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Stovicek V, Lengeler KB, Wendt T, Rasmussen M, Katz M, Förster J. Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast. N Biotechnol 2024; 82:92-106. [PMID: 38788897 DOI: 10.1016/j.nbt.2024.05.006] [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: 01/05/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
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Affiliation(s)
- Vratislav Stovicek
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Klaus B Lengeler
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; Traitomic A/S, J.C. Jacobsens Gade 1, DK-1799 Copenhagen V, Denmark
| | - Magnus Rasmussen
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark.
| | - Jochen Förster
- Carlsberg Research Laboratory, Carlsberg A/S, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark; DTU Biosustain, The Novo Nordisk Foundation Center for Biosustainability, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
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Khoo A, Liu LY, Nyalwidhe JO, Semmes OJ, Vesprini D, Downes MR, Boutros PC, Liu SK, Kislinger T. Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry. Nat Rev Urol 2021; 18:707-724. [PMID: 34453155 PMCID: PMC8639658 DOI: 10.1038/s41585-021-00500-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
Prostate cancer is the second most frequently diagnosed non-skin cancer in men worldwide. Patient outcomes are remarkably heterogeneous and the best existing clinical prognostic tools such as International Society of Urological Pathology Grade Group, pretreatment serum PSA concentration and T-category, do not accurately predict disease outcome for individual patients. Thus, patients newly diagnosed with prostate cancer are often overtreated or undertreated, reducing quality of life and increasing disease-specific mortality. Biomarkers that can improve the risk stratification of these patients are, therefore, urgently needed. The ideal biomarker in this setting will be non-invasive and affordable, enabling longitudinal evaluation of disease status. Prostatic secretions, urine and blood can be sources of biomarker discovery, validation and clinical implementation, and mass spectrometry can be used to detect and quantify proteins in these fluids. Protein biomarkers currently in use for diagnosis, prognosis and relapse-monitoring of localized prostate cancer in fluids remain centred around PSA and its variants, and opportunities exist for clinically validating novel and complimentary candidate protein biomarkers and deploying them into the clinic.
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Affiliation(s)
- Amanda Khoo
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Lydia Y Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julius O Nyalwidhe
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - O John Semmes
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Danny Vesprini
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Canada
| | - Michelle R Downes
- Division of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Vector Institute for Artificial Intelligence, Toronto, Canada.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, Canada.
- Odette Cancer Research Program, Sunnybrook Research Institute, Toronto, Canada.
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.
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Faugeroux V, Pailler E, Oulhen M, Deas O, Brulle-Soumare L, Hervieu C, Marty V, Alexandrova K, Andree KC, Stoecklein NH, Tramalloni D, Cairo S, NgoCamus M, Nicotra C, Terstappen LWMM, Manaresi N, Lapierre V, Fizazi K, Scoazec JY, Loriot Y, Judde JG, Farace F. Genetic characterization of a unique neuroendocrine transdifferentiation prostate circulating tumor cell-derived eXplant model. Nat Commun 2020; 11:1884. [PMID: 32313004 PMCID: PMC7171138 DOI: 10.1038/s41467-020-15426-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/04/2020] [Indexed: 02/07/2023] Open
Abstract
Transformation of castration-resistant prostate cancer (CRPC) into an aggressive neuroendocrine disease (CRPC-NE) represents a major clinical challenge and experimental models are lacking. A CTC-derived eXplant (CDX) and a CDX-derived cell line are established using circulating tumor cells (CTCs) obtained by diagnostic leukapheresis from a CRPC patient resistant to enzalutamide. The CDX and the derived-cell line conserve 16% of primary tumor (PT) and 56% of CTC mutations, as well as 83% of PT copy-number aberrations including clonal TMPRSS2-ERG fusion and NKX3.1 loss. Both harbor an androgen receptor-null neuroendocrine phenotype, TP53, PTEN and RB1 loss. While PTEN and RB1 loss are acquired in CTCs, evolutionary analysis suggest that a PT subclone harboring TP53 loss is the driver of the metastatic event leading to the CDX. This CDX model provides insights on the sequential acquisition of key drivers of neuroendocrine transdifferentiation and offers a unique tool for effective drug screening in CRPC-NE management.
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MESH Headings
- Animals
- Benzamides
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/metabolism
- Cell Line, Tumor
- Cell Transdifferentiation/genetics
- Disease Models, Animal
- Drug Resistance, Neoplasm
- Gene Expression Regulation, Neoplastic
- Homeodomain Proteins/metabolism
- Humans
- Male
- Mice
- Mice, Inbred NOD
- Neoplastic Cells, Circulating/drug effects
- Neoplastic Cells, Circulating/metabolism
- Nitriles
- Phenylthiohydantoin/analogs & derivatives
- Phenylthiohydantoin/pharmacology
- Phylogeny
- Prostate/metabolism
- Prostate/pathology
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Receptors, Androgen/genetics
- Sequence Alignment
- Serine Endopeptidases/metabolism
- Transcription Factors/metabolism
- Transcriptome
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Vincent Faugeroux
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", 94805, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | - Emma Pailler
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", 94805, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | - Marianne Oulhen
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | | | | | - Céline Hervieu
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", 94805, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | - Virginie Marty
- Gustave Roussy, Université Paris-Saclay, Experimental and Translational Pathology Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | - Kamelia Alexandrova
- Gustave Roussy, Université Paris-Saclay, Department of Cell Therapy, 94805, Villejuif, France
| | - Kiki C Andree
- Medical Cell Biophysics Group, Technical Medical Centre, Faculty of Science and Technology, University of Twente, 7522 NB, Enschede, The Netherlands
| | - Nikolas H Stoecklein
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dominique Tramalloni
- Gustave Roussy, Université Paris-Saclay, Department of Cell Therapy, 94805, Villejuif, France
| | | | - Maud NgoCamus
- Gustave Roussy, Université Paris-Saclay, Department of Cancer Medicine, 94805, Villejuif, France
| | - Claudio Nicotra
- Gustave Roussy, Université Paris-Saclay, Department of Cancer Medicine, 94805, Villejuif, France
| | - Leon W M M Terstappen
- Medical Cell Biophysics Group, Technical Medical Centre, Faculty of Science and Technology, University of Twente, 7522 NB, Enschede, The Netherlands
| | | | - Valérie Lapierre
- Gustave Roussy, Université Paris-Saclay, Department of Cell Therapy, 94805, Villejuif, France
| | - Karim Fizazi
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", 94805, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Department of Cancer Medicine, 94805, Villejuif, France
| | - Jean-Yves Scoazec
- Gustave Roussy, Université Paris-Saclay, Experimental and Translational Pathology Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France
| | - Yohann Loriot
- Gustave Roussy, Université Paris-Saclay, Department of Cancer Medicine, 94805, Villejuif, France.
| | | | - Françoise Farace
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", 94805, Villejuif, France.
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, CNRS UMS3655-INSERM US23 AMMICA, 94805, Villejuif, France.
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Lehmann PF, Lemon MB, Ferencak WJ. Antifungal Compounds (“Killer Factors”) Produced byKluyveromycesSpecies and their Detection on an Improved Medium Containing Glycerol. Mycologia 2018. [DOI: 10.1080/00275514.1987.12025461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Paul F. Lehmann
- Department of Microbiology, Medical College of Ohio, C. S. 10008, Toledo, Ohio 43699
| | - Mary B. Lemon
- Department of Microbiology, Medical College of Ohio, C. S. 10008, Toledo, Ohio 43699
| | - William J. Ferencak
- Department of Microbiology, Medical College of Ohio, C. S. 10008, Toledo, Ohio 43699
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5
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Rating of the industrial application potential of yeast strains by molecular characterization. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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6
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Russell I, Stewart GG. Valuable Techniques in the Genetic Manipulation of Industrial Yeast Strains. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-43-0084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- I. Russell
- Production Research Department, Labatt Brewing Company Limited, London, Ontario, Canada N6A 4M3
| | - G. G. Stewart
- Production Research Department, Labatt Brewing Company Limited, London, Ontario, Canada N6A 4M3
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7
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Xiao W, Rank GH. Curing IndustrialSaccharomycesYeasts of Parasitic 2μm Plasmid. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-48-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Wei Xiao
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W0
| | - Gerald H. Rank
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 0W0
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8
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Lauterbach A, Usbeck JC, Behr J, Vogel RF. MALDI-TOF MS typing enables the classification of brewing yeasts of the genus Saccharomyces to major beer styles. PLoS One 2017; 12:e0181694. [PMID: 28792944 PMCID: PMC5549903 DOI: 10.1371/journal.pone.0181694] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/04/2017] [Indexed: 11/19/2022] Open
Abstract
Brewing yeasts of the genus Saccharomyces are either available from yeast distributor centers or from breweries employing their own “in-house strains”. During the last years, the classification and characterization of yeasts of the genus Saccharomyces was achieved by using biochemical and DNA-based methods. The current lack of fast, cost-effective and simple methods to classify brewing yeasts to a beer type, may be closed by Matrix Assisted Laser Desorption/Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) upon establishment of a database based on sub-proteome spectra from reference strains of brewing yeasts. In this study an extendable “brewing yeast” spectra database was established including 52 brewing yeast strains of the most important types of bottom- and top-fermenting strains as well as beer-spoiling S. cerevisiae var. diastaticus strains. 1560 single spectra, prepared with a standardized sample preparation method, were finally compared against the established database and investigated by bioinformatic analyses for similarities and distinctions. A 100% separation between bottom-, top-fermenting and S. cerevisiae var. diastaticus strains was achieved. Differentiation between Alt and Kölsch strains was not achieved because of the high similarity of their protein patterns. Whereas the Ale strains show a high degree of dissimilarity with regard to their sub-proteome. These results were supported by MDS and DAPC analysis of all recorded spectra. Within five clusters of beer types that were distinguished, and the wheat beer (WB) cluster has a clear separation from other groups. With the establishment of this MALDI-TOF MS spectra database proof of concept is provided of the discriminatory power of this technique to classify brewing yeasts into different major beer types in a rapid, easy way, and focus brewing trails accordingly. It can be extended to yeasts for specialty beer types and other applications including wine making or baking.
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Affiliation(s)
- Alexander Lauterbach
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Julia C. Usbeck
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
- * E-mail:
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9
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Xylitol production by genetically modified industrial strain of Saccharomyces cerevisiae using glycerol as co-substrate. ACTA ACUST UNITED AC 2017; 44:961-971. [DOI: 10.1007/s10295-017-1914-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/29/2017] [Indexed: 10/20/2022]
Abstract
Abstract
Xylitol is commercially used in chewing gum and dental care products as a low calorie sweetener having medicinal properties. Industrial yeast strain of S. cerevisiae was genetically modified to overexpress an endogenous aldose reductase gene GRE3 and a xylose transporter gene SUT1 for the production of xylitol. The recombinant strain (XP-RTK) carried the expression cassettes of both the genes and the G418 resistance marker cassette KanMX integrated into the genome of S. cerevisiae. Short segments from the 5′ and 3′ delta regions of the Ty1 retrotransposons were used as homology regions for integration of the cassettes. Xylitol production by the industrial recombinant strain was evaluated using hemicellulosic hydrolysate of the corn cob with glucose as the cosubstrate. The recombinant strain XP-RTK showed significantly higher xylitol productivity (212 mg L−1 h−1) over the control strain XP (81 mg L−1 h−1). Glucose was successfully replaced by glycerol as a co-substrate for xylitol production by S. cerevisiae. Strain XP-RTK showed the highest xylitol productivity of 318.6 mg L−1 h−1 and titre of 47 g L−1 of xylitol at 12 g L−1 initial DCW using glycerol as cosubstrate. The amount of glycerol consumed per amount of xylitol produced (0.47 mol mol−1) was significantly lower than glucose (23.7 mol mol−1). Fermentation strategies such as cell recycle and use of the industrial nitrogen sources were demonstrated using hemicellulosic hydrolysate for xylitol production.
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10
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Stovicek V, Borja GM, Forster J, Borodina I. EasyClone 2.0: expanded toolkit of integrative vectors for stable gene expression in industrial Saccharomyces cerevisiae strains. J Ind Microbiol Biotechnol 2015; 42:1519-31. [PMID: 26376869 PMCID: PMC4607720 DOI: 10.1007/s10295-015-1684-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/02/2015] [Indexed: 12/29/2022]
Abstract
Saccharomyces cerevisiae is one of the key cell factories for production of chemicals and active pharmaceuticals. For large-scale fermentations, particularly in biorefinery applications, it is desirable to use stress-tolerant industrial strains. However, such strains are less amenable for metabolic engineering than the standard laboratory strains. To enable easy delivery and overexpression of genes in a wide range of industrial S. cerevisiae strains, we constructed a set of integrative vectors with long homology arms and dominant selection markers. The vectors integrate into previously validated chromosomal locations via double cross-over and result in homogenous stable expression of the integrated genes, as shown for several unrelated industrial strains. Cre-mediated marker rescue is possible for removing markers positioned on different chromosomes. To demonstrate the applicability of the presented vector set for metabolic engineering of industrial yeast, we constructed xylose-utilizing strains overexpressing xylose isomerase, xylose transporter and five genes of the pentose phosphate pathway.
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Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Gheorghe M Borja
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970, Hørsholm, Denmark.
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12
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Abstract
Prions (infectious proteins) cause fatal neurodegenerative diseases in mammals. In the yeast Saccharomyces cerevisiae, many toxic and lethal variants of the [PSI+] and [URE3] prions have been identified in laboratory strains, although some commonly studied variants do not seem to impair cell growth. Phylogenetic analysis has revealed four major clades of S. cerevisiae that share histories of two prion proteins and largely correspond to different ecological niches of yeast. The [PIN+] prion was most prevalent in commercialized niches, infrequent among wine/vineyard strains, and not observed in ancestral isolates. As previously reported, the [PSI+] and [URE3] prions are not found in any of these strains. Patterns of heterozygosity revealed genetic mosaicism and indicated extensive outcrossing among divergent strains in commercialized environments. In contrast, ancestral isolates were all homozygous and wine/vineyard strains were closely related to each other and largely homozygous. Cellular growth patterns were highly variable within and among clades, although ancestral isolates were the most efficient sporulators and domesticated strains showed greater tendencies for flocculation. [PIN+]-infected strains had a significantly higher likelihood of polyploidy, showed a higher propensity for flocculation compared to uninfected strains, and had higher sporulation efficiencies compared to domesticated, uninfected strains. Extensive phenotypic variability among strains from different environments suggests that S. cerevisiae is a niche generalist and that most wild strains are able to switch from asexual to sexual and from unicellular to multicellular growth in response to environmental conditions. Our data suggest that outbreeding and multicellular growth patterns adapted for domesticated environments are ecological risk factors for the [PIN+] prion in wild yeast.
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Abstract
Genetic engineering has been successfully applied to Saccharomyces cerevisiae laboratory strains for different purposes: extension of substrate range, improvement of productivity and yield, elimination of by-products, improvement of process performance and cellular properties, and extension of product range. The potential of genetically engineered yeasts for the massive production of biofuels as bioethanol and other nonfuel products from renewable resources as lignocellulosic biomass hydrolysates has been recognized. For such applications, robust industrial strains of S. cerevisiae have to be used. Here, some relevant genetic and genomic characteristics of industrial strains are discussed in relation to the problematic of the genetic engineering of such strains. General molecular tools applicable to the manipulation of S. cerevisiae industrial strains are presented and examples of genetically engineered industrial strains developed for the production of bioethanol from lignocellulosic biomass are given.
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Affiliation(s)
- Sylvie Le Borgne
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico.
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Salema-Oom M, De Sousa HR, Assunção M, Gonçalves P, Spencer-Martins I. Derepression of a baker's yeast strain for maltose utilization is associated with severe deregulation of HXT gene expression. J Appl Microbiol 2010; 110:364-74. [PMID: 21091593 DOI: 10.1111/j.1365-2672.2010.04895.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS We undertook to improve an industrial Saccharomyces cerevisiae strain by derepressing it for maltose utilization in the presence of high glucose concentrations. METHODS AND RESULTS A mutant was obtained from an industrial S. cerevisiae strain following random UV mutagenesis and selection on maltose/5-thioglucose medium. The mutant acquired the ability to utilize glucose simultaneously with maltose and possibly also sucrose and galactose. Aerobic sugar metabolism was still largely fermentative, but an enhanced respirative metabolism resulted in a 31% higher biomass yield on glucose. Kinetic characterization of glucose transport in the mutant revealed the predominance of the high-affinity component. Northern blot analysis showed that the mutant strain expresses only the HXT6/7 gene irrespective of the glucose concentration in the medium, indicating a severe deregulation in the induction/repression pathways modulating HXT gene expression. Interestingly, maltose-grown cells of the mutant display inverse diauxy in a glucose/maltose mixture, preferring maltose to glucose. CONCLUSION In the mutant here reported, the glucose transport step seems to be uncoupled from downstream regulation, because it seems to be unable to sense abundant glucose, via both repression and induction pathways. SIGNIFICANCE AND IMPACT OF THE STUDY We report here the isolation of a S. cerevisiae mutant with a novel derepressed phenotype, potentially interesting for the industrial fermentation of mixed sugar substrates.
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Affiliation(s)
- M Salema-Oom
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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15
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Bakalinsky AT, Snow R. Conversion of Wine Strains of Saccharomyces cerevisiae to Heterothallism. Appl Environ Microbiol 2010; 56:849-57. [PMID: 16348171 PMCID: PMC184311 DOI: 10.1128/aem.56.4.849-857.1990] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A general method to convert homothallic strains of the yeast Saccharomyces cerevisiae to heterothallism is described which is applicable to genetically well-behaved diploids, as well as to strains that sporulate poorly or produce few viable and mating-competent spores. The heterothallic (ho) allele was introduced into three widely used wine strains through spore x cell hybridization. The resultant hybrids were sporulated, and heterothallic segregants were isolated for use in successive backcrosses. Heterothallic progeny of opposite mating type and monosomic for chromosome III produced by sixth-backcross hybrids or their progeny were mated together to reconstruct heterothallic derivatives of the wine strain parents. A helpful prerequisite to the introduction of ho was genetic purification of the parental strains based on repeated cycles of sporulation, ascus dissection, and clonal selection. A positive selection to isolate laboratory-wine strain hybrids requiring no prior genetic alteration of the industrial strains, coupled with a partial selection to reduce the number of spore progeny needed to be screened to isolate heterothallic segregants of the proper genotype made the procedure valuable for genetically intractable strains. Trial grape juice fermentations indicated that introduction of ho had no deleterious effect on fermentation behavior.
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Affiliation(s)
- A T Bakalinsky
- Department of Food Science and Technology, Oregon State University, Corvallis, Oregon 97331-6602, and Genetics Department, University of California, Davis, California 95616
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Naumov GI, Naumova ES, Kondratieva VI. The use of hybridization in breeding of eukaryotic microorganisms. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406110147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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İzgü F, Altınbay D, Derinel Y. Immunization of the industrial fermentation starter culture strain of Saccharomyces cerevisiae to a contaminating killer toxin-producing Candida tropicalis. Food Microbiol 2004. [DOI: 10.1016/j.fm.2004.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Olasupo NA, Teniola OD, Okosun R, Omowaye A, Olatope SO, Scott-Emuakpor MB. Studies on an amylolytic strain of Saccharomyces cerevisiae isolated from yam tuber. J Basic Microbiol 1996; 36:283-8. [PMID: 8765084 DOI: 10.1002/jobm.3620360411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An amylolytic yeast strain identified as Saccharomyces cerevisiae was isolated from yam tuber. Studies on the effect of physical agents such as pH and temperature on the activity of the amylase showed that the optimum pH and temperature for the amylase produced by the S. cerevisiae were 5.0 and 60 degrees C, respectively. Heavy metal resistance study on the amylolytic yeast strain indicated different levels of resistance to copper (6.0 mM), zinc (3.0 mM) and manganese (15.0 mM) ions. The results are discussed in relation to the potential use of an amylolytic yeast in the brewing industry in Nigeria.
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Affiliation(s)
- N A Olasupo
- Department of Botany and Microbiology, Lagos State University Ojo, Apapa, Nigeria
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20
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Loray MA, Spencer JF, Spencer DM, de Figueroa LI. Hybrids obtained by protoplast fusion with a salt-tolerant yeast. JOURNAL OF INDUSTRIAL MICROBIOLOGY 1995; 14:508-13. [PMID: 7662292 DOI: 10.1007/bf01573966] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An industrial strain of Saccharomyces cerevisiae was fused with an osmotolerant yeast, Debaryomyces hansenii, to obtain hybrids having increased tolerance to elevated salt concentrations. The hybrids were intermediate to parent species in production of ethanol and polyols.
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Affiliation(s)
- M A Loray
- Universidad Nacional de Tucumán, Argentina
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21
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Nakagawa S, Ouchi K. Construction from a single parent of baker's yeast strains with high freeze tolerance and fermentative activity in both lean and sweet doughs. Appl Environ Microbiol 1994; 60:3499-502. [PMID: 7986027 PMCID: PMC201845 DOI: 10.1128/aem.60.10.3499-3502.1994] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
From a freeze-tolerant baker's yeast (Saccharomyces cerevisiae), 2,333 spore clones were obtained. To improve the leavening ability in lean dough of the parent strain, we selected 555 of the high-maltose-fermentative spore clones by using a method in which a soft agar solution containing maltose and bromocresol purple was overlaid on yeast colonies. By measuring the gassing power in the dough, we selected 66 spore clones with a good leavening ability in lean dough and a total of 694 hybrids were constructed by crossing them. Among these hybrids, we obtained 50 novel freeze-tolerant strains with good leavening ability in all lean, regular, and sweet doughs comparable to that of commercial baker's yeast. Hybrids with improved leavening ability or freeze tolerance compared with the parent yeast and commercial baker's yeasts were also obtained. These results suggest that hybridization between spore clones derived from a single parent strain is effective for improving the properties of baker's yeasts.
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Affiliation(s)
- S Nakagawa
- Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Japan
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22
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Katsuragi T, Kawabata N, Sakai T. Selection of hybrids from protoplast fusion of yeasts by double fluorescence labelling and automatic cell sorting. Lett Appl Microbiol 1994. [DOI: 10.1111/j.1472-765x.1994.tb00913.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Avram D, Petcu I, Radu M, Dan F, Stan R. Electrically induced protoplast fusion for ergosterol-producing yeast strain improvement. J Basic Microbiol 1992; 32:369-72. [PMID: 1487816 DOI: 10.1002/jobm.3620320604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Electrofusion was employed for hybrid construction in ergosterol-producing yeast strains. Some fusion products proved to be hybrid with respect to ergosterol content and to remain stable over several generations.
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Affiliation(s)
- D Avram
- Institute of Biology, Romanian Academy of Sciences, Bucharest
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26
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RANK GH, XIAO W. Alteration of Industrial Food and Beverage Yeasts by Recombinant DNA Technology. Ann N Y Acad Sci 1991. [DOI: 10.1111/j.1749-6632.1991.tb18574.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Abstract
A general procedure is described for determining the chromosomal constitution of industrial strains of Saccharomyces cerevisiae based on analysis of segregation frequencies for input markers among random spore progeny of industrial-laboratory strain hybrids. The multiply auxotrophic haploid testers used carried a dominant erythromycin-resistance marker, allowing hybrids to be selected in mass matings with spores produced by the wild-type industrial strains. Analysis of a number of independent crosses between the haploid testers and an unselected population of spores of each wine strain distinguished between disomic, trisomic and tetrasomic chromosomal complements in the parents. Possible explanations for a significant class of aberrant segregation frequencies are discussed. Results of the analysis indicate that UCD Enology 522 (Montrachet) is diploid and possibly trisomic for chromosome VII; 522X is diploid; UCD Enology 505 (California Champagne) is disomic for chromosome XVI, trisomic for chromosomes I, II, III, VI, VIII, IX, X, XII, XV, tetrasomic for chromosomes IV, XI, XIII, XIV and either trisomic or tetrasomic for chromosomes V and VII; and that UCD Enology 595 (Pasteur Champagne) is disomic for chromosomes I, II, III, IX, XVI, trisomic for chromosomes IV, VI, X, XII, XIV, XV, tetrasomic for chromosomes V, VIII, XI, XIII and either disomic or tetrasomic for chromosome VII.
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Affiliation(s)
- A T Bakalinsky
- Department of Food Science and Technology, Oregon State University, Corvallis 97331-6602
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28
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Witte V, Grossmann B, Emeis CC. Molecular probes for the detection of Kluyveromyces marxianus chromosomal DNA in electrophoretic karyotypes of intergeneric protoplast fusion products. Arch Microbiol 1989; 152:441-6. [PMID: 2573327 DOI: 10.1007/bf00446926] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Random genomic DNA fragments from Kluyveromyces marxianus were cloned in order to identify chromosomal bands in pulsed field electrophoresis patterns of intergneric hybrid strains which were obtained by protoplast fusion. Molecular hybridization data indicated that the K. marxianus parental strain might be triploid, and it showed strong chromosome length polymorphism. We analyzed the karyotype of two Saccharomyces cerevisiae/K. marxianus hybrid strains (St. 1.St.46) with our DNA probes and with a Ty1 specific probe. We found indications for recombinational events which lead to the formation of hybrid chromosomal DNA molecules.
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Affiliation(s)
- V Witte
- Institut für Mikrobiologie/Biologie IV, RWTH Aachen, Federal Republic of Germany
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29
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Oda Y, Ouchi K. Principal-Component Analysis of the Characteristics Desirable in Baker's Yeasts. Appl Environ Microbiol 1989; 55:1495-9. [PMID: 16347943 PMCID: PMC202892 DOI: 10.1128/aem.55.6.1495-1499.1989] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty-seven properties considered to be required for good bakery products were examined in 56 industrial and 2 laboratory yeast strains. The data obtained were applied to principal-component analysis, one of the multivariate statistical analyses. The first and second principal components together were extracted, and these accounted for 77.7% of the variance. The first principal component was interpreted as the glycolytic activity of yeast in dough, and the second one was interpreted as the balance of leavening abilities in sweet and flour doughs from the factor loadings. The scattergram on the two principal components was effective in grouping the 58 yeast strains used.
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Affiliation(s)
- Y Oda
- Tokyo Research Laboratories, Kyowa Hakko Kogyo Co., Ltd., Machida-shi, Tokyo 194, Japan
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30
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Collett MS. The development of biosynthetic vaccines. ADVANCES IN VETERINARY SCIENCE AND COMPARATIVE MEDICINE 1989; 33:109-72. [PMID: 2648773 DOI: 10.1016/b978-0-12-039233-9.50008-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M S Collett
- Molecular Genetics, Inc., Minnetonka, Minnesota
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Weber H, Barth G. Nonconventional yeasts: their genetics and biotechnological applications. Crit Rev Biotechnol 1988; 7:281-337. [PMID: 3064923 DOI: 10.3109/07388558809150535] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To date, more than 500 species of yeasts have been described. Most of the genetic and biochemical studies have, however, been carried out with Saccharomyces cerevisiae. Although a considerable amount of knowledge has been accumulated on fundamental processes and biotechnological applications of this industrially important yeast, the large variety of other yeast genera and species may offer various advantages for experimental study as well as for product formation in biotechnology. The genetic investigation of these so-called unconventional yeasts is poorly developed and information about corresponding data is dispersed. It is the aim of this review to summarize and discuss the main results of genetic studies and biotechnological applications of unconventional yeasts and to serve as a guide for scientists who wish to enter this field or are interested in only some aspects of these yeasts.
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Affiliation(s)
- H Weber
- Central Institute of Microbiology and Experimental Therapy, Academy of Science GDR, Jena
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36
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Baumann H, Bühler M, Fochem H, Hirsinger F, Zoebelein H, Falbe J. Natürliche Fette und Öle – nachwachsende Rohstoffe für die chemische Industrie. Angew Chem Int Ed Engl 1988. [DOI: 10.1002/ange.19881000107] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Gupthar AS. Construction of a series of Pichia stipitis strains with increased DNA contents. Curr Genet 1987. [DOI: 10.1007/bf00368063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Petersen JGL, Nilsson-Tillgren T, Kielland-Brandt MC, Gjermansenl C, Holmber S. Structural heterozygosis at genes IL V2 and IL V5 in Saccharomyces carlsbergensiss. Curr Genet 1987. [DOI: 10.1007/bf00436875] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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39
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Richard MS, van Broock MRG, Figueroa LIC. Restoration of respiratory competence in the yeastCandida utilis after somatic fusion withSaccharomyces cerevisiae. Curr Microbiol 1987. [DOI: 10.1007/bf01588181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Nayak K, Hirlekar M, Pandey N. Conditions for fat production by a recombinant strain of yeast. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0385-6380(87)90115-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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42
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Isolation of yeast with killer activity and its breeding with an industrial baking strain by protoplast fusion. Appl Microbiol Biotechnol 1986. [DOI: 10.1007/bf00294599] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Reymond P, Fevre M. Recombination following protoplast fusion of Penicillium strains used in the dairy industry. Enzyme Microb Technol 1986. [DOI: 10.1016/0141-0229(86)90009-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Alcoholic fermentation of starch containing media using yeast protoplast fusion products. Biotechnol Lett 1985. [DOI: 10.1007/bf01025566] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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de Figueroa LIC, de van Broock MRG. Spheroplast fusion of a brewing yeast strain with Saccharomyces diastaticus. Appl Microbiol Biotechnol 1985. [DOI: 10.1007/bf00295123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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46
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47
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48
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Interspecific protoplast fusion of the Baker's yeast Saccharomyces cerevisiae and Saccharomyces diastaticus. Biotechnol Lett 1984. [DOI: 10.1007/bf00140049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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