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Yang Y, Hou J, Luan J. Resistance mechanisms of Saccharomyces cerevisiae against silver nanoparticles with different sizes and coatings. Food Chem Toxicol 2024; 186:114581. [PMID: 38460669 DOI: 10.1016/j.fct.2024.114581] [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: 08/12/2023] [Revised: 01/15/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
To investigate the underlying resistance mechanisms of Saccharomyces cerevisiae against Ag-NPs with different particle sizes and coatings, transcriptome sequencing (RNA-seq) technology was used to characterize the transcriptomes from S. cerevisiae exposed to 20-PVP-Ag, 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag, respectively. The steroid biosynthesis was found as a general pathway for Ag-NPs stress responding, in which ERG6 and ERG3 were inhibited and ERG11, ERG25 and ERG5 were significantly up-regulated to resist the stress by supporting the later mutation and resistance and modulate drug efflux indirectly. The resistance mechanism of S. cerevisiae to 20-PVP-Ag seems different from that of 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag. Under the 20-PVP-Ag, transmembrane transporter activity, transition metal ion homeostasis and oxidative phosphorylation pathway were main resistance pathways to enhance cell transport processes. While 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag mainly impacted RNA binding, structural constituent of ribosome and ribosome pathway which can provide more energy to maintain the number and function of protein in cells. This study reveals the differences in resistance mechanisms of S. cerevisiae to Ag-NPs with different particle sizes and coatings, and explains several main regulatory mechanisms used to respond to silver stress. It will provide theoretical basis for the study of chemical risk assessment.
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Affiliation(s)
- Yue Yang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, PR China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, PR China.
| | - Jian Luan
- College of Life Sciences, Jilin Normal University, Jilin, 136000, PR China
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Huang M, Shen S, Meng Z, Si G, Wu X, Feng T, Liu C, Chen J, Duan C. Mechanisms involved in the sequestration and resistance of cadmium for a plant-associated Pseudomonas strain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115527. [PMID: 37806135 DOI: 10.1016/j.ecoenv.2023.115527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/07/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023]
Abstract
Understanding Cd-resistant bacterial cadmium (Cd) resistance systems is crucial for improving microremediation in Cd-contaminated environments. However, these mechanisms are not fully understood in plant-associated bacteria. In the present study, we investigated the mechanisms underlying Cd sequestration and resistance in the strain AN-B15. These results showed that extracellular Cd sequestration by complexation in strain AN-B15 was primarily responsible for the removal of Cd from the solution. Transcriptome analyses have shown that the mechanisms of Cd resistance at the transcriptional level involve collaborative processes involving multiple metabolic pathways. The AN-B15 strain upregulated the expression of genes related to exopolymeric substance synthesis, metal transport, Fe-S cluster biogenesis, iron recruitment, reactive oxygen species oxidative stress defense, and DNA and protein repair to resist Cd-induced stress. Furthermore, inoculation with AN-B15 alleviated Cd-induced toxicity and reduced Cd uptake in the shoots of wheat seedlings, indicating its potential for remediation. Overall, the results improve our understanding of the mechanisms involved in Cd resistance in bacteria and thus have important implications for improving microremediation.
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Affiliation(s)
- Mingyu Huang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Shili Shen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Zhuang Meng
- School of Agriculture, Yunnan University, Kunming 650091, China
| | - Guangzheng Si
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Xinni Wu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Tingting Feng
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Chang'e Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China
| | - Jinquan Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Changqun Duan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China; School of Agriculture, Yunnan University, Kunming 650091, China.
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Hosseini F, Hadian M, Lashani E, Moghimi H. Simultaneous bioreduction of tellurite and selenite by Yarrowia lipolytica, Trichosporon cutaneum, and their co-culture along with characterization of biosynthesized Te-Se nanoparticles. Microb Cell Fact 2023; 22:193. [PMID: 37749532 PMCID: PMC10519092 DOI: 10.1186/s12934-023-02204-0] [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: 05/24/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Natural and anthropogenic activities, such as weathering of rocks and industrial processes, result in the release of toxic oxyanions such as selenium (Se) and tellurium (Te) into the environment. Due to the high toxicity of these compounds, their removal from the environment is vital. RESULTS In this study, two yeast strains, Yarrowia lipolytica and Trichosporon cutaneum, were selected as the superior strains for the bioremediation of tellurium and selenium. The reduction analyses showed that exposure to selenite induced more detrimental effects on the strains compared to tellurite. In addition, co-reduction of pollutants displayed almost the same results in selenite reduction and more than ~ 20% higher tellurite reduction in 50 h, which shows that selenite triggered higher tellurite reduction in both strains. The selenite and tellurite kinetics of removal were consistent with the first-order model because of their inhibitory behavior. The result of several characterization experiments, such as FE-SEM (Field emission scanning electron microscopy), dynamic light scattering (DLS), Fourier-transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD), and dispersive X-ray (EDX) on Te-Se nanoparticles (NPs) revealed that the separated Te-Se NPs were needle-like, spherical, and amorphous, consisted of Te-Se NPs ranging from 25 to 171 nm in size, and their surface was covered with different biomolecules. CONCLUSIONS Remarkably, this work shows, for the first time, the simultaneous bioreduction of tellurite and selenite and the production of Te-Se NPs using yeast strains, indicating their potential in this area, which may be applied to the nanotechnology industry and environmental remediation.
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Affiliation(s)
- Firooz Hosseini
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Hadian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Elham Lashani
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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Zhang X, Li F, Ji C, Wu H. Toxicological mechanism of cadmium in the clam Ruditapes philippinarum using combined ionomic, metabolomic and transcriptomic analyses. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121286. [PMID: 36791949 DOI: 10.1016/j.envpol.2023.121286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd) contamination in marine environment poses great risks to the organisms due to its potential adverse effects. In the present study, the toxicological effects and mechanisms of Cd at environmentally relevant concentrations (5 and 50 μg/L) on clam Ruditapes philippinarum after 21 days were investigated by combined ionomic, metabolomic, and transcriptomic analyses. Results showed that the uptake of Cd significantly decreased the concentrations of Cu, Zn, Sr, Se, and Mo in the whole soft tissue from 50 μg/L Cd-treated clams. Significantly negative correlations were observed between Cd and essential elements (Zn, Sr, Se, and Mo). Altered essential elements homeostasis was associated with the gene regulation of transport and detoxification, including ATP-binding cassette protein subfamily B member 1 (ABCB1) and metallothioneins (MT). The crucial contribution of Se to Cd detoxification was also found in clams. Additionally, gene set enrichment analysis showed that Cd could interfere with proteolysis by peptidases and decrease the translation efficiency at 50 μg/L. Cd inhibited lipid metabolism in clams and increased energy demand by up-regulating glycolysis and TCA cycle. Osmotic pressure was regulated by free amino acids, including alanine, glutamate, taurine, and homarine. Meanwhile, significant alterations of some differentially expressed genes, such as dopamine-β-hydroxylase (DBH), neuroligin (NLGN), NOTCH 1, and chondroitin sulfate proteoglycan 1 (CSPG1) were observed in clams, which implied potential interference with synaptic transmission. Overall, through integrating multiple omics, this study provided new insights into the toxicological mechanisms of Cd, particularly in those mediated by dysregulation of essential element homeostasis.
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Affiliation(s)
- Xiaoyu Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao, 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao, 266071, PR China.
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Xing D, Magdouli S, Zhang J, Bouafif H, Koubaa A. A Comparative Study on Heavy Metal Removal from CCA-Treated Wood Waste by Yarrowia lipolytica: Effects of Metal Stress. J Fungi (Basel) 2023; 9:jof9040469. [PMID: 37108923 PMCID: PMC10145133 DOI: 10.3390/jof9040469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Bioremediation is an effective way to remove heavy metals from pollutants. This study investigated the effects of Yarrowia lipolytica (Y. lipolytica) on the bioremediation of chromated copper arsenate (CCA)-treated wood wastes. Copper ions stressed the yeast strains to improve their bioremediation efficiency. A comparison of changes in morphology, chemical composition, and metal content of CCA wood before and after bioremediation was conducted. The amount of arsenic (As), chromium (Cr), and copper (Cu) was quantified by microwave plasma atomic emission spectrometer. The results showed that yeast strains remained on the surface of CCA-treated wood after bioremediation. The morphologies of the strains changed from net to spherical because of the Cu2+ stress. Fourier-transform infrared spectroscopy showed that carboxylic acid groups of wood were released after removing heavy metals. A large amount of oxalic acid was observed when the optical density (OD600nm) was 0.05 on the 21st day. Meanwhile, the highest removal rate of Cu, As, and Cr was 82.8%, 68.3%, and 43.1%, respectively. Furthermore, the Cu removal from CCA-treated wood increased by about 20% after Cu2+ stress. This study showed that it is feasible to remove heavy metals from CCA-treated wood by Y. lipolytica without destroying the wood structure, especially by copper-induced Y. lipolytica.
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Affiliation(s)
- Dan Xing
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC J9X 5E4, Canada
| | - Sara Magdouli
- Lassonde School of Engineering, York University, Toronto, ON M3J 1P3, Canada
| | - Jingfa Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Hassine Bouafif
- Centre Technologique des Résidus Industriels en Abitibi Témiscamingue, 433 Boulevard du Collège, Rouyn-Noranda, QC J9X 0E1, Canada
| | - Ahmed Koubaa
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC J9X 5E4, Canada
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Mashabela MD, Masamba P, Kappo AP. Applications of Metabolomics for the Elucidation of Abiotic Stress Tolerance in Plants: A Special Focus on Osmotic Stress and Heavy Metal Toxicity. PLANTS (BASEL, SWITZERLAND) 2023; 12:269. [PMID: 36678982 PMCID: PMC9860948 DOI: 10.3390/plants12020269] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Plants undergo metabolic perturbations under various abiotic stress conditions; due to their sessile nature, the metabolic network of plants requires continuous reconfigurations in response to environmental stimuli to maintain homeostasis and combat stress. The comprehensive analysis of these metabolic features will thus give an overview of plant metabolic responses and strategies applied to mitigate the deleterious effects of stress conditions at a biochemical level. In recent years, the adoption of metabolomics studies has gained significant attention due to the growing technological advances in analytical biochemistry (plant metabolomics). The complexity of the plant biochemical landscape requires sophisticated, advanced analytical methods. As such, technological advancements in the field of metabolomics have been realized, aided much by the development and refinement of separatory techniques, including liquid and gas chromatography (LC and GC), often hyphenated to state-of-the-art detection instruments such as mass spectrometry (MS) or nuclear resonance magnetic (NMR) spectroscopy. Significant advances and developments in these techniques are briefly highlighted in this review. The enormous progress made thus far also comes with the dawn of the Internet of Things (IoT) and technology housed in machine learning (ML)-based computational tools for data acquisition, mining, and analysis in the 4IR era allowing for broader metabolic coverage and biological interpretation of the cellular status of plants under varying environmental conditions. Thus, scientists can paint a holistic and comprehensive roadmap and predictive models for metabolite-guided crop improvement. The current review outlines the application of metabolomics and related technological advances in elucidating plant responses to abiotic stress, mainly focusing on heavy metal toxicity and subsequent osmotic stress tolerance.
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Sánchez-Rojas T, Espinoza-Culupú A, Ramírez P, Iwai LK, Montoni F, Macedo-Prada D, Sulca-López M, Durán Y, Farfán-López M, Herencia J. Proteomic Study of Response to Copper, Cadmium, and Chrome Ion Stress in Yarrowia lipolytica Strains Isolated from Andean Mine Tailings in Peru. Microorganisms 2022; 10:microorganisms10102002. [PMID: 36296278 PMCID: PMC9611812 DOI: 10.3390/microorganisms10102002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/22/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Mine tailings are produced by mining activities and contain diverse heavy metal ions, which cause environmental problems and have negative impacts on ecosystems. Different microorganisms, including yeasts, play important roles in the absorption and/or adsorption of these heavy metal ions. This work aimed to analyze proteins synthesized by the yeast Yarrowia lipolytica AMJ6 (Yl-AMJ6), isolated from Andean mine tailings in Peru and subjected to stress conditions with common heavy metal ions. Yeast strains were isolated from high Andean water samples impacted by mine tailings from Yanamate (Pasco, Peru). Among all the isolated yeasts, the Yl-AMJ6 strain presented LC50 values of 1.06 mM, 1.42 mM, and 0.49 mM for the Cr+6, Cu+2, and Cd+2 ions, respectively. Proteomic analysis of theYl-AMJ6 strain under heavy metal stress showed that several proteins were up- or downregulated. Biological and functional analysis of these proteins showed that they were involved in the metabolism of proteins, nucleic acids, and carbohydrates; response to oxidative stress and protein folding; ATP synthesis and ion transport; membrane and cell wall; and cell division. The most prominent proteins that presented the greatest changes were related to the oxidative stress response and carbohydrate metabolism, suggesting the existence of a defense mechanism in these yeasts to resist the impact of environmental contamination by heavy metal ions.
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Affiliation(s)
- Tito Sánchez-Rojas
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
- Correspondence: (T.S.-R.); (A.E.-C.)
| | - Abraham Espinoza-Culupú
- Laboratory Research on Health Science, Universidad Señor de Sipán, Chiclayo 14001, Peru
- Correspondence: (T.S.-R.); (A.E.-C.)
| | - Pablo Ramírez
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Leo Kei Iwai
- Laboratory for Applied Toxinology Center of Toxins, Immune-Response and Cell Signaling (LETA/CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Fabio Montoni
- Laboratory for Applied Toxinology Center of Toxins, Immune-Response and Cell Signaling (LETA/CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Diego Macedo-Prada
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Marcos Sulca-López
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Yerson Durán
- Laboratory of Environmental Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Mariella Farfán-López
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Jennifer Herencia
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
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Regulation of heme utilization and homeostasis in Candida albicans. PLoS Genet 2022; 18:e1010390. [PMID: 36084128 PMCID: PMC9491583 DOI: 10.1371/journal.pgen.1010390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/21/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Heme (iron-protoporphyrin IX) is an essential but potentially toxic cellular cofactor. While most organisms are heme prototrophs, many microorganisms can utilize environmental heme as iron source. The pathogenic yeast Candida albicans can utilize host heme in the iron-poor host environment, using an extracellular cascade of soluble and anchored hemophores, and plasma membrane ferric reductase-like proteins. To gain additional insight into the C. albicans heme uptake pathway, we performed an unbiased genetic selection for mutants resistant to the toxic heme analog Ga3+-protoporphyrin IX at neutral pH, and a secondary screen for inability to utilize heme as iron source. Among the mutants isolated were the genes of the pH-responsive RIM pathway, and a zinc finger transcription factor related to S. cerevisiae HAP1. In the presence of hemin in the medium, C. albicans HAP1 is induced, the Hap1 protein is stabilized and Hap1-GFP localizes to the nucleus. In the hap1 mutant, cytoplasmic heme levels are elevated, while influx of extracellular heme is lower. Gene expression analysis indicated that in the presence of extracellular hemin, Hap1 activates the heme oxygenase HMX1, which breaks down excess cytoplasmic heme, while at the same time it also activates all the known heme uptake genes. These results indicate that Hap1 is a heme-responsive transcription factor that plays a role both in cytoplasmic heme homeostasis and in utilization of extracellular heme. The induction of heme uptake genes by C. albicans Hap1 under iron satiety indicates that preferential utilization of host heme can be a dietary strategy in a heme prototroph. The yeast Candida albicans is a human commensal organism, as well as an important opportunistic systemic pathogen. During tissue invasion, systemic pathogens are confronted with iron scarcity, which they can overcome by scavenging host heme as iron source. It was however not known whether C. albicans can sense the presence of host heme independently of iron sensing. Using a forward genetics approach, we identified a transcription factor that regulates both homeostasis of internal heme and uptake of external heme. This transcription factor allows activation of the heme uptake pathway even in iron-rich medium, suggesting that heme can be a preferred iron source over elemental iron, and that heme prototrophs can scavenge host heme as a source for cellular heme.
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Chen H, Zheng Y, Wang M, Wu Y, Yao M. Gene-Regulated Release of Distinctive Volatile Organic Compounds from Stressed Living Cells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9546-9555. [PMID: 35729728 DOI: 10.1021/acs.est.2c01774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Breath-borne volatile organic compounds (VOCs) have been increasingly studied as non-invasive biomarkers in both medical diagnosis and environmental health research. Recently, changes in breath-borne VOC fingerprints were demonstrated in rats and humans following pollutant exposures. In this study, the eukaryotic model Saccharomyces cerevisiae was used to study the release of cellular VOCs resulting from toxicant exposures (i.e., O3, H2O2, and CO2) and its underlying biological mechanism. Our results showed that different toxicant exposures caused the release of distinctive VOC profiles of yeast cells. The levels of ethyl acetate and ethyl n-propionate were altered in response to all the toxicants used in this study and could thus be targeted for future environmental toxicity monitoring. The RNA-seq results revealed significant changes in the metabolic or signaling pathways related to the ribosome, carbohydrate, and amino acid metabolisms after exposures. Notably, the shift from glycolysis to the pentose phosphate pathway of carbohydrate metabolism and the inhabitation of the aspartate pathway in the lysine synthesis was essential to the cellular antioxidation by providing reduced nicotinamide adenine dinucleotide phosphate (NADPH). The reprogrammed metabolisms could have resulted in the observed changes of VOCs released, e.g., the production of ethyl acetate for detoxification from yeast cells. This study provides further evidence that VOCs released from living organisms could be used to monitor and guard against toxic exposures while providing better mechanistic insights of the changes in breath-borne VOCs previously observed in rats and humans exposed to air toxicants.
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Affiliation(s)
- Haoxuan Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yunhao Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yan Wu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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Qin W, Stärk HJ, Müller S, Reemtsma T. Exploring the Extent of Phosphorus and Heavy Metal Uptake by Single Cells of Saccharomyces cerevisiae and Their Effects on Intrinsic Elements by SC-ICP-TOF-MS. Front Microbiol 2022; 13:870931. [PMID: 35547146 PMCID: PMC9082303 DOI: 10.3389/fmicb.2022.870931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The effect of six heavy metals, namely, silver (Ag), lead (Pb), palladium (Pd), copper (Cu), nickel (Ni), and chromium (Cr), on phosphorus (P) uptake by yeast was investigated by single-cell analysis using inductively coupled plasma time-of-flight mass spectrometry (SC-ICP-TOF-MS). It was found that the P content in cells with 1.55 g L–1 P feeding after P starvation was increased by ∼70% compared to control cells. Heavy metals at 10 ppm, except Cu, had a negative impact on P accumulation by cells. Pd reduced the P content by 26% in single cells compared to control cells. Metal uptake was strongest for Ag and Pd (0.7 × 10–12 L cell–1) and weakest for Cr (0.05 × 10–12 L cell–1). Exposure to Cr markedly reduced (−50%) Mg in cells and had the greatest impact on the intrinsic element composition. The SC-ICP-TOF-MS shows the diversity of elemental content in single cells: for example, the P content under standard conditions varied between 12.4 and 890 fg cell–1. This technique allows studying both the uptake of elements and sublethal effects on physiology at a single-cell level.
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Affiliation(s)
- Wen Qin
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
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11
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Halloum I, Al-Attrache H, El-Ghoz K, Hammoud L, Abdel-Razzak Z. Dose-dependent interaction of two heavy metals with amiodarone toxicity in Saccharomyces cerevisiae. Toxicol Ind Health 2022; 38:249-258. [PMID: 35513769 DOI: 10.1177/07482337221088354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Amiodarone (AMD) is an antiarrhythmic drug that induces idiosyncratic toxicity. Environmental pollutants, including heavy metals, could interact with its toxicity by affecting pharmacokinetics and pharmacodynamics. Other levels of interaction could exist in yeast, such as oxidative stress and the general stress response. In this study, we investigated the interaction of mercury chloride (HgCl2) and cadmium chloride (CdCl2) with AMD toxicity on Saccharomyces cerevisiae. Interaction type - synergistic, additive, or antagonistic - was determined by median drug effect analysis using "CompuSyn". HgCl2 potentiated AMD toxicity at high doses (≥ 71.4 μm, which yielded more than 60% inhibition). CdCl2 acted similarly at high doses (≥ 57.9 μm). An antagonistic effect appeared at lower doses with both heavy metals (≤ 49.4 μm for HgCl2 and AMD; ≤ 18.9 μm for CdCl2 and AMD). The threshold concentrations (HgCl2 or CdCl2 combined with AMD) that switched the interaction from antagonistic to additive, and then to synergistic, were decreased in the yeast strain mutant in catalase (CTT1), suggesting an important role for this enzyme. Moreover, mutation of the nutrient sensing receptor gene GPR1 caused the synergistic interaction of CdCl2, but not HgCl2, with AMD to occur at the lowest tested concentrations (1.2 μm). The reverse was obtained with the mutant strain in calcium-manganese transporter gene PMR1, where the synergistic interaction of HgCl2 with AMD occurred at concentrations (20.7 μm) lower than that of the wild type (71.4 μm). These results demonstrated a dose-dependent interaction between the two heavy metals with AMD toxicity, and the involvement of oxidative stress, calcium homeostasis, and nutrient sensing in the observed interaction.
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Affiliation(s)
- Iman Halloum
- 63572Lebanese University, FS1, Rafic Hariri Campus, Beirut. Lebanon
| | - Houssein Al-Attrache
- 63572Lebanese University, FS1, Rafic Hariri Campus, Beirut. Lebanon.,Faculty of Sciences, Section III, 63572Lebanese University, Tripoli, Lebanon.,Faculty of Public Health, Section IV, 63572Lebanese University, Zahleh, Lebanon
| | - Katia El-Ghoz
- 63572Lebanese University, FS1, Rafic Hariri Campus, Beirut. Lebanon
| | - Lara Hammoud
- Faculty of Sciences, Section III, 63572Lebanese University, Tripoli, Lebanon
| | - Ziad Abdel-Razzak
- 63572Lebanese University, FS1, Rafic Hariri Campus, Beirut. Lebanon.,EDST, AZM biotechnology research center, LBA3B, Tripoli, Lebanon
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12
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Grosjean N, Le Jean M, Armengaud J, Schikora A, Chalot M, Gross EM, Blaudez D. Combined omics approaches reveal distinct responses between light and heavy rare earth elements in Saccharomyces cerevisiae. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127830. [PMID: 34896703 DOI: 10.1016/j.jhazmat.2021.127830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The rapid development of green energy sources and new medical technologies contributes to the increased exploitation of rare earth elements (REEs). They can be subdivided into light (LREEs) and heavy (HREEs) REEs. Mining, industrial processing, and end-use practices of REEs has led to elevated environmental concentrations and raises concerns about their toxicity to organisms and their impact on ecosystems. REE toxicity has been reported, but its precise underlying molecular effects have not been well described. Here, transcriptomic and proteomic approaches were combined to decipher the molecular responses of the model organism Saccharomyces cerevisiae to La (LREE) and Yb (HREE). Differences were observed between the early and late responses to La and Yb. Several crucial pathways were modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and pheromone signalling pathways were identified, and these responses have not been reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, with strong discrepancies between La and Yb. These findings are valuable for prioritizing key genes and proteins involved in La and Yb detoxification mechanisms that deserve further characterization to better understand REE environmental and human health toxicity.
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Affiliation(s)
- Nicolas Grosjean
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France; Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Marie Le Jean
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, D-38104 Braunschweig, Germany
| | - Michel Chalot
- Université de Bourgogne Franche-Comté, CNRS, Laboratoire Chrono-Environnement, F-25000 Besançon, France; Université de Lorraine, F-54000 Nancy, France
| | | | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France.
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13
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Mediator dynamics during heat shock in budding yeast. Genome Res 2021; 32:111-123. [PMID: 34785526 PMCID: PMC8744673 DOI: 10.1101/gr.275750.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/13/2021] [Indexed: 11/25/2022]
Abstract
The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy shows similar dependence on Mediator under normal and heat shock conditions. However, although Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Unexpectedly, Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1Δ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.
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14
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Rico-Díaz A, Barreiro-Alonso A, Rey-Souto C, Becerra M, Lamas-Maceiras M, Cerdán ME, Vizoso-Vázquez Á. The HMGB Protein KlIxr1, a DNA Binding Regulator of Kluyveromyces lactis Gene Expression Involved in Oxidative Metabolism, Growth, and dNTP Synthesis. Biomolecules 2021; 11:biom11091392. [PMID: 34572607 PMCID: PMC8465852 DOI: 10.3390/biom11091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
In the traditional fermentative model yeast Saccharomyces cerevisiae, ScIxr1 is an HMGB (High Mobility Group box B) protein that has been considered as an important regulator of gene transcription in response to external changes like oxygen, carbon source, or nutrient availability. Kluyveromyces lactis is also a useful eukaryotic model, more similar to many human cells due to its respiratory metabolism. We cloned and functionally characterized by different methodologies KlIXR1, which encodes a protein with only 34.4% amino acid sequence similarity to ScIxr1. Our data indicate that both proteins share common functions, including their involvement in the response to hypoxia or oxidative stress induced by hydrogen peroxide or metal treatments, as well as in the control of key regulators for maintenance of the dNTP (deoxyribonucleotide triphosphate) pool and ribosome synthesis. KlIxr1 is able to bind specific regulatory DNA sequences in the promoter of its target genes, which are well conserved between S. cerevisiae and K. lactis. Oppositely, we found important differences between ScIrx1 and KlIxr1 affecting cellular responses to cisplatin or cycloheximide in these yeasts, which could be dependent on specific and non-conserved domains present in these two proteins.
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15
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Chaturvedi S, Sadaf A, Bhattacharya A, Rout PK, Nain L, Khare SK. Environment‐Friendly Synergistic Abiotic Stress for Enhancing the Yield of Lipids from Oleaginous Yeasts. EUR J LIPID SCI TECH 2021. [DOI: 10.1002/ejlt.202000376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shivani Chaturvedi
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Ayesha Sadaf
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Prasant Kumar Rout
- Phytochemistry Division CSIR‐Central Institute of medicinal and Aromatic Plants Lucknow Uttar Pradesh 226015 India
| | - Lata Nain
- Division of Microbiology ICAR‐Indian Agricultural Research Institute New Delhi 110014 India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory Department of Chemistry Indian Institute of Technology New Delhi 110016 India
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16
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Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Res 2021; 49:7925-7938. [PMID: 34255854 PMCID: PMC8373080 DOI: 10.1093/nar/gkab553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/25/2023] Open
Abstract
Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. In contrast, epigenomic accessibility data like MNase-seq, DNase-seq, and ATAC-seq provide insight into the chromatin landscape of all factors bound along the genome, but with little insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin accessibility data with nucleotide sequence to jointly compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors. We apply RoboCOP to MNase-seq and ATAC-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome, and show that our model makes better predictions than existing methods. We also compute a chromatin occupancy profile of the yeast genome under cadmium stress, revealing chromatin dynamics associated with transcriptional regulation.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Trung Q Tran
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA.,Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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17
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Rumbo C, Espina CC, Gassmann J, Tosoni O, Barros García R, Martín SM, Tamayo-Ramos JA. In vitro safety evaluation of rare earth-lean alloys for permanent magnets manufacturing. Sci Rep 2021; 11:12633. [PMID: 34135388 PMCID: PMC8209147 DOI: 10.1038/s41598-021-91890-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/02/2021] [Indexed: 12/02/2022] Open
Abstract
Due to their exceptional physico-chemical and magnetic characteristics, rare earth (RE) permanent magnets are applied in multiple critical technologies. However, several environmental and economic difficulties arising from obtaining RE elements have prompted the search of alternatives with acceptable magnetic properties but containing a lower percentage of these elements in their composition. The aim of this work was to perform a preliminary toxicological evaluation of three forms of newly developed RE-lean alloys (one NdFeTi and two NdFeSi alloys) applying different in vitro assays, using as a benchmark a commercial NdFeB alloy. Thus, the effects of the direct exposure to powder suspensions and to their derived leachates were analysed in two model organisms (the A549 human cell line and the yeast Saccharomyces cerevisiae) applying both viability and oxidative stress assays. Moreover, the impact of the alloy leachates on the bioluminescence of Vibrio fischeri was also investigated. The obtained data showed that only the direct interaction of the alloys particulates with the applied organisms resulted in harmful effects, having all the alloys a comparable toxicological potential to that presented by the reference material in the conditions tested. Altogether, this study provides new insights about the safety of NdFeTi and NdFeSi alloys.
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Affiliation(s)
- Carlos Rumbo
- International Research Center in Critical Raw Materials-ICCRAM, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
| | - Cristina Cancho Espina
- International Research Center in Critical Raw Materials-ICCRAM, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - Jürgen Gassmann
- Fraunhofer Research Institution for Materials Recycling and Resource Strategies IWKS, Aschaffenburger Straße 121, 63457, Hanau, Germany
| | | | - Rocío Barros García
- International Research Center in Critical Raw Materials-ICCRAM, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - Sonia Martel Martín
- International Research Center in Critical Raw Materials-ICCRAM, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials-ICCRAM, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain.
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18
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Horstmann C, Davenport V, Zhang M, Peters A, Kim K. Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review. Genes (Basel) 2021; 12:genes12060794. [PMID: 34070957 PMCID: PMC8224664 DOI: 10.3390/genes12060794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.
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Affiliation(s)
- Cullen Horstmann
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (V.D.); (M.Z.); (A.P.)
- Jordan Valley Innovation Center, Missouri State University, 542 N Boonville, Springfield, MO 65806, USA
| | - Victoria Davenport
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (V.D.); (M.Z.); (A.P.)
- Jordan Valley Innovation Center, Missouri State University, 542 N Boonville, Springfield, MO 65806, USA
| | - Min Zhang
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (V.D.); (M.Z.); (A.P.)
- Jordan Valley Innovation Center, Missouri State University, 542 N Boonville, Springfield, MO 65806, USA
| | - Alyse Peters
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (V.D.); (M.Z.); (A.P.)
- Jordan Valley Innovation Center, Missouri State University, 542 N Boonville, Springfield, MO 65806, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (V.D.); (M.Z.); (A.P.)
- Correspondence:
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19
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Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res 2021; 31:1035-1046. [PMID: 33893157 PMCID: PMC8168580 DOI: 10.1101/gr.267237.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins—including histones, transcription factors (TFs), and polymerases—interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. Whereas gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA-binding factors. Using these signatures, we identified associations between chromatin dynamics and transcriptional regulation, not only for known cadmium response genes, but across the entire genome, including antisense transcripts. Those associations allowed us to develop generalizable models that predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.
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Affiliation(s)
- Trung Q Tran
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Vinay Tripuraneni
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sneha Mitra
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
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20
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Robinson JR, Isikhuemhen OS, Anike FN. Fungal-Metal Interactions: A Review of Toxicity and Homeostasis. J Fungi (Basel) 2021; 7:225. [PMID: 33803838 PMCID: PMC8003315 DOI: 10.3390/jof7030225] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
Metal nanoparticles used as antifungals have increased the occurrence of fungal-metal interactions. However, there is a lack of knowledge about how these interactions cause genomic and physiological changes, which can produce fungal superbugs. Despite interest in these interactions, there is limited understanding of resistance mechanisms in most fungi studied until now. We highlight the current knowledge of fungal homeostasis of zinc, copper, iron, manganese, and silver to comprehensively examine associated mechanisms of resistance. Such mechanisms have been widely studied in Saccharomyces cerevisiae, but limited reports exist in filamentous fungi, though they are frequently the subject of nanoparticle biosynthesis and targets of antifungal metals. In most cases, microarray analyses uncovered resistance mechanisms as a response to metal exposure. In yeast, metal resistance is mainly due to the down-regulation of metal ion importers, utilization of metallothionein and metallothionein-like structures, and ion sequestration to the vacuole. In contrast, metal resistance in filamentous fungi heavily relies upon cellular ion export. However, there are instances of resistance that utilized vacuole sequestration, ion metallothionein, and chelator binding, deleting a metal ion importer, and ion storage in hyphal cell walls. In general, resistance to zinc, copper, iron, and manganese is extensively reported in yeast and partially known in filamentous fungi; and silver resistance lacks comprehensive understanding in both.
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Affiliation(s)
| | - Omoanghe S. Isikhuemhen
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, 1601 East Market Street, Greensboro, NC 27411, USA; (J.R.R.); (F.N.A.)
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21
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Čanadi Jurešić G, Ćurko-Cofek B, Barbarić M, Mumiši N, Blagović B, Jamnik P. Response of Saccharomyces cerevisiae W303 to Iron and Lead Toxicity in Overloaded Conditions. Curr Microbiol 2021; 78:1188-1201. [PMID: 33624192 DOI: 10.1007/s00284-021-02390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/07/2021] [Indexed: 11/29/2022]
Abstract
Yeast Saccharomyces cerevisiae is an ideal model organism for studying molecular mechanisms of the stress response provoked by metals. In this work, yeast cells response to iron (Fe3+) or lead (Pb2+) exposure was tested and compared. Survival test was used to determine testing doses of metal ions-for Fe3+ it was 4 mM and for Pb2+ 8 mM. These (high, over-loaded) doses provoked comparable values of growth inhibition, but different values in vitality measurement. The percentage of metabolically active cells, determined by fluorescent FUN-1 dye, was lower in Pb2+ than in Fe3+ treated cells. Besides, endogenous antioxidant defence systems in the cells treated with Pb2+ were less efficient compared to Fe3+. At the mitochondrial level, the effects of metal ions were in correlation with the results of cell metabolic activity. The mitochondrial proteome of Pb2+ treated cells showed the domination of protein downregulation. Yeast cells treated either with Fe3+ or Pb2+ shared 19 common significantly changed proteins. The affected proteins were involved in different cellular process and amongst them only five proteins belong to energy and carbohydrate metabolism, and protein biosynthesis. Based on all obtained results, it is possible to conclude that the effects of Fe3+ and Pb2+ on yeast cells show rather specific patterns of toxicity and stress response.
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Affiliation(s)
- Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000, Rijeka, Croatia.
| | - Božena Ćurko-Cofek
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000, Rijeka, Croatia
| | - Martina Barbarić
- Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000, Rijeka, Croatia
| | - Nermina Mumiši
- Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000, Rijeka, Croatia
| | - Branka Blagović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000, Rijeka, Croatia
| | - Polona Jamnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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22
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De Oliveira VH, Ullah I, Dunwell JM, Tibbett M. Bioremediation potential of Cd by transgenic yeast expressing a metallothionein gene from Populus trichocarpa. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110917. [PMID: 32800252 DOI: 10.1016/j.ecoenv.2020.110917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Cadmium (Cd) is an extremely toxic environmental pollutant with high mobility in soils, which can contaminate groundwater, increasing its risk of entering the food chain. Yeast biosorption can be a low-cost and effective method for removing Cd from contaminated aqueous solutions. We transformed wild-type Saccharomyces cerevisiae (WT) with two versions of a Populus trichocarpa gene (PtMT2b) coding for a metallothionein: one with the original sequence (PtMT2b 'C') and the other with a mutated sequence, with an amino acid substitution (C3Y, named here: PtMT2b 'Y'). WT and both transformed yeasts were grown under Cd stress, in agar (0; 10; 20; 50 μM Cd) and liquid medium (0; 10; 20 μM Cd). Yeast growth was assessed visually and by spectrometry OD600. Cd removal from contaminated media and intracellular accumulation were also quantified. PtMT2b 'Y' was also inserted into mutant strains: fet3fet4, zrt1zrt2 and smf1, and grown under Fe-, Zn- and Mn-deficient media, respectively. Yeast strains had similar growth under 0 μM, but differed under 20 μM Cd, the order of tolerance was: WT < PtMT2b 'C' < PtMT2b 'Y', the latter presenting 37% higher growth than the strain with PtMT2b 'C'. It also extracted ~80% of the Cd in solution, and had higher intracellular Cd than WT. Mutant yeasts carrying PtMT2b 'Y' had slightly higher growth in Mn- and Fe-deficient media than their non-transgenic counterparts, suggesting the transgenic protein may chelate these metals. S. cerevisiae carrying the altered poplar gene offers potential for bioremediation of Cd from wastewaters or other contaminated liquids.
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Affiliation(s)
- Vinicius Henrique De Oliveira
- Department of Sustainable Land Management & Soil Research Centre, School of Agricultura, Policy and Development, University of Reading, RG6 6AR, UK
| | - Ihsan Ullah
- School of Agriculture, Policy and Development, University of Reading, RG6 6AR, UK
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, RG6 6AR, UK
| | - Mark Tibbett
- Department of Sustainable Land Management & Soil Research Centre, School of Agricultura, Policy and Development, University of Reading, RG6 6AR, UK.
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23
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Shi HB, Chen N, Zhu XM, Su ZZ, Wang JY, Lu JP, Liu XH, Lin FC. The casein kinase MoYck1 regulates development, autophagy, and virulence in the rice blast fungus. Virulence 2020; 10:719-733. [PMID: 31392921 PMCID: PMC8647852 DOI: 10.1080/21505594.2019.1649588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Casein kinases are serine/threonine protein kinases that are evolutionarily conserved in yeast and humans and are involved in a range of important cellular processes. However, the biological functions of casein kinases in the fungus Magnaporthe oryzae, the causal agent of destructive rice blast disease, are not characterized. Here, two casein kinases, MoYCK1 and MoHRR25, were identified and targeted for replacement, but only MoYCK1 was further characterized due to the possible nonviability of the MoHRR25 deletion mutant. Disruption of MoYCK1 caused pleiotropic defects in growth, conidiation, conidial germination, and appressorium formation and penetration, therefore resulting in reduced virulence in rice seedlings and barley leaves. Notably, the MoYCK1 deletion triggered quick lipidation of MoAtg8 and degradation of the autophagic marker protein GFP-MoAtg8 under nitrogen starvation conditions, in contrast to the wild type, indicating that autophagy activity was negatively regulated by MoYck1. Furthermore, we found that HOPS (homotypic fusion and vacuolar protein sorting) subunit MoVps41, a putative substrate of MoYck1, was co-located with MoAtg8 and positively required for the degradation of MoAtg8-PE and GFP-MoAtg8. In addition, MoYCK1 is also involved in the response to ionic hyperosmotic and heavy metal cation stresses. Taken together, our results revealed crucial roles of the casein kinase MoYck1 in regulating development, autophagy and virulence in M. oryzae.
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Affiliation(s)
- Huan-Bin Shi
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China.,b State Key Laboratory of Rice Biology, China National Rice Research Institute , Hangzhou , China
| | - Nan Chen
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China
| | - Xue-Ming Zhu
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China
| | - Zhen-Zhu Su
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China
| | - Jiao-Yu Wang
- c State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Science , Hangzhou , China
| | - Jian-Ping Lu
- d College of Life Sciences, Zhejiang University , Hangzhou , China
| | - Xiao-Hong Liu
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China
| | - Fu-Cheng Lin
- a State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University , Hangzhou , China
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Paesano L, Marmiroli M, Bianchi MG, White JC, Bussolati O, Zappettini A, Villani M, Marmiroli N. Differences in toxicity, mitochondrial function and miRNome in human cells exposed in vitro to Cd as CdS quantum dots or ionic Cd. JOURNAL OF HAZARDOUS MATERIALS 2020; 393:122430. [PMID: 32155524 DOI: 10.1016/j.jhazmat.2020.122430] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Cadmium is toxic to humans, although Cd-based quantum dots exerts less toxicity. Human hepatocellular carcinoma cells (HepG2) and macrophages (THP-1) were exposed to ionic Cd, Cd(II), and cadmium sulfide quantum dots (CdS QDs), and cell viability, cell integrity, Cd accumulation, mitochondrial function and miRNome profile were evaluated. Cell-type and Cd form-specific responses were found: CdS QDs affected cell viability more in HepG2 than in THP-1; respective IC20 values were ∼3 and ∼50 μg ml-1. In both cell types, Cd(II) exerted greater effects on viability. Mitochondrial membrane function in HepG2 cells was reduced 70 % with 40 μg ml-1 CdS QDs but was totally inhibited by Cd(II) at corresponding amounts. In THP-1 cells, CdS QDs has less effect on mitochondrial function; 50 μg ml-1 CdS QDs or equivalent Cd(II) caused 30 % reduction or total inhibition, respectively. The different in vitro effects of CdS QDs were unrelated to Cd uptake, which was greater in THP-1 cells. For both cell types, changes in the expression of miRNAs (miR-222, miR-181a, miR-142-3p, miR-15) were found with CdS QDs, which may be used as biomarkers of hazard nanomaterial exposure. The cell-specific miRNome profiles were indicative of a more conservative autophagic response in THP-1 and as apoptosis as in HepG2.
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Affiliation(s)
- Laura Paesano
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Marta Marmiroli
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Massimiliano G Bianchi
- University of Parma, Department of Medicine and Surgery, Laboratory of General Pathology, Via Volturno 39, 43125 Parma, Italy
| | - Jason C White
- Department of Analytical Chemistry, The Connecticut Agricultural Experiment Station (CAES), New Haven, CT 06504, United States
| | - Ovidio Bussolati
- University of Parma, Department of Medicine and Surgery, Laboratory of General Pathology, Via Volturno 39, 43125 Parma, Italy
| | - Andrea Zappettini
- Institute of Materials for Electronics and Magnetism (IMEM-CNR), Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Marco Villani
- Institute of Materials for Electronics and Magnetism (IMEM-CNR), Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 11/A, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze 93/A, 43124 Parma, Italy.
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25
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Stultz LK, Hunsucker A, Middleton S, Grovenstein E, O'Leary J, Blatt E, Miller M, Mobley J, Hanson PK. Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. Metallomics 2020; 12:876-890. [PMID: 32329475 PMCID: PMC7362344 DOI: 10.1039/d0mt00008f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Like platinum-based chemotherapeutics, the anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(iii)], or KP1019, damages DNA, induces apoptosis, and causes tumor regression in animal models. Unlike platinum-based drugs, KP1019 showed no dose-limiting toxicity in a phase I clinical trial. Despite these advances, the mechanism(s) and target(s) of KP1019 remain unclear. For example, the drug may damage DNA directly or by causing oxidative stress. Likewise, KP1019 binds cytosolic proteins, suggesting DNA is not the sole target. Here we use the budding yeast Saccharomyces cerevisiae as a model in a proteomic study of the cellular response to KP1019. Mapping protein level changes onto metabolic pathways revealed patterns consistent with elevated synthesis and/or cycling of the antioxidant glutathione, suggesting KP1019 induces oxidative stress. This result was supported by increased fluorescence of the redox-sensitive dye DCFH-DA and increased KP1019 sensitivity of yeast lacking Yap1, a master regulator of the oxidative stress response. In addition to oxidative and DNA stress, bioinformatic analysis revealed drug-dependent increases in proteins involved ribosome biogenesis, translation, and protein (re)folding. Consistent with proteotoxic effects, KP1019 increased expression of a heat-shock element (HSE) lacZ reporter. KP1019 pre-treatment also sensitized yeast to oxaliplatin, paralleling prior research showing that cancer cell lines with elevated levels of translation machinery are hypersensitive to oxaliplatin. Combined, these data suggest that one of KP1019's many targets may be protein metabolism, which opens up intriguing possibilities for combination therapy.
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Affiliation(s)
- Laura K Stultz
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Alexandra Hunsucker
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Sydney Middleton
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Evan Grovenstein
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Jacob O'Leary
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Eliot Blatt
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Mary Miller
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, School of Medicine, Birmingham, AL 35294, USA
| | - Pamela K Hanson
- Department of Biology, Furman University, Greenville, SC 29613, USA.
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26
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Nguyen KCT, Nguyen PV, Truong HTH. Heavy Metal Tolerance of Novel Papiliotrema Yeast Isolated from Vietnamese Mangosteen. MYCOBIOLOGY 2020; 48:296-303. [PMID: 32952412 PMCID: PMC7476527 DOI: 10.1080/12298093.2020.1767020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Three yeast strains (Hue-1, Hue-8, and Hue-19) with strong heavy metal tolerance were isolated from mangosteen from Hue city, Vietnam. They exhibited identical phenotype and phylogeny. Sequence analysis of the D1/D2 region of the LSU rRNA gene and the internal transcribed spacer (ITS) region demonstrated that the closest relative of these strains is Papiliotrema sp. with 2.12% and 3.55-3.7% divergence in the D1/D2 domain, and ITS domain, respectively. Based on the physiological, biochemical, and molecular data, the three strains belong to a novel species of Papiliotrema genus, for which the name Papiliotrema huenov sp. nov. is proposed. These strains are highly tolerant of heavy metals compared to other yeasts, being able to grow in the presence of 2 mM Pb (II), 2 mM Cd (II), and up to 5 mM Ni (II), but no growth was observed in the presence of 1 mM As (III).
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Affiliation(s)
| | - Phu Van Nguyen
- Faculty of Science, Charles
University, Prague, Czech Republic
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27
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Harnessing the Residual Nutrients in Anaerobic Digestate for Ethanol Fermentation and Digestate Remediation Using Saccharomyces cerevisiae. FERMENTATION 2020. [DOI: 10.3390/fermentation6020052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study evaluated the feasibility of concomitant nutrient removal, cleaner water recovery, and improved ethanol production via glucose fermentation in the liquid fraction of anaerobic digestate (ADE) by Saccharomyces cerevisiae. The 25%, 50%, and 100% (v/v) ADE supported the growth of S. cerevisiae, glucose utilization (~100 g/L) and ethanol production (up to 50.4 ± 6.4 g/L). After a 144 h fermentation in the 50% ADE, the concentrations of ammonia, total nitrogen, phosphate, and total phosphorus decreased 1000-, 104.43-, 1.94-, and 2.20-fold, respectively. Notably, only 0.40 ± 0.61 mg/L ammonia was detected in the 50% ADE post-fermentation. Similarly, the concentrations of aluminum, copper, magnesium, manganese, molybdenum, potassium, sodium, iron, sulfur, zinc, chloride, and sulfate decreased significantly in the ADE. Further analysis suggests that the nitrogen (ammonia and protein), phosphate, and the metal contents of the digestate work in tandem to promote growth and ethanol production. Among these, ammonia and protein appear to exert considerable effects on S. cerevisiae. These results represent a significant first step towards repurposing ADE as a resource in bio-production of fuels and chemicals, whilst generating effluent that is economically treatable by conventional wastewater treatment technologies.
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Mitra S, Zhong J, MacAlpine DM, Hartemink AJ. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2020; 12074:136-151. [PMID: 34386808 PMCID: PMC8356533 DOI: 10.1007/978-3-030-45257-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. RoboCOP can be applied to any epigenomic dataset that provides quantitative insight into chromatin accessibility in any organism, but here we apply it to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model more accurately predicts the binding of these factors genome-wide.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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Ruas FAD, Guerra-Sá R. In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii. Front Microbiol 2020; 11:236. [PMID: 32140149 PMCID: PMC7042463 DOI: 10.3389/fmicb.2020.00236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Recently, there has been an increasing interest in the use of yeast to produce biosorbent materials, because yeast is economical to use, adaptable to a variety of conditions, and amenable to morphological manipulations to yield better raw biomaterials. Previous studies from our laboratory have shown that Meyerozyma guilliermondii, a non-pathogenic haploid yeast (ascomycete), exhibits excellent biosorption capacity for Mn2+, as demonstrated by kinetic analyses. Shotgun/bottom-up analyses of soluble fractions revealed a total of 1257 identified molecules, with 117 proteins expressed in the absence of Mn2+ and 69 expressed only in the presence of Mn2+. In this article, we describe the first in silico prediction and screening of protein–protein interactions (PPIs) in M. guilliermondii using experimental data from shotgun/bottom-up analyses. We also present the categorization of biological processes (BPs), molecular functions (MFs), and metabolic pathways of 71 proteins upregulated in the M. guilliermondii proteome in response to stress caused by an excess of Mn2+ ions. Most of the annotated proteins were related to oxidation–reduction processes, metabolism, and response to oxidative stress. We identified seven functional enrichments and 42 metabolic pathways; most proteins belonged to pathways related to metabolic pathways (19 proteins) followed by the biosynthesis of secondary metabolites (10 proteins) in the presence of Mn2+. Using our data, it is possible to infer that defense mechanisms minimize the impact of Mn2+ via the expression of antioxidant proteins, thus allowing adjustment during the defense response. Previous studies have not considered protein interactions in this genus in a manner that permits comparisons. Consequently, the findings of the current study are innovative, highly relevant, and provide a description of interactive complexes and networks that yield insight into the cellular processes of M. guilliermondii. Collectively, our data will allow researchers to explore the biotechnological potential of M. guilliermondii in future bioremediation processes.
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Affiliation(s)
- France Anne Dias Ruas
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológica (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renata Guerra-Sá
- Laboratório de Bioquímica e Biologia Molecular, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológica (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, Brazil
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30
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Kolhe N, Zinjarde S, Acharya C. Impact of uranium exposure on marine yeast, Yarrowia lipolytica: Insights into the yeast strategies to withstand uranium stress. JOURNAL OF HAZARDOUS MATERIALS 2020; 381:121226. [PMID: 31557712 DOI: 10.1016/j.jhazmat.2019.121226] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/17/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
A marine yeast, Yarrowia lipolytica, was evaluated for morphological, physiological and biochemical responses towards uranium (U) exposure at pH 7.5. The yeast revealed biphasic U binding - a rapid biosorption resulting in ∼35% U binding within 15-30 min followed by a slow biomineralization process, binding up to ∼45.5% U by 24 h on exposure to 50 μM of uranyl carbonate. Scanning electron microscopy coupled with Energy Dispersive X-ray spectroscopy analysis of 24 h U challenged cells revealed the deposition of uranyl precipitates due to biomineralization. The loss of intracellular structures together with surface and subcellular localization of uranyl precipitates in 24 h U exposed cells were visualized by transmission electron microscopy. Cells treated with 50 μM U exhibited membrane permeabilization which was higher at 200 μM U. Enhanced reactive oxygen species (ROS) accumulation and lipid peroxidation, transient RNA degradation and protein oxidation were observed in U exposed cells. High superoxide dismutase levels coupled with uranium binding and bioprecipitation possibly helped in counteracting U stress in 50 μM U treated cells. Resistance to U toxicity apparently developed under prolonged uranyl (50 μM) incubations. However, cells could not cope up with toxicity at 200 μM U due to impairment of resistance mechanisms.
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Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai, 400094, India.
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31
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Rajakumar S, Abhishek A, Selvam GS, Nachiappan V. Effect of cadmium on essential metals and their impact on lipid metabolism in Saccharomyces cerevisiae. Cell Stress Chaperones 2020; 25:19-33. [PMID: 31823289 PMCID: PMC6985397 DOI: 10.1007/s12192-019-01058-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/14/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
Cadmium (Cd) is a toxic heavy metal that induces irregularity in numerous lipid metabolic pathways. Saccharomyces cerevisiae, a model to study lipid metabolism, has been used to establish the molecular basis of cellular responses to Cd toxicity in relation to essential minerals and lipid homeostasis. Multiple pathways sense these environmental stresses and trigger the mineral imbalances specifically calcium (Ca) and zinc (Zn). This review is aimed to elucidate the role of Cd toxicity in yeast, in three different perspectives: (1) elucidate stress response and its adaptation to Cd, (2) understand the physiological role of a macromolecule such as lipids, and (3) study the stress rescue mechanism. Here, we explored the impact of Cd interference on the essential minerals such as Zn and Ca and their influence on endoplasmic reticulum stress and lipid metabolism. Cd toxicity contributes to lipid droplet synthesis by activating OLE1 that is essential to alleviate lipotoxicity. In this review, we expanded our current findings about the effect of Cd on lipid metabolism of budding yeast.
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Affiliation(s)
- Selvaraj Rajakumar
- Eukaryotic Biology Lab, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India.
- Biomembrane Lab, Department of Biochemistry, Centre for Excellence in Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
- Department of Pediatrics, Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada.
| | - Albert Abhishek
- Eukaryotic Biology Lab, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Govindan Sadasivam Selvam
- Eukaryotic Biology Lab, Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Vasanthi Nachiappan
- Biomembrane Lab, Department of Biochemistry, Centre for Excellence in Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
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32
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Horstmann C, Kim DS, Campbell C, Kim K. Transcriptome Profile Alteration with Cadmium Selenide/Zinc Sulfide Quantum Dots in Saccharomyces cerevisiae. Biomolecules 2019; 9:biom9110653. [PMID: 31731522 PMCID: PMC6920935 DOI: 10.3390/biom9110653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023] Open
Abstract
Quantum Dots (QDs) are becoming more prevalent in products used in our daily lives, such as TVs and laptops, due to their unique and tunable optical properties. The possibility of using QDs as fluorescent probes in applications, such as medical imaging, has been a topic of interest for some time, but their potential toxicity and long-term effects on the environment are not well understood. In the present study, we investigated the effects of yellow CdSe/ZnS-QDs on Saccharomyces cerevisiae. We utilized growth assays, RNA-seq, reactive oxygen species (ROS) detection assays, and cell wall stability experiments to investigate the potential toxic effects of CdSe/ZnS-QDs. We found CdSe/ZnS-QDs had no negative effects on cell viability; however, cell wall-compromised cells showed more sensitivity in the presence of 10 µg/mL CdSe/ZnS-QDs compared to non-treated cells. In CdSe/ZnS-treated and non-treated cells, no significant change in superoxide was detected, but according to our transcriptomic analysis, thousands of genes in CdSe/ZnS-treated cells became differentially expressed. Four significantly differentiated genes found, including FAF1, SDA1, DAN1, and TIR1, were validated by consistent results with RT-qPCR assays. Our transcriptome analysis led us to conclude that exposure of CdSe/ZnS-QDs on yeast significantly affected genes implicated in multiple cellular processes.
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Affiliation(s)
- Cullen Horstmann
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
| | - Daniel S Kim
- Kickapoo High School, 3710 South Jefferson Ave, Springfield, MO 65807, USA;
| | - Chelsea Campbell
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65897, USA; (C.H.); (C.C.)
- Correspondence: ; Tel.: +1-417-836-5440; Fax: +1-417-836-5126
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Fallahzadeh RA, Mahvi AH, Meybodi MN, Ghaneian MT, Dalvand A, Salmani MH, Fallahzadeh H, Ehrampoush MH. Application of photo-electro oxidation process for amoxicillin removal from aqueous solution: Modeling and toxicity evaluation. KOREAN J CHEM ENG 2019. [DOI: 10.1007/s11814-019-0259-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Phenylpyrrole fungicides act on triosephosphate isomerase to induce methylglyoxal stress and alter hybrid histidine kinase activity. Sci Rep 2019; 9:5047. [PMID: 30911085 PMCID: PMC6433957 DOI: 10.1038/s41598-019-41564-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/06/2019] [Indexed: 01/03/2023] Open
Abstract
Fludioxonil, a natural product of pyrrolnitrin, is a potent fungicide used on crops worldwide. Drug action requires the presence of a group III hybrid histidine kinase (HHK) and the high osmolarity glycerol (HOG) pathway. We have reported that the drug does not act directly on HHK, but triggers the conversion of the kinase to a phosphatase, which dephosphorylates Ypd1 to constitutively activate HOG signaling. Still, the direct drug target remains unknown and mode of action ill defined. Here, we heterologously expressed a group III HHK, dimorphism-regulating kinase 1 (Drk1) in Saccharomyces cerevisae to delineate fludioxonil’s target and action. We show that the drug interferes with triosephosphate isomerase (TPI) causing release of methylglyoxal (MG). MG activates the group III HHK and thus the HOG pathway. Drug action involved Drk1 cysteine 392, as a C392S substitution increased drug resistance in vivo. Drug sensitivity was reversed by dimedone treatment, indicating Drk1 responds in vivo to an aldehydic stress. Fludioxonil treatment triggered elevated cytosolic methylglyoxal. Likewise, methylglyoxal treatment of Drk1-expressing yeast phenocopied treatment with fludioxonil. Fludioxonil directly inhibited TPI and also caused it to release methylglyoxal in vitro. Thus, TPI is a drug target of the phenylpyrrole class of fungicides, inducing elevated MG which alters HHK activity, likely converting the kinase to a phosphatase that acts on Ypd1 to trigger HOG pathway activation and fungal cell death.
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35
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Mukherjee A, Yadav R, Marmeisse R, Fraissinet-Tachet L, Reddy MS. Heavy metal hypertolerant eukaryotic aldehyde dehydrogenase isolated from metal contaminated soil by metatranscriptomics approach. Biochimie 2019; 160:183-192. [PMID: 30905733 DOI: 10.1016/j.biochi.2019.03.010] [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: 11/03/2018] [Accepted: 03/18/2019] [Indexed: 10/27/2022]
Abstract
Constant addition of heavy metal pollutants in soil resulting from anthropogenic activities can prove detrimental to both macro and micro life forms inhabiting the ecosystem. The potential functional roles of eukaryotic microbes in such environment were explored in this study by metatranscriptomics approach. Sized eukaryotic cDNA libraries, library A (<0.5 kb), library B (0.5-1.0 kb), and library C (>1 kb) were constructed from the soil RNA and screened for copper (Cu) tolerance genes by using copper sensitive yeast mutant strain cup1Δ. Screening of the cDNA libraries yielded different clones capable of growing in Cu amended medium. In the present investigation, one of the transcripts PLCc38 from the library C was characterized and tested for its ability to tolerate different heavy metals by using metal sensitive yeast mutants. Sequence analysis PLCc38 showed homology with aldehyde dehydrogenase (ALDH) and capable of tolerating high concentrations of Cu (150-1000 μM). Aldeyde dehydrogenases are stress response enzymes capable of eliminating toxic levels of aldehydes generated due to abiotic environmental stresses. The cDNA PLCc38 also provided tolerance to wide range of Cd (40-100 μM), Zn (10-13 mM) and Co (2-50 mM) concentrations. Oxidative stress tolerance potential of PLCc38 was also confirmed in presence of different concentrations of H2O2. This study proves that PLCc38 is a potent gene associated with metal tolerance which could be used to revegetate heavy metal polluted soil or as a biomarker for detection of metal contamination.
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Affiliation(s)
- Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Rajiv Yadav
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622 Villeurbanne, France
| | - Roland Marmeisse
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622 Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622 Villeurbanne, France
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.
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36
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Ruas FAD, Barboza NR, Castro-Borges W, Guerra-Sá R. Manganese alters expression of proteins involved in the oxidative stress of Meyerozyma guilliermondii. J Proteomics 2019; 196:173-188. [DOI: 10.1016/j.jprot.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 01/12/2023]
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37
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Kumar Babele P. Zinc oxide nanoparticles impose metabolic toxicity by de-regulating proteome and metabolome in Saccharomyces cerevisiae. Toxicol Rep 2018; 6:64-73. [PMID: 30581761 PMCID: PMC6297892 DOI: 10.1016/j.toxrep.2018.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/28/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
Untargeted proteomic and metabolic approaches provide complete toxicity assessment. ZnO-NPs de-regulate the proteome and metabolome of S. cerevisiae. ZnO-NPs affect the key metabolites of central metabolic pathways. Protein and/or metabolite can be used as biomarker specific to the ZnO-NPs induced toxicity.
As zinc oxide nanoparticles are being increasingly used in various applications, it is important to assess their potential toxic implications. Stress responses and adaptations are primarily controlled by modulation in cellular proteins (enzyme) and concentration of metabolites. To date proteomics or metabolomics applications in nanotoxicity assessment have been applied to a restricted extent. Here we utilized 2DE and 1H NMR based proteomics and metabolomics respectively to delineate the toxicity mechanism of zinc oxide nanoparticles (ZnO-NPs) in budding yeast S. cerevisiae. We found that the physiological and metabolic processes were altered in the S. cerevisiae upon ZnO-NPs exposure. Almost 40% proteins were down-regulated in ZnO-NPs (10 mg L−1) exposed cell as compared to control. Metabolomics and system biology based pathway analysis, revealed that ZnO-NPs repressed a wide range of key metabolites involved in central carbon metabolism, cofactors synthesis, amino acid and fatty acid biosynthesis, purines and pyrimidines, nucleoside and nucleotide biosynthetic pathways. These metabolic changes may be associated with the energy metabolism, antioxidation, DNA and protein damage and membrane stability. We concluded that untargeted proteomic and metabolic approaches provide more complete measurements and suggest probable molecular mechanisms of nanomaterials toxicity.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, 462066, Madhya Pradesh, India
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Heavy metal sensitivities of gene deletion strains for ITT1 and RPS1A connect their activities to the expression of URE2, a key gene involved in metal detoxification in yeast. PLoS One 2018; 13:e0198704. [PMID: 30231023 PMCID: PMC6145592 DOI: 10.1371/journal.pone.0198704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 11/19/2022] Open
Abstract
Heavy metal and metalloid contaminations are among the most concerning types of pollutant in the environment. Consequently, it is important to investigate the molecular mechanisms of cellular responses and detoxification pathways for these compounds in living organisms. To date, a number of genes have been linked to the detoxification process. The expression of these genes can be controlled at both transcriptional and translational levels. In baker’s yeast, Saccharomyces cerevisiae, resistance to a wide range of toxic metals is regulated by glutathione S-transferases. Yeast URE2 encodes for a protein that has glutathione peroxidase activity and is homologous to mammalian glutathione S-transferases. The URE2 expression is critical to cell survival under heavy metal stress. Here, we report on the finding of two genes, ITT1, an inhibitor of translation termination, and RPS1A, a small ribosomal protein, that when deleted yeast cells exhibit similar metal sensitivity phenotypes to gene deletion strain for URE2. Neither of these genes were previously linked to metal toxicity. Our gene expression analysis illustrates that these two genes affect URE2 mRNA expression at the level of translation.
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Pontieri P, Hartings H, Di Salvo M, Massardo DR, De Stefano M, Pizzolante G, Romano R, Troisi J, Del Giudice A, Alifano P, Del Giudice L. Mitochondrial ribosomal proteins involved in tellurite resistance in yeast Saccharomyces cerevisiae. Sci Rep 2018; 8:12022. [PMID: 30104660 PMCID: PMC6089990 DOI: 10.1038/s41598-018-30479-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/23/2018] [Indexed: 11/22/2022] Open
Abstract
A considerable body of evidence links together mitochondrial dysfunctions, toxic action of metalloid oxyanions, and system and neurodegenerative disorders. In this study we have used the model yeast Saccharomyces cerevisiae to investigate the genetic determinants associated with tellurite resistance/sensitivity. Nitrosoguanidine-induced K2TeO3-resistant mutants were isolated, and one of these mutants, named Sc57-Te5R, was characterized. Both random spore analysis and tetrad analysis and growth of heterozygous (TeS/Te5R) diploid from Sc57-Te5R mutant revealed that nuclear and recessive mutation(s) was responsible for the resistance. To get insight into the mechanisms responsible for K2TeO3-resistance, RNA microarray analyses were performed with K2TeO3-treated and untreated Sc57-Te5R cells. A total of 372 differentially expressed loci were identified corresponding to 6.37% of the S. cerevisiae transcriptome. Of these, 288 transcripts were up-regulated upon K2TeO3 treatment. About half of up-regulated transcripts were associated with the following molecular functions: oxidoreductase activity, structural constituent of cell wall, transporter activity. Comparative whole-genome sequencing allowed us to identify nucleotide variants distinguishing Sc57-Te5R from parental strain Sc57. We detected 15 CDS-inactivating mutations, and found that 3 of them affected genes coding mitochondrial ribosomal proteins (MRPL44 and NAM9) and mitochondrial ribosomal biogenesis (GEP3) pointing out to alteration of mitochondrial ribosome as main determinant of tellurite resistance.
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Affiliation(s)
- Paola Pontieri
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy
| | - Hans Hartings
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via Stezzano 24, Bergamo, 24126, Italy
| | - Marco Di Salvo
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce, 73100, Italy
| | - Domenica R Massardo
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy
| | - Mario De Stefano
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Via A. Vivaldi 43, Caserta, 81100, Italy
| | - Graziano Pizzolante
- ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Roberta Romano
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Università di Bologna, Via Terracini 28, Bologna, 40131, Italy
| | - Jacopo Troisi
- Theoreo srl - Spin off dell' Università di Salerno, Via Salvatore Derenzi 50, Montecorvino Pugliano, 84125, (SA), Italy
| | - Angelica Del Giudice
- Amb di allergologia Osp Martini asl città di Torino, via Tofane 71, Torino, 10171, Italy
| | - Pietro Alifano
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce, 73100, Italy
| | - Luigi Del Giudice
- Istituto di Bioscienze e BioRisorse-UOS Portici-CNR c/o Dipartimento di Biologia, Sezione di Igiene, Via Mezzocannone 16, Napoli, 80134, Italy.
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Sousa CA, Soares HMVM, Soares EV. Nickel Oxide (NiO) Nanoparticles Induce Loss of Cell Viability in Yeast Mediated by Oxidative Stress. Chem Res Toxicol 2018; 31:658-665. [PMID: 30043610 DOI: 10.1021/acs.chemrestox.8b00022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present work aimed to elucidate whether the toxic effects of nickel oxide (NiO) nanoparticles (NPs) on the yeast Saccharomyces cerevisiae were associated with oxidative stress (OS) and what mechanisms may have contributed to this OS. Cells exposed to NiO NPs accumulated superoxide anions and hydrogen peroxide, which were intracellularly generated. Yeast cells coexposed to NiO NPs and antioxidants (l-ascorbic acid and N- tert-butyl-α-phenylnitrone) showed quenching of reactive oxygen species (ROS) and increased resistance to NiO NPs, indicating that the loss of cell viability was associated with ROS accumulation. Mutants lacking mitochondrial DNA (ρ0) displayed reduced levels of ROS and increased resistance to NiO NPs, which suggested the involvement of the mitochondrial respiratory chain in ROS production. Yeast cells exposed to NiO NPs presented decreased levels of reduced glutathione (GSH). Mutants deficient in GSH1 ( gsh1Δ) or GSH2 ( gsh2Δ) genes displayed increased levels of ROS and increased sensitivity to NiO NPs, which underline the central role of GSH against NiO NPs-induced OS. This work suggests that the increased levels of intracellular ROS (probably due to the perturbation of the electron transfer chain in mitochondria) combined with the depletion of GSH pool constitute important mechanisms of NiO NPs-induced loss of cell viability in the yeast S. cerevisiae.
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Affiliation(s)
- Cátia A Sousa
- Bioengineering Laboratory-CIETI, Chemical Engineering Department , ISEP-School of Engineering of Polytechnic Institute of Porto , Rua Dr. António Bernardino de Almeida, 431 , 4249-015 Porto , Portugal.,CEB-Centre of Biological Engineering , University of Minho , 4710-057 Braga , Portugal.,REQUIMTE/LAQV, Departamento de Engenharia Química, Faculdade de Engenharia , Universidade do Porto , Rua Dr. Roberto Frias, s/n , 4200-465 Porto , Portugal
| | - Helena M V M Soares
- REQUIMTE/LAQV, Departamento de Engenharia Química, Faculdade de Engenharia , Universidade do Porto , Rua Dr. Roberto Frias, s/n , 4200-465 Porto , Portugal
| | - Eduardo V Soares
- Bioengineering Laboratory-CIETI, Chemical Engineering Department , ISEP-School of Engineering of Polytechnic Institute of Porto , Rua Dr. António Bernardino de Almeida, 431 , 4249-015 Porto , Portugal.,CEB-Centre of Biological Engineering , University of Minho , 4710-057 Braga , Portugal
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Transcriptomic Profiles in Zebrafish Liver Permit the Discrimination of Surface Water with Pollution Gradient and Different Discharges. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081648. [PMID: 30081495 PMCID: PMC6122030 DOI: 10.3390/ijerph15081648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 01/23/2023]
Abstract
The present study aims to evaluate the potential of transcriptomic profiles in evaluating the impacts of complex mixtures of pollutants at environmentally relevant concentrations on aquatic vertebrates. The changes in gene expression were determined using microarray in the liver of male zebrafish (Danio rerio) exposed to surface water collected from selected locations on the Hun River, China. The numbers of differentially expressed genes (DEGs) in each treatment ranged from 728 to 3292, which were positively correlated with chemical oxygen demand (COD). Predominant transcriptomic responses included peroxisome proliferator-activated receptors (PPAR) signaling and steroid biosynthesis. Key pathways in immune system were also affected. Notably, two human diseases related pathways, insulin resistance and Salmonella infection were enriched. Clustering analysis and principle component analysis with DEGs differentiated the upstream and downstream site of Shenyang City, and the mainstream and the tributary sites near the junction. Comparison the gene expression profiles of zebrafish exposed to river surface water with those to individual chemicals found higher similarity of the river water with estradiol than several other organic pollutants and metals. Results suggested that the transcriptomic profiles of zebrafish is promising in differentiating surface water with pollution gradient and different discharges and in providing valuable information to support discharge management.
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Rathod J, Tu HP, Chang YI, Chu YH, Tseng YY, Jean JS, Wu WS. YARG: A repository for arsenic-related genes in yeast. PLoS One 2018; 13:e0201204. [PMID: 30048518 PMCID: PMC6062094 DOI: 10.1371/journal.pone.0201204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/10/2018] [Indexed: 11/30/2022] Open
Abstract
Arsenic is a toxic metalloid. Moderate levels of arsenic exposure from drinking water can cause various human health problems such as skin lesions, circulatory disorders and cancers. Thus, arsenic toxicity is a key focus area for environmental and toxicological investigations. Many arsenic-related genes in yeast have been identified by experimental strategies such as phenotypic screening and transcriptional profiling. These identified arsenic-related genes are valuable information for studying arsenic toxicity. However, the literature about these identified arsenic-related genes is widely dispersed and cannot be easily acquired by researchers. This prompts us to develop YARG (Yeast Arsenic-Related Genes) database, which comprehensively collects 3396 arsenic-related genes in the literature. For each arsenic-related gene, the number and types of experimental evidence (phenotypic screening and/or transcriptional profiling) are provided. Users can use both search and browse modes to query arsenic-related genes in YARG. We used two case studies to show that YARG can return biologically meaningful arsenic-related information for the query gene(s). We believe that YARG is a useful resource for arsenic toxicity research. YARG is available at http://cosbi4.ee.ncku.edu.tw/YARG/.
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Ping Tu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yung-I Chang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Han Chu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Jiin-Shuh Jean
- Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
- * E-mail:
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Liu J, Hernández SE, Swift S, Singhal N. Estrogenic activity of cylindrospermopsin and anatoxin-a and their oxidative products by Fe III-B*/H 2O 2. WATER RESEARCH 2018; 132:309-319. [PMID: 29339303 DOI: 10.1016/j.watres.2018.01.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/03/2018] [Accepted: 01/07/2018] [Indexed: 06/07/2023]
Abstract
The cyanotoxins released into waters during cyanobacterial blooms can pose serious hazards to humans and animals. Apart from their toxicological mechanisms, cyanotoxins have been shown to be involved in estrogenic activity by in vivo and in vitro assays; however, there is limited information on the change in estrogenicity of cyanotoxins following chemical oxidation. In this study, the estrogenic activity of cylindrospermopsin (CYL) and anatoxin-a (ANA) at concentrations ranging from 2.4 × 10-7 M to 2.4 × 10-12 M (CYL) and 7.1 × 10-6 M to 7.1 × 10-11 M (ANA), and after treatment by the FeIII-B*/H2O2 catalyst system, was investigated by the yeast estrogen screen (YES) assay. The results indicate that CYL and ANA acted as agonists in the YES assay (CYL logEC50 = -8.901; ANA logEC50 = -6.789), their binding affinity to estrogen receptors is associated with their intrinsic properties, including ring structures and toxicant properties. CYL and ANA were shown to simulate endocrine disrupting chemicals (EDCs) to modulate the 17β-estradiol-induced estrogenic activity, resulting in non-monotonic dose responses. The treated CYL showed a significantly altered estrogenicity compared to the untreated CYL (T(2) = 8.168, p ≤ .05), while the estrogenicity of the treated ANA was not significantly different to the untreated ANA (T(2) = 1.295, p > .05). Intermediate products generated from CYL and ANA oxidized by FeIII-B*/H2O2 were identified using Q-Exactive Tandem Mass Spectrometry (LC-MS/MS). Treatment with FeIII-B*/H2O2 yielded open-ring by-products which likely resulted in CYL's reduced binding affinity to estrogen receptors. The insignificant change in the estrogenicity of treated ANA was possibly a result of its multiple ring structure products, which were likely able to bind to estrogen receptors. The comparisons for the estrogenicity of these cyanotoxins before and after FeIII-B*/H2O2 treatment suggest that the reductions in estrogenicity achieved by oxidation were dependent on the levels of cyanotoxins removed, as well as the estrogenicity of the degradation products. This is the first study on the change in the estrogenicity of CYL and ANA upon oxidation by FeIII-B*/H2O2, a high activity catalyst system.
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Affiliation(s)
- Jishan Liu
- Department of Civil & Environmental Engineering, The University of Auckland, Auckland 1142, New Zealand
| | - Sandra E Hernández
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico
| | - Simon Swift
- Molecular Medicine and Pathology, The University of Auckland, Auckland 1142, New Zealand
| | - Naresh Singhal
- Department of Civil & Environmental Engineering, The University of Auckland, Auckland 1142, New Zealand.
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44
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Heavy metal tolerance in marine strains of Yarrowia lipolytica. Extremophiles 2018; 22:617-628. [DOI: 10.1007/s00792-018-1022-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/11/2018] [Indexed: 12/21/2022]
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45
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Pan J, Huang X, Li Y, Li M, Yao N, Zhou Z, Li X. Zinc protects against cadmium-induced toxicity by regulating oxidative stress, ions homeostasis and protein synthesis. CHEMOSPHERE 2017; 188:265-273. [PMID: 28886561 DOI: 10.1016/j.chemosphere.2017.08.106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/14/2017] [Accepted: 08/19/2017] [Indexed: 06/07/2023]
Abstract
The widespread environmental toxin cadmium (Cd) is associated with numerous human diseases. The essential trace element zinc (Zn) strongly counteracts Cd-induced toxicity; however, the mechanism is incompletely understood. Here, we conducted RNA sequencing and bioinformatics analyses to determine the global gene expression profiles of yeast cells exposed to Cd or Cd plus Zn. We identified 912 Cd-induced and 627 Cd plus Zn-induced differentially expressed genes (DEGs). Adding Zn during Cd exposure efficiently reversed the expression of 92.1% of Cd-induced DEGs; that of 48.7% was entirely reversed. Gene Ontology, Cluster of Orthologous Group and KEGG Ontology analyses revealed that the response of yeasts to Cd or Cd plus Zn was mainly involved in metal-specific oxidative stress; energy production and conversion; ion homeostasis and ribosome biogenesis and translation. Exposure of yeasts to Cd plus Zn protected them from oxidative stress by efficiently inhibiting the expression of genes associated with Cd-triggered oxidative stress and preventing the disruption of Fe- and Zn-ion homeostasis and reduced glutathione and partially restored mitochondrial membrane potential. Moreover, Zn reduced the intracellular level of Cd to prevent the replacement by Cd of elements required for antioxidant enzyme activity and to protect protein sulphydryl groups against oxidation by free radicals. Further, Zn inhibited the synthesis alterations of Cd-induced ribosomal proteins, S-containing amino acids, S-rich proteins and antioxidant enzymes. Conversely, the investigation results of our study on the yeast model revealed that the Cd-treated protective effects of Zn on Cd-induced toxicity might be partially protective.
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Affiliation(s)
- Jingmei Pan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xinhe Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yuxing Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Ming Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Ning Yao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhengdong Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xueru Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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Andreeva N, Kulakovskaya E, Zvonarev A, Penin A, Eliseeva I, Teterina A, Lando A, Kulakovskiy IV, Kulakovskaya T. Transcriptome profile of yeast reveals the essential role of PMA2 and uncharacterized gene YBR056W-A (MNC1) in adaptation to toxic manganese concentration. Metallomics 2017; 9:175-182. [PMID: 28128390 DOI: 10.1039/c6mt00210b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Adaptation of S. cerevisiae to toxic concentrations of manganese provides a physiological model of heavy metal homeostasis. Transcriptome analysis of adapted yeast cells reveals upregulation of cell wall and plasma membrane proteins including membrane transporters. The gene expression in adapted cells differs from that of cells under short-term toxic metal stress. Among the most significantly upregulated genes are PMA2, encoding an ortholog of Pma1 H+-ATPase of the plasma membrane, and YBR056W-A, encoding a putative membrane protein Mnc1 that belongs to the CYSTM family and presumably chelates manganese at the cell surface. We demonstrate that these genes are essential for the adaptation to toxic manganese concentration and propose an extended scheme of manganese detoxification in yeast.
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Affiliation(s)
- N Andreeva
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, Pushchino, 142290, Russia.
| | - E Kulakovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, Pushchino, 142290, Russia.
| | - A Zvonarev
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, Pushchino, 142290, Russia.
| | - A Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia and Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, 420012, Russia and Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - I Eliseeva
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Institutskaya 4, Pushchino, 142290, Russia
| | - A Teterina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, GSP-1, 119991, Russia
| | - A Lando
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, GSP-1, 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
| | - I V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, GSP-1, 119991, Russia and Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, GSP-1, 119991, Russia.
| | - T Kulakovskaya
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, pr. Nauki 5, Pushchino, 142290, Russia.
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Chen YY, Chan KM. Transcriptional inhibition of TCDD-mediated induction of cytochrome P450 1A1 and alteration of protein expression in a zebrafish hepatic cell line following the administration of TCDD and Cd 2. Toxicol Lett 2017; 282:121-135. [PMID: 29107029 DOI: 10.1016/j.toxlet.2017.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/27/2022]
Abstract
We studied the effects of Cd2+ on TCDD-mediated induction of the cytochrome P450 1A1 (cyp1a1) gene using a zebrafish liver cell line (ZFL). Our results showed that Cd2+ inhibited the TCDD-mediated induction of the cyp1a1 protein, enzyme activity, and mRNA expression level. Cd2+ also down-regulated levels of the aryl hydrocarbon receptor (ahr2) and the aryl hydrocarbon receptor nuclear translocator 2b (arnt2b) mRNAs. Compared with TCDD (3nM) treatment alone, co-treatment with Cd2+ (0-30μM) and TCDD (3nM) significantly inhibited the activity of the luciferase reporter gene constructs harboring the distal promoter region (P-2626/-2009) of CYP1A1 and the synthetic 3XRE gene promoter. This indicates that Cd2+ decreased the level of TCDD-induced cyp1a1 through transcriptional inhibition. Proteomic analysis was also used to evaluate the effect of Cd2+ on TCDD-altered protein expression in ZFL cells. The identified proteins are mainly enzymes of the glycolysis pathway and proteasomes, and have anti-oxidative and anti-stress effects.
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Affiliation(s)
- Ying Ying Chen
- School of Life Sciences, Faculty of Science, Chinese University, Sha Tin, Hong Kong
| | - King Ming Chan
- School of Life Sciences, Faculty of Science, Chinese University, Sha Tin, Hong Kong.
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Serna-Galvis EA, Berrio-Perlaza KE, Torres-Palma RA. Electrochemical treatment of penicillin, cephalosporin, and fluoroquinolone antibiotics via active chlorine: evaluation of antimicrobial activity, toxicity, matrix, and their correlation with the degradation pathways. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23771-23782. [PMID: 28864919 DOI: 10.1007/s11356-017-9985-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Antibiotics are pharmaceuticals widely consumed and frequently detected in environmental water, where they can induce toxic effects and development of resistant bacteria. Their structural variety makes the problem of antibiotics in natural water more complex. In this work, six highly used antibiotics (at 40 μmol L-1) belonging to three different classes (penicillins, cephalosporins, and fluoroquinolones) were treated using an electrochemical system with a Ti/IrO2 anode and a Zr cathode in the presence of NaCl (0.05 μmol L-1). The attack of electrogenerated active chlorine was found to be the main degradation route. After only 20 min of treatment, the process decreased more than 90% of the initial concentration of antibiotics, following the degradation order: fluoroquinolones > penicillins > cephalosporins. The primary interactions of the degrading agent with fluoroquinolones occurred at the cyclic amine (i.e., piperazyl ring) and the benzene ring. Meanwhile, the cephalosporins and penicillins were initially attacked on the β-lactam and sulfide groups. However, the tested penicillins presented an additional reaction on the central amide. In all cases, the transformations of antibiotics led to the antimicrobial activity decreasing. On the contrary, the toxicity level showed diverse results: increasing, decreasing, and no change, depending on the antibiotic type. In fact, due to the conservation of quinolone nucleus in the fluoroquinolone by-products, the toxicity of the treated solutions remained unchanged. With penicillins, the production of chloro-phenyl-isoxazole fragments increased the toxicity level of the resultant solution. However, the opening of β-lactam ring of cephalosporin antibiotics decreased the toxicity level of the treated solutions. Finally, the application of the treatment to synthetic hospital wastewater and seawater containing a representative antibiotic showed that the high amount of chloride ions in seawater accelerates the pollutant degradation. In contrast, the urea and ammonium presence in the hospital wastewater retarded the removal of this pharmaceutical.
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Affiliation(s)
- Efraím A Serna-Galvis
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Karen E Berrio-Perlaza
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Ricardo A Torres-Palma
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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Robinson C, Denison C, Burkenstock A, Nutter C, Gordon D. Cellular conditions that modulate the fungicidal activity of occidiofungin. J Appl Microbiol 2017; 123:380-391. [DOI: 10.1111/jam.13496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023]
Affiliation(s)
- C.A. Robinson
- Department of Biological Sciences; Mississippi State University; Mississippi State MS USA
| | - C. Denison
- Department of Biological Sciences; Mississippi State University; Mississippi State MS USA
| | - A. Burkenstock
- Department of Biological Sciences; Mississippi State University; Mississippi State MS USA
| | - C. Nutter
- Department of Biological Sciences; Mississippi State University; Mississippi State MS USA
| | - D.M. Gordon
- Department of Biological Sciences; Mississippi State University; Mississippi State MS USA
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Improvement of Lead Tolerance of Saccharomyces cerevisiae by Random Mutagenesis of Transcription Regulator SPT3. Appl Biochem Biotechnol 2017; 184:155-167. [PMID: 28656551 DOI: 10.1007/s12010-017-2531-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/04/2017] [Indexed: 10/19/2022]
Abstract
Bioremediation of heavy metal pollution with biomaterials such as bacteria and fungi usually suffer from limitations because of microbial sensitivity to high concentration of heavy metals. Herein, we adopted a novel random mutagenesis technique called RAISE to manipulate the transcription regulator SPT3 of Saccharomyces cerevisiae to improve cell lead tolerance. The best strain Mutant VI was selected from the random mutagenesis libraries on account of the growth performance, with higher specific growth rate than the control strain (0.068 vs. 0.040 h-1) at lead concentration as high as 1.8 g/L. Combined with the transcriptome analysis of S. cerevisiae, expressing the SPT3 protein was performed to make better sense of the global regulatory effects of SPT3. The data analysis revealed that 57 of S. cerevisiae genes were induced and 113 genes were suppressed, ranging from those for trehalose synthesis, carbon metabolism, and nucleotide synthesis to lead resistance. Especially, the accumulation of intracellular trehalose in S. cerevisiae under certain conditions of stress is considered important to lead resistance. The above results represented that SPT3 was acted as global transcription regulator in the exponential phase of strain and accordingly improved heavy metal tolerance in the heterologous host S. cerevisiae. The present study provides a route to complex phenotypes that are not readily accessible by traditional methods.
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