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Coltman BL, Rebnegger C, Gasser B, Zanghellini J. Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii. Microb Biotechnol 2024; 17:e14386. [PMID: 38206275 PMCID: PMC10832545 DOI: 10.1111/1751-7915.14386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024] Open
Abstract
Retentostat cultivations have enabled investigations into substrate-limited near-zero growth for a number of microbes. Quantitative physiology at these near-zero growth conditions has been widely discussed, yet characterisation of the fluxome is relatively under-reported. We investigated the rewiring of metabolism in the transition of a recombinant protein-producing strain of Komagataella phaffii to glucose-limited near-zero growth rates. We used cultivation data from a 200-fold range of growth rates and comprehensive biomass composition data to integrate growth rate dependent biomass equations, generated using a number of different approaches, into a K. phaffii genome-scale metabolic model. Here, we show that a non-growth-associated maintenance value of 0.65 mmol ATP g CDW - 1 h - 1 and a growth-associated maintenance value of 108 mmol ATP g CDW - 1 lead to accurate growth rate predictions. In line with its role as energy source, metabolism is rewired to increase the yield of ATP per glucose. This includes a reduction of flux through the pentose phosphate pathway, and a greater utilisation of glycolysis and the TCA cycle. Interestingly, we observed activity of an external, non-proton translocating NADH dehydrogenase in addition to the malate-aspartate shuttle. Regardless of the method used for the generation of biomass equations, a similar, yet different, growth rate dependent rewiring was predicted. As expected, these differences between the different methods were clearer at higher growth rates, where the biomass equation provides a much greater constraint than at slower growth rates. When placed on an increasingly limited glucose diet, the metabolism of K. phaffii adapts, enabling it to continue to drive critical processes sustaining its high viability at near-zero growth rates.
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Affiliation(s)
- Benjamin Luke Coltman
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Corinna Rebnegger
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Brigitte Gasser
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyViennaAustria
- Department of Analytical ChemistryUniversity of ViennaViennaAustria
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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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3
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Targeted Deletion of Los1 Homologue Affects the Production of a Recombinant Model Protein in Pichia pastoris. IRANIAN BIOMEDICAL JOURNAL 2021; 25:255-64. [PMID: 33992037 PMCID: PMC8334395 DOI: 10.52547/ibj.25.4.255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: The methylotrophic yeast Pichia pastoris is an appealing production host for a variety of recombinant proteins, including biologics. In this sense, various genetic- and non-genetic-based techniques have been implemented to improve the production efficiency of this expression platform. Los1 (loss of supression) encodes a non-essential nuclear tRNA exporter in Saccharomyces cerevisiae, which its deletion extends RLS. Herein, a los1-deficient strain of P. pastoris was generated and characterized. Methods: A gene disruption cassette was prepared and transformed into an anti-CD22-expressing strain of P. pastoris. A δ los1 mutant was isolated and confirmed. The drug sensitivity of the mutant was also assessed. The growth pattern and the level of anti-CD22 ScFv expression were compared between the parent and mutant strains. Results: The los1 homologue was found to be a non-essential gene in P. pastoris. Furthermore, the susceptibility of los1 deletion strain to protein synthesis inhibitors was altered. This strain showed an approximately 1.85-fold increase in the extracellular level of anti-CD22 scFv (p < 0.05). The maximum concentrations of total proteins secreted by δ los1 and parent strains were 125 mg/L and 68 mg/L, respectively. Conclusion: The presented data suggest that the targeted disruption of los1 homologue in P. pastoris can result in a higher expression level of our target protein. Findings of this study may improve the current strategies used in optimizing the productivity of recombinant P. pastoris strains.
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Korpys-Woźniak P, Kubiak P, Białas W, Celińska E. Impact of overproduced heterologous protein characteristics on physiological response in Yarrowia lipolytica steady-state-maintained continuous cultures. Appl Microbiol Biotechnol 2020; 104:9785-9800. [PMID: 33025130 PMCID: PMC7595971 DOI: 10.1007/s00253-020-10937-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022]
Abstract
Overproduction of recombinant secretory proteins triggers numerous physiological perturbations. Depending on a given heterologous protein characteristics, the producer cell is faced with different challenges which lead to varying responses in terms of its physiology and the target protein production rate. In the present study, we used steady-state-maintained Yarrowia lipolytica cells to investigate the impact of different heterologous proteins on the physiological behavior of the host cells. Such an approach allowed to uncouple the impact of the overproduction of a particular protein from the phenomena that result from growth phase or are caused by the heterogeneity of the analyzed populations. Altogether, eight variants of recombinant strains, individually overproducing heterologous proteins of varying molecular weight (27-65 kDa) and reporting activity (enzymatic and fluorescent) were subjected to chemostat cultivations. The steady-state-maintained cells were analyzed in terms of the substrate utilization, biomass and metabolites production, as well as the reporter protein synthesis. Simplified distribution of carbon and nitrogen between the respective products, as well as expression analysis of the heterologous genes were conducted. The here-obtained data suggest that using a more transcriptionally active promoter results in channeling more C flux towards the target protein, giving significantly higher specific amounts and production rates of the target polypeptide, at the cost of biomass accumulation, and with no significant impact on the polyols production. The extent of the reporter protein's post-translational modifications, i.e., the number of disulfide bonds and glycosylation pattern, strongly impacts the synthesis process. Specific responses in terms of the protein formation kinetics, the gene expression levels, and transcript-to-protein linearity were observed.Key Points• Eight expression systems, producing different reporter proteins were analyzed.• The cells were maintained in steady-state by continuous chemostat culturing.• Protein- and promoter-specific effects were observed.
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Affiliation(s)
- Paulina Korpys-Woźniak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
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Gautam A, Sahai V, Mishra S. Development of a dual specific growth rate-based fed-batch process for production of recombinant human granulocyte colony-stimulating factor in Pichia pastoris. Bioprocess Biosyst Eng 2020; 44:103-112. [PMID: 32808048 DOI: 10.1007/s00449-020-02427-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
A number of limitations exist for production of human granulocyte colony-stimulating factor (G-CSF) in Pichia pastoris. In this study, two different specific growth rates (0.015 h-1, 0.01 h-1) were used sequentially in the mixed substrate feeding period during methanol induction phase to enhance the G-CSF titer in the culture broth. Necessary parameters required for implementing the feeding strategy, such as specific product yield on biomass (YP/X) and maintenance coefficient (m) on glycerol, methanol, and sorbitol were estimated using continuous culture technique. Using this strategy, for the same volumetric productivity, about 20% increase in protein titer was achieved over that obtained from the run carried out at a single pre-set value of 0.015 h-1 alone. Thus, implementation of higher specific growth rate (0.015 h-1) set during initial stages of the methanol induction phase followed by a lower specific growth rate (0.01 h-1) helped in achieving increased protein titers.
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Affiliation(s)
- Ashwani Gautam
- Center for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz-Khas, New Delhi, 110016, India
| | - Vikram Sahai
- Care Pro Biosciences Pvt. Ltd., I - 059, Site 5, Kasna Ind Area, Gautam Buddh Nagar, Greater Noida, UP, 201308, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New Delhi, 110016, India.
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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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7
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Nieto-Taype MA, Garrigós-Martínez J, Sánchez-Farrando M, Valero F, Garcia-Ortega X, Montesinos-Seguí JL. Rationale-based selection of optimal operating strategies and gene dosage impact on recombinant protein production in Komagataella phaffii (Pichia pastoris). Microb Biotechnol 2019; 13:315-327. [PMID: 31657146 PMCID: PMC7017824 DOI: 10.1111/1751-7915.13498] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
Its features as a microbial and eukaryotic organism have turned Komagataella phaffii (Pichia pastoris) into an emerging cell factory for recombinant protein production (RPP). As a key step of the bioprocess development, this work aimed to demonstrate the importance of tailor designing the cultivation strategy according to the production kinetics of the cell factory. For this purpose, K. phaffii clones constitutively expressing (PGAP) Candida rugosa lipase 1 (Crl1) with different gene dosage were used as models in continuous and fed‐batch cultures. Production parameters were much greater with a multicopy clone (MCC) than with the single‐copy clone (SCC). Regarding production kinetics, the specific product generation rate (qP) increased linearly with increasing specific growth rate (µ) in SCC; by contrast, qP exhibited saturation in MCC. A transcriptional analysis in chemostat cultures suggested the presence of eventual post‐transcriptional bottlenecks in MCC. After the strain characterization, in order to fulfil overall development of the bioprocess, the performance of both clones was also evaluated in fed‐batch mode. Strikingly, different optimal strategies were determined for both models due to the different production kinetic patterns observed as a trade‐off for product titre, yields and productivity. The combined effect of gene dosage and adequate µ enables rational process development with a view to optimize K. phaffii RPP bioprocesses.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Garrigós-Martínez
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Sánchez-Farrando
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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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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9
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Conacher CG, García-Aparicio MP, Coetzee G, van Zyl WH, Gӧrgens JF. Scalable methanol-free production of recombinant glucuronoyl esterase in Pichia pastoris. BMC Res Notes 2019; 12:596. [PMID: 31533815 PMCID: PMC6751620 DOI: 10.1186/s13104-019-4638-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/11/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Glucuronoyl esterase (GE) is an emerging enzyme that improves fractionation of lignin-carbohydrate complexes. However, the commercial availability of GE is limited, which hinders the research of GE-based bioprocesses for its industrial application in lignocellulose biorefineries. This study evaluated a workable, cost-effective, and commercially scalable production strategy to improve the ease of GE-based research. This strategy consisted of a constitutive and methanol-free enzyme production step coupled with a two-step filtration process. The aim was to determine if this strategy can yield copious amounts of GE, by secretion into the extracellular medium with an acceptable purity that could allow its direct application. This approach was further validated for cellobiose dehydrogenase, another emerging lignocellulose degrading enzyme which is scarcely available at high cost. RESULTS The secreted recombinant enzymes were functionally produced in excess of levels previously reported for constitutive production (1489-2780 mg L-1), and were secreted at moderate to high percentages of the total extracellular protein (51-94%). The constant glycerol feed, implemented during fed-batch fermentation, lead to a decline in growth rate and plateaued productivity. Tangential flow ultrafiltration was used to concentrate cell-free enzyme extracts 5-6-fold, reaching enzyme activity levels (1020-202 U L-1) that could allow their direct application.
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Affiliation(s)
- C. G. Conacher
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - M. P. García-Aparicio
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
- Departments of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - G. Coetzee
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - W. H. van Zyl
- Departments of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - J. F. Gӧrgens
- Departments of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
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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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Peebo K, Neubauer P. Application of Continuous Culture Methods to Recombinant Protein Production in Microorganisms. Microorganisms 2018; 6:E56. [PMID: 29933583 PMCID: PMC6164559 DOI: 10.3390/microorganisms6030056] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/28/2018] [Accepted: 06/19/2018] [Indexed: 11/17/2022] Open
Abstract
Depending on the environmental conditions, cells adapt their metabolism and specific growth rate. Rearrangements occur on many different levels such as macromolecular composition, gene and protein expression, morphology and metabolic flux patterns. As the interplay of these processes also determines the output of a recombinant protein producing system, having control over specific growth rate of the culture is advantageous. Continuous culture methods were developed to grow cells in a constant environment and have been used for decades to study basic microbial physiology in a controlled and reproducible manner. Our review summarizes the uses of continuous cultures in cell physiology studies and process development, with a focus on recombinant protein-producing microorganisms.
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Affiliation(s)
- Karl Peebo
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618 Tallinn, Estonia.
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Peter Neubauer
- Department of Bioprocess Engineering, Technische Universität Berlin, Ackerstraβe 76, ACK24, D-13355 Berlin, Germany.
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12
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Valero F. Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review. Methods Mol Biol 2018; 1835:205-216. [PMID: 30109654 DOI: 10.1007/978-1-4939-8672-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.
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Affiliation(s)
- Francisco Valero
- Departament d'Enginyeria Química, Biològica i Ambiental. EE, Universitat Autònoma de Barcelona, Barcelona, Spain.
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13
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Stress Introduction Rate Alters the Benefit of AcrAB-TolC Efflux Pumps. J Bacteriol 2017; 200:JB.00525-17. [PMID: 29038251 DOI: 10.1128/jb.00525-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022] Open
Abstract
Stress tolerance studies are typically conducted in an all-or-none fashion. However, in realistic settings-such as in clinical or metabolic engineering applications-cells may encounter stresses at different rates. Therefore, how cells tolerate stress may depend on its rate of appearance. To address this, we studied how the rate of stress introduction affects bacterial stress tolerance by focusing on a key stress response mechanism. Efflux pumps, such as AcrAB-TolC of Escherichia coli, are membrane transporters well known for the ability to export a wide variety of substrates, including antibiotics, signaling molecules, and biofuels. Although efflux pumps improve stress tolerance, pump overexpression can result in a substantial fitness cost to the cells. We hypothesized that the ideal pump expression level would involve a rate-dependent trade-off between the benefit of pumps and the cost of their expression. To test this, we evaluated the benefit of the AcrAB-TolC pump under different rates of stress introduction, including a step, a fast ramp, and a gradual ramp. Using two chemically diverse stresses, the antibiotic chloramphenicol and the jet biofuel precursor pinene, we assessed the benefit provided by the pumps. A mathematical model describing these effects predicted the benefit as a function of the rate of stress introduction. Our findings demonstrate that as the rate of introduction is lowered, stress response mechanisms provide a disproportionate benefit to pump-containing strains, allowing cells to survive beyond the original inhibitory concentrations.IMPORTANCE Efflux pumps are ubiquitous in nature and provide stress tolerance in the cells of species ranging from bacteria to mammals. Understanding how pumps provide tolerance has far-reaching implications for diverse fields, from medicine to biotechnology. Here, we investigated how the rate of stressor appearance impacts tolerance. We focused on two distinct substrates of AcrAB-TolC efflux pumps, the antibiotic chloramphenicol and the biofuel precursor pinene. Interestingly, tolerance is highly dependent on the rate of stress introduction. Therefore, it is important to consider not only the total quantity of a stressor but also the rate at which it is applied. The implications of this work are significant because environments are rarely static; antibiotic concentrations change during dosing, and metabolic engineering processes change with time.
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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Zahrl RJ, Peña DA, Mattanovich D, Gasser B. Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res 2017; 17:4093073. [DOI: 10.1093/femsyr/fox068] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
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Ben Azoun S, Kallel H. Investigating the effect of carbon source on rabies virus glycoprotein production in Pichia pastoris by a transcriptomic approach. Microbiologyopen 2017; 6. [PMID: 28523730 PMCID: PMC5552951 DOI: 10.1002/mbo3.489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/14/2017] [Accepted: 03/23/2017] [Indexed: 11/11/2022] Open
Abstract
Several factors affect protein expression in Pichia pastoris, one among them is the carbon source. In this work, we studied the effect of this factor on the expression level of rabies virus glycoprotein (RABV-G) in two recombinant clones harboring seven copies of the gene of interest. The expression was driven either by the constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter or the inducible alcohol oxidase1 (AOX1) promoter. Clones were compared in terms of cell physiology and carbon source metabolism. The transcription levels of 16 key genes involved in the central metabolic pathway, the methanol catabolism, and the oxidative stress were investigated in both clones. Cell size, as a parameter reflecting cell physiological changes, was also monitored. Our results showed that when glucose was used as the sole carbon source, large cells were obtained. Transcript levels of the genes of the central metabolic pathway were also upregulated, whereas antioxidative gene transcript levels were low. By contrast, the use of methanol as a carbon source generated small cells and a shift in carbon metabolism toward the dissimilatory pathway by the upregulation of formaldehyde dehydrogenase gene and the downregulation of those of the central metabolic. These observations are in favor of the use of glucose to enhance the expression of RABV-G in P. pastoris.
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Affiliation(s)
- Safa Ben Azoun
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Biofermentation Unit, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Héla Kallel
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Biofermentation Unit, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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Effects of glycerol supply and specific growth rate on methanol-free production of CALB by P. pastoris: functional characterisation of a novel promoter. Appl Microbiol Biotechnol 2017; 101:3163-3176. [PMID: 28130631 PMCID: PMC5380701 DOI: 10.1007/s00253-017-8123-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/20/2022]
Abstract
As Pichia pastoris (syn. Komagataella sp.) yeast can secrete pure recombinant proteins at high rates, it is a desirable production system. The function of a novel synthetic variant of the AOX1 promoter was characterised comprehensively using a strain secreting Candida antarctica lipase B (CALB) as a model. A new time-saving approach was introduced to determine, in only one experiment, the hitherto unknown relationship between specific product formation rate (qp) and specific growth rate (μ). Tight control of recombinant protein formation was possible in the absence of methanol, while using glycerol as a sole carbon/energy source. CALB was not synthesised during batch cultivation in excess glycerol (>10 g l−1) and at a growth rate close to μmax (0.15 h−1). Between 0.017 and 0.115 h−1 in glycerol-limited fedbatch cultures, basal levels of qp > 0.4 mg g−1 h−1 CALB were reached, independent of the μ at which the culture grew. At μ > 0.04 h−1, an elevated qp occurred temporarily during the first 20 h after changing to fedbatch mode and decreased thereafter to basal. In order to accelerate the determination of the qp(μ) relationship (kinetics of product formation), the entire μ range was covered in a single fedbatch experiment. By linearly increasing and decreasing glycerol addition rates, μ values were repeatedly shifted from 0.004 to 0.074 h−1 and vice versa. Changes in qp were related to changes in μ. A rough estimation of μ range suitable for production was possible in a single fedbatch, thus significantly reducing the experimental input over previous approaches comprising several experiments.
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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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Puxbaum V, Gasser B, Mattanovich D. The bud tip is the cellular hot spot of protein secretion in yeasts. Appl Microbiol Biotechnol 2016; 100:8159-68. [PMID: 27338576 PMCID: PMC4989006 DOI: 10.1007/s00253-016-7674-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/22/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
Abstract
Yeasts are valuable hosts for recombinant protein production. Among them, Pichia pastoris is frequently used for production of secreted proteins, and much effort was made to improve the secretion efficiency of this expression platform. However, the knowledge on the secretion machinery is mainly based on studies in Saccharomyces cerevisiae. Therefore, it is of great interest for targeted improvement of the system to learn more about the secretion process in P. pastoris. Using human serum albumin, a protein which is produced in high quantities in P. pastoris, we show here the secretion pathway of this protein. During passage of the secretory route, the recombinant protein is mainly localized in the endoplasmic reticulum (ER) and in COPII vesicles, and is inherited to the daughter cell via the perinuclear ER. The final release to the cell exterior occurs at the bud, initiating at the bud tip and later spreading over the entire bud surface. The same polarized secretion pattern was observed for a recombinant antibody light chain and the native secretory protein Epx1 of P. pastoris. Clarifying the point of release of secretory proteins will have major impact on engineering the secretory pathway of P. pastoris and other budding yeasts.
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Affiliation(s)
- Verena Puxbaum
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB GmbH), 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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21
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Looser V, Bruhlmann B, Bumbak F, Stenger C, Costa M, Camattari A, Fotiadis D, Kovar K. Cultivation strategies to enhance productivity of Pichia pastoris: A review. Biotechnol Adv 2015; 33:1177-93. [DOI: 10.1016/j.biotechadv.2015.05.008] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
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Abstract
CONTEXT Most syndromes with benign primary excess of a hormone show positive coupling of hormone secretion to size or proliferation in the affected hormone secretory tissue. Syndromes that lack this coupling seem rare and have not been examined for unifying features among each other. EVIDENCE ACQUISITION Selected clinical and basic features were analyzed from original reports and reviews. We examined indices of excess secretion of a hormone and indices of size of secretory tissue within the following three syndromes, each suggestive of uncoupling between these two indices: familial hypocalciuric hypercalcemia, congenital diazoxide-resistant hyperinsulinism, and congenital primary hyperaldosteronism type III (with G151E mutation of the KCNJ5 gene). EVIDENCE SYNTHESIS Some unifying features among the three syndromes were different from features present among common tumors secreting the same hormone. The unifying and distinguishing features included: 1) expression of hormone excess as early as the first days of life; 2) normal size of tissue that oversecretes a hormone; 3) diffuse histologic expression in the hormonal tissue; 4) resistance to treatment by subtotal ablation of the hormone-secreting tissue; 5) causation by a germline mutation; 6) low potential of the same mutation to cause a tumor by somatic mutation; and 7) expression of the mutated molecule in a pathway between sensing of a serum metabolite and secretion of hormone regulating that metabolite. CONCLUSION Some shared clinical and basic features of uncoupling of secretion from size in a hormonal tissue characterize three uncommon states of hormone excess. These features differ importantly from features of common hormonal neoplasm of that tissue.
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Affiliation(s)
- Stephen J Marx
- Genetics and Endocrinology Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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Fed-batch operational strategies for recombinant Fab production with Pichia pastoris using the constitutive GAP promoter. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.07.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Liu Z, Hou J, Martínez JL, Petranovic D, Nielsen J. Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2013; 97:8955-62. [PMID: 23392765 DOI: 10.1007/s00253-013-4715-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 12/22/2022]
Abstract
With the increasing demand for biopharmaceutical proteins and industrial enzymes, it is necessary to optimize the production by microbial fermentation or cell cultures. Yeasts are well established for the production of a wide range of recombinant proteins, but there are also some limitations; e.g., metabolic and cellular stresses have a strong impact on recombinant protein production. In this work, we investigated the effect of the specific growth rate on the production of two different recombinant proteins. Our results show that human insulin precursor is produced in a growth-associated manner, whereas α-amylase tends to have a higher yield on substrate at low specific growth rates. Based on transcriptional analysis, we found that the difference in the production of the two proteins as function of the specific growth rate is mainly due to differences in endoplasmic reticulum processing, protein turnover, cell cycle, and global stress response. We also found that there is a shift at a specific growth rate of 0.1 h(-1) that influences protein production. Thus, for lower specific growth rates, the α-amylase and insulin precursor-producing strains present similar cell responses and phenotypes, whereas for higher specific growth rates, the two strains respond differently to changes in the specific growth rate.
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Affiliation(s)
- Zihe Liu
- Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
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Intracellular interactome of secreted antibody Fab fragment in Pichia pastoris reveals its routes of secretion and degradation. Appl Microbiol Biotechnol 2012; 93:2503-12. [DOI: 10.1007/s00253-012-3933-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/26/2012] [Accepted: 01/28/2012] [Indexed: 12/13/2022]
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