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Atay G, Holyavkin C, Can H, Arslan M, Topaloğlu A, Trotta M, Çakar ZP. Evolutionary engineering and molecular characterization of cobalt-resistant Rhodobacter sphaeroides. Front Microbiol 2024; 15:1412294. [PMID: 38993486 PMCID: PMC11236759 DOI: 10.3389/fmicb.2024.1412294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
With its versatile metabolism including aerobic and anaerobic respiration, photosynthesis, photo-fermentation and nitrogen fixation, Rhodobacter sphaeroides can adapt to diverse environmental and nutritional conditions, including the presence of various stressors such as heavy metals. Thus, it is an important microorganism to study the molecular mechanisms of bacterial stress response and resistance, and to be used as a microbial cell factory for biotechnological applications or bioremediation. In this study, a highly cobalt-resistant and genetically stable R. sphaeroides strain was obtained by evolutionary engineering, also known as adaptive laboratory evolution (ALE), a powerful strategy to improve and characterize genetically complex, desired microbial phenotypes, such as stress resistance. For this purpose, successive batch selection was performed in the presence of gradually increased cobalt stress levels between 0.1-15 mM CoCl2 for 64 passages and without any mutagenesis of the initial population prior to selection. The mutant individuals were randomly chosen from the last population and analyzed in detail. Among these, a highly cobalt-resistant and genetically stable evolved strain called G7 showed significant cross-resistance against various stressors such as iron, magnesium, nickel, aluminum, and NaCl. Growth profiles and flame atomic absorption spectrometry analysis results revealed that in the presence of 4 mM CoCl2 that significantly inhibited growth of the reference strain, the growth of the evolved strain was unaffected, and higher levels of cobalt ions were associated with G7 cells than the reference strain. This may imply that cobalt ions accumulated in or on G7 cells, indicating the potential of G7 for cobalt bioremediation. Whole genome sequencing of the evolved strain identified 23 single nucleotide polymorphisms in various genes that are associated with transcriptional regulators, NifB family-FeMo cofactor biosynthesis, putative virulence factors, TRAP-T family transporter, sodium/proton antiporter, and also in genes with unknown functions, which may have a potential role in the cobalt resistance of R. sphaeroides.
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Affiliation(s)
- Güneş Atay
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Can Holyavkin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Hanay Can
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Mevlüt Arslan
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
| | - Massimo Trotta
- IPCF-CNR Istituto per I processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, İstanbul, Türkiye
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (İTÜ-MOBGAM), Istanbul Technical University, İstanbul, Türkiye
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Holyavkin C, Turanlı-Yıldız B, Yılmaz Ü, Alkım C, Arslan M, Topaloğlu A, Kısakesen Hİ, de Billerbeck G, François JM, Çakar ZP. Genomic, transcriptomic, and metabolic characterization of 2-Phenylethanol-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Front Microbiol 2023; 14:1148065. [PMID: 37113225 PMCID: PMC10127108 DOI: 10.3389/fmicb.2023.1148065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/29/2023] Open
Abstract
2-Phenylethanol is an aromatic compound commonly used in the food, cosmetic, and pharmaceutical industries. Due to increasing demand for natural products by consumers, the production of this flavor by microbial fermentation is gaining interest, as a sustainable alternative to chemical synthesis or expensive plant extraction, both processes relying on the use of fossil resources. However, the drawback of the fermentation process is the high toxicity of 2-phenylethanol to the producing microorganism. The aim of this study was to obtain a 2-phenylethanol-resistant Saccharomyces cerevisiae strain by in vivo evolutionary engineering and characterize the adapted yeast at the genomic, transcriptomic and metabolic levels. For this purpose, the tolerance to 2-phenylethanol was developed by gradually increasing the concentration of this flavor compound through successive batch cultivations, leading to an adapted strain that could tolerate 3.4 g/L of 2-phenylethanol, which was about 3-times better than the reference strain. Genome sequencing of the adapted strain identified point mutations in several genes, notably in HOG1 that encodes the Mitogen-Activated Kinase of the high-osmolarity signaling pathway. As this mutation is localized in the phosphorylation lip of this protein, it likely resulted in a hyperactive protein kinase. Transcriptomic analysis of the adapted strain supported this suggestion by revealing a large set of upregulated stress-responsive genes that could be explained in great part by HOG1-dependent activation of the Msn2/Msn4 transcription factor. Another relevant mutation was found in PDE2 encoding the low affinity cAMP phosphodiesterase, the missense mutation of which may lead to hyperactivation of this enzyme and thereby enhance the stressful state of the 2-phenylethanol adapted strain. In addition, the mutation in CRH1 that encodes a chitin transglycosylase implicated in cell wall remodeling could account for the increased resistance of the adapted strain to the cell wall-degrading enzyme lyticase. Finally, the potent upregulation of ALD3 and ALD4 encoding NAD+ -dependent aldehyde dehydrogenase together with the observed phenylacetate resistance of the evolved strain suggest a resistance mechanism involving conversion of 2-phenylethanol into phenylacetaldehyde and phenylacetate implicating these dehydrogenases.
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Affiliation(s)
- Can Holyavkin
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Burcu Turanlı-Yıldız
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ülkü Yılmaz
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil İbrahim Kısakesen
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | | | - Jean Marie François
- Toulouse Biotechnology Institute (TBI), CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
- *Correspondence: Jean Marie François,
| | - Z. Petek Çakar
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
- Z. Petek Çakar,
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Czajka KM, Nkongolo K. Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress. PLoS One 2022; 17:e0274740. [PMID: 36227867 PMCID: PMC9560071 DOI: 10.1371/journal.pone.0274740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022] Open
Abstract
Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.
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Affiliation(s)
- Karolina M. Czajka
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
- Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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Kocaefe-Özşen N, Yilmaz B, Alkım C, Arslan M, Topaloğlu A, Kısakesen HLB, Gülsev E, Çakar ZP. Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering. Front Microbiol 2022; 13:822864. [PMID: 35283819 PMCID: PMC8911705 DOI: 10.3389/fmicb.2022.822864] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress is a major stress type observed in yeast bioprocesses, resulting in a decrease in yeast growth, viability, and productivity. Thus, robust yeast strains with increased resistance to oxidative stress are in highly demand by the industry. In addition, oxidative stress is also associated with aging and age-related complex conditions such as cancer and neurodegenerative diseases. Saccharomyces cerevisiae, as a model eukaryote, has been used to study these complex eukaryotic processes. However, the molecular mechanisms underlying oxidative stress responses and resistance are unclear. In this study, we have employed evolutionary engineering (also known as adaptive laboratory evolution – ALE) strategies to obtain an oxidative stress-resistant and genetically stable S. cerevisiae strain. Comparative physiological, transcriptomic, and genomic analyses of the evolved strain were then performed with respect to the reference strain. The results show that the oxidative stress-resistant evolved strain was also cross-resistant against other types of stressors, including heat, freeze-thaw, ethanol, cobalt, iron, and salt. It was also found to have higher levels of trehalose and glycogen production. Further, comparative transcriptomic analysis showed an upregulation of many genes associated with the stress response, transport, carbohydrate, lipid and cofactor metabolic processes, protein phosphorylation, cell wall organization, and biogenesis. Genes that were downregulated included those related to ribosome and RNA processing, nuclear transport, tRNA, and cell cycle. Whole genome re-sequencing analysis of the evolved strain identified mutations in genes related to the stress response, cell wall organization, carbohydrate metabolism/transport, which are in line with the physiological and transcriptomic results, and may give insight toward the complex molecular mechanisms of oxidative stress resistance.
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Affiliation(s)
- Nazlı Kocaefe-Özşen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Bahtiyar Yilmaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil L Brahim Kısakesen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Erdinç Gülsev
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Z Petek Çakar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
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5
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Steunou AS, Bourbon M, Babot M, Durand A, Liotenberg S, Yamaichi Y, Ouchane S. Increasing the copper sensitivity of microorganisms by restricting iron supply, a strategy for bio-management practices. Microb Biotechnol 2020; 13:1530-1545. [PMID: 32558275 PMCID: PMC7415376 DOI: 10.1111/1751-7915.13590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
Pollution by copper (Cu2+ ) extensively used as antimicrobial in agriculture and farming represents a threat to the environment and human health. Finding ways to make microorganisms sensitive to lower metal concentrations could help decreasing the use of Cu2 + in agriculture. In this respect, we showed that limiting iron (Fe) uptake makes bacteria much more susceptible to Cu2 + or Cd2+ poisoning. Using efflux mutants of the purple bacterium Rubrivivax gelatinosus, we showed that Cu+ and Cd2+ resistance relies on the expression of the Fur-regulated FbpABC and Ftr iron transporters. To support this conclusion, inactivation of these Fe-importers in the Cu+ or Cd2+ -ATPase efflux mutants gave rise to hypersensitivity towards these ions. Moreover, in metal overloaded cells the expression of FbpA, the periplasmic iron-binding component of the ferric ion transport FbpABC system was induced, suggesting that cells perceived an 'iron-starvation' situation and responded to it by inducing Fe-importers. In this context, the Fe-Sod activity increased in response to Fe homoeostasis dysregulation. Similar results were obtained for Vibrio cholerae and Escherichia coli, suggesting that perturbation of Fe-homoeostasis by metal excess appeared as an adaptive response commonly used by a variety of bacteria. The presented data support a model in which metal excess induces Fe-uptake to support [4Fe-4S] synthesis and thereby induce ROS detoxification system.
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Affiliation(s)
- Anne Soisig Steunou
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marie‐Line Bourbon
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Marion Babot
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Anne Durand
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Sylviane Liotenberg
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Yoshiharu Yamaichi
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
| | - Soufian Ouchane
- Institute for Integrative Biology of the Cell (I2BC)CEACNRSUniversité Paris‐Saclay91198Gif‐sur‐YvetteFrance
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Terzioğlu E, Alkım C, Arslan M, Balaban BG, Holyavkin C, Kısakesen Hİ, Topaloğlu A, Yılmaz Şahin Ü, Gündüz Işık S, Akman S, Çakar ZP. Genomic, transcriptomic and physiological analyses of silver-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Yeast 2020; 37:413-426. [PMID: 33464648 DOI: 10.1002/yea.3514] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/12/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
Silver is a non-essential metal used in medical applications as an antimicrobial agent, but it is also toxic for biological systems. To investigate the molecular basis of silver resistance in yeast, we employed evolutionary engineering using successive batch cultures at gradually increased silver stress levels up to 0.25-mM AgNO3 in 29 populations and obtained highly silver-resistant and genetically stable Saccharomyces cerevisiae strains. Cross-resistance analysis results indicated that the silver-resistant mutants also gained resistance against copper and oxidative stress. Growth physiological analysis results revealed that the highly silver-resistant evolved strain 2E was not significantly inhibited by silver stress, unlike the reference strain. Genomic and transcriptomic analysis results revealed that there were mutations and/or significant changes in the expression levels of the genes involved in cell wall integrity, cellular respiration, oxidative metabolism, copper homeostasis, endocytosis and vesicular transport activities. Particularly the missense mutation in the RLM1 gene encoding a transcription factor involved in the maintenance of cell wall integrity and with 707 potential gene targets might have a key role in the high silver resistance of 2E, along with its improved cell wall integrity, as confirmed by the lyticase sensitivity assay results. In conclusion, the comparative physiological, transcriptomic and genomic analysis results of the silver-resistant S. cerevisiae strain revealed potential key factors that will help understand the complex molecular mechanisms of silver resistance in yeast.
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Affiliation(s)
- Ergi Terzioğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van, Turkey
| | - Berrak Gülçin Balaban
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Can Holyavkin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil İbrahim Kısakesen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ülkü Yılmaz Şahin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Sema Gündüz Işık
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
| | - Süleyman Akman
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey.,Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
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Zhang F, Bian J, Chen X, Huang J, Smith N, Lu W, Xu Y, Lee J, Wu X. Roles for intracellular cation transporters in respiratory growth of yeast. Metallomics 2020; 11:1667-1678. [PMID: 31402362 DOI: 10.1039/c9mt00145j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potassium is involved in copper and iron metabolism in eukaryotic Golgi apparatus, but it is not clear yet whether potassium distributions in other vesicles also affect copper and iron metabolism. Here we show that respiratory growth and iron acquisition by the yeast Saccharomyces cerevisiae relies on potassium (K+) compartmentalization to the mitochondria, as well as the vacuole and late endosome via K+/H+ exchangers Mdm38p, Vnx1p and Nhx1p, respectively. The data indicate that NHX1 and VNX1 knock-out cells grow better than wild type cells on non-fermentable YPEG media, while MDM38 knock-out cells display a growth defect on YPEG media. The over expression of the KHA1 gene located on the Golgi apparatus partially compensates for the growth defect of the MDM38 knock-out strain. The results suggest that the vacuole and late endosome are important potassium storage vesicles and Mdm38p affects the mitochondrial function by regulating copper and iron metabolism. Our study reveals potassium compartmentalization to the subcellular vesicles is relevant for respiratory growth by improving copper utilization and promoting iron absorption.
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Affiliation(s)
- Feng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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8
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Kim HS. Disruption of RIM15 confers an increased tolerance to heavy metals in Saccharomyces cerevisiae. Biotechnol Lett 2020; 42:1193-1202. [PMID: 32248397 DOI: 10.1007/s10529-020-02884-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to identify genes related to a heavy metal tolerance and to elucidate the tolerance mechanism in a eukaryote model using Saccharomyces cerevisiae. RESULTS In this study, one strain tolerant to up to 50 μM Pb(NO3)2 and 30 μM CdCl2 was isolated by screening a transposon-mediated mutant library and the disrupted gene was determined to be RIM15. In addition, this gene's characteristics related to heavy metals-tolerance was proved by deletion and overexpressing of this corresponding gene. The transposon mutant grew faster than the control strain and showed an obvious reduction in the intracellular level of reactive oxygen species (ROS) with activation of MSN4 and CTT1 in YPD medium containing 50 μM Pb(NO3)2 and 30 μM CdCl2 respectively. CONCLUSIONS Disruption of RIM15 in S. cerevisiae results in increased tolerance to heavy metal stress.
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Affiliation(s)
- Hyun-Soo Kim
- Department of Food Science and Technology, Jungwon University, 85, Munmu-ro, Goesan-eup, Goesan-gun, Chungbuk, 367-805, Republic of Korea.
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Evolutionary Engineering of an Iron-Resistant Saccharomyces cerevisiae Mutant and Its Physiological and Molecular Characterization. Microorganisms 2019; 8:microorganisms8010043. [PMID: 31878309 PMCID: PMC7023378 DOI: 10.3390/microorganisms8010043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/31/2022] Open
Abstract
Iron plays an essential role in all organisms and is involved in the structure of many biomolecules. It also regulates the Fenton reaction where highly reactive hydroxyl radicals occur. Iron is also important for microbial biodiversity, health and nutrition. Excessive iron levels can cause oxidative damage in cells. Saccharomyces cerevisiae evolved mechanisms to regulate its iron levels. To study the iron stress resistance in S. cerevisiae, evolutionary engineering was employed. The evolved iron stress-resistant mutant “M8FE” was analysed physiologically, transcriptomically and by whole genome re-sequencing. M8FE showed cross-resistance to other transition metals: cobalt, chromium and nickel and seemed to cope with the iron stress by both avoidance and sequestration strategies. PHO84, encoding the high-affinity phosphate transporter, was the most down-regulated gene in the mutant, and may be crucial in iron-resistance. M8FE had upregulated many oxidative stress response, reserve carbohydrate metabolism and mitophagy genes, while ribosome biogenesis genes were downregulated. As a possible result of the induced oxidative stress response genes, lower intracellular oxidation levels were observed. M8FE also had high trehalose and glycerol production levels. Genome re-sequencing analyses revealed several mutations associated with diverse cellular and metabolic processes, like cell division, phosphate-mediated signalling, cell wall integrity and multidrug transporters.
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10
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Evolutionary engineering and molecular characterization of a caffeine-resistant Saccharomyces cerevisiae strain. World J Microbiol Biotechnol 2019; 35:183. [PMID: 31728740 DOI: 10.1007/s11274-019-2762-2] [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] [Received: 07/27/2019] [Accepted: 11/05/2019] [Indexed: 12/30/2022]
Abstract
Caffeine is a naturally occurring alkaloid, where its major consumption occurs with beverages such as coffee, soft drinks and tea. Despite a variety of reports on the effects of caffeine on diverse organisms including yeast, the complex molecular basis of caffeine resistance and response has yet to be understood. In this study, a caffeine-hyperresistant and genetically stable Saccharomyces cerevisiae mutant was obtained for the first time by evolutionary engineering, using batch selection in the presence of gradually increased caffeine stress levels and without any mutagenesis of the initial population prior to selection. The selected mutant could resist up to 50 mM caffeine, a level, to our knowledge, that has not been reported for S. cerevisiae so far. The mutant was also resistant to the cell wall-damaging agent lyticase, and it showed cross-resistance against various compounds such as rapamycin, antimycin, coniferyl aldehyde and cycloheximide. Comparative transcriptomic analysis results revealed that the genes involved in the energy conservation and production pathways, and pleiotropic drug resistance were overexpressed. Whole genome re-sequencing identified single nucleotide polymorphisms in only three genes of the caffeine-hyperresistant mutant; PDR1, PDR5 and RIM8, which may play a potential role in caffeine-hyperresistance.
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11
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Dias M, Gomes de Lacerda JTJ, Perdigão Cota de Almeida S, de Andrade LM, Oller do Nascimento CA, Rozas EE, Mendes MA. Response mechanism of mine-isolated fungus Aspergillus niger IOC 4687 to copper stress determined by proteomics. Metallomics 2019; 11:1558-1566. [DOI: 10.1039/c9mt00137a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteomic analysis of the fungus Aspergillus niger showed that its capacity to absorb metals was boosted by physiological modification under metal stress conditions.
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Affiliation(s)
- Meriellen Dias
- Dempster MS Lab – Chemical Engineering Department of Polytechnic School of University of São Paulo
- São Paulo-SP
- Brazil
| | | | | | - Lidiane Maria de Andrade
- Dempster MS Lab – Chemical Engineering Department of Polytechnic School of University of São Paulo
- São Paulo-SP
- Brazil
| | | | - Enrique Eduardo Rozas
- Dempster MS Lab – Chemical Engineering Department of Polytechnic School of University of São Paulo
- São Paulo-SP
- Brazil
| | - Maria Anita Mendes
- Dempster MS Lab – Chemical Engineering Department of Polytechnic School of University of São Paulo
- São Paulo-SP
- Brazil
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Tekarslan-Sahin SH, Alkim C, Sezgin T. Physiological and transcriptomic analysis of a salt-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering. Bosn J Basic Med Sci 2018; 18:55-65. [PMID: 28954203 PMCID: PMC5826675 DOI: 10.17305/bjbms.2017.2250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022] Open
Abstract
Salt-resistant yeast strains are highly demanded by industry due to the exposure of yeast cells to high concentrations of salt, in various industrial bioprocesses. The aim of this study was to perform a physiological and transcriptomic analysis of a salt-resistant Saccharomyces cerevisiae (S. cerevisiae) mutant generated by evolutionary engineering. NaCl-resistant S. cerevisiae strains were obtained by ethyl methanesulfonate (EMS) mutagenesis followed by successive batch cultivations in the presence of gradually increasing NaCl concentrations, up to 8.5% w/v of NaCl (1.45 M). The most probable number (MPN) method, high-performance liquid chromatography (HPLC), and glucose oxidase/peroxidase method were used for physiological analysis, while Agilent yeast DNA microarray systems were used for transcriptome analysis. NaCl-resistant mutant strain T8 was highly cross-resistant to LiCl and highly sensitive to AlCl3. In the absence of NaCl stress, T8 strain had significantly higher trehalose and glycogen levels compared to the reference strain. Global transcriptome analysis by means of DNA microarrays showed that the genes related to stress response, carbohydrate transport, glycogen and trehalose biosynthesis, as well as biofilm formation, were upregulated. According to gene set enrichment analysis, 548 genes were upregulated and 22 downregulated in T8 strain, compared to the reference strain. Among the 548 upregulated genes, the highest upregulation was observed for the FLO11 (MUC1) gene (92-fold that of the reference strain). Overall, evolutionary engineering by chemical mutagenesis and increasing NaCl concentrations is a promising approach in developing industrial strains for biotechnological applications.
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Affiliation(s)
- Seyma Hande Tekarslan-Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Turkey; Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey; Department of Pharmaceutical Technology, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
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In vivo evolutionary engineering for ethanol-tolerance of Saccharomyces cerevisiae haploid cells triggers diploidization. J Biosci Bioeng 2017; 124:309-318. [DOI: 10.1016/j.jbiosc.2017.04.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 04/18/2017] [Indexed: 11/20/2022]
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14
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Johnson AJ, Veljanoski F, O'Doherty PJ, Zaman MS, Petersingham G, Bailey TD, Münch G, Kersaitis C, Wu MJ. Molecular insight into arsenic toxicity via the genome-wide deletion mutant screening of Saccharomyces cerevisiae. Metallomics 2016; 8:228-35. [PMID: 26688044 DOI: 10.1039/c5mt00261c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Arsenic is omnipresent in soil, air, food and water. Chronic exposure to arsenic is a serious problem to human health. In-depth understanding of this metalloid's toxicity is a fundamental step towards development of arsenic-free foods and measures for bioremediation. By screening the complete set of gene deletion mutants (4873) of Saccharomyces cerevisiae, this study uncovered 75 sensitive and 39 resistant mutants against arsenite [As(III)]. Functional analysis of the corresponding genes revealed the molecular details for its uptake, toxicity and detoxification. On the basis of the hypersensitivity of yap3Δ, the transcription factor, Yap3p, is for the first time linked to the cell's detoxification against As(III). Apart from confirming the previously described role of the mitogen-activated protein kinase (MAPK) Hog1 pathway in combating arsenic toxicity, the results show that the regulatory subunits (Ckb1p and Ckb2p) of protein kinase CK2 are also involved in the process, suggesting possible crosstalk between the two key protein kinases. The sensitivity to As(III) conferred by deletion of the genes involved in protein degradation and chromatin remodelling demonstrates protein damage is the key mode of toxicity for the metalloid. Furthermore, the resistant phenotype of fps1Δ, snf3Δ and pho81Δ against As(III) links arsenic uptake with the corresponding plasma membrane-bound transporters-aquaglyceroporin (Fps1p), hexose (Snf3p) and phosphate transporters. The molecular details obtained in this screen for As(III) uptake, detoxification and toxicity provide the basis for future investigations into arsenic-related problems in the environment, agriculture and human health.
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Affiliation(s)
- Adam J Johnson
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Filip Veljanoski
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Patrick J O'Doherty
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Mohammad S Zaman
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Gayani Petersingham
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Trevor D Bailey
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Gerald Münch
- Department of Pharmacology, School of Medicine and Molecular Medicine Research Group, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Cindy Kersaitis
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Ming J Wu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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Chen L, Cai C, Chen V, Lu X. Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. BMC Bioinformatics 2016; 17 Suppl 1:9. [PMID: 26818848 PMCID: PMC4895523 DOI: 10.1186/s12859-015-0852-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly controlled transcriptional program. An important and yet challenging task in systems biology is to reconstruct cellular signaling system in a data-driven manner. In this study, we investigate the utility of deep hierarchical neural networks in learning and representing the hierarchical organization of yeast transcriptomic machinery. Results We have designed a sparse autoencoder model consisting of a layer of observed variables and four layers of hidden variables. We applied the model to over a thousand of yeast microarrays to learn the encoding system of yeast transcriptomic machinery. After model selection, we evaluated whether the trained models captured biologically sensible information. We show that the latent variables in the first hidden layer correctly captured the signals of yeast transcription factors (TFs), obtaining a close to one-to-one mapping between latent variables and TFs. We further show that genes regulated by latent variables at higher hidden layers are often involved in a common biological process, and the hierarchical relationships between latent variables conform to existing knowledge. Finally, we show that information captured by the latent variables provide more abstract and concise representations of each microarray, enabling the identification of better separated clusters in comparison to gene-based representation. Conclusions Contemporary deep hierarchical latent variable models, such as the autoencoder, can be used to partially recover the organization of transcriptomic machinery.
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Affiliation(s)
- Lujia Chen
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, 15237, Pittsburgh, PA, USA.
| | - Chunhui Cai
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, 15237, Pittsburgh, PA, USA.
| | - Vicky Chen
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, 15237, Pittsburgh, PA, USA.
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, 15237, Pittsburgh, PA, USA.
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Cell Surface Interference with Plasma Membrane and Transport Processes in Yeasts. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:11-31. [PMID: 26721269 DOI: 10.1007/978-3-319-25304-6_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The wall of the yeast Saccharomyces cerevisiae is a shell of about 120 nm thick, made of two distinct layers, which surrounds the cell. The outer layer is constituted of highly glycosylated proteins and the inner layer is composed of β-glucan and chitin. These two layers are interconnected through covalent linkages leading to a supramolecular architecture that is characterized by physical and chemical properties including rigidity, porosity and biosorption. The later property results from the presence of highly negative charged phosphate and carboxylic groups of the cell wall proteins, allowing the cell wall to act as an efficient barrier to metals ions, toxins and organic compounds. An intimate connection between cell wall and plasma membrane is indicated by the fact that changes in membrane fluidity results in change in cell wall nanomechanical properties. Finally, cell wall contributes to transport processes through the use of dedicated cell wall mannoproteins, as it is the case for Fit proteins implicated in the siderophore-iron bound transport and the Tir/Dan proteins family in the uptake of sterols.
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Johnson AJ, Veljanoski F, O'Doherty PJ, Zaman MS, Petersingham G, Bailey TD, Münch G, Kersaitis C, Wu MJ. Revelation of molecular basis for chromium toxicity by phenotypes of Saccharomyces cerevisiae gene deletion mutants. Metallomics 2016; 8:542-50. [DOI: 10.1039/c6mt00039h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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Zhang MM, Zhao XQ, Cheng C, Bai FW. Improved growth and ethanol fermentation of Saccharomyces cerevisiae in the presence of acetic acid by overexpression of SET5 and PPR1. Biotechnol J 2015; 10:1903-11. [PMID: 26479519 DOI: 10.1002/biot.201500508] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 11/12/2022]
Abstract
To better understand the contribution of zinc-finger proteins to environmental stress tolerance, particularly inhibition from acetic acid, which is a potent inhibitor for cellulosic ethanol production by microbial fermentations, SET5 and PPR1 were overexpressed in Saccharomyces cerevisiae BY4741. With 5 g/L acetic acid addition, engineered strains BY4741/SET5 and BY4741/PPR1 showed improved growth and enhanced ethanol fermentation performance compared to that with the control strain. Similar results were also observed in ethanol production using corn stover hydrolysate. Further studies indicated that SET5 and PPR1 overexpression in S. cerevisiae significantly improved activities of antioxidant enzymes and ATP generation in the presence of acetic acid, and consequently decreased intracellular accumulation of reactive oxygen species (50.9 and 45.7%, respectively). These results revealed the novel functions of SET5 and PPR1 for the improvement of yeast acetic acid tolerance, and also implicated the involvement of these proteins in oxidative stress defense and energy metabolism in S. cerevisiae. This work also demonstrated that overexpression of SET5 and PPR1 would be a feasible strategy to increase cellulosic ethanol production efficiency.
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Affiliation(s)
- Ming-Ming Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Cheng Cheng
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Feng-Wu Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.,State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Schiavone M, Sieczkowski N, Castex M, Dague E, Marie François J. Effects of the strain background and autolysis process on the composition and biophysical properties of the cell wall from two different industrial yeasts. FEMS Yeast Res 2015; 15:fou012. [PMID: 25762053 DOI: 10.1093/femsyr/fou012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Saccharomyces cerevisiae cell surface is endowed with some relevant technological properties, notably antimicrobial and biosorption activities. For these purposes, yeasts are usually processed and packaged in an 'autolysed/dried' formula, which may have some impacts on cell surface properties. In this report, we showed using a combination of biochemical, biophysical and molecular methods that the composition of the cell wall of two wine yeast strains was not altered by the autolysis process. In contrast, this process altered the nanomechanical properties as shown by a 2- to 4-fold increased surface roughness and to a higher adhesion to the atomic force microscope tips of the autolysed cells as compared to live yeast cells. Besides, we found that the two strains harboured differences in biomechanical properties that could be due in part to higher levels of mannan in one of them, and to the fact that the surface of this mannan-enriched strain is decorated with highly adhesive patches forming nanodomains. The presence of these nanodomains could be correlated with the upregulation of flocculin encoding FLO11 as well as to higher expression of few other genes encoding cell wall mannoproteins in this mannan-enriched strain as compared to the other strain.
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Affiliation(s)
- Marion Schiavone
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France CNRS, UMR5504, F-31400 Toulouse, France CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | | | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Etienne Dague
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
| | - Jean Marie François
- Université de Toulouse, INSA, UPS, INP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France CNRS, UMR5504, F-31400 Toulouse, France
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Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory. Curr Opin Biotechnol 2015; 33:183-91. [DOI: 10.1016/j.copbio.2015.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
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21
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Tun NM, O'Doherty PJ, Chen ZH, Wu XY, Bailey TD, Kersaitis C, Wu MJ. Identification of aluminium transport-related genes via genome-wide phenotypic screening of Saccharomyces cerevisiae. Metallomics 2015; 6:1558-64. [PMID: 24926745 DOI: 10.1039/c4mt00116h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genome-wide screening using gene deletion mutants has been widely carried out with numerous toxicants including oxidants and metal ions. The focus of such studies usually centres on identifying sensitive phenotypes against a given toxicant. Here, we screened the complete collection of yeast gene deletion mutants (5047) with increasing concentrations of aluminium sulphate (0.4, 0.8, 1.6 and 3.2 mM) in order to discover aluminium (Al(3+)) tolerant phenotypes. Fifteen genes were found to be associated with Al(3+) transport because their deletion mutants exhibited Al(3+) tolerance, including lem3Δ, hal5Δ and cka2Δ. Deletion of CKA2, a catalytic subunit of tetrameric protein kinase CK2, gives rise to the most pronounced resistance to Al(3+) by showing significantly higher growth compared to the wild type. Functional analysis revealed that both molecular regulation and endocytosis are involved in Al(3+) transport for yeast. Further investigations were extended to all the four subunits of CK2 (CKA1, CKA2, CKB1 and CKB2) and the other 14 identified mutants under a spectrum of metal ions, including Al(3+), Zn(2+), Mn(2+), Fe(2+), Fe(3+), Co(3+), Ga(3+), Cd(2+), In(3+), Ni(2+) and Cu(2+), as well as hydrogen peroxide and diamide, in order to unravel cross-tolerance amongst metal ions and the effect of the oxidants. Finally, the implication of the findings in Al(3+) transport for the other species like plants and humans is discussed.
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Affiliation(s)
- Nay M Tun
- School of Science and Health, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.
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Wan C, Zhang M, Fang Q, Xiong L, Zhao X, Hasunuma T, Bai F, Kondo A. The impact of zinc sulfate addition on the dynamic metabolic profiling of Saccharomyces cerevisiae subjected to long term acetic acid stress treatment and identification of key metabolites involved in the antioxidant effect of zinc. Metallomics 2015; 7:322-32. [DOI: 10.1039/c4mt00275j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zinc modulates cellular amino acid metabolism and redox balance to exert its antioxidant effect.
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Affiliation(s)
- Chun Wan
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Mingming Zhang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Qing Fang
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Liang Xiong
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
| | - Xinqing Zhao
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology
- Kobe University
- Kobe 657-8501, Japan
| | - Fengwu Bai
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian 116024, China
- School of Life Science and Biotechnology
- Shanghai Jiaotong University
| | - Akihiko Kondo
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501, Japan
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Küçükgöze G, Alkım C, Yılmaz Ü, Kısakesen Hİ, Gündüz S, Akman S, Çakar ZP. Evolutionary engineering and transcriptomic analysis of nickel-resistantSaccharomyces cerevisiae. FEMS Yeast Res 2013; 13:731-46. [DOI: 10.1111/1567-1364.12073] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/23/2013] [Accepted: 08/22/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Gökhan Küçükgöze
- Department of Molecular Biology & Genetics; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
- Istanbul Technical University; Dr. Orhan Öcalgiray Molecular Biology; Biotechnology and Genetics Research Center (ITU-MOBGAM); Maslak Istanbul Turkey
| | - Ceren Alkım
- Department of Molecular Biology & Genetics; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
- Istanbul Technical University; Dr. Orhan Öcalgiray Molecular Biology; Biotechnology and Genetics Research Center (ITU-MOBGAM); Maslak Istanbul Turkey
| | - Ülkü Yılmaz
- Department of Molecular Biology & Genetics; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
- Istanbul Technical University; Dr. Orhan Öcalgiray Molecular Biology; Biotechnology and Genetics Research Center (ITU-MOBGAM); Maslak Istanbul Turkey
| | - H. İbrahim Kısakesen
- Department of Molecular Biology & Genetics; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
- Istanbul Technical University; Dr. Orhan Öcalgiray Molecular Biology; Biotechnology and Genetics Research Center (ITU-MOBGAM); Maslak Istanbul Turkey
- SEM Lab A.Ş.; Istanbul Turkey
| | - Sema Gündüz
- Department of Chemistry; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
| | - Süleyman Akman
- Department of Chemistry; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
| | - Z. Petek Çakar
- Department of Molecular Biology & Genetics; Faculty of Science & Letters; Istanbul Technical University; Maslak Istanbul Turkey
- Istanbul Technical University; Dr. Orhan Öcalgiray Molecular Biology; Biotechnology and Genetics Research Center (ITU-MOBGAM); Maslak Istanbul Turkey
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