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Lamers D, van Biezen N, Martens D, Peters L, van de Zilver E, Jacobs-van Dreumel N, Wijffels RH, Lokman C. Selection of oleaginous yeasts for fatty acid production. BMC Biotechnol 2016; 16:45. [PMID: 27233820 PMCID: PMC4884388 DOI: 10.1186/s12896-016-0276-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 05/23/2016] [Indexed: 12/03/2022] Open
Abstract
Background Oleaginous yeast species are an alternative for the production of lipids or triacylglycerides (TAGs). These yeasts are usually non-pathogenic and able to store TAGs ranging from 20 % to 70 % of their cell mass depending on culture conditions. TAGs originating from oleaginous yeasts can be used as the so-called second generation biofuels, which are based on non-food competing “waste carbon sources”. Results In this study the selection of potentially new interesting oleaginous yeast strains is described. Important selection criteria were: a broad maximum temperature and pH range for growth (robustness of the strain), a broad spectrum of carbon sources that can be metabolized (preferably including C-5 sugars), a high total fatty acid content in combination with a low glycogen content and genetic accessibility. Conclusions Based on these selection criteria, among 24 screened species, Schwanniomyces occidentalis (Debaromyces occidentalis) CBS2864 was selected as a promising strain for the production of high amounts of lipids. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0276-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dennis Lamers
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands. .,Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands.
| | - Nick van Biezen
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | - Dirk Martens
- Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands
| | - Linda Peters
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | - Eric van de Zilver
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
| | | | - René H Wijffels
- Bioprocess Engineering, Wageningen University and Research Centre, P.O. Box 8129, , 6700 EV, Wageningen, The Netherlands.,University of Nordland, Faculty of Biosciences and Aquaculture, N-8049, Bodø, Norway
| | - Christien Lokman
- HAN BioCentre, University of Applied Sciences, P.O. Box 6960, , 6503 GL, Nijmegen, The Netherlands
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Kregiel D, Berlowska J, Ambroziak W. Growth and metabolic activity of conventional and non-conventional yeasts immobilized in foamed alginate. Enzyme Microb Technol 2013; 53:229-34. [PMID: 23931687 DOI: 10.1016/j.enzmictec.2013.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/31/2013] [Accepted: 05/31/2013] [Indexed: 11/28/2022]
Abstract
The aim of this research was to study how the cell immobilization technique of forming foamed alginate gels influences the growth, vitality and metabolic activity of different yeasts. Two distinct strains were used, namely conventional yeast (exemplified by Saccharomyces cerevisiae) and a non-conventional strain (exemplified by Debaryomyces occidentalis). The encapsulation of the yeast cells was performed by the traditional process of droplet formation, but from a foamed alginate solution. The activities of two key enzymes, succinate dehydrogenase and pyruvate decarboxylase, together with the ATP content were measured in both the free and immobilized cells. This novel method of yeast cell entrapment had some notable effects. The number of living immobilized cells reached the level of 10(6)-10(7) per single bead, and was stable during the fermentation process. Reductions in both enzyme activity and ATP content were observed in all immobilized yeasts. However, S. cerevisiae showed higher levels of ATP and enzymatic activity than D. occidentalis. Fermentation trials with immobilized repitching cells showed that the tested yeasts adapted to the specific conditions. Nevertheless, the mechanical endurance of the carriers and the internal structure of the gel need to be improved to enable broad applications of alginate gels in industrial fermentation processes, especially with conventional yeasts. This is one of the few papers and patents that describe the technique of cell immobilization in foamed alginate and shows the fermentative capacities and activities of key enzymes in immobilized yeast cells.
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Affiliation(s)
- Dorota Kregiel
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Poland.
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Kretzschmar A, Otto C, Holz M, Werner S, Hübner L, Barth G. Increased homologous integration frequency in Yarrowia lipolytica strains defective in non-homologous end-joining. Curr Genet 2013; 59:63-72. [PMID: 23423527 DOI: 10.1007/s00294-013-0389-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 01/31/2013] [Accepted: 02/08/2013] [Indexed: 01/12/2023]
Abstract
The ascomycetous yeast Yarrowia lipolytica has been established as model system for studies of several research topics as well as for biotechnological processes in the last two decades. However, frequency of heterologous recombination is high in this yeast species, and so knockouts of genes are laborious to achieve. Therefore, the aim of this study was to check whether a reduction of non-homologous end-joining (NHEJ) of double strand breaks (DSB) results in a strong increase of proportion of homologous recombinants. The Ku70-Ku80 heterodimer is known as an essential protein complex of the NHEJ. We show that deletion of YlKU70 and/or YlKU80 results in an increase of the rate of transformants with homologous recombination (HR) up to 85 % in each case. However, it never reaches near 100 % of HR in any case as described for some other yeast. Furthermore, we demonstrated that growth of Δylku strains was similar to that of the wild-type strain. In addition, no differences were detected between the Δylku strains and the parent strain in respect to sensitivity to the mutagenic agent EMS as well as to the antibiotics hygromycin, bleomycin and nourseothricin. However, Δylku70 and Δylku80 strain showed a slightly higher sensitivity against UV rays. Thus, the new constructed Δylku strains are attractive recipient strains for homologous integration of DNA fragments and a valuable tool for directed knockouts of genes. Nevertheless, our data suggest the existence of another system of non-homologous recombination what may be subject of further investigation.
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Affiliation(s)
- Anne Kretzschmar
- Laboratoriumsmedizin Köln, Dres. Med. Wisplinghoff and Kollegen, Classen-Kappelmann-Straße 24, 50931 Köln, Germany
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Assessment of Schwanniomyces occidentalis as a host for protein production using the wide-range Xplor2 expression platform. Appl Microbiol Biotechnol 2012; 97:4443-56. [PMID: 23129184 DOI: 10.1007/s00253-012-4527-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/15/2012] [Accepted: 10/18/2012] [Indexed: 10/27/2022]
Abstract
The wide-range transformation/expression platform, Xplor2, was employed for the assessment of Schwanniomyces occidentalis as a potential producer of the recombinant proteins human IFNα2a (IFNα2a) and S. occidentalis fructofuranosidase (SFfase), and its efficiency was compared to that of Arxula adeninivorans. ADE2 and URA3 genes from both yeast species were isolated, characterized and used as selection markers in combination with the IFNα2a and SFfase expression modules, which used the strong constitutive A. adeninivorans-derived TEF1 promoter. Yeast rDNA integrative expression cassettes and yeast integrative expression cassettes equipped with a selection marker and expression modules were transformed into auxotrophic S. occidentalis and A. adeninivorans strains and a quantitative comparison of the expression efficiency was made. Whilst IFNα2a was mainly accumulated extracellularly (>95 %) in A. adeninivorans, extracellular SFfase (>90 %) was detected in both yeast species. The DNA composition of the selection marker modules and expression modules, especially their open reading frame codon usage, affects auxotrophy recovery as well as protein expression. Auxotrophy recovery was only achieved with selection marker modules of the homologous gene donor yeast. The concentration of recombinant IFNα2a was fivefold higher in A. adeninivorans (1 mg L(-1)), whereas S. occidentalis accumulated 1.5- to 2-fold more SFfase (0.5 Units ml(-1)). These results demonstrate the extension of the use of the wide-range expression platform Xplor2 to another yeast species of biotechnological interest.
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Álvaro-Benito M, Polo A, González B, Fernández-Lobato M, Sanz-Aparicio J. Structural and kinetic analysis of Schwanniomyces occidentalis invertase reveals a new oligomerization pattern and the role of its supplementary domain in substrate binding. J Biol Chem 2010; 285:13930-41. [PMID: 20181943 PMCID: PMC2859555 DOI: 10.1074/jbc.m109.095430] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/09/2010] [Indexed: 11/06/2022] Open
Abstract
Schwanniomyces occidentalis invertase is an extracellular enzyme that hydrolyzes sucrose and releases beta-fructose from various oligosaccharides and essential storage fructan polymers such as inulin. We report here the three-dimensional structure of Sw. occidentalis invertase at 2.9 A resolution and its complex with fructose at 1.9 A resolution. The monomer presents a bimodular arrangement common to other GH32 enzymes, with an N-terminal 5-fold beta-propeller catalytic domain and a C-terminal beta-sandwich domain for which the function has been unknown until now. However, the dimeric nature of Sw. occidentalis invertase reveals a unique active site cleft shaped by both subunits that may be representative of other yeast enzymes reported to be multimeric. Binding of the tetrasaccharide nystose and the polymer inulin was explored by docking analysis, which suggested that medium size and long substrates are recognized by residues from both subunits. The identified residues were mutated, and the enzymatic activity of the mutants against sucrose, nystose, and inulin were investigated by kinetic analysis. The replacements that showed the largest effect on catalytic efficiency were Q228V, a residue putatively involved in nystose and inulin binding, and S281I, involved in a polar link at the dimer interface. Moreover, a significant decrease in catalytic efficiency against inulin was observed in the mutants Q435A and Y462A, both located in the beta-sandwich domain of the second monomer. This highlights the essential function that oligomerization plays in substrate specificity and assigns, for the first time, a direct catalytic role to the supplementary domain of a GH32 enzyme.
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Affiliation(s)
- Miguel Álvaro-Benito
- From the Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular, Consejo Superior de Investigaciones Cientificas-Universidad Autónoma de Madrid (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain and
| | - Aitana Polo
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, Serrano 119, 28006 Madrid, Spain
| | - Beatriz González
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, Serrano 119, 28006 Madrid, Spain
| | - María Fernández-Lobato
- From the Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular, Consejo Superior de Investigaciones Cientificas-Universidad Autónoma de Madrid (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain and
| | - Julia Sanz-Aparicio
- the Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, Serrano 119, 28006 Madrid, Spain
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Suthar DH, Chattoo BB. Expression of Vitreoscilla hemoglobin enhances growth and levels of alpha-amylase in Schwanniomyces occidentalis. Appl Microbiol Biotechnol 2006; 72:94-102. [PMID: 16642333 DOI: 10.1007/s00253-005-0237-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 09/26/2005] [Accepted: 11/01/2005] [Indexed: 11/26/2022]
Abstract
A metabolic engineering approach was exploited to improve growth and protein secretion in the non-conventional yeast, Schwanniomyces occidentalis. Vitreoscilla hemoglobin (VHb) gene was expressed in S. occidentalis under the control of the native alpha-amylase (AMY1) promoter. Expression of VHb was confirmed by reverse transcriptase polymerase chain reaction and Western blot hybridization analysis. Effect of VHb on growth and protein secretion was studied in synthetic medium under both limiting and non-limiting dissolved oxygen conditions. Under both conditions, VHb-expressing cells exhibited higher oxygen uptake and higher specific growth rates. Levels of extracellular alpha-amylase were also elevated in the VHb-transformed strain relative to the control strain. In amylase production medium, VHb-expressing cells showed 3-fold elevated levels of alpha-amylase and a 31% increase in the total secreted protein under oxygen-limiting environment. VHb was found to localize in the mitochondria in addition to its cytoplasmic location. Inhibition of respiration by antimycin A resulted in the loss of the growth-enhancing effects of VHb. A 2.5-fold increase in the cytochrome c oxidase (COX) activity was observed in VHb-expressing cells relative to the control. In addition to this, exogenously added VHb in the assay mixture augmented COX activity.
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Affiliation(s)
- Devesh H Suthar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The M.S. University of Baroda, Vadodara, 390 002, India
| | - Bharat B Chattoo
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The M.S. University of Baroda, Vadodara, 390 002, India.
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Klinner U, Schäfer B. Genetic aspects of targeted insertion mutagenesis in yeasts. FEMS Microbiol Rev 2004; 28:201-23. [PMID: 15109785 DOI: 10.1016/j.femsre.2003.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2003] [Revised: 08/20/2003] [Accepted: 10/02/2003] [Indexed: 11/16/2022] Open
Abstract
Targeted insertion mutagenesis is a main molecular tool of yeast science initially applied in Saccharomyces cerevisiae. The method was extended to fission yeast Schizosaccharomyces pombe and to "non-conventional" yeast species, which show specific properties of special interest to both basic and applied research. Consequently, the behaviour of such non-Saccharomyces yeasts is reviewed against the background of the knowledge of targeted insertion mutagenesis in S. cerevisiae. Data of homologous integration efficiencies obtained with circular, ends-in or ends-out vectors in several yeasts are compared. We follow details of targeted insertion mutagenesis in order to recognize possible rate-limiting steps. The route of the vector to the target and possible mechanisms of its integration into chromosomal genes are considered. Specific features of some yeast species are discussed. In addition, similar approaches based on homologous recombination that have been established for the mitochondrial genome of S. cerevisiae are described.
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Affiliation(s)
- U Klinner
- RWTH Aachen, Institut für Biologie IV (Mikrobiologie und Genetik), Worringer Weg, D-52056 Aachen, Germany.
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Janatova I, Costaglioli P, Wesche J, Masson JM, Meilhoc E. Development of a reporter system for the yeast Schwanniomyces occidentalis: influence of DNA composition and codon usage. Yeast 2003; 20:687-701. [PMID: 12794930 DOI: 10.1002/yea.997] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In this paper we report on searching for suitable reporters to monitor gene expression and protein secretion in the amylolytic yeast Schwanniomyces occidentalis. Several potential reporter and marker genes, formerly shown to be functional in other yeasts, were cloned downstream from the homologous invertase gene (INV) promoter and their activity was followed in conditions of repression and derepression of the INV promoter. However, neither beta-glucuronidase nor beta-lactamase nor phleomycin resistance-conferring gene, all originating from E. coli, were expressed in S. occidentalis cells to such a level to allow for monitoring of their activity. All the reporter genes tested have a higher percentage of GC (47-62%) in their DNA compared to the DNA composition of S. occidentalis genes that are more AT-rich (36% GC). The codon usage of all the reporter genes also varies from that of 16 so far sequenced S. occidentalis genes. This suggests that an appropriate composition of DNA and a codon usage similar to S. occidentalis genes might be very important parameters for an efficient expression of a heterologous gene in Schwanniomyces occidentalis. Indeed, two genes originating from Staphylococcus aureus, with an AT-content in their DNA similar to that of S. occidentalis, were functionally expressed in S. occidentalis cells. Both a phleomycin resistance-conferring gene and a chloramphenicol acetyltransferase-encoding gene thus represent suitable reporters of gene expression and protein secretion in S. occidentalis. Additionally, we show in this work that the transcription-regulating region and the signal peptide sequence of the S. occidentalis invertase gene were efficient to direct gene expression and subsequent protein secretion in Saccharomyces cerevisiae.
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Affiliation(s)
- Ivana Janatova
- Laboratory of Cell Reproduction, Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
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Carmona TA, Barrado P, Jiménez A, Fernández Lobato M. Molecular and functional analysis of a MIG1 homologue from the yeast Schwanniomyces occidentalis. Yeast 2002; 19:459-65. [PMID: 11921094 DOI: 10.1002/yea.846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A putative glucose repressor MIG1-homologue (SoMIG1) was isolated from the amylolytic yeast Schwanniomyces occidentalis. Degenerate primers were designed from the conserved zinc finger regions of Mig1 and CreA proteins from different organisms. PCR using these primers and S. occidentalis genomic DNA as template yielded a single 128 bp product. This fragment was used as a DNA probe to screen a S. occidentalis genomic library. Analysis of the positive clones led to the isolation by PCR of a DNA fragment, which contained an open reading frame (ORF) that would encode a 458 amino acid polypeptide. The DNA binding and effector domains of this putative protein showed an identity of 71% and 15%, respectively, to those of the Mig1 protein from Saccharomyces cerevisiae. The SoMIG1 gene complemented a mig1 mutant of this yeast, which suggests that in S. occidentalis SoMIG1 is a glucose repressor. The Accession No. is AJ417892.
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Affiliation(s)
- Teresa A Carmona
- Centro de Biología Molecular 'Severo Ochoa', Departamento de Biología Molecular (CSIC-UAM), Universidad Autónoma Madrid, Cantoblanco, 28049 Madrid, Spain
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Carmona TA, Jiménez A, Fernández Lobato M. Analysis of the Schwanniomyces occidentalis SWA2 gene promoter in Saccharomyces cerevisiae. FEMS Microbiol Lett 2002; 207:69-73. [PMID: 11886753 DOI: 10.1111/j.1574-6968.2002.tb11030.x] [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: 11/26/2022] Open
Abstract
The effect of different carbon sources on the expression in Saccharomyces cerevisiae of the SWA2 alpha-amylase gene from Schwanniomyces occidentalis was studied from constructs containing its 5' region (-223 to +15), which were fused in-frame to the lacZ gene coding sequence. Maximal expression was achieved with the non-fermentable substrates ethanol and/or glycerol, whereas lower levels were found with maltose or galactose. In contrast, glucose repressed it, even in the presence of any of these other carbon sources. Deletion analyses of the -233 to -85 SWA2 promoter region permitted the identification of two fragments involved in both glucose repression and ethanol activation. A possible region required for cAMP regulation was localised. The SWA2 promoter contains a MIG1-binding GC box whose deletion caused a five-fold increase in the glucose-repressed reporter expression. Despite this, expression of the SWA2 promoter was not MIG1-dependent.
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Affiliation(s)
- T A Carmona
- Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular (CSIC-UAM), Universidad Autónoma Madrid, Cantoblanco, 28049 Madrid, Spain
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Chen WB, Han YF, Jong SC, Chang SC. Isolation, purification, and characterization of a killer protein from Schwanniomyces occidentalis. Appl Environ Microbiol 2000; 66:5348-52. [PMID: 11097913 PMCID: PMC92467 DOI: 10.1128/aem.66.12.5348-5352.2000] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Schwanniomyces occidentalis produces a killer toxin lethal to sensitive strains of Saccharomyces cerevisiae. Killer activity is lost after pepsin and papain treatment, suggesting that the toxin is a protein. We purified the killer protein and found that it was composed of two subunits with molecular masses of approximately 7.4 and 4.9 kDa, respectively, but was not detectable with periodic acid-Schiff staining. A BLAST search revealed that residues 3 to 14 of the 4.9-kDa subunit had 75% identity and 83% similarity with killer toxin K2 from S. cerevisiae at positions 271 to 283. Maximum killer activity was between pH 4.2 and 4.8. The protein was stable between pH 2.0 and 5.0 and inactivated at temperatures above 40 degrees C. The killer protein was chromosomally encoded. Mannan, but not beta-glucan or laminarin, prevented sensitive yeast cells from being killed by the killer protein, suggesting that mannan may bind to the killer protein. Identification and characterization of a killer strain of S. occidentalis may help reduce the risk of contamination by undesirable yeast strains during commercial fermentations.
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Affiliation(s)
- W B Chen
- Department of Biochemistry, National Yang-Ming University, Taipei 112, Taiwan, Republic of China
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