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Meng X, Liu X, Bao Y, Luo T, Wang J. Effect of citric acid on cell membrane structure and function of Issatchenkia terricola WJL-G4. J Appl Microbiol 2024; 135:lxae057. [PMID: 38449343 DOI: 10.1093/jambio/lxae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/17/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024]
Abstract
AIMS This study aimed to investigate the changes of cell membrane structure and function of Issatchenkia terricola under citric acid by performing physiological analysis. METHODS AND RESULTS The membrane integrity, surface hydrophobicity, structure, fluidity, apoptosis, and fatty acid methyl esters composition of I. terricola WJL-G4 cells were determined by propidium iodide staining, microbial adhesion to hydrocarbon test, transmission electron microscopy analysis, fluorescence anisotropy, flow cytometry, and gas chromatography-mass, respectively. The results showed that with the increasing of citric acid concentrations, the cell vitality, membrane integrity, and fluidity of I. terricola reduced; meanwhile, apoptosis rate, membrane permeable, hydrophobicity, and ergosterol contents augmented significantly. Compared to control, the activities of Na+, K+-ATPase, and Ca2+, Mg2+-ATPase increased by 3.73-fold and 6.70-fold, respectively, when citric acid concentration increased to 20 g l-1. The cells cracked and their cytoplasm effused when the citric acid concentration reached 80 g l-1. CONCLUSIONS I. terricola could successfully adjust its membrane structure and function below 60 g l-1 of citric acid. However, for citric acid concentrations above 80 g l-1, its structure and function were dramatically changed, which might result in reduced functionality.
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Affiliation(s)
- Xiangfeng Meng
- College of Life Science, Northeast Forestry University, No. 26, Hexing St., Harbin 150040, China
| | - Xinyi Liu
- College of Life Science, Northeast Forestry University, No. 26, Hexing St., Harbin 150040, China
| | - Yihong Bao
- College of Life Science, Northeast Forestry University, No. 26, Hexing St., Harbin 150040, China
- Key Laboratory of Forest Food Resources Utilization of Heilongjiang Province, No. 26, Hexing St., Harbin 150040, China
| | - Ting Luo
- State Key Laboratory of Food Science and Technology, Nanchang University, No. 999, Xuefu St., Nanchang 330047, China
| | - Jinling Wang
- College of Life Science, Northeast Forestry University, No. 26, Hexing St., Harbin 150040, China
- Key Laboratory of Forest Food Resources Utilization of Heilongjiang Province, No. 26, Hexing St., Harbin 150040, China
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2
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Antunes M, Sá-Correia I. The role of ion homeostasis in adaptation and tolerance to acetic acid stress in yeasts. FEMS Yeast Res 2024; 24:foae016. [PMID: 38658183 PMCID: PMC11092280 DOI: 10.1093/femsyr/foae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024] Open
Abstract
Maintenance of asymmetric ion concentrations across cellular membranes is crucial for proper yeast cellular function. Disruptions of these ionic gradients can significantly impact membrane electrochemical potential and the balance of other ions, particularly under stressful conditions such as exposure to acetic acid. This weak acid, ubiquitous to both yeast metabolism and industrial processes, is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeast. Acetic acid toxicity depends on medium composition, especially on the pH (H+ concentration), but also on other ions' concentrations. Regulation of ion fluxes is essential for effective yeast response and adaptation to acetic acid stress. However, the intricate interplay among ion balancing systems and stress response mechanisms still presents significant knowledge gaps. This review offers a comprehensive overview of the mechanisms governing ion homeostasis, including H+, K+, Zn2+, Fe2+/3+, and acetate, in the context of acetic acid toxicity, adaptation, and tolerance. While focus is given on Saccharomyces cerevisiae due to its extensive physiological characterization, insights are also provided for biotechnologically and clinically relevant yeast species whenever available.
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Affiliation(s)
- Miguel Antunes
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
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3
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Salas-Navarrete PC, Rosas-Santiago P, Suárez-Rodríguez R, Martínez A, Caspeta L. Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12556-7. [PMID: 37178307 DOI: 10.1007/s00253-023-12556-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Ethanol fermentations can be prematurely halted as Saccharomyces cerevisiae faces adverse conditions, such as acidic pH, presence of acetic acid, and supraoptimal temperatures. The knowledge on yeast responses to these conditions is essential to endowing a tolerant phenotype to another strain by targeted genetic manipulation. In this study, physiological and whole-genome analyses were conducted to obtain insights on molecular responses which potentially render yeast tolerant towards thermoacidic conditions. To this end, we used thermotolerant TTY23, acid tolerant AT22, and thermo-acid tolerant TAT12 strains previously generated by adaptive laboratory evolution (ALE) experiments. The results showed an increase in thermoacidic profiles in the tolerant strains. The whole-genome sequence revealed the importance of genes related to: H+, iron, and glycerol transport (i.e., PMA1, FRE1/2, JEN1, VMA2, VCX1, KHA1, AQY3, and ATO2); transcriptional regulation of stress responses to drugs, reactive oxygen species and heat-shock (i.e., HSF1, SKN7, BAS1, HFI1, and WAR1); and adjustments of fermentative growth and stress responses by glucose signaling pathways (i.e., ACS1, GPA1/2, RAS2, IRA2, and REG1). At 30 °C and pH 5.5, more than a thousand differentially expressed genes (DEGs) were identified in each strain. The integration of results revealed that evolved strains adjust their intracellular pH by H+ and acetic acid transport, modify their metabolism and stress responses via glucose signaling pathways, control of cellular ATP pools by regulating translation and de novo synthesis of nucleotides, and direct the synthesis, folding and rescue of proteins throughout the heat-shock stress response. Moreover, the motifs analysis in mutated transcription factors suggested a significant association of SFP1, YRR1, BAS1, HFI1, HSF1, and SKN7 TFs with DEGs found in thermoacidic tolerant yeast strains. KEY POINTS: • All the evolved strains overexpressed the plasma membrane H+ -ATPase PMA1 at optimal conditions • Tolerant strain TAT12 mutated genes encoding weak acid and heat response TFs HSF1, SKN7, and WAR1 • TFs HSF1 and SKN7 likely controlled the transcription of metabolic genes associated to heat and acid tolerance.
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Affiliation(s)
- Prisciluis Caheri Salas-Navarrete
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Paul Rosas-Santiago
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Ramón Suárez-Rodríguez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Alfredo Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Luis Caspeta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México.
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4
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Zhu H, Li T, Li C, Liu Y, Miao Y, Liu D, Shen Q. Intracellular kynurenine promotes acetaldehyde accumulation, further inducing the apoptosis in soil beneficial fungi Trichoderma guizhouense NJAU4742 under acid stress. Environ Microbiol 2023; 25:331-351. [PMID: 36367399 DOI: 10.1111/1462-2920.16286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
In this study, the growth of fungi Trichoderma guizhouense NJAU4742 was significantly inhibited under acid stress, and the genes related to acid stress were identified based on transcriptome analysis. Four genes including tna1, adh2/4, and bna3 were significantly up-regulated. Meanwhile, intracellular hydrogen ions accumulated under acid stress, and ATP synthesis was induced to transport hydrogen ions to maintain hydrogen ion balance. The enhancement of glycolysis pathway was also detected, and a large amount of pyruvic acid from glycolysis was accumulated due to the activity limitation of PDH enzymes. Finally, acetaldehyde accumulated, resulting in the induction of adh2/4. In order to cope with stress caused by acetaldehyde, cells enhanced the synthesis of NAD+ by increasing the expression of tna1 and bna3 genes. NAD+ effectively improved the antioxidant capacity of cells, but the NAD+ supplement pathway mediated by bna3 could also cause the accumulation of kynurenine (KYN), which was an inducer of apoptosis. In addition, KYN had a specific promoting effect on acetaldehyde synthesis by improving the expression of eno2 gene, which led to the extremely high intracellular acetaldehyde in the cell under acidic stress. Our findings provided a route to better understand the response of filamentous fungi under acid stress.
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Affiliation(s)
- Han Zhu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Tuo Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Chi Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Yang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Jiangsu, People's Republic of China
- Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
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5
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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6
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Ye PL, Wang XQ, Yuan B, Liu CG, Zhao XQ. Manipulating cell flocculation-associated protein kinases in Saccharomyces cerevisiae enables improved stress tolerance and efficient cellulosic ethanol production. BIORESOURCE TECHNOLOGY 2022; 348:126758. [PMID: 35134528 DOI: 10.1016/j.biortech.2022.126758] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Cell self-flocculation endows yeast strains with improved environmental stress tolerance that benefits bioproduction. Exploration of the metabolic and regulatory network differences between the flocculating and non-flocculating cells is conducive to developing strains with satisfactory fermentation efficiency. In this work, integrated analyses of transcriptome, proteome, and phosphoproteome were performed using flocculating yeast Saccharomyces cerevisiae SPSC01 and its non-flocculating mutant grown under acetic acid stress, and the results revealed prominent changes in protein kinases. Overexpressing the mitogen-activated protein kinase Hog1 upregulated by flocculation led to reduced ROS accumulation and increased glutathione peroxidase activity, leading to improved ethanol production under stress. Among the seven genes encoding protein kinases that were tested, AKL1 showed the best performance when overexpressed, achieving higher ethanol productivity in both corncob hydrolysate and simulated corn stover hydrolysate. These results provide alternative strategies for improving cellulosic ethanol production by engineering key protein kinases in S. cerevisiae.
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Affiliation(s)
- Pei-Liang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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7
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Crosstalk between Yeast Cell Plasma Membrane Ergosterol Content and Cell Wall Stiffness under Acetic Acid Stress Involving Pdr18. J Fungi (Basel) 2022; 8:jof8020103. [PMID: 35205858 PMCID: PMC8880318 DOI: 10.3390/jof8020103] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/02/2023] Open
Abstract
Acetic acid is a major inhibitory compound in several industrial bioprocesses, in particular in lignocellulosic yeast biorefineries. Cell envelope remodeling, involving cell wall and plasma membrane composition, structure and function, is among the mechanisms behind yeast adaptation and tolerance to stress. Pdr18 is a plasma membrane ABC transporter of the pleiotropic drug resistance family and a reported determinant of acetic acid tolerance mediating ergosterol transport. This study provides evidence for the impact of Pdr18 expression in yeast cell wall during adaptation to acetic acid stress. The time-course of acetic-acid-induced transcriptional activation of cell wall biosynthetic genes (FKS1, BGL2, CHS3, GAS1) and of increased cell wall stiffness and cell wall polysaccharide content in cells with the PDR18 deleted, compared to parental cells, is reported. Despite the robust and more intense adaptive response of the pdr18Δ population, the stress-induced increase of cell wall resistance to lyticase activity was below parental strain levels, and the duration of the period required for intracellular pH recovery from acidification and growth resumption was higher in the less tolerant pdr18Δ population. The ergosterol content, critical for plasma membrane stabilization, suffered a drastic reduction in the first hour of cultivation under acetic acid stress, especially in pdr18Δ cells. Results revealed a crosstalk between plasma membrane ergosterol content and cell wall biophysical properties, suggesting a coordinated response to counteract the deleterious effects of acetic acid.
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8
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Adewara OA, Ogunbanwo ST. Acid stress responses of Lactobacillus amylovorus and Candida kefyr isolated from fermented sorghum gruel and their application in food fermentation. Can J Microbiol 2022; 68:269-280. [PMID: 35038286 DOI: 10.1139/cjm-2021-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Exposure of Lactic Acid Bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress, consequently, microbes develop adaptive responses. In this study, the physiological and proteomic responses of LAB and yeast to acid stress, and their application in food fermentation was investigated. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry method, SDS-PAGE and LC-MS/MS respectively. The technique previously reported by Association of Official Analytical Chemists (AOAC) were employed for evaluation of the physiocochemical and organoleptic properties of the sorghum gruel fermented using the LAB and yeast in singly and combination as starter cultures and spontaneous fermentation as control. Growth of L. amylovorus LS07 was optimal at pH 1.0 and C. kefyr YSI2 at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was noted at pH 1 and 4 respectively suggesting increased microbial metabolism thereby reducing stress encountered. Sorghum gruel produced with combined starters had the highest crude protein (10.94 %), Iron content (0.0085 %), organoleptic acceptability (7.29) significantly different from products produced with the single starters and control. The combined starter's (L. amylovorus LS07 and C. kefyr YSI2 as starter) adapted stress yielded foods with improved sensory properties, mineral and reduced anti-nutrient contents.
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Affiliation(s)
- Oluwaseun Adeola Adewara
- University of Ibadan, 58987, Microbiology, Ibadan, Ibadan, Nigeria.,Caleb University, 202110, Biological Sciences and Biotechnology, Lagos, Lagos, Nigeria;
| | - S T Ogunbanwo
- University of Ibadan, Microbiology, P.O. Box 22346, University of Ibadan, Ibadan, Nigeria, Ibadan, Oyo, Nigeria, +234;
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9
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Extending the Proteomic Characterization of Candida albicans Exposed to Stress and Apoptotic Inducers through Data-Independent Acquisition Mass Spectrometry. mSystems 2021; 6:e0094621. [PMID: 34609160 PMCID: PMC8547427 DOI: 10.1128/msystems.00946-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Candida albicans is a commensal fungus that causes systemic infections in immunosuppressed patients. In order to deal with the changing environment during commensalism or infection, C. albicans must reprogram its proteome. Characterizing the stress-induced changes in the proteome that C. albicans uses to survive should be very useful in the development of new antifungal drugs. We studied the C. albicans global proteome after exposure to hydrogen peroxide (H2O2) and acetic acid (AA), using a data-independent acquisition mass spectrometry (DIA-MS) strategy. More than 2,000 C. albicans proteins were quantified using an ion library previously constructed using data-dependent acquisition mass spectrometry (DDA-MS). C. albicans responded to treatment with H2O2 with an increase in the abundance of many proteins involved in the oxidative stress response, protein folding, and proteasome-dependent catabolism, which led to increased proteasome activity. The data revealed a previously unknown key role for Prn1, a protein similar to pirins, in the oxidative stress response. Treatment with AA resulted in a general decrease in the abundance of proteins involved in amino acid biosynthesis, protein folding, and rRNA processing. Almost all proteasome proteins declined, as did proteasome activity. Apoptosis was observed after treatment with H2O2 but not AA. A targeted proteomic study of 32 proteins related to apoptosis in yeast supported the results obtained by DIA-MS and allowed the creation of an efficient method to quantify relevant proteins after treatment with stressors (H2O2, AA, and amphotericin B). This approach also uncovered a main role for Oye32, an oxidoreductase, suggesting this protein as a possible apoptotic marker common to many stressors. IMPORTANCE Fungal infections are a worldwide health problem, especially in immunocompromised patients and patients with chronic disorders. Invasive candidiasis, caused mainly by C. albicans, is among the most common fungal diseases. Despite the existence of treatments to combat candidiasis, the spectrum of drugs available is limited. For the discovery of new drug targets, it is essential to know the pathogen response to different stress conditions. Our study provides a global vision of proteomic remodeling in C. albicans after exposure to different agents, such as hydrogen peroxide, acetic acid, and amphotericin B, that can cause apoptotic cell death. These results revealed the significance of many proteins related to oxidative stress response and proteasome activity, among others. Of note, the discovery of Prn1 as a key protein in the defense against oxidative stress as well the increase in the abundance of Oye32 protein when apoptotic process occurred point them out as possible drug targets.
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10
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The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan. Microorganisms 2021; 9:microorganisms9091871. [PMID: 34576766 PMCID: PMC8472237 DOI: 10.3390/microorganisms9091871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.
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11
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Shoket H, Pandita M, Sharma M, Kumar R, Rakwal A, Wazir S, Verma V, Salunke DB, Bairwa NK. Genetic interaction between F-box motif encoding YDR131C and retrograde signaling-related RTG1 regulates the stress response and apoptosis in Saccharomyces cerevisiae. J Biochem Mol Toxicol 2021; 35:e22864. [PMID: 34309121 DOI: 10.1002/jbt.22864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
The retrograde signaling pathway is well conserved from yeast to humans, which regulates cell adaptation during stress conditions and prevents cell death. One of its components, RTG1 encoded Rtg1p in association with Rtg3p communicates between mitochondria, nucleus, and peroxisome during stress for adaptation, by regulation of transcription. The F-box motif protein encoded by YDR131C constitutes a part of SCF Ydr131c -E3 ligase complex, with unknown function; however, it is known that retrograde signaling is modulated by the E3 ligase complex. This study reports epistasis interaction between YDR131C and RTG1, which regulates cell growth, response to genotoxic stress, decreased apoptosis, resistance to petite mutation, and cell wall integrity. The cells of ydr131cΔrtg1Δ genetic background exhibits growth rate improvement however, sensitivity to hydroxyurea, itraconazole antifungal agent and synthetic indoloquinazoline-based alkaloid (8-fluorotryptanthrin, RK64), which disrupts the cell wall integrity in Saccharomyces cerevisiae. The epistatic interaction between YDR131C and RTG1 indicates a link between protein degradation and retrograde signaling pathways.
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Affiliation(s)
- Heena Shoket
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Monika Pandita
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Meenu Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Ravinder Kumar
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, India
| | - Ayushi Rakwal
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Shreya Wazir
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Vijeshwar Verma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Deepak B Salunke
- Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, India.,National Interdisciplinary Centre of Vaccine, Immunotherapeutic and Antimicrobials, Panjab University, Chandigarh, India
| | - Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
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12
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Chaves SR, Rego A, Martins VM, Santos-Pereira C, Sousa MJ, Côrte-Real M. Regulation of Cell Death Induced by Acetic Acid in Yeasts. Front Cell Dev Biol 2021; 9:642375. [PMID: 34249904 PMCID: PMC8264433 DOI: 10.3389/fcell.2021.642375] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 11/15/2022] Open
Abstract
Acetic acid has long been considered a molecule of great interest in the yeast research field. It is mostly recognized as a by-product of alcoholic fermentation or as a product of the metabolism of acetic and lactic acid bacteria, as well as of lignocellulosic biomass pretreatment. High acetic acid levels are commonly associated with arrested fermentations or with utilization as vinegar in the food industry. Due to its obvious interest to industrial processes, research on the mechanisms underlying the impact of acetic acid in yeast cells has been increasing. In the past twenty years, a plethora of studies have addressed the intricate cascade of molecular events involved in cell death induced by acetic acid, which is now considered a model in the yeast regulated cell death field. As such, understanding how acetic acid modulates cellular functions brought about important knowledge on modulable targets not only in biotechnology but also in biomedicine. Here, we performed a comprehensive literature review to compile information from published studies performed with lethal concentrations of acetic acid, which shed light on regulated cell death mechanisms. We present an historical retrospective of research on this topic, first providing an overview of the cell death process induced by acetic acid, including functional and structural alterations, followed by an in-depth description of its pharmacological and genetic regulation. As the mechanistic understanding of regulated cell death is crucial both to design improved biomedical strategies and to develop more robust and resilient yeast strains for industrial applications, acetic acid-induced cell death remains a fruitful and open field of study.
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Affiliation(s)
- Susana R Chaves
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - António Rego
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Vítor M Martins
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Cátia Santos-Pereira
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal.,Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
| | - Maria João Sousa
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Centre of Biological and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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13
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Ribeiro RA, Vitorino MV, Godinho CP, Bourbon-Melo N, Robalo TT, Fernandes F, Rodrigues MS, Sá-Correia I. Yeast adaptive response to acetic acid stress involves structural alterations and increased stiffness of the cell wall. Sci Rep 2021; 11:12652. [PMID: 34135398 PMCID: PMC8209030 DOI: 10.1038/s41598-021-92069-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/03/2021] [Indexed: 11/08/2022] Open
Abstract
This work describes a coordinate and comprehensive view on the time course of the alterations occurring at the level of the cell wall during adaptation of a yeast cell population to sudden exposure to a sub-lethal stress induced by acetic acid. Acetic acid is a major inhibitory compound in industrial bioprocesses and a widely used preservative in foods and beverages. Results indicate that yeast cell wall resistance to lyticase activity increases during acetic acid-induced growth latency, corresponding to yeast population adaptation to sudden exposure to this stress. This response correlates with: (i) increased cell stiffness, assessed by atomic force microscopy (AFM); (ii) increased content of cell wall β-glucans, assessed by fluorescence microscopy, and (iii) slight increase of the transcription level of the GAS1 gene encoding a β-1,3-glucanosyltransferase that leads to elongation of (1→3)-β-D-glucan chains. Collectively, results reinforce the notion that the adaptive yeast response to acetic acid stress involves a coordinate alteration of the cell wall at the biophysical and molecular levels. These alterations guarantee a robust adaptive response essential to limit the futile cycle associated to the re-entry of the toxic acid form after the active expulsion of acetate from the cell interior.
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Affiliation(s)
- Ricardo A Ribeiro
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Miguel V Vitorino
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
- Departament of Physics, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Cláudia P Godinho
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Tiago T Robalo
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
- Departament of Physics, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Fábio Fernandes
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Mário S Rodrigues
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
- Departament of Physics, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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14
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Guaragnella N, Bettiga M. Acetic acid stress in budding yeast: From molecular mechanisms to applications. Yeast 2021; 38:391-400. [PMID: 34000094 PMCID: PMC8361955 DOI: 10.1002/yea.3651] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/13/2021] [Accepted: 05/11/2021] [Indexed: 12/20/2022] Open
Abstract
Acetic acid stress represents a frequent challenge to counteract for yeast cells under several environmental conditions and industrial bioprocesses. The molecular mechanisms underlying its response have been mostly elucidated in the budding yeast Saccharomyces cerevisiae, where acetic acid can be either a physiological substrate or a stressor. This review will focus on acetic acid stress and its response in the context of cellular transport, pH homeostasis, metabolism and stress‐signalling pathways. This information has been integrated with the results obtained by multi‐omics, synthetic biology and metabolic engineering approaches aimed to identify major cellular players involved in acetic acid tolerance. In the production of biofuels and renewable chemicals from lignocellulosic biomass, the improvement of acetic acid tolerance is a key factor. In this view, how this knowledge could be used to contribute to the development and competitiveness of yeast cell factories for sustainable applications will be also discussed. Acetic acid stress is a frequent challenge for budding yeast. Signalling pathways dissection and system‐wide approaches reveal a complex picture. Cell fitness and adaptation under acid stress conditions is environment dependent. Tolerance to acetic acid is a key factor in yeast‐based industrial biotechnology. There is no ‘magic bullet’: An integrated approach is advantageous to develop performing yeast cell factories.
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Affiliation(s)
- Nicoletta Guaragnella
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari A.Moro, Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Rome, Italy
| | - Maurizio Bettiga
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Bioeconomy Division, EviKrets Biobased Processes Consultants, Landvetter, Sweden
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15
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Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
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Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, 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, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
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16
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de Castro Andreassa E, Santos MDMD, Wassmandorf R, Wippel HH, Carvalho PC, Fischer JDSDG, Souza TDACBD. Proteomic changes in Trypanosoma cruzi epimastigotes treated with the proapoptotic compound PAC-1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140582. [PMID: 33285319 DOI: 10.1016/j.bbapap.2020.140582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]
Abstract
Apoptosis is a highly regulated process of cell death in metazoans. Therefore, understanding the biochemical changes associated with apoptosis-like death in Trypanosoma cruzi is key to drug development. PAC-1 was recently shown to induce apoptosis in T. cruzi; with this as motivation, we used quantitative proteomics to unveil alterations of PAC-1-treated versus untreated epimastigotes. The PAC-1 treatment reduced the abundance of putative vesicle-associated membrane protein, putative eukaryotic translation initiation factor 1 eIF1, coatomer subunit beta, putative amastin, and a putative cytoskeleton-associated protein. Apoptosis-like signaling also increases the abundance of proteins associated with actin cytoskeleton remodeling, cell polarization, apoptotic signaling, phosphorylation, methylation, ergosterol biosynthesis, vacuolar proteins associated with autophagy, and flagellum motility. We shortlist seventeen protein targets for possible use in chemotherapy for Chagas disease. Almost all differentially abundant proteins belong to a family of proteins previously associated with apoptosis in metazoans, suggesting that the apoptotic pathway's key functions have been preserved from trypanosomatids and metazoans. SIGNIFICANCE: Approximately 8 million people worldwide are infected with Trypanosoma cruzi. The treatment of Chagas disease comprises drugs with severe side effects, thus limiting their application. Thus, developing new pharmaceutical solutions is relevant, and several molecules targeting apoptosis are therapeutically efficient for parasitic, cardiac, and neurological diseases. Apoptotic processes lead to specific morphological features that have been previously observed in T. cruzi. Here, we investigate changes in epimastigotes' proteomic profile treated with the proapoptotic compound PAC-1, providing data concerning the regulation of both metabolic and cellular processes in nonmetazoan apoptotic cells. We shortlist seventeen protein target candidates for use in chemotherapy for Chagas disease.
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Affiliation(s)
- Emanuella de Castro Andreassa
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Marlon Dias Mariano Dos Santos
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Rafaela Wassmandorf
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Helisa Helena Wippel
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Paulo Costa Carvalho
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
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17
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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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18
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Zimmermann A, Tadic J, Kainz K, Hofer SJ, Bauer MA, Carmona-Gutierrez D, Madeo F. Transcriptional and epigenetic control of regulated cell death in yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 352:55-82. [PMID: 32334817 DOI: 10.1016/bs.ircmb.2019.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Unicellular organisms like yeast can undergo controlled demise in a manner that is partly reminiscent of mammalian cell death. This is true at the levels of both mechanistic and functional conservation. Yeast offers the combination of unparalleled genetic amenability and a comparatively simple biology to understand both the regulation and evolution of cell death. In this minireview, we address the capacity of the nucleus as a regulatory hub during yeast regulated cell death (RCD), which is becoming an increasingly central question in yeast RCD research. In particular, we explore and critically discuss the available data on stressors and signals that specifically impinge on the nucleus. Moreover, we also analyze the current knowledge on nuclear factors as well as on transcriptional control and epigenetic events that orchestrate yeast RCD. Altogether we conclude that the functional significance of the nucleus for yeast RCD in undisputable, but that further exploration beyond correlative work is necessary to disentangle the role of nuclear events in the regulatory network.
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Affiliation(s)
- Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; Division of Immunology and Pathophysiology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Maria A Bauer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | | | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; BioTechMed Graz, Graz, Austria.
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19
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Hu J, Dong Y, Wang W, Zhang W, Lou H, Chen Q. Deletion of Atg22 gene contributes to reduce programmed cell death induced by acetic acid stress in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:298. [PMID: 31890026 PMCID: PMC6933646 DOI: 10.1186/s13068-019-1638-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/12/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Programmed cell death (PCD) induced by acetic acid, the main by-product released during cellulosic hydrolysis, cast a cloud over lignocellulosic biofuel fermented by Saccharomyces cerevisiae and became a burning problem. Atg22p, an ignored integral membrane protein located in vacuole belongs to autophagy-related genes family; prior study recently reported that it is required for autophagic degradation and efflux of amino acids from vacuole to cytoplasm. It may alleviate the intracellular starvation of nutrition caused by Ac and increase cell tolerance. Therefore, we investigate the role of atg22 in cell death process induced by Ac in which attempt is made to discover new perspectives for better understanding of the mechanisms behind tolerance and more robust industrial strain construction. RESULTS In this study, we compared cell growth, physiological changes in the absence and presence of Atg22p under Ac exposure conditions. It is observed that disruption and overexpression of Atg22p delays and enhances acetic acid-induced PCD, respectively. The deletion of Atg22p in S. cerevisiae maintains cell wall integrity, and protects cytomembrane integrity, fluidity and permeability upon Ac stress by changing cytomembrane phospholipids, sterols and fatty acids. More interestingly, atg22 deletion increases intracellular amino acids to aid yeast cells for tackling amino acid starvation and intracellular acidification. Further, atg22 deletion upregulates series of stress response genes expression such as heat shock protein family, cell wall integrity and autophagy. CONCLUSIONS The findings show that Atg22p possessed the new function related to cell resistance to Ac. This may help us have a deeper understanding of PCD induced by Ac and provide a new strategy to improve Ac resistance in designing industrial yeast strains for bioethanol production during lignocellulosic biofuel fermentation.
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Affiliation(s)
- Jingjin Hu
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Yachen Dong
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Wei Wang
- Institute of Quality and Standard for Agriculture Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Wei Zhang
- Department of Cardiovascular & Metabolic Sciences, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA
| | - Hanghang Lou
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Qihe Chen
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
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20
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Kumar P, Kundu D, Mondal AK, Nain V, Puria R. Inhibition of TOR signalling in lea1 mutant induces apoptosis in Saccharomyces cerevisiae. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1422-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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21
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Zhang MM, Xiong L, Tang YJ, Mehmood MA, Zhao ZK, Bai FW, Zhao XQ. Enhanced acetic acid stress tolerance and ethanol production in Saccharomyces cerevisiae by modulating expression of the de novo purine biosynthesis genes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:116. [PMID: 31168321 PMCID: PMC6509782 DOI: 10.1186/s13068-019-1456-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/02/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Yeast strains that are tolerant to multiple environmental stresses are highly desired for various industrial applications. Despite great efforts in identifying key genes involved in stress tolerance of budding yeast Saccharomyces cerevisiae, the effects of de novo purine biosynthesis genes on yeast stress tolerance are still not well explored. Our previous studies showed that zinc sulfate addition improved yeast acetic acid tolerance, and key genes involved in yeast stress tolerance were further investigated in this study. RESULTS Three genes involved in de novo purine biosynthesis, namely, ADE1, ADE13, and ADE17, showed significantly increased transcription levels by zinc sulfate supplementation under acetic acid stress, and overexpression of these genes in S. cerevisiae BY4741 enhanced cell growth under various stress conditions. Meanwhile, ethanol productivity was also improved by overexpression of the three ADE genes under stress conditions, among which the highest improvement attained 158.39% by ADE17 overexpression in the presence of inhibitor mixtures derived from lignocellulosic biomass. Elevated levels of adenine-nucleotide pool "AXP" ([ATP] + [ADP] + [AMP]) and ATP content were observed by overexpression of ADE17, both under control condition and under acetic acid stress, and is consistent with the better growth of the recombinant yeast strain. The global intracellular amino acid profiles were also changed by overexpression of the ADE genes. Among the changed amino acids, significant increase of the stress protectant γ-aminobutyric acid (GABA) was revealed by overexpression of the ADE genes under acetic acid stress, suggesting that overexpression of the ADE genes exerts control on both purine biosynthesis and amino acid biosynthesis to protect yeast cells against the stress. CONCLUSION We proved that the de novo purine biosynthesis genes are useful targets for metabolic engineering of yeast stress tolerance. The engineered strains developed in this study with improved tolerance against multiple inhibitors can be employed for efficient lignocellulosic biorefinery to produce biofuels and biochemicals.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024 China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, 430068 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Muhammad Aamer Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, 38000 Pakistan
| | - Zongbao Kent Zhao
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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22
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Martins VM, Fernandes TR, Lopes D, Afonso CB, Domingues MRM, Côrte-Real M, Sousa MJ. Contacts in Death: The Role of the ER-Mitochondria Axis in Acetic Acid-Induced Apoptosis in Yeast. J Mol Biol 2018; 431:273-288. [PMID: 30414966 DOI: 10.1016/j.jmb.2018.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/12/2018] [Accepted: 11/05/2018] [Indexed: 02/08/2023]
Abstract
Endoplasmic reticulum-mitochondria contact sites have been a subject of increasing scientific interest since the discovery that these structures are disrupted in several pathologies. Due to the emerging data that correlate endoplasmic reticulum-mitochondria contact sites function with known events of the apoptotic program, we aimed to dissect this interplay using our well-established model of acetic acid-induced apoptosis in Saccharomyces cerevisiae. Until recently, the only known tethering complex between ER and mitochondria in this organism was the ER-mitochondria encounter structure (ERMES). Following our results from a screening designed to identify genes whose deletion rendered cells with an altered sensitivity to acetic acid, we hypothesized that the ERMES complex could be involved in cell death mediated by this stressor. Herein we demonstrate that single ablation of the ERMES components Mdm10p, Mdm12p and Mdm34p increases the resistance of S. cerevisiae to acetic acid-induced apoptosis, which is associated with a prominent delay in the appearance of several apoptotic markers. Moreover, abrogation of Mdm10p or Mdm34p abolished cytochrome c release from mitochondria. Since these two proteins are embedded in the mitochondrial outer membrane, we propose that the ERMES complex plays a part in cytochrome c release, a key event of the apoptotic cascade. In all, these findings will aid in targeted therapies for diseases where apoptosis is disrupted, as well as assist in the development of acetic acid-resistant strains for industrial processes.
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Affiliation(s)
- Vítor M Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tânia R Fernandes
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Lopes
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Chemistry & CESAM & ECOMARE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Catarina B Afonso
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria R M Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Chemistry & CESAM & ECOMARE, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria J Sousa
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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23
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Guo ZP, Khoomrung S, Nielsen J, Olsson L. Changes in lipid metabolism convey acid tolerance in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:297. [PMID: 30450126 PMCID: PMC6206931 DOI: 10.1186/s13068-018-1295-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/15/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND The yeast Saccharomyces cerevisiae plays an essential role in the fermentation of lignocellulosic hydrolysates. Weak organic acids in lignocellulosic hydrolysate can hamper the use of this renewable resource for fuel and chemical production. Plasma-membrane remodeling has recently been found to be involved in acquiring tolerance to organic acids, but the mechanisms responsible remain largely unknown. Therefore, it is essential to understand the underlying mechanisms of acid tolerance of S. cerevisiae for developing robust industrial strains. RESULTS We have performed a comparative analysis of lipids and fatty acids in S. cerevisiae grown in the presence of four different weak acids. The general response of the yeast to acid stress was found to be the accumulation of triacylglycerols and the degradation of steryl esters. In addition, a decrease in phosphatidic acid, phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine, and an increase in phosphatidylinositol were observed. Loss of cardiolipin in the mitochondria membrane may be responsible for the dysfunction of mitochondria and the dramatic decrease in the rate of respiration of S. cerevisiae under acid stress. Interestingly, the accumulation of ergosterol was found to be a protective mechanism of yeast exposed to organic acids, and the ERG1 gene in ergosterol biosynthesis played a key in ergosterol-mediated acid tolerance, as perturbing the expression of this gene caused rapid loss of viability. Interestingly, overexpressing OLE1 resulted in the increased levels of oleic acid (18:1n-9) and an increase in the unsaturation index of fatty acids in the plasma membrane, resulting in higher tolerance to acetic, formic and levulinic acid, while this change was found to be detrimental to cells exposed to lipophilic cinnamic acid. CONCLUSIONS Comparison of lipid profiles revealed different remodeling of lipids, FAs and the unsaturation index of the FAs in the cell membrane in response of S. cerevisiae to acetic, formic, levulinic and cinnamic acid, depending on the properties of the acid. In future work, it will be necessary to combine lipidome and transcriptome analysis to gain a better understanding of the underlying regulation network and interactions between central carbon metabolism (e.g., glycolysis, TCA cycle) and lipid biosynthesis.
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Affiliation(s)
- Zhong-peng Guo
- Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Present Address: LISBP, INSA, INRA, CNRS, Université de Toulouse, Toulouse, France
| | - Sakda Khoomrung
- Department of Biochemistry and Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, 2800 Kongens Lyngby, Denmark
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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24
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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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25
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Wang D, Wu D, Yang X, Hong J. Transcriptomic analysis of thermotolerant yeastKluyveromyces marxianusin multiple inhibitors tolerance. RSC Adv 2018; 8:14177-14192. [PMID: 35540752 PMCID: PMC9079866 DOI: 10.1039/c8ra00335a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/09/2018] [Indexed: 11/21/2022] Open
Abstract
Global transcriptional response ofK. marxianusto multiple inhibitors including acetic acid, phenols, furfural and HMF at 42 °C.
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Affiliation(s)
- Dongmei Wang
- School of Life Sciences
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Dan Wu
- School of Life Sciences
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Xiaoxue Yang
- School of Life Sciences
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Jiong Hong
- School of Life Sciences
- University of Science and Technology of China
- Hefei
- P. R. China
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26
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Samanfar B, Shostak K, Moteshareie H, Hajikarimlou M, Shaikho S, Omidi K, Hooshyar M, Burnside D, Márquez IG, Kazmirchuk T, Naing T, Ludovico P, York-Lyon A, Szereszewski K, Leung C, Jin JY, Megarbane R, Smith ML, Babu M, Holcik M, Golshani A. The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A. PeerJ 2017; 5:e4037. [PMID: 29158977 PMCID: PMC5691786 DOI: 10.7717/peerj.4037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
The presence of acetic acid during industrial alcohol fermentation reduces the yield of fermentation by imposing additional stress on the yeast cells. The biology of cellular responses to stress has been a subject of vigorous investigations. Although much has been learned, details of some of these responses remain poorly understood. Members of heat shock chaperone HSP proteins have been linked to acetic acid and heat shock stress responses in yeast. Both acetic acid and heat shock have been identified to trigger different cellular responses including reduction of global protein synthesis and induction of programmed cell death. Yeast HSC82 and HSP82 code for two important heat shock proteins that together account for 1–2% of total cellular proteins. Both proteins have been linked to responses to acetic acid and heat shock. In contrast to the overall rate of protein synthesis which is reduced, the expression of HSC82 and HSP82 is induced in response to acetic acid stress. In the current study we identified two yeast genes DOM34 and RPL36A that are linked to acetic acid and heat shock sensitivity. We investigated the influence of these genes on the expression of HSP proteins. Our observations suggest that Dom34 and RPL36A influence translation in a CAP-independent manner.
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Affiliation(s)
- Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Kristina Shostak
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sarah Shaikho
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Center for Cancer Therapeutics, Ottawa, Ontario, Canada
| | - Daniel Burnside
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Imelda Galván Márquez
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Tom Kazmirchuk
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Thet Naing
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Portugal
| | - Anna York-Lyon
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kama Szereszewski
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Cindy Leung
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jennifer Yixin Jin
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rami Megarbane
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Myron L Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Martin Holcik
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada.,Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
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27
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Guerreiro JF, Mira NP, Santos AXS, Riezman H, Sá-Correia I. Membrane Phosphoproteomics of Yeast Early Response to Acetic Acid: Role of Hrk1 Kinase and Lipid Biosynthetic Pathways, in Particular Sphingolipids. Front Microbiol 2017; 8:1302. [PMID: 28747907 PMCID: PMC5506226 DOI: 10.3389/fmicb.2017.01302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/28/2017] [Indexed: 01/02/2023] Open
Abstract
Saccharomyces cerevisiae response and tolerance to acetic acid is critical in industrial biotechnology and in acidic food and beverages preservation. The HRK1 gene, encoding a protein kinase of unknown function belonging to the “Npr1-family” of kinases known to be involved in the regulation of plasma membrane transporters, is an important determinant of acetic acid tolerance. This study was performed to identify the alterations occurring in yeast membrane phosphoproteome profile during the adaptive early response to acetic acid stress (following 1 h of exposure to a sub-lethal inhibitory concentration; 50 mM at pH 4.0) and the effect of HRK1 expression on the phosphoproteome. Results from mass spectrometry analysis following the prefractionation and specific enrichment of phosphorylated peptides using TiO2 beads highlight the contribution of processes related with translation, protein folding and processing, transport, and cellular homeostasis in yeast response to acetic acid stress, with particular relevance for changes in phosphorylation of transport-related proteins, found to be highly dependent on the Hrk1 kinase. Twenty different phosphoproteins known to be involved in lipid and sterol metabolism were found to be differently phosphorylated in response to acetic acid stress, including several phosphopeptides that had not previously been described as being phosphorylated. The suggested occurrence of cellular lipid composition remodeling during the short term yeast response to acetic acid was confirmed: Hrk1 kinase-independent reduction in phytoceramide levels and a reduction in phosphatidylcholine and phosphatidylinositol levels under acetic acid stress in the more susceptible hrk1Δ strain were revealed by a lipidomic analysis.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Nuno P Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | - Aline X S Santos
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Howard Riezman
- Department of Biochemistry, University of GenevaGeneva, Switzerland
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
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28
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Dong Y, Hu J, Fan L, Chen Q. RNA-Seq-based transcriptomic and metabolomic analysis reveal stress responses and programmed cell death induced by acetic acid in Saccharomyces cerevisiae. Sci Rep 2017; 7:42659. [PMID: 28209995 PMCID: PMC5314350 DOI: 10.1038/srep42659] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
Abstract
As a typical harmful inhibitor in cellulosic hydrolyzates, acetic acid not only hinders bioethanol production, but also induces cell death in Saccharomyces cerevisiae. Herein, we conducted both transcriptomic and metabolomic analyses to investigate the global responses under acetic acid stress at different stages. There were 295 up-regulated and 427 down-regulated genes identified at more than two time points during acetic acid treatment (150 mM, pH 3.0). These differentially expressed genes (DEGs) were mainly involved in intracellular homeostasis, central metabolic pathway, transcription regulation, protein folding and stabilization, ubiquitin-dependent protein catabolic process, vesicle-mediated transport, protein synthesis, MAPK signaling pathways, cell cycle, programmed cell death, etc. The interaction network of all identified DEGs was constructed to speculate the potential regulatory genes and dominant pathways in response to acetic acid. The transcriptional changes were confirmed by metabolic profiles and phenotypic analysis. Acetic acid resulted in severe acidification in both cytosol and mitochondria, which was different from the effect of extracellular pH. Additionally, the imbalance of intracellular acetylation was shown to aggravate cell death under this stress. Overall, this work provides a novel and comprehensive understanding of stress responses and programmed cell death induced by acetic acid in yeast.
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Affiliation(s)
- Yachen Dong
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jingjin Hu
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Linlin Fan
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Qihe Chen
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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29
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Henriques SF, Mira NP, Sá-Correia I. Genome-wide search for candidate genes for yeast robustness improvement against formic acid reveals novel susceptibility (Trk1 and positive regulators) and resistance (Haa1-regulon) determinants. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:96. [PMID: 28428821 PMCID: PMC5395885 DOI: 10.1186/s13068-017-0781-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Formic acid is an inhibitory compound present in lignocellulosic hydrolysates. Understanding the complex molecular mechanisms underlying Saccharomyces cerevisiae tolerance to this weak acid at the system level is instrumental to guide synthetic pathway engineering for robustness improvement of industrial strains envisaging their use in lignocellulosic biorefineries. RESULTS This study was performed to identify, at a genome-wide scale, genes whose expression confers protection or susceptibility to formic acid, based on the screening of a haploid deletion mutant collection to search for these phenotypes in the presence of 60, 70 and 80 mM of this acid, at pH 4.5. This chemogenomic analysis allowed the identification of 172 determinants of tolerance and 41 determinants of susceptibility to formic acid. Clustering of genes required for maximal tolerance to this weak acid, based on their biological function, indicates an enrichment of those involved in intracellular trafficking and protein synthesis, cell wall and cytoskeleton organization, carbohydrate metabolism, lipid, amino acid and vitamin metabolism, response to stress, chromatin remodelling, transcription and internal pH homeostasis. Among these genes is HAA1 encoding the main transcriptional regulator of yeast transcriptome reprograming in response to acetic acid and genes of the Haa1-regulon; all demonstrated determinants of acetic acid tolerance. Among the genes that when deleted lead to increased tolerance to formic acid, TRK1, encoding the high-affinity potassium transporter and a determinant of resistance to acetic acid, was surprisingly found. Consistently, genes encoding positive regulators of Trk1 activity were also identified as formic acid susceptibility determinants, while a negative regulator confers protection. At a saturating K+ concentration of 20 mM, the deletion mutant trk1Δ was found to exhibit a much higher tolerance compared with the parental strain. Given that trk1Δ accumulates lower levels of radiolabelled formic acid, compared to the parental strain, it is hypothesized that Trk1 facilitates formic acid uptake into the yeast cell. CONCLUSIONS The list of genes resulting from this study shows a few marked differences from the list of genes conferring protection to acetic acid and provides potentially valuable information to guide improvement programmes for the development of more robust strains against formic acid.
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Affiliation(s)
- Sílvia F. Henriques
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Nuno P. Mira
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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30
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Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress. Sci Rep 2016; 6:34304. [PMID: 27678167 PMCID: PMC5039629 DOI: 10.1038/srep34304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/07/2016] [Indexed: 11/08/2022] Open
Abstract
Brettanomyces bruxellensis has been described as the main contaminant yeast in wine production, due to its ability to convert the hydroxycinnamic acids naturally present in the grape phenolic derivatives, into volatile phenols. Currently, there are no studies in B. bruxellensis which explains the resistance mechanisms to hydroxycinnamic acids, and in particular to p-coumaric acid which is directly involved in alterations to wine. In this work, we performed a transcriptome analysis of B. bruxellensis LAMAP248rown in the presence and absence of p-coumaric acid during lag phase. Because of reported genetic variability among B. bruxellensis strains, to complement de novo assembly of the transcripts, we used the high-quality genome of B. bruxellensis AWRI1499, as well as the draft genomes of strains CBS2499 and0 g LAMAP2480. The results from the transcriptome analysis allowed us to propose a model in which the entrance of p-coumaric acid to the cell generates a generalized stress condition, in which the expression of proton pump and efflux of toxic compounds are induced. In addition, these mechanisms could be involved in the outflux of nitrogen compounds, such as amino acids, decreasing the overall concentration and triggering the expression of nitrogen metabolism genes.
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31
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Petitjean M, Teste MA, Léger-Silvestre I, François JM, Parrou JL. RETRACTED:A new function for the yeast trehalose-6P synthase (Tps1) protein, as key pro-survival factor during growth, chronological ageing, and apoptotic stress. Mech Ageing Dev 2016; 161:234-246. [PMID: 27507670 DOI: 10.1016/j.mad.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of Marie-Ange Teste, Isabelle Léger-Silvestre, Jean M François and Jean-Luc Parrou. Marjorie Petitjean could not be reached.
The corresponding author identified major issues and brought them to the attention of the Journal.
These issues span from significant errors in the Material and Methods section of the article and major flaws in cytometry data analysis to data fabrication on the part of one of the authors.
Given these errors, the retracting authors state that the only responsible course of action would be to retract the article, to respect scientific integrity and maintain the standards and rigor of literature from the retracting authors' group as well as the Journal.
The retracting authors sincerely apologize to the readers and editors.
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Affiliation(s)
| | - Marie-Ange Teste
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, Université de Toulouse, 118 route de Narbonne, F-31000 Toulouse, France
| | - Jean M François
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean-Luc Parrou
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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32
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Koppram R, Mapelli V, Albers E, Olsson L. The Presence of Pretreated Lignocellulosic Solids from Birch during Saccharomyces cerevisiae Fermentations Leads to Increased Tolerance to Inhibitors--A Proteomic Study of the Effects. PLoS One 2016; 11:e0148635. [PMID: 26849651 PMCID: PMC4743953 DOI: 10.1371/journal.pone.0148635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 01/21/2016] [Indexed: 11/18/2022] Open
Abstract
The fermentation performance of Saccharomyces cerevisiae in the cellulose to ethanol conversion process is largely influenced by the components of pretreated biomass. The insoluble solids in pretreated biomass predominantly constitute cellulose, lignin, and -to a lesser extent- hemicellulose. It is important to understand the effects of water-insoluble solids (WIS) on yeast cell physiology and metabolism for the overall process optimization. In the presence of synthetic lignocellulosic inhibitors, we observed a reduced lag phase and enhanced volumetric ethanol productivity by S. cerevisiae CEN.PK 113-7D when the minimal medium was supplemented with WIS of pretreated birch or spruce and glucose as the carbon source. To investigate the underlying molecular reasons for the effects of WIS, we studied the response of WIS at the proteome level in yeast cells in the presence of acetic acid as an inhibitor. Comparisons were made with cells grown in the presence of acetic acid but without WIS in the medium. Altogether, 729 proteins were detected and quantified, of which 246 proteins were significantly up-regulated and 274 proteins were significantly down-regulated with a fold change≥1.2 in the presence of WIS compared to absence of WIS. The cells in the presence of WIS up-regulated several proteins related to cell wall, glycolysis, electron transport chain, oxidative stress response, oxygen and radical detoxification and unfolded protein response; and down-regulated most proteins related to biosynthetic pathways including amino acid, purine, isoprenoid biosynthesis, aminoacyl-tRNA synthetases and pentose phosphate pathway. Overall, the identified differentially regulated proteins may indicate that the likelihood of increased ATP generation in the presence of WIS was used to defend against acetic acid stress at the expense of reduced biomass formation. Although, comparative proteomics of cells with and without WIS in the acetic acid containing medium revealed numerous changes, a direct effect of WIS on cellular physiology remains to be investigated.
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Affiliation(s)
- Rakesh Koppram
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Valeria Mapelli
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eva Albers
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail:
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33
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Guerreiro JF, Sampaio-Marques B, Soares R, Coelho AV, Leão C, Ludovico P, Sá-Correia I. Mitochondrial proteomics of the acetic acid - induced programmed cell death response in a highly tolerant Zygosaccharomyces bailii - derived hybrid strain. MICROBIAL CELL 2016; 3:65-78. [PMID: 28357336 PMCID: PMC5349105 DOI: 10.15698/mic2016.02.477] [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] [Indexed: 02/04/2023]
Abstract
Very high concentrations of acetic acid at low pH induce programmed cell death
(PCD) in both the experimental model Saccharomyces cerevisiae
and in Zygosaccharomyces bailii, the latter being considered
the most problematic acidic food spoilage yeast due to its remarkable intrinsic
resistance to this food preservative. However, while the mechanisms underlying
S. cerevisiae PCD induced by acetic acid have been
previously examined, the corresponding molecular players remain largely unknown
in Z. bailii. Also, the reason why acetic acid concentrations
known to be necrotic for S. cerevisiae induce PCD with an
apoptotic phenotype in Z. bailii remains to be elucidated. In
this study, a 2-DE-based expression mitochondrial proteomic analysis was
explored to obtain new insights into the mechanisms involved in PCD in the
Z. bailii derived hybrid strain ISA1307. This allowed the
quantitative assessment of expression of protein species derived from each of
the parental strains, with special emphasis on the processes taking place in the
mitochondria known to play a key role in acetic acid - induced PCD. A marked
decrease in the content of proteins involved in mitochondrial metabolism, in
particular, in respiratory metabolism (Cor1, Rip1, Lpd1, Lat1 and Pdb1), with a
concomitant increase in the abundance of proteins involved in fermentation
(Pdc1, Ald4, Dld3) was registered. Other differentially expressed identified
proteins also suggest the involvement of the oxidative stress response, protein
translation, amino acid and nucleotide metabolism, among other processes, in the
PCD response. Overall, the results strengthen the emerging concept of the
importance of metabolic regulation of yeast PCD.
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Affiliation(s)
- Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Ana V Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Cecília Leão
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga 4710-057, Portugal. ; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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Palma M, Roque FDC, Guerreiro JF, Mira NP, Queiroz L, Sá-Correia I. Search for genes responsible for the remarkably high acetic acid tolerance of a Zygosaccharomyces bailii-derived interspecies hybrid strain. BMC Genomics 2015; 16:1070. [PMID: 26673744 PMCID: PMC4681151 DOI: 10.1186/s12864-015-2278-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022] Open
Abstract
Background Zygosaccharomyces bailii is considered the most problematic acidic food spoilage yeast species due to its exceptional capacity to tolerate high concentrations of weak acids used as fungistatic preservatives at low pH. However, the mechanisms underlying its intrinsic remarkable tolerance to weak acids remain poorly understood. The identification of genes and mechanisms involved in Z. bailii acetic acid tolerance was on the focus of this study. For this, a genomic library from the highly acetic acid tolerant hybrid strain ISA1307, derived from Z. bailii and a closely related species and isolated from a sparkling wine production plant, was screened for acetic acid tolerance genes. This screen was based on the transformation of an acetic acid susceptible Saccharomyces cerevisiae mutant deleted for the gene encoding the acetic acid resistance determinant transcription factor Haa1. Results The expression of 31 different DNA inserts from ISA1307 strain genome was found to significantly increase the host cell tolerance to acetic acid. The in silico analysis of these inserts was facilitated by the recently available genome sequence of this strain. In total, 65 complete or truncated ORFs were identified as putative determinants of acetic acid tolerance and an S. cerevisiae gene homologous to most of them was found. These include genes involved in cellular transport and transport routes, protein fate, protein synthesis, amino acid metabolism and transcription. The role of strong candidates in Z. bailii and S. cerevisiae acetic acid tolerance was confirmed based on homologous and heterologous expression analyses. Conclusions ISA1307 genes homologous to S. cerevisiae genes GYP8, WSC4, PMT1, KTR7, RKR1, TIF3, ILV3 and MSN4 are proposed as strong candidate determinants of acetic acid tolerance. The ORF ZBAI_02295 that contains a functional domain associated to the uncharacterised integral membrane proteins of unknown function of the DUP family is also suggested as a relevant tolerance determinant. The genes ZbMSN4 and ZbTIF3, encoding a putative stress response transcription factor and a putative translation initiation factor, were confirmed as determinants of acetic acid tolerance in both Z. bailii and S. cerevisiae. This study provides valuable indications on the cellular components, pathways and processes to be targeted in order to control food spoilage by the highly acetic acid tolerant Z. bailii and Z. bailii-derived strains. Additionally, this information is essential to guide the improvement of yeast cells robustness against acetic acid if the objective is their use as cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2278-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margarida Palma
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Filipa de Canaveira Roque
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Joana Fernandes Guerreiro
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Nuno Pereira Mira
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Lise Queiroz
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
| | - Isabel Sá-Correia
- Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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Longo V, Ždralević M, Guaragnella N, Giannattasio S, Zolla L, Timperio AM. Proteome and metabolome profiling of wild-type and YCA1-knock-out yeast cells during acetic acid-induced programmed cell death. J Proteomics 2015; 128:173-88. [PMID: 26269384 DOI: 10.1016/j.jprot.2015.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/03/2015] [Accepted: 08/05/2015] [Indexed: 01/13/2023]
Abstract
UNLABELLED Caspase proteases are responsible for the regulated disassembly of the cell into apoptotic bodies during mammalian apoptosis. Structural homologues of the caspase family (called metacaspases) are involved in programmed cell death in single-cell eukaryotes, yet the molecular mechanisms that contribute to death are currently undefined. Recent evidence revealed that a programmed cell death process is induced by acetic acid (AA-PCD) in Saccharomyces cerevisiae both in the presence and absence of metacaspase encoding gene YCA1. Here, we report an unexpected role for the yeast metacaspase in protein quality and metabolite control. By using an "omics" approach, we focused our attention on proteins and metabolites differentially modulated en route to AA-PCD either in wild type or YCA1-lacking cells. Quantitative proteomic and metabolomic analyses of wild type and Δyca1 cells identified significant alterations in carbohydrate catabolism, lipid metabolism, proteolysis and stress-response, highlighting the main roles of metacaspase in AA-PCD. Finally, deletion of YCA1 led to AA-PCD pathway through the activation of ceramides, whereas in the presence of the gene yeast cells underwent an AA-PCD pathway characterized by the shift of the main glycolytic pathway to the pentose phosphate pathway and a proteolytic mechanism to cope with oxidative stress. SIGNIFICANCE The yeast metacaspase regulates both proteolytic activities through the ubiquitin-proteasome system and ceramide metabolism as revealed by proteome and metabolome profiling of YCA1-knock-out cells during acetic-acid induced programmed cell death.
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Affiliation(s)
- Valentina Longo
- Department of Ecology and Biology, "La Tuscia" University, Viterbo, Italy
| | - Maša Ždralević
- Institute of Biomembrane and Bioenergetics, CNR, Bari, Italy
| | | | | | - Lello Zolla
- Department of Ecology and Biology, "La Tuscia" University, Viterbo, Italy.
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Determinants of tolerance to inhibitors in hardwood spent sulfite liquor in genome shuffled Pachysolen tannophilus strains. Antonie van Leeuwenhoek 2015; 108:811-34. [PMID: 26231071 DOI: 10.1007/s10482-015-0537-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Genome shuffling was used to obtain Pachysolen tannophilus mutants with improved tolerance to inhibitors in hardwood spent sulfite liquor (HW SSL). Genome shuffled strains (GHW301, GHW302 and GHW303) grew at higher concentrations of HW SSL (80 % v/v) compared to the HW SSL UV mutant (70 % v/v) and the wild-type (WT) strain (50 % v/v). In defined media containing acetic acid (0.70-0.90 % w/v), GHW301, GHW302 and GHW303 exhibited a shorter lag compared to the acetic acid UV mutant, while the WT did not grow. Genome shuffled strains produced more ethanol than the WT at higher concentrations of HW SSL and an aspen hydrolysate. To identify the genetic basis of inhibitor tolerance, whole genome sequencing was carried out on GHW301, GHW302 and GHW303 and compared to the WT strain. Sixty single nucleotide variations were identified that were common to all three genome shuffled strains. Of these, 40 were in gene sequences and 20 were within 5 bp-1 kb either up or downstream of protein encoding genes. Based on the mutated gene products, mutations were grouped into functional categories and affected a variety of cellular functions, demonstrating the complexity of inhibitor tolerance in yeast. Sequence analysis of UV mutants (UAA302 and UHW303) from which GHW301, GHW302 and GHW303 were derived, confirmed the success of our cross-mating based genome shuffling strategy. Whole-genome sequencing analysis allowed identification of potential gene targets for tolerance to inhibitors in lignocellulosic hydrolysates.
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37
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Adaptation and tolerance of bacteria against acetic acid. Appl Microbiol Biotechnol 2015; 99:6215-29. [DOI: 10.1007/s00253-015-6762-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/05/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
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38
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Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance. Appl Microbiol Biotechnol 2015; 99:6391-403. [DOI: 10.1007/s00253-015-6706-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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Si T, Luo Y, Bao Z, Zhao H. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 2015; 4:283-91. [PMID: 24758359 DOI: 10.1021/sb500074a] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A fundamental challenge in basic and applied biology is to reprogram cells with improved or novel traits on a genomic scale. However, the current ability to reprogram a cell on the genome scale is limited to bacterial cells. Here, we report RNA interference (RNAi)-assisted genome evolution (RAGE) as a generally applicable method for genome-scale engineering in the yeast Saccharomyces cerevisiae. Through iterative cycles of creating a library of RNAi induced reduction-of-function mutants coupled with high throughput screening or selection, RAGE can continuously improve target trait(s) by accumulating multiplex beneficial genetic modifications in an evolving yeast genome. To validate the RNAi library constructed with yeast genomic DNA and convergent-promoter expression cassette, we demonstrated RNAi screening in Saccharomyces cerevisiae for the first time by identifying two known and three novel suppressors of a telomerase-deficient mutation yku70Δ. We then showed the application of RAGE for improved acetic acid tolerance, a key trait for microbial production of chemicals and fuels. Three rounds of iterative RNAi screening led to the identification of three gene knockdown targets that acted synergistically to confer an engineered yeast strain with substantially improved acetic acid tolerance. RAGE should greatly accelerate the design and evolution of organisms with desired traits and provide new insights on genome structure, function, and evolution.
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Affiliation(s)
- Tong Si
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yunzi Luo
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Zehua Bao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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40
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Michel S, Keller MA, Wamelink MMC, Ralser M. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genet 2015; 16:13. [PMID: 25887987 PMCID: PMC4331311 DOI: 10.1186/s12863-015-0171-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Studying the survival of yeast in stationary phase, known as chronological lifespan, led to the identification of molecular ageing factors conserved from yeast to higher organisms. To identify functional interactions among yeast chronological ageing genes, we conducted a haploproficiency screen on the basis of previously identified long-living mutants. For this, we created a library of heterozygous Saccharomyces cerevisiae double deletion strains and aged them in a competitive manner. RESULTS Stationary phase survival was prolonged in a double heterozygous mutant of the metabolic enzyme non-quiescent mutant 1 (NQM1), a paralogue to the pentose phosphate pathway enzyme transaldolase (TAL1), and the transcription factor vitamin H response transcription factor 1 (VHR1). We find that cells deleted for the two genes possess increased clonogenicity at late stages of stationary phase survival, but find no indication that the mutations delay initial mortality upon reaching stationary phase, canonically defined as an extension of chronological lifespan. We show that both genes influence the concentration of metabolites of glycolysis and the pentose phosphate pathway, central metabolic players in the ageing process, and affect osmolality of growth media in stationary phase cultures. Moreover, NQM1 is glucose repressed and induced in a VHR1 dependent manner upon caloric restriction, on non-fermentable carbon sources, as well as under osmotic and oxidative stress. Finally, deletion of NQM1 is shown to confer resistance to oxidizing substances. CONCLUSIONS The transaldolase paralogue NQM1 and the transcription factor VHR1 interact haploproficiently and affect yeast stationary phase survival. The glucose repressed NQM1 gene is induced under various stress conditions, affects stress resistance and this process is dependent on VHR1. While NQM1 appears not to function in the pentose phosphate pathway, the interplay of NQM1 with VHR1 influences the yeast metabolic homeostasis and stress tolerance during stationary phase, processes associated with yeast ageing.
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Affiliation(s)
- Steve Michel
- Max Planck Institute for Molecular Genetics, Ihnestr 73, Berlin, 14195, Germany.
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
| | - Mirjam M C Wamelink
- Metabolic Unit, Department of Clinical Chemistry, VU University Medical Centre Amsterdam, Amsterdam, The Netherlands.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Center, University of Cambridge, 80, Tennis, Court Road, Cambridge, CB2 1GA, UK.
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.
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41
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Ding J, Holzwarth G, Penner MH, Patton-Vogt J, Bakalinsky AT. Overexpression of acetyl-CoA synthetase in Saccharomyces cerevisiae increases acetic acid tolerance. FEMS Microbiol Lett 2014; 362:1-7. [PMID: 25673654 DOI: 10.1093/femsle/fnu042] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Acetic acid-mediated inhibition of the fermentation of lignocellulose-derived sugars impedes development of plant biomass as a source of renewable ethanol. In order to overcome this inhibition, the capacity of Saccharomyces cerevisiae to synthesize acetyl-CoA from acetic acid was increased by overexpressing ACS2 encoding acetyl-coenzyme A synthetase. Overexpression of ACS2 resulted in higher resistance to acetic acid as measured by an increased growth rate and shorter lag phase relative to a wild-type control strain, suggesting that Acs2-mediated consumption of acetic acid during fermentation contributes to acetic acid detoxification.
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Affiliation(s)
- Jun Ding
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA Department of Food Science and Technology, Oregon State University, Corvallis, Oregon 97331, USA Research and Development, Medolac Laboratories, 6305 SW Rosewood St, Suite B, Lake Oswego, OR 97035, USA
| | - Garrett Holzwarth
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael H Penner
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Alan T Bakalinsky
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA Department of Food Science and Technology, Oregon State University, Corvallis, Oregon 97331, USA
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42
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Guo Z, Olsson L. Physiological response of Saccharomyces cerevisiae to weak acids present in lignocellulosic hydrolysate. FEMS Yeast Res 2014; 14:1234-48. [PMID: 25331461 DOI: 10.1111/1567-1364.12221] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 10/05/2014] [Accepted: 10/08/2014] [Indexed: 01/15/2023] Open
Abstract
Weak acids are present in lignocellulosic hydrolysate as potential inhibitors that can hamper the use of this renewable resource for fuel and chemical production. To study the effects of weak acids on yeast growth, physiological investigations were carried out in batch cultures using glucose as carbon source in the presence of acetic, formic, levulinic, and vanillic acid at three different concentrations at pH 5.0. The results showed that acids at moderate concentrations can stimulate the glycolytic flux, while higher levels of acid slow down the glycolytic flux for both aerobically and anaerobically grown yeast cells. In particular, the flux distribution between respiratory and fermentative growth was adjusted to achieve an optimal ATP generation to allow a maintained energy level as high as it is in nonstressed cells grown exponentially on glucose under aerobic conditions. In addition, yeast cells exposed to acids suffered from severe reactive oxygen species stress and depletion of reduced glutathione commensurate with exhaustion of the total glutathione pool. Furthermore, a higher cellular trehalose content was observed as compared to control cultivations, and this trehalose probably acts to enhance a number of stress tolerances of the yeast.
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Affiliation(s)
- Zhongpeng Guo
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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43
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Mitochondrial dysfunction in cancer chemoresistance. Biochem Pharmacol 2014; 92:62-72. [DOI: 10.1016/j.bcp.2014.07.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 12/19/2022]
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44
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An J, Kwon H, Kim E, Lee YM, Ko HJ, Park H, Choi IG, Kim S, Kim KH, Kim W, Choi W. Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene. Environ Microbiol 2014; 17:656-69. [DOI: 10.1111/1462-2920.12489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jieun An
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
| | - Hyeji Kwon
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
| | - Eunjung Kim
- Department of Pharmacology, School of Medicine; Ajou University; Suwon 442-749 Korea
| | - Young Mi Lee
- Microbial Resources Research Center; Ewha Womans University; Seoul 120-750 Korea
| | - Hyeok Jin Ko
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Hongjae Park
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - In-Geol Choi
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Sooah Kim
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Kyoung Heon Kim
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Wankee Kim
- Department of Pharmacology, School of Medicine; Ajou University; Suwon 442-749 Korea
| | - Wonja Choi
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
- Microbial Resources Research Center; Ewha Womans University; Seoul 120-750 Korea
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45
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Swinnen S, Fernández-Niño M, González-Ramos D, van Maris AJA, Nevoigt E. The fraction of cells that resume growth after acetic acid addition is a strain-dependent parameter of acetic acid tolerance in Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:642-53. [PMID: 24645649 DOI: 10.1111/1567-1364.12151] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 11/28/2022] Open
Abstract
High acetic acid tolerance of Saccharomyces cerevisiae is a relevant phenotype in industrial biotechnology when using lignocellulosic hydrolysates as feedstock. A screening of 38 S. cerevisiae strains for tolerance to acetic acid revealed considerable differences, particularly with regard to the duration of the latency phase. To understand how this phenotype is quantitatively manifested, four strains exhibiting significant differences were studied in more detail. Our data show that the duration of the latency phase is primarily determined by the fraction of cells within the population that resume growth. Only this fraction contributed to the exponential growth observed after the latency phase, while all other cells persisted in a viable but non-proliferating state. A remarkable variation in the size of the fraction was observed among the tested strains differing by several orders of magnitude. In fact, only 11 out of 10(7) cells of the industrial bioethanol production strain Ethanol Red resumed growth after exposure to 157 mM acetic acid at pH 4.5, while this fraction was 3.6 × 10(6) (out of 10(7) cells) in the highly acetic acid tolerant isolate ATCC 96581. These strain-specific differences are genetically determined and represent a valuable starting point to identify genetic targets for future strain improvement.
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Affiliation(s)
- Steve Swinnen
- School of Engineering and Science, Jacobs University gGmbH, Bremen, Germany
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46
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Sousa M, Duarte AM, Fernandes TR, Chaves SR, Pacheco A, Leão C, Côrte-Real M, Sousa MJ. Genome-wide identification of genes involved in the positive and negative regulation of acetic acid-induced programmed cell death in Saccharomyces cerevisiae. BMC Genomics 2013; 14:838. [PMID: 24286259 PMCID: PMC4046756 DOI: 10.1186/1471-2164-14-838] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acetic acid is mostly known as a toxic by-product of alcoholic fermentation carried out by Saccharomyces cerevisiae, which it frequently impairs. The more recent finding that acetic acid triggers apoptotic programmed cell death (PCD) in yeast sparked an interest to develop strategies to modulate this process, to improve several biotechnological applications, but also for biomedical research. Indeed, acetate can trigger apoptosis in cancer cells, suggesting its exploitation as an anticancer compound. Therefore, we aimed to identify genes involved in the positive and negative regulation of acetic acid-induced PCD by optimizing a functional analysis of a yeast Euroscarf knock-out mutant collection. RESULTS The screen consisted of exposing the mutant strains to acetic acid in YPD medium, pH 3.0, in 96-well plates, and subsequently evaluating the presence of culturable cells at different time points. Several functional categories emerged as greatly relevant for modulation of acetic acid-induced PCD (e.g.: mitochondrial function, transcription of glucose-repressed genes, protein synthesis and modifications, and vesicular traffic for protection, or amino acid transport and biosynthesis, oxidative stress response, cell growth and differentiation, protein phosphorylation and histone deacetylation for its execution). Known pro-apoptotic and anti-apoptotic genes were found, validating the approach developed. Metabolism stood out as a main regulator of this process, since impairment of major carbohydrate metabolic pathways conferred resistance to acetic acid-induced PCD. Among these, lipid catabolism arose as one of the most significant new functions identified. The results also showed that many of the cellular and metabolic features that constitute hallmarks of tumour cells (such as higher glycolytic energetic dependence, lower mitochondrial functionality, increased cell division and metabolite synthesis) confer sensitivity to acetic acid-induced PCD, potentially explaining why tumour cells are more susceptible to acetate than untransformed cells and reinforcing the interest in exploiting this acid in cancer therapy. Furthermore, our results clearly establish a connection between cell proliferation and cell death regulation, evidencing a conserved developmental role of programmed cell death in unicellular eukaryotes. CONCLUSIONS This work advanced the characterization of acetic acid-induced PCD, providing a wealth of new information on putative molecular targets for its control with impact both in biotechnology and biomedicine.
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Affiliation(s)
- Marlene Sousa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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47
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Smethurst DG, Dawes IW, Gourlay CW. Actin - a biosensor that determines cell fate in yeasts. FEMS Yeast Res 2013; 14:89-95. [DOI: 10.1111/1567-1364.12119] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 01/22/2023] Open
Affiliation(s)
| | - Ian W. Dawes
- School of Biotechnology and Biomolecular Sciences; University of NSW; Kensington Sydney NSW Australia
| | - Campbell W. Gourlay
- Kent Fungal Group; School of Biosciences; University of Kent; Canterbury Kent UK
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48
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Swinnen E, Ghillebert R, Wilms T, Winderickx J. Molecular mechanisms linking the evolutionary conserved TORC1-Sch9 nutrient signalling branch to lifespan regulation in Saccharomyces cerevisiae. FEMS Yeast Res 2013; 14:17-32. [PMID: 24102693 DOI: 10.1111/1567-1364.12097] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/09/2013] [Accepted: 09/06/2013] [Indexed: 01/13/2023] Open
Abstract
The knowledge on the molecular aspects regulating ageing in eukaryotic organisms has benefitted greatly from studies using the budding yeast Saccharomyces cerevisiae. Indeed, many aspects involved in the control of lifespan appear to be well conserved among species. Of these, the lifespan-extending effects of calorie restriction (CR) and downregulation of nutrient signalling through the target of rapamycin (TOR) pathway are prime examples. Here, we present an overview on the molecular mechanisms by which these interventions mediate lifespan extension in yeast. Several models have been proposed in the literature, which should be seen as complementary, instead of contradictory. Results indicate that CR mediates a large amount of its effect by downregulating signalling through the TORC1-Sch9 branch. In addition, we note that Sch9 is more than solely a downstream effector of TORC1, and documented connections with sphingolipid metabolism may be particularly interesting for future research on ageing mechanisms. As Sch9 comprises the yeast orthologue of the mammalian PKB/Akt and S6K1 kinases, future studies in yeast may continue to serve as an attractive model to elucidate conserved mechanisms involved in ageing and age-related diseases in humans.
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49
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Silva A, Sampaio-Marques B, Fernandes Â, Carreto L, Rodrigues F, Holcik M, Santos MAS, Ludovico P. Involvement of yeast HSP90 isoforms in response to stress and cell death induced by acetic acid. PLoS One 2013; 8:e71294. [PMID: 23967187 PMCID: PMC3744546 DOI: 10.1371/journal.pone.0071294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/27/2013] [Indexed: 11/18/2022] Open
Abstract
Acetic acid-induced apoptosis in yeast is accompanied by an impairment of the general protein synthesis machinery, yet paradoxically also by the up-regulation of the two isoforms of the heat shock protein 90 (HSP90) chaperone family, Hsc82p and Hsp82p. Herein, we show that impairment of cap-dependent translation initiation induced by acetic acid is caused by the phosphorylation and inactivation of eIF2α by Gcn2p kinase. A microarray analysis of polysome-associated mRNAs engaged in translation in acetic acid challenged cells further revealed that HSP90 mRNAs are over-represented in this polysome fraction suggesting preferential translation of HSP90 upon acetic acid treatment. The relevance of HSP90 isoform translation during programmed cell death (PCD) was unveiled using genetic and pharmacological abrogation of HSP90, which suggests opposing roles for HSP90 isoforms in cell survival and death. Hsc82p appears to promote survival and its deletion leads to necrotic cell death, while Hsp82p is a pro-death molecule involved in acetic acid-induced apoptosis. Therefore, HSP90 isoforms have distinct roles in the control of cell fate during PCD and their selective translation regulates cellular response to acetic acid stress.
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Affiliation(s)
- Alexandra Silva
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ângela Fernandes
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Laura Carreto
- Department of Biology and Centre d’Enseignement de la Statistique Appliquée à la Médecine, University of Aveiro, Aveiro, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Martin Holcik
- Apoptosis Research Centre, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Manuel A. S. Santos
- Department of Biology and Centre d’Enseignement de la Statistique Appliquée à la Médecine, University of Aveiro, Aveiro, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
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Wang X, Jin M, Balan V, Jones AD, Li X, Li BZ, Dale BE, Yuan YJ. Comparative metabolic profiling revealed limitations in xylose-fermenting yeast during co-fermentation of glucose and xylose in the presence of inhibitors. Biotechnol Bioeng 2013; 111:152-64. [DOI: 10.1002/bit.24992] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xin Wang
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Mingjie Jin
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing Michigan
- Department of Chemistry; Michigan State University; East Lansing Michigan
| | - Xia Li
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
| | - Bruce E. Dale
- Biomass Conversion Research Laboratory (BCRL); Department of Chemical Engineering and Materials Science; Michigan State University; 3900 Collins Road MBI International Building Lansing Michigan 48910
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering; Ministry of Education; Department of Pharmaceutical Engineering; School of Chemical Engineering and Technology; Tianjin University; Tianjin 300072 P.R. China
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