1
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Das PK, Sahoo A, Veeranki VD. Recombinant monoclonal antibody production in yeasts: Challenges and considerations. Int J Biol Macromol 2024; 266:131379. [PMID: 38580014 DOI: 10.1016/j.ijbiomac.2024.131379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Monoclonal antibodies (mAbs) are laboratory-based engineered protein molecules with a monovalent affinity or multivalent avidity towards a specific target or antigen, which can mimic natural antibodies that are produced in the human immune systems to fight against detrimental pathogens. The recombinant mAb is one of the most effective classes of biopharmaceuticals produced in vitro by cloning and expressing synthetic antibody genes in a suitable host. Yeast is one of the potential hosts among others for the successful production of recombinant mAbs. However, there are very few yeast-derived mAbs that got the approval of the regulatory agencies for direct use for treatment purposes. Certain challenges encountered by yeasts for recombinant antibody productions need to be overcome and a few considerations related to antibody structure, host engineering, and culturing strategies should be followed for the improved production of mAbs in yeasts. In this review, the drawbacks related to the metabolic burden of the host, culturing conditions including induction mechanism and secretion efficiency, solubility and stability, downstream processing, and the pharmacokinetic behavior of the antibody are discussed, which will help in developing the yeast hosts for the efficient production of recombinant mAbs.
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Affiliation(s)
- Prabir Kumar Das
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Venkata Dasu Veeranki
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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2
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Rußmayer H, Buchetics M, Mattanovich M, Neubauer S, Steiger M, Graf AB, Koellensperger G, Hann S, Sauer M, Gasser B, Mattanovich D. Customizing amino acid metabolism of Pichia pastoris for recombinant protein production. Biotechnol J 2023; 18:e2300033. [PMID: 37668396 DOI: 10.1002/biot.202300033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/31/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Amino acids are the building blocks of proteins. In this respect, a reciprocal effect of recombinant protein production on amino acid biosynthesis as well as the impact of the availability of free amino acids on protein production can be anticipated. In this study, the impact of engineering the amino acid metabolism on the production of recombinant proteins was investigated in the yeast Pichia pastoris (syn Komagataella phaffii). Based on comprehensive systems-level analyses of the metabolomes and transcriptomes of different P. pastoris strains secreting antibody fragments, cell engineering targets were selected. Our working hypothesis that increasing intracellular amino acid levels could help unburden cellular metabolism and improve recombinant protein production was examined by constitutive overexpression of genes related to amino acid metabolism. In addition to 12 genes involved in specific amino acid biosynthetic pathways, the transcription factor GCN4 responsible for regulation of amino acid biosynthetic genes was overexpressed. The production of the used model protein, a secreted carboxylesterase (CES) from Sphingopyxis macrogoltabida, was increased by overexpression of pathway genes for alanine and for aromatic amino acids, and most pronounced, when overexpressing the regulator GCN4. The analysis of intracellular amino acid levels of selected clones indicated a direct linkage of improved recombinant protein production to the increased availability of intracellular amino acids. Finally, fed batch cultures showed that overexpression of GCN4 increased CES titers 2.6-fold, while the positive effect of other amino acid synthesis genes could not be transferred from screening to bioreactor cultures.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Matthias Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Copenhagen University, Copenhagen, Denmark
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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3
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Johansson SA, Dulermo T, Jann C, Smith JD, Pryszlak A, Pignede G, Schraivogel D, Colavizza D, Desfougères T, Rave C, Farwick A, Merten CA, Roy KR, Wei W, Steinmetz LM. Large scale microfluidic CRISPR screening for increased amylase secretion in yeast. LAB ON A CHIP 2023; 23:3704-3715. [PMID: 37483015 PMCID: PMC7614956 DOI: 10.1039/d3lc00111c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Key to our ability to increase recombinant protein production through secretion is a better understanding of the pathways that interact to translate, process and export mature proteins to the surrounding environment, including the supporting cellular machinery that supplies necessary energy and building blocks. By combining droplet microfluidic screening with large-scale CRISPR libraries that perturb the expression of the majority of coding and non-coding genes in S. cerevisiae, we identified 345 genes for which an increase or decrease in gene expression resulted in increased secretion of α-amylase. Our results show that modulating the expression of genes involved in the trafficking of vesicles, endosome to Golgi transport, the phagophore assembly site, the cell cycle and energy supply improve α-amylase secretion. Besides protein-coding genes, we also find multiple long non-coding RNAs enriched in the vicinity of genes associated with endosomal, Golgi and vacuolar processes. We validated our results by overexpressing or deleting selected genes, which resulted in significant improvements in α-amylase secretion. The advantages, in terms of precision and speed, inherent to CRISPR based perturbations, enables iterative testing of new strains for increased protein secretion.
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Affiliation(s)
- S Andreas Johansson
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Thierry Dulermo
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Cosimo Jann
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Justin D Smith
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Anna Pryszlak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Georges Pignede
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Didier Colavizza
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Thomas Desfougères
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christophe Rave
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Alexander Farwick
- Lesaffre Institute of Science & Technology, Lesaffre, 59700 Marcq-en-Baroeul, France
| | - Christoph A Merten
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Kevin R Roy
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Wu Wei
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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4
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Chen X, Li C, Liu H. Enhanced Recombinant Protein Production Under Special Environmental Stress. Front Microbiol 2021; 12:630814. [PMID: 33935992 PMCID: PMC8084102 DOI: 10.3389/fmicb.2021.630814] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 01/09/2023] Open
Abstract
Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.
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Affiliation(s)
- Xinyi Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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5
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Sailwal M, Das AJ, Gazara RK, Dasgupta D, Bhaskar T, Hazra S, Ghosh D. Connecting the dots: Advances in modern metabolomics and its application in yeast system. Biotechnol Adv 2020; 44:107616. [DOI: 10.1016/j.biotechadv.2020.107616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
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6
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Guo Z, Zhu Y, Xu W, Luo K, Xiao H, Wang Z. Alteration of Amino Acid Profiling Influenced by the Active Ingredients of DanHong Injection After Prescription Optimization. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:3939-3947. [PMID: 31819368 PMCID: PMC6876559 DOI: 10.2147/dddt.s220314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/12/2019] [Indexed: 11/26/2022]
Abstract
Introduction The aim of this work was to optimize the formulation composition of DanHong injection and to study the disturbance of microscopic components of cerebral ischemia in amino acid metabolites and metabolic pathways. The subtle relationship among these three substances and the influence of metabolic pathways were also studied. Methods In this study, the central composite design (CCD) matrix and response surface methodology (RSM) were used to design the experiments and to evaluate the interactive effects of three substances. Targeted metabolomics was used to detect the amino acid variation in CCD sets. Results Response surfaces were generated, and the formulation was optimized by superimposing the contour plots. It was found that the optimum values of the responses could be obtained at an SAB concentration (x1) of 8–9 mg/kg, a TSN concentration (x2) of 14–16 mg/kg, and an HSYA yellow A concentration (x3) of 6 mg/kg. Statistical analysis showed that the three independent variables had significant effects (p < 0.05) on the responses. A total of 22 experimental runs were performed, and the kinetic data were analyzed using a second-order polynomial. Model algorithm calculation indicated that glutamic acid, serine, leucine, glycine, and valine had a very close correlation with the active ingredients. Methionine, aspartic acid, asparagine, glutamic acid, and valine were important for distinguishing different groups, and they were identified as potential biomarkers. Cluster analysis and pathway analysis indicated that the valine, leucine, and isoleucine degradation (VLI degradation) pathway was the major metabolic pathway. Arginine and proline metabolites were most frequently detected, and they were closely associated with other networks according to the network analysis results. VLI degradation pathway and arginine and proline metabolism pathway had a significant influence on cerebral ischemia. Discussion The integration of CCD and metabolomics may be an effective strategy for optimizing the formulation composition and identifying the mechanism of action of traditional chinese medicine.
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Affiliation(s)
- Zhili Guo
- Chinese Medicine Department, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang, 314000, People's Republic of China
| | - Yan Zhu
- Chinese Medicine Department, Beijing Electric Power Hospital, Capital Medical University, Beijing 10073, People's Republic of China
| | - Wenjuan Xu
- Chinese Medicine Pharmacology, Institute of Basic Research in Clinical Medicine. China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Kaitao Luo
- Chinese Medicine Department, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang, 314000, People's Republic of China
| | - Hongbin Xiao
- Beijing University of Chinese Medicine, Chinese Medicine Institute, Beijing 100029, People's Republic of China
| | - Zhong Wang
- Chinese Medicine Pharmacology, Institute of Basic Research in Clinical Medicine. China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
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8
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Harnessing microbial metabolomics for industrial applications. World J Microbiol Biotechnol 2019; 36:1. [DOI: 10.1007/s11274-019-2775-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
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9
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García-Ortega X, Cámara E, Ferrer P, Albiol J, Montesinos-Seguí JL, Valero F. Rational development of bioprocess engineering strategies for recombinant protein production in Pichia pastoris (Komagataella phaffii) using the methanol-free GAP promoter. Where do we stand? N Biotechnol 2019; 53:24-34. [DOI: 10.1016/j.nbt.2019.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 12/25/2022]
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10
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Nieto-Taype MA, Garrigós-Martínez J, Sánchez-Farrando M, Valero F, Garcia-Ortega X, Montesinos-Seguí JL. Rationale-based selection of optimal operating strategies and gene dosage impact on recombinant protein production in Komagataella phaffii (Pichia pastoris). Microb Biotechnol 2019; 13:315-327. [PMID: 31657146 PMCID: PMC7017824 DOI: 10.1111/1751-7915.13498] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
Its features as a microbial and eukaryotic organism have turned Komagataella phaffii (Pichia pastoris) into an emerging cell factory for recombinant protein production (RPP). As a key step of the bioprocess development, this work aimed to demonstrate the importance of tailor designing the cultivation strategy according to the production kinetics of the cell factory. For this purpose, K. phaffii clones constitutively expressing (PGAP) Candida rugosa lipase 1 (Crl1) with different gene dosage were used as models in continuous and fed‐batch cultures. Production parameters were much greater with a multicopy clone (MCC) than with the single‐copy clone (SCC). Regarding production kinetics, the specific product generation rate (qP) increased linearly with increasing specific growth rate (µ) in SCC; by contrast, qP exhibited saturation in MCC. A transcriptional analysis in chemostat cultures suggested the presence of eventual post‐transcriptional bottlenecks in MCC. After the strain characterization, in order to fulfil overall development of the bioprocess, the performance of both clones was also evaluated in fed‐batch mode. Strikingly, different optimal strategies were determined for both models due to the different production kinetic patterns observed as a trade‐off for product titre, yields and productivity. The combined effect of gene dosage and adequate µ enables rational process development with a view to optimize K. phaffii RPP bioprocesses.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Garrigós-Martínez
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Sánchez-Farrando
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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11
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Systems biology approach in the formulation of chemically defined media for recombinant protein overproduction. Appl Microbiol Biotechnol 2019; 103:8315-8326. [PMID: 31418052 DOI: 10.1007/s00253-019-10048-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
The cell culture medium is an intricate mixture of components which has a tremendous effect on cell growth and recombinant protein production. Regular cell culture medium includes various components, and the decision about which component should be included in the formulation and its optimum amount is an underlying issue in biotechnology industries. Applying conventional techniques to design an optimal medium for the production of a recombinant protein requires meticulous and immense research. Moreover, since the medium formulation for the production of one protein could not be the best choice for another protein, hence, the most suitable media should be determined for each recombinant cell line. Accordingly, medium formulation becomes a laborious, time-consuming, and costly process in biomanufacturing of recombinant protein, and finding alternative strategies for medium development seems to be crucial. In silico modeling is an attractive concept to be adapted for medium formulation due to its high potential to supersede laboratory examinations. By emerging the high-throughput datasets, scientists can disclose the knowledge about the effect of medium components on cell growth and metabolism, and via applying this information through systems biology approach, medium formulation optimization could be accomplished in silico with no need of significant amount of experimentation. This review demonstrates some of the applications of systems biology as a powerful tool for medium development and illustrates the effect of medium optimization with system-level analysis on the production of recombinant proteins in different host cells.
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12
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Zahrl RJ, Gasser B, Mattanovich D, Ferrer P. Detection and Elimination of Cellular Bottlenecks in Protein-Producing Yeasts. Methods Mol Biol 2019; 1923:75-95. [PMID: 30737735 DOI: 10.1007/978-1-4939-9024-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Yeasts are efficient cell factories and are commonly used for the production of recombinant proteins for biopharmaceutical and industrial purposes. For such products high levels of correctly folded proteins are needed, which sometimes requires improvement and engineering of the expression system. The article summarizes major breakthroughs that led to the efficient use of yeasts as production platforms and reviews bottlenecks occurring during protein production. Special focus is given to the metabolic impact of protein production. Furthermore, strategies that were shown to enhance secretion of recombinant proteins in different yeast species are presented.
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Affiliation(s)
- Richard J Zahrl
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Pau Ferrer
- Luxembourg Institute of Science and Technology, Belvaux, Luxembourg. .,Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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13
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Cankorur-Cetinkaya A, Narraidoo N, Kasavi C, Slater NKH, Archer DB, Oliver SG. Process development for the continuous production of heterologous proteins by the industrial yeast, Komagataella phaffii. Biotechnol Bioeng 2018; 115:2962-2973. [PMID: 30267565 PMCID: PMC6283250 DOI: 10.1002/bit.26846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/21/2022]
Abstract
The current trend in industrial biotechnology is to move from batch or fed-batch fermentations to continuous operations. The success of this transition will require the development of genetically stable production strains, the use of strong constitutive promoters, and the development of new medium formulations that allow an appropriate balance between cell growth and product formation. We identified genes that showed high expression in Komagataella phaffii during different steady-state conditions and explored the utility of promoters of these genes (Chr1-4_0586 and FragB_0052) in optimizing the expression of two different r-proteins, human lysozyme (HuLy), and the anti-idiotypic antibody fragment, Fab-3H6, in comparison with the widely used glyceraldehyde-3-phosphate dehydrogenase promoter. Our results showed that the promoter strength was highly dependent on the cultivation conditions and thus constructs should be tested under a range of conditions to determine both the best performing clone and the ideal promoter for the expression of the protein of interest. An important benefit of continuous production is that it facilitates the use of the genome-scale metabolic models in the design of strains and cultivation media. In silico flux distributions showed that production of either protein increased the flux through aromatic amino acid biosynthesis. Tyrosine supplementation increased the productivity for both proteins, whereas tryptophan addition did not cause any significant change and, phenylalanine addition increased the expression of HuLy but decreased that of Fab-3H6. These results showed that a genome-scale metabolic model can be used to assess the metabolic burden imposed by the synthesis of a specific r-protein and then this information can be used to tailor a cultivation medium to increase production.
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Affiliation(s)
- Ayca Cankorur-Cetinkaya
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Nathalie Narraidoo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Ceyda Kasavi
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Nigel K H Slater
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge University West Site, Cambridge, United Kingdom
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Stephen G Oliver
- Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
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14
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Effect of oxygen transfer on yeast growth — Growth kinetic and reactor model to estimate scale-up effects in bioreactors. FOOD AND BIOPRODUCTS PROCESSING 2018. [DOI: 10.1016/j.fbp.2018.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Metabolic engineering of Pichia pastoris. Metab Eng 2018; 50:2-15. [PMID: 29704654 DOI: 10.1016/j.ymben.2018.04.017] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/11/2022]
Abstract
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported. An outstanding early example of metabolic engineering in P. pastoris was the humanization of protein glycosylation. More recently the cell metabolism was engineered also to enhance the productivity of heterologous proteins. The last few years have seen an increased number of metabolic pathway design and engineering in P. pastoris, mainly towards the production of complex (secondary) metabolites. In this review, we discuss the potential role of P. pastoris as a platform for metabolic engineering, its strengths, and major requirements for future developments of chassis strains based on synthetic biology principles.
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Valero F. Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review. Methods Mol Biol 2018; 1835:205-216. [PMID: 30109654 DOI: 10.1007/978-1-4939-8672-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.
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Affiliation(s)
- Francisco Valero
- Departament d'Enginyeria Química, Biològica i Ambiental. EE, Universitat Autònoma de Barcelona, Barcelona, Spain.
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17
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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Zahrl RJ, Peña DA, Mattanovich D, Gasser B. Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res 2017; 17:4093073. [DOI: 10.1093/femsyr/fox068] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
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Zhang M, Yu XW, Xu Y, Jouhten P, Swapna GVT, Glaser RW, Hunt JF, Montelione GT, Maaheimo H, Szyperski T. 13 C metabolic flux profiling of Pichia pastoris grown in aerobic batch cultures on glucose revealed high relative anabolic use of TCA cycle and limited incorporation of provided precursors of branched-chain amino acids. FEBS J 2017; 284:3100-3113. [PMID: 28731268 DOI: 10.1111/febs.14180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/18/2017] [Indexed: 01/02/2023]
Abstract
Carbon metabolism of Crabtree-negative yeast Pichia pastoris was profiled using 13 C nuclear magnetic resonance (NMR) to delineate regulation during exponential growth and to study the import of two precursors for branched-chain amino acid biosynthesis, α-ketoisovalerate and α-ketobutyrate. Cells were grown in aerobic batch cultures containing (a) only glucose, (b) glucose along with the precursors, or (c) glucose and Val. The study provided the following new insights. First, 13 C flux ratio analyses of central metabolism reveal an unexpectedly high anaplerotic supply of the tricarboxylic acid cycle for a Crabtree-negative yeast, and show that a substantial fraction of glucose catabolism proceeds through the pentose phosphate pathway. A comparison with previous flux ratio analyses for batch cultures of Crabtree-negative Pichia stipitis and Crabtree-positive Saccharomyces cerevisiae indicate that the overall regulation of central carbon metabolism in P. pastoris is intermediate in between P. stipitis and S. cerevisiae. Second, excess α-ketoisovalerate in the medium is not transported into the cytoplasm indicating that P. pastoris lacks a suitable transporter. In contrast, excess Val is efficiently taken up and largely fulfills demands for both Val and Leu for protein synthesis. Third, excess α-ketobutyrate is transported into the mitochondria for Ile biosynthesis. However, the import does not efficiently inhibit the synthesis of α-ketobutyrate from pyruvate indicating that P. pastoris has not been optimized evolutionarily to take full advantage of this carbon source. These findings have direct implications for preparing uniformly 2 H,13 C,15 N-labeled proteins containing protonated Ile, Val, and Leu methyl groups in P. pastoris for NMR-based structural biology. ENZYMES Acetohydroxy acid isomeroreductase (EC 1.1.1.86), branched-chain amino acid aminotransferase (BCAT, EC 2.6.1.42), fumarase (EC 4.2.1.2), malic enzyme (EC 1.1.1.39/1.1.1.40), phosphoenolpyruvate carboxykinase (EC 4.1.1.49), pyruvate carboxylase (EC 6.4.1.1), pyruvate kinase (EC 2.7.1.40), l-serine hydroxymethyltransferase (EC 2.1.2.1), threonine aldolase (EC 4.1.2.5), threonine dehydratase (EC 4.3.1.19); transketolase (EC 2.2.1.1), transaldolase (EC 2.2.1.2).
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Affiliation(s)
- Meng Zhang
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiao-Wei Yu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yan Xu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Paula Jouhten
- European Molecular Biology Laboratory Heidelberg, Germany
| | - Gurla V T Swapna
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ralf W Glaser
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, NY, USA
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20
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Adelantado N, Tarazona P, Grillitsch K, García-Ortega X, Monforte S, Valero F, Feussner I, Daum G, Ferrer P. The effect of hypoxia on the lipidome of recombinant Pichia pastoris. Microb Cell Fact 2017; 16:86. [PMID: 28526017 PMCID: PMC5437588 DOI: 10.1186/s12934-017-0699-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/10/2017] [Indexed: 01/17/2023] Open
Abstract
Background Cultivation of recombinant Pichia pastoris (Komagataella sp.) under hypoxic conditions has a strong positive effect on specific productivity when the glycolytic GAP promoter is used for recombinant protein expression, mainly due to upregulation of glycolytic conditions. In addition, transcriptomic analyses of hypoxic P. pastoris pointed out important regulation of lipid metabolism and unfolded protein response (UPR). Notably, UPR that plays a role in the regulation of lipid metabolism, amino acid metabolism and protein secretion, was found to be upregulated under hypoxia. Results To improve our understanding of the interplay between lipid metabolism, UPR and protein secretion, the lipidome of a P. pastoris strain producing an antibody fragment was studied under hypoxic conditions. Furthermore, lipid composition analyses were combined with previously available transcriptomic datasets to further understand the impact of hypoxia on lipid metabolism. Chemostat cultures operated under glucose-limiting conditions under normoxic and hypoxic conditions were analyzed in terms of intra/extracellular product distribution and lipid composition. Integrated analysis of lipidome and transcriptome datasets allowed us to demonstrate an important remodeling of the lipid metabolism under limited oxygen availability. Additionally, cells with reduced amounts of ergosterol through fluconazole treatment were also included in the study to observe the impact on protein secretion and its lipid composition. Conclusions Our results show that cells adjust their membrane composition in response to oxygen limitation mainly by changing their sterol and sphingolipid composition. Although fluconazole treatment results a different lipidome profile than hypoxia, both conditions result in higher recombinant protein secretion levels. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0699-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Núria Adelantado
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain.,Evonik Nutrition & Care GmbH, Hanau, Germany
| | - Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Xavier García-Ortega
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Sergi Monforte
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria. .,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Catalonia, Spain
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21
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Ye R, Huang M, Lu H, Qian J, Lin W, Chu J, Zhuang Y, Zhang S. Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs. BIORESOUR BIOPROCESS 2017; 4:22. [PMID: 28546903 PMCID: PMC5423920 DOI: 10.1186/s40643-017-0152-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/17/2017] [Accepted: 05/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pichia pastoris is one of the most important cell factories for production of industrial enzymes and heterogenous proteins. The genome-scale metabolic model of high quality is crucial for comprehensive understanding of the P. pastoris metabolism. Methods In this paper, we upgraded P. pastoris genome-scale metabolic model based on the combination of latest genome annotations and literatures. Then the performance of the new model was evaluated using the Cobra Toolbox v2.0. Results Compared with the recently published model iMT1026, the reaction number in the new model iRY1243 was increased from 2035 to 2407 and the metabolite number was increased from 1018 to 1094. Accordingly, the unique ORF number was increased from 1026 to 1243. To improve the metabolic functions of P. pastoris genome-scale metabolic model, the biosynthesis pathways of vitamins and cofactors were carefully added. iRY1243 showed good performances when predicting the growth capability on most of the reported carbon and nitrogen sources, the metabolic flux distribution with glucose as a sole carbon source, the essential and partially essential genes, and the effects of gene deletion or overexpression on cell growth and S-adenosyl-l-methionine production. Conclusion iRY1243 is an upgraded P. pastoris genome-scale metabolic model with significant improvements in the metabolic coverage and prediction ability, and thus it will be a potential platform for further systematic investigation of P. pastoris metabolism. Electronic supplementary material The online version of this article (doi:10.1186/s40643-017-0152-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Jiangchao Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Weilu Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, No.130, Meilong Road, Shanghai, 200237 China
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22
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Rapid screening of cellular stress responses in recombinant Pichia pastoris strains using metabolite profiling. J Ind Microbiol Biotechnol 2017; 44:413-417. [PMID: 28160205 PMCID: PMC5329079 DOI: 10.1007/s10295-017-1904-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/07/2017] [Indexed: 10/26/2022]
Abstract
Heterologous protein production in the yeast Pichia pastoris can be limited by biological responses to high expression levels; the unfolded protein response (UPR) is a key determinant of the success of protein production in this organism. Here, we used untargeted NMR metabolic profiling (metabolomics) of a number of different recombinant strains, carried out in a miniaturized format suitable for screening-level experiments. We identified a number of metabolites (from both cell extracts and supernatants) which correlated well with UPR-relevant gene transcripts, and so could be potential biomarkers for future high-throughput screening of large numbers of P. pastoris clones.
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Tomàs-Gamisans M, Ferrer P, Albiol J. Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PLoS One 2016; 11:e0148031. [PMID: 26812499 PMCID: PMC4734642 DOI: 10.1371/journal.pone.0148031] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/12/2016] [Indexed: 01/21/2023] Open
Abstract
Motivation Genome-scale metabolic models (GEMs) are tools that allow predicting a phenotype from a genotype under certain environmental conditions. GEMs have been developed in the last ten years for a broad range of organisms, and are used for multiple purposes such as discovering new properties of metabolic networks, predicting new targets for metabolic engineering, as well as optimizing the cultivation conditions for biochemicals or recombinant protein production. Pichia pastoris is one of the most widely used organisms for heterologous protein expression. There are different GEMs for this methylotrophic yeast of which the most relevant and complete in the published literature are iPP668, PpaMBEL1254 and iLC915. However, these three models differ regarding certain pathways, terminology for metabolites and reactions and annotations. Moreover, GEMs for some species are typically built based on the reconstructed models of related model organisms. In these cases, some organism-specific pathways could be missing or misrepresented. Results In order to provide an updated and more comprehensive GEM for P. pastoris, we have reconstructed and validated a consensus model integrating and merging all three existing models. In this step a comprehensive review and integration of the metabolic pathways included in each one of these three versions was performed. In addition, the resulting iMT1026 model includes a new description of some metabolic processes. Particularly new information described in recently published literature is included, mainly related to fatty acid and sphingolipid metabolism, glycosylation and cell energetics. Finally the reconstructed model was tested and validated, by comparing the results of the simulations with available empirical physiological datasets results obtained from a wide range of experimental conditions, such as different carbon sources, distinct oxygen availability conditions, as well as producing of two different recombinant proteins. In these simulations, the iMT1026 model has shown a better performance than the previous existing models.
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Affiliation(s)
- Màrius Tomàs-Gamisans
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Pau Ferrer
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Joan Albiol
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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Lu H, Liu X, Huang M, Xia J, Chu J, Zhuang Y, Zhang S, Noorman H. Integrated isotope-assisted metabolomics and (13)C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger. Microb Cell Fact 2015; 14:147. [PMID: 26383080 PMCID: PMC4574132 DOI: 10.1186/s12934-015-0329-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus niger is widely used for enzyme production and achievement of high enzyme production depends on the comprehensive understanding of cell’s metabolic regulation mechanisms. Results In this paper, we investigate the metabolic differences and regulation mechanisms between a high glucoamylase-producing strain A. niger DS03043 and its wild-type parent strain A. niger CBS513.88 via an integrated isotope-assisted metabolomics and 13C metabolic flux analysis approach. We found that A. niger DS03043 had higher cell growth, glucose uptake, and glucoamylase production rates but lower oxalic acid and citric acid secretion rates. In response to above phenotype changes, A. niger DS03043 was characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway in contrast to reduced flux through TCA cycle, which were confirmed by consistent changes in pool sizes of metabolites. A higher ratio of ATP over AMP in the high producing strain might contribute to the increase in the PP pathway flux as glucosephosphate isomerase was inhibited at higher ATP concentrations. A. niger CBS513.88, however, was in a higher redox state due to the imbalance of NADH regeneration and consumption, resulting in the secretion of oxalic acid and citric acid, as well as the accumulation of intracellular OAA and PEP, which may in turn result in the decrease in the glucose uptake rate. Conclusions The application of integrated metabolomics and 13C metabolic flux analysis highlights the regulation mechanisms of energy and redox metabolism on flux redistribution in A. niger. An integrated isotope-assisted metabolomics and 13C metabolic flux analysis was was firstly systematically performed in A. niger. In response to enzyme production, the metabolic flux in A. niger DS03043 (high-producing) was redistributed, characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway as well as an increased pool size of pentose. The consistency in 13C metabolic flux analysis and metabolites quantification indicated that an imbalance of NADH formation and consumption led to the accumulation and secretion of organic acids in A. niger CBS513.88 (wild-type) ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0329-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Henk Noorman
- DSM Biotechnology Center, P.O. Box1, 2600 MA, Delft, The Netherlands.
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Russmayer H, Troyer C, Neubauer S, Steiger MG, Gasser B, Hann S, Koellensperger G, Sauer M, Mattanovich D. Metabolomics sampling of Pichia pastoris revisited: rapid filtration prevents metabolite loss during quenching. FEMS Yeast Res 2015; 15:fov049. [PMID: 26091839 DOI: 10.1093/femsyr/fov049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2015] [Indexed: 01/28/2023] Open
Abstract
Metabolomics can be defined as the quantitative assessment of a large number of metabolites of a biological system. A prerequisite for the accurate determination of intracellular metabolite concentrations is a reliable and reproducible sample preparation method, which needs to be optimized for each organism individually. Here, we compare the performance of rapid filtration and centrifugation after quenching of Pichia pastoris cells in cold methanol. During incubation in the quenching solution, metabolites are lost from the cells with a half-life of 70-180 min. Metabolites with lower molecular weights showed lower half-lifes compared to metabolites with higher molecular weight. Rapid filtration within 2 min after quenching leads to only minor losses below 2%, and is thus the preferred method for cell separation.
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Affiliation(s)
- Hannes Russmayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Christina Troyer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Matthias G Steiger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria Institute of Analytical Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
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Quo vadis? The challenges of recombinant protein folding and secretion in Pichia pastoris. Appl Microbiol Biotechnol 2015; 99:2925-38. [DOI: 10.1007/s00253-015-6470-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 10/23/2022]
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichia pastoris. Trends Biotechnol 2014; 32:396-9. [PMID: 24929579 PMCID: PMC4111905 DOI: 10.1016/j.tibtech.2014.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 11/29/2022]
Abstract
The current status of the Pichia pastoris genome is shown to lack extensive functional annotation. GO annotation transfer and literature curation pipelines improve the functional annotation of genomes. Pipelines and tools that can improve the annotation status of the genomes of Pichia pastoris and many industrial microbes are considered. Well-annotated genome sequences will facilitate the utilization of these microbes in a broader range of synthetic biology applications.
The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Valerie Wood
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kim M Rutherford
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Mark D McDowall
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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29
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Jordà J, Rojas HC, Carnicer M, Wahl A, Ferrer P, Albiol J. Quantitative Metabolomics and Instationary 13C-Metabolic Flux Analysis Reveals Impact of Recombinant Protein Production on Trehalose and Energy Metabolism in Pichia pastoris. Metabolites 2014; 4:281-99. [PMID: 24957027 PMCID: PMC4101507 DOI: 10.3390/metabo4020281] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/08/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
Pichia pastoris has been recognized as an effective host for recombinant protein production. In this work, we combine metabolomics and instationary 13C metabolic flux analysis (INST 13C-MFA) using GC-MS and LC-MS/MS to evaluate the potential impact of the production of a Rhizopus oryzae lipase (Rol) on P. pastoris central carbon metabolism. Higher oxygen uptake and CO2 production rates and slightly reduced biomass yield suggest an increased energy demand for the producing strain. This observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain.
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Affiliation(s)
- Joel Jordà
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Hugo Cueto Rojas
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands.
| | - Marc Carnicer
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands.
| | - Pau Ferrer
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Joan Albiol
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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30
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Mattanovich D, Sauer M, Gasser B. Yeast biotechnology: teaching the old dog new tricks. Microb Cell Fact 2014; 13:34. [PMID: 24602262 PMCID: PMC3975642 DOI: 10.1186/1475-2859-13-34] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 02/15/2014] [Indexed: 02/07/2023] Open
Abstract
Yeasts are regarded as the first microorganisms used by humans to process food and alcoholic beverages. The technology developed out of these ancient processes has been the basis for modern industrial biotechnology. Yeast biotechnology has gained great interest again in the last decades. Joining the potentials of genomics, metabolic engineering, systems and synthetic biology enables the production of numerous valuable products of primary and secondary metabolism, technical enzymes and biopharmaceutical proteins. An overview of emerging and established substrates and products of yeast biotechnology is provided and discussed in the light of the recent literature.
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Affiliation(s)
- Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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31
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Anné J, Vrancken K, Van Mellaert L, Van Impe J, Bernaerts K. Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1750-61. [PMID: 24412306 DOI: 10.1016/j.bbamcr.2013.12.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/26/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Proteins secreted by Gram-positive bacteria are released into the culture medium with the obvious benefit that they usually retain their native conformation. This property makes these host cells potentially interesting for the production of recombinant proteins, as one can take full profit of established protocols for the purification of active proteins. Several state-of-the-art strategies to increase the yield of the secreted proteins will be discussed, using Streptomyces lividans as an example and compared with approaches used in some other host cells. It will be shown that approaches such as increasing expression and translation levels, choice of secretion pathway and modulation of proteins thereof, avoiding stress responses by changing expression levels of specific (stress) proteins, can be helpful to boost production yield. In addition, the potential of multi-omics approaches as a tool to understand the genetic background and metabolic fluxes in the host cell and to seek for new targets for strain and protein secretion improvement is discussed. It will be shown that S. lividans, along with other Gram-positive host cells, certainly plays a role as a production host for recombinant proteins in an economically viable way. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Jozef Anné
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Kristof Vrancken
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Lieve Van Mellaert
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Jan Van Impe
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
| | - Kristel Bernaerts
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
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32
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Abstract
Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.
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Affiliation(s)
- Pau Ferrer
- Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain,
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33
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Gasser B, Prielhofer R, Marx H, Maurer M, Nocon J, Steiger M, Puxbaum V, Sauer M, Mattanovich D. Pichia pastoris: protein production host and model organism for biomedical research. Future Microbiol 2013; 8:191-208. [DOI: 10.2217/fmb.12.133] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pichia pastoris is the most frequently used yeast system for heterologous protein production today. The last few years have seen several products based on this platform reach approval as biopharmaceutical drugs. Successful glycoengineering to humanize N-glycans is further fuelling this development. However, detailed understanding of the yeast’s physiology, genetics and regulation has only developed rapidly in the last few years since published genome sequences have become available. An expanding toolbox of genetic elements and strains for the improvement of protein production is being generated, including promoters, gene copy-number enhancement, gene knockout and high-throughput methods. Protein folding and secretion have been identified as significant bottlenecks in yeast expression systems, pinpointing a major target for strain optimization. At the same time, it has become obvious that P. pastoris, as an evolutionarily more ‘ancient’ yeast, may in some cases be a better model for human cell biology and disease than Saccharomyces cerevisiae.
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Affiliation(s)
- Brigitte Gasser
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Roland Prielhofer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Hans Marx
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Michael Maurer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
- University of Applied Sciences FH-Campus Vienna, School of Bioengineering, 1190 Vienna, Austria
| | - Justyna Nocon
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Matthias Steiger
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Verena Puxbaum
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Michael Sauer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Diethard Mattanovich
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
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34
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Systematic applications of metabolomics in metabolic engineering. Metabolites 2012; 2:1090-122. [PMID: 24957776 PMCID: PMC3901235 DOI: 10.3390/metabo2041090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/29/2012] [Accepted: 12/10/2012] [Indexed: 02/05/2023] Open
Abstract
The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules) to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.
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