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Sánchez-Adriá IE, Sanmartín G, Prieto JA, Estruch F, Fortis E, Randez-Gil F. Adaptive laboratory evolution for acetic acid-tolerance matches sourdough challenges with yeast phenotypes. Microbiol Res 2023; 277:127487. [PMID: 37713908 DOI: 10.1016/j.micres.2023.127487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Acetic acid tolerance of Saccharomyces cerevisiae is an important trait in sourdough fermentation processes, where the accumulation of acid by the growth of lactic acid bacteria reduces the yeast metabolic activity. In this work, we have carried out adaptive laboratory evolution (ALE) experiments in two sourdough isolates of S. cerevisiae exposed to acetic acid, or alternatively to acetic acid and myriocin, an inhibitor of sphingolipid biosynthesis that sped-up the evolutionary adaptation. Evolution approaches resulted in acetic tolerance, and surprisingly, increased lactic susceptibility. Four evolved clones, one from each parental strain and evolutionary scheme, were selected on the basis of their potential for CO2 production in sourdough conditions. Among them, two showed phenotypic instability characterized by strong lactic sensitivity after several rounds of growth under unstressed conditions, while two others, displayed increased constitutive acetic tolerance with no loss of growth in lactic medium. Genome sequencing and ploidy level analysis of all strains revealed aneuploidies, which could account for phenotypic heterogeneity. In addition, copy number variations (CNVs), affecting specially to genes involved in ion transport or flocculation, and single nucleotide polymorphisms (SNPs) were identified. Mutations in several genes, ARG82, KEX1, CTK1, SPT20, IRA2, ASG1 or GIS4, were confirmed as involved in acetic and/or lactic tolerance, and new determinants of these phenotypes, MSN5 and PSP2, identified.
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Affiliation(s)
- Isabel E Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, Paterna, 46980 Valencia, Spain
| | - Gemma Sanmartín
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, Paterna, 46980 Valencia, Spain
| | - Jose A Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, Paterna, 46980 Valencia, Spain
| | - Francisco Estruch
- Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Estefanía Fortis
- Cereal (Center for Research Europastry Advanced Lab), Europastry S.A., Marie Curie, 6, Sant Joan Despí, 08970 Barcelona, Spain
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, Paterna, 46980 Valencia, Spain.
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Cruz-O’Byrne R, Gamez-Guzman A, Piraneque-Gambasica N, Aguirre-Forero S. Genomic sequencing in Colombian coffee fermentation reveals new records of yeast species. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Wu Y, Li B, Miao B, Xie C, Tang YQ. Saccharomyces cerevisiae employs complex regulation strategies to tolerate low pH stress during ethanol production. Microb Cell Fact 2022; 21:247. [DOI: 10.1186/s12934-022-01974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Industrial bioethanol production may involve a low pH environment caused by inorganic acids, improving the tolerance of Saccharomyces cerevisiae to a low pH environment is of industrial importance to increase ethanol yield, control bacterial contamination, and reduce production cost. In our previous study, acid tolerance of a diploid industrial Saccharomyces cerevisiae strain KF-7 was chronically acclimatized by continuous ethanol fermentation under gradually increasing low-pH stress conditions. Two haploid strains B3 and C3 having excellent low pH tolerance were derived through the sporulation of an isolated mutant. Diploid strain BC3 was obtained by mating these two haploids. In this study, B3, C3, BC3, and the original strain KF-7 were subjected to comparison transcriptome analysis to investigate the molecular mechanism of the enhanced phenotype.
Result
The comparison transcriptome analysis results suggested that the upregulated vitamin B1 and B6 biosynthesis contributed to the low pH tolerance. Amino acid metabolism, DNA repairment, and general stress response might also alleviate low pH stress.
Conclusion
Saccharomyces cerevisiae seems to employ complex regulation strategies to tolerate low pH during ethanol production. The findings provide guides for the construction of low pH-tolerant industrial strains that can be used in industrial fermentation processes.
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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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Alkalbani NS, Osaili TM, Al-Nabulsi AA, Olaimat AN, Liu SQ, Shah NP, Apostolopoulos V, Ayyash MM. Assessment of Yeasts as Potential Probiotics: A Review of Gastrointestinal Tract Conditions and Investigation Methods. J Fungi (Basel) 2022; 8:jof8040365. [PMID: 35448596 PMCID: PMC9027893 DOI: 10.3390/jof8040365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
Probiotics are microorganisms (including bacteria, yeasts and moulds) that confer various health benefits to the host, when consumed in sufficient amounts. Food products containing probiotics, called functional foods, have several health-promoting and therapeutic benefits. The significant role of yeasts in producing functional foods with promoted health benefits is well documented. Hence, there is considerable interest in isolating new yeasts as potential probiotics. Survival in the gastrointestinal tract (GIT), salt tolerance and adherence to epithelial cells are preconditions to classify such microorganisms as probiotics. Clear understanding of how yeasts can overcome GIT and salt stresses and the conditions that support yeasts to grow under such conditions is paramount for identifying, characterising and selecting probiotic yeast strains. This study elaborated the adaptations and mechanisms underlying the survival of probiotic yeasts under GIT and salt stresses. This study also discussed the capability of yeasts to adhere to epithelial cells (hydrophobicity and autoaggregation) and shed light on in vitro methods used to assess the probiotic characteristics of newly isolated yeasts.
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Affiliation(s)
- Nadia S. Alkalbani
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Tareq M. Osaili
- Department Clinical Nutrition and Dietetics, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates;
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Anas A. Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P. O. Box 330127, Zarqa 13133, Jordan;
| | - Shao-Quan Liu
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, S14 Level 5, Science Drive 2, Singapore 117542, Singapore;
| | - Nagendra P. Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong 999077, China;
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia;
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Mutamed M. Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
- Correspondence:
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Ren M, Li R, Han B, You Y, Huang W, Du G, Zhan J. Involvement of the High-Osmolarity Glycerol Pathway of Saccharomyces Cerevisiae in Protection against Copper Toxicity. Antioxidants (Basel) 2022; 11:antiox11020200. [PMID: 35204083 PMCID: PMC8868352 DOI: 10.3390/antiox11020200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 01/05/2023] Open
Abstract
Although essential for life, copper is also potentially toxic in concentrations that surpass physiological thresholds. The high-osmolarity glycerol pathway of yeast is the main regulator of adaptive responses and is known to play crucial roles in the responses to various stressors. The objective of this research is to determine whether the HOG pathway could be activated and to investigate the possible interplay of the HOG pathway and oxidative stress due to copper exposure. In this research, we demonstrate that copper could induce oxidative stress, including the elevated concentrations of reactive oxygen species (ROS) and malondialdehyde (MDA). Increased combination with GSH, increased intracellular SOD activity, and the up-regulation of relevant genes can help cells defend themselves against oxidative toxicity. The results show that copper treatment triggers marked and prolonged Hog1 phosphorylation. Significantly, oxidative stress generated by copper toxicity is essential for the activation of Hog1. Activated Hog1 is translocated to the nucleus to regulate the expressions of genes such as CTT1, GPD1, and HSP12, among others. Furthermore, copper exposure induced significant G1-phase cell cycle arrest, while Hog1 partially participated in the regulation of cell cycle progression. These novel findings reveal another role for Hog1 in the regulation of copper-induced cellular stress.
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Affiliation(s)
- Mengmeng Ren
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
| | - Ruilong Li
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
| | - Bin Han
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
| | - Yilin You
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
| | - Weidong Huang
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
| | - Gang Du
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
- Correspondence: (G.D.); (J.Z.)
| | - Jicheng Zhan
- Beijing Key Laboratory of Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Tsinghua East Road 17, Haidian District, Beijing 100083, China; (M.R.); (R.L.); (B.H.); (Y.Y.); (W.H.)
- Correspondence: (G.D.); (J.Z.)
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Coradini ALV, da Silveira Bezerra de Mello F, Furlan M, Maneira C, Carazzolle MF, Pereira GAG, Teixeira GS. QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:239. [PMID: 34915919 PMCID: PMC8675505 DOI: 10.1186/s13068-021-02079-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae is largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first- and second-generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background-including low pH tolerance. RESULTS In this work, we pioneer the use of QTL mapping to uncover the genetic basis that confers to the industrial strain Pedra-2 (PE-2) acidic tolerance during growth at low pH. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome X as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed the allele GAS1, encoding a β-1,3-glucanosyltransferase, as the casual variant in this region. The GAS1 sequence alignment of distinct S. cerevisiae strains pointed out a non-synonymous mutation (A631G) prevalence in wild-type isolates, which is absent in laboratory strains. We further showcase that GAS1 allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process. CONCLUSION This work revealed GAS1 as one of the main causative genes associated with tolerance to growth at low pH in PE-2. We also showcase how GAS1PE-2 can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains. Our results collectively show the importance of tailored industrial isolated strains in discovering the genetic architecture of relevant traits and its implications over productivity.
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Affiliation(s)
- Alessandro L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Fellipe da Silveira Bezerra de Mello
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Monique Furlan
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Marcelo F Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Gonçalo Amarante Guimaraes Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
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Queiroz MG, Elsztein C, Strahl S, de Morais Junior MA. The Saccharomyces cerevisiae Ncw2 protein works on the chitin/β-glucan organisation of the cell wall. Antonie van Leeuwenhoek 2021; 114:1141-1153. [PMID: 33945065 DOI: 10.1007/s10482-021-01584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/17/2021] [Indexed: 11/28/2022]
Abstract
The NCW2 gene was recently described as encoding a GPI-bounded protein that assists in the re-modelling of the Saccharomyces cerevisiae cell wall (CW) and in the repair of damage caused by the polyhexamethylene biguanide (PHMB) polymer to the cell wall. Its absence produces a re-organization of the CW structure that result in resistance to lysis by glucanase. Hence, the present study aimed to extend the analysis of the Ncw2 protein (Ncw2p) to determine its physiological role in the yeast cell surface. The results showed that Ncw2p is transported to the cell surface upon O-mannosylation mediated by the Pmt1p-Pmt2p enzyme complex. It co-localises with the yeast bud scars, a region in cell surface formed by chitin deposition. Once there, Ncw2p enables correct chitin/β-glucan structuring during the exponential growth. The increase in molecular mass by hyper-mannosylation coincides with the increasing in chitin deposition, and leads to glucanase resistance. Treatment of the yeast cells with PHMB produced the same biological effects observed for the passage from exponential to stationary growth phase. This might be a possible mechanism of yeast protection against cationic biocides. In conclusion, we propose that Ncw2p takes part in the mechanism involved in the control of cell surface rigidity by aiding on the linkage between chitin and glucan layers in the modelling of the cell wall during cell growth.
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Affiliation(s)
- Maise Gomes Queiroz
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Carolina Elsztein
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Sabine Strahl
- Laboratory of Glycobiology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Marcos Antonio de Morais Junior
- Laboratory of Microbial Genetics, Department of Genetics, Federal University of Pernambuco, Recife, Brazil. .,Departamento de Genética, Universidade Federal de Pernambuco, Av. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50.670-901, Brasil.
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9
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Songserm P, Srimongkol P, Thitiprasert S, Tanasupawat S, Cheirsilp B, Assabumrungrat S, Karnchanatat A, Thongchul N. Differential Gene Expression Analysis
of Aspergillus terreus Reveals Metabolic
Response and Transcription Suppression under Dissolved Oxygen and
pH Stress. J EVOL BIOCHEM PHYS+ 2020. [DOI: 10.1134/s0022093020060101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Lucena RM, Dolz-Edo L, Brul S, de Morais MA, Smits G. Extreme Low Cytosolic pH Is a Signal for Cell Survival in Acid Stressed Yeast. Genes (Basel) 2020; 11:genes11060656. [PMID: 32560106 PMCID: PMC7349538 DOI: 10.3390/genes11060656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast biomass is recycled in the process of bioethanol production using treatment with dilute sulphuric acid to control the bacterial population. This treatment can lead to loss of cell viability, with consequences on the fermentation yield. Thus, the aim of this study was to define the functional cellular responses to inorganic acid stress. Saccharomyces cerevisiae strains with mutation in several signalling pathways, as well as cells expressing pH-sensitive GFP derivative ratiometric pHluorin, were tested for cell survival and cytosolic pH (pHc) variation during exposure to low external pH (pHex). Mutants in calcium signalling and proton extrusion were transiently sensitive to low pHex, while the CWI slt2Δ mutant lost viability. Rescue of this mutant was observed when cells were exposed to extreme low pHex or glucose starvation and was dependent on the induced reduction of pHc. Therefore, a lowered pHc leads to a complete growth arrest, which protects the cells from lethal stress and keeps cells alive. Cytosolic pH is thus a signal that directs the growth stress-tolerance trade-off in yeast. A regulatory model was proposed to explain this mechanism, indicating the impairment of glucan synthesis as the primary cause of low pHex sensitivity.
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Affiliation(s)
- Rodrigo Mendonça Lucena
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Laura Dolz-Edo
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Marcos Antonio de Morais
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Correspondence: (G.S.); (M.A.d.M.J.)
| | - Gertien Smits
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
- Correspondence: (G.S.); (M.A.d.M.J.)
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CgSTE11 mediates cross tolerance to multiple environmental stressors in Candida glabrata. Sci Rep 2019; 9:17036. [PMID: 31745168 PMCID: PMC6863853 DOI: 10.1038/s41598-019-53593-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
Candida glabrata is a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeast Saccharomyces cerevisiae than other Candida spp. Compared with S. cerevisiae, C. glabrata exhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms of C. glabrata adaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome resequencing identified fixation of mutations in CgSTE11 in all parallel evolved populations. The CgSTE11 homolog in S. cerevisiae plays crucial roles in various mitogen-activated protein kinase (MAPK) signaling pathways, but its role is less understood in C. glabrata. Subsequent verification confirmed that CgSTE11 is important in hyperthermal tolerance and the observed extensive cross-tolerance to other environmental stressors. These results support the hypothesis that CgSTE11 mediates cross-talks between MAPK signaling pathways in C. glabrata in response to environmental challenges.
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Queiroz MG, Elsztein C, de Morais MA. The effects of the Ncw2 protein of Saccharomyces cerevisiae on the positioning of chitin in response to cell wall damage. Antonie van Leeuwenhoek 2019; 113:265-277. [PMID: 31598818 DOI: 10.1007/s10482-019-01335-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
The recently described NCW2 gene encodes a protein that is assumed to be located in the cell wall (CW). This protein was proposed to participate in the repair of CW damages induced by polyhexamethylene biguanide (PHMB). However, much of the information on the biological function(s) of Ncw2p still remains unclear. In view of this, this study seeks to extend the analysis of this gene in light of the way its protein functions in the Cell Wall Integrity (CWI) mechanism. Deletion of the NCW2 gene led to constitutive overexpression of some key CWI genes and increased chitin deposition in the walls of cells exposed to PHMB. This means the lack of Ncw2p might activate a compensatory mechanism that upregulates glucan CWI genes for cell protection by stiffening the CW. This condition seems to alleviate the response through the HOG pathway and makes cells sensitive to osmotic stress. However, Ncw2p may not have been directly involved in tolerance to osmotic stress itself. The results obtained definitely place the NCW2 gene in the list of CWI genes of S. cerevisiae and indicate that its protein has an auxiliary function in the maintenance of the glucan/chitin balance and ensuring the correct structure of the yeast cell wall.
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Affiliation(s)
- Maíse Gomes Queiroz
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brasil
| | - Carolina Elsztein
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brasil
| | - Marcos Antonio de Morais
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235. Cidade Universitária, Recife, PE, 50.670-901, Brasil.
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Hou Q, He Q, Liu G, Lu X, Zong H, Chen W, Zhuge B. Identification and application of novel low pH-inducible promoters for lactic acid production in the tolerant yeast Candida glycerinogenes. J Biosci Bioeng 2019; 128:8-12. [DOI: 10.1016/j.jbiosc.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/03/2019] [Accepted: 01/10/2019] [Indexed: 11/27/2022]
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Mendonça AA, da Silva PKN, Calazans TLS, de Souza RB, de Barros Pita W, Elsztein C, de Morais Junior MA. Lactobacillus vini: mechanistic response to stress by medium acidification. Microbiology (Reading) 2019; 165:26-36. [DOI: 10.1099/mic.0.000738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | | | | | - Will de Barros Pita
- 3Department of Antibiotics, Federal University of Pernambuco, Recife, Brazil
| | - Carolina Elsztein
- 1Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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15
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Beyer R, Jandric Z, Zutz C, Gregori C, Willinger B, Jacobsen ID, Kovarik P, Strauss J, Schüller C. Competition of Candida glabrata against Lactobacillus is Hog1 dependent. Cell Microbiol 2018; 20:e12943. [PMID: 30112857 PMCID: PMC6283251 DOI: 10.1111/cmi.12943] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/04/2018] [Accepted: 08/07/2018] [Indexed: 12/30/2022]
Abstract
Candida glabrata is a common human fungal commensal and opportunistic pathogen. This fungus shows remarkable resilience as it can form recalcitrant biofilms on indwelling catheters, has intrinsic resistance against azole antifungals, and is causing vulvovaginal candidiasis. As a nosocomial pathogen, it can cause life-threatening bloodstream infections in immune-compromised patients. Here, we investigate the potential role of the high osmolarity glycerol response (HOG) MAP kinase pathway for C. glabrata virulence. The C. glabrata MAP kinase CgHog1 becomes activated by a variety of environmental stress conditions such as osmotic stress, low pH, and carboxylic acids and subsequently accumulates in the nucleus. We found that CgHog1 allows C. glabrata to persist within murine macrophages, but it is not required for systemic infection in a mouse model. C. glabrata and Lactobacilli co-colonise mucosal surfaces. Lactic acid at a concentration produced by vaginal Lactobacillus spp. causes CgHog1 phosphorylation and accumulation in the nucleus. In addition, CgHog1 enables C. glabrata to tolerate different Lactobacillus spp. and their metabolites when grown in co-culture. Using a phenotypic diverse set of clinical C. glabrata isolates, we find that the HOG pathway is likely the main quantitative determinant of lactic acid stress resistance. Taken together, our data indicate that CgHog1 has an important role in the confrontation of C. glabrata with the common vaginal flora.
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Affiliation(s)
- Reinhard Beyer
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences, Vienna (BOKU)TullnAustria
| | - Zeljkica Jandric
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences, Vienna (BOKU)TullnAustria
| | - Christoph Zutz
- Department of Farm Animal and Veterinary Public HealthInstitute of Milk Hygiene, Milk Technology and Food ScienceViennaAustria
- Platform Bioactive Microbial Metabolites (BiMM)
| | - Christa Gregori
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences, Vienna (BOKU)TullnAustria
| | - Birgit Willinger
- Division of Clinical Microbiology, Department of Laboratory MedicineMedical University of ViennaViennaAustria
| | - Ilse D. Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection BiologyHans‐Knöll‐Institute (HKI)JenaGermany
| | - Pavel Kovarik
- Max F. Perutz LaboratoriesUniversity of Vienna, Vienna Biocenter (VBC)ViennaAustria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences, Vienna (BOKU)TullnAustria
- Platform Bioactive Microbial Metabolites (BiMM)
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ)University of Natural Resources and Life Sciences, Vienna (BOKU)TullnAustria
- Platform Bioactive Microbial Metabolites (BiMM)
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Effect of Cation Influx on the Viability of Freeze-Dried Lactobacillus brevis WiKim0069. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8112189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Extension of the storage stability of freeze-dried lactic acid bacteria is important for industrialization. In this study, the effect of cation influx from soy powder, which contains high amounts of cations, as a cryoprotective agent on the viability of freeze-dried Lactobacillus brevis WiKim0069 was tested. Compared to that in the absence of the soy powder, bacterial viability was significantly higher in the presence of soy powder. Approximately 4.7% of L. brevis WiKim0069 survived in the absence of the protective agent, whereas 92.8% viability was observed in the presence of soy powder. However, when cations were removed from the soy powder by using ethylenediaminetetraacetic acid (EDTA) and a cationic resin filter, the viability of L. brevis WiKim0069 decreased to 22.9–24.7%. When the soy powder was treated with ethylene glycol tetraacetic acid, the viability was higher than when it was pretreated with EDTA and a cationic resin filter, suggesting that Mg2+ had a role in enhancing the viability of L. brevis WiKim0069. Cold adaptation at 10 °C prior to freeze-drying had a positive effect on the storage stability of freeze-dried L. brevis WiKim0069, with 60.6% viability after 56 days of storage. A decrease in the fluorescence polarization value indicated an increase in membrane fluidity, which regulates the activity of ion channels present in the cell membrane. Cold adaptation caused activation of the cation channels, resulting in increased intracellular influx of cations, i.e., Ca2+ and Mg2+. These results suggest that cold adaptation can be used to improve the storage stability of L. brevis WiKim0069.
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Jiang L, Wang L, Fang T, Papadopoulos V. Disruption of ergosterol and tryptophan biosynthesis, as well as cell wall integrity pathway and the intracellular pH homeostasis, lead to mono-(2-ethylhexyl)-phthalate toxicity in budding yeast. CHEMOSPHERE 2018; 206:643-654. [PMID: 29783050 DOI: 10.1016/j.chemosphere.2018.05.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/13/2018] [Accepted: 05/12/2018] [Indexed: 06/08/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are substances in the environment, food, and consumer products that interfere with hormone homeostasis, metabolism or reproduction in humans and animals. One such EDC, the plasticizer di-(2-ethylhexyl)-phthalate (DEHP), exerts its function through its principal bioactive metabolite, mono-(2-ethylhexyl)-phthalate (MEHP). To fully understand the effects of MEHP on cellular processes and metabolism as well as to assess the impact of genetic alteration on the susceptibility to MEHP-induced toxicity, we screened MEHP-sensitive mutations on a genome-scale in the eukaryotic model organism Saccharomyces cerevisiae. We identified a total of 96 chemical-genetic interactions between MEHP and gene mutations in this study. In response to MEHP treatment, most of these gene mutants accumulated higher intracellular MEHP content, which correlated with their MEHP sensitivity. Twenty-seven of these genes are involved in the metabolism, twenty-two of them play roles in protein sorting, and ten of them regulate ion homeostasis. Functional categorization of these genes indicated that the biosynthetic pathways of both ergosterol and tryptophan, as well as cell wall integrity and the intracellular pH homeostasis, were involved in the protective response of yeast cells to the MEHP toxicity. Our study demonstrated that a collection of yeast gene deletion mutants is useful for a functional toxicogenomic analysis of EDCs, which could provide important clues to the effects of EDCs on higher eukaryotic organisms.
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Affiliation(s)
- Linghuo Jiang
- Laboratory for Yeast Molecular and Cell Biology, The Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong 255000, China.
| | - Litong Wang
- Laboratory for Yeast Molecular and Cell Biology, The Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong 255000, China
| | - Tianshu Fang
- Laboratory for Yeast Molecular and Cell Biology, The Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong 255000, China
| | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada; Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
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Mount HO, Revie NM, Todd RT, Anstett K, Collins C, Costanzo M, Boone C, Robbins N, Selmecki A, Cowen LE. Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs. PLoS Genet 2018; 14:e1007319. [PMID: 29702647 PMCID: PMC5922528 DOI: 10.1371/journal.pgen.1007319] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
Invasive fungal infections caused by the pathogen Candida albicans have transitioned from a rare curiosity to a major cause of human mortality. This is in part due to the emergence of resistance to the limited number of antifungals available to treat fungal infections. Azoles function by targeting the biosynthesis of ergosterol, a key component of the fungal cell membrane. Loss-of-function mutations in the ergosterol biosynthetic gene ERG3 mitigate azole toxicity and enable resistance that depends upon fungal stress responses. Here, we performed a genome-wide synthetic genetic array screen in Saccharomyces cerevisiae to map ERG3 genetic interactors and uncover novel circuitry important for azole resistance. We identified nine genes that enabled erg3-mediated azole resistance in the model yeast and found that only two of these genes had a conserved impact on resistance in C. albicans. Further, we screened a C. albicans homozygous deletion mutant library and identified 13 genes for which deletion enhances azole susceptibility. Two of the genes, RGD1 and PEP8, were also important for azole resistance acquired by diverse mechanisms. We discovered that loss of function of retrograde transport protein Pep8 overwhelms the functional capacity of the stress response regulator calcineurin, thereby abrogating azole resistance. To identify the mechanism through which the GTPase activator protein Rgd1 enables azole resistance, we selected for mutations that restore resistance in strains lacking Rgd1. Whole genome sequencing uncovered parallel adaptive mechanisms involving amplification of both chromosome 7 and a large segment of chromosome 3. Overexpression of a transporter gene on the right portion of chromosome 3, NPR2, was sufficient to enable azole resistance in the absence of Rgd1. Thus, we establish a novel mechanism of adaptation to drug-induced stress, define genetic circuitry underpinning azole resistance, and illustrate divergence in resistance circuitry over evolutionary time. Fungal infections caused by the pathogen Candida albicans pose a serious threat to human health. Treating these infections relies heavily on the azole antifungals, however, resistance to these drugs develops readily demanding novel therapeutic strategies. We performed large-scale systematic screens in both C. albicans and the model yeast Saccharomyces cerevisiae to identify genes that enable azole resistance. Our genome-wide screen in S. cerevisiae identified nine determinants of azole resistance, only two of which were important for resistance in C. albicans. Our screen of C. albicans mutants identified 13 genes for which deletion enhances susceptibility to azoles, including RGD1 and PEP8. We found that loss of Pep8 overwhelms the functional capacity of a key stress response regulator, calcineurin. In contrast, amplification of chromosome 7 and the right portion of chromosome 3 can restore resistance in strains lacking Rgd1, suggesting that Rgd1 may enable azole resistance by inducing genes in these amplified regions. Specifically, overexpression of a gene involved in transport on chromosome 3, NPR2, was sufficient to restore azole resistance in the absence of Rgd1. Thus, we establish novel circuitry important for antifungal drug resistance, and uncover adaptive mechanisms involving genomic plasticity that occur in response to drug induced stress.
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Affiliation(s)
| | - Nicole M. Revie
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robert T. Todd
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Kaitlin Anstett
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cathy Collins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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19
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Ji H, Lu X, Zong H, Zhuge B. A synthetic hybrid promoter for D-xylonate production at low pH in the tolerant yeast Candida glycerinogenes. Bioengineered 2017; 8:700-706. [PMID: 28471311 DOI: 10.1080/21655979.2017.1312229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The tolerant yeast Candida glycerinogenes, with high D-xylonate and low-pH tolerances, was used as the host for D-xylonate production at low pH in this study. A low-pH inducible promoter, pGUKd, was engineered using the core promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (pGAP) combined with the upstream activating sequence of the promoter of the guanylate kinase gene (pGUK1) that had substituted pH-responsive TF binding sites. The recombinant cells that expressed GFP from the hybrid promoter pGUKd displayed dramatically increased fluorescence intensity at pH 2.5, thus verifying that pGUKd is a low-pH inducible promoter. The promoter pGUKd was then used to express the D-xylose dehydrogenase gene xylB, resulting in increased expression levels of xylB at low pH. The recombinant protein exhibited higher specific activities under lower pH conditions and produced 38 g/l D-xylonate at pH 2.5. This rate is much higher than that produced by fermentation at pH 5.5. These results suggest that the novel hybrid promoter pGUKd functions to direct the production of D-xylonate at low pH, and we provide a candidate genetic tool for the stress tolerant yeast C. glycerinogenes.
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Affiliation(s)
- Hao Ji
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xinyao Lu
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Hong Zong
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Bin Zhuge
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
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20
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The high osmotic response and cell wall integrity pathways cooperate to regulate morphology, microsclerotia development, and virulence in Metarhizium rileyi. Sci Rep 2016; 6:38765. [PMID: 27941838 PMCID: PMC5150533 DOI: 10.1038/srep38765] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/02/2016] [Indexed: 01/28/2023] Open
Abstract
Microsclerotia (MS) formation was successfully induced in Metarhizium rileyi under changing liquid culture conditions. Mitogen-activated protein kinases (MAPKs) play important roles in fungal development and in coordinating many stress responses. To investigate how M. rileyi transduces growth stress and regulates MS differentiation, we characterized the roles of two MAPKs, Hog1- and Slt2-type orthologues, in M. rileyi. Compared with the wild-type strain, the deletion mutants of Mrhog1 (ΔMrhog1) and Mrslt2 (ΔMrslt2) delayed germination and vegetative growth, displayed sensitivities to various stress, and produced morphologically abnormal clones. The ΔMrhog1 and ΔMrslt2 mutants significantly reduced conidial (42–99%) and MS (96–99%) yields. A transcriptional analysis showed that the two MAPKs regulate MS development in a cooperative manner. Insect bioassays revealed that ΔMrhog1 and ΔMrslt2 had decreased virulence levels in topical (36–56%) and injection (78–93%) bioassays. Our results confirmed the roles of MrHog1 and MrSlt2 in sensing growth-related stress and in regulating MS differentiation.
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21
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Rajkumar AS, Liu G, Bergenholm D, Arsovska D, Kristensen M, Nielsen J, Jensen MK, Keasling JD. Engineering of synthetic, stress-responsive yeast promoters. Nucleic Acids Res 2016; 44:e136. [PMID: 27325743 PMCID: PMC5041464 DOI: 10.1093/nar/gkw553] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/01/2023] Open
Abstract
Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducible by specific endogenous or environmental conditions is still rarely undertaken. In this study, we engineered and characterized a set of strong, synthetic promoters for budding yeast Saccharomyces cerevisiae that are inducible under acidic conditions (pH ≤ 3). Using available expression and transcription factor binding data, literature on transcriptional regulation, and known rules of promoter architecture we improved the low-pH performance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activation sequence. The engineering strategy outlined for the YGP1 promoter was subsequently applied to create a response to low pH in the unrelated CCW14 promoter. We applied our best promoter variants to low-pH fermentations, enabling ten-fold increased production of lactic acid compared to titres obtained with the commonly used, native TEF1 promoter. Our findings outline and validate a general strategy to iteratively design and engineer synthetic yeast promoters inducible to environmental conditions or stresses of interest.
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Affiliation(s)
- Arun S Rajkumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Guodong Liu
- Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - David Bergenholm
- Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Dushica Arsovska
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark Department of Biology and Biological Engineering, Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark Joint BioEnergy Institute, Emeryville, CA 94608, USA Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA 94720, USA
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Saxena A, Sitaraman R. Osmoregulation in Saccharomyces cerevisiae via mechanisms other than the high-osmolarity glycerol pathway. Microbiology (Reading) 2016; 162:1511-1526. [DOI: 10.1099/mic.0.000360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Abhishek Saxena
- Department of Biotechnology, TERI University, New Delhi, India
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NCW2, a Gene Involved in the Tolerance to Polyhexamethylene Biguanide (PHMB), May Help in the Organisation of β-1,3-Glucan Structure of Saccharomyces cerevisiae Cell Wall. Curr Microbiol 2016; 73:341-345. [DOI: 10.1007/s00284-016-1067-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
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de Lucena RM, Elsztein C, Barros de Souza R, de Barros Pita W, Paiva SDSL, de Morais MA. Genetic Interaction between HOG1 and SLT2 Genes in Signalling the Cellular Stress Caused by Sulphuric Acid in Saccharomyces cerevisiae. J Mol Microbiol Biotechnol 2016; 25:423-7. [PMID: 26845706 DOI: 10.1159/000443309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022] Open
Abstract
In fuel ethanol production, recycling of yeast biomass includes treatment of cells with diluted sulphuric acid in order to control bacterial population. However, this strategy might lead to a loss of cell viability, with potential negative consequences to the fermentation yield. In a recent paper we showed that the proteins Slt2 and Hog1 are essential for yeast tolerance to sulphuric acid. As a complement of the aforementioned work, we used DNA microarray technology to search for differentially expressed genes in hog1Δ and slt2Δ deletion mutants after treatment with sulphuric acid. Our results show how Slt2p and Hog1p could coordinate the interplay among protein kinase A (PKA), protein kinase C and high-osmolarity glycerol pathways. Moreover, the SSK22 and KDX1 genes may be part of this network, although their proteins were shown to be non-essential for cell growth/survival at low pH. These proteins might work by enhancing the signal which downregulates the PKA pathway leading to cell cycle arrest, in order to regenerate the integrity of yeast cell wall and cell homeostasis under acid shock.
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Affiliation(s)
- Rodrigo Mendonça de Lucena
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, Brazil
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25
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Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes. Toxins (Basel) 2015; 7:4099-110. [PMID: 26473925 PMCID: PMC4626723 DOI: 10.3390/toxins7104099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/17/2022] Open
Abstract
Most pathogenic, non-O1/non-O139 serogroup Vibrio cholerae strains cause diarrheal disease in the absence of cholera toxin. Instead, many use Type 3 Secretion System (T3SS) mediated mechanisms to disrupt host cell homeostasis. We identified a T3SS effector protein, VopX, which is translocated into mammalian cells during in vitro co-culture. In a S. cerevisiae model system, we found that expression of VopX resulted in a severe growth defect that was partially suppressed by a deletion of RLM1, encoding the terminal transcriptional regulator of the Cell Wall Integrity MAP kinase (CWI) regulated pathway. Growth of yeast cells in the presence of sorbitol also suppressed the defect, supporting a role for VopX in destabilizing the cell wall. Expression of VopX activated expression of β-galactosidase from an RLM1-reponsive element reporter fusion, but failed to do so in cells lacking MAP kinases upstream of Rlm1. The results suggest that VopX inhibits cell growth by stimulating the CWI pathway through Rlm1. Rlm1 is an ortholog of mammalian MEF2 transcription factors that are proposed to regulate cell differentiation, proliferation, and apoptosis. The collective findings suggest that VopX contributes to disease by activating MAP kinase cascades that elicit changes in cellular transcriptional programs.
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26
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Transcriptomic response of Saccharomyces cerevisiae for its adaptation to sulphuric acid-induced stress. Antonie van Leeuwenhoek 2015; 108:1147-60. [DOI: 10.1007/s10482-015-0568-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/20/2015] [Indexed: 01/13/2023]
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27
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de Souza RB, de Menezes JAS, de Souza RDFR, Dutra ED, de Morais MA. Mineral composition of the sugarcane juice and its influence on the ethanol fermentation. Appl Biochem Biotechnol 2014; 175:209-22. [PMID: 25248994 DOI: 10.1007/s12010-014-1258-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
In the present work, we evaluated the mineral composition of three sugarcane varieties from different areas in northeast Brazil and their influence on the fermentation performance of Saccharomyces cerevisiae. The mineral composition was homogeneous in the different areas investigated. However, large variation coefficients were observed for concentrations of copper, magnesium, zinc and phosphorus. Regarding the fermentation performances, the sugarcane juices with the highest magnesium concentration showed the highest ethanol yield. Synthetic media supplemented with magnesium also showed the highest yield (0.45 g g(-1)) while the excess of copper led to the lowest yield (0.35 g g(-1)). According to our results, the magnesium is the principal responsible for the increase on the ethanol yield, and it also seems to be able to disguise the inhibitory effects of the toxic minerals present in the sugarcane juice.
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Affiliation(s)
- Rafael Barros de Souza
- Interdepartmental Research Group in Metabolic Engineering, Department of Genetics, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, 50670-901, Recife, PE, Brazil
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28
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Rego A, Duarte AM, Azevedo F, Sousa MJ, Côrte-Real M, Chaves SR. Cell wall dynamics modulate acetic acid-induced apoptotic cell death of Saccharomyces cerevisiae. MICROBIAL CELL 2014; 1:303-314. [PMID: 28357256 PMCID: PMC5349133 DOI: 10.15698/mic2014.09.164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Acetic acid triggers apoptotic cell death in Saccharomyces
cerevisiae, similar to mammalian apoptosis. To uncover novel
regulators of this process, we analyzed whether impairing MAPK signaling
affected acetic acid-induced apoptosis and found the mating-pheromone response
and, especially, the cell wall integrity pathways were the major mediators,
especially the latter, which we characterized further. Screening downstream
effectors of this pathway, namely targets of the transcription factor Rlm1p,
highlighted decreased cell wall remodeling as particularly important for acetic
acid resistance. Modulation of cell surface dynamics therefore emerges as a
powerful strategy to increase acetic acid resistance, with potential application
in industrial fermentations using yeast, and in biomedicine to exploit the
higher sensitivity of colorectal carcinoma cells to apoptosis induced by acetate
produced by intestinal propionibacteria.
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Affiliation(s)
- António Rego
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Ana M Duarte
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Flávio Azevedo
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Maria J Sousa
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Manuela Côrte-Real
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
| | - Susana R Chaves
- Centro de Biologia Molecular e Ambiental, Departamento de Biologia, Universidade do Minho, Braga, Portugal
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29
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Abstract
Yeast cells need to respond to a variety of stresses found in such different conditions as gastrointestinal tract after probiotic ingestion or fermentation vat during ethanol production. In the present study, H+ neutralisation capacity, membrane fatty acid composition, H+-ATPase activity, and cytosolic Ca2+ concentration were evaluated in yeast cells used for probiotic (Saccharomyces boulardii) and laboratory (Saccharomyces cerevisiae W303) purposes, as well as in some W303 mutant strains for ENA1 gene and S. cerevisiae BY4741. Results show that the H+ internal concentration of yeast is regulated by several systems, including the plasma membrane H+-ATPase, and that Ena1p has an important but undefined role in the cellular response to acid. Membrane fatty acid composition of S. cerevisiae W303 strain was affected by exposure to acidic pH, but the presence of 86 mM NaCl prevented this effect, whereas membrane fatty acid composition of S. boulardii was unaffected by acidic pH. We also demonstrated that the acid stress response is dependent on calcium metabolism and blocked by FK 506.
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30
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Pereira LF, Lucatti E, Basso LC, de Morais MA. The fermentation of sugarcane molasses by Dekkera bruxellensis and the mobilization of reserve carbohydrates. Antonie van Leeuwenhoek 2013; 105:481-9. [PMID: 24370978 DOI: 10.1007/s10482-013-0100-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/12/2013] [Indexed: 01/13/2023]
Abstract
The yeast Dekkera bruxellensis is considered to be very well adapted to industrial environments, in Brazil, USA, Canada and European Countries, when different substrates are used in alcoholic fermentations. Our previous study described its fermentative profile with a sugarcane juice substrate. In this study, we have extended its physiological evaluation to fermentation situations by using sugarcane molasses as a substrate to replicate industrial working conditions. The results have confirmed the previous reports of the low capacity of D. bruxellensis cells to assimilate sucrose, which seems to be the main factor that can cause a bottleneck in its use as fermentative yeast. Furthermore, the cells of D. bruxellensis showed a tendency to deviate most of sugar available for biomass and organic acids (lactic and acetic) compared with Saccharomyces cerevisiae, when calculated on the basis of their respective yields. As well as this, the acetate production from molasses medium by both yeasts was in marked contrast with the previous data on sugarcane juice. Glycerol and ethanol production by D. bruxellensis cells achieved levels of 33 and 53 % of the S. cerevisiae, respectively. However, the ethanol yield was similar for both yeasts. It is worth noting that this yeast did not accumulate trehalose when the intracellular glycogen content was 30 % lower than in S. cerevisiae. The lack of trehalose did not affect yeast viability under fermentation conditions. Thus, the adaptive success of D. bruxellensis under industrial fermentation conditions seems to be unrelated to the production of these reserve carbohydrates.
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Affiliation(s)
- Luciana Filgueira Pereira
- Interdepartmental Research Group on Metabolic Engineering, Federal University of Pernambuco, Recife, Brazil
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31
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González-Ramos D, van den Broek M, van Maris AJA, Pronk JT, Daran JMG. Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:48. [PMID: 23552365 PMCID: PMC3621596 DOI: 10.1186/1754-6834-6-48] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/22/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND n-Butanol and isobutanol produced from biomass-derived sugars are promising renewable transport fuels and solvents. Saccharomyces cerevisiae has been engineered for butanol production, but its high butanol sensitivity poses an upper limit to product titers that can be reached by further pathway engineering. A better understanding of the molecular basis of butanol stress and tolerance of S. cerevisiae is important for achieving improved tolerance. RESULTS By combining a screening of the haploid S. cerevisiae knock-out library, gene overexpression, and genome analysis of evolutionary engineered n-butanol-tolerant strains, we established that protein degradation plays an essential role in tolerance. Strains deleted in genes involved in the ubiquitin-proteasome system and in vacuolar degradation of damaged proteins showed hypersensitivity to n-butanol. Overexpression of YLR224W, encoding the subunit responsible for the recognition of damaged proteins of an ubiquitin ligase complex, resulted in a strain with a higher n-butanol tolerance. Two independently evolved n-butanol-tolerant strains carried different mutations in both RPN4 and RTG1, which encode transcription factors involved in the expression of proteasome and peroxisomal genes, respectively. Introduction of these mutated alleles in the reference strain increased butanol tolerance, confirming their relevance in the higher tolerance phenotype. The evolved strains, in addition to n-butanol, were also more tolerant to 2-butanol, isobutanol and 1-propanol, indicating a common molecular basis for sensitivity and tolerance to C3 and C4 alcohols. CONCLUSIONS This study shows that maintenance of protein integrity plays an essential role in butanol tolerance and demonstrates new promising targets to engineer S. cerevisiae for improved tolerance.
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Affiliation(s)
- Daniel González-Ramos
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, Delft 2600 GA, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, Delft 2600 GA, The Netherlands
| | - Antonius JA van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, Delft 2600 GA, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, Delft 2600 GA, The Netherlands
- Platform for Green Synthetic Biology, P.O. Box 5057, Delft 2600 GA, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft 2628 BC, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, Delft 2600 GA, The Netherlands
- Platform for Green Synthetic Biology, P.O. Box 5057, Delft 2600 GA, The Netherlands
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32
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Ullah A, Lopes MI, Brul S, Smits GJ. Intracellular pH homeostasis in Candida glabrata in infection-associated conditions. Microbiology (Reading) 2013; 159:803-813. [DOI: 10.1099/mic.0.063610-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Azmat Ullah
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, The Netherlands
| | - Maria Inês Lopes
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, The Netherlands
| | - Gertien J. Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, The Netherlands
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