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Bitar L, Isella B, Bertella F, Bettker Vasconcelos C, Harings J, Kopp A, van der Meer Y, Vaughan TJ, Bortesi L. Sustainable Bombyx mori's silk fibroin for biomedical applications as a molecular biotechnology challenge: A review. Int J Biol Macromol 2024; 264:130374. [PMID: 38408575 DOI: 10.1016/j.ijbiomac.2024.130374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Silk is a natural engineering material with a unique set of properties. The major constituent of silk is fibroin, a protein widely used in the biomedical field because of its mechanical strength, toughness and elasticity, as well as its biocompatibility and biodegradability. The domestication of silkworms allows large amounts of fibroin to be extracted inexpensively from silk cocoons. However, the industrial extraction process has drawbacks in terms of sustainability and the quality of the final medical product. The heterologous production of fibroin using recombinant DNA technology is a promising approach to address these issues, but the production of such recombinant proteins is challenging and further optimization is required due to the large size and repetitive structure of fibroin's DNA and amino acid sequence. In this review, we describe the structure-function relationship of fibroin, the current extraction process, and some insights into the sustainability of silk production for biomedical applications. We focus on recent advances in molecular biotechnology underpinning the production of recombinant fibroin, working toward a standardized, successful and sustainable process.
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Affiliation(s)
- Lara Bitar
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands; Fibrothelium GmbH, Philipsstraße 8, 52068 Aachen, Germany
| | - Benedetta Isella
- Fibrothelium GmbH, Philipsstraße 8, 52068 Aachen, Germany; Biomechanics Research Centre (BioMEC), Biomedical Engineering, School of Engineering, College of Science and Engineering, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Francesca Bertella
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands; B4Plastics, IQ Parklaan 2A, 3650 Dilsen-Stokkem, Belgium
| | - Carolina Bettker Vasconcelos
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands; Umlaut GmbH, Am Kraftversorgungsturm 3, 52070 Aachen, Germany
| | - Jules Harings
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands
| | - Alexander Kopp
- Fibrothelium GmbH, Philipsstraße 8, 52068 Aachen, Germany
| | - Yvonne van der Meer
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands
| | - Ted J Vaughan
- Biomechanics Research Centre (BioMEC), Biomedical Engineering, School of Engineering, College of Science and Engineering, University of Galway, University Road, H91 TK33 Galway, Ireland
| | - Luisa Bortesi
- Maastricht University-Aachen Maastricht Institute for Biobased Materials (AMIBM), Urmonderbaan 22, 6167 RD Geleen, the Netherlands.
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Vogeleer P, Millard P, Arbulú ASO, Pflüger-Grau K, Kremling A, Létisse F. Metabolic impact of heterologous protein production in Pseudomonas putida: Insights into carbon and energy flux control. Metab Eng 2024; 81:26-37. [PMID: 37918614 DOI: 10.1016/j.ymben.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
For engineered microorganisms, the production of heterologous proteins that are often useless to host cells represents a burden on resources, which have to be shared with normal cellular processes. Within a certain metabolic leeway, this competitive process has no impact on growth. However, once this leeway, or free capacity, is fully utilized, the extra load becomes a metabolic burden that inhibits cellular processes and triggers a broad cellular response, reducing cell growth and often hindering the production of heterologous proteins. In this study, we sought to characterize the metabolic rearrangements occurring in the central metabolism of Pseudomonas putida at different levels of metabolic load. To this end, we constructed a P. putida KT2440 strain that expressed two genes encoding fluorescent proteins, one in the genome under constitutive expression to monitor the free capacity, and the other on an inducible plasmid to probe heterologous protein production. We found that metabolic fluxes are considerably reshuffled, especially at the level of periplasmic pathways, as soon as the metabolic load exceeds the free capacity. Heterologous protein production leads to the decoupling of anabolism and catabolism, resulting in large excess energy production relative to the requirements of protein biosynthesis. Finally, heterologous protein production was found to exert a stronger control on carbon fluxes than on energy fluxes, indicating that the flexible nature of P. putida's central metabolic network is solicited to sustain energy production.
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Affiliation(s)
- Philippe Vogeleer
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, UPS, Toulouse, France
| | - Pierre Millard
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, UPS, Toulouse, France; MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Ana-Sofia Ortega Arbulú
- Technical University Munich, TUM School of Engineering and Design, Department of Energy and Process Engineering, Systems Biotechnology, Germany
| | - Katharina Pflüger-Grau
- Technical University Munich, TUM School of Engineering and Design, Department of Energy and Process Engineering, Systems Biotechnology, Germany
| | - Andreas Kremling
- Technical University Munich, TUM School of Engineering and Design, Department of Energy and Process Engineering, Systems Biotechnology, Germany
| | - Fabien Létisse
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, UPS, Toulouse, France.
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Liu D, Garrigues S, de Vries RP. Heterologous protein production in filamentous fungi. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12660-8. [PMID: 37405433 PMCID: PMC10386965 DOI: 10.1007/s00253-023-12660-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Filamentous fungi are able to produce a wide range of valuable proteins and enzymes for many industrial applications. Recent advances in fungal genomics and experimental technologies are rapidly changing the approaches for the development and use of filamentous fungi as hosts for the production of both homologous and heterologous proteins. In this review, we highlight the benefits and challenges of using filamentous fungi for the production of heterologous proteins. We review various techniques commonly employed to improve the heterologous protein production in filamentous fungi, such as strong and inducible promoters, codon optimization, more efficient signal peptides for secretion, carrier proteins, engineering of glycosylation sites, regulation of the unfolded protein response and endoplasmic reticulum associated protein degradation, optimization of the intracellular transport process, regulation of unconventional protein secretion, and construction of protease-deficient strains. KEY POINTS: • This review updates the knowledge on heterologous protein production in filamentous fungi. • Several fungal cell factories and potential candidates are discussed. • Insights into improving heterologous gene expression are given.
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Affiliation(s)
- Dujuan Liu
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Department of Food Biotechnology, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
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Vidal LEL, Figueira-Mansur J, Jurgilas PB, Argondizzo APC, Pestana CP, Martins FO, da Silva Junior HC, Miguez M, Loureiro BO, Marques CDFS, Trinta KS, da Silva LBR, de Mello MB, da Silva ED, Bastos RC, Esteves G. Process development and characterization of recombinant nucleocapsid protein for its application on COVID-19 diagnosis. Protein Expr Purif 2023; 207:106263. [PMID: 36921810 PMCID: PMC10012136 DOI: 10.1016/j.pep.2023.106263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2). The nucleocapsid (N) protein from Sars-CoV-2 is a highly immunogenic antigen and responsible for genome packing. Serological assays are important tools to detect previous exposure to SARS-CoV-2, complement epidemiological studies, vaccine evaluation and also in COVID-19 surveillance. SARS-CoV-2 N (r2N) protein was produced in Escherichia coli, characterized, and the immunological performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and beads-based array immunoassay. r2N protein oligomers were evidenced when it is associated to nucleic acid. Benzonase treatment reduced host nucleic acid associated to r2N protein, but crosslinking assay still demonstrates the presence of higher-order oligomers. Nevertheless, after RNase treatment the higher-order oligomers reduced, and dimer form increased, suggesting RNA contributes to the oligomer formation. Structural analysis revealed nucleic acid did not interfere with the thermal stability of the recombinant protein. Interestingly, nucleic acid was able to prevent r2N protein aggregation even with increasing temperature while the protein benzonase treated begin aggregation process above 55 °C. In immunological characterization, ELISA performed with 233 serum samples presented a sensitivity of 97.44% (95% Confidence Interval, CI, 91.04%, 99.69%) and a specificity of 98.71% (95% CI, 95.42%, 99.84%) while beads-based array immunoassay carried out with 217 samples showed 100% sensitivity and 98.6% specificity. The results exhibited an excellent immunological performance of r2N protein in serologic assays showing that, even in presence of nucleic acid, it can be used as a component of an immunoassay for the sensitive and specific detection of SARS-CoV-2 antibodies.
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Affiliation(s)
- Luãnna Elisa Liebscher Vidal
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil.
| | - Janaina Figueira-Mansur
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Patrícia Barbosa Jurgilas
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Ana Paula Correa Argondizzo
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Cristiane Pinheiro Pestana
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Fernanda Otaviano Martins
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Haroldo Cid da Silva Junior
- Immunological Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Mariana Miguez
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Bernardo Oliveira Loureiro
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Christiane de Fátima Silva Marques
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Karen Soares Trinta
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Leila Botelho Rodrigues da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Marcelle Bral de Mello
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Edimilson Domingos da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Renata Chagas Bastos
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Gabriela Esteves
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
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Ye B, Tao Q, Yan X. A transposon system for random insertion of a gene expression cassette into the chromosome of Bacillus subtilis. J Biotechnol 2023; 361:66-73. [PMID: 36494011 DOI: 10.1016/j.jbiotec.2022.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Bacillus subtilis is a robust industrial workhorse for the production of heterologous proteins. Chromosomal integration-based protein production has advantages over plasmid-based methods. Considering that the expression level of a gene is affected by its location in the chromosome, it is important to find an optimal integration site for the gene to be expressed. This work establishes a method for random insertion of a gene expression cassette into chromosomes, enabling the screening of optimal integration sites for high-level protein production. Specifically, a gene expression cassette and a chloromycetin-resistance marker are assembled into a transposon. This transposon is inserted between the promoter and the ribosomal binding site of the zeocin-resistance marker in the chromosome, which blocks the transcription of the zeocin-resistance gene. Transposase Himar1-mediated transposition of this transposon activates the zeocin-resistance marker, which can be selected on plates containing both chloromycetin and zeocin. The transposition frequency was over 10-5. This method was used to select proper insertion sites for the expression cassette of methyl parathion hydrolase (MPH). Compared with the common integration site amyE, the expression level of MPH was increased up to 50 % at the yjbH site.
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Affiliation(s)
- Bin Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; Institute of Microbe and Host Health, College of Agriculture and Forestry, Linyi University, Linyi, Shandong 276000, PR China
| | - Qing Tao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Ergün BG, Laçın K, Çaloğlu B, Binay B. Second generation Pichia pastoris strain and bioprocess designs. Biotechnol Biofuels Bioprod 2022; 15:150. [PMID: 36581872 PMCID: PMC9798597 DOI: 10.1186/s13068-022-02234-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/04/2022] [Indexed: 12/30/2022]
Abstract
Yeast was the first microorganism used by mankind for biotransformation processes that laid the foundations of industrial biotechnology. In the last decade, Pichia pastoris has become the leading eukaryotic host organism for bioproduct generation. Most of the P. pastoris bioprocess operations has been relying on toxic methanol and glucose feed. In the actual bioeconomy era, for sustainable value-added bioproduct generation, non-conventional yeast P. pastoris bioprocess operations should be extended to low-cost and renewable substrates for large volume bio-based commodity productions. In this review, we evaluated the potential of P. pastoris for the establishment of circular bioeconomy due to its potential to generate industrially relevant bioproducts from renewable sources and waste streams in a cost-effective and environmentally friendly manner. Furthermore, we discussed challenges with the second generation P. pastoris platforms and propose novel insights for future perspectives. In this regard, potential of low cost substrate candidates, i.e., lignocellulosic biomass components, cereal by-products, sugar industry by-products molasses and sugarcane bagasse, high fructose syrup by-products, biodiesel industry by-product crude glycerol, kitchen waste and other agri-food industry by products were evaluated for P. pastoris cell growth promoting effects and recombinant protein production. Further metabolic pathway engineering of P. pastoris to construct renewable and low cost substrate utilization pathways was discussed. Although, second generation P. pastoris bioprocess operations for valorisation of wastes and by-products still in its infancy, rapidly emerging synthetic biology tools and metabolic engineering of P. pastoris will pave the way for more sustainable environment and bioeconomy. From environmental point of view, second generation bioprocess development is also important for waste recycling otherwise disposal of carbon-rich effluents creates environmental concerns. P. pastoris high tolerance to toxic contaminants found in lignocellulosic biomass hydrolysate and industrial waste effluent crude glycerol provides the yeast with advantages to extend its applications toward second generation P. pastoris strain design and bioprocess engineering, in the years to come.
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Affiliation(s)
- Burcu Gündüz Ergün
- grid.18376.3b0000 0001 0723 2427National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey ,Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey
| | - Kübra Laçın
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Buse Çaloğlu
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Barış Binay
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey ,grid.448834.70000 0004 0595 7127BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400 Gebze Kocaeli, Turkey
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Liu B, Zhao Y, Zhou H, Zhang J. Enhancing xylanase expression of Komagataella phaffii induced by formate through Mit1 co-expression. Bioprocess Biosyst Eng 2022; 45:1515-1525. [PMID: 35881246 DOI: 10.1007/s00449-022-02760-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Komagataella phaffii (K. phaffii) is a famous microbial cell of heterologous protein and value-added chemicals production because of its strict and strong promoter (alcohol oxidase 1 promoter, PAOX1). Formate is an attractive substitute of traditional inducer methanol because methanol is toxic and explosive. To obtain high level of Aspergillus niger ATCC1015 xylanase as a model of heterologous protein by K. phaffii at formate induction, insertion of three-copy cis-acting element W3A into PAOX1 additionally, and co-expression of transcription factor Mit1 under another PAOX1 were carried out separately and simultaneously. The yield of xylanase increased by 41% at formate induction when Mit1 was co-expressed. Furtherly, the yield of xylanase increased by 42% using sorbitol as supplemental carbon source with the result of 408.3 × 103 U‧L-1 xylanase. Therefore, a non-methanol needed and inducible heterologous protein expression system of Komagataella phaffii was developed successfully.
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Affiliation(s)
- Bing Liu
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Yixin Zhao
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Hualan Zhou
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Jianguo Zhang
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093.
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Gast V, Sandegren A, Dunås F, Ekblad S, Güler R, Thorén S, Tous Mohedano M, Molin M, Engqvist MKM, Siewers V. Engineering Saccharomyces cerevisiae for the production and secretion of Affibody molecules. Microb Cell Fact 2022; 21:36. [PMID: 35264156 PMCID: PMC8905840 DOI: 10.1186/s12934-022-01761-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background Affibody molecules are synthetic peptides with a variety of therapeutic and diagnostic applications. To date, Affibody molecules have mainly been produced by the bacterial production host Escherichia coli. There is an interest in exploring alternative production hosts to identify potential improvements in terms of yield, ease of production and purification advantages. In this study, we evaluated the feasibility of Saccharomyces cerevisiae as a production chassis for this group of proteins. Results We examined the production of three different Affibody molecules in S. cerevisiae and found that these Affibody molecules were partially degraded. An albumin-binding domain, which may be attached to the Affibody molecules to increase their half-life, was identified to be a substrate for several S. cerevisiae proteases. We tested the removal of three vacuolar proteases, proteinase A, proteinase B and carboxypeptidase Y. Removal of one of these, proteinase A, resulted in intact secretion of one of the targeted Affibody molecules. Removal of either or both of the two additional proteases, carboxypeptidase Y and proteinase B, resulted in intact secretion of the two remaining Affibody molecules. The produced Affibody molecules were verified to bind their target, human HER3, as potently as the corresponding molecules produced in E. coli in an in vitro surface-plasmon resonance binding assay. Finally, we performed a fed-batch fermentation with one of the engineered protease-deficient S. cerevisiae strains and achieved a protein titer of 530 mg Affibody molecule/L. Conclusion This study shows that engineered S. cerevisiae has a great potential as a production host for recombinant Affibody molecules, reaching a high titer, and for proteins where endotoxin removal could be challenging, the use of S. cerevisiae obviates the need for endotoxin removal from protein produced in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01761-0.
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Affiliation(s)
- Veronica Gast
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | | | | | | | - Marta Tous Mohedano
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mikael Molin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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9
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Abstract
The availability of exceptionally strong and tightly regulated promoters is a key feature of Komagataella phaffii (syn. Pichia pastoris), a widely applied yeast expression system for heterologous protein production. Most commonly, the methanol-inducible promoter of the alcohol oxidase 1 gene (PAOX1) and the constitutive promoter of the glyceraldehyde 3 phosphate dehydrogenase gene (PGAP) have been used. Recently, also promising novel constitutive (PGCW14), regulated (PGTH1, PCAT1), and bidirectional promoters (histone promoters and synthetic hybrid variants) have been reported.As natural promoters showed so far limited tunability of expression levels and regulatory profiles, various promoter engineering efforts have been undertaken for P. pastoris . PAOX1, PDAS2, PGAP, and PGCW14 have been engineered by systematic deletion studies or random mutagenesis of upstream regulatory sequences. New engineering strategies have focused on PAOX1 core promoter modifications by random or rational approaches and transcriptional regulatory circuits to render PAOX1 independent of methanol induction. These promoter engineering efforts in P. pastoris have resulted in improved, sequence-diversified synthetic promoter variants allowing coordinated fine-tuning of gene expression for a multitude of biotechnological applications.
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Affiliation(s)
- Thomas Vogl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria.
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10
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Roux C, Etienne TA, Hajnsdorf E, Ropers D, Carpousis AJ, Cocaign-Bousquet M, Girbal L. The essential role of mRNA degradation in understanding and engineering E. coli metabolism. Biotechnol Adv 2021; 54:107805. [PMID: 34302931 DOI: 10.1016/j.biotechadv.2021.107805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022]
Abstract
Metabolic engineering strategies are crucial for the development of bacterial cell factories with improved performance. Until now, optimal metabolic networks have been designed based on systems biology approaches integrating large-scale data on the steady-state concentrations of mRNA, protein and metabolites, sometimes with dynamic data on fluxes, but rarely with any information on mRNA degradation. In this review, we compile growing evidence that mRNA degradation is a key regulatory level in E. coli that metabolic engineering strategies should take into account. We first discuss how mRNA degradation interacts with transcription and translation, two other gene expression processes, to balance transcription regulation and remove poorly translated mRNAs. The many reciprocal interactions between mRNA degradation and metabolism are also highlighted: metabolic activity can be controlled by changes in mRNA degradation and in return, the activity of the mRNA degradation machinery is controlled by metabolic factors. The mathematical models of the crosstalk between mRNA degradation dynamics and other cellular processes are presented and discussed with a view towards novel mRNA degradation-based metabolic engineering strategies. We show finally that mRNA degradation-based strategies have already successfully been applied to improve heterologous protein synthesis. Overall, this review underlines how important mRNA degradation is in regulating E. coli metabolism and identifies mRNA degradation as a key target for innovative metabolic engineering strategies in biotechnology.
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Affiliation(s)
- Charlotte Roux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Thibault A Etienne
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; Univ. Grenoble Alpes, Inria, 38000 Grenoble, France.
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | | | - A J Carpousis
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; LMGM, Université de Toulouse, CNRS, UPS, CBI, 31062 Toulouse, France.
| | | | - Laurence Girbal
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France.
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11
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Barrero JJ, Pagazartaundua A, Glick BS, Valero F, Ferrer P. Bioreactor-scale cell performance and protein production can be substantially increased by using a secretion signal that drives co-translational translocation in Pichia pastoris. N Biotechnol 2021; 60:85-95. [PMID: 33045421 PMCID: PMC7680431 DOI: 10.1016/j.nbt.2020.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 11/25/2022]
Abstract
Pichia pastoris (Komagataella spp.) has become one of the most important host organisms for production of heterologous proteins of biotechnological interest, many of them extracellular. The protein secretion pathway has been recognized as a limiting process in which many roadblocks have been pinpointed. Recently, we have identified a bottleneck at the ER translocation level. In earlier exploratory studies, this limitation could be largely overcome by using an improved chimeric secretion signal to drive proteins through the co-translational translocation pathway. Here, we have further tested at bioreactor scale the improved secretion signal consisting of the pre-Ost1 signal sequence, which drives proteins through co-translational translocation, followed by the pro region from the secretion signal of the Saccharomyces cerevisiae α-factor mating pheromone. For comparison, the commonly used full-length α-factor secretion signal, which drives proteins through post-translational translocation, was tested. These two secretion signals were fused to three different model proteins: the tetrameric red fluorescent protein E2-Crimson, which can be used to visualize roadblocks in the secretory pathway; the lipase 2 from Bacillus thermocatenulatus (BTL2); and the Rhizopus oryzae lipase (ROL). All strains were tested in batch cultivation to study the different growth parameters obtained. The strains carrying the improved secretion signal showed increased final production of the proteins of interest. Interestingly, they were able to grow at significantly higher maximum specific growth rates than their counterparts carrying the conventional secretion signal. These results were corroborated in a 5 L fed-batch cultivation, where the final product concentration and volumetric productivity were also shown to be improved.
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Affiliation(s)
- Juan J Barrero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain; Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Alejandro Pagazartaundua
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain; Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Benjamin S Glick
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain; Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain; Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain; Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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12
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Jurischka S, Bida A, Dohmen-Olma D, Kleine B, Potzkei J, Binder S, Schaumann G, Bakkes PJ, Freudl R. A secretion biosensor for monitoring Sec-dependent protein export in Corynebacterium glutamicum. Microb Cell Fact 2020; 19:11. [PMID: 31964372 PMCID: PMC6975037 DOI: 10.1186/s12934-019-1273-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, the industrial workhorse Corynebacterium glutamicum has gained increasing interest as a host organism for the secretory production of heterologous proteins. Generally, the yield of a target protein in the culture supernatant depends on a multitude of interdependent biological and bioprocess parameters which have to be optimized. So far, the monitoring of such optimization processes depends on the availability of a direct assay for the respective target protein that can be handled also in high throughput approaches. Since simple assays, such as standard enzymatic activity assays, are not always at hand, the availability of a general protein secretion biosensor is highly desirable. RESULTS High level secretion of proteins via the Sec protein export pathway leads to secretion stress, a phenomenon that is thought to be caused by the accumulation of incompletely or misfolded proteins at the membrane-cell envelope interface. We have analyzed the transcriptional responses of C. glutamicum to the secretory production of two different heterologous proteins and found that, in both cases, the expression of the gene encoding a homologue of the extracytosolic HtrA protease was highly upregulated. Based on this finding, a C. glutamicum Sec secretion biosensor strain was constructed in which the htrA gene on the chromosome was replaced by the eyfp gene. The fluorescence of the resulting reporter strain responded to the secretion of different heterologous proteins (cutinase from Fusarium solani pisi and alkaline phosphatase PhoA from Escherichia coli) in a dose-dependent manner. In addition, three differently efficient signal peptides for the secretory production of the cutinase could be differentiated by the biosensor signal. Furthermore, we have shown that an efficient signal peptide can be separated from a poor signal peptide by using the biosensor signal of the respective cells in fluorescence activated cell sorting experiments. CONCLUSIONS We have succeeded in the construction of a C. glutamicum biosensor strain that allows for the monitoring of Sec-dependent secretion of heterologous proteins in a dose-dependent manner, independent of a direct assay for the desired target protein.
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Affiliation(s)
- Sarah Jurischka
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), 52425, Jülich, Germany
| | - Astrid Bida
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Doris Dohmen-Olma
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Britta Kleine
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Janko Potzkei
- SenseUp GmbH, c/o Campus Forschungszentrum, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Stephan Binder
- SenseUp GmbH, c/o Campus Forschungszentrum, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Georg Schaumann
- SenseUp GmbH, c/o Campus Forschungszentrum, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Patrick J Bakkes
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Roland Freudl
- Institut für Bio- und Geowissenschaften 1, IBG1: Biotechnologie, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), 52425, Jülich, Germany.
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13
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Kanno AI, Leite LCDC, Pereira LR, de Jesus MJR, Andreata-Santos R, Alves RPDS, Durigon EL, Ferreira LCDS, Gonçalves VM. Optimization and scale-up production of Zika virus ΔNS1 in Escherichia coli: application of Response Surface Methodology. AMB Express 2019; 10:1. [PMID: 31893321 PMCID: PMC6938527 DOI: 10.1186/s13568-019-0926-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/03/2019] [Indexed: 02/01/2023] Open
Abstract
Diagnosing Zika virus (ZIKV) infections has been challenging due to the cross-reactivity of induced antibodies with other flavivirus. The concomitant occurrence of ZIKV and Dengue virus (DENV) in endemic regions requires diagnostic tools with the ability to distinguish these two viral infections. Recent studies demonstrated that immunoassays using the C-terminal fragment of ZIKV NS1 antigen (ΔNS1) can be used to discriminate ZIKV from DENV infections. In order to be used in serological tests, the expression/solubility of ΔNS1 and growth of recombinant E. coli strain were optimized by Response Surface Methodology. Temperature, time and IPTG concentration were evaluated. According to the model, the best condition determined in small scale cultures was 21 °C for 20 h with 0.7 mM of IPTG, which predicted 7.5 g/L of biomass and 962 mg/L of ΔNS1. These conditions were validated and used in a 6-L batch in the bioreactor, which produced 6.4 g/L of biomass and 500 mg/L of ΔNS1 in 12 h of induction. The serological ELISA test performed with purified ΔNS1 showed low cross-reactivity with antibodies from DENV-infected human subjects. Denaturation of ΔNS1 decreased the detection of anti-ZIKV antibodies, thus indicating the contribution of conformational epitopes and confirming the importance of properly folded ΔNS1 for the specificity of the serological analyses. Obtaining high yields of soluble ΔNS1 supports the viability of an effective serologic diagnostic test capable of differentiating ZIKV from other flavivirus infections.
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Söderberg JJ, Grgic M, Hjerde E, Haugen P. Aliivibrio wodanis as a production host: development of genetic tools for expression of cold-active enzymes. Microb Cell Fact 2019; 18:197. [PMID: 31711487 PMCID: PMC6844050 DOI: 10.1186/s12934-019-1247-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/31/2019] [Indexed: 01/16/2023] Open
Abstract
Background Heterologous production of cold-adapted proteins currently represents one of the greatest bottlenecks in the ongoing bioprospecting efforts to find new enzymes from low-temperature environments, such as, the polar oceans that represent essentially untapped resources in this respect. In mesophilic expression hosts such as Escherichia coli, cold-adapted enzymes often form inactive aggregates. Therefore it is necessary to develop new low-temperature expression systems, including identification of new host organisms and complementary genetic tools. Psychrophilic bacteria, including Pseudoalteromonas haloplanktis, Shewanella and Rhodococcus erythropolis have all been explored as candidates for such applications. However to date none of these have found widespread use as efficient expression systems, or are commercially available. In the present work we explored the use of the sub-Arctic bacterium Aliivibrio wodanis as a potential host for heterologous expression of cold-active enzymes. Results We tested 12 bacterial strains, as well as available vectors, promoters and reporter systems. We used RNA-sequencing to determine the most highly expressed genes and their intrinsic promoters in A. wodanis. In addition we examined a novel 5′-fusion to stimulate protein production and solubility. Finally we tested production of a set of “difficult-to-produce” enzymes originating from various bacteria and one Archaea. Our results show that cold-adapted enzymes can be produced in soluble and active form, even in cases when protein production failed in E. coli due to the formation of inclusion bodies. Moreover, we identified a 60-bp/20-aa fragment from the 5′-end of the AW0309160_00174 gene that stimulates expression of Green Fluorescent Protein and improves production of cold-active enzymes when used as a 5′-fusion. A 25-aa peptide from the same protein enhanced secretion of a 25-aa-sfGFP fusion. Conclusions Our results indicate the use of A. wodanis and associated genetic tools for low-temperature protein production and indicate that A. wodanis represents an interesting platform for further development of a protein production system that can promote further cold-enzyme discoveries.
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Affiliation(s)
- Jenny Johansson Söderberg
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Miriam Grgic
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB) and The Norwegian Structural Biology Centre (NorStruct), Faculty of Science and Technology, UiT -The Arctic University of Norway, 9037, Tromsø, Norway.
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15
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Cai D, Zhang B, Rao Y, Li L, Zhu J, Li J, Ma X, Chen S. Improving the utilization rate of soybean meal for efficient production of bacitracin and heterologous proteins in the aprA-deficient strain of Bacillus licheniformis. Appl Microbiol Biotechnol 2019; 103:4789-4799. [PMID: 31025072 DOI: 10.1007/s00253-019-09804-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
Soybean meal is commonly applied as the raw material in the bio-fermentation industry, and bacitracin is a widely used feed additive in the feed industry. In this study, we investigated the influence of subtilisin enhancement on soybean meal utilization and bacitracin production in Bacillus licheniformis DW2, an industrial strain for bacitracin production. Firstly, blocking sRNA aprA expression benefited bacitracin synthesis, and the bacitracin yield produced by aprA-deficient strain DW2△PaprA reached 931.43 U/mL, 18.92% higher than that of DW2 (783.25 U/mL). The bacitracin yield was reduced by 14.27% in the aprA overexpression strain. Furthermore, our results showed that deficiency of aprA led to a 6.54-fold increase of the aprE transcriptional level and a 1.84-fold increase of subtilisin activity, respectively, which led to the increases of soybean meal utilization rate (28.86%) and precursor amino acid supplies for bacitracin synthesis. Additionally, strengthening the utilization rate of soybean meal also benefited heterologous protein production, and the α-amylase and nattokinase activities were respectively enhanced by 59.81% and 50.53% in aprA-deficient strains. Collectively, this research demonstrated that strengthening subtilisin production could improve the utilization rate of soybean meal and thereby enhance bacitracin and target protein production; also, this strategy would be useful for the improvement of protein/peptide production using soybean meal as the main nitrogen source in the fermentation process.
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Affiliation(s)
- Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Bowen Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Lingfeng Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Junhui Li
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China.
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16
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Barrero JJ, Casler JC, Valero F, Ferrer P, Glick BS. An improved secretion signal enhances the secretion of model proteins from Pichia pastoris. Microb Cell Fact 2018; 17:161. [PMID: 30314480 PMCID: PMC6182871 DOI: 10.1186/s12934-018-1009-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
Background Proteins can be secreted from a host organism with the aid of N-terminal secretion signals. The budding yeast Pichia pastoris (Komagataella sp.) is widely employed to secrete proteins of academic and industrial interest. For this yeast, the most commonly used secretion signal is the N-terminal portion of pre-pro-α-factor from Saccharomyces cerevisiae. However, this secretion signal promotes posttranslational translocation into the endoplasmic reticulum (ER), so proteins that can fold in the cytosol may be inefficiently translocated and thus poorly secreted. In addition, if a protein self-associates, the α-factor pro region can potentially cause aggregation, thereby hampering export from the ER. This study addresses both limitations of the pre-pro-α-factor secretion signal. Results We engineered a hybrid secretion signal consisting of the S. cerevisiae Ost1 signal sequence, which promotes cotranslational translocation into the ER, followed by the α-factor pro region. Secretion and intracellular localization were assessed using as a model protein the tetrameric red fluorescent protein E2-Crimson. When paired with the α-factor pro region, the Ost1 signal sequence yielded much more efficient secretion than the α-factor signal sequence. Moreover, an allelic variant of the α-factor pro region reduced aggregation of the E2-Crimson construct in the ER. The resulting improved secretion signal enhanced secretion of E2-Crimson up to 20-fold compared to the levels obtained with the original α-factor secretion signal. Similar findings were obtained with the lipase BTL2, which exhibited 10-fold enhanced secretion with the improved secretion signal. Conclusions The improved secretion signal confers dramatic benefits for the secretion of certain proteins from P. pastoris. These benefits are likely to be most evident for proteins that can fold in the cytosol and for oligomeric proteins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1009-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan J Barrero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain.,Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Jason C Casler
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain.,Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA.
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Noguchi Y, Kashiwagi N, Uzura A, Ogino C, Kondo A, Ikeda H, Sota M. Development of a strictly regulated xylose-induced expression system in Streptomyces. Microb Cell Fact 2018; 17:151. [PMID: 30241528 PMCID: PMC6149001 DOI: 10.1186/s12934-018-0991-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Genetic tools including constitutive and inducible promoters have been developed over the last few decades for strain engineering in Streptomyces. Inducible promoters are useful for controlling gene expression, however only a limited number are applicable to Streptomyces. The aim of this study is to develop a controllable protein expression system based on an inducible promoter using sugar inducer, which has not yet been widely applied in Streptomyces. Results To determine a candidate promoter, inducible protein expression was first examined in Streptomyces avermitilis MA-4680 using various carbon sources. Xylose isomerase (xylA) promoter derived from xylose (xyl) operon was selected due to strong expression of xylose isomerase (XylA) in the presence of d-xylose. Next, a xylose-inducible protein expression system was constructed by investigating heterologous protein expression (chitobiase as a model protein) driven by the xylA promoter in Streptomyces lividans. Chitobiase activity was detected at high levels in S. lividans strain harboring an expression vector with xylA promoter (pXC), under both xylose-induced and non-induced conditions. Thus, S. avermitilis xylR gene, which encodes a putative repressor of xyl operon, was introduced into constructed vectors in order to control protein expression by d-xylose. Among strains constructed in the study, XCPR strain harboring pXCPR vector exhibited strict regulation of protein expression. Chitobiase activity in the XCPR strain was observed to be 24 times higher under xylose-induced conditions than that under non-induced conditions. Conclusion In this study, a strictly regulated protein expression system was developed based on a xylose-induced system. As far as we could ascertain, this is the first report of engineered inducible protein expression in Streptomyces by means of a xylose-induced system. This system might be applicable for controllable expression of toxic products or in the field of synthetic biology using Streptomyces strains. Electronic supplementary material The online version of this article (10.1186/s12934-018-0991-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuji Noguchi
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Atsuko Uzura
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Masahiro Sota
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
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Canales C, Altamirano C, Berrios J. The growth of Pichia pastoris Mut + on methanol-glycerol mixtures fits to interactive dual-limited kinetics: model development and application to optimised fed-batch operation for heterologous protein production. Bioprocess Biosyst Eng 2018; 41:1827-1838. [PMID: 30196441 DOI: 10.1007/s00449-018-2005-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 09/05/2018] [Indexed: 11/26/2022]
Abstract
The methanol-glycerol co-feeding during the induction stage for heterologous protein production in Pichia pastoris has shown significant productive applications. Available model analysis applied to this dual-limited condition is scarce and normally does not consider the interaction effects between the substrates. In this work, a dual-limited growth model of P. pastoris considering an interactive kinetic effect was applied to an optimised fed-batch process production of heterologous Rhizopus oryzae lipase (ROL). In the proposed model, the growth kinetics on glycerol is fully expressed, whereas methanol kinetics is modulated by the co-metabolisation of glycerol, resulting in an enhancing effect of glycerol-specific growth rate. The modelling approach of fed-batch cultures also included the methanol volatilisation caused by the aeration that was found to be a not-negligible phenomenon. The model predicts the ability of P. pastoris to keep control of the methanol concentration in the broth during ROL-optimised production process in fed batch and fits satisfactorily the specific cell growth rate and ROL production. Implications of interaction effect are discussed applying the general procedure of modelling approach.
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Affiliation(s)
- Christian Canales
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaiso, 2340000, Chile
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción, 4080871, Chile
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaiso, 2340000, Chile
| | - Julio Berrios
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaiso, 2340000, Chile.
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Carrillo Rincón AF, Magdevska V, Kranjc L, Fujs Š, Müller R, Petković H. Production of extracellular heterologous proteins in Streptomyces rimosus, producer of the antibiotic oxytetracycline. Appl Microbiol Biotechnol 2018; 102:2607-2620. [PMID: 29417200 DOI: 10.1007/s00253-018-8793-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/13/2018] [Accepted: 01/16/2018] [Indexed: 11/29/2022]
Abstract
Among the Streptomyces species, Streptomyces lividans has often been used for the production of heterologous proteins as it can secrete target proteins directly into the culture medium. Streptomyces rimosus, on the other hand, has for long been used at an industrial scale for oxytetracycline production, and it holds 'Generally Recognised As Safe' status. There are a number of properties of S. rimosus that make this industrial strain an attractive candidate as a host for heterologous protein production, including (1) rapid growth rate; (2) growth as short fragments, as for Escherichia coli; (3) high efficiency of transformation by electroporation; and (4) secretion of proteins into the culture medium. In this study, we specifically focused our efforts on an exploration of the use of the Sec secretory pathway to export heterologous proteins in a S. rimosus host. We aimed to develop a genetic tool kit for S. rimosus and to evaluate the extracellular production of target heterologous proteins of this industrial host. This study demonstrates that S. rimosus can produce the industrially important enzyme phytase AppA extracellularly, and analogous to E. coli as a host, application of His-Tag/Ni-affinity chromatography provides a simple and rapid approach to purify active phytase AppA in S. rimosus. We thus demonstrate that S. rimosus can be used as a potential alternative protein expression system.
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Affiliation(s)
- Andrés Felipe Carrillo Rincón
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, CSIC, C/Albert Einstein, 22, 39011, Santander, Spain.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Vasilka Magdevska
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, SI, Slovenia.,Acies Bio, d.o.o. Tehnološki Park 21, 1000, Ljubljana, SI, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, SI, Slovenia
| | - Štefan Fujs
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, SI, Slovenia.,Acies Bio, d.o.o. Tehnološki Park 21, 1000, Ljubljana, SI, Slovenia
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Hrvoje Petković
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, CSIC, C/Albert Einstein, 22, 39011, Santander, Spain. .,Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, SI, Slovenia. .,Acies Bio, d.o.o. Tehnološki Park 21, 1000, Ljubljana, SI, Slovenia.
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Jong WSP, Vikström D, Houben D, van den Berg van Saparoea HB, de Gier JW, Luirink J. Application of an E. coli signal sequence as a versatile inclusion body tag. Microb Cell Fact 2017; 16:50. [PMID: 28320377 PMCID: PMC5359840 DOI: 10.1186/s12934-017-0662-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/10/2017] [Indexed: 12/18/2022] Open
Abstract
Background Heterologous protein production in Escherichia coli often suffers from bottlenecks such as proteolytic degradation, complex purification procedures and toxicity towards the expression host. Production of proteins in an insoluble form in inclusion bodies (IBs) can alleviate these problems. Unfortunately, the propensity of heterologous proteins to form IBs is variable and difficult to predict. Hence, fusing the target protein to an aggregation prone polypeptide or IB-tag is a useful strategy to produce difficult-to-express proteins in an insoluble form. Results When screening for signal sequences that mediate optimal targeting of heterologous proteins to the periplasmic space of E. coli, we observed that fusion to the 39 amino acid signal sequence of E. coli TorA (ssTorA) did not promote targeting but rather directed high-level expression of the human proteins hEGF, Pla2 and IL-3 in IBs. Further analysis revealed that ssTorA even mediated IB formation of the highly soluble endogenous E. coli proteins TrxA and MBP. The ssTorA also induced aggregation when fused to the C-terminus of target proteins and appeared functional as IB-tag in E. coli K-12 as well as B strains. An additive effect on IB-formation was observed upon fusion of multiple ssTorA sequences in tandem, provoking almost complete aggregation of TrxA and MBP. The ssTorA-moiety was successfully used to produce the intrinsically unstable hEGF and the toxic fusion partner SymE, demonstrating its applicability as an IB-tag for difficult-to-express and toxic proteins. Conclusions We present proof-of-concept for the use of ssTorA as a small, versatile tag for robust E. coli-based expression of heterologous proteins in IBs. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0662-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wouter S P Jong
- Abera Bioscience AB, 11145, Stockholm, Sweden. .,Department of Molecular Cell Biology, Section Molecular Microbiology, Faculty of Earth and Life Sciences, VU University, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | | | | | | | - Jan-Willem de Gier
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Joen Luirink
- Abera Bioscience AB, 11145, Stockholm, Sweden. .,Department of Molecular Cell Biology, Section Molecular Microbiology, Faculty of Earth and Life Sciences, VU University, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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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: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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de Ruijter JC, Frey AD. Analysis of antibody production in Saccharomyces cerevisiae: effects of ER protein quality control disruption. Appl Microbiol Biotechnol 2015; 99:9061-71. [PMID: 26184977 DOI: 10.1007/s00253-015-6807-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/17/2015] [Accepted: 06/27/2015] [Indexed: 12/21/2022]
Abstract
One of the main limitations for heterologous protein production in the yeast Saccharomyces cerevisiae is the protein-folding capacity in the endoplasmic reticulum (ER). Accumulation of unfolded proteins triggers the unfolded protein response (UPR), which resolves the stress by increasing the capacity for protein folding and removal of unfolded proteins by the ER-associated degradation (ERAD) system. In order to analyze the influence of ERAD on production of a human IgG, we disrupted ERAD at different stages by deletion of the HTM1, YOS9, HRD1, HRD3, or UBC7 gene, with or without a disruption of the UPR by deletion of the IRE1 gene. All deletion strains were viable and did not exhibit a growth phenotype under normal growth conditions. Deletion of HTM1 resulted in a small increase in antibody production, whereas a small decrease in antibody production was observed in the Δhrd1, Δhrd3, and Δubc7 yeast strains, and a stronger decrease in the Δyos9 yeast strain. Deletion of the IRE1 gene had contrasting effects in the ERAD mutants, with a strongly decreased production in wild-type cells and partially reversed effects in combination with the Δhtm1 or the Δyos9 deletions. In order to study IgG clearance from the ER, an assay was developed using the inhibitory effect of glucose on the GAL1 promoter that is driving IgG expression. The Δyos9Δire1and Δhtm1Δire1 strains showed a delayed IgG clearance from the cells, showing that removal of components for the generation and recognition of the glycan signal needed for ERAD-mediated protein degradation might increase the IgG ER residence time.
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Affiliation(s)
- Jorg C de Ruijter
- 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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