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Dong Z, Yang S, Dong X, Yang Y, Yan X, Su J, Tang C, Yao L, Kan Y. Characteristics, Protein Engineering, Heterologous Production, and Industrial Applications of Microbial Isoamylases. STARCH-STARKE 2021. [DOI: 10.1002/star.202100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
| | - Shuangshuang Yang
- College of Physical Education Nanyang Normal University Nanyang 473061 China
| | - Xiaoxiao Dong
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
| | - Yongna Yang
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
| | - Xueting Yan
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
| | - Jiejie Su
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
| | - Cunduo Tang
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
- China‐UK‐NYNU‐RRes Joint Laboratory of Insect Biology Henan Key Laboratory of Insect Biology in Funiu Mountain Nanyang Normal University Nanyang Henan 473061 China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
- Henan Key Laboratory of Ecological Security for Water Region of Mid‐line of South‐to‐North Nanyang Normal University Nanyang 473061 China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insect Bio‐reactor College of Life Science and Agricultural Engineering Nanyang Normal University Nanyang 473061 China
- China‐UK‐NYNU‐RRes Joint Laboratory of Insect Biology Henan Key Laboratory of Insect Biology in Funiu Mountain Nanyang Normal University Nanyang Henan 473061 China
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Doughty TW, Domenzain I, Millan-Oropeza A, Montini N, de Groot PA, Pereira R, Nielsen J, Henry C, Daran JMG, Siewers V, Morrissey JP. Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. Nat Commun 2020; 11:2144. [PMID: 32358542 PMCID: PMC7195364 DOI: 10.1038/s41467-020-16073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 04/09/2020] [Indexed: 11/20/2022] Open
Abstract
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology. Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.
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Affiliation(s)
- Tyler W Doughty
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Aaron Millan-Oropeza
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Noemi Montini
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland
| | - Philip A de Groot
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Rui Pereira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland.
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3
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A review of integration strategies of lignocelluloses and other wastes in 1st generation bioethanol processes. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.09.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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4
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Lee JY, Im YK, Ko HM, Chin JE, Kim IC, Lee HB, Bai S. Direct utilization of purple sweet potato by sake yeasts to produce an anthocyanin-rich alcoholic beverage. Biotechnol Lett 2015; 37:1439-45. [DOI: 10.1007/s10529-015-1811-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
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Abstract
This article surveys methods for the enzymatic conversion of starch, involving hydrolases and nonhydrolyzing enzymes, as well as the role of microorganisms producing such enzymes. The sources of the most common enzymes are listed. These starch conversions are also presented in relation to their applications in the food, pharmaceutical, pulp, textile, and other branches of industry. Some sections are devoted to the fermentation of starch to ethanol and other products, and to the production of cyclodextrins, along with the properties of these products. Light is also shed on the enzymes involved in the digestion of starch in human and animal organisms. Enzymatic processes acting on starch are useful in structural studies of the substrates and in understanding the characteristics of digesting enzymes. One section presents the application of enzymes to these problems. The information that is included covers the period from the early 19th century up to 2009.
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van Zyl WH, Bloom M, Viktor MJ. Engineering yeasts for raw starch conversion. Appl Microbiol Biotechnol 2012; 95:1377-88. [PMID: 22797599 DOI: 10.1007/s00253-012-4248-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 11/29/2022]
Abstract
Next to cellulose, starch is the most abundant hexose polymer in plants, an import food and feed source and a preferred substrate for the production of many industrial products. Efficient starch hydrolysis requires the activities of both α-1,4 and α-1,6-debranching hydrolases, such as endo-amylases, exo-amylases, debranching enzymes, and transferases. Although amylases are widely distributed in nature, only about 10 % of amylolytic enzymes are able to hydrolyse raw or unmodified starch, with a combination of α-amylases and glucoamylases as minimum requirement for the complete hydrolysis of raw starch. The cost-effective conversion of raw starch for the production of biofuels and other important by-products requires the expression of starch-hydrolysing enzymes in a fermenting yeast strain to achieve liquefaction, hydrolysis, and fermentation (Consolidated Bioprocessing, CBP) by a single organism. The status of engineering amylolytic activities into Saccharomyces cerevisiae as fermentative host is highlighted and progress as well as challenges towards a true CBP organism for raw starch is discussed. Conversion of raw starch by yeast secreting or displaying α-amylases and glucoamylases on their surface has been demonstrated, although not at high starch loading or conversion rates that will be economically viable on industrial scale. Once efficient conversion of raw starch can be demonstrated at commercial level, engineering of yeast to utilize alternative substrates and produce alternative chemicals as part of a sustainable biorefinery can be pursued to ensure the rightful place of starch converting yeasts in the envisaged bio-economy of the future.
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Affiliation(s)
- W H van Zyl
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa.
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Reduction of PDC1 expression in S. cerevisiae with xylose isomerase on xylose medium. Bioprocess Biosyst Eng 2011; 35:183-9. [PMID: 21989637 DOI: 10.1007/s00449-011-0638-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
Abstract
Ethanol production using hemicelluloses has recently become a focus of many researchers. In order to promote D: -xylose fermentation, we cloned the bacterial xylA gene encoding for xylose isomerase with 434 amino acid residues from Agrobacterium tumefaciens, and successfully expressed it in Saccharomyces cerevisiae, a non-xylose assimilating yeast. The recombinant strain S. cerevisiae W303-1A/pAGROXI successfully colonized a minimal medium containing D: -xylose as a sole carbon source and was capable of growth in minimal medium containing 2% xylose via aerobic shake cultivation. Although the recombinant strain assimilates D: -xylose, its ethanol productivity is quite low during fermentation with D: -xylose alone. In order to ascertain the key enzyme in ethanol production from D: -xylose, we checked the expression levels of the gene clusters involved in the xylose assimilating pathway. Among the genes classified into four groups by their expression patterns, the mRNA level of pyruvate decarboxylase (PDC1) was reduced dramatically in xylose media. This reduced expression of PDC1, an enzyme which converts pyruvate to acetaldehyde, may cause low ethanol productivity in xylose medium. Thus, the enhancement of PDC1 gene expression may provide us with a useful tool for the fermentation of ethanol from hemicellulose.
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Raw starch fermentation to ethanol by an industrial distiller’s yeast strain of Saccharomyces cerevisiae expressing glucoamylase and α-amylase genes. Biotechnol Lett 2011; 33:1643-8. [DOI: 10.1007/s10529-011-0613-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
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9
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Heterologous expression and efficient ethanol production of a Rhizopus glucoamylase gene in Saccharomyces cerevisiae. Mol Biol Rep 2010; 38:59-64. [DOI: 10.1007/s11033-010-0077-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 03/05/2010] [Indexed: 10/19/2022]
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10
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Construction of a direct starch-fermenting industrial strain of Saccharomyces cerevisiae producing glucoamylase, α-amylase and debranching enzyme. Biotechnol Lett 2010; 32:713-9. [DOI: 10.1007/s10529-010-0212-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/13/2010] [Accepted: 01/14/2010] [Indexed: 11/26/2022]
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Kumar P, Satyanarayana T. Microbial glucoamylases: characteristics and applications. Crit Rev Biotechnol 2009; 29:225-55. [DOI: 10.1080/07388550903136076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Efficient production of ethanol from raw starch by a mated diploid Saccharomyces cerevisiae with integrated α-amylase and glucoamylase genes. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.01.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Development of a serial bioreactor system for direct ethanol production from starch usingAspergillus niger andSaccharomyces cerevisiae. BIOTECHNOL BIOPROC E 2007. [DOI: 10.1007/bf02931356] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ghang DM, Yu L, Lim MH, Ko HM, Im SY, Lee HB, Bai S. Efficient one-step starch utilization by industrial strains of Saccharomyces cerevisiae expressing the glucoamylase and α-amylase genes from Debaryomyces occidentalis. Biotechnol Lett 2007; 29:1203-8. [PMID: 17505783 DOI: 10.1007/s10529-007-9371-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Accepted: 03/08/2007] [Indexed: 11/30/2022]
Abstract
Amylolytic industrial polyploid strains of Saccharomyces cerevisiae (ATCC 4126, ATCC 9763 and ATCC 24858) expressing a glucoamylase gene (GAM1) or an alpha-amylase gene (AMY) from Debaryomyces occidentalis were developed. The glucoamylase activity of S. cerevisiae ATCC 9763 expressing the GAM1 gene was 3.7-times higher than that of D. occidentalis. On the other hand, alpha-amylase activity in the corresponding strain expressing the D. occidentalis AMY gene increased 10-times relative to D. occidentalis. These two recombinant yeast strains expressing the GAM1 gene and AMY gene, respectively were cultured simultaneously to produce both glucoamylase and alpha-amylase for efficient one-step utilization of starch. Growth, substrate utilization and enzyme activity of these strains are described.
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Affiliation(s)
- Dong-Myeong Ghang
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, 500-757, Korea
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Toksoy Oner E. Optimization of ethanol production from starch by an amylolytic nuclear petite Saccharomyces cerevisiae strain. Yeast 2006; 23:849-56. [PMID: 17001624 DOI: 10.1002/yea.1399] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Ethanol fermentation characteristics of the 100% respiratory-deficient nuclear petite amylolytic Saccharomyces cerevisiae NPB-G strain was investigated in both shake-flask and controlled bioreactor cultivation conditions, and comparison with the earlier reported results revealed 54.6% increase in ethanol yield. Efforts to improve the starch utilization rate by increasing the selection pressure or supplying the fermentation medium with glucose did not prevent the observed decrease in time-dependent amylolytic activity. Response surface methodology (RSM) was then used as a statistical tool to optimize the initial yeast extract and starch contents of the medium, which resulted in a substantial increase in the stability of the expression plasmid in both the respiratory-deficient NPB-G and the parental respiratory-sufficient WTPB-G strains, with concomitant improvement in their amylolytic potentials. High ethanol yields on substrate values of the bioreactor cultures, which were very close to the theoretical yield, indicated that the amylolytic respiratory-deficient NPB-G strain was effective in the direct fermentation of starch into ethanol.
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Affiliation(s)
- Ebru Toksoy Oner
- Department of Chemical Engineering, Marmara University, Goztepe 34722, Istanbul, Turkey.
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Toksoy Oner E, Oliver SG, Kirdar B. Production of ethanol from starch by respiration-deficient recombinant Saccharomyces cerevisiae. Appl Environ Microbiol 2005; 71:6443-5. [PMID: 16204577 PMCID: PMC1266001 DOI: 10.1128/aem.71.10.6443-6445.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 100%-respiration-deficient nuclear petite amylolytic Saccharomyces cerevisiae NPB-G strain was generated, and its employment for direct fermentation of starch into ethanol was investigated. In a comparison of ethanol fermentation performances with the parental respiration-sufficient WTPB-G strain, the NPB-G strain showed an increase of ca. 48% in both ethanol yield and ethanol productivity.
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Affiliation(s)
- Ebru Toksoy Oner
- Marmara University, Faculty of Engineering, Department of Chemical Engineering, Goztepe 34722 Istanbul, Turkey.
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Khaw TS, Katakura Y, Koh J, Kondo A, Ueda M, Shioya S. Evaluation of performance of different surface-engineered yeast strains for direct ethanol production from raw starch. Appl Microbiol Biotechnol 2005; 70:573-9. [PMID: 16133340 DOI: 10.1007/s00253-005-0101-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 07/11/2005] [Accepted: 07/13/2005] [Indexed: 10/25/2022]
Abstract
Four types of cell-surface-engineered yeast Saccharomyces cerevisiae displaying glucoamylase, namely, systems A, B, C, and D, were constructed to evaluate their performance in direct ethanol fermentation from raw corn starch. Systems A and B were glucoamylase-displaying nonflocculent yeast (YF237) types that secrete alpha-amylase into the culture medium and codisplay alpha-amylase on the cell surface, respectively. Systems C and D were flocculent yeast counterparts (YF207) for systems A and B, respectively. In batch fermentations, the specific ethanol production rates of systems A, B, C, and D were 0.18, 0.06, 0.06, and 0.04 g (g cell)(-1) h(-1), respectively. In repeated fermentations, the specific ethanol production rate of system A decreased with the number of repetitions, whereas, that of system B was maintained. In all systems, the rate-limiting step was the conversion of starch to oligosaccharide because oligosaccharide and glucose were not accumulated throughout the fermentations.
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Affiliation(s)
- Teik Seong Khaw
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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MarıÌn D, Jiménez A, Fernández Lobato M. Construction of an efficient amylolytic industrial yeast strain containing DNA exclusively derived from yeast. FEMS Microbiol Lett 2001. [DOI: 10.1111/j.1574-6968.2001.tb10764.x] [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] Open
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Juretzek T, Le Dall M, Mauersberger S, Gaillardin C, Barth G, Nicaud J. Vectors for gene expression and amplification in the yeast Yarrowia lipolytica. Yeast 2001; 18:97-113. [PMID: 11169753 DOI: 10.1002/1097-0061(20010130)18:2<97::aid-yea652>3.0.co;2-u] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
New vector systems were developed for gene expression in Y. lipolytica. These plasmids contain: (a) as integration target sequences, either a rDNA region or the long terminal repeat zeta of the Y. lipolytica retrotransposon Ylt1; (b) the YlURA3 gene as selection marker for Y. lipolytica, either as the non-defective ura3d1 allele for single integration or the promotor truncated ura3d4 allele for multiple integration; (c) the inducible ICL1 or XPR2 promoters for gene expression; and (d) unique restriction sites for gene insertion. Multiple plasmid integration occurred as inserted tandem-repeats, which are present at 3-39 copies per cell. A correlation between gene copy number and the expressed enzyme activity was demonstrated with Escherichia coli lacZ as reporter gene under the control of the regulated ICL1 promoter. Increases in copy numbers from 5 to 13 for the lacZ expression cassettes resulted in an up to 10-11-fold linear increase of the beta-galactosidase activity in multicopy transformants during their growth on ethanol or glucose, compared with the low-copy replicative plasmid transformants (1.6 plasmid copies). These new tools will enhance the interest in Y. lipolytica as an alternative host for heterologous protein production.
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Affiliation(s)
- T Juretzek
- Institut für Mikrobiologie, Technische Universität Dresden, Mommsenstrasse 13, D-01062 Dresden, Germany
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