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Hidalgo-Gajardo A, Gutiérrez N, Lamazares E, Espinoza F, Escobar-Riquelme F, Leiva MJ, Villavicencio C, Mena-Ulecia K, Montesino R, Altamirano C, Sánchez O, Rivas CI, Ruíz Á, Toledo JR. Co-Formulation of Recombinant Porcine IL-18 Enhances the Onset of Immune Response in a New Lawsonia intracellularis Vaccine. Vaccines (Basel) 2023; 11:1788. [PMID: 38140192 PMCID: PMC10747595 DOI: 10.3390/vaccines11121788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Pig is one of the most consumed meats worldwide. One of the main conditions for pig production is Porcine Enteropathy caused by Lawsonia intracellularis. Among the effects of this disease is chronic mild diarrhea, which affects the weight gain of pigs, generating economic losses. Vaccines available to prevent this condition do not have the desired effect, but this limitation can be overcome using adjuvants. Pro-inflammatory cytokines, such as interleukin 18 (IL-18), can improve an immune response, reducing the immune window of protection. In this study, recombinant porcine IL-18 was produced and expressed in Escherichia coli and Pichia pastoris. The protein's biological activity was assessed in vitro and in vivo, and we determined that the P. pastoris protein had better immunostimulatory activity. A vaccine candidate against L. intracellularis, formulated with and without IL-18, was used to determine the pigs' cellular and humoral immune responses. Animals injected with the candidate vaccine co-formulated with IL-18 showed a significant increase of Th1 immune response markers and an earlier increase of antibodies than those vaccinated without the cytokine. This suggests that IL-18 acts as an immunostimulant and vaccine adjuvant to boost the immune response against the antigens, reducing the therapeutic window of recombinant protein-based vaccines.
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Affiliation(s)
- Angela Hidalgo-Gajardo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Nicolás Gutiérrez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Emilio Lamazares
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Felipe Espinoza
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Fernanda Escobar-Riquelme
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - María J. Leiva
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Carla Villavicencio
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, IX Región, Temuco 4813302, Chile;
| | - Raquel Montesino
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Claudia Altamirano
- Laboratorio de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, V Región, Valparaíso 2362803, Chile;
| | - Oliberto Sánchez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Coralia I. Rivas
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Álvaro Ruíz
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, XVI Región, Chillán 3812120, Chile;
| | - Jorge R. Toledo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
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Gao L, Meng J, Dai W, Zhang Z, Dong H, Yuan Q, Zhang W, Liu S, Wu X. Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production. Biotechnol Biofuels Bioprod 2023; 16:178. [PMID: 37978550 PMCID: PMC10655344 DOI: 10.1186/s13068-023-02428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Single-cell protein (SCP) production in the methylotrophic yeast Pichia pastoris has the potential to achieve a sustainable protein supply. However, improving the methanol fermentation efficiency and reducing carbon loss has been a long-standing challenge with far-reaching scientific and practical implications. Here, comparative transcriptomics revealed that PAS_0305, a gene directly associated with cell wall thickness under methanol stress, can be used as a target for unlocking cell wall sensors. Intracellular trehalose accumulation confirmed that cell wall sensors were activated after knocking out PAS_0305, which resulted in increased cell wall permeability. Genome-wide signal perturbations were transduced through the HOG module and the CWI pathway, which was confirmed to connected by Pbs2-Mkk. As a consequence of CWI pathway activation, ΔPAS_0305 elicited a rescue response of cell wall remodeling by increasing the β-1,3-glucan content and decreasing the chitin/mannose content. Remarkably, perturbations in global stress signals led to a fine-tuning of the metabolic network of ΔPAS_0305, resulting in a superior phenotype with highest crude protein and methanol conversion rate of 67.21% and 0.46 gDCW/g. Further genome-scale metabolic models were constructed to validate the experimental results, confirming that unlocking cell wall sensors resulted in maximized flux from methanol towards SCP and effectively addressing the issue of carbon loss in methanol fermentation. This work sheds new light on the potential of manipulating cellular signaling pathways to optimize metabolic networks and achieve exceptional phenotypic characteristics, providing new strategies for constructing versatile cell factories in P. pastoris.
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Affiliation(s)
- Le Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Jiao Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Wuling Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Zhaokun Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Haofan Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Qianqian Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Shuguang Liu
- Beijing Chasing future Biotechnology Co., Ltd, Beijing, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, Tianjin, 300308, China.
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Àvila-Cabré S, Pérez-Trujillo M, Albiol J, Ferrer P. Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid. Microb Cell Fact 2023; 22:237. [PMID: 37978380 PMCID: PMC10655335 DOI: 10.1186/s12934-023-02241-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Methanol is increasingly gaining attraction as renewable carbon source to produce specialty and commodity chemicals, as it can be generated from renewable sources such as carbon dioxide (CO2). In this context, native methylotrophs such as the yeast Komagataella phaffii (syn Pichia pastoris) are potentially attractive cell factories to produce a wide range of products from this highly reduced substrate. However, studies addressing the potential of this yeast to produce bulk chemicals from methanol are still scarce. 3-Hydroxypropionic acid (3-HP) is a platform chemical which can be converted into acrylic acid and other commodity chemicals and biopolymers. 3-HP can be naturally produced by several bacteria through different metabolic pathways. RESULTS In this study, production of 3-HP via the synthetic β-alanine pathway has been established in K. phaffii for the first time by expressing three heterologous genes, namely panD from Tribolium castaneum, yhxA from Bacillus cereus, and ydfG from Escherichia coli K-12. The expression of these key enzymes allowed a production of 1.0 g l-1 of 3-HP in small-scale cultivations using methanol as substrate. The addition of a second copy of the panD gene and selection of a weak promoter to drive expression of the ydfG gene in the PpCβ21 strain resulted in an additional increase in the final 3-HP titer (1.2 g l-1). The 3-HP-producing strains were further tested in fed-batch cultures. The best strain (PpCβ21) achieved a final 3-HP concentration of 21.4 g l-1 after 39 h of methanol feeding, a product yield of 0.15 g g-1, and a volumetric productivity of 0.48 g l-1 h-1. Further engineering of this strain aiming at increasing NADPH availability led to a 16% increase in the methanol consumption rate and 10% higher specific productivity compared to the reference strain PpCβ21. CONCLUSIONS Our results show the potential of K. phaffii as platform cell factory to produce organic acids such as 3-HP from renewable one-carbon feedstocks, achieving the highest volumetric productivities reported so far for a 3-HP production process through the β-alanine pathway.
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Affiliation(s)
- Sílvia Àvila-Cabré
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Míriam Pérez-Trujillo
- Servei de Ressonància Magnètica Nuclear, Facultat de Ciències i Biociències, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.
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Zhou H, Wang Z, Qian J. Engineering of the hypoxia-induced Pichia stipitis ADH2 promoter to construct a promoter library for Pichia pastoris. J Biotechnol 2023; 376:24-32. [PMID: 37690664 DOI: 10.1016/j.jbiotec.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Hypoxia-inducible promoters of a wide range of activities are desirable for fine-tuning gene expression in response to oxygen limitation, especially for the Crabtree negative yeast Pichia pastoris (Komagataella phaffii) with a high oxygen consumption rate in large-scale fermentations. Here we constructed a hypoxia-inducible promoter library for P. pastoris through error-prone PCR of Pichia stipitis ADH2 promoter (PsADH2). The library of 30 selected promoters showing 0.4- to 5.5-fold of the PsADH2 activity was obtained through high-throughput screening in microplates using the reporter yeast-enhanced green fluorescent protein. Two strong promoters, AM23 and AM30, were further characterized in shake flask cultures at high and low dissolved oxygen levels. They responded more sensitively to the low dissolved oxygen level, achieving a 4.6-, 7.9-fold and 3.6-, 7.7-fold higher fluorescence intensity and transcript level, respectively, than the wild-type PsADH2. Their hypoxia-inducible properties were confirmed with two additional reporters: β-galactosidase and Vitreoscilla hemoglobin, to demonstrate the broad applicability of the promoter library. During the typical fermentation process in shake flasks, the promoter AM30 showed strong expression with cell growth and decreased oxygen levels, without any additional chemical inducers or operations. Since the potent industrial host P. pastoris is recognized as an easy to scale-up system, it is reasonable to expect that the obtained hypoxia-inducible promoter library may have great potential to enable convenient regulation of gene expression under industrial fermentations which are usually run under oxygen limitation due to high cell density cultivations.
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Affiliation(s)
- Hangcheng Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Zhipeng Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jiangchao Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China.
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Zhang L, Wang B, Shen Y, Nie Y. An online soft sensor method for biochemical reaction process based on JS-ISSA-XGBoost. BMC Biotechnol 2023; 23:49. [PMID: 37940925 PMCID: PMC10634092 DOI: 10.1186/s12896-023-00816-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND A method combining offline techniques and the just-in-time learning strategy (JITL) is proposed, because the biochemical reaction process often encounters changing features and parameters over time. METHODS Firstly, multiple sub-databases in the fermentation process are constructed offline by an improved fuzzy C-means algorithm and the sample data are adaptively pruned by a similarity query threshold. Secondly, an improved eXtreme Gradient Boosting (XGBoost) method is used on the online modeling stage to build soft sensor models, and the multi-similarity-driven just-in-time learning strategy is used to increase the diversity of the model. Finally, to improve the generalization of the whole algorithm, the output of the base learner is fused by an improved Stacking integration model and then the predictive output is performed. RESULTS Applying the constructed soft sensor model to the problem of predicting cell concentration and product concentration in Pichia pastoris fermentation process. The experimental results show that the root mean square error of the cell concentration is 0.0260, the coefficient of determination is 0.9945, the root mean square error of the product concentration is 2.6688, and the coefficient of determination is 0.9970. It shows that the proposed method has the advantages of timely prediction and high prediction accuracy, which validates the effectiveness and practicality of the method. CONCLUSION The JS-ISSA-XGBoost is an extensive and excellent soft measurement model that meets the practical needs for real-time monitoring of parameters and prediction of control in biochemical reactions.
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Affiliation(s)
- Ligang Zhang
- School of Electrical and Information Engineering, JiangSu University, ZhenJiang, 212013, JiangSu, China
| | - Bo Wang
- School of Electrical and Information Engineering, JiangSu University, ZhenJiang, 212013, JiangSu, China.
| | - Yao Shen
- School of Electrical and Information Engineering, JiangSu University, ZhenJiang, 212013, JiangSu, China
| | - Yongxin Nie
- School of Electrical and Information Engineering, JiangSu University, ZhenJiang, 212013, JiangSu, China
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Lisov A, Belova O, Lisova Z, Nagel A, Shadrin A, Andreeva-Kovalevskaya Z, Nagornykh M, Zakharova M, Leontievsky A. Two β-glucanases from bacterium Cellulomonas flavigena: expression in Pichia pastoris, properties, biotechnological potential. Prep Biochem Biotechnol 2023; 53:1313-1321. [PMID: 37093814 DOI: 10.1080/10826068.2023.2201934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In the genome of Cellulomonas flavigena, two genes that potentially encode endoglucanases - Cfla_2912 and Cfla_2913 were identified. We cloned the genes and created Pichia pastoris-based recombinant producers of two proteins that were expressed from the AOX1 promoter. Each of the endoglucanase molecules contains a GH6 catalytic domain, CBM2 carbohydrate-binding module, and TAT signal peptide. The fermentation of the producers was carried out in a 10 L fermenter; Cfla_2912 and Cfla_2913 were purified using affinity chromatography. The yield comprised 10.3 mg/ml (430 U/ml) for Cfla_2913 and 9 mg/ml (370 U/ml) for Cfla_2912. Cfla_2912 and Cfla_2913 were found to have a high activity against barley β-glucan and lichenan, a weak activity against carboxymethyl cellulose (CMC), phosphoric-acid treated cellulose, and no activity against laminarin, xylan, soluble starch, microcrystalline cellulose, cellobiose, and cellotriose. Thus, the proteins exhibited β-glucanase activity. Both proteins had a neutral pH optimum of about 7.0 and were more stable at neutral and slightly alkaline pH ranging from 7.0 to 9.0. Cfla_2912 and Cfla_2913 showed a moderate thermal stability. The products of barley β-glucan hydrolysis by Cfla_2912 and Cfla_2913 were trisaccharide, tetrasaccharide, and cellobiose. Cfla_2912 and Cfla_2913 efficiently hydrolyzed cereal polysaccharides, which indicate that they may have biotechnological potential.
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Affiliation(s)
- Alexander Lisov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Belova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zoya Lisova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Nagel
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Shadrin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Zhanna Andreeva-Kovalevskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Maxim Nagornykh
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Marina Zakharova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Leontievsky
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow, Russia
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Wang Y, Wang B, Gao Y, Nakanishi H, Gao XD, Li Z. Highly efficient expression and secretion of human lysozyme using multiple strategies in Pichia pastoris. Biotechnol J 2023; 18:e2300259. [PMID: 37470505 DOI: 10.1002/biot.202300259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Human lysozyme (hLYZ), an emerging antibacterial agent, has extensive application in the food and pharmaceutical industries. However, the source of hLYZ is particularly limited. RESULTS To achieve highly efficient expression and secretion of hLYZ in Pichia pastoris, multiple strategies including G418 sulfate screening, signal sequence optimization, vacuolar sorting receptor VPS10 disruption, and chaperones/transcription factors co-expression were applied. The maximal enzyme activity of extracellular hLYZ in a shaking flask was 81,600 ± 5230 U mL-1 , which was about five times of original strain. To further reduce the cost, the optimal medium RDMY was developed and the highest hLYZ activity reached 352,000 ± 16,696.5 U mL-1 in a 5 L fermenter. CONCLUSION This research provides a very useful and cost-effective approach for the hLYZ production in P. pastoris and can also be applied to the production of other recombinant proteins.
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Affiliation(s)
- Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Buqing Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Yahui Gao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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Liu Q, Huo X, Tian Q, Wang P, Zhao F, Yang C, Su J. The oral antigen-adjuvant fusion vaccine P-MCP-FlaC provides effective protective effect against largemouth bass ranavirus infection. Fish Shellfish Immunol 2023; 142:109179. [PMID: 37863125 DOI: 10.1016/j.fsi.2023.109179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Largemouth bass ranavirus (LMBV) is highly contagious and lethal to largemouth bass, causing significant economic losses to the aquaculture industry. Oral vaccination is generally considered the most ideal strategy for protecting fish from viral infection. In this study, the fusion protein MCP-FlaC, consisting of the main capsid protein (MCP) as the antigen and flagellin C (FlaC) as the adjuvant, was intracellularly expressed in Pichia pastoris. Subsequently, the recombinant P. pastoris was freeze-dried to prepare the oral vaccine P-MCP-FlaC. Transmission electron microscopy and scanning electron microscopy analysis showed that the morphology and structure of the freeze-dried recombinant P. pastoris vaccine remained intact. The experiment fish (n = 100) was divided into five groups (P-MCP-FlaC, P-MCP, P-FlaC, P-pPIC3.5K, control) to evaluate the protective efficacy of the recombinant vaccine. Oral P-MCP-FlaC vaccine effectively up-regulated the serum enzymes activity (total superoxide dismutase, lysozyme, total antioxidant capacity, and complement component 3). The survival rate of P-MCP-FlaC group was significantly higher than that of the other groups. The mRNA expression of crucial immune genes (IL-1β, TNF-α, MHC-II, IFN-γ, Mx, IgM, IgT) was also signally elevated in P-MCP-FlaC group. Vaccine P-MCP-FlaC markedly inhibited the replication of LMBV in the spleen, head kidney, and intestine, while reducing the degree of lesion in the spleen. These results suggest that the oral P-MCP-FlaC vaccine could effectively control LMBV infection, proving an effective strategy for viral diseases prevention in aquaculture.
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Affiliation(s)
- Qian Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingchen Huo
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingqing Tian
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pengxu Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengxia Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunrong Yang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Schwob M, Kugler V, Wagner R. Cloning and Overexpressing Membrane Proteins Using Pichia pastoris (Komagataella phaffii). Curr Protoc 2023; 3:e936. [PMID: 37933574 DOI: 10.1002/cpz1.936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Understanding the structure and function of key proteins located within biological membranes is essential for fundamental knowledge and therapeutic applications. Robust cell systems allowing their actual overexpression are required, among which stands the methylotrophic yeast Pichia pastoris. This system proves highly efficient in producing many eukaryotic membrane proteins of various functions and structures at levels and quality compatible with their subsequent isolation and molecular investigation. This article describes a set of basic guidelines and directions to clone and select recombinant P. pastoris clones overexpressing eukaryotic membrane proteins. Illustrative results obtained for a panel of mammalian membrane proteins are presented, and hints are given on a series of experimental parameters that may substantially improve the amount and/or the functionality of the expressed proteins. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Designing and cloning a P. pastoris expression vector Basic Protocol 2: Integrative transformation of P. pastoris and selection of recombinant clones Basic Protocol 3: Culturing transformed P. pastoris for membrane protein expression Basic Protocol 4: Yeast cell lysis and membrane preparation Basic Protocol 5: Immunodetection of expressed membrane proteins: western blot Alternate Protocol 1: Immunodetection of expressed membrane proteins: dot blot Alternate Protocol 2: Immunodetection of expressed membrane proteins: yeastern blot Basic Protocol 6: Activity assay: ligand-binding analysis of an expressed GPCR.
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Affiliation(s)
- Magali Schwob
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
- Department of Structural Biology, NovAliX, Strasbourg, France
| | - Valérie Kugler
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
| | - Renaud Wagner
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
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Wang YS, Gong MH, Wang JH, Yu JC, Li MJ, Xue YP, Zheng YG. Heterologous expression of a deacetylase and its application in L-glufosinate preparation. Bioprocess Biosyst Eng 2023; 46:1639-1650. [PMID: 37733076 DOI: 10.1007/s00449-023-02925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
With potent herbicidal activity, biocatalysis synthesis of L-glufosinate has drawn attention. In present research, NAP-Das2.3, a deacetylase capable of stereoselectively resolving N-acetyl-L-glufosinate to L-glufosinate mined from Arenimonas malthae, was heterologously expressed and characterized. In Escherichia coli, NAP-Das2.3 activity only reached 0.25 U/L due to the formation of inclusive bodies. Efficient soluble expression of NAP-Das2.3 was achieved in Pichia pastoris. In shake flask and 5 L bioreactor fermentation, NAP-Das2.3 activity by recombinant P. pastoris reached 107.39 U/L and 1287.52 U/L, respectively. The optimum temperature and pH for N-acetyl-glufosinate hydrolysis by NAP-Das2.3 were 45 °C and pH 8.0, respectively. The Km and Vmax of NAP-Das2.3 towards N-acetyl-glufosinate were 25.32 mM and 19.23 μmol mg-1 min-1, respectively. Within 90 min, 92.71% of L-enantiomer in 100 mM racemic N-acetyl-glufosinate was converted by NAP-Das2.3. L-glufosinate with high optical purity (e.e.P above 99.9%) was obtained. Therefore, the recombinant NAP-Das2.3 might be an alternative for L-glufosinate biosynthesis.
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Affiliation(s)
- Yuan-Shan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Mei-Hua Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jin-Hao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jia-Cheng Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Mei-Jing Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Luo H, Zhou T, Cao J, Gao L, Wang S, Gui Z, Shi Y, Xie F, Yang R. Utilization of lignocellulosic biomass by glycerol organosolv pretreatment for biobutanol production integrated with bioconversion of residual glycerol into value-added products. Bioresour Technol 2023; 387:129661. [PMID: 37573976 DOI: 10.1016/j.biortech.2023.129661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Glycerol organosolv pretreatment (GOP) is considered an efficient method to deconstruct lignocellulose for producing fermentable sugars. Herein, the liquid fraction containing glycerol after GOP was utilized for recycled pretreatment of corn stover (CS) for four cycles. Enzymatic yield of glucose after recycled pretreatment was enhanced by 2.4-3.5 folds compared with untreated CS. Meanwhile, residual glycerol was used as carbon source for cultivation of Pichia pastoris to obtain high cell-density, and a final titer of 1.3 g/L human lysozyme was produced by P. pastoris under low temperature methanol induction strategy. Additionally, the pretreated CS was mixed with cassava as fermentable substrates for butanol production by wild-type Clostridium acetobutylicum ATCC 824. Final butanol production of 13.9 g/L was obtained from mixed substrates (25%:75% of CS/cassava) at 10% solids loading by simultaneous saccharification and fermentation. Overall, integration of residual glycerol utilization and butanol production by microbial fermentation provided an efficient strategy for biorefinery.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Tairan Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jin Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Lei Gao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Shijie Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Gui
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yongjiang Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Fang Xie
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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Chronopoulou S, Tsochantaridis I, Tokamani M, Kokkinopliti KD, Tsomakidis P, Giannakakis A, Galanis A, Pappa A, Sandaltzopoulos R. Expression and purification of human interferon alpha 2a (IFNα2a) in the methylotrophic yeast Pichia pastoris. Protein Expr Purif 2023; 211:106339. [PMID: 37467825 DOI: 10.1016/j.pep.2023.106339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Human interferon alpha 2a (IFNα2a) is a secreted glycoprotein that exerts a wide spectrum of biological effects, such as triggering of antiviral, antitumor and immunosuppressive responses. IFNα2a is used as pharmaceutical polypeptide in chronic hepatitis C virus (HCV) infection, chronic myelogenous leukemia, advanced renal cell carcinoma, and metastatic malignant melanoma. So far, the pharmaceutical polypeptide of this cytokine is produced in prokaryotic expression systems (E. coli). Here we report the expression and purification of recombinant human IFNα2a in the methylotrophic yeast Pichia pastoris. The cDNA encoding for human IFNα2a, modified to bear the P. pastoris codon bias, was cloned into the pPinkα-HC vector in order to be expressed as a secreted protein upon induction. Proper expression and secretion of recombinant human IFNα2a (approximately 19 kDa) was confirmed by PCR-sequencing, SDS-PAGE and Western blot analysis following methanol-induced expression in a number of individual transformed strains. Purification of the recombinant protein was performed by affinity chromatography, achieving a robust yield of purified active form. The purified recombinant protein showed an impressive stability to thermal denaturation as observed by Differential Scanning Fluorimetry. The biological activity of the P. pastoris-produced IFNα2a was confirmed in A549 and HT29 cells by monitoring transcriptional up-regulation of a panel of known interferon-stimulated genes (ISGs). Our results document that the P. pastoris expression system is a suitable system for producing biologically functional IFNα2a in a secreted form.
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Affiliation(s)
- Sofia Chronopoulou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Ilias Tsochantaridis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Maria Tokamani
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | | | - Petros Tsomakidis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Antonis Giannakakis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Alex Galanis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
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Abstract
Lycopene is widely used in cosmetics, food, and nutritional supplements. Microbial production of lycopene has been intensively studied. However, few metabolic engineering studies on Pichia pastoris have been aimed at achieving high-yield lycopene production. In this study, the CRISPR/Cpf1-based gene repression system was developed and the gene editing system was optimized, which were applied to improve lycopene production successfully. In addition, the sterol regulatory element-binding protein SREBP (Sre) was used for the regulation of lipid metabolic pathways to promote lycopene overproduction in P. pastoris for the first time. The final engineered strain produced lycopene at 7.24 g/L and 75.48 mg/g DCW in fed-batch fermentation, representing the highest lycopene yield in P. pastoris reported to date. These findings provide effective strategies for extended metabolic engineering assisted by the CRISPR/Cpf1 system and new insights into metabolic engineering through transcriptional regulation of related metabolic pathways to enhance carotenoid production in P. pastoris.
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Affiliation(s)
- Xinying Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuting Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wenjie Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Denggang Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shupeng Ruan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yuxin Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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Zha J, Liu D, Ren J, Liu Z, Wu X. Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories. J Fungi (Basel) 2023; 9:1027. [PMID: 37888283 PMCID: PMC10608127 DOI: 10.3390/jof9101027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
| | | | | | | | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
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Subash Chandra Bose K, Shah MI, Krishna J, Sankaranarayanan M. Genome-scale metabolic model analysis of Pichia pastoris for enhancing the production of S-adenosyl-L-methionine. Bioprocess Biosyst Eng 2023; 46:1471-1482. [PMID: 37597025 DOI: 10.1007/s00449-023-02913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Komagataella phaffii, formerly Pichia pastoris (P. pastoris), is a promising methylotrophic yeast used in industry to produce recombinant protein and valuable metabolites. In this study, a genome-scale metabolic model (GEMs) was reconstructed and used to assess P. pastoris' metabolic capabilities for the production of S-adenosyl-L-methionine (AdoMet or SAM or SAMe) from individual carbon sources along with the addition of L-methionine. In a model-driven P. pastoris strain, the well-established genome-scale metabolic model iAUKM can be implemented to predict high valuable metabolite production. The model, iAUKM, was created by merging the previously published iMT1026 model and the draught model generated using Raven toolbox from the KEGG database which covered 2309 enzymatic reactions associated with 1033 metabolic genes and 1750 metabolites. The highly curated model was successful in capturing P. pastoris growth on various carbon sources, as well as AdoMet production under various growth conditions. Many overexpression gene targets for increasing AdoMet accumulation in the cell have been predicted for various carbon sources. Inorganic phosphatase (IPP) was one of the predicted overexpression targets as revealed from simulations using iAUKM. When IPP gene was integrated into P. pastoris, we found that AdoMet accumulation increased by 16% and 14% using glucose and glycerol as carbon sources, respectively. Our in silico results shed light on the factors limiting AdoMet production, as well as key pathways for rationalized engineering to increase AdoMet yield.
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Affiliation(s)
| | - Mohd Imran Shah
- Department of Biotechnology, Anna University, Chennai, Tamil Nadu, India
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Yu F, Zhao X, Zhou J, Lu W, Li J, Chen J, Du G. Biosynthesis of High-Active Hemoproteins by the Efficient Heme-Supply Pichia Pastoris Chassis. Adv Sci (Weinh) 2023; 10:e2302826. [PMID: 37649147 PMCID: PMC10602571 DOI: 10.1002/advs.202302826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/17/2023] [Indexed: 09/01/2023]
Abstract
Microbial synthesis of valuable hemoproteins has become a popular research topic, and Pichia pastoris is a versatile platform for the industrial production of recombinant proteins. However, the inadequate supply of heme limits the synthesis of high-active hemoproteins. Here a strategy for enhancing intracellular heme biosynthesis to improve the titers and functional activities of hemoproteins is reported. After selecting a suitable expressional strategy for globins, the efficient heme-supply P. pastoris chassis is established by removing the spatial segregation during heme biosynthesis, optimizing precursor synthesis, assembling rate-limiting enzymes using protein scaffolds, and inhibiting heme degradation. This robust chassis produces several highly active hemoproteins, including porcine myoglobin, soy hemoglobin, Vitreoscilla hemoglobin, and P450-BM3, which can be used in the development of artificial meat, high-cell-density fermentation, and whole-cell catalytic synthesis of high-value-added compounds. Furthermore, the engineered chassis strain has great potential for producing and applying other hemoproteins with high activities in various fields.
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Affiliation(s)
- Fei Yu
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Xinrui Zhao
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Jingwen Zhou
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Wei Lu
- Dongsheng Biotech Co., Ltd.91–92 Junmin RoadTaixingJiangsu225432China
| | - Jianghua Li
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Jian Chen
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Guocheng Du
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan University1800 Lihu RoadWuxiJiangsu214122China
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Xiao D, Li X, Zhang Y, Wang F. Efficient Expression of Candida antarctica Lipase B in Pichia pastoris and Its Application in Biodiesel Production. Appl Biochem Biotechnol 2023; 195:5933-5949. [PMID: 36723721 DOI: 10.1007/s12010-023-04374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/02/2023]
Abstract
Lipase B from Candida antarctica (CALB) is an important biocatalyst with many potential applications. However, original CALB is usually with lower enzyme activity and also costly to produce from Candida antarctica; hence, it is often necessary to prepare recombinant CALB through gene heterologous expression. In this research, seven promoters and five signal peptides were compared respectively for expressing codon-optimized CALB in Pichia pastoris, and then recombinant P. pastoris containing 3 copies of calb gene were obtained by screening with high concentrations of antibiotics under the condition of the optimal combination. In a 1.3-L bioreactor, the maximum CALB activity and total protein content reached 444.46 ± 18.81 U/mL and 5.41 ± 0.1 g/L, respectively, after about 9 days of incubation in FM22 medium, which were 34 times and 20 times higher than the initial strains, respectively. In addition, the obtained CALB was used to catalyze the transesterification of acidified gutter oil with methanol, suggesting a promising pathway to convert waste or low quality of bio-oil feedstocks with high amount of free fatty acids into biodiesel by using recombinant CALB as catalyst. The results can provide with a good reference for efficient expression of CALB and enhancing lipase production in P. pastoris. It is supposed to bring with new possibility for the bio-production of other valuable proteins.
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Affiliation(s)
- Dunchi Xiao
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China
| | - Xun Li
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Zhang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China
| | - Fei Wang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China.
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037, China.
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68
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Meng J, Liu S, Gao L, Hong K, Liu S, Wu X. Economical production of Pichia pastoris single cell protein from methanol at industrial pilot scale. Microb Cell Fact 2023; 22:198. [PMID: 37770920 PMCID: PMC10540378 DOI: 10.1186/s12934-023-02198-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Methanol, synthesized from CO2, is a potentially sustainable one-carbon (C1) resource for biomanufacturing. The use of methanol as a feedstock to produce single cell protein (SCP) has been investigated for decades as an alternative to alleviate the high global demand for animal-derived proteins. The methylotrophic yeast Pichia pastoris is an ideal host for methanol-based SCP synthesis due to its natural methanol assimilation ability. However, improving methanol utilization, tolerance to higher temperature, and the protein content of P. pastoris are also current challenges, which are of great significance to the economical industrial application using methanol as a feedstock for SCP production. RESULTS In the present work, adaptive laboratory evolution (ALE) has been employed to overcome the low methanol utilization efficiency and intolerance to a higher temperature of 33 °C in P. pastoris, associated with reduced carbon loss due to the lessened detoxification of intracellular formaldehyde through the dissimilation pathway and cell wall rearrangement to temperature stress resistance following long-term evolution as revealed by transcriptomic and phenotypic analysis. By strengthening nitrogen metabolism and impairing cell wall synthesis, metabolic engineering further increased protein content. Finally, the engineered strain via multi-strategy produced high levels of SCP from methanol in a pilot-scale fed-batch culture at 33 °C with a biomass of 63.37 g DCW/L, methanol conversion rate of 0.43 g DCW/g, and protein content of 0.506 g/g DCW. SCP obtained from P. pastoris contains a higher percentage of protein compared to conventional foods like soy, fish, meat, whole milk, and is a source of essential amino acids, including methionine, lysine, and branched-chain amino acids (BCAAs: valine, isoleucine, leucine). CONCLUSIONS This study clarified the unique mechanism of P. pastoris for efficient methanol utilization, higher temperature resistance, and high protein synthesis, providing a P. pastoris cell factory for SCP production with environmental, economic, and nutritional benefits.
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Affiliation(s)
- Jiao Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Shufan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Le Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Kai Hong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Shuguang Liu
- Ningxia Future Biotechnology Co., Ltd, Jingsan Road, Ningdong Linhe Industrial Zone, Ningdong Town, Ningxia, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China.
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69
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Makeeva A, Muzaev D, Shubert M, Ianshina T, Sidorin A, Sambuk E, Rumyantsev A, Padkina M. Alternative PCR-Based Approaches for Generation of Komagataella phaffii Strains. Microorganisms 2023; 11:2297. [PMID: 37764140 PMCID: PMC10536657 DOI: 10.3390/microorganisms11092297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Komagataella phaffii (Pichia pastoris) is a widely known microbial host for recombinant protein production and an emerging model organism in fundamental research. The development of new materials and techniques on this yeast improves heterologous protein synthesis. One of the most prominent ways to enhance protein production efficiency is to select K. phaffii strains with multiple expression cassettes and generate MutS strains using various vectors. In this study, we demonstrate approaches to expand the applications of pPICZ series vectors. Procedures based on PCR amplification and in vivo cloning allow rapid exchange of selectable markers. The combination of PCR amplification with split-marker-mediated transformation allows the development of K. phaffii MutS strains with two expression cassettes using pPICZ vectors. Both PCR-based approaches were applied to efficiently produce interleukin-2 mimetic Neo-2/15 in K. phaffii. The described techniques provide alternative ways to generate and improve K. phaffii strains without the need for obtaining new specific vectors or additional cloning of expression cassettes.
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Affiliation(s)
| | | | | | | | | | | | - Andrey Rumyantsev
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Marina Padkina
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
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70
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Incze DJ, Poppe L, Bata Z. Optimization Workflow of Fumonisin Esterase Production for Biocatalytic Degradation of Fumonisin B 1. Life (Basel) 2023; 13:1885. [PMID: 37763289 PMCID: PMC10533188 DOI: 10.3390/life13091885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Industrial enzyme production with the Pichia pastoris expression system requires a well-characterized production strain and a competitively priced fermentation medium to meet the expectations of the industry. The present work shows a workflow that allows the rapid and reliable screening of transformants of single copy insertion of the target production cassette. A constitutive expression system with the glyceraldehyde-3-phosphate dehydrogenase promoter (pGAP) with homology arms for the glycerol kinase 1 (GUT1) was constructed for the targeted integration of the expression plasmid in a KU70 deficient Pichia pastoris and the production of a bacterial fumonisin esterase enzyme (CFE). A robust colony qPCR method was developed for the copy number estimation of the expression cassette. Optimization of the protein production medium and the scale-up ability was aided by design of experiments (DOE) approach resulting in optimized production conditions at a semi-industrial scale. A novel fermentation medium containing 3% inactivated yeast and 2% dextrose in an ammonium-citrate buffer (IYD) was shown to be a promising alternative to YPD media (containing yeast extract, peptone, and dextrose), as similar protein titers could be obtained, while the cost of the medium was reduced 20-fold. In a demonstration-scale 48 h long fed-batch fermentation, the IYD media outperformed the small-scale YPD cultivation by 471.5 ± 22.6%.
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Affiliation(s)
- Dániel János Incze
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem Rakpart 3, H-1111 Budapest, Hungary;
- Research and Development Laboratory, Dr. Bata Ltd., Bajcsy-Zsilinszky utca 139, H-2364 Ócsa, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem Rakpart 3, H-1111 Budapest, Hungary;
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Strada Arany János 11, RO-400028 Cluj-Napoca, Romania
| | - Zsófia Bata
- Research and Development Laboratory, Dr. Bata Ltd., Bajcsy-Zsilinszky utca 139, H-2364 Ócsa, Hungary
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71
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Qiao S, Bai F, Cai P, Zhou YJ, Yao L. An improved CRISPRi system in Pichia pastoris. Synth Syst Biotechnol 2023; 8:479-485. [PMID: 37692202 PMCID: PMC10485788 DOI: 10.1016/j.synbio.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 09/12/2023] Open
Abstract
CRISPR interference (CRISPRi) has been developed and widely used for gene repression in various hosts. Here we report an improved CRISPRi system in Pichia pastoris by fusing dCas9 with endogenous transcriptional repressor domains. The CRISPRi system shows strong repression of eGFP, with the highest efficiency of 85%. Repression of native genes is demonstrated by targeting AOX1 promoter. AOX1 is efficiently repressed and the mutant strains show much slower growth in methanol medium. Effects of gRNA expression and processing on CRISPRi efficiency is also investigated. It is found that gRNA processing by HH/HDV ribozymes or Csy4 endoribonuclease generating clean gRNA is critical to achieve strong repression, and Csy4 cleavage shows higher repression efficiency. However, gRNA expression using native tRNA transcription and processing systems results in relatively weaker repression of eGFP. By expression of two gRNAs targeting promoters of eGFP and AOX1 in an array together with Cys4 recognition sites, both genes can be repressed simultaneously. Cys4-mediated gRNA array processing is further applied to repress fatty acyl-CoA synthetase genes (FAA1 and FAA2). Both genes are efficiently repressed, demonstrating that Cys4 endoribonuclease has the ability to cleave gRNAs array and can be can be used for multiplexed gene repression in P. pastoris.
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Affiliation(s)
- Shujing Qiao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Bai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Peng Cai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J. Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, PR China
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72
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Wang X, Li Y, Jin Z, Liu X, Gao X, Guo S, Yu T. A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris. Synth Syst Biotechnol 2023; 8:445-451. [PMID: 37448527 PMCID: PMC10336193 DOI: 10.1016/j.synbio.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The methylotrophic budding yeast Pichia pastoris has been utilized to the production of a variety of heterologous recombinant proteins owing to the strong inducible alcohol oxidase promoter (pAOX1). However, it is difficult to use P. pastoris as the chassis cell factory for high-valuable metabolite biosynthesis due to the low homologous recombination (HR) efficiency and the limitation of handy selective markers, especially in the condition of multistep biosynthetic pathways. Hence, we developed a novel CRISPR/Cas9 system with highly editing efficiencies and recyclable auxotrophic selective marker (HiEE-ReSM) to facilitate cell factory in P. pastoris. Firstly, we improved the HR rates of P. pastoris through knocking out the non-homologous-end-joining gene (Δku70) and overexpressing HR-related proteins (RAD52 and RAD59), resulting in higher positive rate compared to the basal strain, achieved 97%. Then, we used the uracil biosynthetic genes PpURA3 as the reverse screening marker, which can improve the recycling efficiency of marker. Meanwhile, the HR rate is still 100% in uracil auxotrophic yeast. Specially, we improved the growth rate of uracil auxotrophic yeast strains by overexpressing the uracil transporter (scFUR4) to increase the uptake of exogenous uracil from medium. Meanwhile, we explored the optimal concentration of uracil (90 mg/L) for strain growth. In the end, the HiEE-ReSM system has been applied for the inositol production (250 mg/L) derived from methanol in P. pastoris. The systems will contribute to P. pastoris as an attractive cell factory for the complex compound biosynthesis through multistep metabolic pathway engineering and will be a useful tool to improve one carbon (C1) bio-utilization.
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Affiliation(s)
- Xiang Wang
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Li
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhehao Jin
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiangjian Liu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiang Gao
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology of CAS, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academic of Science, Shenzhen, 518055, China
| | - Shuyuan Guo
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Tao Yu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
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73
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Sarwar A, Lee EY. Methanol-based biomanufacturing of fuels and chemicals using native and synthetic methylotrophs. Synth Syst Biotechnol 2023; 8:396-415. [PMID: 37384124 PMCID: PMC10293595 DOI: 10.1016/j.synbio.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/03/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023] Open
Abstract
Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Escherichia coli. Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.
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74
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Akentyev P, Sokolova D, Korzhenkov A, Gubaidullin I, Kozlov D. Expression level of SOR1 is a bottleneck for efficient sorbitol utilization by yeast Komagataella kurtzmanii. Yeast 2023; 40:414-424. [PMID: 37272406 DOI: 10.1002/yea.3884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023] Open
Abstract
The yeast strain Komagataella kurtzmanii VKPM Y-727 shows a significant defect in sorbitol utilization compared to closely related yeast K. phaffii (including strains formerly identified as Pichia pastoris). Our aim was to investigate the factors that determine the phenotype of the wild-type strain and to obtain a K. kurtzmanii strain with an improved ability to utilize sorbitol. We sequenced and annotated the genome of K. kurtzmanii VKPM Y-727 and compared it with that of K. phaffii GS115. Five K. phaffii GS115 genes that might be involved in sorbitol metabolism were selected and transferred into K. kurtzmanii Y-727. The transfer of the modified SOR1 gene resulted in an increased growth rate of K. kurtzmanii in sorbitol, despite the fact that Y-727 already contains its own SOR1 gene without any apparent mutations. The enzymes encoded by the SOR1 genes were analyzed in vitro and found to have similar properties. Differences in promoter activity were assessed using lacZ as a reporter gene, and the PSDH727 (promoter of SOR1 (SDH727) from K. kurtzmanii Y-727) promoter was shown to be 1.5-2.0 times weaker than PSDH115 (promoter of SOR1 (SDH115) from K. phaffii GS115). Moreover, both promoters were less active in K. kurtzmanii than in K. phaffii when evaluated in cells grown in synthetic complete media with glucose or sorbitol. Thus, SOR1 gene expression was identified as a bottleneck in sorbitol metabolism in K. kurtzmanii. Also, the positive effect of additional modified SOR1 gene copies was observed in both yeasts, as K. kurtzmanii and K. phaffii could grow on synthetic complete media with sorbitol three times faster than the original K. phaffii GS115 strain.
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Affiliation(s)
- Philipp Akentyev
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - Daria Sokolova
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | | | - Irek Gubaidullin
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | - Dmitry Kozlov
- National Research Center "Kurchatov Institute", Moscow, Russia
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75
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Zhou Z, Liao B, Wang S, Tang J, Zhao H, Tong M, Li K, Xiong S. Improved Production of Anti-FGF-2 Nanobody Using Pichia pastoris and Its Effect on Antiproliferation of Keratinocytes and Alleviation of Psoriasis. Arch Immunol Ther Exp (Warsz) 2023; 71:20. [PMID: 37632545 DOI: 10.1007/s00005-023-00685-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 08/28/2023]
Abstract
Fibroblast growth factor 2 (FGF-2) is not only an angiogenic factor, but also a mitogen for epidermal keratinocytes. FGF-2 has been shown to be positively immunoreactive in the basal layer of psoriatic lesions. In previous work, we used the Escherichia coli (E. coli) expression system to biosynthesize a biologically active anti-FGF-2 nanobody (Nb) screened by phage display technology, but the low yield limited its clinical application. In this study, we aimed to increase the yield of anti-FGF-2 Nb, and evaluate its therapeutic potential for psoriasis by inhibiting FGF-2-mediated mitogenic signaling in psoriatic epidermal keratinocytes. We demonstrated a 16-fold improvement in the yield of anti-FGF-2 Nb produced in the Pichia pastoris (P. pastoris) compared to the E. coli expression system. In vitro, the FGF-2-induced HaCaT cell model (FHCM) was established to mimic the key feature of keratinocyte overproliferation in psoriasis. Anti-FGF-2 Nb was able to effectively inhibit the proliferation and migration of FHCM. In vivo, anti-FGF-2 Nb attenuated the severity of imiquimod (IMQ)-induced psoriatic lesions in mice, and also improved the inflammatory microenvironment by inhibiting the secretion of inflammatory cytokines (IL-1β, IL-6, IL-23, and TNF-α), chemokines (CXCL1 and CCL20), and neutrophil infiltration in skin lesions. These were mainly related to the suppression of FGF-2-mediated mitogenic signaling in psoriatic keratinocytes. In conclusion, we have improved the production of anti-FGF-2 Nb and demonstrated the modality of attenuating the abnormal proliferative behavior of psoriatic keratinocytes by inhibiting FGF-2-mediated mitogenic signaling, which offers the possibility of treating psoriasis.
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Affiliation(s)
- Zhenlong Zhou
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, People's Republic of China
| | - Baixin Liao
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Shengli Wang
- Institute of Biomedical Transformation, School of Basic Medicine and Public Health, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Jian Tang
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Hui Zhao
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Mingjie Tong
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Keting Li
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Sheng Xiong
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China.
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76
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Velastegui E, Quezada J, Altamirano C, Berrios J, Fickers P. Co-feeding strategy alleviates hypoxic stress in large-scale bioreactor for optimal production of secretory recombinant proteins in Pichia pastoris. J Biotechnol 2023; 373:20-23. [PMID: 37379887 DOI: 10.1016/j.jbiotec.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/23/2023] [Indexed: 06/30/2023]
Abstract
The loss of mixing efficiency inherent to bioreactor process operated at large-scale yields to the formation of concentration gradient and thus to heterogeneous culture conditions. For processes operated with methanol feeding, P. pastoris faces oscillatory culture conditions that significantly affect the cell ability to produce secretory recombinant proteins at high yield. Extended cell residence time in microenvironments of high methanol concentration and low oxygen availability that are typically found in the upper part of the bioreactor near the feeding point, triggers the unfolded protein response (UPR) and thus impairs proper protein secretion. Methanol co-feeding with sorbitol was shown herein to reduce the UPR response and to restore productivity of secreted protein.
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Affiliation(s)
- Edgar Velastegui
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
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De-Thier JS, Pyati P, Bell J, Readshaw JJ, Brown AP, Fitches EC. Heterologous production of the insecticidal pea seed albumin PA1 protein by Pichia pastoris and protein engineering to potentiate aphicidal activity via fusion to snowdrop lectin Galanthus nivalis agglutinin; GNA). Microb Cell Fact 2023; 22:157. [PMID: 37592258 PMCID: PMC10436433 DOI: 10.1186/s12934-023-02176-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND New bioinsecticides with novel modes of action are urgently needed to minimise the environmental and safety hazards associated with the use of synthetic chemical pesticides and to combat growing levels of pesticide resistance. The pea seed albumin PA1b knottin peptide is the only known proteinaceous inhibitor of insect vacuolar adenosine triphosphatase (V-ATPase) rotary proton pumps. Oral toxicity towards insect pests and an absence of activity towards mammals makes Pa1b an attractive candidate for development as a bioinsecticide. The purpose of this study was to investigate if Pichia pastoris could be used to express a functional PA1b peptide and if it's insecticidal activity could be enhanced via engineering to produce a fusion protein comprising the pea albumin protein fused to the mannose-specific snowdrop lectin (Galanthus nivalis agglutinin; GNA). RESULTS We report the production of a recombinant full-length pea albumin protein (designated PAF) and a fusion protein (PAF/GNA) comprised of PAF fused to the N-terminus of GNA in the yeast Pichia pastoris. PAF was orally toxic to pea (Acyrthosiphon pisum) and peach potato (Myzus persicae) aphids with respective, Day 5 LC50 values of 54 µM and 105 µM derived from dose-response assays. PAF/GNA was significantly more orally toxic as compared to PAF, with LC50 values tenfold (5 µM) and 3.3-fold (32 µM) lower for pea and peach potato aphids, respectively. By contrast, no phenotypic effects were observed for worker bumble bees (Bombus terristrus) fed PAF, GNA or PAF/GNA in acute toxicity assays. Confocal microscopy of pea aphid guts after pulse-chase feeding fluorescently labelled proteins provides evidence that enhanced efficacy of the fusion protein is attributable to localisation and retention of PAF/GNA to the gut epithelium. In contact assays the fusion protein was also found to be significantly more toxic towards A. pisum as compared to PAF, GNA or a combination of the two proteins. CONCLUSIONS Our results suggest that GNA mediated binding to V-type ATPase pumps acts to potentiate the oral and contact aphicidal activity of PAF. This work highlights potential for the future commercial development of plant protein-based bioinsecticides that offer enhanced target specificity as compared to chemical pesticides, and compatibility with integrated pest management strategies.
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Affiliation(s)
- Jake S De-Thier
- School of Biosciences, University of Durham, Durham, DH1 3LE, UK
- FUJIFILM Diosynth Biotechnologies Billingham, Billingham, TS23 1LH, UK
| | - Prashant Pyati
- School of Biosciences, University of Durham, Durham, DH1 3LE, UK
- Plant Biotechnology Research Centre, Ajeet Seeds Pvt. Ltd, Aurangabad, 431133, India
| | - Jack Bell
- School of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | | | - Adrian P Brown
- School of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Elaine C Fitches
- School of Biosciences, University of Durham, Durham, DH1 3LE, UK.
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78
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Guo F, Qiao Y, Xin F, Zhang W, Jiang M. Bioconversion of C1 feedstocks for chemical production using Pichia pastoris. Trends Biotechnol 2023; 41:1066-1079. [PMID: 36967258 DOI: 10.1016/j.tibtech.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Bioconversion of C1 feedstocks for chemical production offers a promising solution to global challenges such as the energy and food crises and climate change. The methylotroph Pichia pastoris is an attractive host system for the production of both recombinant proteins and chemicals from methanol. Recent studies have also demonstrated its potential for utilizing CO2 through metabolic engineering or coupling with electrocatalysis. This review focuses on the bioconversion of C1 feedstocks for chemical production using P. pastoris. Herein the challenges and feasible strategies for chemical production in P. pastoris are discussed. The potential of P. pastoris to utilize other C1 feedstocks - including CO2 and formate - is highlighted, and new insights from the perspectives of synthetic biology and material science are proposed.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China
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79
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Çobanoğlu Ş, Arslan E, Yazıcı A, Örtücü S. Expression of Human β-defensin 2 (hBD-2) in Pichia Pastoris and Investigation of Its Binding Efficiency with ACE-2. Protein J 2023; 42:399-407. [PMID: 37291459 PMCID: PMC10250178 DOI: 10.1007/s10930-023-10130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2023] [Indexed: 06/10/2023]
Abstract
COVID-19 is a disease that have affected the entire world, and it continues to spread with new variants. A patient's innate immune system plays a critical role in the mild and severe transition of COVID-19. Antimicrobial peptides (AMPs), which are important components of the innate immune system, are potential molecules to fight pathogenic bacteria, fungi, and viruses. Human β-defensin 2 (hBD-2), a 41-amino-acid antimicrobial peptide, is one of the defensins inducibly expressed in the skin, lungs, and trachea in humans. In this study, it was aimed to investigate the interaction of hBD-2 produced recombinantly in Pichia pastoris with the human angiotensin-converting enzyme 2 (ACE-2) under in vitro conditions. First, hBD-2 was cloned in P. pastoris X-33 via the pPICZαA vector, a yeast expression platform, and its expression was confirmed by SDS-PAGE, western blotting, and qRT-PCR. Then, the interaction between recombinant hBD-2 and ACE-2 proteins was revealed by a pull-down assay. In light of these preliminary experiments, we suggest that the recombinantly produced hBD-2 may be protective against SARS-CoV-2 and be used as a supplement in treatment. However, current findings need to be supported by cell culture studies, toxicity analyses, and in vivo experiments.
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Affiliation(s)
- Şeymanur Çobanoğlu
- Faculty of Science, Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey
- High Technology Research and Application Centre (YUTAM), Molecular Microbiology Laboratory, Erzurum Technical University, Erzurum, Turkey
| | - Elif Arslan
- Faculty of Science, Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey
- High Technology Research and Application Centre (YUTAM), Molecular Microbiology Laboratory, Erzurum Technical University, Erzurum, Turkey
| | - Ayşenur Yazıcı
- Faculty of Science, Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey.
- High Technology Research and Application Centre (YUTAM), Molecular Microbiology Laboratory, Erzurum Technical University, Erzurum, Turkey.
| | - Serkan Örtücü
- Faculty of Science, Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum, Turkey
- High Technology Research and Application Centre (YUTAM), Molecular Microbiology Laboratory, Erzurum Technical University, Erzurum, Turkey
- EcoTech Biotechnology, Ata Teknokent, Erzurum, Turkey
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80
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Amadei M, Niro A, Fullone MR, Miele R, Polticelli F, Musci G, Bonaccorsi di Patti MC. Genetic Incorporation of Dansylalanine in Human Ferroportin to Probe the Alternating Access Mechanism of Iron Transport. Int J Mol Sci 2023; 24:11919. [PMID: 37569293 PMCID: PMC10418311 DOI: 10.3390/ijms241511919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Ferroportin (Fpn), a member of the major facilitator superfamily (MFS) of transporters, is the only known iron exporter found in mammals and plays a crucial role in regulating cellular and systemic iron levels. MFSs take on different conformational states during the transport cycle: inward open, occluded, and outward open. However, the precise molecular mechanism of iron translocation by Fpn remains unclear, with conflicting data proposing different models. In this work, amber codon suppression was employed to introduce dansylalanine (DA), an environment-sensitive fluorescent amino acid, into specific positions of human Fpn (V46, Y54, V161, Y331) predicted to undergo major conformational changes during metal translocation. The results obtained indicate that different mutants exhibit distinct fluorescence spectra depending on the position of the fluorophore within the Fpn structure, suggesting that different local environments can be probed. Cobalt titration experiments revealed fluorescence quenching and blue-shifts of λmax in Y54DA, V161DA, and Y331DA, while V46DA exhibited increased fluorescence and blue-shift of λmax. These observations suggest metal-induced conformational transitions, interpreted in terms of shifts from an outward-open to an occluded conformation. Our study highlights the potential of genetically incorporating DA into Fpn, enabling the investigation of conformational changes using fluorescence spectroscopy. This approach holds great promise for the study of the alternating access mechanism of Fpn and advancing our understanding of the molecular basis of iron transport.
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Affiliation(s)
- Matteo Amadei
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, Sapienza University of Rome, 00185 Rome, Italy; (M.A.); (M.R.F.); (R.M.)
| | - Antonella Niro
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.N.); (G.M.)
| | - Maria Rosaria Fullone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, Sapienza University of Rome, 00185 Rome, Italy; (M.A.); (M.R.F.); (R.M.)
| | - Rossella Miele
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, Sapienza University of Rome, 00185 Rome, Italy; (M.A.); (M.R.F.); (R.M.)
| | | | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.N.); (G.M.)
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81
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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82
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Dong C, Li M, Zhang R, Lu W, Xu L, Liu J, Chu X. The Expression of Antibacterial Peptide Turgencin A in Pichia pastoris and an Analysis of Its Antibacterial Activity. Molecules 2023; 28:5405. [PMID: 37513276 PMCID: PMC10384874 DOI: 10.3390/molecules28145405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance to pathogenic bacteria is becoming an increasing public health threat, and identifying alternatives to antibiotics would be an effective solution to the problem of drug resistance. Antimicrobial peptides are small peptides produced by various organisms; they are considered to be adequate antibiotic substitutes because they have intense, broad-spectrum antibacterial activity and stability, are widely available, and target strains do not quickly develop resistance. Recent research on antimicrobial peptides has shown that they have broad potential for applications in medicine, agriculture, food, and animal feed. Turgencin A is a potent antimicrobial peptide isolated from the Arctic sea squirt. We established a His-tagged expression system for Pichia pastoris and developed a rTurgencin A using the recombinant expression in Pichia pastoris with nickel column purification. This antimicrobial peptide showed intense antimicrobial activity against Gram-positive and Gram-negative bacteria and a good stability at most temperatures and pHs, as well as in various protease and salt ion concentrations, but underwent a significant decrease in stability in high-temperature and low-pH environments. Turgencin A induced bacterial membrane rupture, resulting in content leakage and subsequent cell death. It was also shown to have low hemolytic activity. This study provides primary data for the industrial production and application of the antimicrobial peptide Turgencin A.
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Affiliation(s)
- Chunming Dong
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengru Li
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Rui Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Weitao Lu
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Lijun Xu
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jian Liu
- College of Agriculture and Bioengineering, Heze University, Heze 274000, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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83
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Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
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Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
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84
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Vijayakumar VE, Venkataraman K. A Systematic Review of the Potential of Pichia pastoris (Komagataella phaffii) as an Alternative Host for Biologics Production. Mol Biotechnol 2023:10.1007/s12033-023-00803-1. [PMID: 37400712 DOI: 10.1007/s12033-023-00803-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
The methylotrophic yeast Pichia pastoris is garnering interest as a chassis cell factory for the manufacture of recombinant proteins because it effectively satisfies the requirements of both laboratory and industrial set up. The optimisation of P. pastoris cultivation is still necessary due to strain- and product-specific problems such as promoter strength, methanol utilisation type, and culturing conditions to realize the high yields of heterologous protein(s) of interest. Techniques integrating genetic and process engineering have been used to overcome these problems. Insight into the Pichia as an expression system utilizing MUT pathway and the development of methanol free systems are highlighted in this systematic review. Recent developments in the improved production of proteins in P. pastoris by (i) diverse genetic engineering such as codon optimization and gene dosage; (ii) cultivating tactics including co-expression of chaperones; (iii) advances in the use of the 2A peptide system, and (iv) CRISPR/Cas technologies are widely discussed. We believe that by combining these strategies, P. pastoris will become a formidable platform for the production of high value therapeutic proteins.
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Affiliation(s)
- Vijay Elakkya Vijayakumar
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Krishnan Venkataraman
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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85
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Wang B, Liu J, Yu A, Wang H. Development and Optimization of a Novel Soft Sensor Modeling Method for Fermentation Process of Pichia pastoris. Sensors (Basel) 2023; 23:6014. [PMID: 37447863 DOI: 10.3390/s23136014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
This paper introduces a novel soft sensor modeling method based on BDA-IPSO-LSSVM designed to address the issue of model failure caused by varying fermentation data distributions resulting from different operating conditions during the fermentation of different batches of Pichia pastoris. First, the problem of significant differences in data distribution among different batches of the fermentation process is addressed by adopting the balanced distribution adaptation (BDA) method from transfer learning. This method reduces the data distribution differences among batches of the fermentation process, while the fuzzy set concept is employed to improve the BDA method by transforming the classification problem into a regression prediction problem for the fermentation process. Second, the soft sensor model for the fermentation process is developed using the least squares support vector machine (LSSVM). The model parameters are optimized by an improved particle swarm optimization (IPSO) algorithm based on individual differences. Finally, the data obtained from the Pichia pastoris fermentation experiment are used for simulation, and the developed soft sensor model is applied to predict the cell concentration and product concentration during the fermentation process of Pichia pastoris. Simulation results demonstrate that the IPSO algorithm has good convergence performance and optimization performance compared with other algorithms. The improved BDA algorithm can make the soft sensor model adapt to different operating conditions, and the proposed soft sensor method outperforms existing methods, exhibiting higher prediction accuracy and the ability to accurately predict the fermentation process of Pichia pastoris under different operating conditions.
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Affiliation(s)
- Bo Wang
- Key Laboratory of Agricultural Measurement and Control Technology and Equipment for Mechanical Industrial Facilities, School of Electrical and Information Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jun Liu
- Key Laboratory of Agricultural Measurement and Control Technology and Equipment for Mechanical Industrial Facilities, School of Electrical and Information Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Ameng Yu
- Key Laboratory of Agricultural Measurement and Control Technology and Equipment for Mechanical Industrial Facilities, School of Electrical and Information Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Haibo Wang
- Key Laboratory of Agricultural Measurement and Control Technology and Equipment for Mechanical Industrial Facilities, School of Electrical and Information Engineering, Jiangsu University, Zhenjiang 212013, China
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86
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Fina A, Millard P, Albiol J, Ferrer P, Heux S. High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux. Microb Cell Fact 2023; 22:117. [PMID: 37380999 DOI: 10.1186/s12934-023-02123-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/27/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Production of 3-hydroxypropionic acid (3-HP) through the malonyl-CoA pathway has yielded promising results in Pichia pastoris (Komagataella phaffii), demonstrating the potential of this cell factory to produce this platform chemical and other acetyl-CoA-derived products using glycerol as a carbon source. However, further metabolic engineering of the original P. pastoris 3-HP-producing strains resulted in unexpected outcomes, e.g., significantly lower product yield and/or growth rate. To gain an understanding on the metabolic constraints underlying these observations, the fluxome (metabolic flux phenotype) of ten 3-HP-producing P. pastoris strains has been characterized using a high throughput 13C-metabolic flux analysis platform. Such platform enabled the operation of an optimised workflow to obtain comprehensive maps of the carbon flux distribution in the central carbon metabolism in a parallel-automated manner, thereby accelerating the time-consuming strain characterization step in the design-build-test-learn cycle for metabolic engineering of P. pastoris. RESULTS We generated detailed maps of the carbon fluxes in the central carbon metabolism of the 3-HP producing strain series, revealing the metabolic consequences of different metabolic engineering strategies aimed at improving NADPH regeneration, enhancing conversion of pyruvate into cytosolic acetyl-CoA, or eliminating by-product (arabitol) formation. Results indicate that the expression of the POS5 NADH kinase leads to a reduction in the fluxes of the pentose phosphate pathway reactions, whereas an increase in the pentose phosphate pathway fluxes was observed when the cytosolic acetyl-CoA synthesis pathway was overexpressed. Results also show that the tight control of the glycolytic flux hampers cell growth due to limited acetyl-CoA biosynthesis. When the cytosolic acetyl-CoA synthesis pathway was overexpressed, the cell growth increased, but the product yield decreased due to higher growth-associated ATP costs. Finally, the six most relevant strains were also cultured at pH 3.5 to assess the effect of a lower pH on their fluxome. Notably, similar metabolic fluxes were observed at pH 3.5 compared to the reference condition at pH 5. CONCLUSIONS This study shows that existing fluoxomics workflows for high-throughput analyses of metabolic phenotypes can be adapted to investigate P. pastoris, providing valuable information on the impact of genetic manipulations on the metabolic phenotype of this yeast. Specifically, our results highlight the metabolic robustness of P. pastoris's central carbon metabolism when genetic modifications are made to increase the availability of NADPH and cytosolic acetyl-CoA. Such knowledge can guide further metabolic engineering of these strains. Moreover, insights into the metabolic adaptation of P. pastoris to an acidic pH have also been obtained, showing the capability of the fluoxomics workflow to assess the metabolic impact of environmental changes.
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Affiliation(s)
- Albert Fina
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain.
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
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87
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Popova LG, Khramov DE, Nedelyaeva OI, Volkov VS. Yeast Heterologous Expression Systems for the Study of Plant Membrane Proteins. Int J Mol Sci 2023; 24:10768. [PMID: 37445944 DOI: 10.3390/ijms241310768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Researchers are often interested in proteins that are present in cells in small ratios compared to the total amount of proteins. These proteins include transcription factors, hormones and specific membrane proteins. However, sufficient amounts of well-purified protein preparations are required for functional and structural studies of these proteins, including the creation of artificial proteoliposomes and the growth of protein 2D and 3D crystals. This aim can be achieved by the expression of the target protein in a heterologous system. This review describes the applications of yeast heterologous expression systems in studies of plant membrane proteins. An initial brief description introduces the widely used heterologous expression systems of the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Pichia pastoris. S. cerevisiae is further considered a convenient model system for functional studies of heterologously expressed proteins, while P. pastoris has the advantage of using these yeast cells as factories for producing large quantities of proteins of interest. The application of both expression systems is described for functional and structural studies of membrane proteins from plants, namely, K+- and Na+-transporters, various ATPases and anion transporters, and other transport proteins.
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Affiliation(s)
- Larissa G Popova
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Dmitrii E Khramov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Olga I Nedelyaeva
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
| | - Vadim S Volkov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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88
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Fauzee YNBM, Yoshida Y, Kimata Y. Endoplasmic stress sensor Ire1 is involved in cytosolic/nuclear protein quality control in Pichia pastoris cells independent of HAC1. Front Microbiol 2023; 14:1157146. [PMID: 37415818 PMCID: PMC10321714 DOI: 10.3389/fmicb.2023.1157146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023] Open
Abstract
In eukaryotic species, dysfunction of the endoplasmic reticulum (ER), namely, ER stress, provokes a cytoprotective transcription program called the unfolded protein response (UPR). The UPR is triggered by transmembrane ER-stress sensors, including Ire1, which acts as an endoribonuclease to splice and mature the mRNA encoding the transcription factor Hac1 in many fungal species. Through analyses of the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii), we revealed a previously unknown function of Ire1. In P. pastoris cells, the IRE1 knockout mutation (ire1Δ) and HAC1 knockout mutation (hac1Δ) caused only partially overlapping gene expression changes. Protein aggregation and the heat shock response (HSR) were induced in ire1Δ cells but not in hac1Δ cells even under non-stress conditions. Moreover, Ire1 was further activated upon high-temperature culturing and conferred heat stress resistance to P. pastoris cells. Our findings cumulatively demonstrate an intriguing case in which the UPR machinery controls cytosolic protein folding status and the HSR, which is known to be activated upon the accumulation of unfolded proteins in the cytosol and/or nuclei.
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Li C, Cao H, Wu W, Meng G, Zhao C, Cao Y, Yuan J. Expression and characterization of α-L-arabinofuranosidase derived from Aspergillus awamori and its enzymatic degradation of corn byproducts with xylanase. Bioresour Technol 2023:129278. [PMID: 37290707 DOI: 10.1016/j.biortech.2023.129278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
In this study, α-L-arabinofuranosidase (AF) from Aspergillus awamori was heterologously expressed in Pichia pastoris X33, with a 1-fold increase in AF activity after codon and vector optimization. AF remained stable at 60-65 °C and displayed a broad pH stability range of 2.5-8.0. It also demonstrated considerable resistance to pepsin and trypsin. Furthermore, compared with xylanase alone, AF with xylanase exhibited a marked synergistic effect in the degradation of expanded corn bran, corn bran, and corn distillers' dried grains with solubles, reducing sugars by 3.6-fold, 1.4-fold, and 6.5-fold, respectively, with the degree of synergy increasing to 4.61, 2.44, and 5.4, respectively, while in vitro dry matter digestibility values were 17.6%, 5.2%, and 8.8%, respectively. After enzymatic saccharification, corn byproducts were converted to prebiotic xylo-oligosaccharides and arabinoses, thereby demonstrating the favorable properties of AF in the degradation of corn biomass and its byproducts.
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Affiliation(s)
- Chunyue Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Heng Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Meng
- Ningxia Eppen Biotech Co., Ltd., China Agricultural University, Beijing 100193, China
| | - Chunguang Zhao
- Ningxia Eppen Biotech Co., Ltd., China Agricultural University, Beijing 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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90
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Smith ET, Kruppa M, Johnson DA, Van Haeften J, Chen X, Leahy D, Peake J, Harris JM. High yield expression in Pichia pastoris of human neutrophil elastase fused to cytochrome B5. Protein Expr Purif 2023; 206:106255. [PMID: 36822453 PMCID: PMC10118287 DOI: 10.1016/j.pep.2023.106255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Recombinant human neutrophil elastase (rHNE), a serine protease, was expressed in Pichia pastoris. Glycosylation sites were removed via bioengineering to prevent hyper-glycosylation (a common problem with this system) and the cDNA was codon optimized for translation in Pichia pastoris. The zymogen form of rHNE was secreted as a fusion protein with an N-terminal six histidine tag followed by the heme binding domain of Cytochrome B5 (CytB5) linked to the N-terminus of the rHNE sequence via an enteropeptidase cleavage site. The CytB5 fusion balanced the very basic rHNE (pI = 9.89) to give a colored fusion protein (pI = 6.87), purified via IMAC. Active rHNE was obtained via enteropeptidase cleavage, and purified via cation exchange chromatography, resulting in a single protein band on SDS PAGE (Mr = 25 KDa). Peptide mass fingerprinting analysis confirmed the rHNE amino acid sequence, the absence of glycosylation and the absence of an 8 amino acid C-terminal peptide as opposed to the 20 amino acids usually missing from the C-terminus of native enzyme. The yield of active rHNE was 0.41 mg/L of baffled shaker flask culture medium. Active site titration with alpha-1 antitrypsin, a potent irreversible elastase inhibitor, quantified the concentration of purified active enzyme. The Km of rHNE with methoxy-succinyl-AAPVpNA was identical with that of the native enzyme within the assay's limit of accuracy. This is the first report of full-length rHNE expression at high yields and low cost facilitating further studies on this major human neutrophil enzyme.
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Affiliation(s)
- Eliot T Smith
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA
| | - Michael Kruppa
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA
| | - David A Johnson
- Departments of Biomedical Sciences and Medical Education, James H. Quillen College of Medicine, East Tennessee State University, Box 70582, Johnson City, Tennessee, USA.
| | - Jessica Van Haeften
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Xingchen Chen
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Darren Leahy
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Jonathan Peake
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
| | - Jonathan M Harris
- Queensland University of Technology, Molecular Simulation Group, Institute of Health and Biomedical Innovation, Corner Blamey Street & Musk Avenue, Kelvin Grove Urban Village, Queensland, 4059, Australia
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91
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Shirvani R, Bartik A, Alves GAS, Garcia de Otazo Hernandez D, Müller S, Föttinger K, Steiger MG. Nitrogen recovery from low-value biogenic feedstocks via steam gasification to methylotrophic yeast biomass. Front Bioeng Biotechnol 2023; 11:1179269. [PMID: 37362211 PMCID: PMC10289294 DOI: 10.3389/fbioe.2023.1179269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Carbon and nitrogen are crucial elements for life and must be efficiently regenerated in a circular economy. Biomass streams at the end of their useful life, such as sewage sludge, are difficult to recycle even though they contain organic carbon and nitrogen components. Gasification is an emerging technology to utilize such challenging waste streams and produce syngas that can be further processed into, e.g., Fischer-Tropsch fuels, methane, or methanol. Here, the objective is to investigate if nitrogen can be recovered from product gas cleaning in a dual fluidized bed (DFB) after gasification of softwood pellets to form yeast biomass. Yeast biomass is a protein-rich product, which can be used for food and feed applications. An aqueous solution containing ammonium at a concentration of 66 mM was obtained and by adding other nutrients it enables the growth of the methylotrophic yeast Komagataella phaffii to form 6.2 g.L-1 dry yeast biomass in 3 days. To further integrate the process, it is discussed how methanol can be obtained from syngas by chemical catalysis, which is used as a carbon source for the yeast culture. Furthermore, different gas compositions derived from the gasification of biogenic feedstocks including sewage sludge, bark, and chicken manure are evaluated for their ability to yield methanol and yeast biomass. The different feedstocks are compared based on their potential to yield methanol and ammonia, which are required for the generation of yeast biomass. It was found that the gasification of bark and chicken manure yields a balanced carbon and nitrogen source for the formation of yeast biomass. Overall, a novel integrated process concept based on renewable, biogenic feedstocks is proposed connecting gasification with methanol synthesis to enable the formation of protein-rich yeast biomass.
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Affiliation(s)
- Roghayeh Shirvani
- Research Group Biochemistry, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
| | - Alexander Bartik
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
- Research group Industrial Plant Engineering and Application of Digital Methods, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Gustavo A. S. Alves
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
- Research Group Technical Catalysis, Institute of Materials Chemistry, TU Wien, Vienna, Austria
| | | | - Stefan Müller
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
- Research group Industrial Plant Engineering and Application of Digital Methods, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Karin Föttinger
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
- Research Group Technical Catalysis, Institute of Materials Chemistry, TU Wien, Vienna, Austria
| | - Matthias G. Steiger
- Research Group Biochemistry, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- Doctoral College CO2Refinery, Faculty of Technical Chemistry, TU Wien, Vienna, Austria
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92
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Utami N, Nurdiani D, Hariyatun H, Putro EW, Patria FP, Kusharyoto W. Full-length versus truncated α-factor secretory signal sequences for expression of recombinant human insulin precursor in yeast Pichia pastoris: a comparison. J Genet Eng Biotechnol 2023; 21:67. [PMID: 37212962 DOI: 10.1186/s43141-023-00521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Human insulin was the first FDA-approved biopharmaceutical drug produced through recombinant DNA technology. The previous studies successfully expressed recombinant human insulin precursors (HIP) in Pichia pastoris truncated and full-length α-factor recombinant clones. The matting α-factor (Matα), a signal secretion, direct the HIP protein into the culture media. This study aimed to compare the HIP expression from full-length and truncated α-factor secretory signals clones that grown in two types of media, buffered methanol complex medium (BMMY) and methanol basal salt medium (BSMM). RESULTS ImageJ analysis of the HIP's SDS-PAGE shows that the average HIP expression level of the recombinant P. pastoris truncated α-factor clone (CL4) was significantly higher compared to the full-length (HF7) when expressed in both media. Western blot analysis showed that the expressed protein was the HIP. The α-factor protein structure was predicted using the AlphaFold and visualized using UCSF ChimeraX to confirm the secretion ability for both clones. CONCLUSIONS CL4 clone, which utilized a truncated α-factor in the P. pastoris HIP expression cassette, significantly expressed HIP 8.97 times (in BMMY) and 1.17 times (in BSMM) higher than HF7 clone, which used a full-length α-factor secretory signal. This research confirmed that deletion of some regions of the secretory signal sequence significantly improved the efficiency of HIP protein expression in P. pastoris.
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Affiliation(s)
- Nuruliawaty Utami
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911, Indonesia.
| | - Dini Nurdiani
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911, Indonesia
| | - Hariyatun Hariyatun
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911, Indonesia
| | - Eko Wahyu Putro
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911, Indonesia
| | - Fadillah Putri Patria
- Laboratory Department, Indonesia International Institute for Life Sciences (i3L), Jakarta, Timur, 13210, Indonesia
| | - Wien Kusharyoto
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Cibinong, Bogor, 16911, Indonesia
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93
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Jayachandran D, Banerjee S, Chundawat SPS. Plant cellulose synthase membrane protein isolation directly from Pichia pastoris protoplasts, liposome reconstitution, and its enzymatic characterization. Protein Expr Purif 2023:106309. [PMID: 37211149 DOI: 10.1016/j.pep.2023.106309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Cellulose is synthesized by a plant cell membrane-integrated processive glycosyltransferase (GT) called cellulose synthase (CesA). Since only a few of these plant CesAs have been purified and characterized to date, there are huge gaps in our mechanistic understanding of these enzymes. The biochemistry and structural biology studies of CesAs are currently hampered by challenges associated with their expression and extraction at high yields. To aid in understanding CesA reaction mechanisms and to provide a more efficient CesA extraction method, two putative plant CesAs - PpCesA5 from Physcomitrella patens and PttCesA8 from Populus tremula x tremuloides that are involved in primary and secondary cell wall formation in plants were expressed using Pichia pastoris as an expression host. We developed a protoplast-based membrane protein extraction approach to directly isolate these membrane-bound enzymes, as confirmed by immunoblotting and mass spectrometry-based analyses. Our method gives 3-4-fold higher purified protein yield than the standard cell homogenization protocol. Our method resulted in liposome reconstituted CesA5 and CesA8 enzymes with similar Michaelis-Menten kinetic constants, Km = 167 μM, 108 μM and Vmax = 7.88 × 10-5 μmol/min, 4.31 × 10-5 μmol/min, respectively, in concurrence with the previous studies for enzymes isolated using the standard protocol. Taken together, these results suggest that CesAs involved in primary and secondary cell wall formation can be expressed and purified using a simple and more efficient extraction method. This protocol could help isolate enzymes that unravel the mechanism of native and engineered cellulose synthase complexes involved in plant cell wall biosynthesis.
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Affiliation(s)
- Dharanidaran Jayachandran
- Department of Chemical and Biochemical Engineering, Rutgers-The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Shoili Banerjee
- Department of Chemical and Biochemical Engineering, Rutgers-The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers-The State University of New Jersey, Piscataway, NJ, 08854, USA.
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94
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Karaoğlan M. Alternative secretory signal sequences for recombinant protein production in Pichia pastoris. Enzyme Microb Technol 2023; 168:110256. [PMID: 37196384 DOI: 10.1016/j.enzmictec.2023.110256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Extracellular protein production is primarily preferred to facilitate the downstream processes in recombinant protein production. Secretion of recombinant proteins is mediated by the processing of signal peptides in their N-terminal portion by the secretory mechanism of host expression systems. These molecular elements involved in secretion are functionally interchangeable between different species and secretion sequence screening is one of the widely used approaches to improve extracellular protein production. In this study, α-mating and protein internal repeats (PIR) secretion sequences isolated from different yeasts (Kluyveromyces lactis, Kluyveromyces marxianus and Hansenula polymorpha) were tested in Pichia pastoris for the production of two different proteins (α-amylase and xylanase) and compared with the well-known secretory signals, S. cerevisiae α-mating factor (Sc-MF) and P. pastoris protein internal repeats PIR (PpPIR). The results obtained showed the potential of signal sequences tested. Among the tested peptides, the highest yields were achieved with H. polymorpha protein internal repeats (HpPIR) and K. lactis α-mating factor (Kl-MF) for xylanase and K. marxianus protein internal repeats (KmPIR) and K. lactis α-mating factor (Kl-MF) for amylase. In further studies, these sequences can be evaluated as alternatives in the production of different proteins in P. pastoris and in the production of recombinant proteins in different expression systems.
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Affiliation(s)
- Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
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95
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Corucci G, Batchu KC, Luchini A, Santamaria A, Frewein MPK, Laux V, Haertlein M, Yamaryo-Botté Y, Botté CY, Sheridan T, Tully M, Maestro A, Martel A, Porcar L, Fragneto G. Developing advanced models of biological membranes with hydrogenous and deuterated natural glycerophospholipid mixtures. J Colloid Interface Sci 2023; 645:870-881. [PMID: 37178564 DOI: 10.1016/j.jcis.2023.04.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Cellular membranes are complex systems that consist of hundreds of different lipid species. Their investigation often relies on simple bilayer models including few synthetic lipid species. Glycerophospholipids (GPLs) extracted from cells are a valuable resource to produce advanced models of biological membranes. Here, we present the optimisation of a method previously reported by our team for the extraction and purification of various GPL mixtures from Pichia pastoris. The implementation of an additional purification step by High Performance Liquid Chromatography-Evaporative Light Scattering Detector (HPLC-ELSD) enabled for a better separation of the GPL mixtures from the neutral lipid fraction that includes sterols, and also allowed for the GPLs to be purified according to their different polar headgroups. Pure GPL mixtures at significantly high yields were produced through this approach. For this study, we utilised phoshatidylcholine (PC), phosphatidylserine (PS) and phosphatidylglycerol (PG) mixtures. These exhibit a single composition of the polar head, i.e., PC, PS or PG, but contain several molecular species consisting of acyl chains of varying length and unsaturation, which were determined by Gas Chromatography (GC). The lipid mixtures were produced both in their hydrogenous (H) and deuterated (D) versions and were used to form lipid bilayers both on solid substrates and as vesicles in solution. The supported lipid bilayers were characterised by quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR), whereas the vesicles by small angle X-ray (SAXS) and neutron scattering (SANS). Our results show that despite differences in the acyl chain composition, the hydrogenous and deuterated extracts produced bilayers with very comparable structures, which makes them valuable to design experiments involving selective deuteration with techniques such as NMR, neutron scattering or infrared spectroscopy.
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Affiliation(s)
- Giacomo Corucci
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France
| | | | - Alessandra Luchini
- European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden; Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andreas Santamaria
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Moritz Paul Karl Frewein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, 8010, Austria
| | - Valèrie Laux
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Cyrille Y Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thomas Sheridan
- University College Dublin, Belfield, Dublin 4, Dublin, Ireland; AbbVie, Clonshaugh, Dublin 7, Co. Dublin, Ireland
| | - Mark Tully
- European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Armando Maestro
- Centro de Física de Materiales (CSIC, UPV/EHU) - Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; IKERBASQUE - Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France; European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden.
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Ondracka A, Gasset A, García-Ortega X, Hubmayr D, van Wijngaarden J, Montesinos-Seguí JL, Valero F, Manzano T. CPV of the Future: AI-Powered Continued Process Verification for Bioreactor Processes. PDA J Pharm Sci Technol 2023; 77:146-165. [PMID: 36122916 DOI: 10.5731/pdajpst.2021.012665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
According to the standard guidelines by the FDA, process validation in biopharma manufacturing encompasses a life cycle consisting of three stages: process design (PD), process qualification (PQ), and continued process verification (CPV). The validity and efficiency of the analytics methods employed during the CPV require extensive knowledge of the process. However, for new processes and new drugs, such knowledge is often not available from Process performance qualification and Validation (PPQV). In this work, the suitability of methods based on machine learning/artificial intelligence (ML/AI) for the CPV applied in bioprocess monitoring and cell physiological control of the yeast Pichia pastoris (Komagataella phaffii) was studied with limited historical data. In particular, the production of recombinant Candida rugosa lipase 1 (Crl1) under hypoxic conditions in fed-batch cultures was considered as a case study. Supervised and unsupervised machine learning models using data from fed-batch bioprocesses with different gene dosage clones under normoxic and hypoxic conditions were evaluated. Firstly, a multivariate anomaly detection (isolation forest) model was applied to the batch phase of the bioprocess. Secondly, a supervised random forest model for prediction of required operator's control actions during the semiautomated fed-batch phase under hypoxic conditions was assessed to maintain the respiratory quotient (RQ) within the desired range for maximizing the specific production rate (qP ). The performance of these models was tested on historical data using independent evaluation of the process by the process control engineer (subject matter expert-SME), and on real-time data in the case of manual action prediction, where the model was implemented to guide the control of the bioprocess. The work presented here constitutes a proof-of-concept that multivariate analytics methods, based on machine learning, can be a valuable tool for real-time monitoring and control of biopharma manufacturing bioprocesses to improve its efficiency and to assure product quality.
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Affiliation(s)
| | - Arnau Gasset
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Xavier García-Ortega
- QuBilab, Departament de Biociències, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain; and
| | - David Hubmayr
- Process Development & Breakthrough Technologies R&D, CSL Behring AG, Wankdorfstrasse 10, 3014 Bern, Switzerland
| | | | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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97
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Zhou K, Zhou Y, Zhou H, Cheng H, Xu G. Kinetic process of the biosorption of Cu(II), Ni(II) and Cr(VI) by waste Pichia pastoris cells. Environ Technol 2023; 44:1730-1750. [PMID: 34842065 DOI: 10.1080/09593330.2021.2012266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Waste biomass of Pichia pastoris (P.pastoris) cells from the fermentation industry is an environmentally friendly biosorption material. The present study aimed to explore the biosorption behaviour of waste P.pastoris cells for Cu(II), Ni(II) and Cr(VI) in aqueous solution conditions. The results showed that the adsorption kinetics of three kinds of metals were well-fitted with lineared Elovich, pseudo-second-order kinetics models, non-linear kinetics and adsorption isotherms. The effective biosorption rates for Cu(II), Ni(II) and Cr(VI) removal were 71.3%, 59.7% and 16.25% respectively. The maximum Cu(II) adsorption capacity of waste P.pastoris was 40 mg/g at pH = 4 and 225 mg/L of solute concentration for 0.4 g biomass, better than that of the living yeasts. The pattern of Fourier transform infrared (FTIR) indicated that functional groups such as -NH, -OH, Si-O, P-O-C were involved in Cu(II) adsorption process. The analysis of SEM-EDS, XRD and TEM-EDS can be concluded that Cu(II) occupied Ca(II) binding sites by ion exchange mechanism to remove flocculation, and Cu(II) adsorbed onto the diatomite containing in the industrial waste P.pastoris. Thus the adsorption mechanism of the industrial waste P.pastoris was proposed taking Cu(II) as the example. And consecutive biosorption/desorption cycles were used for the evaluation of the regeneration efficiency, suggesting the good regeneration and reusability of waste P.pastoris.
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Affiliation(s)
- Kaiyan Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, People's Republic of China
| | - Yulu Zhou
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Hongbo Zhou
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Haina Cheng
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Gang Xu
- Hunan Flag Bio-Tech Co., Ltd., Changsha, People's Republic of China
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Erden-Karaoğlan F, Karaoğlan M. Improvement of recombinant L-Asparaginase production in Pichia pastoris. 3 Biotech 2023; 13:164. [PMID: 37159589 PMCID: PMC10163189 DOI: 10.1007/s13205-023-03600-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023] Open
Abstract
Pichia pastoris is a successful expression system that is frequently preferred in the secretion of proteins for both basic research and industrial purposes. In this study, recombinant Rhizomucor miehei (RmASNase) L-asparaginase was produced in Pichia pastoris. The impact of gene copy number on increasing protein production was examined with six clones harboring various gene copy numbers (1-5 and 5 +). The results demonstrated that the clone with three copies of the expression cassette integrated had the highest production level. Also, biochemical characterization of the enzyme was performed. It was determined that the optimum pH and temperature values of the purified enzyme were pH 7.0 and 50 °C, respectively. Stability analyses of the enzyme showed that it maintains its activity of 80% in the pH range of 5-9 and 67% in the temperature range of 20-50 °C. Ca+2 and Mn+2 ions increased the enzyme activity to 121% and 138%, respectively. In future studies, it is also possible to improve the activity and stability values of the enzyme with advanced molecular techniques and to increase production efficiency by producing at fermenter scale and under optimum conditions.
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Affiliation(s)
- Fidan Erden-Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye
| | - Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye
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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.
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Affiliation(s)
- Pieter De Brabander
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Evelien Uitterhaegen
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Karel De Winter
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
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100
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An R, Zhang R, Guo Y, Geng J, Si M, Wang S, Gao M, Wang J. Biological Activity of Optimized Codon Bovine Type III Interferon Expressed in Pichia pastoris. Viruses 2023; 15:v15051101. [PMID: 37243187 DOI: 10.3390/v15051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Type III interferons (IFN-λs) exhibit potent antiviral activity and immunomodulatory effects in specific cells. Nucleotide fragments of the bovine ifn-λ (boifn-λ) gene were synthetized after codon optimization. The boifn-λ gene was then amplified by splicing using overlap extension PCR (SOE PCR), resulting in the serendipitous acquisition of the mutated boIFN-λ3V18M. The recombinant plasmid pPICZαA-boIFN-λ3/λ3V18M was constructed, and the corresponding proteins were expressed in Pichia pastoris with a high-level extracellular soluble form. Dominant expression strains of boIFN-λ3/λ3V18M were selected by Western blot and ELISA and cultured on a large scale, and the recombinant proteins purified by ammonium sulfate precipitation and ion exchange chromatography yielded 1.5g/L and 0.3 g/L, with 85% and 92% purity, respectively. The antiviral activity of boIFN-λ3/λ3V18M exceeded 106 U/mg, and they were neutralized with IFN-λ3 polyclonal antibodies, were susceptible to trypsin, and retained stability within defined pH and temperature ranges. Furthermore, boIFN-λ3/λ3V18M exerted antiproliferative effects on MDBK cells without cytotoxicity at 104 U/mL. Overall, boIFN-λ3 and boIFN-λ3V18M did not differ substantially in biological activity, except for reduced glycosylation of the latter. The development of boIFN-λ3 and comparative evaluation with the mutant provide theoretical insights into the antiviral mechanisms of boIFN-λs and provide material for therapeutic development.
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Affiliation(s)
- Ran An
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Runxiang Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Yongli Guo
- Heilongjiang Provincial Key Laboratory for Infection and Immunity, Department of Immunology, Harbin Medical University, Harbin 150030, China
| | - Jinfeng Geng
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Minglu Si
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shuangfeng Wang
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Mingchun Gao
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Junwei Wang
- Heilongjiang Provincial Key Laboratory of Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
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