1
|
Yuan B, Wang WB, Wang XQ, Liu CG, Hasunuma T, Kondo A, Zhao XQ. The chromatin remodeler Ino80 regulates yeast stress tolerance and cell metabolism through modulating nitrogen catabolite repression. Int J Biol Macromol 2024; 258:129041. [PMID: 38154715 DOI: 10.1016/j.ijbiomac.2023.129041] [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: 06/08/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Chromatin remodelers are important in maintaining the dynamic chromatin state in eukaryotic cells, which is essential for epigenetic regulation. Among the remodelers, the multi-subunits complex INO80 plays crucial roles in transcriptional regulation. However, current knowledge of chromatin regulation of the core subunit Ino80 on stress adaptation remains mysterious. Here we revealed that overexpressing the chromatin remodeler Ino80 elevated tolerance to multiple stresses in budding yeast Saccharomyces cerevisiae. Analyses of differential chromatin accessibility and global transcription levels revealed an enrichment of genes involved in NCR (nitrogen catabolite repression) under acetic acid stress. We demonstrated that Ino80 overexpression reduced the histone H3 occupancy in the promoter region of the glutamate dehydrogenase gene GDH2 and the allantoinase gene DAL1. Consistently, the decreased occupancy of nucleosome was revealed in the Ino80-inactivation mutant. Further analyses showed that Ino80 was recruited to the specific DNA locus in the promoter region of GDH2. Consistently, Ino80 overexpression facilitated the utilization of non-preferred nitrogen source to enhance ethanol yield under prolonged acetic acid stress. These results demonstrate that Ino80 plays a crucial role in coordinating carbon and nitrogen metabolism during stress adaptation.
Collapse
Affiliation(s)
- Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan; Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan; Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
2
|
Zhao B, Zhao J, Wang M, Guo Y, Mehmood A, Wang W, Xiong Y, Luo S, Wei DQ, Zhao XQ, Wang Y. Exploring microproteins from various model organisms using the mip-mining database. BMC Genomics 2023; 24:661. [PMID: 37919660 PMCID: PMC10623795 DOI: 10.1186/s12864-023-09735-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Microproteins, prevalent across all kingdoms of life, play a crucial role in cell physiology and human health. Although global gene transcription is widely explored and abundantly available, our understanding of microprotein functions using transcriptome data is still limited. To mitigate this problem, we present a database, Mip-mining ( https://weilab.sjtu.edu.cn/mipmining/ ), underpinned by high-quality RNA-sequencing data exclusively aimed at analyzing microprotein functions. The Mip-mining hosts 336 sets of high-quality transcriptome data from 8626 samples and nine representative living organisms, including microorganisms, plants, animals, and humans, in our Mip-mining database. Our database specifically provides a focus on a range of diseases and environmental stress conditions, taking into account chemical, physical, biological, and diseases-related stresses. Comparatively, our platform enables customized analysis by inputting desired data sets with self-determined cutoff values. The practicality of Mip-mining is demonstrated by identifying essential microproteins in different species and revealing the importance of ATP15 in the acetic acid stress tolerance of budding yeast. We believe that Mip-mining will facilitate a greater understanding and application of microproteins in biotechnology. Moreover, it will be beneficial for designing therapeutic strategies under various biological conditions.
Collapse
Affiliation(s)
- Bowen Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muyao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yangfan Guo
- Central Laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650051, China
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weibin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, China.
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, 518055, Guangdong, China.
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
3
|
Comparative Transcriptome Analysis to Investigate the Immunotoxicity Mechanism Triggered by Dimethomorph on Human Jurkat T Cell Lines. Foods 2022; 11:foods11233848. [PMID: 36496656 PMCID: PMC9738110 DOI: 10.3390/foods11233848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
Dimethomorph (DMM) is a broad-spectrum fungicide used globally in agricultural production, but little is known regarding the immunotoxicity of DMM in humans. In this study, the immunotoxicity of DMM on human Jurkat T cells was evaluated in vitro. The results indicated that the half-effective concentration (EC50) of DMM for Jurkat cells was 126.01 mg/L (0.32 mM). To further elucidate the underlying mechanism, transcriptomics based on RNA sequencing for exposure doses of EC25 (M21) and EC10 (L4) was performed. The results indicated that compared to untreated samples (Ctr), 121 genes (81 upregulated, 40 downregulated) and 30 genes (17 upregulated, 13 downregulated) were significantly differentially regulated in the L4 and M21 samples, respectively. A gene ontology analysis indicated that the significantly differentially expressed genes (DEGs) were mostly enriched in the negative regulation of cell activities, and a KEGG pathway analysis indicated that the DEGs were mainly enriched in the immune regulation and signal transduction pathways. A quantitative real-time PCR for the selected genes showed that compared to the high-dose exposure (M21), the effect of the low-dose DMM exposure (L4) on gene expression was more significant. The results indicated that DMM has potential immunotoxicity for humans, and this toxicity cannot be ignored even at low concentrations.
Collapse
|
4
|
Tullio V. Yeast Genomics and Its Applications in Biotechnological Processes: What Is Our Present and Near Future? J Fungi (Basel) 2022; 8:jof8070752. [PMID: 35887507 PMCID: PMC9315801 DOI: 10.3390/jof8070752] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Since molecular biology and advanced genetic techniques have become important tools in a variety of fields of interest, including taxonomy, identification, classification, possible production of substances and proteins, applications in pharmacology, medicine, and the food industry, there has been significant progress in studying the yeast genome and its potential applications. Because of this potential, as well as their manageability, safety, ease of cultivation, and reproduction, yeasts are now being extensively researched in order to evaluate a growing number of natural and sustainable applications to provide many benefits to humans. This review will describe what yeasts are, how they are classified, and attempt to provide a rapid overview of the many current and future applications of yeasts. The review will then discuss how yeasts—including those molecularly modified—are used to produce biofuels, proteins such as insulin, vaccines, probiotics, beverage preparations, and food additives and how yeasts could be used in environmental bioremediation and biocontrol for plant infections. This review does not delve into the issues raised during studies and research, but rather presents the positive outcomes that have enabled several industrial, clinical, and agricultural applications in the past and future, including the most recent on cow-free milk.
Collapse
Affiliation(s)
- Vivian Tullio
- Department Public Health and Pediatrics, Microbiology Division, University of Turin, Via Santena 9, 10126 Torino, Italy
| |
Collapse
|
5
|
Abstract
Biofuel consists of non-fossil fuel derived from the organic biomass of renewable resources, including plants, animals, microorganisms, and waste. Energy derived from biofuel is known as bioenergy. The reserve of fossil fuels is now limited and continuing to decrease, while at the same time demand for energy is increasing. In order to overcome this scarcity, it is vital for human beings to transfer their dependency on fossil fuels to alternative types of fuel, including biofuels, which are effective methods of fulfilling present and future demands. The current review therefore focusses on second-generation lignocellulosic biofuels obtained from non-edible plant biomass (i.e., cellulose, lignin, hemi-celluloses, non-food material) in a more sustainable manner. The conversion of lignocellulosic feedstock is an important step during biofuel production. It is, however, important to note that, as a result of various technical restrictions, biofuel production is not presently cost efficient, thus leading to the need for improvement in the methods employed. There remain a number of challenges for the process of biofuel production, including cost effectiveness and the limitations of various technologies employed. This leads to a vital need for ongoing and enhanced research and development, to ensure market level availability of lignocellulosic biofuel.
Collapse
|
6
|
Sá-Correia I, Godinho CP. Exploring the biological function of efflux pumps for the development of superior industrial yeasts. Curr Opin Biotechnol 2021; 74:32-41. [PMID: 34781103 DOI: 10.1016/j.copbio.2021.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/23/2021] [Accepted: 10/18/2021] [Indexed: 01/02/2023]
Abstract
Among the mechanisms used by yeasts to overcome the deleterious effects of chemical and other environmental stresses is the activity of plasma membrane efflux pumps involved in multidrug resistance (MDR), a role on the focus of intensive research for years in pathogenic yeasts. More recently, these active transporters belonging to the MFS (Drug: H+ antiporters) or the ABC superfamily have been involved in resistance to xenobiotic compounds and in the transport of substrates with a clear physiological role. This review paper focuses on these putative efflux pumps concerning their tolerance phenotypes towards bioprocess-specific multiple stress factors, expression levels, physiological roles, and mechanisms by which they may lead to multistress resistance. Their association with the increased secretion of metabolites and other bioproducts and in the development of more robust superior strains for Yeast Chemical Biotechnology is highlighted.
Collapse
Affiliation(s)
- Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory Institute for Health and Bioeconomy i4HB at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - Cláudia P Godinho
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Associate Laboratory Institute for Health and Bioeconomy i4HB at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
7
|
Dogra V, Kaur G, Kumar R, Kumar S. Toxicity profiling of metallosurfactant based ruthenium and ruthenium oxide nanoparticles towards the eukaryotic model organism Saccharomyces cerevisiae. CHEMOSPHERE 2021; 270:128650. [PMID: 33131730 DOI: 10.1016/j.chemosphere.2020.128650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
In the present study, a facile method was used to synthesize the ruthenium and ruthenium oxide (RuO2) nanoparticles (NPs) derived from three different metallosurfactants. Firstly, three metallosurfactants were fabricated i.e. RuCTAC (Bishexadecyltrimethylammonium ruthenium tetrachloride), RuDDA (Bisdodecylamine ruthenium dichloride), and RuHEXA (Bishexadecylamine ruthenium dichloride) and characterized by CHN, FTIR, and 1HNMR. These metallosurfactants were further utilized to fabricate the mixed type of NPs (Ru and RuO2 NPs) using the biocompatible microemulsion technique and NPs were then characterized. Subsequently, the nanotoxicity of mixed NPs (Ru & RuO2) was studied towards Saccharomyces cerevisiae. The detailed study of nanotoxicity against the S. cerevisiae cells was done by employing optical microscopy, FESEM, anti-yeast activity assay, circular dichroism, and gel electrophoresis techniques. FESEM and optical microscopy analyses indicated that RuCTAC nanosuspension (Ns) has the most toxic effect on the S. cerevisiae cells. FESEM analysis confirmed the harmful impact of Ru and RuO2 NPs on the S. cerevisiae cells. From the FESEM analysis, complete alteration in the morphology, cell membrane breakage, and formation of the holes on the cell wall of S. cerevisiae was affirmed in presence of all three types of Ns i.e. RuCTAC, RuDDA, and RuHEXA Ns. Genotoxicity of the NPs was confirmed by circular dichroism and gel electrophoresis and it was found that RuCTAC and RuHEXA Ns have the most damaging influence on the yeast genomic DNA.
Collapse
Affiliation(s)
- Varsha Dogra
- Department of Environment Studies, Panjab University, Chandigarh, India
| | - Gurpreet Kaur
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, India.
| | - Rajeev Kumar
- Department of Environment Studies, Panjab University, Chandigarh, India
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science & Technology, Hisar, 125 001, Haryana, India
| |
Collapse
|
8
|
Genome-wide toxicogenomic study of the lanthanides sheds light on the selective toxicity mechanisms associated with critical materials. Proc Natl Acad Sci U S A 2021; 118:2025952118. [PMID: 33903247 DOI: 10.1073/pnas.2025952118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lanthanides are a series of critical elements widely used in multiple industries, such as optoelectronics and healthcare. Although initially considered to be of low toxicity, concerns have emerged during the last few decades over their impact on human health. The toxicological profile of these metals, however, has been incompletely characterized, with most studies to date solely focusing on one or two elements within the group. In the current study, we assessed potential toxicity mechanisms in the lanthanide series using a functional toxicogenomics approach in baker's yeast, which shares many cellular pathways and functions with humans. We screened the homozygous deletion pool of 4,291 Saccharomyces cerevisiae strains with the lanthanides and identified both common and unique functional effects of these metals. Three very different trends were observed within the lanthanide series, where deletions of certain proteins on membranes and organelles had no effect on the cellular response to early lanthanides while inducing yeast sensitivity and resistance to middle and late lanthanides, respectively. Vesicle-mediated transport (primarily endocytosis) was highlighted by both gene ontology and pathway enrichment analyses as one of the main functions disturbed by the majority of the metals. Protein-protein network analysis indicated that yeast response to lanthanides relied on proteins that participate in regulatory paths used for calcium (and other biologically relevant cations), and lanthanide toxicity included disruption of biosynthetic pathways by enzyme inhibition. Last, multiple genes and proteins identified in the network analysis have human orthologs, suggesting that those may also be targeted by lanthanides in humans.
Collapse
|
9
|
Martins LC, Palma M, Angelov A, Nevoigt E, Liebl W, Sá-Correia I. Complete Utilization of the Major Carbon Sources Present in Sugar Beet Pulp Hydrolysates by the Oleaginous Red Yeasts Rhodotorula toruloides and R. mucilaginosa. J Fungi (Basel) 2021; 7:jof7030215. [PMID: 33802726 PMCID: PMC8002571 DOI: 10.3390/jof7030215] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Agro-industrial residues are low-cost carbon sources (C-sources) for microbial growth and production of value-added bioproducts. Among the agro-industrial residues available, those rich in pectin are generated in high amounts worldwide from the sugar industry or the industrial processing of fruits and vegetables. Sugar beet pulp (SBP) hydrolysates contain predominantly the neutral sugars d-glucose, l-arabinose and d-galactose, and the acidic sugar d-galacturonic acid. Acetic acid is also present at significant concentrations since the d-galacturonic acid residues are acetylated. In this study, we have examined and optimized the performance of a Rhodotorula mucilaginosa strain, isolated from SBP and identified at the molecular level during this work. This study was extended to another oleaginous red yeast species, R. toruloides, envisaging the full utilization of the C-sources from SBP hydrolysate (at pH 5.0). The dual role of acetic acid as a carbon and energy source and as a growth and metabolism inhibitor was examined. Acetic acid prevented the catabolism of d-galacturonic acid and l-arabinose after the complete use of the other C-sources. However, d-glucose and acetic acid were simultaneously and efficiently metabolized, followed by d-galactose. SBP hydrolysate supplementation with amino acids was crucial to allow d-galacturonic acid and l-arabinose catabolism. SBP valorization through the production of lipids and carotenoids by Rhodotorula strains, supported by complete catabolism of the major C-sources present, looks promising for industrial implementation.
Collapse
Affiliation(s)
- Luís C. Martins
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Margarida Palma
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Angel Angelov
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (A.A.); (W.L.)
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany;
| | - Wolfgang Liebl
- TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; (A.A.); (W.L.)
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences/i4HB—Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (L.C.M.); (M.P.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Correspondence:
| |
Collapse
|
10
|
Bereketoglu C, Nacar G, Sari T, Mertoglu B, Pradhan A. Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae. PeerJ 2021; 9:e10794. [PMID: 33614281 PMCID: PMC7882136 DOI: 10.7717/peerj.10794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022] Open
Abstract
Nonylphenol (NP) is a bioaccumulative environmental estrogen that is widely used as a nonionic surfactant. We have previously examined short-term effects of NP on yeast cells using microarray technology. In the present study, we investigated the adaptive response of Saccharomyces cerevisiae BY4742 cells to NP exposure by analyzing genome-wide transcriptional profiles using RNA-sequencing. We used 2 mg/L NP concentration for 40 days of exposure. Gene expression analysis showed that a total of 948 genes were differentially expressed. Of these, 834 genes were downregulated, while 114 genes were significantly upregulated. GO enrichment analysis revealed that 369 GO terms were significantly affected by NP exposure. Further analysis showed that many of the differentially expressed genes were associated with oxidative phosphorylation, iron and copper acquisition, autophagy, pleiotropic drug resistance and cell cycle progression related processes such as DNA and mismatch repair, chromosome segregation, spindle checkpoint activity, and kinetochore organization. Overall, these results provide considerable information and a comprehensive understanding of the adaptive response to NP exposure at the gene expression level.
Collapse
Affiliation(s)
- Ceyhun Bereketoglu
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Iskenderun Technical University, Hatay, Turkey
| | - Gozde Nacar
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Tugba Sari
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
| |
Collapse
|
11
|
Soares EV, Soares HMVM. Harmful effects of metal(loid) oxide nanoparticles. Appl Microbiol Biotechnol 2021; 105:1379-1394. [PMID: 33521847 PMCID: PMC7847763 DOI: 10.1007/s00253-021-11124-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/04/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023]
Abstract
The incorporation of nanomaterials (NMs), including metal(loid) oxide (MOx) nanoparticles (NPs), in the most diversified consumer products, has grown enormously in recent decades. Consequently, the contact between humans and these materials increased, as well as their presence in the environment. This fact has raised concerns and uncertainties about the possible risks of NMs to human health and the adverse effects on the environment. These concerns underline the need and importance of assessing its nanosecurity. The present review focuses on the main mechanisms underlying the MOx NPs toxicity, illustrated with different biological models: release of toxic ions, cellular uptake of NPs, oxidative stress, shading effect on photosynthetic microorganisms, physical restrain and damage of cell wall. Additionally, the biological models used to evaluate the potential hazardous of nanomaterials are briefly presented, with particular emphasis on the yeast Saccharomyces cerevisiae, as an alternative model in nanotoxicology. An overview containing recent scientific advances on cellular responses (toxic symptoms exhibited by yeasts) resulting from the interaction with MOx NPs (inhibition of cell proliferation, cell wall damage, alteration of function and morphology of organelles, presence of oxidative stress bio-indicators, gene expression changes, genotoxicity and cell dead) is critically presented. The elucidation of the toxic modes of action of MOx NPs in yeast cells can be very useful in providing additional clues about the impact of NPs on the physiology and metabolism of the eukaryotic cell. Current and future trends of MOx NPs toxicity, regarding their possible impacts on the environment and human health, are discussed. KEY POINTS: • The potential hazardous effects of MOx NPs are critically reviewed. • An overview of the main mechanisms associated with MOx NPs toxicity is presented. • Scientific advances about yeast cell responses to MOx NPs are updated and discussed.
Collapse
Affiliation(s)
- Eduardo V Soares
- Bioengineering Laboratory-CIETI, ISEP-School of Engineering, Polytechnic Institute of Porto, rua Dr António Bernardino de Almeida, 431, 4249-015, Porto, Portugal.
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, 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
| |
Collapse
|
12
|
Mota MN, Martins LC, Sá-Correia I. The Identification of Genetic Determinants of Methanol Tolerance in Yeast Suggests Differences in Methanol and Ethanol Toxicity Mechanisms and Candidates for Improved Methanol Tolerance Engineering. J Fungi (Basel) 2021; 7:90. [PMID: 33513997 PMCID: PMC7911966 DOI: 10.3390/jof7020090] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 12/15/2022] Open
Abstract
Methanol is a promising feedstock for metabolically competent yeast strains-based biorefineries. However, methanol toxicity can limit the productivity of these bioprocesses. Therefore, the identification of genes whose expression is required for maximum methanol tolerance is important for mechanistic insights and rational genomic manipulation to obtain more robust methylotrophic yeast strains. The present chemogenomic analysis was performed with this objective based on the screening of the Euroscarf Saccharomyces cerevisiae haploid deletion mutant collection to search for susceptibility phenotypes in YPD medium supplemented with 8% (v/v) methanol, at 35 °C, compared with an equivalent ethanol concentration (5.5% (v/v)). Around 400 methanol tolerance determinants were identified, 81 showing a marked phenotype. The clustering of the identified tolerance genes indicates an enrichment of functional categories in the methanol dataset not enriched in the ethanol dataset, such as chromatin remodeling, DNA repair and fatty acid biosynthesis. Several genes involved in DNA repair (eight RAD genes), identified as specific for methanol toxicity, were previously reported as tolerance determinants for formaldehyde, a methanol detoxification pathway intermediate. This study provides new valuable information on genes and potential regulatory networks involved in overcoming methanol toxicity. This knowledge is an important starting point for the improvement of methanol tolerance in yeasts capable of catabolizing and copying with methanol concentrations present in promising bioeconomy feedstocks, including industrial residues.
Collapse
Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (M.N.M.); (L.C.M.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Luís C. Martins
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (M.N.M.); (L.C.M.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; (M.N.M.); (L.C.M.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| |
Collapse
|
13
|
Godinho CP, Costa R, Sá‐Correia I. The ABC transporter Pdr18 is required for yeast thermotolerance due to its role in ergosterol transport and plasma membrane properties. Environ Microbiol 2021; 23:69-80. [PMID: 32985771 PMCID: PMC7891575 DOI: 10.1111/1462-2920.15253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022]
Abstract
Among the mechanisms by which yeast overcomes multiple stresses is the expression of genes encoding ATP-binding cassette (ABC) transporters required for resistance to a wide range of toxic compounds. These substrates may include weak acids, alcohols, agricultural pesticides, polyamines, metal cations, as in the case of Pdr18. This pleotropic drug resistance transporter was previously proposed to transport ergosterol at the plasma membrane (PM) level contributing to the maintenance of PM lipid organization and reduced diffusional permeation induced by lipophilic compounds. The present work reports a novel phenotype associated with the putative drug/xenobiotic-efflux-pump transporter Pdr18: the resistance to heat shock and to long-term growth at supra-optimal temperatures. Cultivation at 40°C was demonstrated to lead to higher PM permeabilization of a pdr18Δ cell population with the PDR18 gene deleted compared with the parental strain population, as indicated by flow cytometry analysis of propidium iodide stained cells. Cells of pdr18Δ grown at 40°C also exhibited increased transcription levels from genes of the ergosterol biosynthetic pathway, compared with parental cells. However, this adaptive response at 40°C was not enough to maintain PM physiological ergosterol levels in the population lacking the Pdr18 transporter and free ergosterol precursors accumulate in the deletion mutant cells.
Collapse
Affiliation(s)
- Cláudia P. Godinho
- iBB ‐ Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisbonPortugal
| | - Rute Costa
- iBB ‐ Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisbonPortugal
- Department of BioengineeringInstituto Superior Técnico, Universidade de LisboaLisbonPortugal
| | - Isabel Sá‐Correia
- iBB ‐ Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisbonPortugal
- Department of BioengineeringInstituto Superior Técnico, Universidade de LisboaLisbonPortugal
| |
Collapse
|
14
|
Cytotoxicity of Oleandrin Is Mediated by Calcium Influx and by Increased Manganese Uptake in Saccharomyces cerevisiae Cells. Molecules 2020; 25:molecules25184259. [PMID: 32957533 PMCID: PMC7570853 DOI: 10.3390/molecules25184259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 11/22/2022] Open
Abstract
Oleandrin, the main component of Nerium oleander L. extracts, is a cardiotoxic glycoside with multiple pharmacological implications, having potential anti-tumoral and antiviral characteristics. Although it is accepted that the main mechanism of oleandrin action is the inhibition of Na+/K+-ATPases and subsequent increase in cell calcium, many aspects which determine oleandrin cytotoxicity remain elusive. In this study, we used the model Saccharomyces cerevisiae to unravel new elements accounting for oleandrin toxicity. Using cells expressing the Ca2+-sensitive photoprotein aequorin, we found that oleandrin exposure resulted in Ca2+ influx into the cytosol and that failing to pump Ca2+ from the cytosol to the vacuole increased oleandrin toxicity. We also found that oleandrin exposure induced Mn2+ accumulation by yeast cells via the plasma membrane Smf1 and that mutants with defects in Mn2+ homeostasis are oleandrin-hypersensitive. Our data suggest that combining oleandrin with agents which alter Ca2+ or Mn2+ uptake may be a way of controlling oleandrin toxicity.
Collapse
|
15
|
Ruta LL, Farcasanu IC. Saccharomyces cerevisiae and Caffeine Implications on the Eukaryotic Cell. Nutrients 2020; 12:nu12082440. [PMID: 32823708 PMCID: PMC7468979 DOI: 10.3390/nu12082440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Caffeine-a methylxanthine analogue of the purine bases adenine and guanine-is by far the most consumed neuro-stimulant, being the active principle of widely consumed beverages such as coffee, tea, hot chocolate, and cola. While the best-known action of caffeine is to prevent sleepiness by blocking the adenosine receptors, caffeine exerts a pleiotropic effect on cells, which lead to the activation or inhibition of various cell integrity pathways. The aim of this review is to present the main studies set to investigate the effects of caffeine on cells using the model eukaryotic microorganism Saccharomyces cerevisiae, highlighting the caffeine synergy with external cell stressors, such as irradiation or exposure to various chemical hazards, including cigarette smoke or chemical carcinogens. The review also focuses on the importance of caffeine-related yeast phenotypes used to resolve molecular mechanisms involved in cell signaling through conserved pathways, such as target of rapamycin (TOR) signaling, Pkc1-Mpk1 mitogen activated protein kinase (MAPK) cascade, or Ras/cAMP protein kinase A (PKA) pathway.
Collapse
|
16
|
Martins LC, Monteiro CC, Semedo PM, Sá-Correia I. Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges. Appl Microbiol Biotechnol 2020; 104:6527-6547. [PMID: 32474799 PMCID: PMC7347521 DOI: 10.1007/s00253-020-10697-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/19/2020] [Indexed: 01/29/2023]
Abstract
Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.
Collapse
Affiliation(s)
- Luís C Martins
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina C Monteiro
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Paula M Semedo
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
17
|
Gallo V, Srivastava V, Bulone V, Zappettini A, Villani M, Marmiroli N, Marmiroli M. Proteomic Analysis Identifies Markers of Exposure to Cadmium Sulphide Quantum Dots (CdS QDs). NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1214. [PMID: 32580447 PMCID: PMC7353101 DOI: 10.3390/nano10061214] [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: 04/06/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022]
Abstract
The use of cadmium sulphide quantum dot (CdS QD)-enabled products has become increasingly widespread. The prospect of their release in the environment is raising concerns. Here we have used the yeast model Saccharomyces cerevisiae to determine the potential impact of CdS QD nanoparticles on living organisms. Proteomic analyses and cell viability assays performed after 9 h exposure revealed expression of proteins involved in oxidative stress and reduced lethality, respectively, whereas oxidative stress declined, and lethality increased after 24 h incubation in the presence of CdS QDs. Quantitative proteomics using the iTRAQ approach (isobaric tags for relative and absolute quantitation) revealed that key proteins involved in essential biological pathways were differentially regulated over the time course of the experiment. At 9 h, most of the glycolytic functions increased, and the abundance of the number of heat shock proteins increased. This contrasts with the situation at 24 h where glycolytic functions, some heat shock proteins as well as oxidative phosphorylation and ATP synthesis were down-regulated. It can be concluded from our data that cell exposure to CdS QDs provokes a metabolic shift from respiration to fermentation, comparable to the situation reported in some cancer cell lines.
Collapse
Affiliation(s)
- Valentina Gallo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
| | - Vaibhav Srivastava
- Royal Institute of Technology (KTH), Department of Chemistry, Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, SE-106 91 Stockholm, Sweden; (V.S.); (V.B.)
| | - Vincent Bulone
- Royal Institute of Technology (KTH), Department of Chemistry, Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, SE-106 91 Stockholm, Sweden; (V.S.); (V.B.)
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Urbrae, SA 5064, Australia
| | - Andrea Zappettini
- Department of Nanomaterials, Institute of Materials for Electronics and Magnetism (IMEM)Department of Nanomaterials, National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Marco Villani
- Department of Nanomaterials, Institute of Materials for Electronics and Magnetism (IMEM)Department of Nanomaterials, National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
- The Italian National Interuniversity Consortium for Environmental Sciences (CINSA), 43124 Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
| |
Collapse
|
18
|
Xie Z, Fong WP, Tsang PWK. Engineering and optimization of phosphate-responsive phytase expression in Pichia pastoris yeast for phytate hydrolysis. Enzyme Microb Technol 2020; 137:109533. [PMID: 32423670 DOI: 10.1016/j.enzmictec.2020.109533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 10/25/2022]
Abstract
Phytate is the major storage form of phosphorus in plants. It is present in cereals and raw materials of vegetable origin used in animal and human diets. However, non-ruminant animals have little phytase activity in their guts and, therefore, cannot digest phytate. As a result, almost all dietary phytate is discharged into the environment, causing phosphorus pollution. Phytate is also considered as an "antinutrient" for its ability to form insoluble and stable complexes with metal ions, thus reducing dietary absorption of essential minerals. It is a dire need to develop sustainable approaches for environmentally-friendly utilization for this valuable and abundant natural resource. To this end, we engineered Pichia pastoris to express and secrete phytase in a "made-to-order" fashion in response to external level of inorganic phosphate (Pi). Responsiveness to external Pi level was achieved by generating a Pi-responsive promoter library using directed evolution. The resultant yeast strains were proven to liberate Pi from wheat-based meal in a simulated in vitro digestion model. These yeast-based whole cell biocatalysts may serve as platform hosts with potential applications in food processing industry and animal waste treatment.
Collapse
Affiliation(s)
- Zhenming Xie
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing-Ping Fong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Paul Wai-Kei Tsang
- Technological and Higher Education Institute of Hong Kong, Hong Kong, China.
| |
Collapse
|
19
|
Huang X, Tang S, Zheng L, Teng Y, Yang Y, Zhu J, Lu X. Construction of an Efficient and Robust Aspergillus terreus Cell Factory for Monacolin J Production. ACS Synth Biol 2019; 8:818-825. [PMID: 30856313 DOI: 10.1021/acssynbio.8b00489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monacolin J is a key precursor for the synthesis of the cholesterol-lowering drug simvastatin. Industrially, monacolin J is manufactured through the alkaline hydrolysis of the fungal polyketide lovastatin, which is relatively complex and environmentally unfriendly. A cell factory for monacolin J production was created by heterologously introducing lovastatin hydrolase into Aspergillus terreus in our previous study. However, residual lovastatin remained a problem for the downstream product purification. In this study, we used combined metabolic engineering strategies to create a more efficient and robust monacolin J-producing cell factory that completely lacks lovastatin residue. The complete deletion of the key gene lovF blocked the biosynthesis of lovastatin and led to a large accumulation of monacolin J without any lovastatin residue. Additionally, the overexpression of the specific transcription factor lovE under the P gpdAt promoter further increased the titer of monacolin J by 52.5% to 5.5 g L-1. Interestingly, the fermentation robustness was also significantly improved by the expression of lovE. This improvement not only avoids the process of alkaline hydrolysis but also simplifies the downstream separation process.
Collapse
Affiliation(s)
| | - Shen Tang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Linghui Zheng
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou 318000, China
| | - Yun Teng
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou 318000, China
| | - Yong Yang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou 318000, China
| | - Jinwei Zhu
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou 318000, China
| | - Xuefeng Lu
- Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Wenhai Rd 1, Aoshanwei, Qingdao 266003, China
| |
Collapse
|
20
|
Pagano L, Caldara M, Villani M, Zappettini A, Marmiroli N, Marmiroli M. In Vivo-In Vitro Comparative Toxicology of Cadmium Sulphide Quantum Dots in the Model Organism Saccharomyces cerevisiae. NANOMATERIALS 2019; 9:nano9040512. [PMID: 30986968 PMCID: PMC6523553 DOI: 10.3390/nano9040512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022]
Abstract
The aim of this work was to use the yeast Saccharomyces cerevisiae as a tool for toxicogenomic studies of Engineered Nanomaterials (ENMs) risk assessment, in particular focusing on cadmium based quantum dots (CdS QDs). This model has been exploited for its peculiar features: a short replication time, growth on both fermentable and oxidizable carbon sources, and for the contextual availability of genome wide information in the form of genetic maps, DNA microarray, and collections of barcoded mutants. The comparison of the whole genome analysis with the microarray experiments (99.9% coverage) and with the phenotypic analysis of 4688 barcoded haploid mutants (80.2% coverage), shed light on the genes involved in the response to CdS QDs, both in vivo and in vitro. The results have clarified the mechanisms involved in the exposure to CdS QDs, and whether these ENMs and Cd2+ exploited different pathways of response, in particular related to oxidative stress and to the maintenance of mitochondrial integrity and function. Saccharomyces cerevisiae remains a versatile and robust alternative for organismal toxicological studies, with a high level of heuristic insights into the toxicology of more complex eukaryotes, including mammals.
Collapse
Affiliation(s)
- Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
| | - Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
| | | | | | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA), University of Parma, 43123 Parma, Italy.
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
| |
Collapse
|
21
|
Palma M, Sá-Correia I. Physiological Genomics of the Highly Weak-Acid-Tolerant Food Spoilage Yeasts of Zygosaccharomyces bailii sensu lato. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:85-109. [PMID: 30911890 DOI: 10.1007/978-3-030-13035-0_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Zygosaccharomyces bailii and two closely related species, Z. parabailii and Z. pseudobailii ("Z. bailii species complex", "Z. bailii sensu lato" or simply "Z. bailii (s.l.)"), are frequently implicated in the spoilage of acidified preserved foods and beverages due to their tolerance to very high concentrations of weak acids used as food preservatives. The recent sequencing and annotation of these species' genomes have clarified their genomic organization and phylogenetic relationship, which includes events of interspecies hybridization. Mechanistic insights into their adaptation and tolerance to weak acids (e.g., acetic and lactic acids) are also being revealed. Moreover, the potential of Z. bailii (s.l.) to be used in industrial biotechnological processes as interesting cell factories for the production of organic acids, reduction of the ethanol content, increase of alcoholic beverages aroma complexity, as well as of genetic source for increasing weak acid resistance in yeast, is currently being considered. This chapter includes taxonomical, ecological, physiological, and biochemical aspects of Z. bailii (s.l.). The focus is on the exploitation of physiological genomics approaches that are providing the indispensable holistic knowledge to guide the effective design of strategies to overcome food spoilage or the rational exploitation of these yeasts as promising cell factories.
Collapse
Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences (iBB) and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences (iBB) and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| |
Collapse
|
22
|
Gil FN, Gonçalves AC, Becker JD, Viegas CA. Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:871-889. [PMID: 29611082 DOI: 10.1007/s10646-018-1929-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
Accidental spills and misuse of pesticides may lead to current and/or legacy environmental contamination and may pose concerns regarding possible risks towards non-target microbes and higher eukaryotes in ecosystems. The present study was aimed at comparing transcriptomic responses to effects of sub-lethal levels of six environmentally relevant pesticide active substances in the Saccharomyces cerevisiae eukaryotic model. The insecticide carbofuran, the fungicide pyrimethanil and the herbicides alachlor, S-metolachlor, diuron and methyl(4-chloro-2-methylphenoxy)acetate were studied. Some are currently used agricultural pesticides, while others are under restricted utilization or banned in Europe and/or North America albeit being used in other geographical locations. In the present work transcriptional profiles representing genome-wide responses in a standardized yeast population upon 2 h of exposure to concentrations of each compound exerting equivalent toxic effects, i.e., inhibition of growth by 20% relative to the untreated control cells, were examined. Hierarchical clustering and Venn analyses of the datasets of differentially expressed genes pointed out transcriptional patterns distinguishable between the six active substances. Functional enrichment analyses allowed predicting mechanisms of pesticide toxicity and response to pesticide stress in the yeast model. In general, variations in transcript numbers of selected genes assessed by Real-Time quantitative reverse transcription polymerase chain reaction confirmed microarray data and correlated well with growth inhibitory effects. A possible biological relevance of mechanistic predictions arising from these comparative transcriptomic analyses is discussed in the context of better understanding potential modes of action and adverse side-effects of pesticides.
Collapse
Affiliation(s)
- Fátima N Gil
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Alina C Gonçalves
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande N°6, 2780-156, Oeiras, Portugal
| | - Cristina A Viegas
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av Rovisco Pais, 1049-001, Lisboa, Portugal.
- Department of Bioengineering, IST, UL, Av Rovisco Pais, 1049-001, Lisboa, Portugal.
| |
Collapse
|
23
|
Godinho CP, Prata CS, Pinto SN, Cardoso C, Bandarra NM, Fernandes F, Sá-Correia I. Pdr18 is involved in yeast response to acetic acid stress counteracting the decrease of plasma membrane ergosterol content and order. Sci Rep 2018; 8:7860. [PMID: 29777118 PMCID: PMC5959924 DOI: 10.1038/s41598-018-26128-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/04/2018] [Indexed: 11/11/2022] Open
Abstract
Saccharomyces cerevisiae has the ability to become less sensitive to a broad range of chemically and functionally unrelated cytotoxic compounds. Among multistress resistance mechanisms is the one mediated by plasma membrane efflux pump proteins belonging to the ABC superfamily, questionably proposed to enhance the kinetics of extrusion of all these compounds. This study provides new insights into the biological role and impact in yeast response to acetic acid stress of the multistress resistance determinant Pdr18 proposed to mediate ergosterol incorporation in plasma membrane. The described coordinated activation of the transcription of PDR18 and of several ergosterol biosynthetic genes (ERG2-4, ERG6, ERG24) during the period of adaptation to acetic acid inhibited growth provides further support to the involvement of Pdr18 in yeast response to maintain plasma membrane ergosterol content in stressed cells. Pdr18 role in ergosterol homeostasis helps the cell to counteract acetic acid-induced decrease of plasma membrane lipid order, increase of the non-specific membrane permeability and decrease of transmembrane electrochemical potential. Collectively, our results support the notion that Pdr18-mediated multistress resistance is closely linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties.
Collapse
Affiliation(s)
- Cláudia P Godinho
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Catarina S Prata
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Sandra N Pinto
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.,Centro de Química-Física Molecular, Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Carlos Cardoso
- DivAV, IPMA - Instituto Português do Mar e da Atmosfera, Rua Alfredo Magalhães Ramalho 6, 1495-006, Lisbon, Portugal
| | - Narcisa M Bandarra
- DivAV, IPMA - Instituto Português do Mar e da Atmosfera, Rua Alfredo Magalhães Ramalho 6, 1495-006, Lisbon, Portugal
| | - Fábio Fernandes
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.,Centro de Química-Física Molecular, Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- IBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| |
Collapse
|
24
|
Pinu FR, Granucci N, Daniell J, Han TL, Carneiro S, Rocha I, Nielsen J, Villas-Boas SG. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test. Metabolomics 2018; 14:43. [PMID: 30830324 DOI: 10.1007/s11306-018-1339-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/07/2018] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. MATERIALS AND METHODS The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow. CONCLUSIONS Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.
Collapse
Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
| | - Ninna Granucci
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Daniell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
- LanzaTech, Skokie, IL, 60077, USA
| | - Ting-Li Han
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Sonia Carneiro
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Isabel Rocha
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
25
|
Nickel oxide (NiO) nanoparticles disturb physiology and induce cell death in the yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2018; 102:2827-2838. [PMID: 29423633 DOI: 10.1007/s00253-018-8802-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/18/2018] [Accepted: 01/20/2018] [Indexed: 10/18/2022]
Abstract
The increasing use of nanoparticles (NPs) has spurred concerns about their toxic effects. This work aimed to assess the potential hazards of nickel oxide (NiO) NPs using the yeast Saccharomyces cerevisiae as a cell model. Yeast cells exposed for 6 h to 100 mg/L NiO NPs presented reduced metabolic activity (esterase activity and FUN-1 dye processing) and enhanced accumulation of reactive oxygen species. NiO NPs induced the loss of cell viability in a dose-dependent manner. Study of the dissolution of NiO NPs in aqueous media, together with the toxicological data, suggests that the nickel released by the NPs cannot explain all the toxic effects observed in S. cerevisiae caused by the NPs. Transmission electron microscopy observations revealed that NiO NPs were adsorbed onto cell surface but did not enter into yeast cells. Isogenic mutants (cwp1∆ and cwp2∆) with increased cell wall porosity did not display enhanced susceptibility to NiO NPs compared to the wild type strain. Our results suggest that NiO NPs exert their toxic effect by an indirect mechanism. This work contributes to knowledge of the potential hazards of NiO NPs and to the elucidation of their mechanisms of toxic action.
Collapse
|
26
|
Lazard M, Dauplais M, Blanquet S, Plateau P. Recent advances in the mechanism of selenoamino acids toxicity in eukaryotic cells. Biomol Concepts 2018; 8:93-104. [PMID: 28574376 DOI: 10.1515/bmc-2017-0007] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/03/2017] [Indexed: 12/31/2022] Open
Abstract
Selenium is an essential trace element due to its incorporation into selenoproteins with important biological functions. However, at high doses it is toxic. Selenium toxicity is generally attributed to the induction of oxidative stress. However, it has become apparent that the mode of action of seleno-compounds varies, depending on its chemical form and speciation. Recent studies in various eukaryotic systems, in particular the model organism Saccharomyces cerevisiae, provide new insights on the cytotoxic mechanisms of selenomethionine and selenocysteine. This review first summarizes current knowledge on reactive oxygen species (ROS)-induced genotoxicity of inorganic selenium species. Then, we discuss recent advances on our understanding of the molecular mechanisms of selenocysteine and selenomethionine cytotoxicity. We present evidences indicating that both oxidative stress and ROS-independent mechanisms contribute to selenoamino acids cytotoxicity. These latter mechanisms include disruption of protein homeostasis by selenocysteine misincorporation in proteins and/or reaction of selenols with protein thiols.
Collapse
|
27
|
Zhang M, Zhang K, Mehmood MA, Zhao ZK, Bai F, Zhao X. Deletion of acetate transporter gene ADY2 improved tolerance of Saccharomyces cerevisiae against multiple stresses and enhanced ethanol production in the presence of acetic acid. BIORESOURCE TECHNOLOGY 2017; 245:1461-1468. [PMID: 28606754 DOI: 10.1016/j.biortech.2017.05.191] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/27/2017] [Accepted: 05/29/2017] [Indexed: 05/24/2023]
Abstract
The aim of this work was to study the effects of deleting acetate transporter gene ADY2 on growth and fermentation of Saccharomyces cerevisiae in the presence of inhibitors. Comparative transcriptome analysis revealed that three genes encoding plasma membrane carboxylic acid transporters, especially ADY2, were significantly downregulated under the zinc sulfate addition condition in the presence of acetic acid stress, and the deletion of ADY2 improved growth of S. cerevisiae under acetic acid, ethanol and hydrogen peroxide stresses. Consistently, a concomitant increase in ethanol production by 14.7% in the presence of 3.6g/L acetic acid was observed in the ADY2 deletion mutant of S. cerevisiae BY4741. Decreased intracellular acetic acid, ROS accumulation, and plasma membrane permeability were observed in the ADY2 deletion mutant. These findings would be useful for developing robust yeast strains for efficient ethanol production.
Collapse
Affiliation(s)
- Mingming Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Keyu Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Aamer Mehmood
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Zongbao Kent Zhao
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
28
|
Bereketoglu C, Arga KY, Eraslan S, Mertoglu B. Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure. Physiol Genomics 2017; 49:549-566. [PMID: 28887370 DOI: 10.1152/physiolgenomics.00034.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/17/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023] Open
Abstract
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a nonionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/l; <15% cell number reduction) and high (5 mg/l; >65% cell number reduction) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/l NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed. Similarly, 678 (168 repressed, 510 induced) and 688 genes (215 repressed, 473 induced) were differentially expressed in cells exposed to 5 mg/l NP for 120 and 180 min, respectively. Only 15 downregulated and 63 upregulated genes were common between low and high NP inhibitory concentration exposure for 120 min, whereas 16 downregulated and 31 upregulated genes were common after the 180-min exposure. Several processes/pathways were prominently affected by either low or high inhibitory concentration exposure, while certain processes were affected by both inhibitory concentrations, including ion transport, response to chemicals, transmembrane transport, cellular amino acids, and carbohydrate metabolism. While minimal expression changes were observed with low inhibitory concentration exposure, 5 mg/l NP treatment induced substantial expression changes in genes involved in oxidative phosphorylation, cell wall biogenesis, ribosomal biogenesis, and RNA processing, and encoding heat shock proteins and ubiquitin-conjugating enzymes. Collectively, these results provide considerable information on effects of NP at the molecular level.
Collapse
Affiliation(s)
- Ceyhun Bereketoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey; .,Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University; Baglarbasi, Gumushane, Turkey; and
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| | - Serpil Eraslan
- Department of Chemical Engineering, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Bulent Mertoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University; Goztepe, Kadikoy, Istanbul, Turkey
| |
Collapse
|
29
|
André C, Gagné F. Effect of the periodic properties of toxic stress on the oscillatory behaviour of glycolysis in yeast-evidence of a toxic effect frequency. Comp Biochem Physiol C Toxicol Pharmacol 2017; 196:36-43. [PMID: 28286097 DOI: 10.1016/j.cbpc.2017.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 01/19/2023]
Abstract
Starving and nondividing yeast cells induce changes in the electron donor nicotinamide adenine dinucleotide (NADH) levels in a cyclic and wave-like manner for over 90min. Yeast suspensions were used to examine the toxic effects of contaminants on the cyclic behaviour of metabolite changes during anaerobic glycolysis. The cyclic behaviour NADH levels in yeast cell suspensions starved for 2 to 5h was studied after the addition of 10mM glucose for 5min followed by 10mM KCN to block aerobic glycolysis. The effects of three toxic elements (CuSO4, silver nanoparticles-nAg, and GdCl3), known for their potential to alter glycolsysis, on NADH levels over time were examined during the 3-h starvation step. The data were analyzed using spectral analysis (Fourier transformation) to characterize the cyclic behaviour of NADH levels during anaerobic glycolysis. Increasing the starvation time by 3h increased the amplitude of changes in NADH levels with characteristic periods of 3 to 8min. Longer starvation times decreased the amplitude of oscillations during these periods, with the appearance of NADH changes at higher frequencies. Moreover, the amplitude changes in NADH were proportional to the starvation time. Exposure to the above chemicals during the 3-h starvation time led to the formation of higher frequencies with concentration-dependent amplitude changes. In comparison with nAg and Gd3+, Cu2+ was the most toxic (decreased viability the most) and produce changes at higher frequencies as well. It is noteworthy that each element produced a characteristic change in the frequency profiles, which suggests different mechanisms of action in which the severity of toxicity shifted NADH changes at higher frequencies. In conclusion, the appearance of synchronized oscillations in dense yeast populations following synchronization stress could be induced by starvation and exposure to chemicals. However, synchronicity could be abolished when cells desynchronize as a result of loss of cell viability, which contributes to heterogeneity in yeast populations, translating into NADH changes at higher frequencies. This is the first report on the influence of environmental contaminants on the cyclic or wave-like behaviour of biochemical changes in cells.
Collapse
Affiliation(s)
- C André
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, 105 McGill St., Montréal, QC H2Y 2E7, Canada
| | - F Gagné
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, 105 McGill St., Montréal, QC H2Y 2E7, Canada.
| |
Collapse
|
30
|
Yeast response and tolerance to benzoic acid involves the Gcn4- and Stp1-regulated multidrug/multixenobiotic resistance transporter Tpo1. Appl Microbiol Biotechnol 2017; 101:5005-5018. [PMID: 28409382 PMCID: PMC5486834 DOI: 10.1007/s00253-017-8277-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/22/2017] [Accepted: 03/27/2017] [Indexed: 11/27/2022]
Abstract
The action of benzoic acid in the food and beverage industries is compromised by the ability of spoilage yeasts to cope with this food preservative. Benzoic acid occurs naturally in many plants and is an intermediate compound in the biosynthesis of many secondary metabolites. The understanding of the mechanisms underlying the response and resistance to benzoic acid stress in the eukaryotic model yeast is thus crucial to design more suitable strategies to deal with this toxic lipophilic weak acid. In this study, the Saccharomyces cerevisiae multidrug transporter Tpo1 was demonstrated to confer resistance to benzoic acid. TPO1 transcript levels were shown to be up-regulated in yeast cells suddenly exposed to this stress agent. This up-regulation is under the control of the Gcn4 and Stp1 transcription factors, involved in the response to amino acid availability, but not under the regulation of the multidrug resistance transcription factors Pdr1 and Pdr3 that have binding sites in TPO1 promoter region. Benzoic acid stress was further shown to affect the intracellular pool of amino acids and polyamines. The observed decrease in the concentration of these nitrogenous compounds, registered upon benzoic acid stress exposure, was not found to be dependent on Tpo1, although the limitation of yeast cells on nitrogenous compounds was found to activate Tpo1 expression. Altogether, the results described in this study suggest that Tpo1 is one of the key players standing in the crossroad between benzoic acid stress response and tolerance and the control of the intracellular concentration of nitrogenous compounds. Also, results can be useful to guide the design of more efficient preservation strategies and the biotechnological synthesis of benzoic acid or benzoic acid-derived compounds.
Collapse
|
31
|
Exposure to selenomethionine causes selenocysteine misincorporation and protein aggregation in Saccharomyces cerevisiae. Sci Rep 2017; 7:44761. [PMID: 28303947 PMCID: PMC5355996 DOI: 10.1038/srep44761] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/13/2017] [Indexed: 12/23/2022] Open
Abstract
Selenomethionine, a dietary supplement with beneficial health effects, becomes toxic if taken in excess. To gain insight into the mechanisms of action of selenomethionine, we screened a collection of ≈5900 Saccharomyces cerevisiae mutants for sensitivity or resistance to growth-limiting amounts of the compound. Genes involved in protein degradation and synthesis were enriched in the obtained datasets, suggesting that selenomethionine causes a proteotoxic stress. We demonstrate that selenomethionine induces an accumulation of protein aggregates by a mechanism that requires de novo protein synthesis. Reduction of translation rates was accompanied by a decrease of protein aggregation and of selenomethionine toxicity. Protein aggregation was supressed in a ∆cys3 mutant unable to synthetize selenocysteine, suggesting that aggregation results from the metabolization of selenomethionine to selenocysteine followed by translational incorporation in the place of cysteine. In support of this mechanism, we were able to detect random substitutions of cysteinyl residues by selenocysteine in a reporter protein. Our results reveal a novel mechanism of toxicity that may have implications in higher eukaryotes.
Collapse
|
32
|
Pasquali F, Agrimonti C, Pagano L, Zappettini A, Villani M, Marmiroli M, White JC, Marmiroli N. Nucleo-mitochondrial interaction of yeast in response to cadmium sulfide quantum dot exposure. JOURNAL OF HAZARDOUS MATERIALS 2017; 324:744-752. [PMID: 27890358 DOI: 10.1016/j.jhazmat.2016.11.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Cell sensitivity to quantum dots (QDs) has been attributed to a cascade triggered by oxidative stress leading to apoptosis. The role and function of mitochondria in animal cells are well understood but little information is available on the complex genetic networks that regulate nucleo-mitochondrial interaction. The effect of CdS QD exposure in yeast Saccharomyces cerevisiae was assessed under conditions of limited lethality (<10%), using cell physiological and morphological endpoints. Whole-genomic array analysis and the screening of a deletion mutant library were also carried out. The results showed that QDs: increased the level of reactive oxygen species (ROS) and decreased the level of reduced vs oxidized glutathione (GSH/GSSG); reduced oxygen consumption and the abundance of respiratory cytochromes; disrupted mitochondrial membrane potentials and affected mitochondrial morphology. Exposure affected the capacity of cells to grow on galactose, which requires nucleo-mitochondrial involvement. However, QDs exposure did not materially induce respiratory deficient (RD) mutants but only RD phenocopies. All of these cellular changes were correlated with several key nuclear genes, including TOM5 and FKS1, involved in the maintenance of mitochondrial organization and function. The consequences of these cellular effects are discussed in terms of dysregulation of cell function in response to these "pathological mitochondria".
Collapse
Affiliation(s)
| | | | - Luca Pagano
- Department of Life Sciences, University of Parma, Parma, Italy; Stockbridge school of Agriculture, University of Massachusetts, Amherst, MA, USA; The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Andrea Zappettini
- IMEM-CNR - Istituto dei Materiali per l'Elettronica ed il Magnetismo, Parma, Italy
| | - Marco Villani
- IMEM-CNR - Istituto dei Materiali per l'Elettronica ed il Magnetismo, Parma, Italy
| | - Marta Marmiroli
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parma, Italy; CINSA - Consorzio Interuniversitario Nazionale per le Scienze Ambientali, University of Parma, Parma, Italy.
| |
Collapse
|
33
|
Watanabe D, Takagi H. Yeasts for Global Happiness: report of the 14th International Congress on Yeasts (ICY14) held in Awaji Island. Genes Cells 2017; 22:130-134. [PMID: 28105742 DOI: 10.1111/gtc.12471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
The 14th International Congress on Yeasts (ICY14) was held at Awaji Yumebutai International Conference Center (Awaji, Hyogo) in Japan from 11 to 15 September 2016. The main slogan of ICY14 was 'Yeasts for Global Happiness', which enabled us to acknowledge the high-potential usefulness of yeasts contributing to the global happiness in terms of food/beverage, health/medicine and energy/environment industries, as well as to basic biosciences. In addition, two more concepts were introduced: 'from Japan to the world' and 'from senior to junior'. As it was the first ICY meeting held in Japan or other Asian countries, ICY14 provided a good opportunity to widely spread the great achievements by Japanese and Asian yeast researchers, such as those by the 2016 Nobel Laureate Dr. Yoshinori Ohsumi, and also, to convey the fun and importance of yeasts to the next generation of researchers from Asia and all over the world. As a result, a total of 426 yeast lovers from 42 countries (225 overseas and 201 domestic participants) with different generations attended ICY14 to share the latest knowledge of a wide range of yeast research fields and to join active and constructive scientific discussions.
Collapse
Affiliation(s)
- Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| |
Collapse
|
34
|
Henriques SF, Mira NP, Sá-Correia I. Genome-wide search for candidate genes for yeast robustness improvement against formic acid reveals novel susceptibility (Trk1 and positive regulators) and resistance (Haa1-regulon) determinants. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:96. [PMID: 28428821 PMCID: PMC5395885 DOI: 10.1186/s13068-017-0781-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4.5. This chemogenomic analysis allowed the identification of 172 determinants of tolerance and 41 determinants of susceptibility to formic acid. Clustering of genes required for maximal tolerance to this weak acid, based on their biological function, indicates an enrichment of those involved in intracellular trafficking and protein synthesis, cell wall and cytoskeleton organization, carbohydrate metabolism, lipid, amino acid and vitamin metabolism, response to stress, chromatin remodelling, transcription and internal pH homeostasis. Among these genes is HAA1 encoding the main transcriptional regulator of yeast transcriptome reprograming in response to acetic acid and genes of the Haa1-regulon; all demonstrated determinants of acetic acid tolerance. Among the genes that when deleted lead to increased tolerance to formic acid, TRK1, encoding the high-affinity potassium transporter and a determinant of resistance to acetic acid, was surprisingly found. Consistently, genes encoding positive regulators of Trk1 activity were also identified as formic acid susceptibility determinants, while a negative regulator confers protection. At a saturating K+ concentration of 20 mM, the deletion mutant trk1Δ was found to exhibit a much higher tolerance compared with the parental strain. Given that trk1Δ accumulates lower levels of radiolabelled formic acid, compared to the parental strain, it is hypothesized that Trk1 facilitates formic acid uptake into the yeast cell. CONCLUSIONS The list of genes resulting from this study shows a few marked differences from the list of genes conferring protection to acetic acid and provides potentially valuable information to guide improvement programmes for the development of more robust strains against formic acid.
Collapse
Affiliation(s)
- Sílvia F. Henriques
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Nuno P. Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| |
Collapse
|
35
|
Sphingolipid biosynthesis upregulation by TOR complex 2-Ypk1 signaling during yeast adaptive response to acetic acid stress. Biochem J 2016; 473:4311-4325. [PMID: 27671892 DOI: 10.1042/bcj20160565] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 02/07/2023]
Abstract
Acetic acid-induced inhibition of yeast growth and metabolism limits the productivity of industrial fermentation processes, especially when lignocellulosic hydrolysates are used as feedstock in industrial biotechnology. Tolerance to acetic acid of food spoilage yeasts is also a problem in the preservation of acidic foods and beverages. Thus understanding the molecular mechanisms underlying adaptation and tolerance to acetic acid stress is increasingly important in industrial biotechnology and the food industry. Prior genetic screens for Saccharomyces cerevisiae mutants with increased sensitivity to acetic acid identified loss-of-function mutations in the YPK1 gene, which encodes a protein kinase activated by the target of rapamycin (TOR) complex 2 (TORC2). We show in the present study by several independent criteria that TORC2-Ypk1 signaling is stimulated in response to acetic acid stress. Moreover, we demonstrate that TORC2-mediated Ypk1 phosphorylation and activation is necessary for acetic acid tolerance, and occurs independently of Hrk1, a protein kinase previously implicated in the cellular response to acetic acid. In addition, we show that TORC2-Ypk1-mediated activation of l-serine:palmitoyl-CoA acyltransferase, the enzyme complex that catalyzes the first committed step of sphingolipid biosynthesis, is required for acetic acid tolerance. Furthermore, analysis of the sphingolipid pathway using inhibitors and mutants indicates that it is production of certain complex sphingolipids that contributes to conferring acetic acid tolerance. Consistent with that conclusion, promoting sphingolipid synthesis by adding exogenous long-chain base precursor phytosphingosine to the growth medium enhanced acetic acid tolerance. Thus appropriate modulation of the TORC2-Ypk1-sphingolipid axis in industrial yeast strains may have utility in improving fermentations of acetic acid-containing feedstocks.
Collapse
|
36
|
Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Curr Genet 2016; 63:253-274. [DOI: 10.1007/s00294-016-0633-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/14/2016] [Accepted: 07/16/2016] [Indexed: 01/06/2023]
|
37
|
Gil FN, Bellí G, Viegas CA. TheSaccharomyces cerevisiaeresponse to stress caused by the herbicidal active substance alachlor requires the iron regulon transcription factor Aft1p. Environ Microbiol 2016; 19:485-499. [DOI: 10.1111/1462-2920.13439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Fátima N. Gil
- iBB-Institute for Bioengineering and Biosciences; Instituto Superior Técnico (IST), Universidade de Lisboa (UL); Av. Rovisco Pais Lisboa 1049-001 Portugal
| | - Gemma Bellí
- Department of Basic Medical Sciences; IRBLleida, University of Lleida; Rovira Roure 80 Lleida 25198 Spain
| | - Cristina A. Viegas
- iBB-Institute for Bioengineering and Biosciences; Instituto Superior Técnico (IST), Universidade de Lisboa (UL); Av. Rovisco Pais Lisboa 1049-001 Portugal
- Department of Bioengineering; Instituto Superior Técnico (IST), Universidade de Lisboa (UL); Av. Rovisco Pais Lisboa 1049-001 Portugal
| |
Collapse
|
38
|
Hinkle KL, Anderson CC, Forkey B, Griffin J, Cone K, Vitzthum C, Olsen D. Exposure to the lampricide 3-trifluoromethyl-4-nitrophenol results in increased expression of carbohydrate transporters in Saccharomyces cerevisiae. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:1727-1732. [PMID: 26606276 PMCID: PMC5076018 DOI: 10.1002/etc.3314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/10/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) is used to control sea lamprey (Petromyzon marinus) populations in freshwater lakes. Although TFM can have sublethal and lethal effects, little is known about gene expression changes with TFM exposure. Microarray analysis was used to determine differential gene expression over 4 h of exposure in Saccharomyces cerevisiae. Among the most significantly up-regulated genes were regulators of carbohydrate transport, including HXT1, HXT3, HXT4, IMA5, MIG2, and YKR075C. Environ Toxicol Chem 2016;35:1727-1732. © 2015 SETAC.
Collapse
Affiliation(s)
- Karen L. Hinkle
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
| | - Chad C. Anderson
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
| | - Blake Forkey
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
| | - Jacob Griffin
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
- Department of Mathematics, Norwich University, Northfield, VT USA
| | - Kelsey Cone
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
| | - Carl Vitzthum
- Department of Biology and Physical Education, Norwich University, Northfield, VT USA
| | - Darlene Olsen
- Department of Mathematics, Norwich University, Northfield, VT USA
| |
Collapse
|
39
|
Graziano S, Gullì M, Maestri E, Marmiroli N. The global effect of exposing bakers' yeast to 5-fluoruracil and nystatin; a view to Toxichip. CHEMOSPHERE 2016; 145:470-479. [PMID: 26694798 DOI: 10.1016/j.chemosphere.2015.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/07/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
A genome-wide screen of a haploid deletion library of bakers' yeast (Saccharomyces cerevisiae) was conducted to document the phenotypic and transcriptional impact of exposure to each of the two pharmaceutical products 5-fluorouracil (an anti-tumor agent) and nystatin (an anti-fungal agent). The combined data set was handled by applying a systems biology perspective. A Gene Ontology analysis identified functional categories previously characterized as likely targets for both compounds. Induced transcription profiles were well correlated in yeast and human HepG2 cells. The identified molecular targets for both compounds were used to suggest a small set of human orthologues as appropriate for testing on human material. The yeast system developed here (denoted "Toxichip") has likely utility for identifying biomarkers relevant for health and environmental risk assessment applications required as part of the development process for novel pharmaceuticals.
Collapse
Affiliation(s)
- Sara Graziano
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Mariolina Gullì
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Elena Maestri
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.
| |
Collapse
|