1
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Sauty SM, Fisher A, Dolson A, Yankulov K. Mutations in the DNA processivity factor POL30 predisposes the FLO11 locus to epigenetic instability in S. cerevisiae. J Cell Sci 2024; 137:jcs262006. [PMID: 39552290 DOI: 10.1242/jcs.262006] [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: 02/02/2024] [Accepted: 11/07/2024] [Indexed: 11/19/2024] Open
Abstract
The FLO genes in Saccharomyces cerevisiae are repressed by heterochromatin formation, involving histone deacetylases, transcription factors and non-coding RNAs. Here, we report that mutations in the processivity factor POL30 (PCNA) that show transient derepression at the subtelomeres and the mating-type loci do not derepress FLO loci. However, deletions of the replisome stability factors RRM3 and TOF1 along with pol30 mutations induced flocculation phenotypes. The phenotypes correlated with increased expression of reporter proteins driven by the FLO11 promoter, the frequency of silent to active conversions of FLO11, and reduced expression of the regulatory long non-coding RNAs ICR1 and PWR1. Alterations in the local replication landscape of FLO11 indicate a link between defects in the fork protection complex and the stability of gene silencing. Analyses of these mutants at the subtelomeres and the HMLα locus showed a similar derepression phenotype and suggest transient instability of both active and silent states of FLO11. We conclude that RRM3 and TOF1 interact differentially with the pol30 mutations to promote transient derepression or complete epigenetic conversions of FLO11. We suggest that the interaction between POL30, RRM3 and TOF1 is essential to maintain epigenetic stability at the studied loci.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Ashley Fisher
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Andrew Dolson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G2W1, Canada
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2
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Xu L, Bai X, Joong Oh E. Strategic approaches for designing yeast strains as protein secretion and display platforms. Crit Rev Biotechnol 2024:1-18. [PMID: 39138023 DOI: 10.1080/07388551.2024.2385996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 08/15/2024]
Abstract
Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.
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Affiliation(s)
- Luping Xu
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
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3
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Le Montagner P, Bakhtiar Y, Miot-Sertier C, Guilbaud M, Albertin W, Moine V, Dols-Lafargue M, Masneuf-Pomarède I. Effect of abiotic and biotic factors on Brettanomyces bruxellensis bioadhesion properties. Food Microbiol 2024; 120:104480. [PMID: 38431326 DOI: 10.1016/j.fm.2024.104480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 03/05/2024]
Abstract
Biofilms are central to microbial life because of the advantage that this mode of life provides, whereas the planktonic form is considered to be transient in the environment. During the winemaking process, grape must and wines host a wide diversity of microorganisms able to grow in biofilm. This is the case of Brettanomyces bruxellensis considered the most harmful spoilage yeast, due to its negative sensory effect on wine and its ability to colonise stressful environments. In this study, the effect of different biotic and abiotic factors on the bioadhesion and biofilm formation capacities of B. bruxellensis was analyzed. Ethanol concentration and pH had negligible effect on yeast surface properties, pseudohyphal cell formation or bioadhesion, while the strain and genetic group factors strongly modulated the phenotypes studied. From a biotic point of view, the presence of two different strains of B. bruxellensis did not lead to a synergistic effect. A competition between the strains was rather observed during biofilm formation which seemed to be driven by the strain with the highest bioadhesion capacity. Finally, the presence of wine bacteria reduced the bioadhesion of B. bruxellensis. Due to biofilm formation, O. oeni cells were observed attached to B. bruxellensis as well as extracellular matrix on the surface of the cells.
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Affiliation(s)
- Paul Le Montagner
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Biolaffort, Floirac, France
| | - Yacine Bakhtiar
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Cecile Miot-Sertier
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Morgan Guilbaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120, Palaiseau, France
| | - Warren Albertin
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSMAC, Bordeaux INP, 33600, Pessac, France
| | | | - Marguerite Dols-Lafargue
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSMAC, Bordeaux INP, 33600, Pessac, France
| | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Science Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Bordeaux Sciences Agro, 33175, Gradignan, France.
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4
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Pangestu R, Kahar P, Ogino C, Kondo A. Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation. Yeast 2024; 41:192-206. [PMID: 38081785 DOI: 10.1002/yea.3917] [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: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/23/2023] [Indexed: 04/09/2024] Open
Abstract
While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.
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Affiliation(s)
- Radityo Pangestu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
- National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Hyogo, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation (STIN), Kobe University, Kobe, Hyogo, Japan
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5
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Malavia-Jones D, Farrer RA, Stappers MH, Edmondson MB, Borman AM, Johnson EM, Lipke PN, Gow NA. Strain and temperature dependent aggregation of Candida auris is attenuated by inhibition of surface amyloid proteins. Cell Surf 2023; 10:100110. [PMID: 37559873 PMCID: PMC10407437 DOI: 10.1016/j.tcsw.2023.100110] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Candida auris is a multi-drug resistant human fungal pathogen that has become a global threat to human health due to its drug resistant phenotype, persistence in the hospital environment and propensity for patient to patient spread. Isolates display variable aggregation that may affect the relative virulence of strains. Therefore, dissection of this phenotype has gained substantial interest in recent years. We studied eight clinical isolates from four different clades (I-IV); four of which had a strongly aggregating phenotype and four of which did not. Genome analysis identified polymorphisms associated with loss of cell surface proteins were enriched in weakly-aggregating strains. Additionally, we identified down-regulation of chitin synthase genes involved in the synthesis of the chitinous septum. Characterisation of the cells revealed no ultrastructural defects in cytokinesis or cell separation in aggregating isolates. Strongly and weakly aggregating strains did not differ in net surface charge or in cell surface hydrophobicity. The capacity for aggregation and for adhesion to polystyrene microspheres were also not correlated. However, aggregation and extracellular matrix formation were all increased at higher growth temperatures, and treatment with the amyloid protein inhibitor Thioflavin-T markedly attenuated aggregation. Genome analysis further indicated strain specific differences in the genome content of GPI-anchored proteins including those encoding genes with the potential to form amyloid proteins. Collectively our data suggests that aggregation is a complex strain and temperature dependent phenomenon that may be linked in part to the ability to form extracellular matrix and cell surface amyloids.
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Affiliation(s)
- Dhara Malavia-Jones
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rhys A. Farrer
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mark H.T. Stappers
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Matt B. Edmondson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew M. Borman
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Elizabeth M. Johnson
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- UKHSA Mycology Reference Laboratory, National Infection Services, UKHSA South West Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Peter N. Lipke
- Biology Department, Brooklyn College of City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| | - Neil A.R. Gow
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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6
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Zhao Z, Wei Y, Zou X, Jiang S, Chen Y, Ye J, Xu F, Wang H, Shao X. Tryptophol Improves the Biocontrol Efficacy of Scheffersomyces spartinae against the Gray Mold of Strawberries by Quorum Sensing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19739-19748. [PMID: 38041637 DOI: 10.1021/acs.jafc.3c06676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Previously, we reported that marine yeast Scheffersomyces spartinae exhibited biocontrol efficacy against the gray mold of strawberries caused by Botrytis cinerea. Herein, tryptophol, a quorum-sensing molecule, was identified in the metabolites of S. spartinae. Subsequently, we found that 25 μM tryptophol promoted population density, biofilm formation, and cell aggregation of S. spartinae. Furthermore, 25 μM tryptophol improved the biocontrol efficacy of S. spartinae against B. cinerea in vitro and in the strawberry fruit. Under a scanning electronic microscope, tryptophol facilitated colonization and biofilm formation on strawberry wounds, showing that tryptophol increased the biocontrol efficacy of S. spartinae via quorum sensing. Transcriptome analysis revealed that tryptophol upregulated the gene expression of SDS3, DAL81, DSE1, SNF5, SUN41, FLO8, and HOP1, which was associated with cell adhesion or biofilm formation. Thus, to the best of our knowledge, this study was the first to report that tryptophol improved the biocontrol efficacy of S. spartinae via quorum sensing.
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Affiliation(s)
- Zichang Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yingying Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xiurong Zou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- School of Food Science, Shaoguan University, Shaoguan 512005, China
| | - Shu Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Jianfen Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Feng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Hongfei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xingfeng Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
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7
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Mohammadi K, Saris PEJ. Antibiofilm Effect of Curcumin on Saccharomyces boulardii during Beer Fermentation and Bottle Aging. Biomolecules 2023; 13:1367. [PMID: 37759767 PMCID: PMC10526157 DOI: 10.3390/biom13091367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
In a prior study, we elucidated the biofilm formation of Saccharomyces boulardii on glass surfaces during beer bottle aging. Here, we supplemented brewing wort with curcumin at 25 μg/mL concentration to mitigate S. boulardii biofilm and enhance beer's functional and sensory attributes. An assessment encompassing biofilm growth and development, fermentation performance, FLO gene expression, yeast ultrastructure, bioactive content, and consumer acceptance of the beer was conducted throughout fermentation and aging. Crystal violet (CV) and XTT reduction assays unveiled a significant (p < 0.05) reduction in biofilm formation and development. Fluorescent staining (FITC-conA) and imaging with confocal laser scanning microscopy provided visual evidence regarding reduced exopolysaccharide content and biofilm thickness. Transcriptional analyses showed that key adhesins (FLO1, FLO5, FLO9, and FLO10) were downregulated, whereas FLO11 expression remained relatively stable. Although there were initial variations in terms of yeast population and fermentation performance, by day 6, the number of S. boulardii in the test group had almost reached the level of the control group (8.3 log CFU/mL) and remained stable thereafter. The supplementation of brewing wort with curcumin led to a significant (p < 0.05) increase in the beer's total phenolic and flavonoid content. In conclusion, curcumin shows promising potential for use as an additive in beer, offering potential antibiofilm and health benefits without compromising the beer's overall characteristics.
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Affiliation(s)
- Khosrow Mohammadi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland;
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8
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Le Montagner P, Guilbaud M, Miot-Sertier C, Brocard L, Albertin W, Ballestra P, Dols-Lafargue M, Renouf V, Moine V, Bellon-Fontaine MN, Masneuf-Pomarède I. High intraspecific variation of the cell surface physico-chemical and bioadhesion properties in Brettanomyces bruxellensis. Food Microbiol 2023; 112:104217. [PMID: 36906300 DOI: 10.1016/j.fm.2023.104217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
Brettanomyces bruxellensis is the most damaging spoilage yeast in the wine industry because of its negative impact on the wine organoleptic qualities. The strain persistence in cellars over several years associated with recurrent wine contamination suggest specific properties to persist and survive in the environment through bioadhesion phenomena. In this work, the physico-chemical surface properties, morphology and ability to adhere to stainless steel were studied both on synthetic medium and on wine. More than 50 strains representative of the genetic diversity of the species were considered. Microscopy techniques made it possible to highlight a high morphological diversity of the cells with the presence of pseudohyphae forms for some genetic groups. Analysis of the physico-chemical properties of the cell surface reveals contrasting behaviors: most of the strains display a negative surface charge and hydrophilic behavior while the Beer 1 genetic group has a hydrophobic behavior. All strains showed bioadhesion abilities on stainless steel after only 3 h with differences in the concentration of bioadhered cells ranging from 2.2 × 102 cell/cm2 to 7.6 × 106 cell/cm2. Finally, our results show high variability of the bioadhesion properties, the first step in the biofilm formation, according to the genetic group with the most marked bioadhesion capacity for the beer group.
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Affiliation(s)
- Paul Le Montagner
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Laboratoire EXCELL, Floirac, France; Biolaffort, Floirac, France.
| | - Morgan Guilbaud
- Univ. Paris-Saclay, SayFood, AgroParisTech, INRAE UMR 782, 91300, Massy, France
| | - Cécile Miot-Sertier
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Lysiane Brocard
- Univ. Bordeaux, Plant Imaging Platform, Bordeaux Imaging Center, UMS 3420, CNRS, 33000, Bordeaux, France
| | - Warren Albertin
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Patricia Ballestra
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSCBP, Bordeaux INP, 33600, Pessac, France
| | | | | | | | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Bordeaux Sciences Agro, 33175, Gradignan, France
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9
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Johnston N, Cline G, Strobel SA. Cells Adapt to Resist Fluoride through Metabolic Deactivation and Intracellular Acidification. Chem Res Toxicol 2022; 35:2085-2096. [PMID: 36282204 PMCID: PMC9683101 DOI: 10.1021/acs.chemrestox.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 01/09/2023]
Abstract
Fluoride is highly abundant in the environment. Many organisms have adapted specific defense mechanisms against high concentrations of fluoride, including the expression of proteins capable of removing fluoride from cells. However, these fluoride transporters have not been identified in all organisms, and even organisms that express fluoride transporters vary in tolerance capabilities across species, individuals, and even tissue types. This suggests that alternative factors influence fluoride tolerance. We screened for adaptation against fluoride toxicity through an unbiased mutagenesis assay conducted on Saccharomyces cerevisiae lacking the fluoride exporter FEX, the primary mechanism of fluoride resistance. Over 80 independent fluoride-hardened strains were generated, with anywhere from 100- to 1200-fold increased fluoride tolerance compared to the original strain. The whole genome of each mutant strain was sequenced and compared to the wild type. The fluoride-hardened strains utilized a combination of phenotypes that individually conferred fluoride tolerance. These included intracellular acidification, cellular dormancy, nutrient storage, and a communal behavior reminiscent of flocculation. Of particular importance to fluoride resistance was intracellular acidification, which served to reverse the accumulation of fluoride and lead to its excretion from the cell as HF without the activity of a fluoride-specific protein transporter. This transport mechanism was also observed in wild-type yeast through a manual mutation to lower their cytoplasmic pH. The results demonstrate that the yeast developed a protein-free adaptation for removing an intracellular toxicant.
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Affiliation(s)
- Nichole
R. Johnston
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
| | - Gary Cline
- Department
of Internal Medicine, Yale School of Medicine, New Haven 06510, Connecticut, United States
| | - Scott A. Strobel
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
- Department
of Chemistry, Yale University, New Haven 06477, Connecticut, United States
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10
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Krause DJ, Hittinger CT. Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae. Mol Biol Evol 2022; 39:6711080. [PMID: 36134526 PMCID: PMC9551191 DOI: 10.1093/molbev/msac202] [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: 12/15/2022] Open
Abstract
The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.
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Affiliation(s)
- David J Krause
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI
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11
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Day TC, Márquez-Zacarías P, Bravo P, Pokhrel AR, MacGillivray KA, Ratcliff WC, Yunker PJ. Varied solutions to multicellularity: The biophysical and evolutionary consequences of diverse intercellular bonds. BIOPHYSICS REVIEWS 2022; 3:021305. [PMID: 35673523 PMCID: PMC9164275 DOI: 10.1063/5.0080845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
The diversity of multicellular organisms is, in large part, due to the fact that multicellularity has independently evolved many times. Nonetheless, multicellular organisms all share a universal biophysical trait: cells are attached to each other. All mechanisms of cellular attachment belong to one of two broad classes; intercellular bonds are either reformable or they are not. Both classes of multicellular assembly are common in nature, having independently evolved dozens of times. In this review, we detail these varied mechanisms as they exist in multicellular organisms. We also discuss the evolutionary implications of different intercellular attachment mechanisms on nascent multicellular organisms. The type of intercellular bond present during early steps in the transition to multicellularity constrains future evolutionary and biophysical dynamics for the lineage, affecting the origin of multicellular life cycles, cell-cell communication, cellular differentiation, and multicellular morphogenesis. The types of intercellular bonds used by multicellular organisms may thus result in some of the most impactful historical constraints on the evolution of multicellularity.
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Affiliation(s)
- Thomas C. Day
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | | | - Aawaz R. Pokhrel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Peter J. Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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12
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Shoket H, Parvez S, Sharma M, Pandita M, Sharma V, Kumar P, Bairwa NK. Deletion of autophagy related, ATG1 and F-box motif encoding YDR131C, together, lead to synthetic growth defects and flocculation behavior in Saccharomyces cerevisiae. J Biochem Mol Toxicol 2022; 36:e23064. [PMID: 35385166 DOI: 10.1002/jbt.23064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/09/2022]
Abstract
Ubiquitin proteasome system (UPS) and autophagy both pathways are involved in clearing the nonessential cellular components and also crosstalk during cellular response to normal and stress conditions. The F-box motif proteins constitute the SCF-E3 ligase complex of the UPS pathway in Saccharomyces cerevisiae and are involved in the substrate recruitment for ubiquitination. The ATG1 encoded Atg1p, a conserved serine-threonine kinase is crucial for the autophagy process. Here in this study, we report that loss of F-box motif encoding YDR131C and ATG1 together results in growth defects, floc formation, sensitivity to hydroxyurea, methyl methanesulfonate, and hydrogen peroxide. Both the genes also interact with the flocculation-related genes (FLO) and associate with gene ontology terms "ubiquitin-protein transferase activity" and "cellular catabolic process." Based on in silico analysis and experimental evidence we conclude that YDR131C and ATG1 function in parallel pathways to regulate the growth, flocculation, and stress response.
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Affiliation(s)
- Heena Shoket
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Sadia Parvez
- 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
| | - Monika Pandita
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Vishali Sharma
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Prabhat Kumar
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
| | - Narendra K Bairwa
- Genome Stability Regulation Lab, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu & Kashmir, India
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13
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Kahar P, Itomi A, Tsuboi H, Ishizaki M, Yasuda M, Kihira C, Otsuka H, Azmi NB, Matsumoto H, Ogino C, Kondo A. The flocculant Saccharomyces cerevisiae strain gains robustness via alteration of the cell wall hydrophobicity. Metab Eng 2022; 72:82-96. [DOI: 10.1016/j.ymben.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
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14
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FLO8 deletion leads to decreased adhesion and virulence with downregulated expression of EPA1, EPA6, and EPA7 in Candida glabrata. Braz J Microbiol 2022; 53:727-738. [PMID: 35122657 PMCID: PMC9151949 DOI: 10.1007/s42770-022-00703-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/01/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Candida glabrata does not develop into a pathogenic hiphal form; however, it has become the second most common pathogen of fungal infections in humans, partly because of its adhesion ability and virulence. OBJECTIVES The present study aimed to determine whether Flo8, a transcription factor that plays an important role in the virulence and drug resistance in Candida albicans, has a similar role in C. glabrata. METHODS We constructed FLO8 null strains of a C. glabrata standard strain and eight clinical strains from different sources, and a FLO8 complemented strain. Real-time quantitative PCR, biofilm formation assays, hydrophobicity tests, adhesion tests, Caenorhabditis elegans survival assay, and drug-susceptibility were then performed. RESULTS Compared with the wild-type strains, the biofilm formation, hydrophobicity, adhesion, and virulence of the FLO8-deficient strains decreased, accompanied by decreased expression of EPA1, EPA6, and EPA7. On the other hand, it showed no changes in antifungal drug resistance, although the expression levels of CDR1, CDR2, and SNQ2 increased after FLO8 deletion. CONCLUSIONS These results indicated that Flo8 is involved in the adhesion and virulence of C. glabrata, with FLO8 deletion leading to decreased expression of EPA1, EPA6, and EPA7 and decreased biofilm formation, hydrophobicity, adhesion, and virulence.
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15
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:foab059. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey
- Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
- Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
- Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
- Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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16
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FLO11, a Developmental Gene Conferring Impressive Adaptive Plasticity to the Yeast Saccharomyces cerevisiae. Pathogens 2021; 10:pathogens10111509. [PMID: 34832664 PMCID: PMC8617999 DOI: 10.3390/pathogens10111509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has a remarkable ability to adapt its lifestyle to fluctuating or hostile environmental conditions. This adaptation most often involves morphological changes such as pseudofilaments, biofilm formation, or cell aggregation in the form of flocs. A prerequisite for these phenotypic changes is the ability to self-adhere and to adhere to abiotic surfaces. This ability is conferred by specialized surface proteins called flocculins, which are encoded by the FLO genes family in this yeast species. This mini-review focuses on the flocculin encoded by FLO11, which differs significantly from other flocculins in domain sequence and mode of genetic and epigenetic regulation, giving it an impressive plasticity that enables yeast cells to swiftly adapt to hostile environments or into new ecological niches. Furthermore, the common features of Flo11p with those of adhesins from pathogenic yeasts make FLO11 a good model to study the molecular mechanism underlying cell adhesion and biofilm formation, which are part of the initial step leading to fungal infections.
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17
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Willaert RG, Kayacan Y, Devreese B. The Flo Adhesin Family. Pathogens 2021; 10:pathogens10111397. [PMID: 34832553 PMCID: PMC8621652 DOI: 10.3390/pathogens10111397] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
The first step in the infection of fungal pathogens in humans is the adhesion of the pathogen to host tissue cells or abiotic surfaces such as catheters and implants. One of the main players involved in this are the expressed cell wall adhesins. Here, we review the Flo adhesin family and their involvement in the adhesion of these yeasts during human infections. Firstly, we redefined the Flo adhesin family based on the domain architectures that are present in the Flo adhesins and their functions, and set up a new classification of Flo adhesins. Next, the structure, function, and adhesion mechanisms of the Flo adhesins whose structure has been solved are discussed in detail. Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. These yeasts are discussed in relation to their adhesion characteristics and involvement in infections.
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Affiliation(s)
- Ronnie G. Willaert
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Correspondence: ; Tel.: +32-2629-1846
| | - Yeseren Kayacan
- Research Group Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bart Devreese
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Laboratory for Microbiology, Gent University (UGent), 9000 Gent, Belgium
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18
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Bouyx C, Schiavone M, Teste MA, Dague E, Sieczkowski N, Julien A, François JM. The dual role of amyloid-β-sheet sequences in the cell surface properties of FLO11-encoded flocculins in Saccharomyces cerevisiae. eLife 2021; 10:e68592. [PMID: 34467855 PMCID: PMC8457840 DOI: 10.7554/elife.68592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/29/2021] [Indexed: 11/21/2022] Open
Abstract
Fungal adhesins (Als) or flocculins are family of cell surface proteins that mediate adhesion to diverse biotic and abiotic surfaces. A striking characteristic of Als proteins originally identified in the pathogenic Candida albicans is to form functional amyloids that mediate cis-interaction leading to the formation of adhesin nanodomains and trans-interaction between amyloid sequences of opposing cells. In this report, we show that flocculins encoded by FLO11 in Saccharomyces cerevisiae behave like adhesins in C. albicans. To do so, we show that the formation of nanodomains under an external physical force requires a threshold number of amyloid-forming sequences in the Flo11 protein. Then, using a genome editing approach, we constructed strains expressing variants of the Flo11 protein under the endogenous FLO11 promoter, leading to the demonstration that the loss of amyloid-forming sequences strongly reduces cell-cell interaction but has no effect on either plastic adherence or invasive growth in agar, both phenotypes being dependent on the N- and C-terminal ends of Flo11p. Finally, we show that the location of Flo11 is not altered either by the absence of amyloid-forming sequences or by the removal of the N- or C-terminus of the protein.
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Affiliation(s)
- Clara Bouyx
- Toulouse Biotechnology Institute, INSAToulouseFrance
| | - Marion Schiavone
- Toulouse Biotechnology Institute, INSAToulouseFrance
- Lallemand, Lallemand SASBlagnacFrance
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19
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High Foam Phenotypic Diversity and Variability in Flocculant Gene Observed for Various Yeast Cell Surfaces Present as Industrial Contaminants. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7030127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many contaminant yeast strains that survive inside fuel ethanol industrial vats show detrimental cell surface phenotypes. These harmful effects may include filamentation, invasive growth, flocculation, biofilm formation, and excessive foam production. Previous studies have linked some of these phenotypes to the expression of FLO genes, and the presence of gene length polymorphisms causing the expansion of FLO gene size appears to result in stronger flocculation and biofilm formation phenotypes. We performed here a molecular analysis of FLO1 and FLO11 gene polymorphisms present in contaminant strains of Saccharomyces cerevisiae from Brazilian fuel ethanol distilleries showing vigorous foaming phenotypes during fermentation. The size variability of these genes was correlated with cellular hydrophobicity, flocculation, and highly foaming phenotypes in these yeast strains. Our results also showed that deleting the primary activator of FLO genes (the FLO8 gene) from the genome of a contaminant and highly foaming industrial strain avoids complex foam formation, flocculation, invasive growth, and biofilm production by the engineered (flo8∆::BleR/flo8Δ::kanMX) yeast strain. Thus, the characterization of highly foaming yeasts and the influence of FLO8 in this phenotype open new perspectives for yeast strain engineering and optimization in the sugarcane fuel-ethanol industry.
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20
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Shaban K, Sauty SM, Yankulov K. Variation, Variegation and Heritable Gene Repression in S. cerevisiae. Front Genet 2021; 12:630506. [PMID: 33747046 PMCID: PMC7970126 DOI: 10.3389/fgene.2021.630506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Phenotypic heterogeneity provides growth advantages for a population upon changes of the environment. In S. cerevisiae, such heterogeneity has been observed as "on/off" states in the expression of individual genes in individual cells. These variations can persist for a limited or extended number of mitotic divisions. Such traits are known to be mediated by heritable chromatin structures, by the mitotic transmission of transcription factors involved in gene regulatory circuits or by the cytoplasmic partition of prions or other unstructured proteins. The significance of such epigenetic diversity is obvious, however, we have limited insight into the mechanisms that generate it. In this review, we summarize the current knowledge of epigenetically maintained heterogeneity of gene expression and point out similarities and converging points between different mechanisms. We discuss how the sharing of limiting repression or activation factors can contribute to cell-to-cell variations in gene expression and to the coordination between short- and long- term epigenetic strategies. Finally, we discuss the implications of such variations and strategies in adaptation and aging.
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Affiliation(s)
- Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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21
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Abstract
Multicellularity has evolved many times. A new study explores why some forms of multicellularity may be better than others.
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22
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Sun P, Li X, Yang M, Zhao X, Zhang Z, Wei D. Deletion of a small, secreted and cysteine-rich protein Cpl1 leads to increased invasive growth of Cryptococcus neoformans into nutrient agar. Microbiol Res 2020; 241:126570. [PMID: 32805526 DOI: 10.1016/j.micres.2020.126570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/13/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
Invasive growth of yeast cells into nutrient agar is induced by different stresses and contributes to the survival of yeast cells under several adverse conditions. The mechanism of invasive growth of Saccharomyces cerevisiae has been extensively investigated. However, there is very little information about the mechanism of invasive growth of another human pathogen yeast Cryptococcus neoformans. Here, we report that deletion of a small and secreted cysteine-rich protein Cpl1 in C. neoformans JEC21 leads to increased adhesive and invasive growth into nutrient agar. The increased adhesive and invasive growth does not depend on the only known adhesion protein Cfl1 and its main controller Znf2. Cpl1Δ accumulates significantly higher level of intracellular labile zinc ion, leading to increased glucose uptake, higher level of mitochondrial membrane potential, ATP and Reactive Oxygen Species(ROS) production. Higher level of ROS activates Snf1, leading to invasive growth of Cpl1Δ. Three cysteine residues at the N-terminals of the cysteine-rich domain controls the increased invasive growth under nutrient sufficient conditions. This is the first report that a small and secreted cysteine-rich protein negatively regulates invasive growth of C. neoformans through regulating the intracellular labile zinc ion level. The function of this cysteine-rich domain was systematically investigated by site-directed mutagenensis in C. neoformans. The work contributes to understanding the function of this protein family and the invasive growth mechanism in C. neoformans.
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Affiliation(s)
- Pei Sun
- National Key Program of Microbiology and Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Li
- National Key Program of Microbiology and Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mengdi Yang
- National Key Program of Microbiology and Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xueru Zhao
- National Key Program of Microbiology and Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhijun Zhang
- National Engineering Technology Research Center for Preservation of Agricultural Products, Key Laboratory of Storage of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage of Agricultural Products, Tianjin, 300384, China.
| | - Dongsheng Wei
- National Key Program of Microbiology and Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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23
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Yeast Flocculin: Methods for Quantitative Analysis of Flocculation in Yeast Cells. Methods Mol Biol 2020. [PMID: 32306350 DOI: 10.1007/978-1-0716-0430-4_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Flocculation, the clump forming property of yeast, has long been appreciated in breweries and utilized as an off-cost method to enable the reuse of yeast cells. Members of the flocculin protein family were identified as the adherent proteins on the cell surface responsible for flocculation, and their properties have been investigated. Crystal structures of the adhesion domain of flocculins revealed their unique mode of ligand binding where a calcium ion is located in the middle of the interface between flocculin and the interacting sugar. Here we describe the most commonly used flocculation assay. The method is simple and easy, yet it is the most direct and reliable assay to evaluate the flocculation cellular phenotype.
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24
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Colomer MS, Chailyan A, Fennessy RT, Olsson KF, Johnsen L, Solodovnikova N, Forster J. Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications. Front Microbiol 2020; 11:637. [PMID: 32373090 PMCID: PMC7177047 DOI: 10.3389/fmicb.2020.00637] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Brettanomyces yeasts have gained popularity in many sectors of the biotechnological industry, specifically in the field of beer production, but also in wine and ethanol production. Their unique properties enable Brettanomyces to outcompete conventional brewer’s yeast in industrially relevant traits such as production of ethanol and pleasant flavors. Recent advances in next-generation sequencing (NGS) and high-throughput screening techniques have facilitated large population studies allowing the selection of appropriate yeast strains with improved traits. In order to get a better understanding of Brettanomyces species and its potential for beer production, we sequenced the whole genome of 84 strains, which we make available to the scientific community and carried out several in vitro assays for brewing-relevant properties. The collection includes isolates from different substrates and geographical origin. Additionally, we have included two of the oldest Carlsberg Research Laboratory isolates. In this study, we reveal the phylogenetic pattern of Brettanomyces species by comparing the predicted proteomes of each strain. Furthermore, we show that the Brettanomyces collection is well described using similarity in genomic organization, and that there is a direct correlation between genomic background and phenotypic characteristics. Particularly, genomic patterns affecting flavor production, maltose assimilation, beta-glucosidase activity, and phenolic off-flavor (POF) production are reported. This knowledge yields new insights into Brettanomyces population survival strategies, artificial selection pressure, and loss of carbon assimilation traits. On a species-specific level, we have identified for the first time a POF negative Brettanomyces anomalus strain, without the main spoilage character of Brettanomyces species. This strain (CRL-90) has lost DaPAD1, making it incapable of converting ferulic acid to 4-ethylguaiacol (4-EG) and 4-ethylphenol (4-EP). This loss of function makes CRL-90 a good candidate for the production of characteristic Brettanomyces flavors in beverages, without the contaminant increase in POF. Overall, this study displays the potential of exploring Brettanomyces yeast species biodiversity to find strains with relevant properties applicable to the brewing industry.
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Affiliation(s)
- Marc Serra Colomer
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark.,National Institute for Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Chailyan
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Ross T Fennessy
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Kim Friis Olsson
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | | | | | - Jochen Forster
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
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25
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Varela C, Bartel C, Nandorfy DE, Borneman A, Schmidt S, Curtin C. Identification of flocculant wine yeast strains with improved filtration-related phenotypes through application of high-throughput sedimentation rate assays. Sci Rep 2020; 10:2738. [PMID: 32066762 PMCID: PMC7026045 DOI: 10.1038/s41598-020-59579-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/30/2020] [Indexed: 11/24/2022] Open
Abstract
In most yeast-driven biotechnological applications, biomass is separated from the aqueous phase after fermentation or production has finished. During winemaking, yeasts are removed after fermentation by racking, filtration, or centrifugation, which add costs to the overall process and may reduce product yield. Theoretically, clarification and filtration can be aided through use of yeast strains that form flocs due to cell-cell binding, a process known as flocculation. However, because early flocculation can cause stuck/sluggish fermentations, this phenotype is not common amongst commercially available wine yeasts. In this study we sought to identify wine strains that exhibit late-fermentation flocculant behaviour using two complementary approaches; a high-throughput sedimentation rate assay of individual strains and a competitive sedimentation assay using a barcoded yeast collection. Amongst 103 wine strains, several exhibited strong sedimentation at the end of the wine fermentation process under various environmental conditions. Two of these strains, AWRI1688 and AWRI1759, were further characterised during red winemaking trials. Shiraz wines produced with both strains displayed improved filtration-related properties. AWRI1759 produced wines with greater filterability, whereas AWRI1688 enabled the recovery of larger wine volumes after racking. Thus, this study demonstrates the effective use of sedimentation screening assays to identify wine yeasts with practical winemaking applications.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia. .,Department of Wine & Food Science, University of Adelaide, Glen Osmond, SA 5064, Adelaide, Australia.
| | - Caroline Bartel
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | | | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Simon Schmidt
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Chris Curtin
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.,College of Agricultural Sciences, Oregon State University, Wiegand Hall, 3051 SW Campus Way, Corvallis, OR, 97331, USA
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26
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Abstract
Flocculation or cell aggregation is a well-appreciated characteristic of industrial brewer’s strains, since it allows removal of the cells from the beer in a cost-efficient and environmentally-friendly manner. However, many industrial strains are non-flocculent and genetic interference to increase the flocculation characteristics are not appreciated by the consumers. We applied adaptive laboratory evolution (ALE) to three non-flocculent, industrial Saccharomyces cerevisiae brewer’s strains using small continuous bioreactors (ministats) to obtain an aggregative phenotype, i.e., the “snowflake” phenotype. These aggregates could increase yeast sedimentation considerably. We evaluated the performance of these evolved strains and their produced flavor during lab scale beer fermentations. The small aggregates did not result in a premature sedimentation during the fermentation and did not result in major flavor changes of the produced beer. These results show that ALE could be used to increase the sedimentation behavior of non-flocculent brewer’s strains.
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Salazar AN, Gorter de Vries AR, van den Broek M, Brouwers N, de la Torre Cortès P, Kuijpers NGA, Daran JMG, Abeel T. Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization. BMC Genomics 2019; 20:916. [PMID: 31791228 PMCID: PMC6889557 DOI: 10.1186/s12864-019-6263-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history. RESULTS To fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains. CONCLUSIONS Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.
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Affiliation(s)
- Alex N Salazar
- Delft Bioinformatics Lab, Delft University of Technology, 2628, CD, Delft, The Netherlands
| | - Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Pilar de la Torre Cortès
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Niels G A Kuijpers
- HEINEKEN Supply Chain B.V., Global Innovation and Research, Zoeterwoude, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, 2628, CD, Delft, The Netherlands.
- Broad Institute of MIT and Harvard, Boston, MA, 02142, USA.
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Rowlands H, Shaban K, Cheng A, Foster B, Yankulov K. Dysfunctional CAF-I reveals its role in cell cycle progression and differential regulation of gene silencing. Cell Cycle 2019; 18:3223-3236. [PMID: 31564230 DOI: 10.1080/15384101.2019.1673100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Chromatin Assembly Factor I (CAF-I) plays a central role in the reassembly of H3/H4 histones during DNA replication. In S. cerevisiae CAF-I is not essential and its loss is associated with reduced gene silencing at telomeres and increased sensitivity to DNA damage. Two kinases, Cyclin Dependent Kinase (CDK) and Dbf4-Dependent Kinase (DDK), are known to phosphorylate the Cac1p subunit of CAF-I, but their role in the regulation of CAF-I activity is not well understood. In this study we systematically mutated the phosphorylation target sites of these kinases. We show that concomitant mutations of the CDK and DDK target sites of Cac1p lead to growth retardation and significant cell cycle defects, altered cell morphology and increased sensitivity to DNA damage. Surprisingly, some mutations also produced flocculation, a phenotype that is lost in most laboratory strains, and displayed elevated expression of FLO genes. None of these effects is observed upon the destruction of CAF-I. In contrast, the mutations that caused flocculation did not affect gene silencing at the mating type and subtelomeric loci. We conclude that dysfunctional CAF-I produces severe phenotypes, which reveal a possible role of CAF-I in the coordination of DNA replication, chromatin reassembly and cell cycle progression. Our study highlights the role of phosphorylation of Cac1p by CDK and a putative role for DDK in the transmission and re-assembly of chromatin during DNA replication.
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Affiliation(s)
- Hollie Rowlands
- Department of Molecular and Cellular Biology, University of Guelph , Guelph , Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph , Guelph , Canada
| | - Ashley Cheng
- Department of Molecular and Cellular Biology, University of Guelph , Guelph , Canada
| | - Barret Foster
- Department of Molecular and Cellular Biology, University of Guelph , Guelph , Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph , Guelph , Canada
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29
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Su Y, Chen J, Huang Y. Disruption of ppr3, ppr4, ppr6 or ppr10 induces flocculation and filamentous growth in Schizosaccharomyces pombe. FEMS Microbiol Lett 2019; 365:5033677. [PMID: 29878109 DOI: 10.1093/femsle/fny141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are major players in mitochondrial and chloroplast RNA metabolism, which is essential for normal organellar function. The fission yeast Schizosaccharomyces pombe has 10 PPR proteins. We have previously reported that loss of ppr3, ppr4, ppr6 or ppr10 perturbs iron homeostasis leading to accumulation of reactive oxygen species and apoptotic cell death. In the present study, we show that loss of ppr3, ppr4, ppr6 or ppr10 can cause non-sexual flocculation and filamentous growth of cells. Furthermore, expression of a number of genes encoding cell-surface flocculins and cell wall-remodeling enzymes are induced in these ppr-deletion mutants. We also show that Δppr10 cells, and, to a lesser extent, Δppr4 and Δppr6 cells, exhibited increased tolerance to H2O2 toxicity compared with the wild-type strain. Finally, we found that overexpression of genes involved in iron uptake and/or iron homeostasis could cause the flocculation of wild-type cells. Our findings suggest that an elevated level of intracellular iron in the mutant caused by loss of ppr3, ppr4, ppr6 or ppr10 may result in flocculation and filamentous growth in S. pombe.
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Affiliation(s)
- Yang Su
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jie Chen
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genetics, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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30
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Rowlands H, Shaban K, Foster B, Proteau Y, Yankulov K. Histone chaperones and the Rrm3p helicase regulate flocculation in S. cerevisiae. Epigenetics Chromatin 2019; 12:56. [PMID: 31547833 PMCID: PMC6757361 DOI: 10.1186/s13072-019-0303-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022] Open
Abstract
Background Biofilm formation or flocculation is a major phenotype in wild type budding yeasts but rarely seen in laboratory yeast strains. Here, we analysed flocculation phenotypes and the expression of FLO genes in laboratory strains with various genetic backgrounds. Results We show that mutations in histone chaperones, the helicase RRM3 and the Histone Deacetylase HDA1 de-repress the FLO genes and partially reconstitute flocculation. We demonstrate that the loss of repression correlates to elevated expression of several FLO genes, to increased acetylation of histones at the promoter of FLO1 and to variegated expression of FLO11. We show that these effects are related to the activity of CAF-1 at the replication forks. We also demonstrate that nitrogen starvation or inhibition of histone deacetylases do not produce flocculation in W303 and BY4742 strains but do so in strains compromised for chromatin maintenance. Finally, we correlate the de-repression of FLO genes to the loss of silencing at the subtelomeric and mating type gene loci. Conclusions We conclude that the deregulation of chromatin maintenance and transmission is sufficient to reconstitute flocculation in laboratory yeast strains. Consequently, we propose that a gain in epigenetic silencing is a major contributing factor for the loss of flocculation phenotypes in these strains. We suggest that flocculation in yeasts provides an excellent model for addressing the challenging issue of how epigenetic mechanisms contribute to evolution.
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Affiliation(s)
- Hollie Rowlands
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Barret Foster
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Yannic Proteau
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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31
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Sariki SK, Kumawat R, Singh V, Tomar RS. Flocculation ofSaccharomyces cerevisiaeis dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway. Mol Microbiol 2019; 112:1350-1369. [DOI: 10.1111/mmi.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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32
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Ogawa M, Bisson LF, García-Martínez T, Mauricio JC, Moreno-García J. New insights on yeast and filamentous fungus adhesion in a natural co-immobilization system: proposed advances and applications in wine industry. Appl Microbiol Biotechnol 2019; 103:4723-4731. [PMID: 31079167 DOI: 10.1007/s00253-019-09870-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 11/29/2022]
Abstract
Fungi possess extraordinary strength in attachment to biotic and abiotic surfaces. This review focuses on adhesion mechanisms of yeast and filamentous fungi and the proposed combination of the adhesive forces of both organisms in an immobilization system called yeast biocapsules, whereby Saccharomyces cerevisiae cells are attached to the hyphae of Penicillium chrysogenum. The natural adherent properties of each organism, one multicellular and another unicellular, allow yeast to be fixated securely on the filamentous fungi and complete alcoholic fermentation. Following alcoholic fermentation, the hyphae become an inert support for yeast cells while maintaining shape and integrity. Biocapsules have been used successfully in both wine and bioethanol production. Investigation of the potential genes involved in fungal-yeast fusion suggests that natural hydrophobic interactions of both organisms play a major role. Analysis of the possible mechanisms involved in fungus and yeast adhesion, future perspectives on improving yeast immobilization, and proposed applications of the biocapsules are explored.
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Affiliation(s)
- Minami Ogawa
- Department of Microbiology, University of Córdoba, Córdoba, Spain.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Linda F Bisson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | | | - Juan C Mauricio
- Department of Microbiology, University of Córdoba, Córdoba, Spain
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33
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Bui TT, Harting R, Braus-Stromeyer SA, Tran VT, Leonard M, Höfer A, Abelmann A, Bakti F, Valerius O, Schlüter R, Stanley CE, Ambrósio A, Braus GH. Verticillium dahliae transcription factors Som1 and Vta3 control microsclerotia formation and sequential steps of plant root penetration and colonisation to induce disease. THE NEW PHYTOLOGIST 2019; 221:2138-2159. [PMID: 30290010 DOI: 10.1111/nph.15514] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Verticillium dahliae nuclear transcription factors Som1 and Vta3 can rescue adhesion in a FLO8-deficient Saccharomyces cerevisiae strain. Som1 and Vta3 induce the expression of the yeast FLO1 and FLO11 genes encoding adhesins. Som1 and Vta3 are sequentially required for root penetration and colonisation of the plant host by V. dahliae. The SOM1 and VTA3 genes were deleted and their functions in fungus-induced plant pathogenesis were studied using genetic, cell biology, proteomic and plant pathogenicity experiments. Som1 supports fungal adhesion and root penetration and is required earlier than Vta3 in the colonisation of plant root surfaces and tomato plant infection. Som1 controls septa positioning and the size of vacuoles, and subsequently hyphal development including aerial hyphae formation and normal hyphal branching. Som1 and Vta3 control conidiation, microsclerotia formation, and antagonise in oxidative stress responses. The molecular function of Som1 is conserved between the plant pathogen V. dahliae and the opportunistic human pathogen Aspergillus fumigatus. Som1 controls genes for initial steps of plant root penetration, adhesion, oxidative stress response and VTA3 expression to allow subsequent root colonisation. Both Som1 and Vta3 regulate developmental genetic networks required for conidiation, microsclerotia formation and pathogenicity of V. dahliae.
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Affiliation(s)
- Tri-Thuc Bui
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Susanna A Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Van-Tuan Tran
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
- Department of Microbiology, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, 100000, Hanoi, Vietnam
| | - Miriam Leonard
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Annalena Höfer
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Anja Abelmann
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Fruzsina Bakti
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, D-17489, Greifswald, Germany
| | - Claire E Stanley
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Alinne Ambrósio
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
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Tek EL, Sundstrom JF, Gardner JM, Oliver SG, Jiranek V. Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment. FEMS Microbiol Ecol 2019; 94:4831476. [PMID: 29394344 DOI: 10.1093/femsec/fix188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Abstract
Commercially available active dried wine yeasts are regularly used by winemakers worldwide to achieve reliable fermentations and obtain quality wine. This practice has led to increased evidence of traces of commercial wine yeast in the vineyard, winery and uninoculated musts. The mechanism(s) that enables commercial wine yeast to persist in the winery environment and the influence to native microbial communities on this persistence is poorly understood. This study has investigated the ability of commercial wine yeasts to form biofilms and adhere to plastic. The results indicate that the biofilms formed by commercial yeasts consist of cells with a combination of different lifestyles (replicative and non-replicative) and growth modes including invasive growth, bud elongation, sporulation and a mat sectoring-like phenotype. Invasive growth was greatly enhanced on grape pulp regardless of strain, while adhesion on plastic varied between strains. The findings suggest a possible mechanism that allows commercial yeast to colonise and survive in the winery environment, which may have implications for the indigenous microbiota profile as well as the population profile in uninoculated fermentations if their dissemination is not controlled.
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Affiliation(s)
- Ee Lin Tek
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Joanna F Sundstrom
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Gardner
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
| | - Stephen G Oliver
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK
| | - Vladimir Jiranek
- Department of Wine and Food Science, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.,Australian Research Council Training Centre for Innovative Wine Production, University of Adelaide, Waite Campus, Australia
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Perpetuini G, Tittarelli F, Suzzi G, Tofalo R. Cell Wall Surface Properties of Kluyveromyces marxianus Strains From Dairy-Products. Front Microbiol 2019; 10:79. [PMID: 30766524 PMCID: PMC6366010 DOI: 10.3389/fmicb.2019.00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/15/2019] [Indexed: 01/30/2023] Open
Abstract
Thirty-three Kluyveromyces marxianus strains were tested for the ability to form biofilm and mat structures in YPD and whey and for cell surface hydrophobicity. To identify genes potentially involved in adhesion properties, a RT-qPCR analysis was performed. Eight strains were able to adhere on polystyrene plates in both media and formed a mature mat structure. These strains showed a different level of hydrophobicity ranging from 55 to 66% in YPD and from 69 to 81% in whey. Four K. marxianus orthologs genes (FLO11, STE12, TPK3, and WSC4), known from studies in other yeast to be involved in biofilm formation, have been studied. FLO11 and STE12 showed the highest fold changes in all conditions tested and especially in whey: 15.05 and 11.21, respectively. TPK3 was upregulated only in a strain, and WSC4 in 3 strains. In YPD, fold changes were lower than in whey with STE12 and FLO11 genes showing the highest fold changes. In mat structures FLO11 and STE12 fold changes ranged from 3.6-1.3 to 2-1.17, respectively. Further studies are necessary to better understand the role of these genes in K. marxianus adhesion ability.
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Affiliation(s)
| | | | | | - Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
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36
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Moreno-García J, Martín-García FJ, Ogawa M, García-Martínez T, Moreno J, Mauricio JC, Bisson LF. FLO1, FLO5 and FLO11 Flocculation Gene Expression Impacts Saccharomyces cerevisiae Attachment to Penicillium chrysogenum in a Co-immobilization Technique. Front Microbiol 2018; 9:2586. [PMID: 30429833 PMCID: PMC6220091 DOI: 10.3389/fmicb.2018.02586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/10/2018] [Indexed: 11/14/2022] Open
Abstract
A reoccurring flaw of most yeast immobilization systems that limits the potential of the technique is leakage of the cells from the matrix. Leakage may be due to weakly adherent cells, deterioration of the matrix, or to new growth and loss of non-adherent daughter cells. Yeast biocapsules are a spontaneous, cost effective system of immobilization whereby Saccharomyces cerevisiae cells are attached to the hyphae of Penicillium chrysogenum, creating hollow spheres that allow recovery and reutilization. This attachment is based on naturally occurring adherent properties of the yeast cell surface. We hypothesized that proteins associated with flocculation might play a role in adherence to fungal hyphae. To test this hypothesis, yeast strains with overexpressed and deleted flocculation genes (FLO1, FLO5, and FLO11) were evaluated for biocapsule formation to observe the impact of gene expression on biocapsule diameter, number, volume, dry mass, and percent immobilized versus non-immobilized cells. Overexpression of all three genes enhanced immobilization and resulted in larger diameter biocapsules. In particular, overexpression of FLO11 resulted in a five fold increase of absorbed cells versus the wild type isogenic strain. In addition, deletion of FLO1 and FLO11 significantly decreased the number of immobilized yeast cells compared to the wild type BY4742. These results confirm the role of natural adherent properties of yeast cells in attachment to fungal hyphae and offer the potential to create strongly adherent cells that will produce adherent progeny thereby reducing the potential for cell leakage from the matrix.
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Affiliation(s)
- Jaime Moreno-García
- Department of Microbiology, University of Córdoba, Córdoba, Spain
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Minami Ogawa
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Juan Moreno
- Department of Agricultural Chemistry, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Microbiology, University of Córdoba, Córdoba, Spain
| | - Linda F. Bisson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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37
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Willaert RG. Adhesins of Yeasts: Protein Structure and Interactions. J Fungi (Basel) 2018; 4:jof4040119. [PMID: 30373267 PMCID: PMC6308950 DOI: 10.3390/jof4040119] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
The ability of yeast cells to adhere to other cells or substrates is crucial for many yeasts. The budding yeast Saccharomyces cerevisiae can switch from a unicellular lifestyle to a multicellular one. A crucial step in multicellular lifestyle adaptation is self-recognition, self-interaction, and adhesion to abiotic surfaces. Infectious yeast diseases such as candidiasis are initiated by the adhesion of the yeast cells to host cells. Adhesion is accomplished by adhesin proteins that are attached to the cell wall and stick out to interact with other cells or substrates. Protein structures give detailed insights into the molecular mechanism of adhesin-ligand interaction. Currently, only the structures of a very limited number of N-terminal adhesion domains of adhesins have been solved. Therefore, this review focuses on these adhesin protein families. The protein architectures, protein structures, and ligand interactions of the flocculation protein family of S. cerevisiae; the epithelial adhesion family of C. glabrata; and the agglutinin-like sequence protein family of C. albicans are reviewed and discussed.
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Affiliation(s)
- Ronnie G Willaert
- Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), IJRG VUB-EPFL NanoBiotechnology & NanoMedicine (NANO), Research Group Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
- Department Bioscience Engineering, University Antwerp, 2020 Antwerp, Belgium.
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38
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Yang L, Zheng C, Chen Y, Ying H. FLO Genes Family and Transcription Factor MIG1 Regulate Saccharomyces cerevisiae Biofilm Formation During Immobilized Fermentation. Front Microbiol 2018; 9:1860. [PMID: 30210459 PMCID: PMC6119776 DOI: 10.3389/fmicb.2018.01860] [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: 05/05/2018] [Accepted: 07/24/2018] [Indexed: 01/26/2023] Open
Abstract
Saccharomyces cerevisiae immobilization is commonly used for efficient ethanol fuel production in industry due to the relatively higher ethanol stress resistance of S. cerevisiae in biofilms relative to planktonic cells. The mechanisms of biofilm formation and stress resistance, however, remain ambiguous. By analyzing biofilm and planktonic cell transcriptomes, this study observed that MIG1 (encoding a transcription factor) expression in cells increases during the biofilm formation process. To identify the role of MIG1 in yeast biofilm formation and the ethanol resistance of these cells, MIG1 was deleted and complemented in S. cerevisiae 1308. Results showed the MIG1 deletion mutant strain demonstrated weaker biofilm formation ability both on fibers and plastic than the wild-type and these could be restored by expressing MIG1 in deletion mutant. To verify the ability of MIG1 to regulate the expression of FLO genes, which encode adhesions responsible for yeast biofilm formation, FLO gene transcription levels were measured via qRT-PCR. Relative to wild-type S. cerevisiae, the adhesion genes FLO1, 5, and 9 which also demonstrate increased expression in the transcriptome of yeast cells during biofilm formation, but not FLO11, were down-regulated in the MIG1 mutant strain. Additionally, the MIG1 mutant lost a majority of its flocculation ability, which depended on cell-cell adhesions and its slightly invasive growth ability, dependent on cell-substrate adhesion. Deleting FLO1, 5, and 9 decreased biofilm formation on plastics, suggesting these FLO genes contribute to the biofilm formation process alongside FLO11. Moreover, the ethanol tolerance of yeast decreased in the MIG1 deletion mutant as well as the FLO11 deletion mutant, resulting in reduced biofilm formation during fermentation. It remains possible that in the later period of fermentation, when ethanol has accumulated, an over-expression of the FLO1, 5, and 9 genes regulated by MIG1 would enhanced cell-cell adhesions and thus protect cells in the outer layer of biofilms from ethanol, a function primarily dependent on cell-cell adhesions. This work offers a possible explanation for how biofilm formation is regulated during the immobilized fermentation process, and can enhance environmental tolerance in industrial production.
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Affiliation(s)
- Leyun Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Cheng Zheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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39
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40
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Yamada R, Nishikawa R, Wakita K, Ogino H. Rapid and stable production of 2,3-butanediol by an engineered Saccharomyces cerevisiae strain in a continuous airlift bioreactor. J Ind Microbiol Biotechnol 2018; 45:305-311. [PMID: 29605870 DOI: 10.1007/s10295-018-2033-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/26/2018] [Indexed: 12/26/2022]
Abstract
Utilization of renewable feedstocks for the production of bio-based bulk chemicals, such as 2,3-butanediol (2,3-BDO), by engineered strains of the non-pathogenic yeast, Saccharomyces cerevisiae, has recently become an attractive option. In this study, to realize rapid production of 2,3-BDO, a flocculent, 2,3-BDO-producing S. cerevisiae strain YPH499/dPdAdG/BDN6-10/FLO1 was constructed from a previously developed 2,3-BDO-producing strain. Continuous 2,3-BDO fermentation was carried out by the flocculent strain in an airlift bioreactor. The strain consumed more than 90 g/L of glucose, which corresponded to 90% of the input, and stably produced more than 30 g/L of 2,3-BDO over 380 h. The maximum 2,3-BDO productivity was 7.64 g/L/h at a dilution rate of 0.200/h, which was higher than the values achieved by continuous fermentation using pathogenic bacteria in the previous reports. These results demonstrate that continuous 2,3-BDO fermentation with flocculent 2,3-BDO-producing S. cerevisiae is a promising strategy for practical 2,3-BDO production.
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Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Riru Nishikawa
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Kazuki Wakita
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
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41
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Karabín M, Jelínek L, Kotrba P, Cejnar R, Dostálek P. Enhancing the performance of brewing yeasts. Biotechnol Adv 2017; 36:691-706. [PMID: 29277309 DOI: 10.1016/j.biotechadv.2017.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/23/2017] [Accepted: 12/20/2017] [Indexed: 12/26/2022]
Abstract
Beer production is one of the oldest known traditional biotechnological processes, but is nowadays facing increasing demands not only for enhanced product quality, but also for improved production economics. Targeted genetic modification of a yeast strain is one way to increase beer quality and to improve the economics of beer production. In this review we will present current knowledge on traditional approaches for improving brewing strains and for rational metabolic engineering. These research efforts will, in the near future, lead to the development of a wider range of industrial strains that should increase the diversity of commercial beers.
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Affiliation(s)
- Marcel Karabín
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Lukáš Jelínek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Kotrba
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Rudolf Cejnar
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Dostálek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic.
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42
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Wertheimer NB, Stone N, Berman J. Ploidy dynamics and evolvability in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0461. [PMID: 28080987 PMCID: PMC5095540 DOI: 10.1098/rstb.2015.0461] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Noa Blutraich Wertheimer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
| | - Neil Stone
- Institute of Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
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FLO5 gene controls flocculation phenotype and adhesive properties in a Saccharomyces cerevisiae sparkling wine strain. Sci Rep 2017; 7:10786. [PMID: 28883485 PMCID: PMC5589750 DOI: 10.1038/s41598-017-09990-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Flocculation is an important feature for yeast survival in adverse conditions. The natural diversity of flocculating genes in Saccharomyces cerevisiae can also be exploited in several biotechnological applications. Flocculation is mainly regulated by the expression of genes belonging to the FLO family. These genes have a similar function, but their specific contribution to flocculation ability is still unclear. In this study, the distribution of FLO1, FLO5 and FLO8 genes in four S. cerevisiae wine strains was investigated. Subsequently, both FLO1 and FLO5 genes were separately deleted in a flocculent S. cerevisiae wine strain. After gene disruption, flocculation ability and agar adhesion were evaluated. FLO1 and FLO5 genes inheritance was also monitored. All strains presented different lengths for FLO1 and FLO5 genes. Results confirm that in S. cerevisiae strain F6789, the FLO5 gene drives flocculation and influences adhesive properties. Flocculation ability monitoring after a cross with a non-flocculent strain revealed that FLO5 is the gene responsible for flocculation development.
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44
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Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth. Metab Eng 2017; 41:46-56. [DOI: 10.1016/j.ymben.2017.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/10/2017] [Accepted: 03/08/2017] [Indexed: 12/20/2022]
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45
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Mei M, Zhou Y, Peng W, Yu C, Ma L, Zhang G, Yi L. Application of modified yeast surface display technologies for non-Antibody protein engineering. Microbiol Res 2017; 196:118-128. [DOI: 10.1016/j.micres.2016.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 02/07/2023]
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46
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Gravity-Driven Adaptive Evolution of an Industrial Brewer’s Yeast Strain towards a Snowflake Phenotype in a 3D-Printed Mini Tower Fermentor. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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47
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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Tofalo R, Perpetuini G, Di Gianvito P, Arfelli G, Schirone M, Corsetti A, Suzzi G. Characterization of specialized flocculent yeasts to improve sparkling wine fermentation. J Appl Microbiol 2016; 120:1574-84. [DOI: 10.1111/jam.13113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 02/10/2016] [Accepted: 02/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- R. Tofalo
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Perpetuini
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - P. Di Gianvito
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Arfelli
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - M. Schirone
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - A. Corsetti
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
| | - G. Suzzi
- Faculty of BioScience and Technology for Food; Agriculture and Environment; University of Teramo; Mosciano Sant' Angelo (TE) Italy
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Rossouw D, Bagheri B, Setati ME, Bauer FF. Co-Flocculation of Yeast Species, a New Mechanism to Govern Population Dynamics in Microbial Ecosystems. PLoS One 2015; 10:e0136249. [PMID: 26317200 PMCID: PMC4552943 DOI: 10.1371/journal.pone.0136249] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Flocculation has primarily been studied as an important technological property of Saccharomyces cerevisiae yeast strains in fermentation processes such as brewing and winemaking. These studies have led to the identification of a group of closely related genes, referred to as the FLO gene family, which controls the flocculation phenotype. All naturally occurring S. cerevisiae strains assessed thus far possess at least four independent copies of structurally similar FLO genes, namely FLO1, FLO5, FLO9 and FLO10. The genes appear to differ primarily by the degree of flocculation induced by their expression. However, the reason for the existence of a large family of very similar genes, all involved in the same phenotype, has remained unclear. In natural ecosystems, and in wine production, S. cerevisiae growth together and competes with a large number of other Saccharomyces and many more non-Saccharomyces yeast species. Our data show that many strains of such wine-related non-Saccharomyces species, some of which have recently attracted significant biotechnological interest as they contribute positively to fermentation and wine character, were able to flocculate efficiently. The data also show that both flocculent and non-flocculent S. cerevisiae strains formed mixed species flocs (a process hereafter referred to as co-flocculation) with some of these non-Saccharomyces yeasts. This ability of yeast strains to impact flocculation behaviour of other species in mixed inocula has not been described previously. Further investigation into the genetic regulation of co-flocculation revealed that different FLO genes impact differently on such adhesion phenotypes, favouring adhesion with some species while excluding other species from such mixed flocs. The data therefore strongly suggest that FLO genes govern the selective association of S. cerevisiae with specific species of non-Saccharomyces yeasts, and may therefore be drivers of ecosystem organisational patterns. Our data provide, for the first time, insights into the role of the FLO gene family beyond intraspecies cellular association, and suggest a wider evolutionary role for the FLO genes. Such a role would explain the evolutionary persistence of a large multigene family of genes with apparently similar function.
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Affiliation(s)
- Debra Rossouw
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Bahareh Bagheri
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Mathabatha Evodia Setati
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Florian Franz Bauer
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch, 7600, South Africa
- * E-mail:
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50
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Petruzzi L, Rosaria Corbo M, Sinigaglia M, Bevilacqua A. Brewer’s yeast in controlled and uncontrolled fermentations, with a focus on novel, nonconventional, and superior strains. FOOD REVIEWS INTERNATIONAL 2015. [DOI: 10.1080/87559129.2015.1075211] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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