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Pham DN, Linova MY, Smith WK, Brown H, Elhanafi D, Fan J, Lavoie J, Woodley JM, Carbonell RG. Novel multimodal cation-exchange membrane for the purification of a single-chain variable fragment from Pichia pastoris supernatant. J Chromatogr A 2024; 1718:464682. [PMID: 38341900 DOI: 10.1016/j.chroma.2024.464682] [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: 11/21/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/13/2024]
Abstract
A novel salt-tolerant cation-exchange membrane, prepared with a multimodal ligand, 2-mercaptopyridine-3-carboxylic acid (MMC-MPCA), was examined for its purification properties in a bind-and-elute mode from the high conductivity supernatant of a Pichia pastoris fermentation producing and secreting a single-chain variable fragment (scFv). If successful, this approach would eliminate the need for a buffer exchange prior to product capture by ion-exchange. Two fed-batch fermentations of Pichia pastoris resulted in fermentation supernatants reaching an scFv titer of 395.0 mg/L and 555.7 mg/L, both with a purity of approximately 83 %. The MMC-MPCA membrane performance was characterized in terms of pH, residence time (RT), scFv load, and scFv concentration to identify the resulting dynamic binding capacity (DBC), yield, and purity achieved under optimal conditions. The MMC-MPCA membrane exhibited the highest DBC of 39.06 mg/mL at pH 5.5, with a residence time of 1 min, while reducing the pH below 5.0 resulted in a significant decrease of the DBC to around 2.5 mg/mL. With almost no diffusional limitations, reducing the RT from 2 to 0.2 min did not negatively impact the DBC of the MMC-MPCA membrane, resulting in a significant improvement in productivity of up to 180 mg/mL/min at 0.2 min RT. Membrane fouling was observed when reusing the membranes at 0.2 and 0.5 min RT, likely due to the enhanced adsorption of impurities on the membrane. Changing the amount of scFv loaded onto the membrane column did not show any changes in yield, instead a 10-20 % loss of scFv was observed, which suggested that some of the produced scFv were fragmented or had aggregated. When performing the purification under the optimized conditions, the resulting purity of the product improved from 83 % to approximately 92-95 %.
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Affiliation(s)
- Dan N Pham
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marina Y Linova
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - William K Smith
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Hunter Brown
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Driss Elhanafi
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jinxin Fan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
| | - Joseph Lavoie
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7905, USA
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Ruben G Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7905, USA.
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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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3
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De Groeve M, Laukens B, Schotte P. Optimizing expression of Nanobody® molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions. Microb Cell Fact 2023; 22:135. [PMID: 37481525 PMCID: PMC10362571 DOI: 10.1186/s12934-023-02132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/24/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. RESULTS Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. CONCLUSION Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
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Affiliation(s)
- Manu De Groeve
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Bram Laukens
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Peter Schotte
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium.
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Shrivastava A, Pal M, Sharma RK. Pichia as Yeast Cell Factory for Production of Industrially Important Bio-Products: Current Trends, Challenges, and Future Prospects. JOURNAL OF BIORESOURCES AND BIOPRODUCTS 2023. [DOI: 10.1016/j.jobab.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Yeast-produced fructosamine-3-kinase retains mobility after ex vivo intravitreal injection in human and bovine eyes as determined by Fluorescence Correlation Spectroscopy. Int J Pharm 2022; 621:121772. [PMID: 35487399 DOI: 10.1016/j.ijpharm.2022.121772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/20/2022]
Abstract
Globally, over 2 billion people suffer from vision impairment. Despite complex multifactorial etiology, advanced glycation end products are involved in the pathogenesis of many causative age- and diabetes-related eye diseases. Deglycating enzyme fructosamine-3-kinase (FN3K) was recently proposed as a potential therapeutic, but for further biopharmaceutical development, knowledge on its manufacturability and stability and mobility in the vitreous fluid of the eye is indispensable. We evaluated recombinant production of FN3K in two host systems, and its diffusion behavior in both bovine and human vitreous. Compared to Escherichia coli, intracellular production in Pichia pastoris yielded more and higher purity FN3K. The yeast-produced enzyme was used in a first attempt to use fluorescence correlation spectroscopy to study protein mobility in non-sonicated bovine vitreous, human vitreous, and intact bovine eyes. It was demonstrated that FN3K retained mobility upon intravitreal injection, although a certain delay in diffusion was observed. Alkylation of free cysteines was tolerated both in terms of enzymatic activity and vitreous diffusion. Ex vivo diffusion data gathered and the availability of yeast-produced high purity enzyme now clear the path for in vivo pharmacokinetics studies of FN3K.
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Bustos C, Quezada J, Veas R, Altamirano C, Braun-Galleani S, Fickers P, Berrios J. Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production. Metabolites 2022; 12:346. [PMID: 35448535 PMCID: PMC9027633 DOI: 10.3390/metabo12040346] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.
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Affiliation(s)
- Cristina Bustos
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Rhonda Veas
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Stephanie Braun-Galleani
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
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Irani V, Soliman C, Raftis MA, Guy AJ, Elbourne A, Ramsland PA. Expression of monoclonal antibodies for functional and structural studies. METHODS IN MICROBIOLOGY 2022. [DOI: 10.1016/bs.mim.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Jennifer S, Corinna R, Thomas D, Nils L, Diethard M, Brigitte G. Going beyond the limit: Increasing global translation activity leads to increased productivity of recombinant secreted proteins in Pichia pastoris. Metab Eng 2022; 70:181-195. [DOI: 10.1016/j.ymben.2022.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/06/2023]
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9
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Expression and Characterization of a Potent Long-Acting GLP-1 Receptor Like Agonist, Exendin-4-Fc. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractHuman GLP-1 (glucagon-like peptide-1) can produce a remarkable improvement in glycemic control in patients with type 2 diabetes. However, its clinical benefits are limited by its short half-life, which is less than 2 min because of its small size and rapid enzymatic inactivation by dipeptidyl peptidase IV. We engineered Exendin-4-Fc, a 66-kDa fusion protein by linking an IgG2 Fc to Exendin-4. A stably transfected Chinese hamster ovary cell line was obtained using electroporation. Exendin-4-Fc stimulated insulin secretion in INS-1 cells in a dose- and glucose-dependent manner and increased insulin mRNA expression. The plasma half-life of Exendin-4-Fc in cynomolgus monkeys was approximately 133.92 ± 25.1 h. In the KKAy mouse model of diabetes, one intraperitoneal injection of Exendin-4-Fc (1 mg/kg) reduced blood glucose levels for 5 days. A 4-week repeat-administration study identified sustained effects on blood glucose levels. Oral glucose tolerance tests conducted at the beginning and end of this 4-week period showed that Exendin-4-Fc produced a stable glucose lowering effect. In addition, KKAy mice treated with Exendin-4-Fc showed statistically significant weight loss from day 23. In conclusion, these properties of Exendin-4-Fc demonstrated that it could be a potential long-acting GLP-1 receptor agonist for the treatment of type 2 diabetes.
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Valli M, Grillitsch K, Grünwald-Gruber C, Tatto NE, Hrobath B, Klug L, Ivashov V, Hauzmayer S, Koller M, Tir N, Leisch F, Gasser B, Graf AB, Altmann F, Daum G, Mattanovich D. A subcellular proteome atlas of the yeast Komagataella phaffii. FEMS Yeast Res 2021; 20:5700286. [PMID: 31922548 PMCID: PMC6981350 DOI: 10.1093/femsyr/foaa001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.
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Affiliation(s)
- Minoska Valli
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Karlheinz Grillitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Nadine E Tatto
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Bernhard Hrobath
- Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Lisa Klug
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Vasyl Ivashov
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Sandra Hauzmayer
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Martina Koller
- School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Nora Tir
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Statistics, University of Natural Resources and Life Sciences, Peter-Jordan-Straße 82, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH-Campus Vienna, Muthgasse 11, 1190 Vienna, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Günther Daum
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Brooks SM, Alper HS. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat Commun 2021; 12:1390. [PMID: 33654085 PMCID: PMC7925609 DOI: 10.1038/s41467-021-21740-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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Zhu W, Xu R, Gong G, Xu L, Hu Y, Xie L. Medium optimization for high yield production of human serum albumin in Pichia pastoris and its efficient purification. Protein Expr Purif 2021; 181:105831. [PMID: 33508474 DOI: 10.1016/j.pep.2021.105831] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To improve the yield of recombinant human serum albumin (HSA) in Pichia pastoris by medium optimization and establish the related purification scheme. RESULTS A simplified version of the generally used buffered glycerol complex medium (BMGY), which contained yeast extract, glycerol and potassium salts, was found to be applicable. By decreasing the salt concentration of basal salt medium (BSM) to half of the original formula further, we achieved a high yield of 17.47 g/L HSA in the supernatant within a 192 h induction, which is the highest rHSA yield ever reported as far as we know. Accompanied with a three-step purification procedure which recovered two thirds of the desired protein at high purity, our work lays a solid foundation for large-scale industrial production of HSA. CONCLUSION Medium optimization plays a significant role in improving the yield of desired protein, lowering the production cost and helping to explore the producing strain's character.
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Affiliation(s)
- Wen Zhu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China
| | - Renren Xu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China
| | - Guihua Gong
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China
| | - Lei Xu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China
| | - Youjia Hu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China
| | - Liping Xie
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, PR China.
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13
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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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14
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Dalvie NC, Leal J, Whittaker CA, Yang Y, Brady JR, Love KR, Love JC. Host-Informed Expression of CRISPR Guide RNA for Genomic Engineering in Komagataella phaffii. ACS Synth Biol 2020; 9:26-35. [PMID: 31825599 PMCID: PMC7814401 DOI: 10.1021/acssynbio.9b00372] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is growing interest in the use of nonmodel microorganisms as hosts for biopharmaceutical manufacturing. These hosts require genomic engineering to meet clinically relevant product qualities and titers, but the adaptation of tools for editing genomes, such as CRISPR-Cas9, has been slow for poorly characterized hosts. Specifically, a lack of biochemical characterization of RNA polymerase III transcription has hindered reliable expression of guide RNAs in new hosts. Here, we present a sequencing-based strategy for the design of host-specific cassettes for modular, reliable, expression of guide RNAs. Using this strategy, we achieved up to 95% gene editing efficiency in the methylotrophic yeast Komagataella phaffii. We applied this approach for the rapid, multiplexed engineering of a complex phenotype, achieving humanized product glycosylation in two sequential steps of engineering. Reliable extension of simple gene editing tools to nonmodel manufacturing hosts will enable rapid engineering of manufacturing strains tuned for specific product profiles and potentially decrease the costs and timelines for process development.
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Affiliation(s)
- Neil C. Dalvie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Justin Leal
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Charles A. Whittaker
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Yuchen Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Joseph R. Brady
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Kerry R. Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - J. Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
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15
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Torres P, Saa PA, Albiol J, Ferrer P, Agosin E. Contextualized genome-scale model unveils high-order metabolic effects of the specific growth rate and oxygenation level in recombinant Pichia pastoris. Metab Eng Commun 2019; 9:e00103. [PMID: 31720218 PMCID: PMC6838487 DOI: 10.1016/j.mec.2019.e00103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022] Open
Abstract
Pichia pastoris is recognized as a biotechnological workhorse for recombinant protein expression. The metabolic performance of this microorganism depends on genetic makeup and culture conditions, amongst which the specific growth rate and oxygenation level are critical. Despite their importance, only their individual effects have been assessed so far, and thus their combined effects and metabolic consequences still remain to be elucidated. In this work, we present a comprehensive framework for revealing high-order (i.e., individual and combined) metabolic effects of the above parameters in glucose-limited continuous cultures of P. pastoris, using thaumatin production as a case study. Specifically, we employed a rational experimental design to calculate statistically significant metabolic effects from multiple chemostat data, which were later contextualized using a refined and highly predictive genome-scale metabolic model of this yeast under the simulated conditions. Our results revealed a negative effect of the oxygenation on the specific product formation rate (thaumatin), and a positive effect on the biomass yield. Notably, we identified a novel positive combined effect of both the specific growth rate and oxygenation level on the specific product formation rate. Finally, model predictions indicated an opposite relationship between the oxygenation level and the growth-associated maintenance energy (GAME) requirement, suggesting a linear GAME decrease of 0.56 mmol ATP/gDCW per each 1% increase in oxygenation level, which translated into a 44% higher metabolic cost under low oxygenation compared to high oxygenation. Overall, this work provides a systematic framework for mapping high-order metabolic effects of different culture parameters on the performance of a microbial cell factory. Particularly in this case, it provided valuable insights about optimal operational conditions for protein production in P. pastoris.
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Affiliation(s)
- Paulina Torres
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
| | - Pedro A Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860, Santiago, Chile
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16
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Statistically Designed Medium Reveals Interactions between Metabolism and Genetic Information Processing for Production of Stable Human Serum Albumin in Pichia pastoris. Biomolecules 2019; 9:biom9100568. [PMID: 31590267 PMCID: PMC6843683 DOI: 10.3390/biom9100568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
Human serum albumin (HSA), sourced from human serum, has been an important therapeutic protein for several decades. Pichia pastoris is strongly considered as an expression platform, but proteolytic degradation of recombinant HSA in the culture filtrate remains a major bottleneck for use of this system. In this study, we have reported the development of a medium that minimized proteolytic degradation across different copy number constructs. A synthetic codon-optimized copy of HSA was cloned downstream of α-factor secretory signal sequence and expressed in P. pastoris under the control of Alcohol oxidase 1 promoter. A two-copy expression cassette was also prepared. Culture conditions and medium components were identified and optimized using statistical tools to develop a medium that supported stable production of HSA. Comparative analysis of transcriptome data obtained by cultivation on optimized and unoptimized medium indicated upregulation of genes involved in methanol metabolism, alternate nitrogen assimilation, and DNA transcription, whereas enzymes of translation and secretion were downregulated. Several new genes were identified that could serve as possible targets for strain engineering of this yeast.
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17
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Coats MT, Bydlinski N, Maresch D, Diendorfer A, Klanert G, Borth N. mRNA Transfection into CHO-Cells Reveals Production Bottlenecks. Biotechnol J 2019; 15:e1900198. [PMID: 31475780 DOI: 10.1002/biot.201900198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/27/2019] [Indexed: 12/19/2022]
Abstract
Obtaining highly productive Chinese hamster ovary (CHO)-cell clones for the production of therapeutic proteins relies on multiple time-consuming selection steps. Several CHO-cell strains with high degrees of genomic and epigenetic variation are available. Each harbor potential advantages and disadvantages for any given product, particularly those considered difficult to express. A simple test system to quickly assess compatibility of cell line and product may therefore prove useful. Transient plasmid transfection falls short of the specific productivities of stable producer cells, making it unsuitable for the elucidation of high specific productivity bottlenecks. The aim of the study is to reach specific productivities approaching those of industrial production cell lines by transfection of in vitro transcribed mRNA. The system is characterized with respect to transfection efficacy (by quantitative PCR) and protein production (by flow cytometry and biolayer interferometry). Fluorescence of intracellular eGFP saturates at higher amounts of mRNA per cell, while the amount of secreted and intracellular EPO-Fc remain linearly correlated to the amount of mRNA taken up. Nevertheless, MS shows a severe reduction in N-glycosylation quality. This method allows for rapid elucidation of bottlenecks that would otherwise remain undetected until later during cell line development, giving insight into suitable strategies for preemptive targeted metabolic engineering and host cell line optimization.
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Affiliation(s)
- Michael T Coats
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Nina Bydlinski
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, BOKU University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | | | - Gerald Klanert
- Austrian Centre of Industrial Biotechnology GmbH, 8010, Graz, Austria
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology GmbH, 8010, Graz, Austria
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18
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Sifniotis V, Cruz E, Eroglu B, Kayser V. Current Advancements in Addressing Key Challenges of Therapeutic Antibody Design, Manufacture, and Formulation. Antibodies (Basel) 2019; 8:E36. [PMID: 31544842 PMCID: PMC6640721 DOI: 10.3390/antib8020036] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022] Open
Abstract
Therapeutic antibody technology heavily dominates the biologics market and continues to present as a significant industrial interest in developing novel and improved antibody treatment strategies. Many noteworthy advancements in the last decades have propelled the success of antibody development; however, there are still opportunities for improvement. In considering such interest to develop antibody therapies, this review summarizes the array of challenges and considerations faced in the design, manufacture, and formulation of therapeutic antibodies, such as stability, bioavailability and immunological engagement. We discuss the advancement of technologies that address these challenges, highlighting key antibody engineered formats that have been adapted. Furthermore, we examine the implication of novel formulation technologies such as nanocarrier delivery systems for the potential to formulate for pulmonary delivery. Finally, we comprehensively discuss developments in computational approaches for the strategic design of antibodies with modulated functions.
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Affiliation(s)
- Vicki Sifniotis
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia.
| | - Esteban Cruz
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia.
| | - Barbaros Eroglu
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia.
| | - Veysel Kayser
- School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia.
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19
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Tackling Cancer with Yeast-Based Technologies. Trends Biotechnol 2019; 37:592-603. [DOI: 10.1016/j.tibtech.2018.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/24/2018] [Accepted: 11/30/2018] [Indexed: 12/19/2022]
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20
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Vorauer-Uhl K, Lhota G. Quantification of Recombinant Products in Yeast. Methods Mol Biol 2019; 1923:385-428. [PMID: 30737753 DOI: 10.1007/978-1-4939-9024-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantification of various proteins expressed in yeast can be performed by different methods. In this respect, classical as well as advanced techniques can be applied, where the analysis of crude supernatants is of special interest in screening but also manufacturing.The following chapter addresses the analytical background of the introduced methods followed by specific recommendations for the quantification of different products of industrial interest. The method portfolio includes electrophoresis, chromatography, and ELISA as classical techniques, but also biosensor-based, microfluidic and automated, miniaturized methods are introduced. Furthermore, individual strengths and perceived limitations are summarized.Although prominent examples are described, it should be noted that individual modifications are required according to host and cultivation mode.
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Affiliation(s)
- Karola Vorauer-Uhl
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria.
| | - Gabriele Lhota
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
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21
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Jain KK, Kumar S, Bhardwaj KN, Kuhad RC. Functional Expression of a Thermostable Endoglucanase from Thermoascus aurantiacus RCKK in Pichia pastoris X-33 and Its Characterization. Mol Biotechnol 2018; 60:736-748. [PMID: 30076532 DOI: 10.1007/s12033-018-0106-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Thermostable cellulases offer several advantages like higher rates of substrate hydrolysis, lowered risk of contamination, and increased flexibility with respect to process design. In the present study, a thermostable native endoglucanase nEG (EC 3.2.1.4) was purified and characterized from T. aurantiacus RCKK. Further, it was cloned in P. pastoris X-33 and processed for over expression. Expression of recombinant endoglucanase (rEG) of molecular size ~ 33 kDa was confirmed by SDS-PAGE and western blotting followed by in gel activity determination by zymogram analysis. Similar to nEG, the purified rEG was characterized to harbor high thermostability while retaining 50% of its initial activity even after 6- and 10-h incubation at 80 and 70 °C, respectively, and exhibited considerable stability in pH range 3.0-7.0. CD spectroscopy revealed more than 20% β-sheets in protein structure consistently when incubated upto 85 °C as a speculated reason for protein high thermostability. Interestingly, both nEG and rEG were found tolerant up to 10% of the presence of 1-ethyl-3-methylimidazolium acetate [C2mim][OAc]. Values of the catalytic constants Km and Vmax for rEG were recorded as 2.5 mg/ml and 303.4 µmol/mg/min, respectively. Thermostability, pH stability, and resistance to the presence of ionic liquid signify the potential applicability of present enzyme in cellulose hydrolysis and enzymatic deinking of recycled paper pulp.
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Affiliation(s)
- Kavish Kumar Jain
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.,Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Sandeep Kumar
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kailash N Bhardwaj
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.,Uttarakhan State Council of Science and Technology [UCOST], Vigyan Dham, Post Office- Jhajra, Dehradun, Uttarakhand, 248007, India
| | - Ramesh Chander Kuhad
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,Central University of Haryana, Jant-Pali Village, Mahendergarh District, Haryana, 123029, India.
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22
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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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23
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The yeast stands alone: the future of protein biologic production. Curr Opin Biotechnol 2018; 53:50-58. [DOI: 10.1016/j.copbio.2017.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/13/2022]
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24
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Zhu W, Gong G, Pan J, Han S, Zhang W, Hu Y, Xie L. High level expression and purification of recombinant human serum albumin in Pichia pastoris. Protein Expr Purif 2018. [DOI: 10.1016/j.pep.2018.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Nambu-Nishida Y, Nishida K, Hasunuma T, Kondo A. Genetic and physiological basis for antibody production by Kluyveromyces marxianus. AMB Express 2018; 8:56. [PMID: 29651657 PMCID: PMC5897269 DOI: 10.1186/s13568-018-0588-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022] Open
Abstract
Kluyveromyces marxianus is a thermotolerant, crabtree-negative yeast, which preferentially directs metabolism (e.g., from the tricarboxylic acid cycle) to aerobic alcoholic fermentation. Thus K. marxianus has great potential for engineering to produce various materials under aerobic cultivation conditions. In this study, we engineered K. marxianus to produce and secrete a single-chain antibody (scFv), a product that is highly valuable but has historically proven difficult to generate at large scale. scFv production was obtained with strains carrying either plasmid-borne or genomically integrated constructs using various combinations of promoters (PMDH1 or PACO1) and secretion signal peptides (KmINUss or Scα-MFss). As the wild-type K. marxianus secretes endogenous inulinase predominantly, the corresponding INU1 gene was disrupted using a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)—associated protein (CRISPR–Cas9) system to re-direct resources to scFv production. Genomic integration was used to replace INU1 with sequences encoding a fusion of the INU1 signal peptide to scFv; the resulting construct yielded the highest scFv production among the strains tested. Optimization of growth conditions revealed that scFv production by this strain was enhanced by incubation at 30 °C in xylose medium containing 200 mM MgSO4. These results together demonstrate that K. marxianus has the potential to serve as a host strain for antibody production.
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26
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Zahrl RJ, Mattanovich D, Gasser B. The impact of ERAD on recombinant protein secretion in Pichia pastoris (syn Komagataella spp.). MICROBIOLOGY-SGM 2018. [PMID: 29533745 DOI: 10.1099/mic.0.000630] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The yeast Pichia pastoris (syn. Komagataella spp.) is a popular cell factory for recombinant protein production. Yeasts in general provide a good starting point for cell factory engineering. They are intrinsically robust and easy to manipulate and cultivate. However, their secretory pathway is not evolutionarily adapted to high loads of secretory protein. In particular, more complex proteins, like the antibody fragment (Fab) used in this study, overwhelm the folding and secretion capacity. This triggers cellular stress responses, which may cause excessive intracellular degradation. Previous results have shown that, in fact, about 60 % of the newly synthesized Fab is intracellularly degraded. Endoplasmic reticulum-associated protein degradation (ERAD) is one possible intracellular degradation pathway for proteins aimed for secretion. We therefore targeted ERAD for cell factory engineering and investigated the impact on recombinant protein secretion in P. pastoris. Three components of the ERAD-L complex, which is involved in the degradation of luminal proteins, and a protein involved in proteasomal degradation, were successfully disrupted in Fab-secreting P. pastoris. Contrary to expectation, the effect on secretion was marginal. In the course of more detailed investigation of the impact of ERAD, we took a closer look at the intracellular variants of the recombinant protein. This enabled us to further zero in on the issue of intracellular Fab degradation and exclude an overshooting ER quality control. We propose that a major fraction of the Fab is actually degraded before entering the secretory pathway.
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Affiliation(s)
- Richard J Zahrl
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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27
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Sigar M, Maity N, Mishra S. Enhancing granulocyte colony-stimulating factor expression in Pichia pastoris through fusion with human serum albumin. Prep Biochem Biotechnol 2017; 47:364-370. [DOI: 10.1080/10826068.2016.1252922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Moolchand Sigar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Nitu Maity
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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28
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Saitua F, Torres P, Pérez-Correa JR, Agosin E. Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris. BMC SYSTEMS BIOLOGY 2017; 11:27. [PMID: 28222737 PMCID: PMC5320773 DOI: 10.1186/s12918-017-0408-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/09/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Pichia pastoris shows physiological advantages in producing recombinant proteins, compared to other commonly used cell factories. This yeast is mostly grown in dynamic cultivation systems, where the cell's environment is continuously changing and many variables influence process productivity. In this context, a model capable of explaining and predicting cell behavior for the rational design of bioprocesses is highly desirable. Currently, there are five genome-scale metabolic reconstructions of P. pastoris which have been used to predict extracellular cell behavior in stationary conditions. RESULTS In this work, we assembled a dynamic genome-scale metabolic model for glucose-limited, aerobic cultivations of Pichia pastoris. Starting from an initial model structure for batch and fed-batch cultures, we performed pre/post regression diagnostics to ensure that model parameters were identifiable, significant and sensitive. Once identified, the non-relevant ones were iteratively fixed until a priori robust modeling structures were found for each type of cultivation. Next, the robustness of these reduced structures was confirmed by calibrating the model with new datasets, where no sensitivity, identifiability or significance problems appeared in their parameters. Afterwards, the model was validated for the prediction of batch and fed-batch dynamics in the studied conditions. Lastly, the model was employed as a case study to analyze the metabolic flux distribution of a fed-batch culture and to unravel genetic and process engineering strategies to improve the production of recombinant Human Serum Albumin (HSA). Simulation of single knock-outs indicated that deviation of carbon towards cysteine and tryptophan formation improves HSA production. The deletion of methylene tetrahydrofolate dehydrogenase could increase the HSA volumetric productivity by 630%. Moreover, given specific bioprocess limitations and strain characteristics, the model suggests that implementation of a decreasing specific growth rate during the feed phase of a fed-batch culture results in a 25% increase of the volumetric productivity of the protein. CONCLUSION In this work, we formulated a dynamic genome scale metabolic model of Pichia pastoris that yields realistic metabolic flux distributions throughout dynamic cultivations. The model can be calibrated with experimental data to rationally propose genetic and process engineering strategies to improve the performance of a P. pastoris strain of interest.
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Affiliation(s)
- Francisco Saitua
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - Paulina Torres
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - José Ricardo Pérez-Correa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
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Wang M, Jiang S, Wang Y. Recent advances in the production of recombinant subunit vaccines in Pichia pastoris. Bioengineered 2017; 7:155-65. [PMID: 27246656 DOI: 10.1080/21655979.2016.1191707] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recombinant protein subunit vaccines are formulated using defined protein antigens that can be produced in heterologous expression systems. The methylotrophic yeast Pichia pastoris has become an important host system for the production of recombinant subunit vaccines. Although many basic elements of P. pastoris expression system are now well developed, there is still room for further optimization of protein production. Codon bias, gene dosage, endoplasmic reticulum protein folding and culture condition are important considerations for improved production of recombinant vaccine antigens. Here we comment on current advances in the application of P. pastoris for the synthesis of recombinant subunit vaccines.
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Affiliation(s)
- Man Wang
- a Institute for Translational Medicine, Medical College of Qingdao University , Qingdao , China
| | - Shuai Jiang
- b State Key Laboratory of Virology , College of Life Sciences, Wuhan University , Wuhan , China
| | - Yefu Wang
- b State Key Laboratory of Virology , College of Life Sciences, Wuhan University , Wuhan , China
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30
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Love KR, Shah KA, Whittaker CA, Wu J, Bartlett MC, Ma D, Leeson RL, Priest M, Borowsky J, Young SK, Love JC. Comparative genomics and transcriptomics of Pichia pastoris. BMC Genomics 2016; 17:550. [PMID: 27495311 PMCID: PMC4974788 DOI: 10.1186/s12864-016-2876-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/05/2016] [Indexed: 11/24/2022] Open
Abstract
Background Pichia pastoris has emerged as an important alternative host for producing recombinant biopharmaceuticals, owing to its high cultivation density, low host cell protein burden, and the development of strains with humanized glycosylation. Despite its demonstrated utility, relatively little strain engineering has been performed to improve Pichia, due in part to the limited number and inconsistent frameworks of reported genomes and transcriptomes. Furthermore, the co-mingling of genomic, transcriptomic and fermentation data collected about Komagataella pastoris and Komagataella phaffii, the two strains co-branded as Pichia, has generated confusion about host performance for these genetically distinct species. Generation of comparative high-quality genomes and transcriptomes will enable meaningful comparisons between the organisms, and potentially inform distinct biotechnological utilies for each species. Results Here, we present a comprehensive and standardized comparative analysis of the genomic features of the three most commonly used strains comprising the tradename Pichia: K. pastoris wild-type, K. phaffii wild-type, and K. phaffii GS115. We used a combination of long-read (PacBio) and short-read (Illumina) sequencing technologies to achieve over 1000X coverage of each genome. Construction of individual genomes was then performed using as few as seven individual contigs to create gap-free assemblies. We found substantial syntenic rearrangements between the species and characterized a linear plasmid present in K. phaffii. Comparative analyses between K. phaffii genomes enabled the characterization of the mutational landscape of the GS115 strain. We identified and examined 35 non-synonomous coding mutations present in GS115, many of which are likely to impact strain performance. Additionally, we investigated transcriptomic profiles of gene expression for both species during cultivation on various carbon sources. We observed that the most highly transcribed genes in both organisms were consistently highly expressed in all three carbon sources examined. We also observed selective expression of certain genes in each carbon source, including many sequences not previously reported as promoters for expression of heterologous proteins in yeasts. Conclusions Our studies establish a foundation for understanding critical relationships between genome structure, cultivation conditions and gene expression. The resources we report here will inform and facilitate rational, organism-wide strain engineering for improved utility as a host for protein production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2876-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kerry R Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 76-253, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Kartik A Shah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 76-253, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Charles A Whittaker
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jie Wu
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - M Catherine Bartlett
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 76-253, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Rachel L Leeson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 76-253, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Margaret Priest
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jonathan Borowsky
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sarah K Young
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 76-253, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Pichia pastoris Exhibits High Viability and a Low Maintenance Energy Requirement at Near-Zero Specific Growth Rates. Appl Environ Microbiol 2016; 82:4570-4583. [PMID: 27208115 PMCID: PMC4984280 DOI: 10.1128/aem.00638-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 12/16/2022] Open
Abstract
The yeast Pichia pastoris is a widely used host for recombinant protein production. Understanding its physiology at extremely low growth rates is a first step in the direction of decoupling product formation from cellular growth and therefore of biotechnological relevance. Retentostat cultivation is an excellent tool for studying microbes at extremely low specific growth rates but has so far not been implemented for P. pastoris. Retentostat feeding regimes were based on the maintenance energy requirement (mS) and maximum biomass yield on glucose (YX/Smax) estimated from steady-state glucose-limited chemostat cultures. Aerobic retentostat cultivation enabled reproducible, smooth transitions from a specific growth rate (μ) of 0.025 h−1 to near-zero specific growth rates (μ < 0.001 h−1). At these near-zero specific growth rates, viability remained at least 97%. The value of mS at near-zero growth rates was 3.1 ± 0.1 mg glucose per g biomass and h, which was 3-fold lower than the mS estimated from faster-growing chemostat cultures. This difference indicated that P. pastoris reduces its maintenance energy requirement at extremely low μ, a phenomenon not previously observed in eukaryotes. Intracellular levels of glycogen and trehalose increased, while μ progressively declined during retentostat cultivation. Transcriptional reprogramming toward zero growth included the upregulation of many transcription factors as well as stress-related genes and the downregulation of cell cycle genes. This study underlines the relevance of comparative analysis of maintenance energy metabolism, which has an important impact on large-scale industrial processes. IMPORTANCE The yeast Pichia pastoris naturally lives on trees and can utilize different carbon sources, among them glucose, glycerol, and methanol. In biotechnology, it is widely used for the production of recombinant proteins. For both the understanding of life in its natural habitat and optimized production processes, a better understanding of cell physiology at an extremely low growth rate would be of extraordinary value. Therefore, we have grown P. pastoris in a retentostat, which allows the cultivation of metabolically active cells even at zero growth. Here we reached doubling times as long as 38 days and found that P. pastoris decreases its maintenance energy demand 3-fold during very slow growth, which enables it to survive with a much lower substrate supply than baker's yeast.
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Landes N, Gasser B, Vorauer-Uhl K, Lhota G, Mattanovich D, Maurer M. The vitamin-sensitive promoter PTHI11enables pre-defined autonomous induction of recombinant protein production inPichia pastoris. Biotechnol Bioeng 2016; 113:2633-2643. [DOI: 10.1002/bit.26041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Nils Landes
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Brigitte Gasser
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Karola Vorauer-Uhl
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
| | - Gabriele Lhota
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
| | - Diethard Mattanovich
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Michael Maurer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
- School of Bioengineering; University of Applied Sciences; FH Campus Vienna Austria
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A step forward to improve recombinant protein production in Pichia pastoris : From specific growth rate effect on protein secretion to carbon-starving conditions as advanced strategy. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Yang Y, Chen F, Wan D, Liu Y, Yang L, Feng H, Cui X, Gao X, Song H. Expression and Characterization of a Potent Long-Acting GLP-1 Receptor Agonist, GLP-1-IgG2σ-Fc. PLoS One 2016; 11:e0156449. [PMID: 27232339 PMCID: PMC4883776 DOI: 10.1371/journal.pone.0156449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/13/2016] [Indexed: 01/13/2023] Open
Abstract
Human GLP-1 (glucagon-like peptide-1) can produce a remarkable improvement in glycemic control in patients with type 2 diabetes. However, its clinical benefits are limited by its short half-life, which is less than 2 min because of its small size and rapid enzymatic inactivation by dipeptidyl peptidase IV. We engineered GLP-1-IgG2σ-Fc, a 68-kDa fusion protein linking a variant human GLP-1 (A8G/G26E/R36G) to a human IgG2σ constant heavy-chain. A stably transfected Chinese hamster ovary cell line was obtained using electroporation. Western blotting showed that the expressed protein was immunoreactive to both GLP-1 and IgG antibodies. GLP-1-IgG2σ-Fc stimulated insulin secretion from INS-1 cells in a dose- and glucose-dependent manner and increased insulin mRNA expression. The half-life of GLP-1-IgG2σ-Fc in cynomolgus monkeys was approximately 57.1 ± 4.5 h. In the KKAy mouse model of diabetes, one intraperitoneal injection of GLP-1-IgG2σ-Fc (1 mg/kg) reduced blood glucose levels for 5 days. A 4-week repeat-administration study identified sustained effects on blood glucose levels. Oral glucose tolerance tests conducted at the beginning and end of this 4-week period showed that GLP-1-IgG2σ-Fc produced a stable glucose lowering effect. In addition, KKAy mice treated with GLP-1-IgG2σ-Fc showed statistically significant weight loss from day 23. In conclusion, these properties of GLP-1-IgG2σ-Fc demonstrated that it represented a potential long-acting GLP-1 receptor agonist for the treatment of type 2 diabetes.
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Affiliation(s)
- Yi Yang
- Anhui Medical University, Hefei, Anhui, China
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Fang Chen
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Deyou Wan
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Yunhui Liu
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Li Yang
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Hongru Feng
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Xinling Cui
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
| | - Xin Gao
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (HS); (XG)
| | - Haifeng Song
- Anhui Medical University, Hefei, Anhui, China
- Research Center of Pharmacokinetics, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (HS); (XG)
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de Ruijter JC, Koskela EV, Frey AD. Enhancing antibody folding and secretion by tailoring the Saccharomyces cerevisiae endoplasmic reticulum. Microb Cell Fact 2016; 15:87. [PMID: 27216259 PMCID: PMC4878073 DOI: 10.1186/s12934-016-0488-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 05/11/2016] [Indexed: 01/20/2023] Open
Abstract
Background The yeast Saccharomyces cerevisiae provides intriguing possibilities for synthetic biology and bioprocess applications, but its use is still constrained by cellular characteristics that limit the product yields. Considering the production of advanced biopharmaceuticals, a major hindrance lies in the yeast endoplasmic reticulum (ER), as it is not equipped for efficient and large scale folding of complex proteins, such as human antibodies. Results Following the example of professional secretory cells, we show that inducing an ER expansion in yeast by deleting the lipid-regulator gene OPI1 can improve the secretion capacity of full-length antibodies up to fourfold. Based on wild-type and ER-enlarged yeast strains, we conducted a screening of a folding factor overexpression library to identify proteins and their expression levels that enhance the secretion of antibodies. Out of six genes tested, addition of the peptidyl-prolyl isomerase CPR5 provided the most beneficial effect on specific product yield while PDI1, ERO1, KAR2, LHS1 and SIL1 had a mild or even negative effect to antibody secretion efficiency. Combining genes for ER enhancement did not induce any significant additional effect compared to addition of just one element. By combining the Δopi1 strain, with the enlarged ER, with CPR5 overexpression, we were able to boost the specific antibody product yield by a factor of 10 relative to the non-engineered strain. Conclusions Engineering protein folding in vivo is a major task for biopharmaceuticals production in yeast and needs to be optimized at several levels. By rational strain design and high-throughput screening applications we were able to increase the specific secreted antibody yields of S. cerevisiae up to 10-fold, providing a promising strain for further process optimization and platform development for antibody production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0488-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorg C de Ruijter
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Essi V Koskela
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Alexander D Frey
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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Saadatirad A, Sardari S, Kazemali M, Zarei N, Davami F, Barkhordari F, Adeli A, Mahboudi F. Expression of a novel chimeric-truncated tPA in Pichia pastoris with improved biochemical properties. Mol Biotechnol 2016; 56:1143-50. [PMID: 25143123 DOI: 10.1007/s12033-014-9794-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombolytic therapy by plasminogen activators (PAs) has been a main goal in the treatment of acute myocardial infarction. Despite improved outcomes of currently available thrombolytic therapies, all these agents have different drawbacks that may result in less than optimal outcomes. In order to make tissue plasminogen activator (tPA) more potent, while being more resistant to plasminogen activator inhibitor-1 (PAI-1) and having a higher affinity to fibrin, a new chimeric-truncated form of tPA (CT tPA) was designed and expressed in Pichia pastoris. This novel variant consists of a finger domain of Desmoteplase, an epidermal growth factor (EGF) domain, a kringle 1 (K1) domain, a kringle 2 (K2) domain, in which the lysine binding site (LBS) was deleted, and a protease domain, where the four amino acids lysine 296, arginine 298, arginine 299, and arginine 304 were substituted by aspartic acid. The chimera CT tPA showed 14-fold increase in its activity in the presence of fibrin compared to the absence of fibrin. Furthermore, CT tPA showed about 10-fold more potency than commercially available full-length tPA (Actylase(®)) and provided 1.2-fold greater affinity to fibrin. A residual activity of only 68 % was observed after incubation of Actylase(®) with PAI-1, however, 91 % activity remained for CT tPA. These promising findings suggest that the novel CT tPA variant might be an acceptable PA with superior characteristics and properties.
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Affiliation(s)
- Amirhossein Saadatirad
- Biotechnology Research Center, Pasteur Institute of Iran (IPI), No. 69, Pasteur Avenue, Tehran, 1316943551, Iran
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Kunert R, Reinhart D. Advances in recombinant antibody manufacturing. Appl Microbiol Biotechnol 2016; 100:3451-61. [PMID: 26936774 PMCID: PMC4803805 DOI: 10.1007/s00253-016-7388-9] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 01/16/2023]
Abstract
Since the first use of Chinese hamster ovary (CHO) cells for recombinant protein expression, production processes have steadily improved through numerous advances. In this review, we have highlighted several key milestones that have contributed to the success of CHO cells from the beginning of their use for monoclonal antibody (mAb) expression until today. The main factors influencing the yield of a production process are the time to accumulate a desired amount of biomass, the process duration, and the specific productivity. By comparing maximum cell densities and specific growth rates of various expression systems, we have emphasized the limiting parameters of different cellular systems and comprehensively described scientific approaches and techniques to improve host cell lines. Besides the quantitative evaluation of current systems, the quality-determining properties of a host cell line, namely post-translational modifications, were analyzed and compared to naturally occurring polyclonal immunoglobulin fractions from human plasma. In summary, numerous different expression systems for mAbs are available and also under scientific investigation. However, CHO cells are the most frequently investigated cell lines and remain the workhorse for mAb production until today.
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Affiliation(s)
- Renate Kunert
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria.
| | - David Reinhart
- Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria
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Narasimhan Janakiraman V, Noubhani A, Venkataraman K, Vijayalakshmi M, Santarelli X. High yield of recombinant human Apolipoprotein A-I expressed in Pichia pastoris
by using mixed-mode chromatography. Biotechnol J 2015; 11:117-26. [DOI: 10.1002/biot.201500245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/19/2015] [Accepted: 11/25/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Vignesh Narasimhan Janakiraman
- IPB, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
- Univ. Bordeaux, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
- Centre for Bio-Separation Technology, VIT University; Vellore India
| | - Abdelmajid Noubhani
- IPB, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
- Univ. Bordeaux, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
| | | | | | - Xavier Santarelli
- IPB, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
- Univ. Bordeaux, Biotechnologie des Protéines Recombinantes à Visée Santé; Bordeaux France
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Irani ZA, Kerkhoven EJ, Shojaosadati SA, Nielsen J. Genome-scale metabolic model ofPichia pastoriswith native and humanized glycosylation of recombinant proteins. Biotechnol Bioeng 2015; 113:961-9. [DOI: 10.1002/bit.25863] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/21/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Zahra Azimzadeh Irani
- Biotechnology Group; Faculty of Chemical Engineering; Tarbiat Modares University; Tehran Iran
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology; Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
| | | | - Jens Nielsen
- Systems and Synthetic Biology; Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
- Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Hørsholm Denmark
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Maity N, Thawani A, Sharma A, Gautam A, Mishra S, Sahai V. Expression and Control of Codon-Optimized Granulocyte Colony-Stimulating Factor in Pichia pastoris. Appl Biochem Biotechnol 2015; 178:159-72. [PMID: 26410223 DOI: 10.1007/s12010-015-1865-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022]
Abstract
Granulocyte colony-stimulating factor (GCSF) has therapeutic applications due to its proven efficacy in different forms of neutropenia and chemotherapy-induced leucopenia. The original 564-bp nucleotide sequence from NCBI was codon optimized and assembled by overlapping PCR method comprising of 16 oligos of 50-nt length with 15 base overhang. The synthetic gene (CO-GCSF) was cloned under glucose utilizing glyceraldehyde 3-phosphate dehydrogenase (GAP) and methanol-utilizing alcohol oxidase (AOX1) promoters and expressed in Pichia pastoris SMD1168 strain. Constitutive expression under GAP resulted in cellular toxicity while AOX1 promoter controlled expression was stable. Variation in the levels of expression was observed among the transformant colonies with transformant #2 secreting up to ∼4 mg/L of GCSF. The molecular mass of the expressed GCSF in P. pastoris was ∼19.0 kDa. Quatitation of the expressed protein was carried out by a highly reproducible gel densitometric method. Effect of several operational and nutritional conditions was studied on GCSF production and the results suggest a general approach for increasing the yield of GCSF several folds (2- to 5-fold) over the standard conditions employed currently. Cultivation of the single-copy integrant in the chemically defined medium in a 5-L fermenter resulted in a volumetric productivity of ∼0.7 mg/L/h at the end of the induction phase, which was about 4-fold higher than attained in the shake flask.
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Affiliation(s)
- Nitu Maity
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ankita Thawani
- Lilly Hall of Biological Sciences, Purdue University - West Lafayette, Indiana, USA
| | - Anshul Sharma
- Biochemical Engineering Department, University College London, London, UK
| | - Ashwani Gautam
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Vikram Sahai
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Noncoding RNAs, post-transcriptional RNA operons and Chinese hamster ovary cells. ACTA ACUST UNITED AC 2015. [DOI: 10.4155/pbp.14.65] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
Current doctoral students who will be the driving force of science in the future. Christian Obinger, speaker of the BioToP Phd program "Biomolecular Technology of Proteins - BioToP", reviews the articles in this BioToP Special issue.
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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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Tscheliessnig A, Satzer P, Hammerschmidt N, Schulz H, Helk B, Jungbauer A. Ethanol precipitation for purification of recombinant antibodies. J Biotechnol 2014; 188:17-28. [DOI: 10.1016/j.jbiotec.2014.07.436] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/27/2014] [Accepted: 07/22/2014] [Indexed: 11/24/2022]
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Mallem M, Warburton S, Li F, Shandil I, Nylen A, Kim S, Jiang Y, Meehl M, d'Anjou M, Stadheim TA, Choi BK. Maximizing recombinant human serum albumin production in a MutsPichia pastorisstrain. Biotechnol Prog 2014; 30:1488-96. [DOI: 10.1002/btpr.1990] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/28/2014] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Fang Li
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Ishaan Shandil
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Adam Nylen
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Sehoon Kim
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Youwei Jiang
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Michael Meehl
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
| | - Marc d'Anjou
- GlycoFi, Biologics Discovery; Merck & Co., Inc. Lebanon NH
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Maccani A, Hackl M, Leitner C, Steinfellner W, Graf AB, Tatto NE, Karbiener M, Scheideler M, Grillari J, Mattanovich D, Kunert R, Borth N, Grabherr R, Ernst W. Identification of microRNAs specific for high producer CHO cell lines using steady-state cultivation. Appl Microbiol Biotechnol 2014; 98:7535-48. [PMID: 25052466 PMCID: PMC4139590 DOI: 10.1007/s00253-014-5911-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 01/06/2023]
Abstract
MicroRNAs are short non-coding RNAs that play an important role in the regulation of gene expression. Hence, microRNAs are considered as potential targets for engineering of Chinese hamster ovary (CHO) cells to improve recombinant protein production. Here, we analyzed and compared the microRNA expression patterns of high, low, and non-producing recombinant CHO cell lines expressing two structurally different model proteins in order to identify microRNAs that are involved in heterologous protein synthesis and secretion and thus might be promising targets for cell engineering to increase productivity. To generate reproducible and comparable data, the cells were cultivated in a bioreactor under steady-state conditions. Global microRNA expression analysis showed that mature microRNAs were predominantly upregulated in the producing cell lines compared to the non-producer. Several microRNAs were significantly differentially expressed between high and low producers, but none of them commonly for both model proteins. The identification of target messenger RNAs (mRNAs) is essential to understand the biological function of microRNAs. Therefore, we negatively correlated microRNA and global mRNA expression data and combined them with computationally predicted and experimentally validated targets. However, statistical analysis of the identified microRNA-mRNA interactions indicated a considerable false positive rate. Our results and the comparison to published data suggest that the reaction of CHO cells to the heterologous protein expression is strongly product- and/or clone-specific. In addition, this study highlights the urgent need for reliable CHO-specific microRNA target prediction tools and experimentally validated target databases in order to facilitate functional analysis of high-throughput microRNA expression data in CHO cells.
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Affiliation(s)
- Andreas Maccani
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria,
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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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