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Pkh1p-Ypk1p and Pkh1p-Sch9p Pathways Are Activated by Acetic Acid to Induce a Mitochondrial-Dependent Regulated Cell Death. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7095078. [PMID: 32318242 PMCID: PMC7154982 DOI: 10.1155/2020/7095078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/20/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022]
Abstract
The yeast Saccharomyces cerevisiae undergoes a mitochondrial-dependent regulated cell death (RCD) exhibiting typical markers of mammalian apoptosis. We have previously shown that ceramide production contributes to RCD induced by acetic acid and is involved in mitochondrial outer membrane permeabilization and cytochrome c release, especially through hydrolysis of complex sphingolipids catalyzed by Isc1p. Recently, we also showed that Sch9p regulates the translocation of Isc1p from the endoplasmic reticulum into mitochondria, perturbing sphingolipid balance and determining cell fate. In this study, we addressed the role of other signaling proteins in acetic acid-induced RCD. We found that single deletion of PKH1 or YPK1, as shown for SCH9 and ISC1, leads to an increase in cell survival in response to acetic acid and that Pkh1/2p-dependent phosphorylation of Ypk1p and Sch9p increases under these conditions. These results indicate that Pkh1p regulates acetic acid-induced RCD through Ypk1p and Sch9p. In addition, our results suggest that Pkh1p-Ypk1p is necessary for isc1Δ resistance to acetic acid-induced RCD. Moreover, double deletion of ISC1 and PKH1 has a drastic effect on cell survival associated with increased ROS accumulation and release of cytochrome c, which is counteracted by overexpression of the PKA pathway negative regulator PDE2. Overall, our results suggest that Pkh1p-Ypk1p and Pkh1p-Sch9p pathways contribute to RCD induced by acetic acid.
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Li B, Xie CY, Yang BX, Gou M, Xia ZY, Sun ZY, Tang YQ. The response mechanisms of industrial Saccharomyces cerevisiae to acetic acid and formic acid during mixed glucose and xylose fermentation. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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53
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Ndukwe JK, Aliyu GO, Onwosi CO, Chukwu KO, Ezugworie FN. Mechanisms of weak acid-induced stress tolerance in yeasts: Prospects for improved bioethanol production from lignocellulosic biomass. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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54
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Relevance and Regulation of Cell Density. Trends Cell Biol 2020; 30:213-225. [PMID: 31980346 DOI: 10.1016/j.tcb.2019.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023]
Abstract
Cell density shows very little variation within a given cell type. For example, in humans variability in cell density among cells of a given cell type is 100 times smaller than variation in cell mass. This tight control indicates that maintenance of a cell type-specific cell density is important for cell function. Indeed, pathological conditions such as cellular senescence are accompanied by changes in cell density. Despite the apparent importance of cell-type-specific density, we know little about how cell density affects cell function, how it is controlled, and how it sometimes changes as part of a developmental process or in response to changes in the environment. The recent development of new technologies to accurately measure the cell density of single cells in suspension and in tissues is likely to provide answers to these important questions.
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55
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Kim MS, Cho KH, Park KH, Jang J, Hahn JS. Activation of Haa1 and War1 transcription factors by differential binding of weak acid anions in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 47:1211-1224. [PMID: 30476185 PMCID: PMC6379682 DOI: 10.1093/nar/gky1188] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 01/03/2023] Open
Abstract
In Saccharomyces cerevisiae, Haa1 and War1 transcription factors are involved in cellular adaptation against hydrophilic weak acids and lipophilic weak acids, respectively. However, it is unclear how these transcription factors are differentially activated depending on the identity of the weak acid. Using a field-effect transistor (FET)-type biosensor based on carbon nanofibers, in the present study we demonstrate that Haa1 and War1 directly bind to various weak acid anions with different affinities. Haa1 is most sensitive to acetate, followed by lactate, whereas War1 is most sensitive to benzoate, followed by sorbate, reflecting their differential activation during weak acid stresses. We show that DNA binding by Haa1 is induced in the presence of acetic acid and that the N-terminal Zn-binding domain is essential for this activity. Acetate binds to the N-terminal 150-residue region, and the transcriptional activation domain is located between amino acid residues 230 and 483. Our data suggest that acetate binding converts an inactive Haa1 to the active form, which is capable of DNA binding and transcriptional activation.
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Affiliation(s)
- Myung Sup Kim
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kyung Hee Cho
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kwang Hyun Park
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jyongsik Jang
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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Day AM, Quinn J. Stress-Activated Protein Kinases in Human Fungal Pathogens. Front Cell Infect Microbiol 2019; 9:261. [PMID: 31380304 PMCID: PMC6652806 DOI: 10.3389/fcimb.2019.00261] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/04/2019] [Indexed: 11/28/2022] Open
Abstract
The ability of fungal pathogens to survive hostile environments within the host depends on rapid and robust stress responses. Stress-activated protein kinase (SAPK) pathways are conserved MAPK signaling modules that promote stress adaptation in all eukaryotic cells, including pathogenic fungi. Activation of the SAPK occurs via the dual phosphorylation of conserved threonine and tyrosine residues within a TGY motif located in the catalytic domain. This induces the activation and nuclear accumulation of the kinase and the phosphorylation of diverse substrates, thus eliciting appropriate cellular responses. The Hog1 SAPK has been extensively characterized in the model yeast Saccharomyces cerevisiae. Here, we use this a platform from which to compare SAPK signaling mechanisms in three major fungal pathogens of humans, Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans. Despite the conservation of SAPK pathways within these pathogenic fungi, evidence is emerging that their role and regulation has significantly diverged. However, consistent with stress adaptation being a common virulence trait, SAPK pathways are important pathogenicity determinants in all these major human pathogens. Thus, the development of drugs which target fungal SAPKs has the exciting potential to generate broad-acting antifungal treatments.
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Affiliation(s)
- Alison M Day
- Faculty of Medicine, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Janet Quinn
- Faculty of Medicine, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
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Lv Z, Zhou J, Zhang Y, Zhou X, Xu N, Xin F, Ma J, Jiang M, Dong W. Techniques for enhancing the tolerance of industrial microbes to abiotic stresses: A review. Biotechnol Appl Biochem 2019; 67:73-81. [PMID: 31206805 DOI: 10.1002/bab.1794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022]
Abstract
The diversity of stress responses and survival strategies evolved by microorganism enables them to survive and reproduce in a multitude of harsh environments, whereas the discovery of the underlying resistance genes or mechanisms laid the foundation for the directional enhancement of microbial tolerance to abiotic stresses encountered in industrial applications. Many biological techniques have been developed for improving the stress resistance of industrial microorganisms, which greatly benefited the bacteria on which industrial production is based. This review introduces the main techniques for enhancing the resistance of microorganisms to abiotic stresses, including evolutionary engineering, metabolic engineering, and process engineering, developed in recent years. In addition, we also discuss problems that are still present in this area and offer directions for future research.
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Affiliation(s)
- Ziyao Lv
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Yue Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Xinhai Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, Peoples' Republic of China
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58
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Janschitz M, Romanov N, Varnavides G, Hollenstein DM, Gérecová G, Ammerer G, Hartl M, Reiter W. Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages. Cell Commun Signal 2019; 17:66. [PMID: 31208443 PMCID: PMC6572760 DOI: 10.1186/s12964-019-0381-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Modern quantitative mass spectrometry (MS)-based proteomics enables researchers to unravel signaling networks by monitoring proteome-wide cellular responses to different stimuli. MS-based analysis of signaling systems usually requires an integration of multiple quantitative MS experiments, which remains challenging, given that the overlap between these datasets is not necessarily comprehensive. In a previous study we analyzed the impact of the yeast mitogen-activated protein kinase (MAPK) Hog1 on the hyperosmotic stress-affected phosphorylome. Using a combination of a series of hyperosmotic stress and kinase inhibition experiments, we identified a broad range of direct and indirect substrates of the MAPK. Here we re-evaluate this extensive MS dataset and demonstrate that a combined analysis based on two software packages, MaxQuant and Proteome Discoverer, increases the coverage of Hog1-target proteins by 30%. Using protein-protein proximity assays we show that the majority of new targets gained by this analysis are indeed Hog1-interactors. Additionally, kinetic profiles indicate differential trends of Hog1-dependent versus Hog1-independent phosphorylation sites. Our findings highlight a previously unrecognized interconnection between Hog1 signaling and the RAM signaling network, as well as sphingolipid homeostasis.
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Affiliation(s)
- Marion Janschitz
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Children’s Cancer Research Institute, St. Anna Kinderspital, Vienna, Austria
| | - Natalie Romanov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Current Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gina Varnavides
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | | | - Gabriela Gérecová
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Gustav Ammerer
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
| | - Markus Hartl
- Department of Biochemistry, Max F. Perutz Laboratories, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
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Xu Q, Bai C, Liu Y, Song L, Tian L, Yan Y, Zhou J, Zhou X, Zhang Y, Cai M. Modulation of acetate utilization in Komagataella phaffii by metabolic engineering of tolerance and metabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:61. [PMID: 30936941 PMCID: PMC6427870 DOI: 10.1186/s13068-019-1404-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Acetate, an economical industrial chemical, which is also the precursor of acetyl-CoA, could serve as an alternative substrate for biomanufacturing. This nontraditional substrate can be widely produced from syngas via hydrolysis or pyrolysis of the cellulosic biomass, chemical or microbial catalysis, anaerobic fermentation in treated wastewater, etc. However, the toxicity of acetate to microorganisms has held back its utilization, especially for the eukaryotes that are good hosts for production of complicated pharmaceuticals or chemicals. This study seeks to improve acetate utilization in a widely used yeast host, Komagataella phaffii (previously Pichia pastoris), by metabolic engineering of acetate tolerance, transport, and metabolism. RESULTS A kinase-deficient library of K. phaffii was firstly used to screen acetate-resistant kinases. The HRK1 knockout strain was sensitive to acetate and overexpression of this gene improved acetate tolerance and cell growth of the strain. Also, overexpression of HRK1 caused a 55% productivity improvement of acetyl-CoA-dependent 6-methylsalicylic acid (6-MSA). However, activation of Hrk1 on membrane H(+)-ATPase Pma1 seemed not to work in the engineered strain. Acetate transporter gene ScFPS1* was further overexpressed, despite of not improving 6-MSA biosynthesis. To enhance acetate metabolism, acetyl-CoA synthesizing related genes, yeast PpACS1, ScACS1*, and E. coli ackA/pta were overexpressed separately. Introduction of PpACS1 and ScACS1* each increased biosynthesis of 6-MSA by approximately 20% on 20 mM acetate. Finally, co-overexpression of HRK1 and ScACS1* improved 6-MSA productivity by 51% on 20 mM acetate, despite that a low expression level of HRK1 happened when genes were expressed under the same promoter. CONCLUSIONS HRK1 screened by K. phaffii kinase-deficient library played an important role in acetate tolerance and was proved to profit the biosynthesis of acetyl-CoA-derived chemicals. It could be a potential target for metabolic engineering of acetate utilization in other eukaryotic hosts as well. A combined strategy of introducing genes for acetate tolerance and metabolism further improved biosynthesis of acetyl-CoA derived reporter compound in K. phaffii. This makes it a good choice for acetyl-CoA-derived chemicals with acetate as substrate or precursor in K. phaffii, which would also extend the use of this chassis host.
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Affiliation(s)
- Qin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Chenxiao Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yiqi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Lin Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yunfeng Yan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Jinfeng Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
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60
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Acid Stress Triggers Resistance to Acetic Acid-Induced Regulated Cell Death through Hog1 Activation Which Requires RTG2 in Yeast. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4651062. [PMID: 30931079 PMCID: PMC6410445 DOI: 10.1155/2019/4651062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/13/2018] [Indexed: 11/29/2022]
Abstract
Acid stress causes resistance to acetic acid-induced regulated cell death (AA-RCD) in budding yeast, resulting in catalase activation. In order to explore the molecular determinants of evasion of AA-RCD triggered by acid stress adaptation, we studied the involvement and the possible interplay of the master regulator of transcription high-osmolarity glycerol 1 (HOG1) and RTG2, a positive regulator of the RTG-dependent mitochondrial retrograde signaling. Viability, DNA fragmentation, and ROS accumulation have been analyzed in wild-type and mutant cells lacking HOG1 and/or RTG2. Catalase activity and transcription of CTT1 and CTA1, coding the cytosolic and peroxisomal/mitochondrial catalase, respectively, as well as Hog1 phosphorylation, were also analyzed. Our results show that HOG1 is essential for resistance to AA-RCD and its activation results in the upregulation of CTT1, but not CTA1, transcription during acid stress adaptation. RTG2 is required for Hog1-dependent CTT1 upregulation upon acid stress, despite failure of RTG pathway activation. We give evidence that Rtg2 has a cytoprotective role and can act as a general cell stress sensor independent of Rtg1/3-dependent transcription.
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61
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Mans R, Hassing EJ, Wijsman M, Giezekamp A, Pronk JT, Daran JM, van Maris AJA. A CRISPR/Cas9-based exploration into the elusive mechanism for lactate export in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 17:4628041. [PMID: 29145596 DOI: 10.1093/femsyr/fox085] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/13/2017] [Indexed: 11/14/2022] Open
Abstract
CRISPR/Cas9-based genome editing allows rapid, simultaneous modification of multiple genetic loci in Saccharomyces cerevisiae. Here, this technique was used in a functional analysis study aimed at identifying the hitherto unknown mechanism of lactate export in this yeast. First, an S. cerevisiae strain was constructed with deletions in 25 genes encoding transport proteins, including the complete aqua(glycero)porin family and all known carboxylic acid transporters. The 25-deletion strain was then transformed with an expression cassette for Lactobacillus casei lactate dehydrogenase (LcLDH). In anaerobic, glucose-grown batch cultures this strain exhibited a lower specific growth rate (0.15 vs. 0.25 h-1) and biomass-specific lactate production rate (0.7 vs. 2.4 mmol g biomass-1 h-1) than an LcLDH-expressing reference strain. However, a comparison of the two strains in anaerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) showed identical lactate production rates. These results indicate that, although deletion of the 25 transporter genes affected the maximum specific growth rate, it did not impact lactate export rates when analysed at a fixed specific growth rate. The 25-deletion strain provides a first step towards a 'minimal transportome' yeast platform, which can be applied for functional analysis of specific (heterologous) transport proteins as well as for evaluation of metabolic engineering strategies.
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Affiliation(s)
- Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Else-Jasmijn Hassing
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Annabel Giezekamp
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Development of Robust Yeast Strains for Lignocellulosic Biorefineries Based on Genome-Wide Studies. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:61-83. [PMID: 30911889 DOI: 10.1007/978-3-030-13035-0_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lignocellulosic biomass has been widely studied as the renewable feedstock for the production of biofuels and biochemicals. Budding yeast Saccharomyces cerevisiae is commonly used as a cell factory for bioconversion of lignocellulosic biomass. However, economic bioproduction using fermentable sugars released from lignocellulosic feedstocks is still challenging. Due to impaired cell viability and fermentation performance by various inhibitors that are present in the cellulosic hydrolysates, robust yeast strains resistant to various stress environments are highly desired. Here, we summarize recent progress on yeast strain development for the production of biofuels and biochemical using lignocellulosic biomass. Genome-wide studies which have contributed to the elucidation of mechanisms of yeast stress tolerance are reviewed. Key gene targets recently identified based on multiomics analysis such as transcriptomic, proteomic, and metabolomics studies are summarized. Physiological genomic studies based on zinc sulfate supplementation are highlighted, and novel zinc-responsive genes involved in yeast stress tolerance are focused. The dependence of host genetic background of yeast stress tolerance and roles of histones and their modifications are emphasized. The development of robust yeast strains based on multiomics analysis benefits economic bioconversion of lignocellulosic biomass.
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63
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Uzcátegui NL, Figarella K, Segnini A, Marsiccobetre S, Lang F, Beitz E, Rodríguez-Acosta A, Bertl A. Trypanosoma brucei aquaglyceroporins mediate the transport of metabolic end-products: Methylglyoxal, D-lactate, L-lactate and acetate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2252-2261. [DOI: 10.1016/j.bbamem.2018.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/26/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
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Watcharawipas A, Watanabe D, Takagi H. Sodium Acetate Responses in Saccharomyces cerevisiae and the Ubiquitin Ligase Rsp5. Front Microbiol 2018; 9:2495. [PMID: 30459728 PMCID: PMC6232821 DOI: 10.3389/fmicb.2018.02495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Recent studies have revealed the feasibility of sodium acetate as a potentially novel inhibitor/stressor relevant to the fermentation from neutralized lignocellulosic hydrolysates. This mini-review focuses on the toxicity of sodium acetate, which is composed of both sodium and acetate ions, and on the involved cellular responses that it elicits, particularly via the high-osmolarity glycerol (HOG) pathway, the Rim101 pathway, the P-type ATPase sodium pumps Ena1/2/5, and the ubiquitin ligase Rsp5 with its adaptors. Increased understanding of cellular responses to sodium acetate would improve our understanding of how cells respond not only to different stimuli but also to composite stresses induced by multiple components (e.g., sodium and acetate) simultaneously. Moreover, unraveling the characteristics of specific stresses under industrially related conditions and the cellular responses evoked by these stresses would be a key factor in the industrial yeast strain engineering toward the increased productivity of not only bioethanol but also advanced biofuels and valuable chemicals that will be in demand in the coming era of bio-based industry.
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Affiliation(s)
- Akaraphol Watcharawipas
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid. ACTA ACUST UNITED AC 2018; 45:735-751. [DOI: 10.1007/s10295-018-2053-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Abstract
Toxic concentrations of monocarboxylic weak acids present in lignocellulosic hydrolyzates affect cell integrity and fermentative performance of Saccharomyces cerevisiae. In this work, we report the deletion of the general catabolite repressor Mig1p as a strategy to improve the tolerance of S. cerevisiae towards inhibitory concentrations of acetic, formic or levulinic acid. In contrast with the wt yeast, where the growth and ethanol production were ceased in presence of acetic acid 5 g/L or formic acid 1.75 g/L (initial pH not adjusted), the m9 strain (Δmig1::kan) produced 4.06 ± 0.14 and 3.87 ± 0.06 g/L of ethanol, respectively. Also, m9 strain tolerated a higher concentration of 12.5 g/L acetic acid (initial pH adjusted to 4.5) without affecting its fermentative performance. Moreover, m9 strain produced 33% less acetic acid and 50–70% less glycerol in presence of weak acids, and consumed acetate and formate as carbon sources under aerobic conditions. Our results show that the deletion of Mig1p provides a single gene deletion target for improving the acid tolerance of yeast strains significantly.
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66
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Quintana JF, Pino RCD, Yamada K, Zhang N. Adaptation and Therapeutic Exploitation of the Plasma Membrane of African Trypanosomes. Genes (Basel) 2018; 9:E368. [PMID: 30037058 PMCID: PMC6071061 DOI: 10.3390/genes9070368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
African trypanosomes are highly divergent from their metazoan hosts, and as part of adaptation to a parasitic life style have developed a unique endomembrane system. The key virulence mechanism of many pathogens is successful immune evasion, to enable survival within a host, a feature that requires both genetic events and membrane transport mechanisms in African trypanosomes. Intracellular trafficking not only plays a role in immune evasion, but also in homeostasis of intracellular and extracellular compartments and interactions with the environment. Significantly, historical and recent work has unraveled some of the connections between these processes and highlighted how immune evasion mechanisms that are associated with adaptations to membrane trafficking may have, paradoxically, provided specific sensitivity to drugs. Here, we explore these advances in understanding the membrane composition of the trypanosome plasma membrane and organelles and provide a perspective for how transport could be exploited for therapeutic purposes.
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Affiliation(s)
- Juan F Quintana
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | | | - Kayo Yamada
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Ning Zhang
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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67
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Wang S, Sun X, Yuan Q. Strategies for enhancing microbial tolerance to inhibitors for biofuel production: A review. BIORESOURCE TECHNOLOGY 2018; 258:302-309. [PMID: 29567023 DOI: 10.1016/j.biortech.2018.03.064] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 05/05/2023]
Abstract
Using lignocellulosic biomass for the production of renewable biofuel provides a sustainable and promising solution to the crisis of energy and environment. However, the processes of biomass pretreatment and biofuel fermentation bring a variety of inhibitors to microbial strains. These inhibitors repress microbial growth, decrease biofuel yields and increase fermentation costs. The production of biofuels from renewable lignocellulosic biomass relies on the development of tolerant and robust microbial strains. In recent years, the advancement of tolerance engineering and evolutionary engineering provides powerful platform for obtaining host strains with desired tolerance for further metabolic engineering of biofuel pathways. In this review, we summarized the inhibitors derived from biomass pretreatment and biofuel fermentation, the mechanisms of inhibitor toxicity, and the strategies for enhancing microbial tolerance.
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Affiliation(s)
- Shizeng Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, PR China.
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68
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Palma M, Guerreiro JF, Sá-Correia I. Adaptive Response and Tolerance to Acetic Acid in Saccharomyces cerevisiae and Zygosaccharomyces bailii: A Physiological Genomics Perspective. Front Microbiol 2018. [PMID: 29515554 PMCID: PMC5826360 DOI: 10.3389/fmicb.2018.00274] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Acetic acid is an important microbial growth inhibitor in the food industry; it is used as a preservative in foods and beverages and is produced during normal yeast metabolism in biotechnological processes. Acetic acid is also a major inhibitory compound present in lignocellulosic hydrolysates affecting the use of this promising carbon source for sustainable bioprocesses. Although the molecular mechanisms underlying Saccharomyces cerevisiae response and adaptation to acetic acid have been studied for years, only recently they have been examined in more detail in Zygosaccharomyces bailii. However, due to its remarkable tolerance to acetic acid and other weak acids this yeast species is a major threat in the spoilage of acidic foods and beverages and considered as an interesting alternative cell factory in Biotechnology. This review paper emphasizes genome-wide strategies that are providing global insights into the molecular targets, signaling pathways and mechanisms behind S. cerevisiae and Z. bailii tolerance to acetic acid, and extends this information to other weak acids whenever relevant. Such comprehensive perspective and the knowledge gathered in these two yeast species allowed the identification of candidate molecular targets, either for the design of effective strategies to overcome yeast spoilage in acidic foods and beverages, or for the rational genome engineering to construct more robust industrial strains. Examples of successful applications are provided.
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Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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69
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Kretschmer M, Lambie S, Croll D, Kronstad JW. Acetate provokes mitochondrial stress and cell death in Ustilago maydis. Mol Microbiol 2018; 107:488-507. [PMID: 29235175 DOI: 10.1111/mmi.13894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022]
Abstract
The fungal pathogen Ustilago maydis causes disease on maize by mating to establish an infectious filamentous cell type that invades the host and induces tumours. We previously found that β-oxidation mutants were defective in virulence and did not grow on acetate. Here, we demonstrate that acetate inhibits filamentation during mating and in response to oleic acid. We therefore examined the influence of different carbon sources by comparing the transcriptomes of cells grown on acetate, oleic acid or glucose, with expression changes for the fungus during tumour formation in planta. Guided by the transcriptional profiling, we found that acetate negatively influenced resistance to stress, promoted the formation of reactive oxygen species, triggered cell death in stationary phase and impaired virulence on maize. We also found that acetate induced mitochondrial stress by interfering with mitochondrial functions. Notably, the disruption of oxygen perception or inhibition of the electron transport chain also influenced filamentation and mating. Finally, we made use of the connections between acetate and β-oxidation to test metabolic inhibitors for an influence on growth and virulence. These experiments identified diclofenac as a potential inhibitor of virulence. Overall, these findings support the possibility of targeting mitochondrial metabolic functions to control fungal pathogens.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Scott Lambie
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Daniel Croll
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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70
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Monteiro B, Ferraz P, Barroca M, da Cruz SH, Collins T, Lucas C. Conditions promoting effective very high gravity sugarcane juice fermentation. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:251. [PMID: 30237826 PMCID: PMC6142328 DOI: 10.1186/s13068-018-1239-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/27/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Applying very high gravity (VHG) fermentation conditions to the sugarcane juice (SCJ) bioethanol industry would improve its environmental and economic sustainability without the need for major infrastructure changes or investments. It could enable a decrease in the consumption of biological and natural resources (cane/land, water and energy) while maintaining acceptable production parameters. The present study attempts to demonstrate and characterise an effective industrially relevant SCJ-VHG fermentation process. RESULTS An industry-like SCJ-VHG bioethanol production process with 30 and 35 °Bx broth was employed to investigate the effects of both the yeast strain used and nitrogen source supplementation on process yield, process productivity, biomass viability, glycerol concentration and retention-associated gene expression. Process performance was shown to be variably affected by the different process conditions investigated. Highest process efficiency, with a 17% (w/v) ethanol yield and only 0.2% (w/v) sugar remaining unfermented, was observed with the Saccharomyces cerevisiae industrial strain CAT-1 in 30 °Bx broth with urea supplementation. In addition, efficient retention of glycerol by the yeast strain was identified as a requisite for better fermentation and was consistent with a higher expression of glycerol permease STL1 and channel FPS1. Urea was shown to promote the deregulation of STL1 expression, overcoming glucose repression. The consistency between Fps1-mediated ethanol secretion and ethanol in the extracellular media reinforces previous suggestions that ethanol might exit the cell through the Fps1 channel. CONCLUSIONS This work brings solid evidence in favour of the utilisation of VHG conditions in SCJ fermentations, bringing it a step closer to industrial application. SCJ concentrated up to 30 °Bx maintains industrially relevant ethanol production yield and productivity, provided the broth is supplemented with a suitable nitrogen source and an appropriate industrial bioethanol-producing yeast strain is used. In addition, the work contributes to a better understanding of the VHG-SCJ process and the variable effects of process parameters on process efficiency and yeast strain response.
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Affiliation(s)
- Bruno Monteiro
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Ferraz
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Mário Barroca
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sandra H. da Cruz
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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71
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Sabir F, Loureiro-Dias MC, Soveral G, Prista C. Functional relevance of water and glycerol channels in Saccharomyces cerevisiae. FEMS Microbiol Lett 2017; 364:3739791. [PMID: 28430948 DOI: 10.1093/femsle/fnx080] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
Our understanding of the functional relevance of orthodox aquaporins and aquaglyceroporins in Saccharomyces cerevisiae is essentially based on phenotypic variations obtained by expression/overexpression/deletion of these major intrinsic proteins in selected strains. These water/glycerol channels are considered crucial during various life-cycle phases, such as sporulation and mating and in some life processes such as rapid freeze-thaw tolerance, osmoregulation and phenomena associated with cell surface. Despite their putative functional roles not only as channels but also as sensors, their underlying mechanisms and their regulation are still poorly understood. In the present review, we summarize and discuss the physiological relevance of S. cerevisiae aquaporins (Aqy1 and Aqy2) and aquaglyceroporins (Fps1 and Yfl054c). In particular, the fact that most S. cerevisiae laboratory strains harbor genes coding for non-functional aquaporins, while wild and industrial strains possess at least one functional aquaporin, suggests that aquaporin activity is required for cell survival under more harsh conditions.
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Affiliation(s)
- Farzana Sabir
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda 1349-017 Lisboa, Portugal.,Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa,1649-003 Lisboa, Portugal
| | - Maria C Loureiro-Dias
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda 1349-017 Lisboa, Portugal
| | - Graça Soveral
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa,1649-003 Lisboa, Portugal
| | - Catarina Prista
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda 1349-017 Lisboa, Portugal
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72
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Lindahl L, Genheden S, Faria-Oliveira F, Allard S, Eriksson LA, Olsson L, Bettiga M. Alcohols enhance the rate of acetic acid diffusion in S. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance. MICROBIAL CELL 2017; 5:42-55. [PMID: 29354649 PMCID: PMC5772038 DOI: 10.15698/mic2018.01.609] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. n-butanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes.
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Affiliation(s)
- Lina Lindahl
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Samuel Genheden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fábio Faria-Oliveira
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Stefan Allard
- Department of Chemistry and Chemical Engineering, Division of Energy and Materials, Nuclear Chemistry, Chalmers University of Technology, Gothenburg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Maurizio Bettiga
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden.,EviKrets Biobased Processes Consultants, Gothenburg, Sweden
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73
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Watcharawipas A, Watanabe D, Takagi H. Enhanced sodium acetate tolerance in Saccharomyces cerevisiae by the Thr255Ala mutation of the ubiquitin ligase Rsp5. FEMS Yeast Res 2017; 17:4587736. [DOI: 10.1093/femsyr/fox083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/01/2017] [Indexed: 12/18/2022] Open
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74
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Brown AJP, Cowen LE, di Pietro A, Quinn J. Stress Adaptation. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0048-2016. [PMID: 28721857 PMCID: PMC5701650 DOI: 10.1128/microbiolspec.funk-0048-2016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/21/2023] Open
Abstract
Fungal species display an extraordinarily diverse range of lifestyles. Nevertheless, the survival of each species depends on its ability to sense and respond to changes in its natural environment. Environmental changes such as fluctuations in temperature, water balance or pH, or exposure to chemical insults such as reactive oxygen and nitrogen species exert stresses that perturb cellular homeostasis and cause molecular damage to the fungal cell. Consequently, fungi have evolved mechanisms to repair this damage, detoxify chemical insults, and restore cellular homeostasis. Most stresses are fundamental in nature, and consequently, there has been significant evolutionary conservation in the nature of the resultant responses across the fungal kingdom and beyond. For example, heat shock generally induces the synthesis of chaperones that promote protein refolding, antioxidants are generally synthesized in response to an oxidative stress, and osmolyte levels are generally increased following a hyperosmotic shock. In this article we summarize the current understanding of these and other stress responses as well as the signaling pathways that regulate them in the fungi. Model yeasts such as Saccharomyces cerevisiae are compared with filamentous fungi, as well as with pathogens of plants and humans. We also discuss current challenges associated with defining the dynamics of stress responses and with the elaboration of fungal stress adaptation under conditions that reflect natural environments in which fungal cells may be exposed to different types of stresses, either sequentially or simultaneously.
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Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Antonio di Pietro
- Departamento de Genética, Universidad de Córdoba, Campus de Rabanales, Edificio Gregor Mendel C5, 14071 Córdoba, Spain
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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75
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Chen Y, Nielsen J. Flux control through protein phosphorylation in yeast. FEMS Yeast Res 2017; 16:fow096. [PMID: 27797916 DOI: 10.1093/femsyr/fow096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2016] [Indexed: 01/26/2023] Open
Abstract
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark
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76
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Kawazoe N, Kimata Y, Izawa S. Acetic Acid Causes Endoplasmic Reticulum Stress and Induces the Unfolded Protein Response in Saccharomyces cerevisiae. Front Microbiol 2017; 8:1192. [PMID: 28702017 PMCID: PMC5487434 DOI: 10.3389/fmicb.2017.01192] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/12/2017] [Indexed: 02/02/2023] Open
Abstract
Since acetic acid inhibits the growth and fermentation ability of Saccharomyces cerevisiae, it is one of the practical hindrances to the efficient production of bioethanol from a lignocellulosic biomass. Although extensive information is available on yeast response to acetic acid stress, the involvement of endoplasmic reticulum (ER) and unfolded protein response (UPR) has not been addressed. We herein demonstrated that acetic acid causes ER stress and induces the UPR. The accumulation of misfolded proteins in the ER and activation of Ire1p and Hac1p, an ER-stress sensor and ER stress-responsive transcription factor, respectively, were induced by a treatment with acetic acid stress (>0.2% v/v). Other monocarboxylic acids such as propionic acid and sorbic acid, but not lactic acid, also induced the UPR. Additionally, ire1Δ and hac1Δ cells were more sensitive to acetic acid than wild-type cells, indicating that activation of the Ire1p-Hac1p pathway is required for maximum tolerance to acetic acid. Furthermore, the combination of mild acetic acid stress (0.1% acetic acid) and mild ethanol stress (5% ethanol) induced the UPR, whereas neither mild ethanol stress nor mild acetic acid stress individually activated Ire1p, suggesting that ER stress is easily induced in yeast cells during the fermentation process of lignocellulosic hydrolysates. It was possible to avoid the induction of ER stress caused by acetic acid and the combined stress by adjusting extracellular pH.
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Affiliation(s)
- Nozomi Kawazoe
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of TechnologyKyoto, Japan
| | - Yukio Kimata
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
| | - Shingo Izawa
- Laboratory of Microbial Technology, Graduate School of Science and Technology, Kyoto Institute of TechnologyKyoto, Japan
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77
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Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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78
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Geng P, Zhang L, Shi GY. Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2017; 33:94. [PMID: 28405910 DOI: 10.1007/s11274-017-2259-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 04/01/2017] [Indexed: 12/31/2022]
Abstract
Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.
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Affiliation(s)
- Peng Geng
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
| | - Gui Yang Shi
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
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79
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Cartwright SP, Darby RAJ, Sarkar D, Bonander N, Gross SR, Ashe MP, Bill RM. Constitutively-stressed yeast strains are high-yielding for recombinant Fps1: implications for the translational regulation of an aquaporin. Microb Cell Fact 2017; 16:41. [PMID: 28279185 PMCID: PMC5345182 DOI: 10.1186/s12934-017-0656-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We previously selected four strains of Saccharomyces cerevisiae for their ability to produce the aquaporin Fps1 in sufficient yield for further study. Yields from the yeast strains spt3Δ, srb5Δ, gcn5Δ and yTHCBMS1 (supplemented with 0.5 μg/mL doxycycline) that had been transformed with an expression plasmid containing 249 base pairs of 5' untranslated region (UTR) in addition to the primary FPS1 open reading frame (ORF) were 10-80 times higher than yields from wild-type cells expressing the same plasmid. One of the strains increased recombinant yields of the G protein-coupled receptor adenosine receptor 2a (A2aR) and soluble green fluorescent protein (GFP). The specific molecular mechanisms underpinning a high-yielding Fps1 phenotype remained incompletely described. RESULTS Polysome profiling experiments were used to analyze the translational state of spt3Δ, srb5Δ, gcn5Δ and yTHCBMS1 (supplemented with 0.5 μg/mL doxycycline); all but gcn5Δ were found to exhibit a clear block in translation initiation. Four additional strains with known initiation blocks (rpl31aΔ, rpl22aΔ, ssf1Δ and nop1Δ) also improved the yield of recombinant Fps1 compared to wild-type. Expression of the eukaryotic transcriptional activator GCN4 was increased in spt3Δ, srb5Δ, gcn5Δ and yTHCBMS1 (supplemented with 0.5 μg/mL doxycycline); these four strains also exhibited constitutive phosphorylation of the eukaryotic initiation factor, eIF2α. Both responses are indicative of a constitutively-stressed phenotype. Investigation of the 5'UTR of FPS1 in the expression construct revealed two untranslated ORFs (uORF1 and uORF2) upstream of the primary ORF. Deletion of either uORF1 or uORF1 and uORF2 further improved recombinant yields in our four strains; the highest yields of the uORF deletions were obtained from wild-type cells. Frame-shifting the stop codon of the native uORF (uORF2) so that it extended into the FPS1 ORF did not substantially alter Fps1 yields in spt3Δ or wild-type cells, suggesting that high-yielding strains are able to bypass 5'uORFs in the FPS1 gene via leaky scanning, which is a known stress-response mechanism. Yields of recombinant A2aR, GFP and horseradish peroxidase could be improved in one or more of the yeast strains suggesting that a stressed phenotype may also be important in high-yielding cell factories. CONCLUSIONS Regulation of Fps1 levels in yeast by translational control may be functionally important; the presence of a native uORF (uORF2) may be required to maintain low levels of Fps1 under normal conditions, but higher levels as part of a stress response. Constitutively-stressed yeast strains may be useful high-yielding microbial cell factories for recombinant protein production.
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Affiliation(s)
- Stephanie P Cartwright
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Richard A J Darby
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.,Thistle Scientific Ltd, Glasgow, G71 6NZ, UK
| | - Debasmita Sarkar
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Nicklas Bonander
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
| | - Stephane R Gross
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Mark P Ashe
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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80
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Romanov N, Hollenstein DM, Janschitz M, Ammerer G, Anrather D, Reiter W. Identifying protein kinase-specific effectors of the osmostress response in yeast. Sci Signal 2017; 10:10/469/eaag2435. [PMID: 28270554 DOI: 10.1126/scisignal.aag2435] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The budding yeast Saccharomyces cerevisiae reacts to increased external osmolarity by modifying many cellular processes. Adaptive signaling relies primarily on the high-osmolarity glycerol (HOG) pathway, which is closely related to the mammalian p38 mitogen-activated protein kinase (MAPK) pathway in core architecture. To identify target proteins of the MAPK Hog1, we designed a mass spectrometry-based high-throughput experiment to measure the impact of Hog1 activation or inhibition on the Scerevisiae phosphoproteome. In addition, we analyzed how deletion of RCK2, which encodes a known effector protein kinase target of Hog1, modulated osmotic stress-induced phosphorylation. Our results not only provide an overview of the diversity of cellular functions that are directly and indirectly affected by the activity of the HOG pathway but also enabled an assessment of the Hog1-independent events that occur under osmotic stress conditions. We extended the number of putative Hog1 direct targets by analyzing the modulation of motifs consisting of serine or threonine followed by a proline (S/T-P motif) and subsequently validated these with an in vivo interaction assay. Rck2 appears to act as a central hub for many Hog1-mediated secondary phosphorylation events. This study clarifies many of the direct and indirect effects of HOG signaling and its stress-adaptive functions.
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Affiliation(s)
- Natalie Romanov
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - David Maria Hollenstein
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Marion Janschitz
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Gustav Ammerer
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Wolfgang Reiter
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
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81
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Martí-Raga M, Peltier E, Mas A, Beltran G, Marullo P. Genetic Causes of Phenotypic Adaptation to the Second Fermentation of Sparkling Wines in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2017; 7:399-412. [PMID: 27903630 PMCID: PMC5295589 DOI: 10.1534/g3.116.037283] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 01/12/2023]
Abstract
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL mapping approach on an F1-progeny population. Three main QTL were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudooverdominance and dominance effects. The molecular dissection of those QTL revealed that the adaptation to second fermentation is related to pH, lipid, or osmotic regulation. Our results suggest that the stressful conditions of second fermentation have driven the selection of rare genetic variants adapted to maintain yeast cell homeostasis and, in particular, to low pH conditions.
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Affiliation(s)
- Maria Martí-Raga
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
| | - Emilien Peltier
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Philippe Marullo
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
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82
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Swinnen S, Henriques SF, Shrestha R, Ho PW, Sá-Correia I, Nevoigt E. Improvement of yeast tolerance to acetic acid through Haa1 transcription factor engineering: towards the underlying mechanisms. Microb Cell Fact 2017; 16:7. [PMID: 28068993 PMCID: PMC5220606 DOI: 10.1186/s12934-016-0621-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/21/2016] [Indexed: 12/28/2022] Open
Abstract
Background Besides being a major regulator of the response to acetic acid in Saccharomyces cerevisiae, the transcription factor Haa1 is an important determinant of the tolerance to this acid. The engineering of Haa1 either by overexpression or mutagenesis has therefore been considered to be a promising avenue towards the construction of more robust strains with improved acetic acid tolerance. Results By applying the concept of global transcription machinery engineering to the regulon-specific transcription factor Haa1, a mutant allele containing two point mutations could be selected that resulted in a significantly higher acetic acid tolerance as compared to the wild-type allele. The level of improvement obtained was comparable to the level obtained by overexpression of HAA1, which was achieved by introduction of a second copy of the native HAA1 gene. Dissection of the contribution of the two point mutations to the phenotype showed that the major improvement was caused by an amino acid exchange at position 135 (serine to phenylalanine). In order to further study the mechanisms underlying the tolerance phenotype, Haa1 translocation and transcriptional activation of Haa1 target genes was compared between Haa1 mutant, overproduction and wild-type strains. While the rapid Haa1 translocation from the cytosol to the nucleus in response to acetic acid was not affected in the Haa1S135F mutant strain, the levels of transcriptional activation of four selected Haa1-target genes by acetic acid were significantly higher in cells of the mutant strain as compared to cells of the wild-type strain. Interestingly, the time-course of transcriptional activation in response to acetic acid was comparable for the mutant and wild-type strain whereas the maximum mRNA levels obtained correlate with each strain’s tolerance level. Conclusion Our data confirms that engineering of the regulon-specific transcription factor Haa1 allows the improvement of acetic acid tolerance in S. cerevisiae. It was also shown that the beneficial S135F mutation identified in the current work did not lead to an increase of HAA1 transcript level, suggesting that an altered protein structure of the Haa1S135F mutant protein led to an increased recruitment of the transcription machinery to Haa1 target genes.
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Affiliation(s)
- Steve Swinnen
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Sílvia F Henriques
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Ranjan Shrestha
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Ping-Wei Ho
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Isabel Sá-Correia
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany.
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83
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The CgHaa1-Regulon Mediates Response and Tolerance to Acetic Acid Stress in the Human Pathogen Candida glabrata. G3-GENES GENOMES GENETICS 2017; 7:1-18. [PMID: 27815348 PMCID: PMC5217100 DOI: 10.1534/g3.116.034660] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
To thrive in the acidic vaginal tract, Candida glabrata has to cope with high concentrations of acetic acid. The mechanisms underlying C. glabrata tolerance to acetic acid at low pH remain largely uncharacterized. In this work, the essential role of the CgHaa1 transcription factor (encoded by ORF CAGL0L09339g) in the response and tolerance of C. glabrata to acetic acid is demonstrated. Transcriptomic analysis showed that CgHaa1 regulates, directly or indirectly, the expression of about 75% of the genes activated under acetic acid stress. CgHaa1-activated targets are involved in multiple physiological functions including membrane transport, metabolism of carbohydrates and amino acids, regulation of the activity of the plasma membrane H+-ATPase, and adhesion. Under acetic acid stress, CgHaa1 increased the activity and the expression of the CgPma1 proton pump and contributed to increased colonization of vaginal epithelial cells by C. glabrata. CgHAA1, and two identified CgHaa1-activated targets, CgTPO3 and CgHSP30, are herein demonstrated to be determinants of C. glabrata tolerance to acetic acid. The protective effect of CgTpo3 and of CgHaa1 was linked to a role of these proteins in reducing the accumulation of acetic acid inside C. glabrata cells. In response to acetic acid stress, marked differences were found in the regulons controlled by CgHaa1 and by its S. cerevisiae ScHaa1 ortholog, demonstrating a clear divergent evolution of the two regulatory networks. The results gathered in this study significantly advance the understanding of the molecular mechanisms underlying the success of C. glabrata as a vaginal colonizer.
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84
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85
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Raguz Nakic Z, Seisenbacher G, Posas F, Sauer U. Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2016; 10:104. [PMID: 27846849 PMCID: PMC5109706 DOI: 10.1186/s12918-016-0350-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/03/2016] [Indexed: 01/08/2023]
Abstract
Background Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousands of phosphorylation sites (phosphosites) in single experiments. However, functionality of the vast majority of these sites remains unclear and we lack suitable approaches to evaluate functional relevance at a pace that matches their detection. Results Here, we assess functionality of 26 phosphosites by introducing phosphodeletion and phosphomimic mutations in 25 metabolic enzymes and regulators from the TOR and HOG signaling pathway in Saccharomyces cerevisiae by phenotypic analysis and untargeted metabolomics. We show that metabolomics largely outperforms growth analysis and recovers 10 out of the 13 previously characterized phosphosites and suggests functionality for several novel sites, including S79 on the TOR regulatory protein Tip41. We analyze metabolic profiles to identify consequences underlying regulatory phosphorylation events and detecting glycerol metabolism to have a so far unknown influence on arginine metabolism via phosphoregulation of the glycerol dehydrogenases. Further, we also find S508 in the MAPKK Pbs2 as a potential link for cross-talking between HOG signaling and the cell wall integrity pathway. Conclusions We demonstrate that metabolic profiles can be exploited for gaining insight into regulatory consequences and biological roles of phosphosites. Altogether, untargeted metabolomics is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of phosphosites. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0350-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zrinka Raguz Nakic
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.,PhD Program on Systems Biology, Life Science Zürich, Zürich, Switzerland
| | - Gerhard Seisenbacher
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard-Hof 1, Zürich, Switzerland.
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86
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87
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Overexpression of ESBP6 improves lactic acid resistance and production in Saccharomyces cerevisiae. J Biosci Bioeng 2016; 122:415-20. [DOI: 10.1016/j.jbiosc.2016.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/12/2016] [Accepted: 03/16/2016] [Indexed: 12/28/2022]
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88
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Ahmadpour D, Maciaszczyk-Dziubinska E, Babazadeh R, Dahal S, Migocka M, Andersson M, Wysocki R, Tamás MJ, Hohmann S. The mitogen-activated protein kinase Slt2 modulates arsenite transport through the aquaglyceroporin Fps1. FEBS Lett 2016; 590:3649-3659. [DOI: 10.1002/1873-3468.12390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Doryaneh Ahmadpour
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
| | | | - Roja Babazadeh
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
| | - Sita Dahal
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
| | | | - Mikael Andersson
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
| | - Robert Wysocki
- Institute of Experimental Biology; University of Wroclaw; Poland
| | - Markus J. Tamás
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology; University of Gothenburg; Sweden
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89
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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.
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90
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Zhang Q, Bhattacharya S, Pi J, Clewell RA, Carmichael PL, Andersen ME. Adaptive Posttranslational Control in Cellular Stress Response Pathways and Its Relationship to Toxicity Testing and Safety Assessment. Toxicol Sci 2016; 147:302-16. [PMID: 26408567 DOI: 10.1093/toxsci/kfv130] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although transcriptional induction of stress genes constitutes a major cellular defense program against a variety of stressors, posttranslational control directly regulating the activities of preexisting stress proteins provides a faster-acting alternative response. We propose that posttranslational control is a general adaptive mechanism operating in many stress pathways. Here with the aid of computational models, we first show that posttranslational control fulfills two roles: (1) handling small, transient stresses quickly and (2) stabilizing the negative feedback transcriptional network. We then review the posttranslational control pathways for major stress responses-oxidative stress, metal stress, hyperosmotic stress, DNA damage, heat shock, and hypoxia. Posttranslational regulation of stress protein activities occurs by reversible covalent modifications, allosteric or non-allosteric enzymatic regulations, and physically induced protein structural changes. Acting in feedback or feedforward networks, posttranslational control may establish a threshold level of cellular stress. Sub-threshold stresses are handled adequately by posttranslational control without invoking gene transcription. With supra-threshold stress levels, cellular homeostasis cannot be maintained and transcriptional induction of stress genes and other gene programs, eg, those regulating cell metabolism, proliferation, and apoptosis, takes place. The loss of homeostasis with consequent changes in cellular function may lead to adverse cellular outcomes. Overall, posttranslational and transcriptional control pathways constitute a stratified cellular defense system, handling stresses coherently across time and intensity. As cell-based assays become a focus for chemical testing anchored on toxicity pathways, examination of proteomic and metabolomic changes as a result of posttranslational control occurring in the absence of transcriptomic alterations deserves more attention.
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Affiliation(s)
- Qiang Zhang
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Sudin Bhattacharya
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Jingbo Pi
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Rebecca A Clewell
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Paul L Carmichael
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Melvin E Andersen
- *Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709; School of Public Health, China Medical University, Shenyang, China; and Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, UK
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91
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Wu X, Zhang L, Jin X, Fang Y, Zhang K, Qi L, Zheng D. Deletion of JJJ1 improves acetic acid tolerance and bioethanol fermentation performance of Saccharomyces cerevisiae strains. Biotechnol Lett 2016; 38:1097-106. [PMID: 27067354 DOI: 10.1007/s10529-016-2085-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/17/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To improve tolerance to acetic acid that is present in lignocellulosic hydrolysates and affects bioethanol production by Saccharomyces cerevisiae. RESULTS Saccharomyces cerevisiae strains with improved tolerance to acetic acid were obtained through deletion of the JJJ1 gene. The lag phase of the JJJ1 deletion mutant BYΔJJJ1 was ~16 h shorter than that of the parent strain, BY4741, when the fermentation medium contained 4.5 g acetic acid/l. Additionally, the specific ethanol production rate of BYΔJJJ1 was increased (0.057 g/g h) compared to that of the parent strain (0.051 g/g h). Comparative transcription and physiological analyses revealed higher long chain fatty acid, trehalose, and catalase contents might be critical factors responsible for the acetic acid resistance of JJJ1 knockout strains. CONCLUSIONS JJJ1 deletion improves acetic acid tolerance and ethanol fermentation performance of S. cerevisiae.
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Affiliation(s)
- Xuechang Wu
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Lijie Zhang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Xinna Jin
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Yahong Fang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Lei Qi
- Ocean College, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Daoqiong Zheng
- Ocean College, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
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92
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Sabir F, Loureiro-Dias MC, Prista C. Comparative analysis of sequences, polymorphisms and topology of yeasts aquaporins and aquaglyceroporins. FEMS Yeast Res 2016; 16:fow025. [DOI: 10.1093/femsyr/fow025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2016] [Indexed: 12/16/2022] Open
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93
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Roy A, Hashmi S, Li Z, Dement AD, Cho KH, Kim JH. The glucose metabolite methylglyoxal inhibits expression of the glucose transporter genes by inactivating the cell surface glucose sensors Rgt2 and Snf3 in yeast. Mol Biol Cell 2016; 27:862-71. [PMID: 26764094 PMCID: PMC4803311 DOI: 10.1091/mbc.e15-11-0789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/05/2016] [Indexed: 01/04/2023] Open
Abstract
Methylglyoxal (MG) is a cytotoxic by-product of glycolysis. MG inhibits the growth of glucose-fermenting yeast cells by inhibiting glycolysis. MG does so by inducing endocytosis and degradation of the cell-surface glucose sensors Rgt2 and Snf3, which are required for glucose induction of HXT (glucose transporter) gene expression. Methylglyoxal (MG) is a cytotoxic by-product of glycolysis. MG has inhibitory effect on the growth of cells ranging from microorganisms to higher eukaryotes, but its molecular targets are largely unknown. The yeast cell-surface glucose sensors Rgt2 and Snf3 function as glucose receptors that sense extracellular glucose and generate a signal for induction of expression of genes encoding glucose transporters (HXTs). Here we provide evidence that these glucose sensors are primary targets of MG in yeast. MG inhibits the growth of glucose-fermenting yeast cells by inducing endocytosis and degradation of the glucose sensors. However, the glucose sensors with mutations at their putative ubiquitin-acceptor lysine residues are resistant to MG-induced degradation. These results suggest that the glucose sensors are inactivated through ubiquitin-mediated endocytosis and degraded in the presence of MG. In addition, the inhibitory effect of MG on the glucose sensors is greatly enhanced in cells lacking Glo1, a key component of the MG detoxification system. Thus the stability of these glucose sensors seems to be critically regulated by intracellular MG levels. Taken together, these findings suggest that MG attenuates glycolysis by promoting degradation of the cell-surface glucose sensors and thus identify MG as a potential glycolytic inhibitor.
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Affiliation(s)
- Adhiraj Roy
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, Washington, DC 20037
| | - Salman Hashmi
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, Washington, DC 20037
| | - Zerui Li
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, Washington, DC 20037
| | - Angela D Dement
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN 47809
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Science, Washington, DC 20037
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94
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Yang X, Wang K, Wang H, Zhang J, Tang L, Mao Z. Control of pH by acetic acid and its effect on ethanol fermentation in an integrated ethanol–methane fermentation process. RSC Adv 2016. [DOI: 10.1039/c6ra04129a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The integrated ethanol–methane fermentation process employing cassava or other feedstock requires pH control to maximize yields.
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Affiliation(s)
- Xinchao Yang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Ke Wang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Huijun Wang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Jianhua Zhang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Lei Tang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Zhonggui Mao
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
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95
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Meijnen JP, Randazzo P, Foulquié-Moreno MR, van den Brink J, Vandecruys P, Stojiljkovic M, Dumortier F, Zalar P, Boekhout T, Gunde-Cimerman N, Kokošar J, Štajdohar M, Curk T, Petrovič U, Thevelein JM. Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:5. [PMID: 26740819 PMCID: PMC4702306 DOI: 10.1186/s13068-015-0421-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/15/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Acetic acid is one of the major inhibitors in lignocellulose hydrolysates used for the production of second-generation bioethanol. Although several genes have been identified in laboratory yeast strains that are required for tolerance to acetic acid, the genetic basis of the high acetic acid tolerance naturally present in some Saccharomyces cerevisiae strains is unknown. Identification of its polygenic basis may allow improvement of acetic acid tolerance in yeast strains used for second-generation bioethanol production by precise genome editing, minimizing the risk of negatively affecting other industrially important properties of the yeast. RESULTS Haploid segregants of a strain with unusually high acetic acid tolerance and a reference industrial strain were used as superior and inferior parent strain, respectively. After crossing of the parent strains, QTL mapping using the SNP variant frequency determined by pooled-segregant whole-genome sequence analysis revealed two major QTLs. All F1 segregants were then submitted to multiple rounds of random inbreeding and the superior F7 segregants were submitted to the same analysis, further refined by sequencing of individual segregants and bioinformatics analysis taking into account the relative acetic acid tolerance of the segregants. This resulted in disappearance in the QTL mapping with the F7 segregants of a major F1 QTL, in which we identified HAA1, a known regulator of high acetic acid tolerance, as a true causative allele. Novel genes determining high acetic acid tolerance, GLO1, DOT5, CUP2, and a previously identified component, VMA7, were identified as causative alleles in the second major F1 QTL and in three newly appearing F7 QTLs, respectively. The superior HAA1 allele contained a unique single point mutation that significantly improved acetic acid tolerance under industrially relevant conditions when inserted into an industrial yeast strain for second-generation bioethanol production. CONCLUSIONS This work reveals the polygenic basis of high acetic acid tolerance in S. cerevisiae in unprecedented detail. It also shows for the first time that a single strain can harbor different sets of causative genes able to establish the same polygenic trait. The superior alleles identified can be used successfully for improvement of acetic acid tolerance in industrial yeast strains.
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Affiliation(s)
- Jean-Paul Meijnen
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Paola Randazzo
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - María R. Foulquié-Moreno
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | | | - Paul Vandecruys
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Marija Stojiljkovic
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Françoise Dumortier
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
| | - Polona Zalar
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Teun Boekhout
- />CBS, Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands
| | - Nina Gunde-Cimerman
- />Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
- />Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Janez Kokošar
- />Genialis d.o.o., Ulica Zore Majcnove 4, 1000 Ljubljana, Slovenia
| | - Miha Štajdohar
- />Genialis d.o.o., Ulica Zore Majcnove 4, 1000 Ljubljana, Slovenia
- />Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Tomaž Curk
- />Faculty of Computer and Information Science, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Uroš Petrovič
- />Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, Ljubljana, Slovenia
| | - Johan M. Thevelein
- />Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- />Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, 3001 Leuven-Heverlee, Belgium
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96
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Casal M, Queirós O, Talaia G, Ribas D, Paiva S. Carboxylic Acids Plasma Membrane Transporters in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:229-251. [PMID: 26721276 DOI: 10.1007/978-3-319-25304-6_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter covers the functionally characterized plasma membrane carboxylic acids transporters Jen1, Ady2, Fps1 and Pdr12 in the yeast Saccharomyces cerevisiae, addressing also their homologues in other microorganisms, as filamentous fungi and bacteria. Carboxylic acids can either be transported into the cells, to be used as nutrients, or extruded in response to acid stress conditions. The secondary active transporters Jen1 and Ady2 can mediate the uptake of the anionic form of these substrates by a H(+)-symport mechanism. The undissociated form of carboxylic acids is lipid-soluble, crossing the plasma membrane by simple diffusion. Furthermore, acetic acid can also be transported by facilitated diffusion via Fps1 channel. At the cytoplasmic physiological pH, the anionic form of the acid prevails and it can be exported by the Pdr12 pump. This review will highlight the mechanisms involving carboxylic acids transporters, and the way they operate according to the yeast cell response to environmental changes, as carbon source availability, extracellular pH and acid stress conditions.
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Affiliation(s)
- Margarida Casal
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Odília Queirós
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra, 1317, 4585-116, Gandra, PRD, Portugal
| | - Gabriel Talaia
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - David Ribas
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sandra Paiva
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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97
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Mota S, Alves R, Carneiro C, Silva S, Brown AJ, Istel F, Kuchler K, Sampaio P, Casal M, Henriques M, Paiva S. Candida glabrata susceptibility to antifungals and phagocytosis is modulated by acetate. Front Microbiol 2015; 6:919. [PMID: 26388859 PMCID: PMC4560035 DOI: 10.3389/fmicb.2015.00919] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/21/2015] [Indexed: 11/13/2022] Open
Abstract
Candida glabrata is considered a major opportunistic fungal pathogen of humans. The capacity of this yeast species to cause infections is dependent on the ability to grow within the human host environment and to assimilate the carbon sources available. Previous studies have suggested that C. albicans can encounter glucose-poor microenvironments during infection and that the ability to use alternative non-fermentable carbon sources, such as carboxylic acids, contributes to the virulence of this fungus. Transcriptional studies on C. glabrata cells identified a similar response, upon nutrient deprivation. In this work, we aimed at analyzing biofilm formation, antifungal drug resistance, and phagocytosis of C. glabrata cells grown in the presence of acetic acid as an alternative carbon source. C. glabrata planktonic cells grown in media containing acetic acid were more susceptible to fluconazole and were better phagocytosed and killed by macrophages than when compared to media lacking acetic acid. Growth in acetic acid also affected the ability of C. glabrata to form biofilms. The genes ADY2a, ADY2b, FPS1, FPS2, and ATO3, encoding putative carboxylate transporters, were upregulated in C. glabrata planktonic and biofilm cells in the presence of acetic acid. Phagocytosis assays with fps1 and ady2a mutant strains suggested a potential role of FPS1 and ADY2a in the phagocytosis process. These results highlight how acidic pH niches, associated with the presence of acetic acid, can impact in the treatment of C. glabrata infections, in particular in vaginal candidiasis.
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Affiliation(s)
- Sandra Mota
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal ; Centre of Health and Environmental Research, School of Allied Health Sciences, Polytechnic Institute of Porto Porto, Portugal
| | - Rosana Alves
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal
| | - Catarina Carneiro
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal
| | - Sónia Silva
- Centre for Biological Engineering, University of Minho Braga, Portugal
| | - Alistair J Brown
- Institute of Medical Sciences - School of Medical Sciences, University of Aberdeen Aberdeen, UK
| | - Fabian Istel
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna Vienna, Austria
| | - Karl Kuchler
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna Vienna, Austria
| | - Paula Sampaio
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal
| | - Mariana Henriques
- Centre for Biological Engineering, University of Minho Braga, Portugal
| | - Sandra Paiva
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho Braga, Portugal
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98
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The Cytosolic pH of Individual Saccharomyces cerevisiae Cells Is a Key Factor in Acetic Acid Tolerance. Appl Environ Microbiol 2015; 81:7813-21. [PMID: 26341199 DOI: 10.1128/aem.02313-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/27/2015] [Indexed: 11/20/2022] Open
Abstract
It was shown recently that individual cells of an isogenic Saccharomyces cerevisiae population show variability in acetic acid tolerance, and this variability affects the quantitative manifestation of the trait at the population level. In the current study, we investigated whether cell-to-cell variability in acetic acid tolerance could be explained by the observed differences in the cytosolic pHs of individual cells immediately before exposure to the acid. Results obtained with cells of the strain CEN.PK113-7D in synthetic medium containing 96 mM acetic acid (pH 4.5) showed a direct correlation between the initial cytosolic pH and the cytosolic pH drop after exposure to the acid. Moreover, only cells with a low initial cytosolic pH, which experienced a less severe drop in cytosolic pH, were able to proliferate. A similar correlation between initial cytosolic pH and cytosolic pH drop was also observed in the more acid-tolerant strain MUCL 11987-9. Interestingly, a fraction of cells in the MUCL 11987-9 population showed initial cytosolic pH values below the minimal cytosolic pH detected in cells of the strain CEN.PK113-7D; consequently, these cells experienced less severe drops in cytosolic pH. Although this might explain in part the difference between the two strains with regard to the number of cells that resumed proliferation, it was observed that all cells from strain MUCL 11987-9 were able to proliferate, independently of their initial cytosolic pH. Therefore, other factors must also be involved in the greater ability of MUCL 11987-9 cells to endure strong drops in cytosolic pH.
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99
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Muir A, Roelants FM, Timmons G, Leskoske KL, Thorner J. Down-regulation of TORC2-Ypk1 signaling promotes MAPK-independent survival under hyperosmotic stress. eLife 2015; 4. [PMID: 26274562 PMCID: PMC4552222 DOI: 10.7554/elife.09336] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/13/2015] [Indexed: 01/10/2023] Open
Abstract
In eukaryotes, exposure to hypertonic conditions activates a MAPK (Hog1 in Saccharomyces cerevisiae and ortholog p38 in human cells). In yeast, intracellular glycerol accumulates to counterbalance the high external osmolarity. To prevent glycerol efflux, Hog1 action impedes the function of the aquaglyceroporin Fps1, in part, by displacing channel co-activators (Rgc1/2). However, Fps1 closes upon hyperosmotic shock even in hog1∆ cells, indicating another mechanism to prevent Fps1-mediated glycerol efflux. In our prior proteome-wide screen, Fps1 was identified as a target of TORC2-dependent protein kinase Ypk1 (Muir et al., 2014). We show here that Fps1 is an authentic Ypk1 substrate and that the open channel state of Fps1 requires phosphorylation by Ypk1. Moreover, hyperosmotic conditions block TORC2-dependent Ypk1-mediated Fps1 phosphorylation, causing channel closure, glycerol accumulation, and enhanced survival under hyperosmotic stress. These events are all Hog1-independent. Our findings define the underlying molecular basis of a new mechanism for responding to hypertonic conditions. DOI:http://dx.doi.org/10.7554/eLife.09336.001
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Affiliation(s)
- Alexander Muir
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Françoise M Roelants
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Garrett Timmons
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Kristin L Leskoske
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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100
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Costa C, Ponte A, Pais P, Santos R, Cavalheiro M, Yaguchi T, Chibana H, Teixeira MC. New Mechanisms of Flucytosine Resistance in C. glabrata Unveiled by a Chemogenomics Analysis in S. cerevisiae. PLoS One 2015; 10:e0135110. [PMID: 26267134 PMCID: PMC4534419 DOI: 10.1371/journal.pone.0135110] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 07/18/2015] [Indexed: 11/19/2022] Open
Abstract
5-Flucytosine is currently used as an antifungal drug in combination therapy, but fungal pathogens are rapidly able to develop resistance against this drug, compromising its therapeutic action. The understanding of the underlying resistance mechanisms is crucial to deal with this problem. In this work, the S. cerevisiae deletion mutant collection was screened for increased resistance to flucytosine. Through this chemogenomics analysis, 183 genes were found to confer resistance to this antifungal agent. Consistent with its known effect in DNA, RNA and protein synthesis, the most significant Gene Ontology terms over-represented in the list of 5-flucytosine resistance determinants are related to DNA repair, RNA and protein metabolism. Additional functional classes include carbohydrate and nitrogen-particularly arginine-metabolism, lipid metabolism and cell wall remodeling. Based on the results obtained for S. cerevisiae as a model system, further studies were conducted in the pathogenic yeast Candida glabrata. Arginine supplementation was found to relieve the inhibitory effect exerted by 5-flucytosine in C. glabrata. Lyticase susceptibility was found to increase within the first 30min of 5-flucytosine exposure, suggesting this antifungal drug to act as a cell wall damaging agent. Upon exponential growth resumption in the presence of 5-flucytosine, the cell wall exhibited higher resistance to lyticase, suggesting that cell wall remodeling occurs in response to 5-flucytosine. Additionally, the aquaglyceroporin encoding genes CgFPS1 and CgFPS2, from C. glabrata, were identified as determinants of 5-flucytosine resistance. CgFPS1 and CgFPS2 were found to mediate 5-flucytosine resistance, by decreasing 5-flucytosine accumulation in C. glabrata cells.
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Affiliation(s)
- Catarina Costa
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Andreia Ponte
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Rui Santos
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Mafalda Cavalheiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
| | - Takashi Yaguchi
- Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB—Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Lisboa, Portugal
- * E-mail:
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