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Tafrishi A, Trivedi V, Xing Z, Li M, Mewalal R, Cutler SR, Blaby I, Wheeldon I. Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library. Metab Eng 2024; 85:73-83. [PMID: 39019250 DOI: 10.1016/j.ymben.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/06/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
CRISPR-based high-throughput genome-wide loss-of-function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold coverage genome-wide sgRNA library for this biotechnologically important yeast containing 30,848 active sgRNAs targeting over 99% of its coding sequences. Conducting fitness screens in the absence of functional non-homologous end joining (NHEJ), the dominant DNA repair mechanism in K. phaffii, provides a quantitative means to assess the activity of each sgRNA in the library. This approach allows for the experimental validation of each guide's targeting activity, leading to more precise screening outcomes. We used this approach to conduct growth screens with glucose as the sole carbon source and identify essential genes. Comparative analysis of the called gene sets identified a core set of K. phaffii essential genes, many of which relate to metabolic engineering targets, including protein production, secretion, and glycosylation. The high activity, genome-wide CRISPR library developed here enables functional genomic screening in K. phaffii, applied here to gene essentiality classification, and promises to enable other genetic screens.
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Affiliation(s)
- Aida Tafrishi
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Varun Trivedi
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Zenan Xing
- Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA
| | - Mengwan Li
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA
| | - Ritesh Mewalal
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sean R Cutler
- Botany and Plant Sciences, University of California-Riverside, Riverside, CA, 92521, USA
| | - Ian Blaby
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA, 92521, USA; Center for Industrial Biotechnology, University of California-Riverside, Riverside, CA, 92521, USA.
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2
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Strawn G, Wong RWK, Young BP, Davey M, Nislow C, Conibear E, Loewen CJR, Mayor T. Genome-wide screen identifies new set of genes for improved heterologous laccase expression in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:36. [PMID: 38287338 PMCID: PMC10823697 DOI: 10.1186/s12934-024-02298-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024] Open
Abstract
The yeast Saccharomyces cerevisiae is widely used as a host cell for recombinant protein production due to its fast growth, cost-effective culturing, and ability to secrete large and complex proteins. However, one major drawback is the relatively low yield of produced proteins compared to other host systems. To address this issue, we developed an overlay assay to screen the yeast knockout collection and identify mutants that enhance recombinant protein production, specifically focusing on the secretion of the Trametes trogii fungal laccase enzyme. Gene ontology analysis of these mutants revealed an enrichment of processes including vacuolar targeting, vesicle trafficking, proteolysis, and glycolipid metabolism. We confirmed that a significant portion of these mutants also showed increased activity of the secreted laccase when grown in liquid culture. Notably, we found that the combination of deletions of OCA6, a tyrosine phosphatase gene, along with PMT1 or PMT2, two genes encoding ER membrane protein-O-mannosyltransferases involved in ER quality control, and SKI3, which encode for a component of the SKI complex responsible for mRNA degradation, further increased secreted laccase activity. Conversely, we also identified over 200 gene deletions that resulted in decreased secreted laccase activity, including many genes that encode for mitochondrial proteins and components of the ER-associated degradation pathway. Intriguingly, the deletion of the ER DNAJ co-chaperone gene SCJ1 led to almost no secreted laccase activity. When we expressed SCJ1 from a low-copy plasmid, laccase secretion was restored. However, overexpression of SCJ1 had a detrimental effect, indicating that precise dosing of key chaperone proteins is crucial for optimal recombinant protein expression. This study offers potential strategies for enhancing the overall yield of recombinant proteins and provides new avenues for further research in optimizing protein production systems.
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Affiliation(s)
- Garrett Strawn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ryan W K Wong
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Barry P Young
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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3
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Zhao M, Ma J, Zhang L, Qi H. Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:32. [PMID: 38247006 PMCID: PMC10801990 DOI: 10.1186/s12934-024-02299-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
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Affiliation(s)
- Meirong Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Jianfan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Lei Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Haishan Qi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China.
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4
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Li Y, Xiao C, Pan Y, Qin L, Zheng L, Zhao M, Huang M. Optimization of Protein Folding for Improved Secretion of Human Serum Albumin Fusion Proteins in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18414-18423. [PMID: 37966975 DOI: 10.1021/acs.jafc.3c05330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The successful expression and secretion of recombinant proteins in cell factories significantly depend on the correct folding of nascent peptides, primarily achieved through disulfide bond formation. Thus, optimizing cellular protein folding is crucial, especially for proteins with complex spatial structures. In this study, protein disulfide isomerases (PDIs) from various species were introduced into Saccharomyces cerevisiae to facilitate proper disulfide bond formation and enhance recombinant protein secretion. The impacts of these PDIs on recombinant protein production and yeast growth metabolism were evaluated by substituting the endogenous PDI1. Heterologous PDIs cannot fully compensate the endogenous PDI. Furthermore, protein folding mediators, PDI and ER oxidoreductase 1 (Ero1), from different species were used to increase the production of complex human serum albumin (HSA) fusion proteins. The validated folding mediators were then introduced into unfolded protein response (UPR)-optimized strains, resulting in a 7.8-fold increase in amylase-HSA and an 18.2-fold increase in albiglutide compared with the control strain. These findings provide valuable insights for optimizing protein folding and expressing HSA-based drugs.
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Affiliation(s)
- Yanling Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Ling Qin
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Lin Zheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mouming Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Guangdong Food Green Processing and Nutrition Regulation Technologies Research Center, Guangzhou 510650, China
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Chen N, Yang S, You D, Shen J, Ruan B, Wu M, Zhang J, Luo X, Tang H. Systematic genetic modifications of cell wall biosynthesis enhanced the secretion and surface-display of polysaccharide degrading enzymes in Saccharomyces cerevisiae. Metab Eng 2023; 77:273-282. [PMID: 37100192 DOI: 10.1016/j.ymben.2023.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023]
Abstract
Saccharomyces cerevisiae is a robust cell factory to secrete or surface-display cellulase and amylase for the conversion of agricultural residues into valuable chemicals. Engineering the secretory pathway is a well-known strategy for overproducing these enzymes. Although cell wall biosynthesis can be tightly linked to the secretory pathway by regulation of all involved processes, the effect of its modifications on protein production has not been extensively studied. In this study, we systematically studied the effect of engineering cell wall biosynthesis on the activity of cellulolytic enzyme β-glucosidase (BGL1) by comparing seventy-nine gene knockout S. cerevisiae strains and newly identified that inactivation of DFG5, YPK1, FYV5, CCW12 and KRE1 obviously improved BGL1 secretion and surface-display. Combinatorial modifications of these genes, particularly double deletion of FVY5 and CCW12, along with the use of rich medium, increased the activity of secreted and surface-displayed BGL1 by 6.13-fold and 7.99-fold, respectively. Additionally, we applied this strategy to improve the activity of the cellulolytic cellobiohydrolase and amylolytic α-amylase. Through proteomic analysis coupled with reverse engineering, we found that in addition to the secretory pathway, regulation of translation processes may also involve in improving enzyme activity by engineering cell wall biosynthesis. Our work provides new insight into the construction of a yeast cell factory for efficient production of polysaccharide degrading enzymes.
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Affiliation(s)
- Nanzhu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuo Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology, 3501 Daxue Road, Jinan, 250353, China
| | - Dawei You
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junfeng Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Banlai Ruan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Mei Wu
- Synceres Biosciences (Shenzhen) Co., Ltd, Nanshan Medical Device Industrial Park, Nanhai Avenue, Shenzhen, 518067, China
| | - Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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Ji W, Wang X, Liu X, Wang Y, Liu F, Xu B, Luo H, Tu T, Zhang W, Xu X, Su X. Combining manipulation of integration loci and secretory pathway on expression of an Aspergillus niger glucose oxidase gene in Trichoderma reesei. Microb Cell Fact 2023; 22:38. [PMID: 36841771 PMCID: PMC9960163 DOI: 10.1186/s12934-023-02046-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/18/2023] [Indexed: 02/27/2023] Open
Abstract
Trichoderma reesei (T. reesei) is well-known for its excellent ability to secret a large quantity of cellulase. However, unlike the endogenous proteins, little is known about the molecular mechanisms governing heterologous protein production. Herein, we focused on the integration loci and the secretory pathway, and investigated their combinatorial effects on heterologous gene expression in T. reesei using a glucose oxidase from Aspergillus niger as a model protein. Integration in the cel3c locus was more efficient than the cbh1 locus in expressing the AnGOx by increasing the transcription of AnGOx in the early stage. In addition, we discovered that interruption of the cel3c locus has an additional effect by increasing the expression of the secretory pathway component genes. Accordingly, overexpressing three secretory pathway component genes, that were snc1, sso2, and rho3, increased AnGOx expression in the cbh1 transformant but not in the cel3c transformant.
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Affiliation(s)
- Wangli Ji
- grid.410727.70000 0001 0526 1937Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing, 100081 China
| | - Xiaolu Wang
- grid.410727.70000 0001 0526 1937Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193 China
| | - Xiaoqing Liu
- grid.410727.70000 0001 0526 1937Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing, 100081 China
| | - Yuan Wang
- grid.410727.70000 0001 0526 1937Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193 China
| | - Fangui Liu
- grid.459577.d0000 0004 1757 6559College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 Guangdong China
| | - Bo Xu
- grid.459577.d0000 0004 1757 6559College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 Guangdong China
| | - Huiying Luo
- grid.410727.70000 0001 0526 1937Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193 China
| | - Tao Tu
- grid.410727.70000 0001 0526 1937Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193 China
| | - Wei Zhang
- grid.410727.70000 0001 0526 1937Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing, 100081 China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing, 100081, China.
| | - Xiaoyun Su
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China.
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7
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Zahrl RJ, Prielhofer R, Ata Ö, Baumann K, Mattanovich D, Gasser B. Pushing and pulling proteins into the yeast secretory pathway enhances recombinant protein secretion. Metab Eng 2022; 74:36-48. [PMID: 36057427 DOI: 10.1016/j.ymben.2022.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022]
Abstract
Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key advantages of yeast host systems is their ability to secrete the recombinant protein into the culture media. However, secretion of some recombinant proteins is less efficient. These proteins include antibody fragments such as Fabs or scFvs. We have recently identified translocation of nascent Fab fragments from the cytosol into the endoplasmic reticulum (ER) as one major bottleneck. Conceptually, this bottleneck requires engineering to increase the flux of recombinant proteins at the translocation step by pushing on the cytosolic side and pulling on the ER side. This engineering strategy is well-known in the field of metabolic engineering. To apply the push-and-pull strategy to recombinant protein secretion, we chose to modulate the cytosolic and ER Hsp70 cycles, which have a key impact on the translocation process. After identifying the relevant candidate factors of the Hsp70 cycles, we combined the push-and-pull factors in a single strain and achieved synergistic effects for antibody fragment secretion. With this concept we were able to successfully engineer strains and improve protein secretion up to 5-fold for different model protein classes. Overall, titers of more than 1.3 g/L Fab and scFv were reached in bioreactor cultivations.
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Affiliation(s)
- Richard J Zahrl
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Roland Prielhofer
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Özge Ata
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Kristin Baumann
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Diethard Mattanovich
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- ACIB GmbH, Muthgasse 11, 1190, Vienna, Austria; Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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8
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Tir N, Heistinger L, Grünwald-Gruber C, Jakob LA, Dickgiesser S, Rasche N, Mattanovich D. From strain engineering to process development: monoclonal antibody production with an unnatural amino acid in Pichia pastoris. Microb Cell Fact 2022; 21:157. [PMID: 35953849 PMCID: PMC9367057 DOI: 10.1186/s12934-022-01882-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Background Expansion of the genetic code is a frequently employed approach for the modification of recombinant protein properties. It involves reassignment of a codon to another, e.g., unnatural, amino acid and requires the action of a pair of orthogonal tRNA and aminoacyl tRNA synthetase modified to recognize only the desired amino acid. This approach was applied for the production of trastuzumab IgG carrying p-azido-l-phenylalanine (pAzF) in the industrial yeast Pichia pastoris. Combining the knowledge of protein folding and secretion with bioreactor cultivations, the aim of the work was to make the production of monoclonal antibodies with an expanded genetic code cost-effective on a laboratory scale. Results Co-translational transport of proteins into the endoplasmic reticulum through secretion signal prepeptide change and overexpression of lumenal chaperones Kar2p and Lhs1p improved the production of trastuzumab IgG and its Fab fragment with incorporated pAzF. In the case of Fab, a knockout of vacuolar targeting for protein degradation further increased protein yield. Fed-batch bioreactor cultivations of engineered P. pastoris strains increased IgG and IgGpAzF productivity by around 50- and 20-fold compared to screenings, yielding up to 238 mg L−1 and 15 mg L−1 of fully assembled tetrameric protein, respectively. Successful site-specific incorporation of pAzF was confirmed by mass spectrometry. Conclusions Pichia pastoris was successfully employed for cost-effective laboratory-scale production of a monoclonal antibody with an unnatural amino acid. Applying the results of this work in glycoengineered strains, and taking further steps in process development opens great possibilities for utilizing P. pastoris in the development of antibodies for subsequent conjugations with, e.g., bioactive payloads. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01882-6.
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Affiliation(s)
- Nora Tir
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Lina Heistinger
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biology, Institute of Biochemistry, ETH Zürich, 8093, Zurich, Switzerland
| | - Clemens Grünwald-Gruber
- University of Natural Resources and Life Sciences, Vienna Core Facility Mass Spectrometry, Muthgasse 18, 1190, Vienna, Austria
| | - Leo A Jakob
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Dickgiesser
- ADCs & Targeted NBE Therapeutics, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Nicolas Rasche
- ADCs & Targeted NBE Therapeutics, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Shi T, Zhou J, Xue A, Lu H, He Y, Yu Y. Characterization and modulation of endoplasmic reticulum stress response target genes in Kluyveromyces marxianus to improve secretory expressions of heterologous proteins. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:236. [PMID: 34906221 PMCID: PMC8670139 DOI: 10.1186/s13068-021-02086-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/30/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND Kluyveromyces marxianus is a promising cell factory for producing bioethanol and that raised a demand for a high yield of heterologous proteins in this species. Expressions of heterologous proteins usually lead to the accumulation of misfolded or unfolded proteins in the lumen of the endoplasmic reticulum (ER) and then cause ER stress. To cope with this problem, a group of ER stress response target genes (ESRTs) are induced, mainly through a signaling network called unfolded protein response (UPR). Characterization and modulation of ESRTs direct the optimization of heterologous expressions. However, ESRTs in K. marxianus have not been identified so far. RESULTS In this study, we characterized the ER stress response in K. marxianus for the first time, by using two ER stress-inducing reagents, dithiothreitol (DTT) and tunicamycin (TM). Results showed that the Kar2-Ire1-Hac1 pathway of UPR is well conserved in K. marxianus. About 15% and 6% of genes were upregulated during treatment of DTT and TM, respectively. A total of 115 upregulated genes were characterized as ESRTs, among which 97 genes were identified as UPR target genes and 37 UPR target genes contained UPR elements in their promoters. Genes related to carbohydrate metabolic process and actin filament organization were identified as new types of UPR target genes. A total of 102 ESRTs were overexpressed separately in plasmids and their effects on productions of two different lignocellulolytic enzymes were systematically evaluated. Overexpressing genes involved in carbohydrate metabolism, including PDC1, PGK and VID28, overexpressing a chaperone gene CAJ1 or overexpressing a reductase gene MET13 substantially improved secretion expressions of heterologous proteins. Meanwhile, overexpressing a novel gene, KLMA_50479 (named ESR1), as well as overexpressing genes involved in ER-associated protein degradation (ERAD), including HRD3, USA1 andYET3, reduced the secretory expressions. ESR1 and the aforementioned ERAD genes were deleted from the genome. Resultant mutants, except the yet3Δ mutant, substantially improved secretions of three different heterologous proteins. During the fed-batch fermentation, extracellular activities of an endoxylanase and a glucanase in hrd3Δ cells improved by 43% and 28%, respectively, compared to those in wild-type cells. CONCLUSIONS Our results unveil the transcriptional scope of the ER stress response in K. marxianus and suggest efficient ways to improve productions of heterologous proteins by manipulating expressions of ESRTs.
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Affiliation(s)
- Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Aijuan Xue
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438 China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
| | - Yungang He
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438 China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438 China
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10
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Pallares RM, An DD, Hébert S, Faulkner D, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Multidimensional genome-wide screening in yeast provides mechanistic insights into europium toxicity. Metallomics 2021; 13:6409834. [PMID: 34694395 DOI: 10.1093/mtomcs/mfab061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022]
Abstract
Europium is a lanthanide metal that is highly valued in optoelectronics. Even though europium is used in many commercial products, its toxicological profile has only been partially characterized, with most studies focusing on identifying lethal doses in different systems or bioaccumulation in vivo. This paper describes a genome-wide toxicogenomic study of europium in Saccharomyces cerevisiae, which shares many biological functions with humans. By using a multidimensional approach and functional and network analyses, we have identified a group of genes and proteins associated with the yeast responses to ameliorate metal toxicity, which include metal discharge paths through vesicle-mediated transport, paths to regulate biologically relevant cations, and processes to reduce metal-induced stress. Furthermore, the analyses indicated that europium promotes yeast toxicity by disrupting the function of chaperones and cochaperones, which have metal-binding sites. Several of the genes and proteins highlighted in our study have human orthologues, suggesting they may participate in europium-induced toxicity in humans. By identifying the endogenous targets of europium as well as the already existing paths that can decrease its toxicity, we can determine specific genes and proteins that may help to develop future therapeutic strategies.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Solène Hébert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA
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11
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Chun J, Ko YH, Kim DH. Interaction between hypoviral-regulated fungal virulence factor laccase3 and small heat shock protein Hsp24 from the chestnut blight fungus Cryphonectria parasitica. J Microbiol 2021; 60:57-62. [PMID: 34826098 DOI: 10.1007/s12275-022-1498-0] [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: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Laccase3 is an important virulence factor of the fungus Cryphonectria parasitica. Laccase3 gene (lac3) transcription is induced by tannic acid, a group of phenolic compounds found in chestnut trees, and its induction is regulated by the hypovirus CHV1 infection. CpHsp24, a small heat shock protein gene of C. parasitica, plays a determinative role in stress adaptation and pathogen virulence. Having uncovered in our previous study that transcriptional regulation of the CpHsp24 gene in response to tannic acid supplementation and CHV1 infection was similar to that of the lac3, and that conserved phenotypic changes of reduced virulence were observed in mutants of both genes, we inferred that both genes were implicated in a common pathway. Building on this finding, in this paper we examined whether the CpHsp24 protein (CpHSP24) was a molecular chaperone for the lac3 protein (LAC3). Our pull-down experiment indicated that the protein products of the two genes directly interacted with each other. Heterologous co-expression of CpHsp24 and lac3 genes using Saccharomyces cerevisiae resulted in more laccase activity in the cotransformant than in a parental lac3-expresssing yeast strain. These findings suggest that CpHSP24 is, in fact, a molecular chaperone for the LAC3, which is critical component of fungal pathogenesis.
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Affiliation(s)
- Jeesun Chun
- Department of Molecular Biology, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Yo-Han Ko
- Department of Molecular Biology, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Dae-Hyuk Kim
- Department of Molecular Biology, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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12
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Kim JE, Son SH, Oh SS, Kim SC, Lee JY. Pairing of orthogonal chaperones with a cytochrome P450 enhances terpene synthesis in Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2000452. [PMID: 34269523 DOI: 10.1002/biot.202000452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022]
Abstract
The supply of terpenes is often limited by their low extraction yield from natural resources, such as plants. Thus, microbial biosynthesis has emerged as an attractive platform for the production of terpenes. Many strategies have been applied to engineer microbes to improve terpene production capabilities; however, functional expression of heterologous proteins such as cytochrome P450 enzymes (P450s) in microbes is a major obstacle. This study reports the successful pairing of cognate chaperones and P450s for functional heterologous expression in Saccharomyces cerevisiae. This chaperone pairing was exploited to facilitate the functional assembly of the protopanaxadiol (PPD) biosynthesis pathway, which consists of a P450 oxygenase and a P450 reductase redox partner originating from Panax ginseng and Arabidopsis thaliana, respectively. We identified several chaperones required for protein folding in P. ginseng and A. thaliana and evaluated the impact of the coexpression of the corresponding chaperones on the synthesis and activity of PPD biosynthesis enzymes. Expression of a chaperone from P. ginseng (PgCPR5), a cognate of PPD biosynthesis enzymes, significantly increased PPD production by more than 2.5-fold compared with that in the corresponding control strain. Thus, pairing of chaperones with heterologous enzymes provides an effective strategy for the construction of challenging biosynthesis pathways in yeast.
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Affiliation(s)
- Jae-Eung Kim
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - So-Hee Son
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.,Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
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13
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Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up. Microb Cell Fact 2021; 20:124. [PMID: 34193127 PMCID: PMC8246677 DOI: 10.1186/s12934-021-01617-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.
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14
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Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
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15
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Koskela EV, Gonzalez Salcedo A, Piirainen MA, Iivonen HA, Salminen H, Frey AD. Mining Data From Plasma Cell Differentiation Identified Novel Genes for Engineering of a Yeast Antibody Factory. Front Bioeng Biotechnol 2020; 8:255. [PMID: 32296695 PMCID: PMC7136540 DOI: 10.3389/fbioe.2020.00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Saccharomyces cerevisiae is a common platform for production of therapeutic proteins, but it is not intrinsically suited for the manufacturing of antibodies. Antibodies are naturally produced by plasma cells (PCs) and studies conducted on PC differentiation provide a comprehensive blueprint for the cellular transformations needed to create an antibody factory. In this study we mined transcriptomics data from PC differentiation to improve antibody secretion by S. cerevisiae. Through data exploration, we identified several new target genes. We tested the effects of 14 genetic modifications belonging to different cellular processes on protein production. Four of the tested genes resulted in improved antibody expression. The ER stress sensor IRE1 increased the final titer by 1.8-fold and smaller effects were observed with PSA1, GOT1, and HUT1 increasing antibody titers by 1. 6-, 1. 4-, and 1.4-fold. When testing combinations of these genes, the highest increases were observed when co-expressing IRE1 with PSA1, or IRE1 with PSA1 and HUT1, resulting in 3.8- and 3.1-fold higher antibody titers. In contrast, strains expressing IRE1 alone or in combination with the other genes produced similar or lower levels of recombinantly expressed endogenous yeast acid phosphatase compared to the controls. Using a genetic UPR responsive GFP reporter construct, we show that IRE1 acts through constitutive activation of the unfolded protein response. Moreover, the positive effect of IRE1 expression was transferable to other antibody molecules. We demonstrate how data exploration from an evolutionary distant, but highly specialized cell type can pinpoint new genetic targets and provide a novel concept for rationalized cell engineering.
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Affiliation(s)
- Essi V Koskela
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | | | - Mari A Piirainen
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Heidi A Iivonen
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Heidi Salminen
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Alexander D Frey
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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16
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Cedras G, Kroukamp H, Van Zyl WH, Den Haan R. The
in vivo
detection and measurement of the unfolded protein response in recombinant cellulase producing
Saccharomyces cerevisiae
strains. Biotechnol Appl Biochem 2020; 67:82-94. [DOI: 10.1002/bab.1819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/16/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Gillian Cedras
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
| | - Heinrich Kroukamp
- Department of Molecular SciencesMacquarie University North Ryde NSW Australia
| | | | - Riaan Den Haan
- Department of BiotechnologyUniversity of the Western Cape Bellville South Africa
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17
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Beal DM, Bastow EL, Staniforth GL, von der Haar T, Freedman RB, Tuite MF. Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo. Antioxid Redox Signal 2019; 31:261-274. [PMID: 30880408 PMCID: PMC6602113 DOI: 10.1089/ars.2018.7615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
Aims: Efficient oxidative protein folding (OPF) in the endoplasmic reticulum (ER) is a key requirement of the eukaryotic secretory pathway. In particular, protein folding linked to the formation of disulfide bonds, an activity dependent on the enzyme protein disulfide isomerase (PDI), is crucial. For the de novo formation of disulfide bonds, reduced PDI must be reoxidized by an ER-located oxidase (ERO1). Despite some knowledge of this pathway, the kinetic parameters with which these components act and the importance of specific parameters, such as PDI reoxidation by Ero1, for the overall performance of OPF in vivo remain poorly understood. Results: We established an in vitro system using purified yeast (Saccharomyces cerevisiae) PDI (Pdi1p) and ERO1 (Ero1p) to investigate OPF. This necessitated the development of a novel reduction/oxidation processing strategy to generate homogenously oxidized recombinant yeast Ero1p. This new methodology enabled the quantitative assessment of the interaction of Pdi1p and Ero1p in vitro by measuring oxygen consumption and reoxidation of reduced RNase A. The resulting quantitative data were then used to generate a simple model that can describe the oxidizing capacity of Pdi1p and Ero1p in vitro and predict the in vivo effect of modulation of the levels of these proteins. Innovation: We describe a model that can be used to explore the OPF pathway and its control in a quantitative way. Conclusion: Our study informs and provides new insights into how OPF works at a molecular level and provides a platform for the design of more efficient heterologous protein expression systems in yeast.
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Affiliation(s)
- Dave M. Beal
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Emma L. Bastow
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Gemma L. Staniforth
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Robert B. Freedman
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Mick F. Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
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18
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Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production. Proc Natl Acad Sci U S A 2018; 115:E11025-E11032. [PMID: 30397111 DOI: 10.1073/pnas.1809921115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Baker's yeast Saccharomyces cerevisiae is one of the most important and widely used cell factories for recombinant protein production. Many strategies have been applied to engineer this yeast for improving its protein production capacity, but productivity is still relatively low, and with increasing market demand, it is important to identify new gene targets, especially targets that have synergistic effects with previously identified targets. Despite improved protein production, previous studies rarely focused on processes associated with intracellular protein retention. Here we identified genetic modifications involved in the secretory and trafficking pathways, the histone deacetylase complex, and carbohydrate metabolic processes as targets for improving protein secretion in yeast. Especially modifications on the endosome-to-Golgi trafficking was found to effectively reduce protein retention besides increasing protein secretion. Through combinatorial genetic manipulations of several of the newly identified gene targets, we enhanced the protein production capacity of yeast by more than fivefold, and the best engineered strains could produce 2.5 g/L of a fungal α-amylase with less than 10% of the recombinant protein retained within the cells, using fed-batch cultivation.
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19
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Engineering folding mechanism through Hsp70 and Hsp40 chaperones for enhancing the production of recombinant human interferon gamma (rhIFN-γ) in Pichia pastoris cell factory. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Sheng J, Flick H, Feng X. Systematic Optimization of Protein Secretory Pathways in Saccharomyces cerevisiae to Increase Expression of Hepatitis B Small Antigen. Front Microbiol 2017; 8:875. [PMID: 28559891 PMCID: PMC5432677 DOI: 10.3389/fmicb.2017.00875] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/01/2017] [Indexed: 11/13/2022] Open
Abstract
Hepatitis B is a major disease that chronically infects millions of people in the world, especially in developing countries. Currently, one of the effective vaccines to prevent Hepatitis B is the Hepatitis B Small Antigen (HBsAg), which is mainly produced by the recombinant yeast Saccharomyces cerevisiae. In order to bring down the price, which is still too high for people in developing countries to afford, it is important to understand key cellular processes that limit protein expression. In this study, we took advantage of yeast knockout collection (YKO) and screened 194 S. cerevisiae strains with single gene knocked out in four major steps of the protein secretory pathway, i.e., endoplasmic-reticulum (ER)-associated protein degradation, protein folding, unfolded protein response (UPR), and translocation and exocytosis. The screening showed that the single deletion of YPT32, SBH1, and HSP42 led to the most significant increase of HBsAg expression over the wild type while the deletion of IRE1 led to a profound decrease of HBsAg expression. The synergistic effects of gene knockout and gene overexpression were next tested. We found that simultaneously deleting YPT32 and overexpressing IRE1 led to a 2.12-fold increase in HBsAg expression over the wild type strain. The results of this study revealed novel genetic targets of protein secretory pathways that could potentially improve the manufacturing of broad scope vaccines in a cost-effective way using recombinant S. cerevisiae.
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Affiliation(s)
- Jiayuan Sheng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, United States
| | - Hunter Flick
- Department of Chemical Engineering, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, United States
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, United States
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21
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Tracking Effects of SIL1 Increase: Taking a Closer Look Beyond the Consequences of Elevated Expression Level. Mol Neurobiol 2017; 55:2524-2546. [PMID: 28401474 DOI: 10.1007/s12035-017-0494-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/14/2017] [Indexed: 12/31/2022]
Abstract
SIL1 acts as a co-chaperone for the major ER-resident chaperone BiP and thus plays a role in many BiP-dependent cellular functions such as protein-folding control and unfolded protein response. Whereas the increase of BiP upon cellular stress conditions is a well-known phenomenon, elevation of SIL1 under stress conditions was thus far solely studied in yeast, and different studies indicated an adverse effect of SIL1 increase. This is seemingly in contrast with the beneficial effect of SIL1 increase in surviving neurons in neurodegenerative disorders such as amyotrophic lateral sclerosis and Alzheimer's disease. Here, we addressed these controversial findings. Applying cell biological, morphological and biochemical methods, we demonstrated that SIL1 increases in various mammalian cells and neuronal tissues upon cellular stress. Investigation of heterozygous SIL1 mutant cells and tissues supported this finding. Moreover, SIL1 protein was found to be stabilized during ER stress. Increased SIL1 initiates ER stress in a concentration-dependent manner which agrees with the described adverse SIL1 effect. However, our results also suggest that protective levels are achieved by the secretion of excessive SIL1 and GRP170 and that moderately increased SIL1 also ameliorates cellular fitness under stress conditions. Our immunoprecipitation results indicate that SIL1 might act in a BiP-independent manner. Proteomic studies showed that SIL1 elevation alters the expression of proteins including crucial players in neurodegeneration, especially in Alzheimer's disease. This finding agrees with our observation of increased SIL1 immunoreactivity in surviving neurons of Alzheimer's disease autopsy cases and supports the assumption that SIL1 plays a protective role in neurodegenerative disorders.
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22
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Møller TSB, Hay J, Saxton MJ, Bunting K, Petersen EI, Kjærulff S, Finnis CJA. Human β-defensin-2 production from S. cerevisiae using the repressible MET17 promoter. Microb Cell Fact 2017; 16:11. [PMID: 28100236 PMCID: PMC5241953 DOI: 10.1186/s12934-017-0627-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background Baker’s yeast Saccharomyces cerevisiae is a proven host for the commercial production of recombinant biopharmaceutical proteins. For the manufacture of heterologous proteins with activities deleterious to the host it can be desirable to minimise production during the growth phase and induce production late in the exponential phase. Protein expression by regulated promoter systems offers the possibility of improving productivity in this way by separating the recombinant protein production phase from the yeast growth phase. Commonly used inducible promoters do not always offer convenient solutions for industrial scale biopharmaceutical production with engineered yeast systems. Results Here we show improved secretion of the antimicrobial protein, human β-defensin-2, (hBD2), using the S. cerevisiae MET17 promoter by repressing expression during the growth phase. In shake flask culture, a higher final concentration of human β-defensin-2 was obtained using the repressible MET17 promoter system than when using the strong constitutive promoter from proteinase B (PRB1) in a yeast strain developed for high-level commercial production of recombinant proteins. Furthermore, this was achieved in under half the time using the MET17 promoter compared to the PRB1 promoter. Cell density, plasmid copy-number, transcript level and protein concentration in the culture supernatant were used to study the effects of different initial methionine concentrations in the culture media for the production of human β-defensin-2 secreted from S. cerevisiae. Conclusions The repressible S. cerevisiae MET17 promoter was more efficient than a strong constitutive promoter for the production of human β-defensin-2 from S. cerevisiae in small-scale culture and offers advantages for the commercial production of this and other heterologous proteins which are deleterious to the host organism. Furthermore, the MET17 promoter activity can be modulated by methionine alone, which has a safety profile applicable to biopharmaceutical manufacturing.
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Affiliation(s)
- Thea S B Møller
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.,Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Joanna Hay
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Malcolm J Saxton
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Karen Bunting
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Evamaria I Petersen
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Søren Kjærulff
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Christopher J A Finnis
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.
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23
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Guan B, Chen F, Su S, Duan Z, Chen Y, Li H, Jin J. Effects of co-overexpression of secretion helper factors on the secretion of a HSA fusion protein (IL2-HSA) in pichia pastoris. Yeast 2016; 33:587-600. [PMID: 27532278 DOI: 10.1002/yea.3183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 07/18/2016] [Accepted: 07/29/2016] [Indexed: 11/12/2022] Open
Abstract
Pichia pastoris is generally considered as an expression host for heterologous proteins with the coding gene under control of the alcohol oxidase 1 (AOX1) promoter. The secretion of heterologous proteins in P. pastoris can be potentially affected by many factors. Based on our previous results, the secretion levels of human albumin (HSA) fusion protein IL2-HSA were only around 500 mg/L or less in fermentor cultures, which decreased more than 50% compared with that of HSA (>1 g/L). In this study, we selected five potential secretion helper factors, in which Ero1, Pdi1 and Kar2 were involved in protein folding and Sec1 and Sly1 were involved in vesicle trafficking. We evaluated the possible effects of individual overexpression of these secretion helper factors on the secretion of IL2-HSA in P. pastoris. Constitutive overexpression of the five selected secretion factors did not have an obvious negative effect on cell growth of the IL2-HSA secreting strain. Individual co-overexpression of Ero1, Kar2, Pdi1, Sec1 and Sly1 improved the secretion level of IL2-HSA to ~2.3-, 1.9-, 2.2-, 2.5- and 1.9-fold that in the control strain respectively in shake flasks. We evaluated the changes in mRNA and protein levels of the intracellular IL2-HSA, as well as the secretion helper factor genes in the co-overexpressing strains. Our results indicated that manipulating the expression level of ER resident protein Pdi1, Ero1, Kar2 and SM protein Sec1 and Sly1 could improve the secretion level of IL2-HSA fusion protein in P. pastoris, which provided new candidates for combinatorial engineering in future study. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Bo Guan
- School of Food Science, Shihezi University, Shihezi, China
| | - Fengxiang Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shuai Su
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zuoying Duan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Chen
- Laboratory of Drug Design axnd Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Huazhong Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Jin
- Laboratory of Drug Design axnd Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
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24
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de Ruijter JC, Koskela EV, Frey AD. Enhancing antibody folding and secretion by tailoring the Saccharomyces cerevisiae endoplasmic reticulum. Microb Cell Fact 2016; 15:87. [PMID: 27216259 PMCID: PMC4878073 DOI: 10.1186/s12934-016-0488-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 05/11/2016] [Indexed: 01/20/2023] Open
Abstract
Background The yeast Saccharomyces cerevisiae provides intriguing possibilities for synthetic biology and bioprocess applications, but its use is still constrained by cellular characteristics that limit the product yields. Considering the production of advanced biopharmaceuticals, a major hindrance lies in the yeast endoplasmic reticulum (ER), as it is not equipped for efficient and large scale folding of complex proteins, such as human antibodies. Results Following the example of professional secretory cells, we show that inducing an ER expansion in yeast by deleting the lipid-regulator gene OPI1 can improve the secretion capacity of full-length antibodies up to fourfold. Based on wild-type and ER-enlarged yeast strains, we conducted a screening of a folding factor overexpression library to identify proteins and their expression levels that enhance the secretion of antibodies. Out of six genes tested, addition of the peptidyl-prolyl isomerase CPR5 provided the most beneficial effect on specific product yield while PDI1, ERO1, KAR2, LHS1 and SIL1 had a mild or even negative effect to antibody secretion efficiency. Combining genes for ER enhancement did not induce any significant additional effect compared to addition of just one element. By combining the Δopi1 strain, with the enlarged ER, with CPR5 overexpression, we were able to boost the specific antibody product yield by a factor of 10 relative to the non-engineered strain. Conclusions Engineering protein folding in vivo is a major task for biopharmaceuticals production in yeast and needs to be optimized at several levels. By rational strain design and high-throughput screening applications we were able to increase the specific secreted antibody yields of S. cerevisiae up to 10-fold, providing a promising strain for further process optimization and platform development for antibody production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0488-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorg C de Ruijter
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Essi V Koskela
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Alexander D Frey
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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Song Y, Ding J, Jin R, Jung J, Li S, Yang J, Wang A, Li Z. Expression and purification of FGF21 in Pichia pastoris and its effect on fibroblast-cell migration. Mol Med Rep 2016; 13:3619-26. [PMID: 26934832 DOI: 10.3892/mmr.2016.4942] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/08/2015] [Indexed: 11/06/2022] Open
Abstract
Fibroblast growth factor (FGF)21 functions in the maintenance of glucose homeostasis and exerts protective effects on the liver, heat and kidneys. However, the roles of FGF21 in other tissue types are yet to be fully elucidated. The present study detected elevated expression levels of FGF21 in skin tissue. Furthermore, it was revealed that FGF21 expression in the skin was induced upon wounding. In addition, β‑klotho expression was detected in the skin tissue. To examine the role of FGF21 in the wound healing process, recombinant human (h)FGF21 was expressed in a the yeast strain Pichia (P.) pastoris, a well‑known system for recombinant protein production. Based on the sequence of hFGF21 and the optimal codon of P. pastoris, codon‑optimized FGF21 open reading frame sequences were obtained using seven pairs of 55‑59‑nt primers with seven rounds of PCR. The recombinant FGF21 was purified and its function was examined in human fibroblast cells using a wound healing cell migration assay. Treatment with FGF21 promoted cell migration, which is an important step in wound healing. Furthermore, FGF21 treatment enhanced the activity of c‑Jun N‑terminal kinase, a key regulator in fibroblast‑cell migration. In conclusion, FGF21 is induced after wounding and FGF21 expressed and purified from yeast markedly accelerates wound healing. The present study was the first to elucidate the function of FGF21 in skin tissues and provided a theoretical basis for the use of FGF21 in the treatment of skin wounds.
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Affiliation(s)
- Yonghuan Song
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Jian Ding
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Rilong Jin
- Department of Orthopedic Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310000, P.R. China
| | - Jinhee Jung
- Molecular Evolution Team, Department of Biotech R&D, Amicogen Inc., Jinju, Yeongnam 660‑852, South Korea
| | - Shi Li
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Jingquan Yang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Anyuan Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Zhijie Li
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
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26
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Zinkevičiūtė R, Bakūnaitė E, Čiplys E, Ražanskas R, Raškevičiūtė J, Slibinskas R. Heat shock at higher cell densities improves measles hemagglutinin translocation and human GRP78/BiP secretion in Saccharomyces cerevisiae. N Biotechnol 2015; 32:690-700. [PMID: 25907596 DOI: 10.1016/j.nbt.2015.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 03/30/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
The yield of heterologous proteins is often limited by several bottlenecks in the secretory pathway of yeast Saccharomyces cerevisiae. It was shown earlier that synthesis of measles virus hemagglutinin (MeH) is inefficient mostly due to a bottleneck in the translocation of viral protein precursors into the endoplasmic reticulum (ER) of yeast cells. Here we report that heat shock with subsequent induction of MeH expression at 37°C improved translocation of MeH precursors when applied at higher cell densities. The amount of MeH glycoprotein increased by about 3-fold after heat shock in the late-log phases of both glucose and ethanol growth. The same temperature conditions increased both secretion titer and yield of another heterologous protein human GRP78/BiP by about 50%. Furthermore, heat shock at the late-log glucose growth phase also improved endogenous invertase yield by approximately 2.7-fold. In contrast, a transfer of yeast culture to lower temperature at diauxic shift followed by protein expression at 20°C almost totally inhibited translocation of MeH precursors. The difference in amounts of MeH glycoprotein under expression at 37°C and 20°C was about 80-fold, while amounts of unglycosylated MeH polypeptides were similar under both conditions. Comparative proteomic analysis revealed that besides over-expressed ER-resident chaperone Kar2, an increased expression of several cytosolic proteins (such as Hsp104, Hsp90 and eEF1A) may contribute to improved translocation of MeH.
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Affiliation(s)
- Rūta Zinkevičiūtė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania
| | - Edita Bakūnaitė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania
| | - Evaldas Čiplys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania
| | - Raimundas Ražanskas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania
| | - Jurgita Raškevičiūtė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania
| | - Rimantas Slibinskas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V.Graiciuno 8, Vilnius, LT-02241, Lithuania.
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27
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Nykänen M, Birch D, Peterson R, Yu H, Kautto L, Gryshyna A, Te'o J, Nevalainen H. Ultrastructural features of the early secretory pathway in Trichoderma reesei. Curr Genet 2015; 62:455-65. [PMID: 26699139 DOI: 10.1007/s00294-015-0555-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 01/07/2023]
Abstract
We have systematically analysed the ultrastructure of the early secretory pathway in the Trichoderma reesei hyphae in the wild-type QM6a, cellulase-overexpressing Rut-C30 strain and a Rut-C30 transformant BV47 overexpressing a recombinant BiP1-VenusYFP fusion protein with an endoplasmic reticulum (ER) retention signal. The hyphae were studied after 24 h of growth using transmission electron microscopy, confocal microscopy and quantitative stereological techniques. All three strains exhibited different spatial organisation of the ER at 24 h in both a cellulase-inducing medium and a minimal medium containing glycerol as a carbon source (non-cellulase-inducing medium). The wild-type displayed a number of ER subdomains including parallel tubular/cisternal ER, ER whorls, ER-isolation membrane complexes with abundant autophagy vacuoles and dense bodies. Rut-C30 and its transformant BV47 overexpressing the BiP1-VenusYFP fusion protein also contained parallel tubular/cisternal ER, but no ER whorls; also, there were very few autophagy vacuoles and an increasing amount of punctate bodies where particularly the recombinant BiP1-VenusYFP fusion protein was localised. The early presence of distinct strain-specific features such as the dominance of ER whorls in the wild type and tub/cis ER in Rut-C30 suggests that these are inherent traits and not solely a result of cellular response mechanisms by the high secreting mutant to protein overload.
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Affiliation(s)
- Marko Nykänen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Debra Birch
- Microscopy Unit, Faculty of Science, Macquarie University, Sydney, NSW, 2109, Australia
| | - Robyn Peterson
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Hong Yu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Westmead Millenium Institute, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia
| | - Liisa Kautto
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Anna Gryshyna
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Junior Te'o
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
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28
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Tang H, Bao X, Shen Y, Song M, Wang S, Wang C, Hou J. Engineering protein folding and translocation improves heterologous protein secretion inSaccharomyces cerevisiae. Biotechnol Bioeng 2015; 112:1872-82. [DOI: 10.1002/bit.25596] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hongting Tang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Yu Shen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Meihui Song
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Shenghuan Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Chengqiang Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Jin Hou
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
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29
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Kim H, Yoo SJ, Kang HA. Yeast synthetic biology for the production of recombinant therapeutic proteins. FEMS Yeast Res 2015; 15:1-16. [PMID: 25130199 DOI: 10.1111/1567-1364.12195] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/12/2014] [Accepted: 08/05/2014] [Indexed: 11/29/2022] Open
Abstract
The production of recombinant therapeutic proteins is one of the fast-growing areas of molecular medicine and currently plays an important role in treatment of several diseases. Yeasts are unicellular eukaryotic microbial host cells that offer unique advantages in producing biopharmaceutical proteins. Yeasts are capable of robust growth on simple media, readily accommodate genetic modifications, and incorporate typical eukaryotic post-translational modifications. Saccharomyces cerevisiae is a traditional baker's yeast that has been used as a major host for the production of biopharmaceuticals; however, several nonconventional yeast species including Hansenula polymorpha, Pichia pastoris, and Yarrowia lipolytica have gained increasing attention as alternative hosts for the industrial production of recombinant proteins. In this review, we address the established and emerging genetic tools and host strains suitable for recombinant protein production in various yeast expression systems, particularly focusing on current efforts toward synthetic biology approaches in developing yeast cell factories for the production of therapeutic recombinant proteins.
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Affiliation(s)
- Hyunah Kim
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Su Jin Yoo
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
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30
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Fidan O, Zhan J. Recent advances in engineering yeast for pharmaceutical protein production. RSC Adv 2015. [DOI: 10.1039/c5ra13003d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Currently available systems and synthetic biology tools can be applied to yeast engineering for improved biopharmaceutical protein production.
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Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
| | - Jixun Zhan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
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31
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Improving the Secretory Production of the Heterologous Protein in Pichia pastoris by Focusing on Protein Folding. Appl Biochem Biotechnol 2014; 175:535-48. [DOI: 10.1007/s12010-014-1292-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/09/2014] [Indexed: 01/07/2023]
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32
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Delic M, Göngrich R, Mattanovich D, Gasser B. Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins. Antioxid Redox Signal 2014; 21:414-37. [PMID: 24483278 DOI: 10.1089/ars.2014.5844] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. RECENT ADVANCES Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. CRITICAL ISSUES While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. FUTURE DIRECTIONS Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.
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Affiliation(s)
- Marizela Delic
- 1 Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
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33
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Improved production of a heterologous amylase in Saccharomyces cerevisiae by inverse metabolic engineering. Appl Environ Microbiol 2014; 80:5542-50. [PMID: 24973076 DOI: 10.1128/aem.00712-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing demand for industrial enzymes and biopharmaceutical proteins relies on robust production hosts with high protein yield and productivity. Being one of the best-studied model organisms and capable of performing posttranslational modifications, the yeast Saccharomyces cerevisiae is widely used as a cell factory for recombinant protein production. However, many recombinant proteins are produced at only 1% (or less) of the theoretical capacity due to the complexity of the secretory pathway, which has not been fully exploited. In this study, we applied the concept of inverse metabolic engineering to identify novel targets for improving protein secretion. Screening that combined UV-random mutagenesis and selection for growth on starch was performed to find mutant strains producing heterologous amylase 5-fold above the level produced by the reference strain. Genomic mutations that could be associated with higher amylase secretion were identified through whole-genome sequencing. Several single-point mutations, including an S196I point mutation in the VTA1 gene coding for a protein involved in vacuolar sorting, were evaluated by introducing these to the starting strain. By applying this modification alone, the amylase secretion could be improved by 35%. As a complement to the identification of genomic variants, transcriptome analysis was also performed in order to understand on a global level the transcriptional changes associated with the improved amylase production caused by UV mutagenesis.
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34
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Biopharmaceutical protein production bySaccharomyces cerevisiae: current state and future prospects. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Andersen JT, Cameron J, Plumridge A, Evans L, Sleep D, Sandlie I. Single-chain variable fragment albumin fusions bind the neonatal Fc receptor (FcRn) in a species-dependent manner: implications for in vivo half-life evaluation of albumin fusion therapeutics. J Biol Chem 2013; 288:24277-85. [PMID: 23818524 DOI: 10.1074/jbc.m113.463000] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Albumin has a serum half-life of 3 weeks in humans. This has been utilized to extend the serum persistence of biopharmaceuticals that are fused to albumin. In light of the fact that the neonatal Fc receptor (FcRn) is a key regulator of albumin homeostasis, it is crucial to address how fusion of therapeutics to albumin impacts binding to FcRn. Here, we report on a detailed molecular investigation on how genetic fusion of a short peptide or an single-chain variable fragment (scFv) fragment to human serum albumin (HSA) influences pH-dependent binding to FcRn from mouse, rat, monkey, and human. We have found that fusion to the N- or C-terminal end of HSA only slightly reduces receptor binding, where the most noticeable effect is seen after fusion to the C-terminal end. Furthermore, in contrast to the observed strong binding to human and monkey FcRn, HSA and all HSA fusions bound very poorly to mouse and rat versions of the receptor. Thus, we demonstrate that conventional rodents are limited as preclinical models for analysis of serum half-life of HSA-based biopharmaceuticals. This finding is explained by cross-species differences mainly found within domain III (DIII) of albumin. Our data demonstrate that although fusion, particularly to the C-terminal end, may slightly reduce the affinity for FcRn, HSA is versatile as a carrier of biopharmaceuticals.
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Affiliation(s)
- Jan Terje Andersen
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0316 Oslo, Norway.
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36
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Feizi A, Österlund T, Petranovic D, Bordel S, Nielsen J. Genome-scale modeling of the protein secretory machinery in yeast. PLoS One 2013; 8:e63284. [PMID: 23667601 PMCID: PMC3646752 DOI: 10.1371/journal.pone.0063284] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/31/2013] [Indexed: 11/19/2022] Open
Abstract
The protein secretory machinery in Eukarya is involved in post-translational modification (PTMs) and sorting of the secretory and many transmembrane proteins. While the secretory machinery has been well-studied using classic reductionist approaches, a holistic view of its complex nature is lacking. Here, we present the first genome-scale model for the yeast secretory machinery which captures the knowledge generated through more than 50 years of research. The model is based on the concept of a Protein Specific Information Matrix (PSIM: characterized by seven PTMs features). An algorithm was developed which mimics secretory machinery and assigns each secretory protein to a particular secretory class that determines the set of PTMs and transport steps specific to each protein. Protein abundances were integrated with the model in order to gain system level estimation of the metabolic demands associated with the processing of each specific protein as well as a quantitative estimation of the activity of each component of the secretory machinery.
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Affiliation(s)
- Amir Feizi
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Österlund
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dina Petranovic
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Sergio Bordel
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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Kazemi Seresht A, Palmqvist EA, Schluckebier G, Pettersson I, Olsson L. The challenge of improved secretory production of active pharmaceutical ingredients inSaccharomyces cerevisiae: A case study on human insulin analogs. Biotechnol Bioeng 2013; 110:2764-74. [DOI: 10.1002/bit.24928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/18/2013] [Accepted: 03/28/2013] [Indexed: 12/27/2022]
Affiliation(s)
| | - Eva A. Palmqvist
- Diabetes Protein Engineering, Diabetes Research Unit; Novo Nordisk A/S; DK-2780; Måløv; Denmark
| | - Gerd Schluckebier
- Diabetes Protein Engineering, Diabetes Research Unit; Novo Nordisk A/S; DK-2780; Måløv; Denmark
| | - Ingrid Pettersson
- Diabetes Protein Engineering, Diabetes Research Unit; Novo Nordisk A/S; DK-2780; Måløv; Denmark
| | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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38
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Current state and recent advances in biopharmaceutical production in Escherichia coli, yeasts and mammalian cells. J Ind Microbiol Biotechnol 2013; 40:257-74. [PMID: 23385853 DOI: 10.1007/s10295-013-1235-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/22/2013] [Indexed: 12/28/2022]
Abstract
Almost all of the 200 or so approved biopharmaceuticals have been produced in one of three host systems: the bacterium Escherichia coli, yeasts (Saccharomyces cerevisiae, Pichia pastoris) and mammalian cells. We describe the most widely used methods for the expression of recombinant proteins in the cytoplasm or periplasm of E. coli, as well as strategies for secreting the product to the growth medium. Recombinant expression in E. coli influences the cell physiology and triggers a stress response, which has to be considered in process development. Increased expression of a functional protein can be achieved by optimizing the gene, plasmid, host cell, and fermentation process. Relevant properties of two yeast expression systems, S. cerevisiae and P. pastoris, are summarized. Optimization of expression in S. cerevisiae has focused mainly on increasing the secretion, which is otherwise limiting. P. pastoris was recently approved as a host for biopharmaceutical production for the first time. It enables high-level protein production and secretion. Additionally, genetic engineering has resulted in its ability to produce recombinant proteins with humanized glycosylation patterns. Several mammalian cell lines of either rodent or human origin are also used in biopharmaceutical production. Optimization of their expression has focused on clonal selection, interference with epigenetic factors and genetic engineering. Systemic optimization approaches are applied to all cell expression systems. They feature parallel high-throughput techniques, such as DNA microarray, next-generation sequencing and proteomics, and enable simultaneous monitoring of multiple parameters. Systemic approaches, together with technological advances such as disposable bioreactors and microbioreactors, are expected to lead to increased quality and quantity of biopharmaceuticals, as well as to reduced product development times.
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39
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Hou J, Osterlund T, Liu Z, Petranovic D, Nielsen J. Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2012. [PMID: 23208612 DOI: 10.1007/s00253-012-4596-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The yeast Saccharomyces cerevisiae is a widely used platform for the production of heterologous proteins of medical or industrial interest. However, heterologous protein productivity is often low due to limitations of the host strain. Heat shock response (HSR) is an inducible, global, cellular stress response, which facilitates the cell recovery from many forms of stress, e.g., heat stress. In S. cerevisiae, HSR is regulated mainly by the transcription factor heat shock factor (Hsf1p) and many of its targets are genes coding for molecular chaperones that promote protein folding and prevent the accumulation of mis-folded or aggregated proteins. In this work, we over-expressed a mutant HSF1 gene HSF1-R206S which can constitutively activate HSR, so the heat shock response was induced at different levels, and we studied the impact of HSR on heterologous protein secretion. We found that moderate and high level over-expression of HSF1-R206S increased heterologous α-amylase yield 25 and 70 % when glucose was fully consumed, and 37 and 62 % at the end of the ethanol phase, respectively. Moderate and high level over-expression also improved endogenous invertase yield 118 and 94 %, respectively. However, human insulin precursor was only improved slightly and this only by high level over-expression of HSF1-R206S, supporting our previous findings that the production of this protein in S. cerevisiae is not limited by secretion. Our results provide an effective strategy to improve protein secretion and demonstrated an approach that can induce ER and cytosolic chaperones simultaneously.
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Affiliation(s)
- Jin Hou
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
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Shen Q, Wu M, Wang HB, Naranmandura H, Chen SQ. The effect of gene copy number and co-expression of chaperone on production of albumin fusion proteins in Pichia pastoris. Appl Microbiol Biotechnol 2012; 96:763-72. [PMID: 22885695 DOI: 10.1007/s00253-012-4337-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/21/2012] [Accepted: 07/24/2012] [Indexed: 12/24/2022]
Abstract
Interleukin-1 receptor antagonist (IL1ra) is known to treat a number of diseases such as rheumatoid arthritis and type 2 diabetes. However, the biological half-life of IL1ra is very short due to its rapid renal clearance. Our present study aimed to increase the biological half-life of IL1ra through fusion with human serum albumin (HSA), and then augmented expression of the IL1ra and HSA fusion protein (IH) in Pichia pastoris strain by increasing IH gene copy number or was co-expressed with chaperone. By comparing clones containing varying copy numbers of IH fusion gene, it was observed that higher levels of secretory IH fusion protein was produced in strain with higher IH gene copy number. In addition, IH protein yield was further improved after being co-expressed with protein disulfide isomerase (PDI). Conversely, it was significantly decreased (i.e., secretory IH in the culture medium) by co-expression of immunoglobulin binding protein. We have also discussed whether the multi-copy strain and co-expressed of PDI could enhance the levels of other secretory albumin fusion protein (e.g., HSA and human growth hormone fusion protein). Interestingly, the level of this fusion protein was apparently also increased by these approaches. In conclusion, our results have demonstrated that increasing copy number and co-expression of PDI may raise yield of albumin fusion protein in P. pastoris, which might probably contribute to the industry for the development of proteinous drugs.
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Affiliation(s)
- Qi Shen
- Department of Pharmacology, Toxicology and Biochemical Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University Hangzhou, Hangzhou, 310058, China
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Park YK, Jung SM, Lim HK, Son YJ, Park YC, Seo JH. Effects of Trx2p and Sec23p expression on stable production of hepatitis B surface antigen S domain in recombinant Saccharomyces cerevisiae. J Biotechnol 2012; 160:151-60. [DOI: 10.1016/j.jbiotec.2012.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 03/14/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022]
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Kazemi Seresht A, Nørgaard P, Palmqvist EA, Andersen AS, Olsson L. Modulating heterologous protein production in yeast: the applicability of truncated auxotrophic markers. Appl Microbiol Biotechnol 2012; 97:3939-48. [PMID: 22782252 DOI: 10.1007/s00253-012-4263-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/19/2012] [Accepted: 06/22/2012] [Indexed: 11/28/2022]
Abstract
The use of auxotrophic Saccharomyces cerevisiae strains for improved production of a heterologous protein was examined. Two different marker genes were investigated, encoding key enzymes in the metabolic pathways for amino acid (LEU2) and pyrimidine (URA3) biosynthesis, respectively. Expression plasmids, carrying the partly defective selection markers LEU2d and URA3d, were constructed. Two CEN.PK-derived strains were chosen and insulin analogue precursor was selected as a model protein. Different truncations of the LEU2 and URA3 promoters were used as the mean to titrate the plasmid copy number and thus the recombinant gene dosage in order to improve insulin productivity. Experiments were initially carried out in batch mode to examine the stability of yeast transformants and to select high yielding mutants. Next, chemostat cultivations were run at high cell density to address industrial applicability and long-term expression stability of the transformants. We found that the choice of auxotrophic marker is crucial for developing a yeast expression system with stable heterologous protein production. The incremental truncation of the URA3 promoter led to higher plasmid copy numbers and IAP yields, whereas the truncation of the LEU2 promoter caused low plasmid stability. We show that the modification of the level of the recombinant gene dosage by varying the degree of promoter truncation can be a strong tool for optimization of productivity. The application of the URA3d-based expression systems showed a high potential for industrial protein production and for further academic studies.
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Affiliation(s)
- Ali Kazemi Seresht
- Protein Expression, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark.
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Hou J, Tyo KE, Liu Z, Petranovic D, Nielsen J. Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae. FEMS Yeast Res 2012; 12:491-510. [DOI: 10.1111/j.1567-1364.2012.00810.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/19/2012] [Accepted: 04/22/2012] [Indexed: 01/02/2023] Open
Affiliation(s)
| | | | - Zihe Liu
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Göteborg; Sweden
| | - Dina Petranovic
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Göteborg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Göteborg; Sweden
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Liu Z, Tyo KEJ, Martínez JL, Petranovic D, Nielsen J. Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae. Biotechnol Bioeng 2012; 109:1259-68. [PMID: 22179756 DOI: 10.1002/bit.24409] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/28/2011] [Accepted: 12/08/2011] [Indexed: 11/06/2022]
Abstract
Yeast Saccharomyces cerevisiae has become an attractive cell factory for production of commodity and speciality chemicals and proteins, such as industrial enzymes and pharmaceutical proteins. Here we evaluate most important expression factors for recombinant protein secretion: we chose two different proteins (insulin precursor (IP) and α-amylase), two different expression vectors (POTud plasmid and CPOTud plasmid) and two kinds of leader sequences (the glycosylated alpha factor leader and a synthetic leader with no glycosylation sites). We used IP and α-amylase as representatives of a simple protein and a multi-domain protein, as well as a non-glycosylated protein and a glycosylated protein, respectively. The genes coding for the two recombinant proteins were fused independently with two different leader sequences and were expressed using two different plasmid systems, resulting in eight different strains that were evaluated by batch fermentations. The secretion level (µmol/L) of IP was found to be higher than that of α-amylase for all expression systems and we also found larger variation in IP production for the different vectors. We also found that there is a change in protein production kinetics during the diauxic shift, that is, the IP was produced at higher rate during the glucose uptake phase, whereas amylase was produced at a higher rate in the ethanol uptake phase. For comparison, we also refer to data from another study, (Tyo et al. submitted) in which we used the p426GPD plasmid (standard vector using URA3 as marker gene and pGPD1 as expression promoter). For the IP there is more than 10-fold higher protein production with the CPOTud vector compared with the standard URA3-based vector, and this vector system therefore represent a valuable resource for future studies and optimization of recombinant protein production in yeast.
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Affiliation(s)
- Zihe Liu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Structure-based mutagenesis reveals the albumin-binding site of the neonatal Fc receptor. Nat Commun 2012; 3:610. [PMID: 22215085 PMCID: PMC3272563 DOI: 10.1038/ncomms1607] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/23/2011] [Indexed: 12/29/2022] Open
Abstract
Albumin is the most abundant protein in blood where it has a pivotal role as a transporter of fatty acids and drugs. Like IgG, albumin has long serum half-life, protected from degradation by pH-dependent recycling mediated by interaction with the neonatal Fc receptor, FcRn. Although the FcRn interaction with IgG is well characterized at the atomic level, its interaction with albumin is not. Here we present structure-based modelling of the FcRn–albumin complex, supported by binding analysis of site-specific mutants, providing mechanistic evidence for the presence of pH-sensitive ionic networks at the interaction interface. These networks involve conserved histidines in both FcRn and albumin domain III. Histidines also contribute to intramolecular interactions that stabilize the otherwise flexible loops at both the interacting surfaces. Molecular details of the FcRn–albumin complex may guide the development of novel albumin variants with altered serum half-life as carriers of drugs. Albumin transport proteins circulate in the blood and are protected from degradation by interaction with the neonatal Fc receptor. Andersen et al. investigate the albumin binding site of the neonatal Fc receptor and find pH sensitive ionic networks at the binding interface.
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Gil DF, García-Fernández R, Alonso-del-Rivero M, Lamazares E, Pérez M, Varas L, Díaz J, Chávez MA, González-González Y, Mansur M. Recombinant expression of ShPI-1A, a non-specific BPTI-Kunitz-type inhibitor, and its protection effect on proteolytic degradation of recombinant human miniproinsulin expressed in Pichia pastoris. FEMS Yeast Res 2011; 11:575-86. [DOI: 10.1111/j.1567-1364.2011.00749.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 06/28/2011] [Accepted: 07/25/2011] [Indexed: 01/28/2023] Open
Affiliation(s)
- Dayrom F. Gil
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - Rossana García-Fernández
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - Maday Alonso-del-Rivero
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - Emilio Lamazares
- Centro de Ingeniería Genética y Biotecnología (CIGB); Cubanacán; La Habana; Cuba
| | - Mariela Pérez
- Centro de Ingeniería Genética y Biotecnología (CIGB); Cubanacán; La Habana; Cuba
| | - Laura Varas
- Centro de Ingeniería Genética y Biotecnología (CIGB); Cubanacán; La Habana; Cuba
| | - Joaquín Díaz
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - María A. Chávez
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - Yamile González-González
- Centro de Estudios de Proteínas; Facultad de Biología; Universidad de La Habana; Plaza de la Revolución; La Habana; Cuba
| | - Manuel Mansur
- Centro de Ingeniería Genética y Biotecnología (CIGB); Cubanacán; La Habana; Cuba
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Martínez-Alonso M, Villaverde A, Ferrer-Miralles N. Cross-system excision of chaperone-mediated proteolysis in chaperone-assisted recombinant protein production. Bioeng Bugs 2011; 1:148-50. [PMID: 21326941 DOI: 10.4161/bbug.1.2.11048] [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: 12/20/2009] [Accepted: 12/29/2009] [Indexed: 11/19/2022] Open
Abstract
Main Escherichia coli cytosolic chaperones such as DnaK are key components of the control quality network designed to minimize the prevalence of polypeptides with aberrant conformations. This is achieved by both favoring refolding activities but also stimulating proteolytic degradation of folding reluctant species. This last activity is responsible for the decrease of the proteolytic stability of recombinant proteins when co-produced along with DnaK, where an increase in solubility might be associated to a decrease in protein yield. However, when DnaK and its co-chaperone DnaJ are co-produced in cultured insect cells or whole insect larvae (and expectedly, in other heterologous hosts), only positive, folding-related effects of these chaperones are observed, in absence of proteolysis-mediated reduction of recombinant protein yield.
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Affiliation(s)
- Mónica Martínez-Alonso
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain
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Finnis CJA, Payne T, Hay J, Dodsworth N, Wilkinson D, Morton P, Saxton MJ, Tooth DJ, Evans RW, Goldenberg H, Scheiber-Mojdehkar B, Ternes N, Sleep D. High-level production of animal-free recombinant transferrin from Saccharomyces cerevisiae. Microb Cell Fact 2010; 9:87. [PMID: 21083917 PMCID: PMC3000842 DOI: 10.1186/1475-2859-9-87] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 11/17/2010] [Indexed: 11/18/2022] Open
Abstract
Background Animal-free recombinant proteins provide a safe and effective alternative to tissue or serum-derived products for both therapeutic and biomanufacturing applications. While recombinant insulin and albumin already exist to replace their human counterparts in cell culture media, until recently there has been no equivalent for serum transferrin. Results The first microbial system for the high-level secretion of a recombinant transferrin (rTf) has been developed from Saccharomyces cerevisiae strains originally engineered for the commercial production of recombinant human albumin (Novozymes' Recombumin® USP-NF) and albumin fusion proteins (Novozymes' albufuse®). A full-length non-N-linked glycosylated rTf was secreted at levels around ten-fold higher than from commonly used laboratory strains. Modification of the yeast 2 μm-based expression vector to allow overexpression of the ER chaperone, protein disulphide isomerase, further increased the secretion of rTf approximately twelve-fold in high cell density fermentation. The rTf produced was functionally equivalent to plasma-derived transferrin. Conclusions A Saccharomyces cerevisiae expression system has enabled the cGMP manufacture of an animal-free rTf for industrial cell culture application without the risk of prion and viral contamination, and provides a high-quality platform for the development of transferrin-based therapeutics.
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Affiliation(s)
- Christopher J A Finnis
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham NG71FD, UK.
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Evans L, Hughes M, Waters J, Cameron J, Dodsworth N, Tooth D, Greenfield A, Sleep D. The production, characterisation and enhanced pharmacokinetics of scFv-albumin fusions expressed in Saccharomyces cerevisiae. Protein Expr Purif 2010; 73:113-24. [PMID: 20546898 DOI: 10.1016/j.pep.2010.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 11/20/2022]
Abstract
An expression system is described for the production of monomeric scFvs and scFv antibody fragments genetically fused to human albumin (at either the N- or C-terminus or both). Based upon strains of Saccharomyces cerevisiae originally developed for the production of a recombinant human albumin (Recombumin) this system has delivered high levels of secreted product into the supernatant of shake flask and high cell density fed-batch fermentations. Specific binding to the corresponding ligand was demonstrated for each of the scFvs and scFv-albumin fusions and pharmacokinetic studies showed that the fusion products had greatly extended circulatory half-lives. The system described provides an attractive alternative to other microbial systems for the manufacture of this type of product.
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Affiliation(s)
- Leslie Evans
- Novozymes Biopharma UK Ltd., Castle Court, 59 Castle Boulevard, Nottingham NG7 1FD, United Kingdom.
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Idiris A, Tohda H, Kumagai H, Takegawa K. Engineering of protein secretion in yeast: strategies and impact on protein production. Appl Microbiol Biotechnol 2010; 86:403-17. [DOI: 10.1007/s00253-010-2447-0] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 01/07/2010] [Accepted: 01/09/2010] [Indexed: 01/08/2023]
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