafA functions mainly as a transcriptional activator through binding to a zinc response sequence located in the regulatory regions of its target genes, although it could also function as a repressor of a limited number of genes. In addition to genes involved in the homeostatic response to zinc deficiency, ZafA also influenced, either directly or indirectly, the expression of many other genes. It is remarkable that the expression of many genes involved in iron uptake and ergosterol biosynthesis is strongly reduced under zinc starvation, even though only the expression of some of these genes appeared to be influenced directly or indirectly by ZafA. In addition, it appears to exist in A. fumigatus a zinc/iron cross-homeostatic network to allow the adaptation of the fungus to grow in media containing unbalanced Zn:Fe ratios. The adaptive response to oxidative stress typically linked to zinc starvation was also mediated by ZafA, as was the strong induction of genes involved in gliotoxin biosynthesis and self-protection against endogenous gliotoxin. This study has expanded our knowledge about the regulatory and metabolic changes displayed by A. fumigatus in response to zinc starvation and has helped us to pinpoint new ZafA target genes that could be important for fungal pathogens to survive and grow within host tissues and, hence, for virulence.
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24
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Choi S, Hu YM, Corkins ME, Palmer AE, Bird AJ. Zinc transporters belonging to the Cation Diffusion Facilitator (CDF) family have complementary roles in transporting zinc out of the cytosol. PLoS Genet 2018. [PMID: 29529046 PMCID: PMC5864093 DOI: 10.1371/journal.pgen.1007262] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Zinc is an essential trace element that is required for the function of a large number of proteins. As these zinc-binding proteins are found within the cytosol and organelles, all eukaryotes require mechanisms to ensure that zinc is delivered to organelles, even under conditions of zinc deficiency. Although many zinc transporters belonging to the Cation Diffusion Facilitator (CDF) families have well characterized roles in transporting zinc into the lumens of intracellular compartments, relatively little is known about the mechanisms that maintain organelle zinc homeostasis. The fission yeast Schizosaccharomyces pombe is a useful model system to study organelle zinc homeostasis as it expresses three CDF family members that transport zinc out of the cytosol into intracellular compartments: Zhf1, Cis4, and Zrg17. Zhf1 transports zinc into the endoplasmic reticulum, and Cis4 and Zrg17 form a heterodimeric complex that transports zinc into the cis-Golgi. Here we have used the high and low affinity ZapCY zinc-responsive FRET sensors to examine cytosolic zinc levels in yeast mutants that lack each of these CDF proteins. We find that deletion of cis4 or zrg17 leads to higher levels of zinc accumulating in the cytosol under conditions of zinc deficiency, whereas deletion of zhf1 results in zinc accumulating in the cytosol when zinc is not limiting. We also show that the expression of cis4, zrg17, and zhf1 is independent of cellular zinc status. Taken together our results suggest that the Cis4/Zrg17 complex is necessary for zinc transport out of the cytosol under conditions of zinc-deficiency, while Zhf1 plays the dominant role in removing zinc from the cytosol when labile zinc is present. We propose that the properties and/or activities of individual CDF family members are fine-tuned to enable cells to control the flux of zinc out of the cytosol over a broad range of environmental zinc stress.
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Affiliation(s)
- Sangyong Choi
- Department of Human Nutrition, The Ohio State University, Columbus, Ohio, United States of America
| | - Ya-Mei Hu
- Department of Human Nutrition, The Ohio State University, Columbus, Ohio, United States of America
| | - Mark E Corkins
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Amy E Palmer
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Amanda J Bird
- Department of Human Nutrition, The Ohio State University, Columbus, Ohio, United States of America.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America.,Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
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25
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Bucci MD, Weisenhorn E, Haws S, Yao Z, Zimmerman G, Gannon M, Taggart J, Lee T, Klionsky DJ, Russell J, Coon J, Eide DJ. An Autophagy-Independent Role for ATG41 in Sulfur Metabolism During Zinc Deficiency. Genetics 2018; 208:1115-1130. [PMID: 29321173 PMCID: PMC5844326 DOI: 10.1534/genetics.117.300679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/05/2018] [Indexed: 01/17/2023] Open
Abstract
The Zap1 transcription factor of Saccharomyces cerevisiae is a key regulator in the genomic responses to zinc deficiency. Among the genes regulated by Zap1 during zinc deficiency is the autophagy-related gene ATG41 Here, we report that Atg41 is required for growth in zinc-deficient conditions, but not when zinc is abundant or when other metals are limiting. Consistent with a role for Atg41 in macroautophagy, we show that nutritional zinc deficiency induces autophagy and that mutation of ATG41 diminishes that response. Several experiments indicated that the importance of ATG41 function to growth during zinc deficiency is not because of its role in macroautophagy, but rather is due to one or more autophagy-independent functions. For example, rapamycin treatment fully induced autophagy in zinc-deficient atg41Δ mutants but failed to improve growth. In addition, atg41Δ mutants showed a far more severe growth defect than any of several other autophagy mutants tested, and atg41Δ mutants showed increased Heat Shock Factor 1 activity, an indicator of protein homeostasis stress, while other autophagy mutants did not. An autophagy-independent function for ATG41 in sulfur metabolism during zinc deficiency was suggested by analyzing the transcriptome of atg41Δ mutants during the transition from zinc-replete to -deficient conditions. Analysis of sulfur metabolites confirmed that Atg41 is needed for the normal accumulation of methionine, homocysteine, and cysteine in zinc-deficient cells. Therefore, we conclude that Atg41 plays roles in both macroautophagy and sulfur metabolism during zinc deficiency.
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Affiliation(s)
- Michael D Bucci
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
| | - Erin Weisenhorn
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Spencer Haws
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
| | - Zhiyuan Yao
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Ginelle Zimmerman
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
| | - Molly Gannon
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
| | - Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
| | - Traci Lee
- Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, Wisconsin 53144
| | - Daniel J Klionsky
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Jason Russell
- Morgridge Institute for Research, Madison, Wisconsin 53715
- Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706
| | - Joshua Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Wisconsin 53706
- Morgridge Institute for Research, Madison, Wisconsin 53715
- Genome Center of Wisconsin, University of Wisconsin-Madison, Wisconsin 53706
- Department of Chemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Wisconsin 53706
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26
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Ochab-Marcinek A, Jędrak J, Tabaka M. Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades. Phys Chem Chem Phys 2018; 19:22580-22591. [PMID: 28809965 DOI: 10.1039/c7cp00743d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An intuition based on deterministic models of chemical kinetics is that population heterogeneity of transcription factor levels in cells is transmitted unchanged downstream to the target genes. We use a stochastic model of a two-gene cascade with a self-regulating upstream gene to show that, counter to the intuition, there is no simple mapping (bimodal to bimodal, unimodal to unimodal) between the shapes of the distributions of transcription factor numbers and target protein numbers in cells. Due to the presence of the two regulations, the system contains two nonlinear transfer functions, defined by the Hill kinetics of transcription factor binding. The transfer function of the regulator can "interfere" with the transfer function of the target, converting the bimodal input into a unimodal output or vice versa. We show that this effect can be predicted by a geometric construction. As an example application of the method, we present a case study of a system of several downstream genes of different sensitivities, controlled by a common transcription factor which also regulates its own transcription. We show that a single regulator can induce qualitatively different patterns (binary or graded) of responses to a signal in different downstream genes, depending on whether the sensitivity regions of the transfer functions of the upstream and downstream genes overlap or not. Alternatively, the same model can be interpreted as describing a single downstream gene that has different sensitivities in different cell lines due to mutations. Our model shows, therefore, a possible kinetic mechanism by which different genes can interpret the same biological signal in a different manner.
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Affiliation(s)
- Anna Ochab-Marcinek
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Jędrak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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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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28
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Taggart J, MacDiarmid CW, Haws S, Eide DJ. Zap1-dependent transcription from an alternative upstream promoter controls translation of RTC4 mRNA in zinc-deficient Saccharomyces cerevisiae. Mol Microbiol 2017; 106:678-689. [PMID: 28963784 DOI: 10.1111/mmi.13851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/14/2022]
Abstract
Maintaining zinc homeostasis is an important property of all organisms. In the yeast Saccharomyces cerevisiae, the Zap1 transcriptional activator is a central player in this process. In response to zinc deficiency, Zap1 activates transcription of many genes and consequently increases accumulation of their encoded proteins. In this report, we describe a new mechanism of Zap1-mediated regulation whereby increased transcription of certain target genes results in reduced protein expression. Transcription of the Zap1-responsive genes RTC4 and RAD27 increases markedly in zinc-deficient cells but, surprisingly, their protein levels decrease. We examined the underlying mechanism further for RTC4 and found that this unusual regulation results from altered transcription start site selection. In zinc-replete cells, RTC4 transcription begins near the protein-coding region and the resulting short transcript leader allows for efficient translation. In zinc-deficient cells, RTC4 RNA with longer transcript leaders are expressed that are not efficiently translated due to the presence of multiple small open reading frames upstream of the coding region. This regulation requires a potential Zap1 binding site located farther upstream of the promoter. Thus, we present evidence for a new mechanism of Zap1-mediated gene regulation and another way that this activator protein can repress protein expression.
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Affiliation(s)
- Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Colin W MacDiarmid
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer Haws
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Eide
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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Bird AJ, Labbé S. The Zap1 transcriptional activator negatively regulates translation of the RTC4 mRNA through the use of alternative 5' transcript leaders. Mol Microbiol 2017; 106:673-677. [PMID: 28971534 DOI: 10.1111/mmi.13856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/28/2017] [Accepted: 09/28/2017] [Indexed: 12/29/2022]
Abstract
The zinc-responsive transcription activator Zap1 plays a central role in zinc homeostasis in the budding yeast Saccharomyces cerevisiae. In zinc-deficient cells, Zap1 binds to zinc responsive elements in target gene promoters and activates gene expression. In most cases, Zap1-dependent gene activation results in increased levels of mRNAs and proteins. However, Zap1-dependent activation of RTC4 results in increased levels of the RTC4 mRNA and decreased levels of the Rtc4 protein. This atypical regulation results from Zap1-mediated changes in the transcriptional start site for RTC4 and the production of a RTC4 transcript with a longer 5' leader. This long RTC4 transcript contains small upstream open reading frames that prevent translation of the downstream RTC4 ORF. The new studies with Zap1 highlight how a transcriptional activator can facilitate decreased protein expression.
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Affiliation(s)
- Amanda J Bird
- Departments of Human Nutrition and Molecular Genetics, The Ohio State University, 1787 Neil Avenue, Columbus, OH 43210, USA
| | - Simon Labbé
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Pavillon Z-8, 3201, Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
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30
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Pinheiro AM, Carreira A, Prescott TAK, Ferreira RB, Monteiro SA. Bridging the Gap to Non-toxic Fungal Control: Lupinus-Derived Blad-Containing Oligomer as a Novel Candidate to Combat Human Pathogenic Fungi. Front Microbiol 2017; 8:1182. [PMID: 28702011 PMCID: PMC5487463 DOI: 10.3389/fmicb.2017.01182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/12/2017] [Indexed: 01/17/2023] Open
Abstract
The lack of antifungal drugs with novel modes of action reaching the clinic is a serious concern. Recently a novel antifungal protein referred to as Blad-containing oligomer (BCO) has received regulatory approval as an agricultural antifungal agent. Interestingly its spectrum of antifungal activity includes human pathogens such as Candida albicans, however, its mode of action has yet to be elucidated. Here we demonstrate that BCO exerts its antifungal activity through inhibition of metal ion homeostasis which results in apoptotic cell death in C. albicans. HIP HOP profiling in Saccharomyces cerevisiae using a panel of signature strains that are characteristic for common modes of action identified hypersensitivity in yeast lacking the iron-dependent transcription factor Aft1 suggesting restricted iron uptake as a mode of action. Furthermore, global transcriptome profiling in C. albicans also identified disruption of metal ion homeostasis as a potential mode of action. Experiments were carried out to assess the effect of divalent metal ions on the antifungal activity of BCO revealing that BCO activity is antagonized by metal ions such as Mn2+, Zn2+, and Fe2+. The transcriptome profile also implicated sterol synthesis as a possible secondary mode of action which was subsequently confirmed in sterol synthesis assays in C. albicans. Animal models for toxicity showed that BCO is generally well tolerated and presents a promising safety profile as a topical applied agent. Given its potent broad spectrum antifungal activity and novel multitarget mode of action, we propose BCO as a promising new antifungal agent for the topical treatment of fungal infections.
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Affiliation(s)
- Ana M Pinheiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Alexandra Carreira
- CEV, SA, Parque Industrial de Cantanhede/Biocant-ParkCantanhede, Portugal
| | | | - Ricardo B Ferreira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Sara A Monteiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal.,CEV, SA, Parque Industrial de Cantanhede/Biocant-ParkCantanhede, Portugal
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31
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Makthal N, Nguyen K, Do H, Gavagan M, Chandrangsu P, Helmann JD, Olsen RJ, Kumaraswami M. A Critical Role of Zinc Importer AdcABC in Group A Streptococcus-Host Interactions During Infection and Its Implications for Vaccine Development. EBioMedicine 2017; 21:131-141. [PMID: 28596134 PMCID: PMC5514391 DOI: 10.1016/j.ebiom.2017.05.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023] Open
Abstract
Bacterial pathogens must overcome host immune mechanisms to acquire micronutrients for successful replication and infection. Streptococcus pyogenes, also known as group A streptococcus (GAS), is a human pathogen that causes a variety of clinical manifestations, and disease prevention is hampered by lack of a human GAS vaccine. Herein, we report that the mammalian host recruits calprotectin (CP) to GAS infection sites and retards bacterial growth by zinc limitation. However, a GAS-encoded zinc importer and a nuanced zinc sensor aid bacterial defense against CP-mediated growth inhibition and contribute to GAS virulence. Immunization of mice with the extracellular component of the zinc importer confers protection against systemic GAS challenge. Together, we identified a key early stage host-GAS interaction and translated that knowledge into a novel vaccine strategy against GAS infection. Furthermore, we provided evidence that a similar struggle for zinc may occur during other streptococcal infections, which raises the possibility of a broad-spectrum prophylactic strategy against multiple streptococcal pathogens. Host employs calprotectin to impose zinc (Zn) limitation on the human pathogen group A streptococcus (GAS) during infection. As a defense, GAS uses a sensor, AdcR, to monitor Zn availability, and a high-affinity transporter, AdcABC, to acquire Zn. Finally, we characterized the extracellular subunit of AdcA as a vaccine candidate to protect mice from GAS infections.
There is an urgent need for a human vaccine to protect against diseases caused by human pathogen, group A streptococcus (GAS). Herein, we identified the key molecular players involved in the battle between the host and invading bacteria for the critical nutrient zinc. The host recruits calprotectin at GAS infection sites to limit zinc availability to the pathogen. The pathogen senses the alterations in zinc availability using a sensor, AdcR, and outcompetes calprotectin by employing a high-affinity zinc uptake system, AdcABC. Using this knowledge, we developed a successful vaccination strategy by immunization with AdcA and demonstrated protection against GAS infections.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Kimberly Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Maire Gavagan
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, United States
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, United States.
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32
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Singh N, Yadav KK, Rajasekharan R. Effect of zinc deprivation on the lipid metabolism of budding yeast. Curr Genet 2017; 63:977-982. [PMID: 28500379 DOI: 10.1007/s00294-017-0704-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 12/21/2022]
Abstract
Zinc is an essential micronutrient for all living cells. It serves as a structural and catalytic cofactor for numerous proteins, hence maintaining a proper level of cellular zinc is essential for normal functioning of the cell. Zinc homeostasis is sustained through various ways under severe zinc-deficient conditions. Zinc-dependent proteins play an important role in biological systems and limitation of zinc causes a drastic change in their expression. In budding yeast, a zinc-responsive transcription factor Zap1p controls the expression of genes required for uptake and mobilization of zinc under zinc-limiting conditions. It also regulates the polar lipid levels under zinc-limiting conditions to maintain membrane integrity. Deletion of ZAP1 causes an increase in triacylglyerol levels which is due to the increased biosynthesis of acetate that serves as a precursor for triacylglycerol biosynthesis. In this review, we expanded our recent work role of Zap1p in nonpolar lipid metabolism of budding yeast.
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Affiliation(s)
- Neelima Singh
- Department of Lipid Science, Council of Scientific and Industrial Research (CSIR), Central Food Technological Research Institute (CFTRI), Mysore, 570020, Karnataka, India
| | - Kamlesh Kumar Yadav
- Department of Lipid Science, Council of Scientific and Industrial Research (CSIR), Central Food Technological Research Institute (CFTRI), Mysore, 570020, Karnataka, India
| | - Ram Rajasekharan
- Department of Lipid Science, Council of Scientific and Industrial Research (CSIR), Central Food Technological Research Institute (CFTRI), Mysore, 570020, Karnataka, India.
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33
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Zhao W, Zheng HZ, Zhou T, Hong XS, Cui HJ, Jiang ZW, Chen HJ, Zhou ZJ, Liu XG. CTT1 overexpression increases the replicative lifespan of MMS-sensitive Saccharomyces cerevisiae deficient in KSP1. Mech Ageing Dev 2017; 164:27-36. [PMID: 28347693 DOI: 10.1016/j.mad.2017.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/06/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022]
Abstract
Ksplp is a nuclear-localized Ser/Thr kinase that is not essential for the vegetative growth of yeast. A global gene function analysis in yeast suggested that Ksplp was involved in the oxidative stress response; however, the underlying mechanism remains unclear. Here, we showed that KSP1-deficient yeast cells exhibit hypersensitivity to the DNA alkylating agent methyl methanesulphonate (MMS), and treatment of the KSP1-deficient strain with MMS could trigger abnormal mitochondrial membrane potential and up-regulate reactive oxygen species (ROS) production. In addition, the mRNA expression level of the catalase gene CTT1 (which encodes cytosolic catalase) and total catalase activity were strongly down-regulated in the KSP1-deleted strain compared with those in wild-type cells. Moreover, the KSP1 deficiency also leads to a shortened replicative lifespan, which could be restored by the increased expression of CTT1. On the other hand, KSP1-overexpressed (KSP1OX) yeast cells exhibited increased resistance towards MMS, an effect that was, at least in part, CTT1 independent. Collectively, these findings highlight the involvement of Ksplp in the DNA damage response and implicate Ksplp as a modulator of the replicative lifespan.
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Affiliation(s)
- Wei Zhao
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Hua-Zhen Zheng
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Tao Zhou
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Xiao-Shan Hong
- Institute of Gynecology, Women and Children's Hospital of Guangdong Province, Guangzhou 511442, China
| | - Hong-Jing Cui
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Zhi-Wen Jiang
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Hui-Ji Chen
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China
| | - Zhong-Jun Zhou
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Xin-Guang Liu
- Institute of Aging Research, Guangdong Medical University, Dongguan 523808, China; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808, China; Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan 523808, China.
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34
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Wu YH, Taggart J, Song PX, MacDiarmid C, Eide DJ. An MSC2 Promoter-lacZ Fusion Gene Reveals Zinc-Responsive Changes in Sites of Transcription Initiation That Occur across the Yeast Genome. PLoS One 2016; 11:e0163256. [PMID: 27657924 PMCID: PMC5033525 DOI: 10.1371/journal.pone.0163256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/05/2016] [Indexed: 11/18/2022] Open
Abstract
The Msc2 and Zrg17 proteins of Saccharomyces cerevisiae form a complex to transport zinc into the endoplasmic reticulum. ZRG17 is transcriptionally induced in zinc-limited cells by the Zap1 transcription factor. In this report, we show that MSC2 mRNA also increases (~1.5 fold) in zinc-limited cells. The MSC2 gene has two in-frame ATG codons at its 5' end, ATG1 and ATG2; ATG2 is the predicted initiation codon. When the MSC2 promoter was fused at ATG2 to the lacZ gene, we found that unlike the chromosomal gene this reporter showed a 4-fold decrease in lacZ mRNA in zinc-limited cells. Surprisingly, β-galactosidase activity generated by this fusion gene increased ~7 fold during zinc deficiency suggesting the influence of post-transcriptional factors. Transcription of MSC2ATG2-lacZ was found to start upstream of ATG1 in zinc-replete cells. In zinc-limited cells, transcription initiation shifted to sites just upstream of ATG2. From the results of mutational and polysome profile analyses, we propose the following explanation for these effects. In zinc-replete cells, MSC2ATG2-lacZ mRNA with long 5' UTRs fold into secondary structures that inhibit translation. In zinc-limited cells, transcripts with shorter unstructured 5' UTRs are generated that are more efficiently translated. Surprisingly, chromosomal MSC2 did not show start site shifts in response to zinc status and only shorter 5' UTRs were observed. However, the shifts that occur in the MSC2ATG2-lacZ construct led us to identify significant transcription start site changes affecting the expression of ~3% of all genes. Therefore, zinc status can profoundly alter transcription initiation across the yeast genome.
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Affiliation(s)
- Yi-Hsuan Wu
- Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Janet Taggart
- Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Pamela Xiyao Song
- Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Colin MacDiarmid
- Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - David J. Eide
- Department of Nutritional Sciences, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail:
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35
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MacDiarmid CW, Taggart J, Jeong J, Kerdsomboon K, Eide DJ. Activation of the Yeast UBI4 Polyubiquitin Gene by Zap1 Transcription Factor via an Intragenic Promoter Is Critical for Zinc-deficient Growth. J Biol Chem 2016; 291:18880-96. [PMID: 27432887 DOI: 10.1074/jbc.m116.743120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 01/20/2023] Open
Abstract
Stability of many proteins requires zinc. Zinc deficiency disrupts their folding, and the ubiquitin-proteasome system may help manage this stress. In Saccharomyces cerevisiae, UBI4 encodes five tandem ubiquitin monomers and is essential for growth in zinc-deficient conditions. Although UBI4 is only one of four ubiquitin-encoding genes in the genome, a dramatic decrease in ubiquitin was observed in zinc-deficient ubi4Δ cells. The three other ubiquitin genes were strongly repressed under these conditions, contributing to the decline in ubiquitin. In a screen for ubi4Δ suppressors, a hypomorphic allele of the RPT2 proteasome regulatory subunit gene (rpt2(E301K)) suppressed the ubi4Δ growth defect. The rpt2(E301K) mutation also increased ubiquitin accumulation in zinc-deficient cells, and by using a ubiquitin-independent proteasome substrate we found that proteasome activity was reduced. These results suggested that increased ubiquitin supply in suppressed ubi4Δ cells was a consequence of more efficient ubiquitin release and recycling during proteasome degradation. Degradation of a ubiquitin-dependent substrate was restored by the rpt2(E301K) mutation, indicating that ubiquitination is rate-limiting in this process. The UBI4 gene was induced ∼5-fold in low zinc and is regulated by the zinc-responsive Zap1 transcription factor. Surprisingly, Zap1 controls UBI4 by inducing transcription from an intragenic promoter, and the resulting truncated mRNA encodes only two of the five ubiquitin repeats. Expression of a short transcript alone complemented the ubi4Δ mutation, indicating that it is efficiently translated. Loss of Zap1-dependent UBI4 expression caused a growth defect in zinc-deficient conditions. Thus, the intragenic UBI4 promoter is critical to preventing ubiquitin deficiency in zinc-deficient cells.
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Affiliation(s)
- Colin W MacDiarmid
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Janet Taggart
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, Massachusetts 01002
| | - Kittikhun Kerdsomboon
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - David J Eide
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
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36
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Zinc sensing and regulation in yeast model systems. Arch Biochem Biophys 2016; 611:30-36. [PMID: 26940262 DOI: 10.1016/j.abb.2016.02.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/23/2022]
Abstract
The Zap1 transcription factor of Saccharomyces cerevisiae and the Loz1 transcription factor of Schizosaccharomyces pombe both play a central role in zinc homeostasis by controlling the expression of genes necessary for zinc metabolism. Zap1 activates gene expression when cells are limited for zinc, while Loz1 is required for gene repression when zinc is in excess. In this review we highlight what is known about the underlying mechanisms by which these factors are regulated by zinc, and how transcriptional activation and repression in eukaryotic cells can be finely tuned according to intracellular zinc availability.
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37
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Taymaz-Nikerel H, Cankorur-Cetinkaya A, Kirdar B. Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. Front Bioeng Biotechnol 2016; 4:17. [PMID: 26925399 PMCID: PMC4757645 DOI: 10.3389/fbioe.2016.00017] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/04/2016] [Indexed: 12/22/2022] Open
Abstract
Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to the changing conditions. Genome-wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors, such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short and long term. This review focuses on response of yeast cells to diverse stress inducing perturbations, including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, and to genetic interventions such as deletion and overexpression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.
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Affiliation(s)
| | | | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University , Istanbul , Turkey
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38
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Jung WH. The Zinc Transport Systems and Their Regulation in Pathogenic Fungi. MYCOBIOLOGY 2015; 43:179-83. [PMID: 26539032 PMCID: PMC4630422 DOI: 10.5941/myco.2015.43.3.179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 05/15/2023]
Abstract
Zinc is an essential micronutrient required for many enzymes that play essential roles in a cell. It was estimated that approximately 3% of the total cellular proteins are required for zinc for their functions. Zinc has long been considered as one of the key players in host-pathogen interactions. The host sequesters intracellular zinc by utilizing multiple cellular zinc importers and exporters as a means of nutritional immunity. To overcome extreme zinc limitation within the host environment, pathogenic microbes have successfully evolved a number of mechanisms to secure sufficient concentrations of zinc for their survival and pathogenesis. In this review, we briefly discuss the zinc uptake systems and their regulation in the model fungus Saccharomyces cerevisiae and in major human pathogenic fungi such as Aspergillus fumigatus, Candida albicans, and Cryptococcus gattii.
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Affiliation(s)
- Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
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39
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Cellular sensing and transport of metal ions: implications in micronutrient homeostasis. J Nutr Biochem 2015; 26:1103-15. [PMID: 26342943 DOI: 10.1016/j.jnutbio.2015.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/23/2015] [Accepted: 08/04/2015] [Indexed: 12/15/2022]
Abstract
Micronutrients include the transition metal ions zinc, copper and iron. These metals are essential for life as they serve as cofactors for many different proteins. On the other hand, they can also be toxic to cell growth when in excess. As a consequence, all organisms require mechanisms to tightly regulate the levels of these metal ions. In eukaryotes, one of the primary ways in which metal levels are regulated is through changes in expression of genes required for metal uptake, compartmentalization, storage and export. By tightly regulating the expression of these genes, each organism is able to balance metal levels despite fluctuations in the diet or extracellular environment. The goal of this review is to provide an overview of how gene expression can be controlled at a transcriptional, posttranscriptional and posttranslational level in response to metal ions in lower and higher eukaryotes. Specifically, I review what is known about how these metalloregulatory factors sense fluctuations in metal ion levels and how changes in gene expression maintain nutrient homeostasis.
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40
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Sanson M, Makthal N, Flores AR, Olsen RJ, Musser JM, Kumaraswami M. Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence. Nucleic Acids Res 2014; 43:418-32. [PMID: 25510500 PMCID: PMC4288194 DOI: 10.1093/nar/gku1304] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Altering zinc bioavailability to bacterial pathogens is a key component of host innate immunity. Thus, the ability to sense and adapt to the alterations in zinc concentrations is critical for bacterial survival and pathogenesis. To understand the adaptive responses of group A Streptococcus (GAS) to zinc limitation and its regulation by AdcR, we characterized gene regulation by AdcR. AdcR regulates the expression of 70 genes involved in zinc acquisition and virulence. Zinc-bound AdcR interacts with operator sequences in the negatively regulated promoters and mediates differential regulation of target genes in response to zinc deficiency. Genes involved in zinc mobilization and conservation are derepressed during mild zinc deficiency, whereas the energy-dependent zinc importers are upregulated during severe zinc deficiency. Further, we demonstrated that transcription activation by AdcR occurs by direct binding to the promoter. However, the repression and activation by AdcR is mediated by its interactions with two distinct operator sequences. Finally, mutational analysis of the metal ligands of AdcR caused impaired DNA binding and attenuated virulence, indicating that zinc sensing by AdcR is critical for GAS pathogenesis. Together, we demonstrate that AdcR regulates GAS adaptive responses to zinc limitation and identify molecular components required for GAS survival during zinc deficiency.
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Affiliation(s)
- Misu Sanson
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA Escuela de Biotecnología y Alimentos, Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Monterrey, NL, Mexico
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - Anthony R Flores
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA Section of Infectious Diseases, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX, USA
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41
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Choi S, Bird AJ. Zinc'ing sensibly: controlling zinc homeostasis at the transcriptional level. Metallomics 2014; 6:1198-215. [PMID: 24722954 DOI: 10.1039/c4mt00064a] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Zinc-responsive transcription factors are found in all kingdoms of life and include the transcriptional activators ZntR, SczA, Zap1, bZip19, bZip23, and MTF-1, and transcriptional repressors Zur, AdcR, Loz1, and SmtB. These factors have two defining features; their activity is regulated by zinc and they all play a central role in zinc homeostasis by controlling the expression of genes that directly affect zinc levels or its availability. This review summarizes what is known about the mechanisms by which each of these factors sense changes in intracellular zinc levels and how they control zinc homeostasis through target gene regulation. Other factors that influence zinc ion sensing are also discussed.
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Affiliation(s)
- Sangyong Choi
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
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42
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Suppression of Placental Metallothionein 1 and Zinc Transporter 1 mRNA Expressions Contributes to Fetal Heart Malformations Caused by Maternal Zinc Deficiency. Cardiovasc Toxicol 2014; 14:329-38. [DOI: 10.1007/s12012-014-9256-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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43
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Staats CC, Kmetzsch L, Schrank A, Vainstein MH. Fungal zinc metabolism and its connections to virulence. Front Cell Infect Microbiol 2013; 3:65. [PMID: 24133658 PMCID: PMC3796257 DOI: 10.3389/fcimb.2013.00065] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/26/2013] [Indexed: 12/03/2022] Open
Abstract
Zinc is a ubiquitous metal in all life forms, as it is a structural component of the almost 10% of eukaryotic proteins, which are called zinc-binding proteins. In zinc-limiting conditions such as those found during infection, pathogenic fungi activate the expression of several systems to enhance the uptake of zinc. These systems include ZIP transporters (solute carrier 39 family) and secreted zincophores, which are proteins that are able to chelate zinc. The expression of some fungal zinc uptake systems are regulated by a master regulator (Zap1), first characterized in the yeast Saccharomyces cerevisiae. In this review, we highlight features of zinc uptake and metabolism in human fungal pathogens and aspects of the relationship between proper zinc metabolism and the expression of virulence factors and adaptation to the host habitat.
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Affiliation(s)
- Charley C Staats
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil ; Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil
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44
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MacDiarmid CW, Taggart J, Kerdsomboon K, Kubisiak M, Panascharoen S, Schelble K, Eide DJ. Peroxiredoxin chaperone activity is critical for protein homeostasis in zinc-deficient yeast. J Biol Chem 2013; 288:31313-27. [PMID: 24022485 DOI: 10.1074/jbc.m113.512384] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Zinc is required for the folding and function of many proteins. In Saccharomyces cerevisiae, homeostatic and adaptive responses to zinc deficiency are regulated by the Zap1 transcription factor. One Zap1 target gene encodes the Tsa1 peroxiredoxin, a protein with both peroxidase and protein chaperone activities. Consistent with its regulation, Tsa1 is critical for growth under low zinc conditions. We previously showed that Tsa1's peroxidase function decreases the oxidative stress that occurs in zinc deficiency. In this report, we show that Tsa1 chaperone, and not peroxidase, activity is the more critical function in zinc-deficient cells. Mutations restoring growth to zinc-deficient tsa1 cells inactivated TRR1, encoding thioredoxin reductase. Because Trr1 is required for oxidative stress tolerance, this result implicated the Tsa1 chaperone function in tolerance to zinc deficiency. Consistent with this hypothesis, the tsa1Δ zinc requirement was complemented by a Tsa1 mutant allele that retained only chaperone function. Additionally, growth of tsa1Δ was also restored by overexpression of holdase chaperones Hsp26 and Hsp42, which lack peroxidase activity, and the Tsa1 paralog Tsa2 contributed to suppression by trr1Δ, even though trr1Δ inactivates Tsa2 peroxidase activity. The essentiality of the Tsa1 chaperone suggested that zinc-deficient cells experience a crisis of disrupted protein folding. Consistent with this model, assays of protein homeostasis suggested that zinc-limited tsa1Δ mutants accumulated unfolded proteins and induced a corresponding stress response. These observations demonstrate a clear physiological role for a peroxiredoxin chaperone and reveal a novel and unexpected role for protein homeostasis in tolerating metal deficiency.
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Affiliation(s)
- Colin W MacDiarmid
- From the Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
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45
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Zinc finger protein Loz1 is required for zinc-responsive regulation of gene expression in fission yeast. Proc Natl Acad Sci U S A 2013; 110:15371-6. [PMID: 24003116 DOI: 10.1073/pnas.1300853110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In Schizosaccharomyces pombe, alcohol dehydrogenase 1 (Adh1) is an abundant zinc-requiring enzyme that catalyses the conversion of acetaldehyde to ethanol during fermentation. In a zinc-replete cell, adh1 is highly expressed. However, in zinc-limited cells, adh1 gene expression is repressed, and cells induce the expression of an alternative alcohol dehydrogenase encoded by the adh4 gene. In our studies examining this zinc-dependent switch in alcohol dehydrogenase gene expression, we isolated an adh1Δ strain containing a partial loss of function mutation that resulted in higher levels of adh4 transcripts in zinc-replete cells. This mutation also led to the aberrant expression of other genes that are typically regulated by zinc. Using linkage analysis, we have mapped the position of this mutation to a single gene called Loss Of Zinc sensing 1 (loz1). Loz1 is a 55-kDa protein that contains a double C2H2-type zinc finger domain. The mapped mutation that disrupts Loz1 function leads to an arginine to glycine substitution in the second zinc finger domain, suggesting that the double zinc finger domain is important for Loz1 function. We show that loz1Δ cells hyperaccumulate zinc and that Loz1 is required for gene repression in zinc-replete cells. We also have found that Loz1 negatively autoregulates its own expression. We propose that Loz1 is a unique metalloregulatory factor that plays a central role in zinc homeostasis in S. pombe.
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46
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Abstract
All living organisms require nutrient minerals for growth and have developed mechanisms to acquire, utilize, and store nutrient minerals effectively. In the aqueous cellular environment, these elements exist as charged ions that, together with protons and hydroxide ions, facilitate biochemical reactions and establish the electrochemical gradients across membranes that drive cellular processes such as transport and ATP synthesis. Metal ions serve as essential enzyme cofactors and perform both structural and signaling roles within cells. However, because these ions can also be toxic, cells have developed sophisticated homeostatic mechanisms to regulate their levels and avoid toxicity. Studies in Saccharomyces cerevisiae have characterized many of the gene products and processes responsible for acquiring, utilizing, storing, and regulating levels of these ions. Findings in this model organism have often allowed the corresponding machinery in humans to be identified and have provided insights into diseases that result from defects in ion homeostasis. This review summarizes our current understanding of how cation balance is achieved and modulated in baker's yeast. Control of intracellular pH is discussed, as well as uptake, storage, and efflux mechanisms for the alkali metal cations, Na(+) and K(+), the divalent cations, Ca(2+) and Mg(2+), and the trace metal ions, Fe(2+), Zn(2+), Cu(2+), and Mn(2+). Signal transduction pathways that are regulated by pH and Ca(2+) are reviewed, as well as the mechanisms that allow cells to maintain appropriate intracellular cation concentrations when challenged by extreme conditions, i.e., either limited availability or toxic levels in the environment.
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47
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Promoter sequence determines the relationship between expression level and noise. PLoS Biol 2013; 11:e1001528. [PMID: 23565060 PMCID: PMC3614515 DOI: 10.1371/journal.pbio.1001528] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/22/2013] [Indexed: 01/01/2023] Open
Abstract
A single transcription factor can activate or repress expression by three different mechanisms: one that increases cell-to-cell variability in target gene expression (noise) and two that decrease noise. The ability of cells to accurately control gene expression levels in response to extracellular cues is limited by the inherently stochastic nature of transcriptional regulation. A change in transcription factor (TF) activity results in changes in the expression of its targets, but the way in which cell-to-cell variability in expression (noise) changes as a function of TF activity, and whether targets of the same TF behave similarly, is not known. Here, we measure expression and noise as a function of TF activity for 16 native targets of the transcription factor Zap1 that are regulated by it through diverse mechanisms. For most activated and repressed Zap1 targets, noise decreases as expression increases. Kinetic modeling suggests that this is due to two distinct Zap1-mediated mechanisms that both change the frequency of transcriptional bursts. Notably, we found that another mechanism of repression by Zap1, which is encoded in the promoter DNA, likely decreases the size of transcriptional bursts, producing a unique transcriptional state characterized by low expression and low noise. In addition, we find that further reduction in noise is achieved when a single TF both activates and represses a single target gene. Our results suggest a global principle whereby at low TF concentrations, the dominant source of differences in expression between promoters stems from differences in burst frequency, whereas at high TF concentrations differences in burst size dominate. Taken together, we show that the precise amount by which noise changes with expression is specific to the regulatory mechanism of transcription and translation that acts at each gene. In response to environmental changes, cells regulate the activity of transcription factors (TFs), which in turn change the expression of dozens of downstream target genes by binding to their promoters. The response of each target gene is determined by the interplay between TF concentration and the context in which TF binding sites occur in each target promoter. To examine the relationship between promoter sequence, mechanism of regulation, and response to TF activity, we measured expression of 16 target genes of a single TF in response to changes in TF concentration in single cells. We found that different native promoters that are all targets of the same TF exhibit diverse responses to changing TF levels in terms of both gene expression level and cell-to-cell variability (noise) in expression. Using computational modeling and mutations of specific promoter elements, we show that the molecular mechanisms of regulation can be inferred by measuring how noise changes with expression. These results show that a single TF can regulate transcription through multiple mechanisms, resulting in similar changes in mean expression but vastly different changes in cell-to-cell variability.
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48
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Ehrensberger KM, Mason C, Corkins ME, Anderson C, Dutrow N, Cairns BR, Dalley B, Milash B, Bird AJ. Zinc-dependent regulation of the Adh1 antisense transcript in fission yeast. J Biol Chem 2012; 288:759-69. [PMID: 23223230 DOI: 10.1074/jbc.m112.406165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In yeast, Adh1 (alcohol dehydrogenase 1) is an abundant zinc-binding protein that is required for the conversion of acetaldehyde to ethanol. Through transcriptome profiling of the Schizosaccharomyces pombe genome, we identified a natural antisense transcript at the adh1 locus that is induced in response to zinc limitation. This antisense transcript (adh1AS) shows a reciprocal expression pattern to that of the adh1 mRNA partner. In this study, we show that increased expression of the adh1AS transcript in zinc-limited cells is necessary for the repression of adh1 gene expression and that the increased level of the adh1AS transcript in zinc-limited cells is a result of two mechanisms. At the transcriptional level, the adh1AS transcript is expressed at a high level in zinc-limited cells. In addition to this transcriptional control, adh1AS transcripts preferentially accumulate in zinc-limited cells when the adh1AS transcript is expressed from a constitutive promoter. This secondary mechanism requires the simultaneous expression of adh1. Our studies reveal how multiple mechanisms can synergistically control the ratio of sense to antisense transcripts and highlight a novel mechanism by which adh1 gene expression can be controlled by cellular zinc availability.
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Affiliation(s)
- Kate M Ehrensberger
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
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49
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Frey AG, Eide DJ. Zinc-responsive coactivator recruitment by the yeast Zap1 transcription factor. Microbiologyopen 2012; 1:105-14. [PMID: 22950018 PMCID: PMC3426420 DOI: 10.1002/mbo3.8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 12/19/2011] [Indexed: 11/11/2022] Open
Abstract
The zinc-responsive Zap1 transcription factor of Saccharomyces cerevisiae controls many genes involved in zinc homeostasis. Zap1 has two activation domains, AD1 and AD2, which are independently regulated by zinc. While AD1 can fully activate most Zap1 target genes, AD2 is active only on a subset of those genes. One hypothesis explaining this promoter specificity was that AD1 and AD2 recruit different coactivators. To address this question, we carried out a genetic screen to identify coactivator complexes that are required for Zap1-mediated activation. SWI/SNF, SAGA, and Mediator complexes were implicated as playing major roles in Zap1 activation. Consistent with this conclusion, we found that these three complexes are recruited to Zap1 target promoters in a zinc-responsive and Zap1-dependent manner. Coactivator recruitment was highly interdependent such that mutations disrupting SAGA impaired recruitment of SWI/SNF and vice versa. Optimal Mediator recruitment was dependent on both SAGA and SWI/SNF. A comparison of the coactivators recruited by AD1 and AD2 found no obvious differences suggesting that recruitment of different coactivators is not likely the mechanism of AD specificity. Rather, our results suggest that AD2 recruits coactivators less effectively than AD1 and is therefore only functional on some promoters.
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Affiliation(s)
- Avery G Frey
- Department of Nutritional Sciences, University of Wisconsin-Madison Madison, Wisconsin
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50
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Zap1 regulates zinc homeostasis and modulates virulence in Cryptococcus gattii. PLoS One 2012; 7:e43773. [PMID: 22916306 PMCID: PMC3423376 DOI: 10.1371/journal.pone.0043773] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 07/25/2012] [Indexed: 11/19/2022] Open
Abstract
Zinc homeostasis is essential for fungal growth, as this metal is a critical structural component of several proteins, including transcription factors. The fungal pathogen Cryptococcus gattii obtains zinc from the stringent zinc-limiting milieu of the host during the infection process. To characterize the zinc metabolism in C. gattii and its relationship to fungal virulence, the zinc finger protein Zap1 was functionally characterized. The C. gattii ZAP1 gene is an ortholog of the master regulatory genes zafA and ZAP1 that are found in Aspergillus fumigatus and Saccharomyces cerevisiae, respectively. There is some evidence to support an association between Zap1 and zinc metabolism in C. gattii: (i) ZAP1 expression is highly induced during zinc deprivation, (ii) ZAP1 knockouts demonstrate impaired growth in zinc-limiting conditions, (iii) Zap1 regulates the expression of ZIP zinc transporters and distinct zinc-binding proteins and (iv) Zap1 regulates the labile pool of intracellular zinc. In addition, the deletion of ZAP1 reduces C. gattii virulence in a murine model of cryptococcosis infection. Based on these observations, we postulate that proper zinc metabolism plays a crucial role in cryptococcal virulence.
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