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Unver Y, Ari B, Acar M, Yildiz Arslan S. A self-inducible heterologous protein expression system in Komagataella phaffii ( Pichia pastoris). 3 Biotech 2024; 14:193. [PMID: 39131177 PMCID: PMC11306816 DOI: 10.1007/s13205-024-04039-x] [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: 04/17/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024] Open
Abstract
Komagataella phaffii (previously described as Pichia pastoris) is a yeast that produces high-level heterologous proteins with a wide range of applications in medicine and industry. The methanol-induced alcohol oxidase I promoter (PAOX1) is frequently used for protein expression in this yeast. However, limitations on the use of methanol have been observed in large-scale production, including its flammability, toxicity, and need for special handling. Here, we propose to develop a system using recombinant cells constitutively expressing pectinmethyl esterase for expression of two reporter proteins, GFP and azurin, under the control of PAOX1 using pectin in production medium. So, this system is coherent with yeast culture medium containing pectin and heterologous gene inserted downstream of PAOX1 can be successfully expressed without the addition of methanol. Therefore, this novel Self-inducibLe heterologous protein EXpression (SILEX) system, which does not require the addition of methanol, can be used for the production of any protein. It can also be adapted for large-scale production. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04039-x.
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Affiliation(s)
- Yagmur Unver
- Department of Molecular Biology and Genetics, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Betul Ari
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Melek Acar
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Seyda Yildiz Arslan
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
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Bachleitner S, Severinsen MM, Lutz G, Mattanovich D. Overexpression of the transcriptional activators Mxr1 and Mit1 enhances lactic acid production on methanol in Komagataellaphaffii. Metab Eng 2024; 85:133-144. [PMID: 39067842 DOI: 10.1016/j.ymben.2024.07.013] [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: 04/24/2024] [Revised: 07/07/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
A bio-based production of chemical building blocks from renewable, sustainable and non-food substrates is one key element to fight climate crisis. Lactic acid, one such chemical building block is currently produced from first generation feedstocks such as glucose and sucrose, both requiring land and water resources. In this study we aimed for lactic acid production from methanol by utilizing Komagataella phaffii as a production platform. Methanol, a single carbon source has potential as a sustainable substrate as technology allows (electro)chemical hydrogenation of CO2 for methanol production. Here we show that expression of the Lactiplantibacillus plantarum derived lactate dehydrogenase leads to L-lactic acid production in Komagataella phaffii, however, production resulted in low titers and cells subsequently consumed lactic acid again. Gene expression analysis of the methanol-utilizing genes AOX1, FDH1 and DAS2 showed that the presence of lactic acid downregulates transcription of the aforementioned genes, thereby repressing the methanol-utilizing pathway. For activation of the methanol-utilizing pathway in the presence of lactic acid, we constructed strains deficient in transcriptional repressors Nrg1, Mig1-1, and Mig1-2 as well as strains with overrepresentation of transcriptional activators Mxr1 and Mit1. While loss of transcriptional repressors had no significant impact on lactic acid production, overexpression of both transcriptional activators, MXR1 and MIT1, increased lactic acid titers from 4 g L-1 to 17 g L-1 in bioreactor cultivations.
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Affiliation(s)
- Simone Bachleitner
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Manja Mølgaard Severinsen
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Gregor Lutz
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria
| | - Diethard Mattanovich
- BOKU University, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, 1190, Vienna, Austria.
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3
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Besleaga M, Zimmermann C, Ebner K, Mach RL, Mach-Aigner AR, Geier M, Glieder A, Spadiut O, Kopp J. Bi-directionalized promoter systems allow methanol-free production of hard-to-express peroxygenases with Komagataella Phaffii. Microb Cell Fact 2024; 23:177. [PMID: 38879507 PMCID: PMC11179361 DOI: 10.1186/s12934-024-02451-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/04/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Heme-incorporating peroxygenases are responsible for electron transport in a multitude of organisms. Yet their application in biocatalysis is hindered due to their challenging recombinant production. Previous studies suggest Komagataella phaffi to be a suitable production host for heme-containing enzymes. In addition, co-expression of helper proteins has been shown to aid protein folding in yeast. In order to facilitate recombinant protein expression for an unspecific peroxygenase (AnoUPO), we aimed to apply a bi-directionalized expression strategy with Komagataella phaffii. RESULTS In initial screenings, co-expression of protein disulfide isomerase was found to aid the correct folding of the expressed unspecific peroxygenase in K. phaffi. A multitude of different bi-directionalized promoter combinations was screened. The clone with the most promising promoter combination was scaled up to bioreactor cultivations and compared to a mono-directional construct (expressing only the peroxygenase). The strains were screened for the target enzyme productivity in a dynamic matter, investigating both derepression and mixed feeding (methanol-glycerol) for induction. Set-points from bioreactor screenings, resulting in the highest peroxygenase productivity, for derepressed and methanol-based induction were chosen to conduct dedicated peroxygenase production runs and were analyzed with RT-qPCR. Results demonstrated that methanol-free cultivation is superior over mixed feeding in regard to cell-specific enzyme productivity. RT-qPCR analysis confirmed that mixed feeding resulted in high stress for the host cells, impeding high productivity. Moreover, the bi-directionalized construct resulted in a much higher specific enzymatic activity over the mono-directional expression system. CONCLUSIONS In this study, we demonstrate a methanol-free bioreactor production strategy for an unspecific peroxygenase, yet not shown in literature. Hence, bi-directionalized assisted protein expression in K. phaffii, cultivated under derepressed conditions, is indicated to be an effective production strategy for heme-containing oxidoreductases. This very production strategy might be opening up further opportunities for biocatalysis.
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Affiliation(s)
- Mihail Besleaga
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Christian Zimmermann
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Katharina Ebner
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Martina Geier
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Anton Glieder
- bisy GmbH, Wünschendorf 292, Hofstätten an der Raab, 8200, Austria
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria
| | - Julian Kopp
- Institute of Chemical, Environmental and Bioscience Engineering, Research Division Integrated Bioprocess Development, Gumpendorfer Straße 1a, Vienna, 1060, Austria.
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Tian E, Shen X, Xiao M, Zhu Z, Yang Y, Yan X, Wang P, Zou G, Zhou Z. An engineered Pichia pastoris platform for the biosynthesis of silk-based nanomaterials with therapeutic potential. Int J Biol Macromol 2024; 269:131954. [PMID: 38697424 DOI: 10.1016/j.ijbiomac.2024.131954] [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: 02/19/2024] [Revised: 04/19/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Silk fibroin (SF) from the cocoon of silkworm has exceptional mechanical properties and biocompatibility and is used as a biomaterial in a variety of fields. Sustainable, affordable, and scalable manufacturing of SF would enable its large-scale use. We report for the first time the high-level secretory production of recombinant SF peptides in engineered Pichia pastoris cell factories and the processing thereof to nanomaterials. Two SF peptides (BmSPR3 and BmSPR4) were synthesized and secreted by P. pastoris using signal peptides and appropriate spacing between hydrophilic sequences. By strain engineering to reduce protein degradation, increase glycyl-tRNA supply, and improve protein secretion, we created the optimized P. pastoris chassis PPGSP-8 to produce BmSPR3 and BmSPR4. The SF fed-batch fermentation titers of the resulting two P. pastoris cell factories were 11.39 and 9.48 g/L, respectively. Protein self-assembly was inhibited by adding Tween 80 to the medium. Recombinant SF peptides were processed to nanoparticles (NPs) and nanofibrils. The physicochemical properties of nanoparticles R3NPs and R4NPs from the recombinant SFs synthesized in P. pastoris cell factories were similar or superior to those of RSFNPs (Regenerated Silk Fibroin NanoParticles) originating from commercially available SF. Our work will facilitate the production by microbial fermentation of functional SF for use as a biomaterial.
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Affiliation(s)
- Ernuo Tian
- School of Pharmacy, East China University of Science and Technology, Shanghai 200037, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Shen
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yi Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200037, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Gen Zou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Zhihua Zhou
- School of Pharmacy, East China University of Science and Technology, Shanghai 200037, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Steimann T, Heite Z, Germer A, Blank LM, Büchs J, Mann M, Magnus JB. Understanding exopolysaccharide byproduct formation in Komagataella phaffii fermentation processes for recombinant protein production. Microb Cell Fact 2024; 23:131. [PMID: 38711081 DOI: 10.1186/s12934-024-02403-3] [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: 02/13/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) has emerged as a common and robust biotechnological platform organism, to produce recombinant proteins and other bioproducts of commercial interest. Key advantage of K. phaffii is the secretion of recombinant proteins, coupled with a low host protein secretion. This facilitates downstream processing, resulting in high purity of the target protein. However, a significant but often overlooked aspect is the presence of an unknown polysaccharide impurity in the supernatant. Surprisingly, this impurity has received limited attention in the literature, and its presence and quantification are rarely addressed. RESULTS This study aims to quantify this exopolysaccharide in high cell density recombinant protein production processes and identify its origin. In stirred tank fed-batch fermentations with a maximal cell dry weight of 155 g/L, the polysaccharide concentration in the supernatant can reach up to 8.7 g/L. This level is similar to the achievable target protein concentration. Importantly, the results demonstrate that exopolysaccharide production is independent of the substrate and the protein production process itself. Instead, it is directly correlated with biomass formation and proportional to cell dry weight. Cell lysis can confidently be ruled out as the source of this exopolysaccharide in the culture medium. Furthermore, the polysaccharide secretion can be linked to a mutation in the HOC1 gene, featured by all derivatives of strain NRRL Y-11430, leading to a characteristic thinner cell wall. CONCLUSIONS This research sheds light on a previously disregarded aspect of K. phaffii fermentations, emphasizing the importance of monitoring and addressing the exopolysaccharide impurity in biotechnological applications, independent of the recombinant protein produced.
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Affiliation(s)
- Thomas Steimann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Zoe Heite
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Marcel Mann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jørgen Barsett Magnus
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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Albacar M, Casamayor A, Ariño J. Harnessing alkaline-pH regulatable promoters for efficient methanol-free expression of enzymes of industrial interest in Komagataella Phaffii. Microb Cell Fact 2024; 23:99. [PMID: 38566096 PMCID: PMC10985989 DOI: 10.1186/s12934-024-02362-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The yeast Komagataella phaffii has become a very popular host for heterologous protein expression, very often based on the use of the AOX1 promoter, which becomes activated when cells are grown with methanol as a carbon source. However, the use of methanol in industrial settings is not devoid of problems, and therefore, the search for alternative expression methods has become a priority in the last few years. RESULTS We recently reported that moderate alkalinization of the medium triggers a fast and wide transcriptional response in K. phaffii. Here, we present the utilization of three alkaline pH-responsive promoters (pTSA1, pHSP12 and pPHO89) to drive the expression of a secreted phytase enzyme by simply shifting the pH of the medium to 8.0. These promoters offer a wide range of strengths, and the production of phytase could be modulated by adjusting the pH to specific values. The TSA1 and PHO89 promoters offered exquisite regulation, with virtually no enzyme production at acidic pH, while limitation of Pi in the medium further potentiated alkaline pH-driven phytase expression from the PHO89 promoter. An evolved strain based on this promoter was able to produce twice as much phytase as the reference pAOX1-based strain. Functional mapping of the TSA1 and HSP12 promoters suggests that both contain at least two alkaline pH-sensitive regulatory regions. CONCLUSIONS Our work shows that the use of alkaline pH-regulatable promoters could be a useful alternative to methanol-based expression systems, offering advantages in terms of simplicity, safety and economy.
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Affiliation(s)
- Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain.
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Rajak N, Dey T, Sharma Y, Bellad V, Rangarajan PN. Unlocking Nature's Toolbox: glutamate-inducible recombinant protein production from the Komagatella phaffii PEPCK promoter. Microb Cell Fact 2024; 23:66. [PMID: 38402195 PMCID: PMC10893637 DOI: 10.1186/s12934-024-02340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Komagataella phaffii (a.k.a. Pichia pastoris) harbors a glutamate utilization pathway in which synthesis of glutamate dehydrogenase 2 and phosphoenolpyruvate carboxykinase (PEPCK) is induced by glutamate. Glutamate-inducible synthesis of these enzymes is regulated by Rtg1p, a cytosolic, basic helix-loop-helix protein. Here, we report food-grade monosodium glutamate (MSG)-inducible recombinant protein production from K. phaffii PEPCK promoter (PPEPCK) using green fluorescent protein (GFP) and receptor binding domain of SARS-CoV-2 virus (RBD) as model proteins. RESULTS PPEPCK-RBD/GFP expression cassette was integrated at two different sites in the genome to improve recombinant protein yield from PPEPCK. The traditional, methanol-inducible alcohol oxidase 1 promoter (PAOX1) was used as the benchmark. Initial studies carried out with MSG as the inducer resulted in low recombinant protein yield. A new strategy employing MSG/ethanol mixed feeding improved biomass generation as well as recombinant protein yield. Cell density of 100-120 A600 units/ml was achieved after 72 h of induction in shake flask cultivations, resulting in recombinant protein yield from PPEPCK that is comparable or even higher than that from PAOX1. CONCLUSIONS We have designed an induction medium for recombinant protein production from K. phaffii PPEPCK in shake flask cultivations. It consists of 1.0% yeast extract, 2.0% peptone, 0.17% yeast nitrogen base with ammonium sulfate, 100 mM potassium phosphate (pH 6.0), 0.4 mg/L biotin, 2.0% MSG, and 2% ethanol. Substitution of ammonium sulphate with 0.5% urea is optional. Carbon source was replenished every 24 h during 72 h induction period. Under these conditions, GFP and RBD yields from PPEPCK equaled and even surpassed those from PAOX1. Compared to the traditional methanol-inducible expression system, the inducers of glutamate-inducible expression system are non-toxic and their metabolism does not generate toxic metabolites such as formaldehyde and hydrogen peroxide. This study sets the stage for MSG-inducible, industrial scale recombinant protein production from K. phaffii PPEPCK in bioreactors.
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Affiliation(s)
- Neetu Rajak
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Trishna Dey
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Yash Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Vedanth Bellad
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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Shen Q, Cui J, Wang Y, Hu ZC, Xue YP, Zheng YG. Identification of a novel growth-associated promoter for biphasic expression of heterogenous proteins in Pichia pastoris. Appl Environ Microbiol 2024; 90:e0174023. [PMID: 38193674 PMCID: PMC10880622 DOI: 10.1128/aem.01740-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Pichia pastoris (P. pastoris) is one of the most popular cell factories for expressing exogenous proteins and producing useful chemicals. The alcohol oxidase 1 promoter (PAOX1) is the most commonly used strong promoter in P. pastoris and has the characteristic of biphasic expression. However, the inducer for PAOX1, methanol, has toxicity and poses risks in industrial settings. In the present study, analyzing transcriptomic data of cells collected at different stages of growth found that the formate dehydrogenase (FDH) gene ranked 4960th in relative expression among 5032 genes during the early logarithmic growth phase but rose to the 10th and 1st during the middle and late logarithmic growth phases, respectively, displaying a strict biphasic expression characteristic. The unique transcriptional regulatory profile of the FDH gene prompted us to investigate the properties of its promoter (PFDH800). Under single-copy conditions, when a green fluorescent protein variant was used as the expression target, the PFDH800 achieved 119% and 69% of the activity of the glyceraldehyde-3-phosphate dehydrogenase promoter and PAOX1, respectively. After increasing the copy number of the expression cassette in the strain to approximately four copies, the expression level of GFPuv driven by PFDH800 increased to approximately 2.5 times that of the strain containing GFPuv driven by a single copy of PAOX1. Our PFDH800-based expression system exhibited precise biphasic expression, ease of construction, minimal impact on normal cellular metabolism, and high strength. Therefore, it has the potential to serve as a new expression system to replace the PAOX1 promoter.IMPORTANCEThe alcohol oxidase 1 promoter (PAOX1) expression system has the characteristics of biphasic expression and high expression levels, making it the most widely used promoter in the yeast Pichia pastoris. However, PAOX1 requires methanol induction, which can be toxic and poses a fire hazard in large quantities. Our research has found that the activity of PFDH800 is closely related to the growth state of cells and can achieve biphasic expression without the need for an inducer. Compared to other reported non-methanol-induced biphasic expression systems, the system based on the PFDH800 offers several advantages, including high expression levels, simple construction, minimal impact on cellular metabolism, no need for an inducer, and the ability to fine-tune expression.
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Affiliation(s)
- Qi Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Jie Cui
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhong-Ce Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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10
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Lai J, Song L, Zhou Y, Zong H, Zhuge B, Lu X. Fine-Tuned Gene Expression Elements from Hybrid Promoter Libraries in Pichia pastoris. ACS Synth Biol 2024; 13:310-318. [PMID: 38150419 DOI: 10.1021/acssynbio.3c00534] [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] [Indexed: 12/29/2023]
Abstract
As a desirable microbial cell factory, Pichia pastoris has garnered extensive utilization in metabolic engineering. Nevertheless, the lack of fine-tuned gene expression components has significantly constrained the potential scope of applications. Here, a gradient strength promoter library was constructed by random hybridization and high-throughput screening. The hybrid promoter, phy47, performed best with 2.93-fold higher GFP expression levels than GAP. The broad applicability of the novel hybrid promoter variants in biotechnological production was further validated in the biosynthesis of pinene and rHuPH20 with higher titers. The upstream regulatory sequences (UASE and URSD) were identified and applied to promoters GAP and ENO1, resulting in a 34 and 43% increase and an 18 and 37% decrease in the expression level, respectively. Yeast one-hybrid analysis showed that transcription factor HAP2 activates the hybrid promoter through a direct interaction with the crucial regulatory region UASH. Furthermore, a short segment of tunable activation sequence (20 bp) was also screened, and artificial promoters were constructed in tandem with the addition of regulatory sequence, resulting in a 61% expansion of the expression range. This study provides a molecular tool and regulatory elements for further synthetic biology research in P. pastoris.
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Affiliation(s)
- Jie Lai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Lingang Song
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuyu Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Lab of Industrial Microorganism & Research and Design Center for Polyols, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Arjmand S. Promoters in Pichia pastoris: A Toolbox for Fine-Tuned Gene Expression. Methods Mol Biol 2024; 2844:159-178. [PMID: 39068339 DOI: 10.1007/978-1-0716-4063-0_11] [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] [Indexed: 07/30/2024]
Abstract
This chapter reviews the different promoters used to control gene expression in the yeast Pichia pastoris, mainly for recombinant protein production. It covers natural inducible, derepressed, and constitutive promoters, as well as engineered synthetic/hybrid promoters, orthologous promoters from related yeasts, and emerging bidirectional promoters. Key examples, characteristics, and regulatory mechanisms are discussed for each promoter class. Recent efforts in promoter engineering through rational design, mutagenesis, and computational approaches are also highlighted. Looking ahead, we anticipate further developments that will enhance promoter design for Pichia pastoris. Overall, this comprehensive overview underscores the importance of promoter choice and engineering for fully harnessing Pichia pastoris biotechnological potential.
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Affiliation(s)
- Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran.
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Current achievements, strategies, obstacles, and overcoming the challenges of the protein engineering in Pichia pastoris expression system. World J Microbiol Biotechnol 2023; 40:39. [PMID: 38062216 DOI: 10.1007/s11274-023-03851-6] [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: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Yeasts serve as exceptional hosts in the manufacturing of functional protein engineering and possess industrial or medical utilities. Considerable focus has been directed towards yeast owing to its inherent benefits and recent advancements in this particular cellular host. The Pichia pastoris expression system is widely recognized as a prominent and widely accepted instrument in molecular biology for the purpose of generating recombinant proteins. The advantages of utilizing the P. pastoris system for protein production encompass the proper folding process occurring within the endoplasmic reticulum (ER), as well as the subsequent secretion mediated by Kex2 as a signal peptidase, ultimately leading to the release of recombinant proteins into the extracellular environment of the cell. In addition, within the P. pastoris expression system, the ease of purifying recombinant protein arises from its restricted synthesis of endogenous secretory proteins. Despite its achievements, scientists often encounter persistent challenges when attempting to utilize yeast for the production of recombinant proteins. This review is dedicated to discussing the current achievements in the usage of P. pastoris as an expression host. Furthermore, it sheds light on the strategies employed in the expression system and the optimization and development of the fermentative process of this yeast. Finally, the impediments (such as identifying high expression strains, improving secretion efficiency, and decreasing hyperglycosylation) and successful resolution of certain difficulties are put forth and deliberated upon in order to assist and promote the expression of complex proteins in this prevalent recombinant host.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
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Flores-Villegas M, Rebnegger C, Kowarz V, Prielhofer R, Mattanovich D, Gasser B. Systematic sequence engineering enhances the induction strength of the glucose-regulated GTH1 promoter of Komagataella phaffii. Nucleic Acids Res 2023; 51:11358-11374. [PMID: 37791854 PMCID: PMC10639056 DOI: 10.1093/nar/gkad752] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/16/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
The promoter of the high-affinity glucose transporter Gth1 (PGTH1) is tightly repressed on glucose and glycerol surplus, and strongly induced in glucose-limitation, thus enabling regulated methanol-free production processes in the yeast production host Komagataella phaffii. To further improve this promoter, an intertwined approach of nucleotide diversification through random and rational engineering was pursued. Random mutagenesis and fluorescence activated cell sorting of PGTH1 yielded five variants with enhanced induction strength. Reverse engineering of individual point mutations found in the improved variants identified two single point mutations with synergistic action. Sequential deletions revealed the key promoter segments for induction and repression properties, respectively. Combination of the single point mutations and the amplification of key promoter segments led to a library of novel promoter variants with up to 3-fold higher activity. Unexpectedly, the effect of gaining or losing a certain transcription factor binding site (TFBS) was highly dependent on its context within the promoter. Finally, the applicability of the novel promoter variants for biotechnological production was proven for the secretion of different recombinant model proteins in fed batch cultivation, where they clearly outperformed their ancestors. In addition to advancing the toolbox for recombinant protein production and metabolic engineering of K. phaffii, we discovered single nucleotide positions and correspondingly affected TFBS that distinguish between glycerol- and glucose-mediated repression of the native promoter.
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Affiliation(s)
- Mirelle Flores-Villegas
- CD-Laboratory for Growth-decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
| | - Corinna Rebnegger
- CD-Laboratory for Growth-decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Prielhofer
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
- ACIB GmbH, Muthgasse 11, 1190 Vienna, Austria
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De Groeve M, Laukens B, Schotte P. Optimizing expression of Nanobody® molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions. Microb Cell Fact 2023; 22:135. [PMID: 37481525 PMCID: PMC10362571 DOI: 10.1186/s12934-023-02132-z] [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: 04/04/2023] [Accepted: 06/24/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. RESULTS Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. CONCLUSION Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
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Affiliation(s)
- Manu De Groeve
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Bram Laukens
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Peter Schotte
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium.
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15
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Liu B, Cong W, Zhao Y, Zhou H, Zhang J. An inducible Komagataella phaffii system for protein expression using sorbitol dehydrogenase promoter. Biotechnol Lett 2023; 45:667-677. [PMID: 37074552 DOI: 10.1007/s10529-023-03370-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 04/20/2023]
Abstract
OBJECTIVES The aim of the present work was to develop a methanol-independent Komagataella phaffii (K. phaffii) strain using a non-methanol promoter. RESULTS In this study, the food grade enzyme xylanase from Aspergillus niger ATCC 1015 was used as the reporter protein, a recombinant K. phaffii containing a cascade gene circus was designed and constructed using sorbitol as inducer. Sorbitol induced PSDH leading to MIT1 expression firstly, and heterologous protein xylanase expression finally. This system showed 1.7 fold of xylanase activity at the condition of single copy number of extra MIT1, and 2.1 fold of xylanase activity at condition of multi-copy extra MIT1 gene. CONCLUSIONS This sorbitol-induced expression system of K. phaffii avoided toxic and explosive methanol. It was a novel cascade gene expression and a food safety system.
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Affiliation(s)
- Bing Liu
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Wenjie Cong
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Yixin Zhao
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Hualan Zhou
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Jianguo Zhang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China.
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Bernat-Camps N, Ebner K, Schusterbauer V, Fischer JE, Nieto-Taype MA, Valero F, Glieder A, Garcia-Ortega X. Enabling growth-decoupled Komagataella phaffii recombinant protein production based on the methanol-free P DH promoter. Front Bioeng Biotechnol 2023; 11:1130583. [PMID: 37034257 PMCID: PMC10076887 DOI: 10.3389/fbioe.2023.1130583] [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: 12/23/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
The current transition towards the circular bioeconomy requires a rational development of biorefineries to sustainably fulfill the present demands. The use of Komagataella phaffii (Pichia pastoris) can meet this challenge, since it has the capability to use crude glycerol as a carbon-source, a by-product from the biodiesel industry, while producing high- and low-added value products. Recombinant protein production (RPP) using K. phaffii has often been driven either by the methanol induced AOX1 promoter (PAOX1) and/or the constitutive GAP promoter (PGAP). In the last years, strong efforts have been focused on developing novel expression systems that expand the toolbox variety of K. phaffii to efficiently produce diverse proteins that requires different strategies. In this work, a study was conducted towards the development of methanol-free expression system based on a heat-shock gene promoter (PDH) using glycerol as sole carbon source. Using this promoter, the recombinant expression is strongly induced in carbon-starving conditions. The classical PGAP was used as a benchmark, taking for both strains the lipase B from Candida antarctica (CalB) as model protein. Titer of CalB expressed under PDH outperformed PGAP controlled expression in shake-flask cultivations when using a slow-release continuous feeding technology, confirming that PDH is induced under pseudo-starving conditions. This increase was also confirmed in fed-batch cultivations. Several optimization rounds were carried out for PDH under different feeding and osmolarity conditions. In all of them the PDH controlled process outperformed the PGAP one in regard to CalB titer. The best PDH approach reached 3.6-fold more specific productivity than PGAP fed-batch at low μ. Compared to the optimum approach for PGAP-based process, the best PDH fed-batch strategy resulted in 2.3-fold higher titer, while the specific productivity was very similar. To summarize, PDH is an inducible promoter that exhibited a non-coupled growth regulation showing high performance, which provides a methanol-free additional solution to the usual growth-coupled systems for RPP. Thus, this novel system emerges as a potential alternative for K. phaffii RPP bioprocess and for revaluing crude glycerol, promoting the transition towards a circular economy.
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Affiliation(s)
- Núria Bernat-Camps
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | | | | | - Miguel Angel Nieto-Taype
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | - Xavier Garcia-Ortega
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- *Correspondence: Xavier Garcia-Ortega,
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Yao Y, Zheng S, Chi S, Chen F, Cai N, Cai Z, Li Z, Ni H. Characterization of the off-flavor from Pichia pastoris GS115 during the overexpression of an α-l-rhamnosidase. J Ind Microbiol Biotechnol 2023; 50:kuad035. [PMID: 37942557 PMCID: PMC10696632 DOI: 10.1093/jimb/kuad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
The off-flavor of Pichia pastoris strains is a negative characteristic of proteins overexpressed with this yeast. In the present study, P. pastoris GS115 overexpressing an α-l-rhamnosidase was taken as the example to characterize the off-flavor via sensory evaluation, gas chromatography-mass spectrometer, gas chromatography-olfaction, and omission test. The result showed that the off-flavor was due to the strong sweaty note, and moderate metallic and plastic notes. Four volatile compounds, that is, tetramethylpyrazine, 2,4-di-tert-butylphenol, isovaleric acid, and 2-methylbutyric acid, were identified to be major contributors to the sweaty note. Dodecanol and 2-acetylbutyrolactone were identified to be contributors to the metallic and plastic notes, respectively. It is the first study on the off-flavor of P. pastoris strains, helping understand metabolites with off-flavor of this yeast. Interestingly, it is the first study illustrating 2-acetylbutyrolactone and dodecanol with plastic and metallic notes, providing new information about the aromatic contributors of biological products. IMPORTANCE The methylotrophic yeast Pichia pastoris is an important host for the industrial expression of functional proteins. In our previous studies, P. pastoris strains have been sniffed with a strong off-flavor during the overexpression of various functional proteins, limiting the application of these proteins. Although many yeast strains have been reported with off-flavor, no attention has been paid to characterize the off-flavor in P. pastoris so far. Considering that P. pastoris has advantages over other established expression systems of functional proteins, it is of interest to identify the compounds with off-flavor synthesized in the overexpression of functional proteins with P. pastoris strains. In this study, the off-flavor synthesized from P. pastoris GS115 was characterized during the overexpression of an α-l-rhamnosidase, which helps understand the aromatic metabolites with off-flavor of P. pastoris strains. In addition, 2-acetylbutyrolactone and dodecanol were newly revealed with plastic and metallic notes, enriching the aromatic contributors of biological products. Thus, this study is important for understanding the metabolites with off-flavor of P. pastoris strains and other organisms, providing important knowledge to improve the flavor of products yielding with P. pastoris strains and other organisms. ONE-SENTENCE SUMMARY Characterize the sensory and chemical profile of the off-flavor produced by one strain of P. pastoris in vitro.
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Affiliation(s)
- YuXuan Yao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, People's Republic of China
| | - ShengLan Zheng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, People's Republic of China
| | - ShiLin Chi
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, People's Republic of China
| | - Feng Chen
- Department of Food, Nutrition and Packaging Sciences, Clemson University, Clemson, SC 29634, USA
| | - Ning Cai
- Xiamen Ocean Vocational College, Xiamen, Fujian 361021, People's Republic of China
| | - ZhenZhen Cai
- Xiamen Ocean Vocational College, Xiamen, Fujian 361021, People's Republic of China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, People's Republic of China
- Key Laboratory of Food Microbiology and Enzyme Engineering Technology of Fujian Province, Xiamen, Fujian 361021, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian 361021, People's Republic of China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, People's Republic of China
- Xiamen Ocean Vocational College, Xiamen, Fujian 361021, People's Republic of China
- Key Laboratory of Food Microbiology and Enzyme Engineering Technology of Fujian Province, Xiamen, Fujian 361021, People's Republic of China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, Fujian 361021, People's Republic of China
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Niu T, Cui Y, Shan X, Qin S, Zhou X, Wang R, Chang A, Ma N, Jing J, He J. Comparative transcriptomic analysis-based identification of the regulation of foreign proteins with different stabilities expressed in Pichia pastoris. Front Microbiol 2022; 13:1074398. [PMID: 36620045 PMCID: PMC9814716 DOI: 10.3389/fmicb.2022.1074398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction The industrial yeast Pichia pastoris is widely used as a cell factory to produce proteins, chemicals and advanced biofuels. We have previously constructed P. pastoris strains that overexpress protein disulfide isomerase (PDI), which is a kind of molecular chaperone that can improve the expression of an exogenous protein when they are co-expressed. Chicken cystatin (cC) is a highly thermostable cysteine protease inhibitor and a homologous protein of human cystatin C (HCC). Wild-type cC and the two mutants, I66Q and ΔW (a truncated cC lacking the á-helix 2) represent proteins with different degrees of stability. Methods Wild-type cC, I66Q and ΔW were each overexpressed in P. pastoris without and with the coexpression of PDI and their extracellular levels were determined and compared. Transcriptomic profiling was performed to compare the changes in the main signaling pathways and cell components (other than endoplasmic reticulum quality control system represented by molecular chaperones) in P. pastoris in response to intracellular folding stress caused by the expression of exogenous proteins with different stabilities. Finally, hub genes hunting was also performed. Results and discussion The coexpression of PDI was able to increase the extracellular levels of both wild-type cC and the two mutants, indicating that overexpression of PDI could prevent the misfolding of unstable proteins or promote the degradation of the misfolded proteins to some extent. For P. pastoris cells that expressed the I66Q or ΔW mutant, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the common DEGs in these cells revealed a significant upregulation of the genes involved in protein processing, but a significant downregulation of the genes enriched in the Ribosome, TCA and Glycolysis/Gluconeogenesis pathways. Hub genes hunting indicated that the most downregulated ribosome protein, C4QXU7 in this case, might be an important target protein that could be manipulated to increase the expression of foreign proteins, especially proteins with a certain degree of instability. Conclusion These findings should shed new light on our understanding of the regulatory mechanism in yeast cells that responds to intracellular folding stress, providing valuable information for the development of a convenient platform that could improve the efficiency of heterologous protein expression in P. pastoris.
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Affiliation(s)
- Tingting Niu
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Yi Cui
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xu Shan
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Shuzhen Qin
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xuejie Zhou
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Rui Wang
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Alan Chang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Nan Ma
- China Academy of Transportation Sciences, Beijing, China,Nan Ma,
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China,Jingjing Jing,
| | - Jianwei He
- School of Life Sciences, Liaoning University, Shenyang, China,*Correspondence: Jianwei He,
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Hashem C, Hochrinner J, Bürgler MB, Rinnofner C, Pichler H, Winkler M. From linoleic acid to hexanal and hexanol by whole cell catalysis with a lipoxygenase, hydroperoxide lyase and reductase cascade in Komagataella phaffii. Front Mol Biosci 2022; 9:965315. [PMID: 36579187 PMCID: PMC9791951 DOI: 10.3389/fmolb.2022.965315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022] Open
Abstract
Green leaf volatiles (GLVs) cover a group of mainly C6-and C9-aldehydes, -alcohols and -esters. Their name refers to their characteristic herbal and fruity scent, which is similar to that of freshly cut grass or vegetables. Lipoxygenases (LOXs) catalyze the peroxidation of unsaturated fatty acids. The resulting hydroperoxy fatty acids are then cleaved into aldehydes and oxo acids by fatty acid hydroperoxide lyases (HPLs). Herein, we equipped the yeast Komagataella phaffii with recombinant genes coding for LOX and HPL, to serve as a biocatalyst for GLV production. We expressed the well-known 13S-specific LOX gene from Pleurotus sapidus and a compatible HPL gene from Medicago truncatula. In bioconversions, glycerol induced strains formed 12.9 mM hexanal using whole cells, and 8 mM hexanol was produced with whole cells induced by methanol. We applied various inducible and constitutive promoters in bidirectional systems to influence the final ratio of LOX and HPL proteins. By implementing these recombinant enzymes in Komagataella phaffii, challenges such as biocatalyst supply and lack of product specificity can finally be overcome.
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Affiliation(s)
- Chiam Hashem
- Institute of Molecular Biotechnology, TU Graz, NAWI Graz, Graz, Austria,Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | - Julius Hochrinner
- Institute of Molecular Biotechnology, TU Graz, NAWI Graz, Graz, Austria
| | - Moritz B. Bürgler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | - Harald Pichler
- Institute of Molecular Biotechnology, TU Graz, NAWI Graz, Graz, Austria,Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria,BioTechMed Graz, Graz, Austria
| | - Margit Winkler
- Institute of Molecular Biotechnology, TU Graz, NAWI Graz, Graz, Austria,Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria,*Correspondence: Margit Winkler,
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20
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Efficient expression of heterologous protein by engineered Komagataella phaffii by harnessing a bioelectrical CO2 reduction system. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Pan Y, Yang J, Wu J, Yang L, Fang H. Current advances of Pichia pastoris as cell factories for production of recombinant proteins. Front Microbiol 2022; 13:1059777. [PMID: 36504810 PMCID: PMC9730254 DOI: 10.3389/fmicb.2022.1059777] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Pichia pastoris (syn. Komagataella spp.) has attracted extensive attention as an efficient platform for recombinant protein (RP) production. For obtaining a higher protein titer, many researchers have put lots of effort into different areas and made some progress. Here, we summarized the most recent advances of the last 5 years to get a better understanding of its future direction of development. The appearance of innovative genetic tools and methodologies like the CRISPR/Cas9 gene-editing system eases the manipulation of gene expression systems and greatly improves the efficiency of exploring gene functions. The integration of novel pathways in microorganisms has raised more ideas of metabolic engineering for enhancing RP production. In addition, some new opportunities for the manufacture of proteins have been created by the application of novel mathematical models coupled with high-throughput screening to have a better overview of bottlenecks in the biosynthetic process.
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Affiliation(s)
- Yingjie Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiao Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianping Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lirong Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China,College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China,*Correspondence: Hao Fang,
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22
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Zhu Q, Liu Q, Yao C, Zhang Y, Cai M. Yeast transcriptional device libraries enable precise synthesis of value-added chemicals from methanol. Nucleic Acids Res 2022; 50:10187-10199. [PMID: 36095129 PMCID: PMC9508829 DOI: 10.1093/nar/gkac765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Natural methylotrophs are attractive methanol utilization hosts, but lack flexible expression tools. In this study, we developed yeast transcriptional device libraries for precise synthesis of value-added chemicals from methanol. We synthesized transcriptional devices by fusing bacterial DNA-binding proteins (DBPs) with yeast transactivation domains, and linking bacterial binding sequences (BSs) with the yeast core promoter. Three DBP–BS pairs showed good activity when working with transactivation domains and the core promoter of PAOX1 in the methylotrophic yeast, Pichia pastoris. Fine-tuning of the tandem BSs, spacers and differentiated input promoters further enabled a constitutive transcriptional device library (cTRDL) composed of 126 transcriptional devices with an expression strength of 16–520% and an inducible TRDL (iTRDL) composed of 162 methanol-inducible transcriptional devices with an expression strength of 30–500%, compared with PAOX1. Selected devices from iTRDL were adapted to the dihydromonacolin L biosynthetic pathway by orthogonal experimental design, reaching 5.5-fold the production from the PAOX1-driven pathway. The full factorial design of the selected devices from the cTRDL was adapted to the downstream pathway of dihydromonacolin L to monacolin J. Monacolin J production from methanol reached 3.0-fold the production from the PAOX1-driven pathway. Our engineered toolsets ensured multilevel pathway control of chemical synthesis in methylotrophic yeasts.
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Affiliation(s)
- Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chaoying Yao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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23
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Haghighi Poodeh S, Ranaei Siadat SO, Arjmand S, Khalifeh Soltani M. Improving AOX1 promoter efficiency by overexpression of Mit1 transcription factor. Mol Biol Rep 2022; 49:9379-9386. [PMID: 36002652 DOI: 10.1007/s11033-022-07790-7] [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: 04/06/2022] [Accepted: 07/12/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Reprogramming in transcriptional regulation provides an effective tool for adjusting cellular metabolic activities. The strong methanol-inducible alcohol oxidase-1 promoter (pAOX1) is commonly used for heterologous gene expression in the yeast Pichia pastoris. Here, we present a novel Pichia pastoris strain engineered to co-express methanol-induced transcription factor 1 (Mit1) and the target protein. Mit1 upregulates pAOX1 in response to methanol. METHODS AND RESULTS Two model proteins (VEGF and eGFP) have been used as the target proteins under the control of pAOX1. The sequence of Mit1 had obtained from the yeast genome and likewise cloned under the control of pAOX1. The results indicated a 1.9 and 2.2 fold increase in the detected VEGF and eGFP, respectively, when co-expressed with Mit1. Furthermore, the double-recombinant cells, containing Mit-1 and eGFP, produced 1.3 fold more eGFP when the methanol feeding concentration was doubled. The real-time PCR indicated a slight increase in the Mit1 expression, probably due to the negative regulatory feedback loop that exists for the intrinsic yeast Mit1. Overexpression of Mit1 also led to duplication of AOX1 enzyme activity, which may enhance the yeast cells' capacity for methanol detoxification. CONCLUSION Overexpression of Mit1 could be considered a promising strategy for upregulation of target recombinant proteins in Pichia pastoris. Intracellular overexpression of Mit1 upregulates the heterologous target gene (eGFP) production, which is expressed under the control of pAOX1.
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Affiliation(s)
- Samin Haghighi Poodeh
- Protein Research Center, Shahid Beheshti University, P.O. Box: 19839, 69411, Tehran, Iran
| | | | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, P.O. Box: 19839, 69411, Tehran, Iran.
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24
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Heterologous (Over) Expression of Human SoLute Carrier (SLC) in Yeast: A Well-Recognized Tool for Human Transporter Function/Structure Studies. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081206. [PMID: 36013385 PMCID: PMC9410066 DOI: 10.3390/life12081206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022]
Abstract
For more than 20 years, yeast has been a widely used system for the expression of human membrane transporters. Among them, more than 400 are members of the largest transporter family, the SLC superfamily. SLCs play critical roles in maintaining cellular homeostasis by transporting nutrients, ions, and waste products. Based on their involvement in drug absorption and in several human diseases, they are considered emerging therapeutic targets. Despite their critical role in human health, a large part of SLCs' is 'orphans' for substrate specificity or function. Moreover, very few data are available concerning their 3D structure. On the basis of the human health benefits of filling these knowledge gaps, an understanding of protein expression in systems that allow functional production of these proteins is essential. Among the 500 known yeast species, S. cerevisiae and P. pastoris represent those most employed for this purpose. This review aims to provide a comprehensive state-of-the-art on the attempts of human SLC expression performed by exploiting yeast. The collected data will hopefully be useful for guiding new attempts in SLCs expression with the aim to reveal new fundamental data that could lead to potential effects on human health.
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25
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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] [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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26
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Heterologous protein expression enhancement of Komagataella phaffii by ammonium formate induction based on transcriptomic analysis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Expanding the promoter toolbox for metabolic engineering of methylotrophic yeasts. Appl Microbiol Biotechnol 2022; 106:3449-3464. [PMID: 35538374 DOI: 10.1007/s00253-022-11948-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/31/2023]
Abstract
Methylotrophic yeasts have been widely recognized as a promising host for production of recombinant proteins and value-added chemicals. Promoters for controlled gene expression are critical for construction of efficient methylotrophic yeasts cell factories. Here, we summarized recent advances in characterizing and engineering promoters in methylotrophic yeasts, such as Komagataella phaffii and Ogataea polymorpha. Constitutive and inducible promoters controlled by methanol or other inducers/repressors were introduced to demonstrate their applications in production of proteins and chemicals. Furthermore, efforts of promoter engineering, including site-directed mutagenesis, hybrid promoter, and transcription factor regulation to expand the promoter toolbox were also summarized. This mini-review also provides useful information on promoters for the application of metabolic engineering in methylotrophic yeasts. KEY POINTS: • The characteristics of six methylotrophic yeasts and their promoters are described. • The applications of Komagataella phaffii and Ogataea polymorpha in metabolic engineeringare expounded. • Three promoter engineering strategies are introduced in order to expand the promoter toolbox.
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28
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Farre JC, Carolino K, Devanneaux L, Subramani S. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. eLife 2022; 11:e75143. [PMID: 35467529 PMCID: PMC9094750 DOI: 10.7554/elife.75143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these pathways enter mitochondria for ATP production and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH-shuttling- and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by a high AMP/ATP ratio. In OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the Δgal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2, and NRG1) controlled by SNF1 signaling. Our results are interpreted in terms of a mechanism by which peroxisomal and mitochondrial proteins and/or metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol, and the nucleus. We discuss the physiological relevance of this work in the context of human OXPHOS deficiencies.
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Affiliation(s)
- Jean-Claude Farre
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Krypton Carolino
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Lou Devanneaux
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
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29
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Bustos C, Quezada J, Veas R, Altamirano C, Braun-Galleani S, Fickers P, Berrios J. Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production. Metabolites 2022; 12:346. [PMID: 35448535 PMCID: PMC9027633 DOI: 10.3390/metabo12040346] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.
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Affiliation(s)
- Cristina Bustos
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Rhonda Veas
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Stephanie Braun-Galleani
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
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30
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Gupta A, Rangarajan PN. Histidine is essential for growth of Komagataella phaffii cultured in YPA medium. FEBS Open Bio 2022; 12:1241-1252. [PMID: 35416413 PMCID: PMC9157411 DOI: 10.1002/2211-5463.13408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 11/08/2022] Open
Abstract
Komagataella phaffii (a.k.a. Pichia pastoris) requires histidine for optimal growth when cultured in a medium containing yeast extract, peptone (YP) and acetate (YPA). We demonstrate that HIS4-deficient, K. phaffii strain GS115 exhibits a growth defect on YP-media containing acetate, but not on other carbon sources. K. phaffii X33, a prototroph, grows better than K. phaffii GS115 (his4), a histidine auxotroph in YPA. Normal growth of GS115 is restored either by the expression of HIS4 or by culturing in YPA containing ≥0.6 mM histidine. In presence of histidine, expression of several genes is altered including those encoding key subunits of mitochondrial ATP synthase, transporters of amino acids and nutrients, as well as biosynthetic enzymes. Thus, histidine should be included as an essential component for optimal growth of K.phaffii histidine auxotrophs cultured in YPA.
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Affiliation(s)
- Aditi Gupta
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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31
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Liu Q, Song L, Peng Q, Zhu Q, Shi X, Xu M, Wang Q, Zhang Y, Cai M. A programmable high-expression yeast platform responsive to user-defined signals. SCIENCE ADVANCES 2022; 8:eabl5166. [PMID: 35148182 PMCID: PMC8836803 DOI: 10.1126/sciadv.abl5166] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rapidly growing yeasts with appropriate posttranslational modifications are favored hosts for protein production in the biopharmaceutical industry. However, limited production capacity and intricate transcription regulation restrict their application and adaptability. Here, we describe a programmable high-expression yeast platform, SynPic-X, which responds to defined signals and is broadly applicable. We demonstrated that a synthetic improved transcriptional signal amplification device (iTSAD) with a bacterial-yeast transactivator and bacterial-yeast promoter markedly increased expression capacity in Pichia pastoris. CRISPR activation and interference devices were designed to strictly regulate iTSAD in response to defined signals. Engineered switches were then constructed to exemplify the response of SynPic-X to exogenous signals. Expression of α-amylase by SynPic-R, a specific SynPic-X, in a bioreactor proved a methanol-free high-production process of recombinant protein. Our SynPic-X platform provides opportunities for protein production in customizable yeast hosts with high expression and regulatory flexibility.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiangqiang Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingqiang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Corresponding author.
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32
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Dalvie NC, Biedermann AM, Rodriguez‐Aponte SA, Naranjo CA, Rao HD, Rajurkar MP, Lothe RR, Shaligram US, Johnston RS, Crowell LE, Castelino S, Tracey MK, Whittaker CA, Love JC. Scalable, methanol-free manufacturing of the SARS-CoV-2 receptor-binding domain in engineered Komagataella phaffii. Biotechnol Bioeng 2022; 119:657-662. [PMID: 34780057 PMCID: PMC8653030 DOI: 10.1002/bit.27979] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 09/10/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022]
Abstract
Prevention of COVID-19 on a global scale will require the continued development of high-volume, low-cost platforms for the manufacturing of vaccines to supply ongoing demand. Vaccine candidates based on recombinant protein subunits remain important because they can be manufactured at low costs in existing large-scale production facilities that use microbial hosts like Komagataella phaffii (Pichia pastoris). Here, we report an improved and scalable manufacturing approach for the SARS-CoV-2 spike protein receptor-binding domain (RBD); this protein is a key antigen for several reported vaccine candidates. We genetically engineered a manufacturing strain of K. phaffii to obviate the requirement for methanol induction of the recombinant gene. Methanol-free production improved the secreted titer of the RBD protein by >5X by alleviating protein folding stress. Removal of methanol from the production process enabled to scale up to a 1200 L pre-existing production facility. This engineered strain is now used to produce an RBD-based vaccine antigen that is currently in clinical trials and could be used to produce other variants of RBD as needed for future vaccines.
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Affiliation(s)
- Neil C. Dalvie
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Andrew M. Biedermann
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Sergio A. Rodriguez‐Aponte
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Christopher A. Naranjo
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | | | | | | | - Ryan S. Johnston
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Laura E. Crowell
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Seraphin Castelino
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mary K. Tracey
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Charles A. Whittaker
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - J. Christopher Love
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Rinnofner C, Felber M, Pichler H. Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris. Methods Mol Biol 2022; 2513:79-112. [PMID: 35781201 DOI: 10.1007/978-1-0716-2399-2_6] [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] [Indexed: 06/15/2023]
Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Affiliation(s)
- Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.
- Bisy GmbH, Hofstaetten/Raab, Austria.
| | - Michael Felber
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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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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35
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Improved Production of Streptomyces sp. FA1 Xylanase in a Dual-Plasmid Pichia pastoris System. Curr Issues Mol Biol 2021; 43:2289-2304. [PMID: 34940135 PMCID: PMC8928940 DOI: 10.3390/cimb43030161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
Methanol is considered as a potential hazard in the methanol-induced yeast expression of food-related enzymes. To increase the production efficiency of recombinant proteins in Pichia pastoris without methanol induction, a novel dual-plasmid system was constructed, for the first time, by a combining the strategies of genomic integration and episomal expression. To obtain a high copy number of the target gene, the autonomously replicating sequence derived from Kluyveromyces lactis (PARS) was used to construct episomal vectors carrying the constitutive promoters PGAP and PGCW14. In addition, an integrative vector carrying the PGCW14 promoter was constructed by replacing the PGAP promoter sequence with a partial PGCW14 promoter. Next, using xylanase XynA from Streptomyces sp. FA1 as the model enzyme, recombination strains were transformed with different combinations of integrating and episomal vectors that were constructed to investigate the changes in the protein yield. Results in shake flasks indicated that the highest enzyme yield was achieved when integrated PGAP and episomal PGCW14 were simultaneously transformed into the host strain. Meanwhile, the copy number of xynA increased from 1.14 ± 0.46 to 3.06 ± 0.35. The yield of XynA was successfully increased to 3925 U·mL-1 after 102 h of fermentation in a 3.6 L fermenter, which was 16.7-fold and 2.86-fold of the yields that were previously reported for the constitutive expression and methanol-induced expression of the identical protein, respectively. Furthermore, the high-cell-density fermentation period was shortened from 132 h to 102 h compared to that of methanol-induced system. Since the risk of methanol toxicity is removed, this novel expression system would be suitable for the production of proteins related to the food and pharmaceutical industries.
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36
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Infanzón B, Herrmann KR, Hofmann I, Willbold S, Ruff AJ, Schwaneberg U. Phytase blends for enhanced phosphorous mobilization of deoiled seeds. Enzyme Microb Technol 2021; 153:109953. [PMID: 34847439 DOI: 10.1016/j.enzmictec.2021.109953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 11/03/2022]
Abstract
Phytases are hydrolytic enzymes capable of a stepwise phosphate release from phytate which is the main phosphorous storage in seeds, cereals and legumes. Limitations such as low enzyme activity or incomplete phytate hydrolysis to inositol are a great challenge in phytase applications in food and feed. Herein we report a phytase blend of two enzymes with additive effects on phytate (InsP6) hydrolysis and its application in the enzymatic phosphorous recovery process. Blending the fast 6-phytase rPhyXT52 with the 3-phytase from Debaryomyces castellii, which is capable of fully hydrolyzing InsP6, we achieved rapid phosphate release with higher yields compared to the individual enzymes and a rapid disappearance of InsP6-3 intermediates, monitored by HPLC. NMR data suggest a nearly complete phytate hydrolysis to inositol and phosphate. The blend was applied for phosphate mobilization from phytate-rich biomass, such as deoiled seeds. For this emerging application, an up to 43% increased phosphate mobilization yield was achieved when using 1000 U of the blend per kg biomass compared to using only the E. coli phytase. Even so, the time of enzyme treatment was decreased by more than half (6 h instead of 16 h) when using 4000 U of blend, we reached a 78-90% reduction of the total phosphorous content in the explored deoiled seeds. In summary, the phytase blend of Dc phyt/rPhyXT52 was proven very efficient to obtain inositol phosphate depleted meal which has its potential application in animal feeding and is concomitant with the production of green phosphate from renewable resources.
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Affiliation(s)
- Belén Infanzón
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Kevin R Herrmann
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Isabell Hofmann
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Sabine Willbold
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany.
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Ergün BG, Berrios J, Binay B, Fickers P. Recombinant protein production in Pichia pastoris: From transcriptionally redesigned strains to bioprocess optimization and metabolic modelling. FEMS Yeast Res 2021; 21:6424904. [PMID: 34755853 DOI: 10.1093/femsyr/foab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Pichia pastoris is one of the most widely used host for the production of recombinant proteins. Expression systems that rely mostly on promoters from genes encoding alcohol oxidase 1 or glyceraldehyde-3-phosphate dehydrogenase have been developed together with related bioreactor operation strategies based on carbon sources such as methanol, glycerol, or glucose. Although, these processes are relatively efficient and easy to use, there have been notable improvements over the last twenty years to better control gene expression from these promoters and their engineered variants. Methanol-free and more efficient protein production platforms have been developed by engineering promoters and transcription factors. The production window of P. pastoris has been also extended by using alternative feedstocks including ethanol, lactic acid, mannitol, sorbitol, sucrose, xylose, gluconate, formate, or rhamnose. Herein, the specific aspects that are emerging as key parameters for recombinant protein synthesis are discussed. For this purpose, a holistic approach has been considered to scrutinize protein production processes from strain design to bioprocess optimization, particularly focusing on promoter engineering, transcriptional circuitry redesign. This review also considers the optimization of bioprocess based on alternative carbon sources and derived co-feeding strategies. Optimization strategies for recombinant protein synthesis through metabolic modelling are also discussed.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey.,Department of Chemical Engineering, Middle East Technical University, 06800 Ankara, Turkey.,UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Patrick Fickers
- TERRA Teaching and Research Centre, University of Liege, Gembloux Agro-Bio Tech, Gembloux, Belgium
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38
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Godinho CP, Palma M, Oliveira J, Mota MN, Antunes M, Teixeira MC, Monteiro PT, Sá-Correia I. The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts. FEMS Yeast Res 2021; 21:6356955. [PMID: 34427650 DOI: 10.1093/femsyr/foab045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract (http://yeastract-plus.org/ncyeastract/) was associated to YEASTRACT + (http://yeastract-plus.org/). The YEASTRACT + portal is a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. N.C.Yeastract gathers all published regulatory associations and TF-binding sites for Komagataellaphaffii (formerly Pichia pastoris), the oleaginous yeast Yarrowia lipolytica, the lactose fermenting species Kluyveromyces lactis and Kluyveromyces marxianus, and the remarkably weak acid-tolerant food spoilage yeast Zygosaccharomyces bailii. The objective of this review paper is to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on these species, exploring all the information available in the global YEASTRACT + portal. Using simple and widely used examples, a guided exploitation is offered for several tools: (i) inference of orthologous genes; (ii) search for putative TF binding sites and (iii) inter-species comparison of transcription regulatory networks and prediction of TF-regulated networks based on documented regulatory associations available in YEASTRACT + for well-studied species. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed.
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Affiliation(s)
- Cláudia P Godinho
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Palma
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | - Marta N Mota
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Antunes
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel C Teixeira
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro T Monteiro
- INESC-ID, Lisbon, Portugal.,Department of Computer Science and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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39
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de Sá Magalhães S, Keshavarz-Moore E. Pichia pastoris ( Komagataella phaffii) as a Cost-Effective Tool for Vaccine Production for Low- and Middle-Income Countries (LMICs). Bioengineering (Basel) 2021; 8:119. [PMID: 34562941 PMCID: PMC8468848 DOI: 10.3390/bioengineering8090119] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 01/26/2023] Open
Abstract
Vaccination is of paramount importance to global health. With the advent of the more recent pandemics, the urgency to expand the range has become even more evident. However, the potential limited availability and affordability of vaccines to resource low- and middle-income countries has created a need for solutions that will ensure cost-effective vaccine production methods for these countries. Pichia pastoris (P. pastoris) (also known as Komagataella phaffii) is one of the most promising candidates for expression of heterologous proteins in vaccines development. It combines the speed and ease of highly efficient prokaryotic platforms with some key capabilities of mammalian systems, potentially reducing manufacturing costs. This review will examine the latest developments in P. pastoris from cell engineering and design to industrial production systems with focus on vaccine development and with reference to specific key case studies.
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Affiliation(s)
| | - Eli Keshavarz-Moore
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK;
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40
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Herrmann KR, Hofmann I, Jungherz D, Wittwer M, Infanzón B, Hamer SN, Davari MD, Ruff AJ, Schwaneberg U. Generation of phytase chimeras with low sequence identities and improved thermal stability. J Biotechnol 2021; 339:14-21. [PMID: 34271055 DOI: 10.1016/j.jbiotec.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/25/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022]
Abstract
Being able to recombine more than two genes with four or more crossover points in a sequence independent manner is still a challenge in protein engineering and limits our capabilities in tailoring enzymes for industrial applications. By computational analysis employing multiple sequence alignments and homology modeling, five fragments of six phytase genes (sequence identities 31-64 %) were identified and efficiently recombined through phosphorothioate-based cloning using the PTRec method. By combinatorial recombination, functional phytase chimeras containing fragments of up to four phytases were obtained. Two variants (PTRec 74 and PTRec 77) with up to 32 % improved residual activity (90 °C, 60 min) and retained specific activities of > 1100 U/mg were identified. Both variants are composed of fragments from the phytases of Citrobacter braakii, Hafnia alvei and Yersinia mollaretii. They exhibit sequence identities of ≤ 80 % to their parental enzymes, highlighting the great potential of DNA recombination strategies to generate new enzymes with low sequences identities that offer opportunities for property right claims.
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Affiliation(s)
- Kevin R Herrmann
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Isabell Hofmann
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Dennis Jungherz
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Malte Wittwer
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Belén Infanzón
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Stefanie Nicole Hamer
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany; DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056, Aachen, Germany.
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41
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Dalvie NC, Biedermann AM, Rodriguez-Aponte SA, Naranjo CA, Rao HD, Rajurkar MP, Lothe RR, Shaligram US, Johnston RS, Crowell LE, Castelino S, Tracey MK, Whittaker CA, Love JC. Scalable, methanol-free manufacturing of the SARS-CoV-2 receptor binding domain in engineered Komagataella phaffii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.15.440035. [PMID: 33880471 PMCID: PMC8057236 DOI: 10.1101/2021.04.15.440035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prevention of COVID-19 on a global scale will require the continued development of high-volume, low-cost platforms for the manufacturing of vaccines to supply on-going demand. Vaccine candidates based on recombinant protein subunits remain important because they can be manufactured at low costs in existing large-scale production facilities that use microbial hosts like Komagataella phaffii ( Pichia pastoris ). Here, we report an improved and scalable manufacturing approach for the SARS-CoV-2 spike protein receptor binding domain (RBD); this protein is a key antigen for several reported vaccine candidates. We genetically engineered a manufacturing strain of K. phaffii to obviate the requirement for methanol-induction of the recombinant gene. Methanol-free production improved the secreted titer of the RBD protein by >5x by alleviating protein folding stress. Removal of methanol from the production process enabled scale up to a 1,200 L pre-existing production facility. This engineered strain is now used to produce an RBD-based vaccine antigen that is currently in clinical trials and could be used to produce other variants of RBD as needed for future vaccines.
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Affiliation(s)
- Neil C. Dalvie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Andrew M. Biedermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Sergio A. Rodriguez-Aponte
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher A. Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | | | | | | | | | - Ryan S. Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Laura E. Crowell
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Seraphin Castelino
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mary Kate Tracey
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Charles A. Whittaker
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - J. Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
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Aggarwal S, Mishra S. Differential role of segments of α-mating factor secretion signal in Pichia pastoris towards granulocyte colony-stimulating factor emerging from a wild type or codon optimized copy of the gene. Microb Cell Fact 2020; 19:199. [PMID: 33121493 PMCID: PMC7597063 DOI: 10.1186/s12934-020-01460-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The methylotrophic yeast, Pichia pastoris has been widely used for the production of human therapeutics, but production of granulocyte colony-stimulating factor (G-CSF) in this yeast is low.The work reported here aimed to improve the extracellular production of G-CSF by introducing mutations in the leader sequence and using a codon optimized copy of G-CSF. Bioinformatic analysis was carried out to propose an explanation for observed effect of mutations on extracellular G-CSF production. RESULTS Mutations in the pro-region of the α-mating type (MAT) secretory signal, when placed next to a codon optimized (CO)-GCSF copy, specifically, the Δ57-70 type, led to highest G-CSF titre of 39.4 ± 1.4 mg/L. The enhanced effect of this deletion was also observed when it preceded the WT copy of the gene. Deletion of the 30-43 amino acids in the pro-peptide, fused with the wild type (WT)-GCSF copy, completely diminished G-CSF secretion, while no effect was observed when this deletion was in front of the CO-GCSF construct. Also, Matα:Δ47-49 deletion preceding the WT-GCSF dampened the secretion of this protein, while no effect was seen when this deletion preceded the CO-GCSF copy of the gene. This indicated that faster rates of translation (as achieved through codon optimization) could overcome the control exercised by these segments. The loss of secretion occurring due to Δ30-43 in the WT-GCSF was partially restored (by 60%) when the Δ57-70 was added. The effect of Δ47-49 segment in the WT-GCSF could also be partially restored (by 60%) by addition of Δ57-70 indicating the importance of the 47-49 region. A stimulatory effect of Δ57-70 was confirmed in the double deletion (Matα:Δ57-70;47-49) construct preceding the CO-GCSF. Secondary and tertiary structures, when predicted using I-TASSER, allowed to understand the relationship between structural changes and their impact on G-CSF secretion. The Δ57-70 amino acids form a major part of 3rd alpha-helix in the pre-pro peptide and its distortion increased the flexibility of the loop, thereby promoting its interaction with the cargo protein. A minimum loop length was found to be necessary for secretion. The strict control in the process of secretion appeared to be overcome by changing the secondary structures in the signal peptides. Such fine tuning can allow enhanced secretion of other therapeutics in this expression system. CONCLUSIONS Among the different truncations (Matα:Δ57-70, Matα:Δ47-49, Matα:Δ30-43, Matα:Δ57-70;30-43, Matα:Δ57-70;47-49) in pro-peptide of α-MAT secretion signal, Matα:Δ57-70 fused to CO-GCSF, led to highest G-CSF titre as compared to other Matα truncations. On the other hand, Matα:Δ30-43 and Matα:Δ47-49 fused to the WT-GCSF dampened the secretion of this protein indicating important role of these segments in the secretion of the cargo protein.
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Affiliation(s)
- Sakshi Aggarwal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India.
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43
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Hashem C, Stolterfoht H, Rinnofner C, Steinberger S, Winkler M, Pichler H. Secretion of Pseudomonas aeruginosa Lipoxygenase by Pichia pastoris upon Glycerol Feed. Biotechnol J 2020; 15:e2000089. [PMID: 32749051 DOI: 10.1002/biot.202000089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Indexed: 01/17/2023]
Abstract
Pseudomonas aeruginosa lipoxygenase (PaLOX) catalyzes the peroxidation of unsaturated fatty acids. Not only linoleic acid, but also linolenic acid and oleic acid are oxidized. The natural host secretes PaLOX into the periplasmic space. Herein, the aim is to secrete PaLOX to the culture supernatant of Pichia pastoris. Since protein background in the culture supernatant is typically rather low, this strategy allows for almost pure production of PaLOX applicable for the valorization of renewable fatty acids, for example for the production of green leaf volatiles. Using the CAT1 promoter system and the well-established α-factor signal sequence for secretion, methanol- and glycerol-induced secretion are compared and the latter shows four times more LOX activity in the culture supernatant under methanol-free conditions. In addition, secreted PaLOX is purified and the specific activity with enzyme in culture supernatant is compared. Notably, the predominant specific activity is achieved for enzyme in culture supernatant - 11.6 U mg-1 - reaching five times higher specific activity than purified PaLOX.
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Affiliation(s)
- Chiam Hashem
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
| | - Holly Stolterfoht
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- bisy GmbH, Wuenschendorf 292, Hofstaetten, 8200, Austria
| | - Stefan Steinberger
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
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44
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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45
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Takagi S, Tsutsumi N, Terui Y, Kong X, Yurimoto H, Sakai Y. Engineering the expression system for Komagataella phaffii (Pichia pastoris): an attempt to develop a methanol-free expression system. FEMS Yeast Res 2020; 19:5549515. [PMID: 31408151 PMCID: PMC6736287 DOI: 10.1093/femsyr/foz059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/11/2019] [Indexed: 11/13/2022] Open
Abstract
The construction of a methanol-free expression system of Komagataella phaffii (Pichia pastoris) was attempted by engineering a strong methanol-inducible DAS1 promoter using Citrobacter braakii phytase production as a model case. Constitutive expression of KpTRM1, formerly PRM1-a positive transcription regulator for methanol-utilization (MUT) genes of K. phaffii,was demonstrated to produce phytase without addition of methanol, especially when a DAS1 promoter was used but not an AOX1 promoter. Another positive regulator, Mxr1p, did not have the same effect on the DAS1 promoter, while it was more effective than KpTrmp1 on the AOX1 promoter. Removing a potential upstream repression sequence (URS) and multiplying UAS1DAS1 in the DAS1 promoter significantly enhanced the yield of C. braakii phytase with methanol-feeding, which surpassed the native AOX1 promoter by 80%. However, multiplying UAS1DAS1 did not affect the yield of methanol-free expression by constitutive KpTrm1p. Another important region to enhance the effect of KpTrm1p under a methanol-free condition was identified in the DAS1 promoter, and was termed ESPDAS1. Nevertheless, methanol-free phytase production using an engineered DAS1 promoter outperformed phytase production with the GAP promoter by 25%. Difference in regulation by known transcription factors on the AOX1 promoter and the DAS1 promoter was also illustrated.
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Affiliation(s)
- Shinobu Takagi
- Novozymes Japan Ltd, CB-6 MTG, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan
| | - Noriko Tsutsumi
- Novozymes Japan Ltd, CB-6 MTG, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan
| | - Yuji Terui
- Novozymes Japan Ltd, CB-6 MTG, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan
| | - XiangYu Kong
- Novozymes (China) Investment Co. Ltd, 14 Xinxi Road, Shangdi Zone, Haidian District, 100085 Beijing, China
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
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Ergün BG, Demir İ, Özdamar TH, Gasser B, Mattanovich D, Çalık P. Engineered Deregulation of Expression in Yeast with Designed Hybrid-Promoter Architectures in Coordination with Discovered Master Regulator Transcription Factor. ACTA ACUST UNITED AC 2020; 4:e1900172. [PMID: 32293158 DOI: 10.1002/adbi.201900172] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/05/2020] [Accepted: 02/14/2020] [Indexed: 12/24/2022]
Abstract
Engineered promoters are key components in the cell-factory design, allowing precise and enhanced expression of genes. Promoters having exceptional strength are attractive candidates for designing metabolic engineering strategies for tailoring de novo production strategies that require directed evolution methods by engineering with de novo synthetic biology tools. Here, the custom-designed AOX1 hybrid-promoter architectures in coordination with targeted transcription factors are shown, transcriptionally rewired the expression over methanol-free substrate-utilization pathway(s) and converted methanol-dependent Pichia pastoris alcohol oxidase 1(AOX1) promoter (PAOX1 ) expression into a non-toxic carbon-source-regulated system. AOX1 promoter variants are engineered by replacing specified cis-regulatory DNA elements with synthetic Adr1, Cat8, and Aca2 cis-acting DNA elements for Mxr1, Cat8, and Aca1 binding, respectively. Applications of the engineered-promoters are validated for eGFP expression and extracellular human serum albumin production. The hybrid-promoter architecture designed with single Cat8 cis-acting DNA element deregulates the expression on ethanol. Compared with PAOX1 on methanol, the expression on ethanol is increased with i) PAOX1/Cat8-L3 (designed with single Cat8 cis-acting element) to 74%, ii) PAOX1/Adr1-L3/Cat8-L3 (designed with single- Cat8 and Adr1 cis-acting elements) to 85%, and for further consolidation of deregulated expression iii) PeAOX1 (designed with triplet- Cat8 and Adr1 cis-acting elements) 1.30-fold, at t = 20 h of batch cultivations.
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Affiliation(s)
- Burcu Gündüz Ergün
- Department of Chemical Engineering, Biochemical Reaction Engineering Laboratory, Middle East Technical University, Ankara, 06800, Turkey.,Department of Biotechnology, Industrial Biotechnology and Metabolic Engineering Laboratory, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - İrem Demir
- Department of Chemical Engineering, Biochemical Reaction Engineering Laboratory, Middle East Technical University, Ankara, 06800, Turkey.,Department of Biotechnology, Industrial Biotechnology and Metabolic Engineering Laboratory, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Tunçer H Özdamar
- Biochemical Reaction Engineering Laboratory, Chemical Engineering Department, Ankara University, Tandoğan, Ankara, 06100, Turkey
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria
| | - Pınar Çalık
- Department of Chemical Engineering, Biochemical Reaction Engineering Laboratory, Middle East Technical University, Ankara, 06800, Turkey.,Department of Biotechnology, Industrial Biotechnology and Metabolic Engineering Laboratory, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, 06800, Turkey
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47
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Vogl T, Fischer JE, Hyden P, Wasmayer R, Sturmberger L, Glieder A. Orthologous promoters from related methylotrophic yeasts surpass expression of endogenous promoters of Pichia pastoris. AMB Express 2020; 10:38. [PMID: 32100120 PMCID: PMC7042429 DOI: 10.1186/s13568-020-00972-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Methylotrophic yeasts such as Komagataella phaffii (syn. Pichia pastoris, Pp), Hansenula polymorpha (Hp), Candida boidinii (Cb) and Pichia methanolica (Pm) are widely used protein production platforms. Typically, strong, tightly regulated promoters of genes coding for their methanol utilization (MUT) pathways are used to drive heterologous gene expression. Despite highly similar open reading frames in the MUT pathways of the four yeasts, the regulation of the respective promoters varies strongly between species. While most endogenous Pp MUT promoters remain tightly repressed after depletion of a repressing carbon, Hp, Cb and Pm MUT promoters are derepressed to up to 70% of methanol induced levels, enabling methanol free production processes in their respective host background. Here, we have tested a series of orthologous promoters from Hp, Cb and Pm in Pp. Unexpectedly, when induced with methanol, the promoter of the HpMOX gene reached very similar expression levels as the strong methanol, inducible, and most frequently used promoter of the Pp alcohol oxidase 1 gene (PPpAOX1). The HpFMD promoter even surpassed PPpAOX1 up to three-fold, when induced with methanol, and reached under methanol-free/derepressed conditions similar expression as the methanol induced PPpAOX1. These results demonstrate that orthologous promoters from related yeast species can give access to otherwise unobtainable regulatory profiles and may even considerably surpass endogenous promoters in P. pastoris.
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Specific growth rate governs AOX1 gene expression, affecting the production kinetics of Pichia pastoris (Komagataella phaffii) P AOX1-driven recombinant producer strains with different target gene dosage. Microb Cell Fact 2019; 18:187. [PMID: 31675969 PMCID: PMC6824138 DOI: 10.1186/s12934-019-1240-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/02/2022] Open
Abstract
Background The PAOX1-based expression system is the most widely used for producing recombinant proteins in the methylotrophic yeast Pichia pastoris (Komagataella phaffii). Despite relevant recent advances in regulation of the methanol utilization (MUT) pathway have been made, the role of specific growth rate (µ) in AOX1 regulation remains unknown, and therefore, its impact on protein production kinetics is still unclear. Results The influence of heterologous gene dosage, and both, operational mode and strategy, on culture physiological state was studied by cultivating the two PAOX1-driven Candida rugosa lipase 1 (Crl1) producer clones. Specifically, a clone integrating a single expression cassette of CRL1 was compared with one containing three cassettes over broad dilution rate and µ ranges in both chemostat and fed-batch cultivations. Chemostat cultivations allowed to establish the impact of µ on the MUT-related MIT1 pool which leads to a bell-shaped relationship between µ and PAOX1-driven gene expression, influencing directly Crl1 production kinetics. Also, chemostat and fed-batch cultivations exposed the favorable effects of increasing the CRL1 gene dosage (up to 2.4 fold in qp) on Crl1 production with no significant detrimental effects on physiological capabilities. Conclusions PAOX1-driven gene expression and Crl1 production kinetics in P. pastoris were successfully correlated with µ. In fact, µ governs MUT-related MIT1 amount that triggers PAOX1-driven gene expression—heterologous genes included—, thus directly influencing the production kinetics of recombinant protein.
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García-Ortega X, Cámara E, Ferrer P, Albiol J, Montesinos-Seguí JL, Valero F. Rational development of bioprocess engineering strategies for recombinant protein production in Pichia pastoris (Komagataella phaffii) using the methanol-free GAP promoter. Where do we stand? N Biotechnol 2019; 53:24-34. [DOI: 10.1016/j.nbt.2019.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 12/25/2022]
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50
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Nieto-Taype MA, Garrigós-Martínez J, Sánchez-Farrando M, Valero F, Garcia-Ortega X, Montesinos-Seguí JL. Rationale-based selection of optimal operating strategies and gene dosage impact on recombinant protein production in Komagataella phaffii (Pichia pastoris). Microb Biotechnol 2019; 13:315-327. [PMID: 31657146 PMCID: PMC7017824 DOI: 10.1111/1751-7915.13498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
Its features as a microbial and eukaryotic organism have turned Komagataella phaffii (Pichia pastoris) into an emerging cell factory for recombinant protein production (RPP). As a key step of the bioprocess development, this work aimed to demonstrate the importance of tailor designing the cultivation strategy according to the production kinetics of the cell factory. For this purpose, K. phaffii clones constitutively expressing (PGAP) Candida rugosa lipase 1 (Crl1) with different gene dosage were used as models in continuous and fed‐batch cultures. Production parameters were much greater with a multicopy clone (MCC) than with the single‐copy clone (SCC). Regarding production kinetics, the specific product generation rate (qP) increased linearly with increasing specific growth rate (µ) in SCC; by contrast, qP exhibited saturation in MCC. A transcriptional analysis in chemostat cultures suggested the presence of eventual post‐transcriptional bottlenecks in MCC. After the strain characterization, in order to fulfil overall development of the bioprocess, the performance of both clones was also evaluated in fed‐batch mode. Strikingly, different optimal strategies were determined for both models due to the different production kinetic patterns observed as a trade‐off for product titre, yields and productivity. The combined effect of gene dosage and adequate µ enables rational process development with a view to optimize K. phaffii RPP bioprocesses.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Garrigós-Martínez
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Sánchez-Farrando
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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