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Altammar KA, Ling JG, Al-Bajalan HM, Chin IS, Mackeen MM, Mahadi NM, Murad AMA, Bakar FDA. Characterization of AnCUT3, a plastic-degrading paucimannose cutinase from Aspergillus niger expressed in Pichia pastoris. Int J Biol Macromol 2022; 222:2353-2367. [DOI: 10.1016/j.ijbiomac.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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2
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Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints. Nat Commun 2022; 13:2969. [PMID: 35624178 PMCID: PMC9142503 DOI: 10.1038/s41467-022-30689-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/12/2022] [Indexed: 01/20/2023] Open
Abstract
Eukaryotic cells are used as cell factories to produce and secrete multitudes of recombinant pharmaceutical proteins, including several of the current top-selling drugs. Due to the essential role and complexity of the secretory pathway, improvement for recombinant protein production through metabolic engineering has traditionally been relatively ad-hoc; and a more systematic approach is required to generate novel design principles. Here, we present the proteome-constrained genome-scale protein secretory model of yeast Saccharomyces cerevisiae (pcSecYeast), which enables us to simulate and explain phenotypes caused by limited secretory capacity. We further apply the pcSecYeast model to predict overexpression targets for the production of several recombinant proteins. We experimentally validate many of the predicted targets for α-amylase production to demonstrate pcSecYeast application as a computational tool in guiding yeast engineering and improving recombinant protein production. Due to the complexity of the protein secretory pathway, strategy suitable for the production of a certain recombination protein cannot be generalized. Here, the authors construct a proteome-constrained genome-scale protein secretory model for yeast and show its application in the production of different misfolded or recombinant proteins.
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Peebo K, Neubauer P. Application of Continuous Culture Methods to Recombinant Protein Production in Microorganisms. Microorganisms 2018; 6:E56. [PMID: 29933583 PMCID: PMC6164559 DOI: 10.3390/microorganisms6030056] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/28/2018] [Accepted: 06/19/2018] [Indexed: 11/17/2022] Open
Abstract
Depending on the environmental conditions, cells adapt their metabolism and specific growth rate. Rearrangements occur on many different levels such as macromolecular composition, gene and protein expression, morphology and metabolic flux patterns. As the interplay of these processes also determines the output of a recombinant protein producing system, having control over specific growth rate of the culture is advantageous. Continuous culture methods were developed to grow cells in a constant environment and have been used for decades to study basic microbial physiology in a controlled and reproducible manner. Our review summarizes the uses of continuous cultures in cell physiology studies and process development, with a focus on recombinant protein-producing microorganisms.
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Affiliation(s)
- Karl Peebo
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618 Tallinn, Estonia.
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Peter Neubauer
- Department of Bioprocess Engineering, Technische Universität Berlin, Ackerstraβe 76, ACK24, D-13355 Berlin, Germany.
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Zhang J, Cai Y, Du G, Chen J, Wang M, Kang Z. Evaluation and application of constitutive promoters for cutinase production by Saccharomyces cerevisiae. J Microbiol 2017; 55:538-544. [PMID: 28664516 DOI: 10.1007/s12275-017-6514-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/01/2017] [Accepted: 03/10/2017] [Indexed: 10/19/2022]
Abstract
Cutinase as a promising biocatalyst has been intensively studied and applied in processes targeted for industrial scale. In this work, the cutinase gene tfu from Thermobifida fusca was artificially synthesized according to codon usage bias of Saccharomyces cerevisiae and investigated in Saccharomyces cerevisiae. Using the α-factor signal peptide, the T. fusca cutinase was successfully overexpressed and secreted with the GAL1 expression system. To increase the cutinase level and overcome some of the drawbacks of induction, four different strong promoters (ADH1, HXT1, TEF1, and TDH3) were comparatively evaluated for cutinase production. By comparison, promoter TEF1 exhibited an outstanding property and significantly increased the expression level. By fed-batch fermentation with a constant feeding approach, the activity of cutinase was increased to 29.7 U/ml. The result will contribute to apply constitutive promoter TEF1 as a tool for targeted cutinase production in S. cerevisiae cell factory.
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Affiliation(s)
- Juan Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China. .,School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China.
| | - Yanqiu Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jian Chen
- School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Miao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Jiangsu, 214122, P. R. China
| | - Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China. .,School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China.
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5
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Abstract
AbstractCutin hydrolase (EC 3.1.1.74), an extracellular polyesterase found in pollens, bacteria and fungi, is an efficient catalyst that exhibits hydrolytic activity on a variety of water-soluble esters, synthetic fibers, plastics and triglycerides. Thus, cutinase can be used in various applications such as ester synthesis, bio-scouring, food and detergent industries. Ancut2 is one of five genes encoding cutinases present in the Aspergillus niger ATCC 10574 genome. The cDNA of Ancut2 comprising of an open reading frame of 816 bp encoding a protein of 271 amino acid residues, was isolated and expressed in Pichia pastoris. The partially purified recombinant cutinase exhibited a molecular mass of approximately 40 kDa. The enzyme showed highest activity at 40°C with a preference for acidic pH (5.0-6.0). AnCUT2 showed hydrolytic activity towards various p-nitrophenyl esters with preference towards shorter chain esters such as p-nitrophenyl butyrate (C4). Scanning Electron Microscopy demonstrated that AnCUT2 was capable of modifying surfaces of synthetic polycaprolactone and polyethylene terephthalate plastics. The properties of this enzyme suggest that it may be applied in synthetic fiber modification and fruit processing industries.
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Mohammad AW, Johar S, Jahim JM, Hassan O. Optimization of Cutinase Purification using a Hydrophobic Interaction Membrane Chromatographic Process by Response Surface Methodology. SEP SCI TECHNOL 2013. [DOI: 10.1080/01496395.2013.788520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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The effect of α-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris. Gene 2013; 519:311-7. [PMID: 23454485 DOI: 10.1016/j.gene.2013.01.062] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 11/21/2022]
Abstract
The methylotrophic yeast, Pichia pastoris, has been genetically engineered to produce many heterologous proteins for industrial and research purposes. In order to secrete proteins for easier purification from the extracellular medium, the coding sequence of recombinant proteins is initially fused to the Saccharomyces cerevisiae α-mating factor secretion signal leader. Extensive site-directed mutagenesis of the prepro-region of the α-mating factor secretion signal sequence was performed in order to determine the effects of various deletions and substitutions on expression. Though some mutations clearly dampened protein expression, deletion of amino acids 57-70, corresponding to the predicted 3rd alpha helix of α-mating factor secretion signal, increased secretion of reporter proteins horseradish peroxidase and lipase at least 50% in small-scale cultures. These findings raise the possibility that the secretory efficiency of the leader can be further enhanced in the future.
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Liu Z, Hou J, Martínez JL, Petranovic D, Nielsen J. Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 97:8955-62. [PMID: 23392765 DOI: 10.1007/s00253-013-4715-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 12/22/2022]
Abstract
With the increasing demand for biopharmaceutical proteins and industrial enzymes, it is necessary to optimize the production by microbial fermentation or cell cultures. Yeasts are well established for the production of a wide range of recombinant proteins, but there are also some limitations; e.g., metabolic and cellular stresses have a strong impact on recombinant protein production. In this work, we investigated the effect of the specific growth rate on the production of two different recombinant proteins. Our results show that human insulin precursor is produced in a growth-associated manner, whereas α-amylase tends to have a higher yield on substrate at low specific growth rates. Based on transcriptional analysis, we found that the difference in the production of the two proteins as function of the specific growth rate is mainly due to differences in endoplasmic reticulum processing, protein turnover, cell cycle, and global stress response. We also found that there is a shift at a specific growth rate of 0.1 h(-1) that influences protein production. Thus, for lower specific growth rates, the α-amylase and insulin precursor-producing strains present similar cell responses and phenotypes, whereas for higher specific growth rates, the two strains respond differently to changes in the specific growth rate.
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Affiliation(s)
- Zihe Liu
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
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Sørensen JD, Petersen EI, Wiebe MG. Production of Fusarium solani f. sp. pisi cutinase in Fusarium venenatum A3/5. Biotechnol Lett 2007; 29:1227-32. [PMID: 17505784 DOI: 10.1007/s10529-007-9369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 03/08/2007] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
Fusarium venenatum A3/5 was transformed using the Aspergillus niger expression plasmid, pIGF, in which the coding sequence for the F. solani f. sp. pisi cutinase gene had been inserted in frame, with a KEX2 cleavage site, with the truncated A. niger glucoamylase gene under control of the A. niger glucoamylase promoter. The transformant produced up to 21 U cutinase l(-1) in minimal medium containing glucose or starch as the primary carbon source. Glucoamylase (165 U l(-1) or 8 mg l(-1)) was also produced. Both the transformant and the parent strain produced cutinase in medium containing cutin.
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Affiliation(s)
- Jacob Dam Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, Aalborg, 9000, Denmark
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Du GC, Zhang SL, Hua ZZ, Zhu Y, Chen J. Enhanced cutinase production withThermobifida fusca by two-stage pH control strategy. Biotechnol J 2007; 2:365-9. [PMID: 17309045 DOI: 10.1002/biot.200600122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A mutant of Thermobifida fusca ATCC 27730 was used for cutinase production. Acetate was the most suitable carbon source for cell growth and cutinase production compared with others. The pH was one of the most important factors affecting cutinase yield and productivity. Batch cutinase fermentations by mutant Thermobifida fusca WSH04 at various pH values ranging from 7.0 to 7.9 were studied. Based on the effects of different pH values on the specific cell growth rate and specific cutinase formation rate, a two-stage pH control strategy was developed, in which the pH was set at 7.3 for the first 20 h, and switched to 7.6 afterwards. By applying this two-stage pH control strategy for cutinase fermentation, the maximal cutinase activity reached 19.8 U/mL.
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Affiliation(s)
- Guo-Cheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Southern Yangtze University, Wuxi, China
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Stagoj MN, Comino A, Komel R. A novel GAL recombinant yeast strain for enhanced protein production. ACTA ACUST UNITED AC 2006; 23:195-9. [PMID: 16707274 DOI: 10.1016/j.bioeng.2006.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 03/20/2006] [Accepted: 03/28/2006] [Indexed: 10/24/2022]
Abstract
A novel strain of Saccharomyces cerevisiae in which the GAL1 gene was replaced with the GAL4 gene has been designed. The GAL1 gene encodes galactokinase (Gal1p), an enzyme that phosphorylates galactose. Gal4p activates genes necessary for galactose metabolism and is among the best characterized transcription activators. Here we describe a GAL recombinant strain that contains the GAL4 gene fused to the natural GAL1 promoter in addition to the normal constitutively expressed chromosomal GAL4 gene. To evaluate whether both gratuitous induction and regulated overexpression of the positive regulator improve protein production, low- and multi-copy expression vectors containing the GAL1 promoter fused to the structural gene for green fluorescent protein (GFP) were introduced into wild-type, gal1 and GAL recombinant strains. In yeast containing the multi-copy plasmid there was an approximately 3.3-fold increase in GFP production in the gal1 mutant strain. Moreover, in the resulting GAL recombinant cells a 4.6-fold increase in fluorescence relative to the wild-type was observed. The GAL recombinant strain should therefore prove useful for maximal expression of heterologous genes driven by a galactose-inducible promoter.
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Affiliation(s)
- Mateja Novak Stagoj
- National Institute of Chemistry, Laboratory for Biosynthesis and Biotransformation, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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Calado CRC, Monteiro SMS, Cabral JMS, Fonseca LP. Effect of pre-fermentation on the production of cutinase by a recombinant Saccharomyces cerevisiae. J Biosci Bioeng 2005; 93:354-9. [PMID: 16233214 DOI: 10.1016/s1389-1723(02)80067-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2001] [Accepted: 12/25/2001] [Indexed: 10/27/2022]
Abstract
The importance of controlling the expression of heterologous cutinase in a recombinant Saccharomyces cerevisiae SU50 strain was investigated. Maximum specific growth rate and the biomass yield increased 1.91 and 1.16 fold, respectively, when cutinase production was induced by galactose in a pre-fermentation step. However, only 19% of specific cell activity was obtained in comparison to other fermentations following a pre-fermentation step without induction of cutinase expression. Thus, the pre-fermentation step was performed using a selective medium not containing galactose, and the fermentation was performed with a cheaper and complex non-selective medium containing galactose. Under these conditions, and with the aim of maximising the specific cutinase activity, a pre-fermentation with low volume and high density of viable cells must be used. However, due to the low pre-fermentation volume, low yeast cell concentrations and low specific cell activities were obtained after 96 h of fermentation. Otherwise, when the aim was to maximise cutinase yield and productivity, a pre-fermentation volume of 10% (v/v) in relation to fermentation and in the exponential growth phase with a cell concentration between 1.1 and 1.8 g dcw/l should be used. A higher pre-fermentation volume, such as 20% (v/v), would still be economical in the case of a pre-fermentation with low cell density or low cell viability.
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Affiliation(s)
- Cecília R C Calado
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais 1049-001 Lisboa, Portugal
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13
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Calado CRC, Ferreira BS, da Fonseca MMR, Cabral JMS, Fonseca LP. Integration of the production and the purification processes of cutinase secreted by a recombinant Saccharomyces cerevisiae SU50 strain. J Biotechnol 2004; 109:147-58. [PMID: 15063623 DOI: 10.1016/j.jbiotec.2003.10.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2002] [Revised: 05/14/2003] [Accepted: 10/14/2003] [Indexed: 10/26/2022]
Abstract
By expanded bed adsorption (EBA) it was possible to simultaneously recover and purify the heterologous cutinase directly from the crude feedstock. However, it was observed that in a highly condensed and consequently economically advantageous purification process as EBA, the cultivation step highly influences the following purification step. Thus, the yeast cultivation and cutinase purification by EBA cannot be considered as independent entities, and the understanding of the interactions between them are crucial for the development of a highly cost effective overall cutinase production process. From the cultivation strategies studied, one batch, one continuous and two fed-batch cultivations, the strategy that resulted in a more economical cutinase overall production process was a fed-batch mode with a feeding in galactose. This last cultivation strategy, exhibited the highest culture cutinase activity and bioreactor productivity, being obtained 3.8-fold higher cutinase activity and 3.0-fold higher productivity that could compensate the 40% higher cultivation medium costs when compared with a fed-batch culture with a feeding on glucose and galactose. Moreover, a 3.8-fold higher effective cutinase dynamic adsorption capacity and 3.8-fold higher effective purification productivity were obtained in relation to the fed-batch culture with the feeding on glucose and galactose. The cultivation strategy with a feeding on galactose, that presented 5.6-fold higher effective purification productivity, could also compensate the 32% effective adsorption capacity obtained with a continuous cultivation broth. Furthermore, a 205-fold higher cutinase activity, 24-fold higher bioreactor productivity and 6% of the cultivation medium costs were obtained in relation to the continuous culture.
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Affiliation(s)
- Cecília R C Calado
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Ferreira BS, Calado CRC, van Keulen F, Fonseca LP, Cabral JMS, da Fonseca MMR. Towards a cost effective strategy for cutinase production by a recombinant Saccharomyces cerevisiae: strain physiological aspects. Appl Microbiol Biotechnol 2003; 61:69-76. [PMID: 12658517 DOI: 10.1007/s00253-002-1196-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2002] [Revised: 11/04/2002] [Accepted: 11/08/2002] [Indexed: 11/29/2022]
Abstract
Although the physiology and metabolism of the growth of yeast strains has been extensively studied, many questions remain unanswered where the induced production of a recombinant protein is concerned. This work addresses the production of a Fusarium solani pisi cutinase by a recombinant Saccharomyces cerevisiae strain induced through the use of a galactose promoter. The strain is able to metabolise the inducer, galactose, which is a much more expensive carbon source than glucose. Both the transport of galactose into the cell-required for the induction of cutinase production-and galactose metabolism are highly repressed by glucose. Different fermentation strategies were tested and the culture behaviour was interpreted in view of the strain metabolism and physiology. A fed-batch fermentation with a mixed feed of glucose and galactose was carried out, during which simultaneous consumption of both hexoses was achieved, as long as the glucose concentration in the medium did not exceed 0.20 g/l. The costs, in terms of hexoses, incurred with this fermentation strategy were reduced to 23% of those resulting from a fermentation carried out using a more conventional strategy, namely a fed-batch fermentation with a feed of galactose.
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Affiliation(s)
- B S Ferreira
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal. bsf@ ist.utl.pt
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Calado CR, Almeida C, Cabral JM, Fonseca LP. Development of a Fed-Batch Cultivation Strategy for the Enhanced production and Secretion of Cutinase by a Recombinant Saccharomyces cerevisiae SU50 Strain. J Biosci Bioeng 2003. [DOI: 10.1016/s1389-1723(03)90116-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Thomassen YE, Meijer W, Sierkstra L, Verrips C. Large-scale production of VHH antibody fragments by Saccharomyces cerevisiae. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(01)00497-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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