1
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Jaswal AS, Elangovan R, Mishra S. Optimization of dilution rate and mixed carbon feed for continuous production of recombinant plant sucrose:sucrose 1-fructosyltransferase in Komagataella phaffii. Bioprocess Biosyst Eng 2024; 47:1499-1514. [PMID: 38904715 DOI: 10.1007/s00449-024-03045-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
The trisaccharide 1-kestose, a major constituent of commercial fructooligosaccharide (FOS) formulations, shows a superior prebiotic effect compared to higher-chain FOS. The plant sucrose:sucrose 1-fructosyltransferases (1-SST) are extensively used for selective synthesis of lower chain FOS. In this study, enhanced recombinant (r) 1-SST production was achieved in Komagataella phaffii (formerly Pichia pastoris) containing three copies of a codon-optimized Festuca arundinacea 1-SST gene. R1-SST production reached 47 U/mL at the shake-flask level after a 96-h methanol induction phase. A chemostat-based strain characterization methodology was adopted to assess the influence of specific growth rate (µ) on cell-specific r1-SST productivity (Qp) and cell-specific oxygen uptake rate (Qo) under two different feeding strategies across dilution rates from 0.02 to 0.05 h-1. The methanol-sorbitol co-feeding strategy significantly reduced Qo by 46 ± 2.4% compared to methanol-only feeding without compromising r1-SST productivity. Based on the data, a dilution rate of 0.025 h-1 was applied for continuous cultivation of recombinant cells to achieve a sustained r1-SST productivity of 5000 ± 64.4 U/L/h for 15 days.
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Affiliation(s)
- Avijeet S Jaswal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India
| | - Ravikrishnan Elangovan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India.
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2
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Adame M, Vázquez H, Juárez-López D, Corzo G, Amezcua M, López D, González Z, Schcolnik-Cabrera A, Morales-Martínez A, Villegas E. Expression and characterization of scFv-6009FV in Pichia pastoris with improved ability to neutralize the neurotoxin Cn2 from Centruroides noxius. Int J Biol Macromol 2024; 275:133461. [PMID: 38945343 DOI: 10.1016/j.ijbiomac.2024.133461] [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: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Small single-chain variable fragments (scFv) are promising biomolecules to inhibit and neutralize toxins and to act as antivenoms. In this work, we aimed to produce a functional scFv-6009FV in the yeast Pichia pastoris, which inhibits the pure Cn2 neurotoxin and the whole venom of Centruroides noxius. We were able to achieve yields of up to 31.6 ± 2 mg/L in flasks. Furthermore, the protein showed a structure of 6.1 % α-helix, 49.1 % β-sheet, and 44.8 % of random coil by CD. Mass spectrometry confirmed the amino acid sequence and showed no glycosylation profile for this molecule. Purified scFv-6009FV allowed us to develop anti-scFvs in rabbits, which were then used in affinity columns to purify other scFvs. Determination of its half-maximal inhibitory concentration value (IC50) was 40 % better than the scFvs produced by E. coli as a control. Finally, we found that scFv-6009FV was able to inhibit ex vivo the pure Cn2 toxin and the whole venom from C. noxius in murine rescue experiments. These results demonstrated that under the conditions assayed here, P. pastoris is suited to produce scFv-6009FV that, compared to scFvs produced by E. coli, maintains the characteristics of an antibody and neutralizes the Cn2 toxin more effectively.
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Affiliation(s)
- Mariel Adame
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hilda Vázquez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Juárez-López
- Instituto de Investigaciones Biomédicas, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mónica Amezcua
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Daniela López
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Zuriel González
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | - Adriana Morales-Martínez
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elba Villegas
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
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3
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Akentyev P, Sokolova D, Korzhenkov A, Gubaidullin I, Kozlov D. Expression level of SOR1 is a bottleneck for efficient sorbitol utilization by yeast Komagataella kurtzmanii. Yeast 2023; 40:414-424. [PMID: 37272406 DOI: 10.1002/yea.3884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023] Open
Abstract
The yeast strain Komagataella kurtzmanii VKPM Y-727 shows a significant defect in sorbitol utilization compared to closely related yeast K. phaffii (including strains formerly identified as Pichia pastoris). Our aim was to investigate the factors that determine the phenotype of the wild-type strain and to obtain a K. kurtzmanii strain with an improved ability to utilize sorbitol. We sequenced and annotated the genome of K. kurtzmanii VKPM Y-727 and compared it with that of K. phaffii GS115. Five K. phaffii GS115 genes that might be involved in sorbitol metabolism were selected and transferred into K. kurtzmanii Y-727. The transfer of the modified SOR1 gene resulted in an increased growth rate of K. kurtzmanii in sorbitol, despite the fact that Y-727 already contains its own SOR1 gene without any apparent mutations. The enzymes encoded by the SOR1 genes were analyzed in vitro and found to have similar properties. Differences in promoter activity were assessed using lacZ as a reporter gene, and the PSDH727 (promoter of SOR1 (SDH727) from K. kurtzmanii Y-727) promoter was shown to be 1.5-2.0 times weaker than PSDH115 (promoter of SOR1 (SDH115) from K. phaffii GS115). Moreover, both promoters were less active in K. kurtzmanii than in K. phaffii when evaluated in cells grown in synthetic complete media with glucose or sorbitol. Thus, SOR1 gene expression was identified as a bottleneck in sorbitol metabolism in K. kurtzmanii. Also, the positive effect of additional modified SOR1 gene copies was observed in both yeasts, as K. kurtzmanii and K. phaffii could grow on synthetic complete media with sorbitol three times faster than the original K. phaffii GS115 strain.
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Affiliation(s)
- Philipp Akentyev
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - Daria Sokolova
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | | | - Irek Gubaidullin
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | - Dmitry Kozlov
- National Research Center "Kurchatov Institute", Moscow, Russia
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4
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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.
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Affiliation(s)
- Pieter De Brabander
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Evelien Uitterhaegen
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Karel De Winter
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
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5
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Singh A, Narang A. PAOX1 expression in mixed-substrate continuous cultures of Komagataella phaffii (Pichia pastoris) is completely determined by methanol consumption regardless of the secondary carbon source. Front Bioeng Biotechnol 2023; 11:1123703. [PMID: 37091330 PMCID: PMC10113526 DOI: 10.3389/fbioe.2023.1123703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
The expression of recombinant proteins by the AOX1 promoter of Komagataella phaffii is typically induced by adding methanol to the cultivation medium. Since growth on methanol imposes a high oxygen demand, the medium is often supplemented with an additional secondary carbon source which serves to reduce the consumption of methanol, and hence, oxygen. Early research recommended the use of glycerol as the secondary carbon source, but more recent studies recommend the use of sorbitol because glycerol represses PAOX1 expression. To assess the validity of this recommendation, we measured the steady state concentrations of biomass, residual methanol, and LacZ expressed from PAOX1 over a wide range of dilution rates (0.02–0.20 h−1) in continuous cultures of the Mut+ strain fed with methanol + glycerol (repressing) and methanol + sorbitol (non-repressing). We find that under these conditions, the specific PAOX1 expression rate (measured as either specific LacZ productivity or specific AOX productivity) is completely determined by the specific methanol consumption rate regardless of the type (repressing/non-repressing) of the secondary carbon source. In both cultures, the specific PAOX1 expression rate is proportional to the specific methanol consumption rate, provided that the latter is below 0.15 g/(gdw-h); beyond this threshold consumption rate, the specific PAOX1 expression rate of both cultures saturates to the same value. Analysis of the data in the literature shows that the same phenomenon also occurs in continuous cultures of Escherichia coli fed with mixtures of lactose plus repressing/non-repressing carbon sources. The specific Plac expression rate is completely determined by the specific lactose consumption rate, regardless of the type of secondary carbon source, glycerol or glucose.
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6
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Heterologous protein expression enhancement of Komagataella phaffii by ammonium formate induction based on transcriptomic analysis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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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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8
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High level production of stable human serum albumin in Pichia pastoris and characterization of the recombinant product. Bioprocess Biosyst Eng 2022; 45:409-424. [PMID: 34999948 DOI: 10.1007/s00449-021-02670-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/21/2021] [Indexed: 12/19/2022]
Abstract
Human serum albumin (HSA) is an important therapeutic used in clinical settings for restoration of blood volume and treatment of chemotherapy induced neutropenia. Currently sourced from human serum, it carries the risk of contamination with viruses. The production of stable extracellular recombinant (r)HSA was achieved at nearly 1 g/L at shake-flask level in Pichia pastoris (syn. Komagataella phaffii) containing a three-copy containing HSA expression cassette, prepared in vitro. The HSA specific transcripts were increased by 1.82- to 2.46-fold in the three-copy containing clones indicating increased transcript levels to result in enhanced production of extracellular rHSA. The purified rHSA displayed secondary structure, zeta potential, size distribution and biological efficacy that matched with that of the commercial HSA. Cultivation strategy was developed at bioreactor level for the single HSA expression cassette containing recombinant which led to productivity of 300 mg/L/d of rHSA with minimum proteolytic cleavage.
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Ergün BG, Berrios J, Binay B, Fickers P. Recombinant protein production in Pichia pastoris: From transcriptionally redesigned strains to bioprocess optimization and metabolic modelling. FEMS Yeast Res 2021; 21:6424904. [PMID: 34755853 DOI: 10.1093/femsyr/foab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Pichia pastoris is one of the most widely used host for the production of recombinant proteins. Expression systems that rely mostly on promoters from genes encoding alcohol oxidase 1 or glyceraldehyde-3-phosphate dehydrogenase have been developed together with related bioreactor operation strategies based on carbon sources such as methanol, glycerol, or glucose. Although, these processes are relatively efficient and easy to use, there have been notable improvements over the last twenty years to better control gene expression from these promoters and their engineered variants. Methanol-free and more efficient protein production platforms have been developed by engineering promoters and transcription factors. The production window of P. pastoris has been also extended by using alternative feedstocks including ethanol, lactic acid, mannitol, sorbitol, sucrose, xylose, gluconate, formate, or rhamnose. Herein, the specific aspects that are emerging as key parameters for recombinant protein synthesis are discussed. For this purpose, a holistic approach has been considered to scrutinize protein production processes from strain design to bioprocess optimization, particularly focusing on promoter engineering, transcriptional circuitry redesign. This review also considers the optimization of bioprocess based on alternative carbon sources and derived co-feeding strategies. Optimization strategies for recombinant protein synthesis through metabolic modelling are also discussed.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey.,Department of Chemical Engineering, Middle East Technical University, 06800 Ankara, Turkey.,UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Patrick Fickers
- TERRA Teaching and Research Centre, University of Liege, Gembloux Agro-Bio Tech, Gembloux, Belgium
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10
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Liu H, Chen SL, Xu JZ, Zhang WG. Dual Regulation of Cytoplasm and Peroxisomes for Improved Α-Farnesene Production in Recombinant Pichia pastoris. ACS Synth Biol 2021; 10:1563-1573. [PMID: 34080850 DOI: 10.1021/acssynbio.1c00186] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microbial production of α-farnesene from renewable raw materials is a feasible alternative to traditional petroleum craft. Recently, the research on improving α-farnesene production in Pichia pastoris mainly focused on cytoplasmic engineering, while comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we first sought to confirm that the isopentenol utilization pathway (IUP) could act as a two-step shortcut for IPP synthesis in P. pastoris peroxisomes. In addition, we proposed dual regulation of cytoplasm and peroxisomes to boost α-farnesene synthesis in P. pastoris X33, thus the resultant strain produced 2.18 ± 0.04 g/L, which was 1.3 times and 2.1 times than that of the strain only with peroxisomal or cytoplasmic engineering, respectively. The α-farnesene production achieved 2.56 ± 0.04 g/L in shake flasks after carbon source cofeeding, which was the highest reported production in worldwide literatures to the best of my knowledge. Therefore, we propose these strategies as efficient approaches to enhancing α-farnesene production in P. pastoris, which might bring new ideas for the biosynthesis of high-value compounds.
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Affiliation(s)
- Hui Liu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, People’s Republic of China
| | - Sheng-Ling Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, People’s Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, People’s Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi 214122, People’s Republic of China
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11
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Filkin SY, Chertova NV, Vavilova EA, Zatsepin SS, Eldarov MA, Sadykhov EG, Fedorov AN, Lipkin AV. Optimization of the Production Method for Recombinant Chymosin in the Methylotrophic Yeast Komagataella phaffii. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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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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13
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Munro R, de Vlugt J, Ladizhansky V, Brown LS. Improved Protocol for the Production of the Low-Expression Eukaryotic Membrane Protein Human Aquaporin 2 in Pichia pastoris for Solid-State NMR. Biomolecules 2020; 10:biom10030434. [PMID: 32168846 PMCID: PMC7175339 DOI: 10.3390/biom10030434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/16/2022] Open
Abstract
Solid-state nuclear magnetic resonance (SSNMR) is a powerful biophysical technique for studies of membrane proteins; it requires the incorporation of isotopic labels into the sample. This is usually accomplished through over-expression of the protein of interest in a prokaryotic or eukaryotic host in minimal media, wherein all (or some) carbon and nitrogen sources are isotopically labeled. In order to obtain multi-dimensional NMR spectra with adequate signal-to-noise ratios suitable for in-depth analysis, one requires high yields of homogeneously structured protein. Some membrane proteins, such as human aquaporin 2 (hAQP2), exhibit poor expression, which can make producing a sample for SSNMR in an economic fashion extremely difficult, as growth in minimal media adds additional strain on expression hosts. We have developed an optimized growth protocol for eukaryotic membrane proteins in the methylotrophic yeast Pichia pastoris. Our new growth protocol uses the combination of sorbitol supplementation, higher cell density, and low temperature induction (LT-SEVIN), which increases the yield of full-length, isotopically labeled hAQP2 ten-fold. Combining mass spectrometry and SSNMR, we were able to determine the nature and the extent of post-translational modifications of the protein. The resultant protein can be functionally reconstituted into lipids and yields excellent resolution and spectral coverage when analyzed by two-dimensional SSNMR spectroscopy.
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Katla S, Pavan SS, Mohan N, Sivaprakasam S. Biocalorimetric monitoring of glycoengineered P. pastoris cultivation for the production of recombinant huIFNα2b: A quantitative study based on mixed feeding strategies. Biotechnol Prog 2020; 36:e2971. [PMID: 31990134 DOI: 10.1002/btpr.2971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 11/05/2022]
Abstract
Real-time monitoring of glycoengineered Pichia pastoris by employing process analytical technology (PAT) tools is vital for gaining deeper insights into the therapeutic protein production process. The present study focuses on influence of mixed feed carbon substrates during the induction phases of glycoengineered P. pastoris cultivation, for recombinant human interferon α2b (huIFNα2b) production by employing calorimetric (biological heat rate, q B ) and respirometric (oxygen uptake rate and carbon dioxide evolution rate) measurements. Mixed feed stream of carbon substrates (methanol + glycerol, methanol + sorbitol) at a predetermined "C-molar ratios" were added during the induction phases. Methanol- and sorbitol-based mixed feeding approach resulted in an improved huIFNα2b titer of 288 mg/L by channeling of methanol predominantly towards an optimal functioning of AOX expression system. A stand-off between biomass yield Y X S and biomass heat yield Y Q X coefficient, degree of reduction of methanol and its cosubstrate (glycerol and sorbitol) determines the fraction of carbon energy channeled toward biomass and protein production, under strict aerobic conditions. Calorespirometric monitoring and assessment of thermal yields enables a reliable prediction of process variables, leading to futuristic efficient PAT-based feed rate control.
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Affiliation(s)
- Srikanth Katla
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Satya Sai Pavan
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Naresh Mohan
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Senthilkumar Sivaprakasam
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Parekh M, Ali A, Ali Z, Bateson S, Abugchem F, Pybus L, Lennon C. Microbioreactor for lower cost and faster optimisation of protein production. Analyst 2020; 145:6148-6161. [DOI: 10.1039/d0an01266a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microbioreactor system, with inset the microbioreactor element, and an example cultivation growth profile showing dissolved oxygen, pH and dry cell weight.
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Affiliation(s)
- Mayur Parekh
- Healthcare Innovation Centre
- School of Health and Life Sciences
- Teesside University
- Middlesbrough
- UK
| | - AbdulAziz Ali
- Healthcare Innovation Centre
- School of Health and Life Sciences
- Teesside University
- Middlesbrough
- UK
| | - Zulfiqur Ali
- Healthcare Innovation Centre
- School of Health and Life Sciences
- Teesside University
- Middlesbrough
- UK
| | - Simon Bateson
- Healthcare Innovation Centre
- School of Health and Life Sciences
- Teesside University
- Middlesbrough
- UK
| | - Fathi Abugchem
- Healthcare Innovation Centre
- School of Health and Life Sciences
- Teesside University
- Middlesbrough
- UK
| | - Leon Pybus
- FUJIFILM Diosynth Biotechnologies
- Billingham
- UK
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16
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Prabhu AA, Kumar JP, Mandal BB, Veeranki VD. Glucose-methanol-based fed-batch fermentation for the production of recombinant human interferon gamma (rhIFN-γ) and evaluation of its antitumor potential. Biotechnol Appl Biochem 2019; 67:973-982. [PMID: 31811672 DOI: 10.1002/bab.1868] [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: 05/10/2019] [Accepted: 12/02/2019] [Indexed: 11/09/2022]
Abstract
Squamous cell carcinoma (SCC) is nonmelanoma skin cancer, which is very common in patients having T-cell immunosuppressant drugs. Anticancerous agents such as cytokines showed effective response on SCC. Human interferon-gamma (hIFN-γ), a type II cytokines, are having potent antiproliferative and immunomodulatory effects. In the current study, the fed-batch cultivation of recombinant Pichia pastoris was carried out, and its effect on cell biomass production, recombinant human interferon-gamma (rhIFN-γ) production, and the overflow metabolites was estimated. P. pastoris GS115 strain coexpressed with 6-phosphogluconolactonase (SOL3) and ribulose-phosphate 3-epimerase (RPE1) gene (GS115/rhIFN-γ/SR) resulted in 60 mg L-1 of rhIFN-γ production, which was twofold higher as compared with the production from GS115/rhIFN-γ strain. The antiproliferative potential of rhIFN-γ was examined on the human squamous carcinoma (A431) cell lines. Cells treated with 80 ng mL-1 of rhIFN-γ exhibited 50% growth inhibition by enhancing the production of intracellular reactive oxygen species levels and disrupting membrane integrity. Our findings highlight a state of art process development strategy for the high-level production of rhIFN-γ and its potential application as a therapeutic drug in SCC therapy.
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Affiliation(s)
- Ashish A Prabhu
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, India
| | - Jadi Praveen Kumar
- Biomaterial and Tissue Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, India
| | - Biman B Mandal
- Biomaterial and Tissue Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, India.,Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Venkata Dasu Veeranki
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam, India
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17
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High-level expression of Humicola insolens cutinase in Pichia pastoris without carbon starvation and its use in cotton fabric bioscouring. J Biotechnol 2019; 304:10-15. [DOI: 10.1016/j.jbiotec.2019.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 07/01/2019] [Accepted: 07/31/2019] [Indexed: 11/19/2022]
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18
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Wang B, Nesbeth D, Keshavarz-Moore E. Sorbitol/methanol mixed induction reduces process impurities and improves centrifugal dewatering in Pichia pastoris culture. Enzyme Microb Technol 2019; 130:109366. [PMID: 31421726 DOI: 10.1016/j.enzmictec.2019.109366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 11/25/2022]
Abstract
This study investigates how sorbitol/methanol mixed induction affects fermentation performance, dewatering characteristics of cells during harvesting and the profile of host cell proteins (HCP) in the process fluid when producing the target recombinant protein aprotinin. Compared to standard methanol induction, sorbitol/methanol (1:1, C-mol/C-mol) mixed induction improved cellular viability from 92.8 ± 0.3% to 97.7 ± 0.1% although resulted in a reduced product yield from 1.65 ± 0.03 g L-1 to 1.12 ± 0.07 g L-1. On the other hand, average oxygen consumption rate (OUR) dropped from 241.4 ± 21.3 mmol L-1 h-1 to 145.5 ± 6.7 mmol L-1 h-1. Cell diameter decreased over time in the mixed induction, resulting in a D50 value of 3.14 μm at harvest compared to 3.85 μm with methanol. The reduction in cell size enhanced the maximum dewatering efficiency from 78.1 ± 3.9% to 84.5 ± 3.3% as evaluated by using an established ultra scale-down methodology that models pilot and industrial scale disc stack centrifugation. Seventy host cell proteins (HCPs) were identified in clarified supernatant when using sorbitol/methanol mixed induction regimen. The total number of HCPs identified with standard methanol induction was nearly one hundred. The downstream process advantage of the mixed induction lies in improved product purity by reducing both cell mortality and level of released whole cell proteins. This needs to be balanced and optimised against the observed reduction in product yield during fermentation.
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Affiliation(s)
- Baolong Wang
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, Bernard Katz Building, London, WC1E 6BT, UK
| | - Darren Nesbeth
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, Bernard Katz Building, London, WC1E 6BT, UK
| | - Eli Keshavarz-Moore
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, Bernard Katz Building, London, WC1E 6BT, UK.
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Theron CW, Berrios J, Steels S, Telek S, Lecler R, Rodriguez C, Fickers P. Expression of recombinant enhanced green fluorescent protein provides insight into foreign gene‐expression differences betweenMut+andMutSstrains ofPichia pastoris. Yeast 2019; 36:285-296. [DOI: 10.1002/yea.3388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/04/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Chrispian W. Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | - Julio Berrios
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Sébastien Steels
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | - Samuel Telek
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | | | | | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
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20
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Velastegui E, Theron C, Berrios J, Fickers P. Downregulation by organic nitrogen of AOX1 promoter used for controlled expression of foreign genes in the yeast Pichia pastoris. Yeast 2019; 36:297-304. [PMID: 30699241 DOI: 10.1002/yea.3381] [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: 09/26/2018] [Revised: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 01/18/2023] Open
Abstract
Pichia pastoris is a well-established cell factory for recombinant protein synthesis. Various optimization strategies of processes based on AOX1 promoter have been investigated, including methanol co-feeding with glycerol or sorbitol during the induction stage. Compared with carbon sources, comparatively little research has been devoted to the effects of nitrogen sources. Several reports have described the benefits of adding casamino acids (CA) to the recombinant protein production medium, however, without considering its effects at the gene expression level. Using enhanced green fluorescent protein as a reporter protein, monitored using flow cytometry, CA was shown to downregulate AOX1 promoter induction. Despite higher growth rates, cultures containing CA exhibited slower transition to the induced state, whereas metabolite analysis revealed that methanol consumption was reduced in the presence of CA compared with its absence. The repressive effect of CA was further confirmed by analysing the synthesis of extracellular recombinant Candida antarctica lipase under control of the AOX1 promoter. These findings highlight nitrogen source selection as an important consideration for AOX1-based protein production.
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Affiliation(s)
- Edgar Velastegui
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Chrispian Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Julio Berrios
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
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Liu WC, Inwood S, Gong T, Sharma A, Yu LY, Zhu P. Fed-batch high-cell-density fermentation strategies for Pichia pastoris growth and production. Crit Rev Biotechnol 2019; 39:258-271. [DOI: 10.1080/07388551.2018.1554620] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Wan-Cang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, U.S.A
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing, P. R. China
| | - Sarah Inwood
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, U.S.A
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ashish Sharma
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, U.S.A
| | - Li-Yan Yu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing, P. R. China
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
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22
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Transcriptome and metabolome analyses reveal global behaviour of a genetically engineered methanol-independent Pichia pastoris strain. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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23
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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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24
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Azadi S, Sadjady SK, Mortazavi SA, Naghdi N, Mahboubi A, Solaimanian R. Bioprocess and downstream optimization of recombinant human growth hormone in Pichia pastoris. Res Pharm Sci 2018; 13:222-238. [PMID: 29853932 PMCID: PMC5921403 DOI: 10.4103/1735-5362.228953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris is a well-established expression host, which is often used in the production of protein pharmaceuticals. This work aimed to evaluate the effect of various concentrations of ascorbic acid in mixed feeding strategy with sorbitol/methanol on productivity of recombinant human growth hormone (r-hGH). The relevant concentration of ascorbic acid (5, 10, or 20 mmol) and 50 g/L sorbitol were added in batch-wise mode to the medium at the beginning of induction phase. The rate of methanol addition was increased stepwise during the first 12 h of production and then kept constant. Total protein and r-hGH concentrations were analyzed and the results compared with sorbitol/methanol feeding using one-way analysis of variance. Moreover, an effective clarification process using activated carbon was developed to remove process contaminants like pigments and endotoxins. Finally, a three-step chromatographic process was applied to purify the product. According to the obtained results, addition of 10 mmol ascorbic acid to sorbitol/methanol co-feeding could significantly increase cell biomass (1.7 fold), total protein (1.14 fold), and r-hGH concentration (1.43 fold). One percent activated carbon could significantly decrease pigments and endotoxins without any significant changes in r-hGH assay. The result of the study concluded that ascorbic acid in combination with sorbitol could effectively enhance the productivity of r-hGH. This study also demonstrated that activated carbon clarification is a simple method for efficient removal of endotoxin and pigment in production of recombinant protein in the yeast expression system.
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Affiliation(s)
- Saeed Azadi
- Pharmaceutical sciences research center, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | | | | | - Nasser Naghdi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Arash Mahboubi
- Food Safety Research Center, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Roya Solaimanian
- Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, I.R. Iran
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25
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Wang J, Wang X, Shi L, Zhang Y, Zhou X, Cai M. Reduced methanol input induces increased protein output by AOX1 promoter in a trans-acting elements engineered Pichia pastoris. ACTA ACUST UNITED AC 2018; 45:25-30. [DOI: 10.1007/s10295-017-1988-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
Abstract
High oxygen consumption and heat release caused by methanol catabolism usually bring difficulties to industrial scale-up and cost for protein expression driven by methanol-induced AOX1 promoter in Pichia pastoris. Here, reduced methanol feeding levels were investigated for expression of insulin precursor in a trans-acting elements engineered P. pastoris strain MF1-IP. Insulin precursor expression level reached 6.69 g/(L supernatant) at the methanol feeding rate of 6.67 mL/(h·L broth), which was 59% higher than that in the wild-type strain WT-IP at the methanol feeding rate of 12 mL/(h·L broth). Correspondingly, the insulin precursor expression level in fermentation broth and maximum specific insulin precursor production rate was 137 and 77% higher than the WT-IP, respectively. However, oxygen consumption and heat evolution were reduced, and the highest oxygen consumption rate and heat evolution rate of the MF1-IP were 18.0 and 37.7% lower than the WT-IP, respectively.
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Affiliation(s)
- Jinjia Wang
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Xiaolong Wang
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Lei Shi
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Yuanxing Zhang
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
- 0000 0001 2163 4895 grid.28056.39 School of Biotechnology East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
- Shanghai Collaborative Innovation Center for Biomanufacturing 130 Meilong Road 200237 Shanghai China
| | - Xiangshan Zhou
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
- 0000 0001 2163 4895 grid.28056.39 School of Biotechnology East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Menghao Cai
- 0000 0001 2163 4895 grid.28056.39 State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
- 0000 0001 2163 4895 grid.28056.39 School of Biotechnology East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
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26
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Theron CW, Berrios J, Delvigne F, Fickers P. Integrating metabolic modeling and population heterogeneity analysis into optimizing recombinant protein production by Komagataella (Pichia) pastoris. Appl Microbiol Biotechnol 2017; 102:63-80. [PMID: 29138907 DOI: 10.1007/s00253-017-8612-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 12/24/2022]
Abstract
The methylotrophic yeast Komagataella (Pichia) pastoris has become one of the most utilized cell factories for the production of recombinant proteins over the last three decades. This success story is linked to its specific physiological traits, i.e., the ability to grow at high cell density in inexpensive culture medium and to secrete proteins at high yield. Exploiting methanol metabolism is at the core of most P. pastoris-based processes but comes with its own challenges. Co-feeding cultures with glycerol/sorbitol and methanol is a promising approach, which can benefit from improved understanding and prediction of metabolic response. The development of profitable processes relies on the construction and selection of efficient producing strains from less efficient ones but also depends on the ability to master the bioreactor process itself. More specifically, how a bioreactor processes could be monitored and controlled to obtain high yield of production. In this review, new perspectives are detailed regarding a multi-faceted approach to recombinant protein production processes by P. pastoris; including gaining improved understanding of the metabolic pathways involved, accounting for variations in transcriptional and translational efficiency at the single cell level and efficient monitoring and control of methanol levels at the bioreactor level.
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Affiliation(s)
- Chrispian W Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium.
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27
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Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: A review. Biotechnol Adv 2017; 36:182-195. [PMID: 29129652 DOI: 10.1016/j.biotechadv.2017.11.002] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 11/24/2022]
Abstract
Pichia pastoris has been recognized as one of the most industrially important hosts for heterologous protein production. Despite its high protein productivity, the optimization of P. pastoris cultivation is still imperative due to strain- and product-specific challenges such as promoter strength, methanol utilization type and oxygen demand. To address the issues, strategies involving genetic and process engineering have been employed. Optimization of codon usage and gene dosage, as well as engineering of promoters, protein secretion pathways and methanol metabolic pathways have proved beneficial to innate protein expression levels. Large-scale production of proteins via high cell density fermentation additionally relies on the optimization of process parameters including methanol feed rate, induction temperature and specific growth rate. Recent progress related to the enhanced production of proteins in P. pastoris via various genetic engineering and cultivation strategies are reviewed. Insight into the regulation of the P. pastoris alcohol oxidase 1 (AOX1) promoter and the development of methanol-free systems are highlighted. Novel cultivation strategies such as mixed substrate feeding are discussed. Recent advances regarding substrate and product monitoring techniques are also summarized. Application of P. pastoris to the production of biodiesel and other value-added products via metabolic engineering are also reviewed. P. pastoris is becoming an indispensable platform through the use of these combined engineering strategies.
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28
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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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29
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Wang J, Lu L, Feng F. Combined strategies for improving production of a thermo-alkali stable laccase in Pichia pastoris. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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30
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Cankorur-Cetinkaya A, Dias JML, Kludas J, Slater NKH, Rousu J, Oliver SG, Dikicioglu D. CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology. MICROBIOLOGY-SGM 2017. [PMID: 28635591 PMCID: PMC5817226 DOI: 10.1099/mic.0.000477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners. In addition, the lack of subsidiary approaches to further investigate critical factors and their interactions prevents the full analysis and exploitation of the biotechnological system. We have addressed these problems and, here, provide a simple-to-use and freely available graphical user interface to empower a broad range of experimental biologists to employ complex evolutionary algorithms to optimize their experimental designs. Our approach exploits a Genetic Algorithm to discover the subspace containing the optimal combination of parameters, and Symbolic Regression to construct a model to evaluate the sensitivity of the experiment to each parameter under investigation. We demonstrate the utility of this method using an example in which the culture conditions for the microbial production of a bioactive human protein are optimized. CamOptimus is available through: (https://doi.org/10.17863/CAM.10257).
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Affiliation(s)
- Ayca Cankorur-Cetinkaya
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Joao M L Dias
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0QQ, UK
| | - Jana Kludas
- Helsinki Institute for Information Technology HIIT; Department of Computer Science, Aalto University, Konemiehentie 2, Espoo, FI-02150, Finland
| | - Nigel K H Slater
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Juho Rousu
- Helsinki Institute for Information Technology HIIT; Department of Computer Science, Aalto University, Konemiehentie 2, Espoo, FI-02150, Finland
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Duygu Dikicioglu
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.,Present address: Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
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Berrios J, Flores MO, Díaz-Barrera A, Altamirano C, Martínez I, Cabrera Z. A comparative study of glycerol and sorbitol as co-substrates in methanol-induced cultures of Pichia pastoris: temperature effect and scale-up simulation. ACTA ACUST UNITED AC 2017; 44:407-411. [DOI: 10.1007/s10295-016-1895-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/22/2016] [Indexed: 11/28/2022]
Abstract
Abstract
The production of recombinant proteins by Pichia pastoris under AOX1 promoter is usually performed using methanol together with either glycerol or sorbitol as co-substrate. Although both co-substrates have been widely used, comparative studies are scarce. In addition, these comparisons have been performed at different specific growth rate (µ) that it is well known that has an important effect on productivity. Thus, the effect of using these co-substrates on the production of Rhyzopus oryzae lipase (ROL) by P. pastoris was compared in continuous cultures growing at the same µ at either 22 or 30 °C. Results show that using glycerol as co-substrate led to higher volumetric productivities, and lower specific and volumetric methanol consumption rates. Scale-up simulation with 10–10,000 L bioreactor sizes indicated that glycerol produced the highest volumetric productivity of ROL with lower aeration requirements. Therefore, glycerol rises as a better option than sorbitol in ROL production.
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Affiliation(s)
- Julio Berrios
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
| | - María-Olga Flores
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
| | - Alvaro Díaz-Barrera
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
| | - Claudia Altamirano
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
| | - Irene Martínez
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
| | - Zaida Cabrera
- grid.8170.e 0000000115375962 School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso Av. Brasil 2085 Valparaíso Chile
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Azadi S, Mahboubi A, Naghdi N, Solaimanian R, Mortazavi SA. Evaluation of Sorbitol-Methanol Co-Feeding Strategy on Production of Recombinant Human Growth Hormone in Pichia Pastoris. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2017; 16:1555-1564. [PMID: 29552064 PMCID: PMC5843317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recombinant protein production in Pichia pastoris is based on alcohol oxidase promoters which are regulated by methanol. However, the use of methanol has several disadvantages, which is why current trends in bioprocess development with Pichia pastoris (P. pastoris) are focusing on methanol mixed feeding strategies. This work aimed to develop a new experimental method and compare the effect of various fractions of sorbitol in mixed feeding strategy with stepwise addition of methanol to maximize the productivity of human growth hormone. Accordingly, fed-batch culture performed with a mixed feed of sorbitol/methanol. Sorbitol at concentrations of 30, 40, 50 and 60 gram per liter was added in batch-wise mode to the medium at the beginning of induction phase and the rate of methanol addition was increased stepwise during the first 12 h of production and then kept constant. In order to understand the effects of various co-substrate feeding strategies on P. pastoris and its production of hGH, cell mass, dry cell weight, total protein, hGH expression level and hGH concentration were analyzed and the results compared with the basic feeding protocol using one-way analysis of variance (ANOVA). According to the obtained results, sorbitol at a concentration of 50 g/L could significantly increase the production yield. Under such optimal conditions cell biomass was 108 g/L (DCW), total protein was 0.807 g/L, expression level was 83.1% and rhGH concentration was 0.667 g/L following 30 h induction.
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Affiliation(s)
- Saeed Azadi
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Arash Mahboubi
- Food Safety Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nasser Naghdi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran.
| | - Roya Solaimanian
- Department of Pharmaceutics, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran.
| | - Seyyed Alireza Mortazavi
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Combined 13C-assisted metabolomics and metabolic flux analysis reveals the impacts of glutamate on the central metabolism of high β-galactosidase-producing Pichia pastoris. BIORESOUR BIOPROCESS 2016; 3:47. [PMID: 27867835 PMCID: PMC5093185 DOI: 10.1186/s40643-016-0124-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/26/2016] [Indexed: 01/01/2023] Open
Abstract
Background Pichia pastoris is a popular recombinant protein expression system for its accessibility of efficient gene manipulation and high protein production. Sufficient supply of precursors, energy, and redox cofactors is crucial for high recombinant protein production. In our present work, we found that the addition of glutamate improved the recombinant β-galactosidase (β-gal) production by P. pastoris G1HL. Methods To elucidate the impacts of glutamate on the central metabolism in detail, a combined 13C-assisted metabolomics and 13C metabolic flux analysis was conducted based on LC–MS/MS and GC–MS data. Results The pool sizes of intracellular amino acids were obviously higher on glucose/glutamate (Glc/Glu). The fluxes in EMP entry reaction and in downstream TCA cycle were 50 and 67% higher on Glc/Glu than on Glc, respectively. While the fluxes in upstream TCA cycle kept almost unaltered, the fluxes in PPP oxidative branch decreased. Conclusion The addition of glutamate leads to a remarkable change on the central metabolism of high β-galactosidase-producing P. pastoris G1HL. To meet the increased demands of redox cofactors and energy for higher β-galactosidase production on Glc/Glu, P. pastoris G1HL redistributes the fluxes in central metabolism through the inhibitions and/or activation of the enzymes in key nodes together with the energy and redox status. Electronic supplementary material The online version of this article (doi:10.1186/s40643-016-0124-6) contains supplementary material, which is available to authorized users.
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Sassi H, Delvigne F, Kar T, Nicaud JM, Coq AMCL, Steels S, Fickers P. Deciphering how LIP2 and POX2 promoters can optimally regulate recombinant protein production in the yeast Yarrowia lipolytica. Microb Cell Fact 2016; 15:159. [PMID: 27651221 PMCID: PMC5028966 DOI: 10.1186/s12934-016-0558-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 11/13/2022] Open
Abstract
Background In recent years, the non-conventional model yeast species Yarrowia lipolytica has received much attention because it is a useful cell factory for producing recombinant proteins. In this species, expression vectors involving LIP2 and POX2 promoters have been developed and used successfully for protein production at yields similar to or even higher than those of other cell factories, such as Pichia pastoris. However, production processes involving these promoters can be difficult to manage, especially if carried out at large scales in fed-batch bioreactors, because they require hydrophobic inducers, such as oleic acid or methyl oleate. Thus, the challenge has become to reduce loads of hydrophobic substrates while simultaneously promoting recombinant protein production. One possible solution is to replace a portion of the inducer with a co-substrate that can serve as an alternative energy source. However, implementing such an approach would require detailed knowledge of how carbon sources impact promoter regulation, which is surprisingly still lacking for the LIP2 and POX2 promoters. This study’s aim was thus to better characterize promoter regulation and cell metabolism in Y. lipolytica cultures grown in media supplemented with different carbon sources. Results pPOX2 induction could be detected when glucose or glycerol was used as sole carbon source, which meant these carbon source could not prevent promoter induction. In addition, when a mixture of glucose and oleic acid was used in complex medium, pPOX2 induction level was lower that that of pLIP2. In contrast, pLIP2 induction was absent when glucose was present in the culture medium, which meant that cell growth could occur without any recombinant gene expression. When a 40/60 mixture of glucose and oleic acid (w/w) was used, a tenfold increase in promoter induction, as compared to when an oleic-acid-only medium was observed. It was also clear that individual cells were adapting metabolically to use both glucose and oleic acid. Indeed, no distinct subpopulations that specialized on glucose versus oleic acid were observed; such an outcome would have led to producer and non-producer phenotypes. In medium containing both glucose and oleic acid, cells tended to directly metabolize oleic acid instead of storing it in lipid bodies. Conclusions This study found that pLIP2 is a promoter of choice as compared to pPOX2 to drive gene expression for recombinant protein production by Y. lipolytica used as cell factory. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0558-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hosni Sassi
- Biotechnology and Bioprocesses, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium
| | - Frank Delvigne
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Tambi Kar
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en Josas, France
| | - Sebastien Steels
- Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium
| | - Patrick Fickers
- Biotechnology and Bioprocesses, Université libre de Bruxelles, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium. .,Microbial Processes and Interactions, University of Liège-Gembloux AgroBio Tech, Passage des Déportés, 2, B-5030, Gembloux, Belgium.
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35
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Camattari A, Goh A, Yip LY, Tan AHM, Ng SW, Tran A, Liu G, Liachko I, Dunham MJ, Rancati G. Characterization of a panARS-based episomal vector in the methylotrophic yeast Pichia pastoris for recombinant protein production and synthetic biology applications. Microb Cell Fact 2016; 15:139. [PMID: 27515025 PMCID: PMC4981965 DOI: 10.1186/s12934-016-0540-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022] Open
Abstract
Background Recombinant protein production in the methylotrophic yeast Pichia pastoris largely relies on integrative vectors. Although the stability of integrated expression cassettes is well appreciated for most applications, the availability of reliable episomal vectors for this host would represent a useful tool to expedite cloning and high-throughput screening, ameliorating also the relatively high clonal variability reported in transformants from integrative vectors caused by off-target integration in the P. pastoris genome. Recently, heterologous and endogenous autonomously replicating sequences (ARS) were identified in P. pastoris by genome mining, opening the possibility of expanding the available toolbox to include efficient episomal plasmids. The aim of this technical report is to validate a 452-bp sequence (“panARS”) in context of P. pastoris expression vectors, and to compare their performance to classical integrative plasmids. Moreover, we aimed to test if such episomal vectors would be suitable to sustain in vivo recombination, using fragments for transformation, directly in P. pastoris cells. Results A panARS-based episomal vector was evaluated using blue fluorescent protein (BFP) as a reporter gene. Normalized fluorescence from colonies carrying panARS-BFP outperformed the level of signal obtained from integrative controls by several-fold, whereas endogenous sequences, identified from the P. pastoris genome, were not as efficient in terms of protein production. At the single cell level, panARS-BFP clones showed lower interclonal variability but higher intraclonal variation compared to their integrative counterparts, supporting the idea that heterologous protein production could benefit from episomal plasmids. Finally, efficiency of 2-fragment and 3-fragment in vivo recombination was tested using varying lengths of overlapping regions and molar ratios between fragments. Upon optimization, minimal background was obtained for in vivo assembled vectors, suggesting this could be a quick and efficient method to generate of episomal plasmids of interest. Conclusions An expression vector based on the panARS sequence was shown to outperform its integrative counterparts in terms of protein productivity and interclonal variability, facilitating recombinant protein expression and screening. Using optimized fragment lengths and ratios, it was possible to perform reliable in vivo recombination of fragments in P. pastoris. Taken together, these results support the applicability of panARS episomal vectors for synthetic biology approaches.
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Affiliation(s)
- Andrea Camattari
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
| | - Amelia Goh
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Lian Yee Yip
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Andy Hee Meng Tan
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Sze Wai Ng
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Anthony Tran
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
| | - Gaowen Liu
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Giulia Rancati
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
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Müller JM, Bruhn S, Flaschel E, Friehs K, Risse JM. GAP promoter-based fed-batch production of highly bioactive core streptavidin byPichia pastoris. Biotechnol Prog 2016; 32:855-64. [DOI: 10.1002/btpr.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jakob Michael Müller
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Simon Bruhn
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Erwin Flaschel
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Karl Friehs
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Joe Max Risse
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
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Carly F, Niu H, Delvigne F, Fickers P. Influence of methanol/sorbitol co-feeding rate on pAOX1 induction in a Pichia pastoris Mut+ strain in bioreactor with limited oxygen transfer rate. ACTA ACUST UNITED AC 2016; 43:517-23. [DOI: 10.1007/s10295-015-1722-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/11/2015] [Indexed: 11/28/2022]
Abstract
Abstract
High Pichia pastoris biomass density could be obtained using high co-feeding rate of methanol and sorbitol in a fed-batch or continuous culture, while further higher feeding rate finally leads to oxygen limitation in bioreactor. In the literature, there is lack of report about AOX1 promoter regulation with regard to dissolved oxygen level (DO). Therefore, in this work, chemostat cultures were performed to investigate the cell growth, metabolism and regulation of the AOX1 promoter (pAOX1) regarding co-feeding rate of optimized methanol/sorbitol mixture (methanol fraction 0.60 C-mol/C-mol) using a P. pastoris Mut+/pAOX1-lacZ strain. The oxygen transfer rates (OTR) in bioreactor were kept in the range of typical values of large bioreactor, i.e., 4–8 g/(L h) if DO equals 30 % saturation or 5–10 g/(L h) if DO nears zero. For DO >0, an increase of the carbon fed led to an increase of pAOX1 induction. By contrast, when dissolved oxygen was completely depleted, methanol accumulated, causing a 30 % decrease of pAOX1 induction. However, this decrease is more likely to be lined to methanol accumulation than to low level of dissolved oxygen (<4 % DO). Methanol/sorbitol co-feeding allowed cells to adapt to oxygen transient limitations that often occur at industrial scale with reduced effect on pAOX1 induction. The optimal feeding rate tested here was 6.6 mmol C (DCW h)−1 at an OTR of 8.28 g O2(L h)−1 with over fivefold pAOX1 induction (probably directly associated with target protein productivity) compared with previous work.
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Affiliation(s)
- F Carly
- grid.4989.c 0000000123480746 Unité de Biotechnologies et Bioprocédés Université libre de Bruxelles Av Roosevelt 52, CP152/51 1050 Brussels Belgium
| | - H Niu
- grid.7445.2 0000000121138111 Department of Chemical Engineering, Centre for Process Systems Engineering Imperial College London South Kensington Campus SW7 2AZ London England, UK
| | - F Delvigne
- grid.410510.1 0000000122979043 Microbial Processes and Interactions Université de Liège – Gembloux AgroBio Tech Passage des Déportés, 2 5030 Gembloux Belgium
| | - P Fickers
- grid.4989.c 0000000123480746 Unité de Biotechnologies et Bioprocédés Université libre de Bruxelles Av Roosevelt 52, CP152/51 1050 Brussels Belgium
- grid.410510.1 0000000122979043 Microbial Processes and Interactions Université de Liège – Gembloux AgroBio Tech Passage des Déportés, 2 5030 Gembloux Belgium
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Capone S, Horvat J, Herwig C, Spadiut O. Development of a mixed feed strategy for a recombinant Pichia pastoris strain producing with a de-repression promoter. Microb Cell Fact 2015; 14:101. [PMID: 26156850 PMCID: PMC4561368 DOI: 10.1186/s12934-015-0292-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/25/2015] [Indexed: 01/25/2023] Open
Abstract
Background Recombinant protein production in the yeast Pichia pastoris is usually based on the alcohol oxidase promoters pAOX1 and pAOX2, which are regulated by methanol and strongly repressed by other C-sources, like glycerol and glucose. However, the use of methanol brings several disadvantages, which is why current trends in bioprocess development with P. pastoris are focussing on minimizing the required amount of methanol or even avoid its employment. In this respect novel promoter systems which do not rely on methanol have been investigated and promoter variants were designed to fine-tune gene expression. Amongst these novel promoter systems, mutated AOX promoters, which are regulated by available carbon source concentration (so-called de-repressed promoters), are currently raising attention. However, the main disadvantage of such a production system is that expression and growth usually cannot happen concomitantly resulting in low space–time-yields. Results Here we show the development of a mixed-feed strategy for an industrial recombinant P. pastoris de-repression strain aiming at increased productivity and maximum space–time-yield. By doing dynamic experiments we determined a ratio between the specific substrate uptake rates of glycerol and sorbitol allowing a more than 2-fold increased productivity compared to the conventional single substrate de-repression strategy. Conclusion Based on our results we recommend adjusting qs glycerol = 0.04 g g−1 h−1 and qs sorbitol = 0.055 g g−1 h−1 to obtain highest productivity with a P. pastoris de-repression strain. Our methodological approach of designing mixed-feed strategies based on physiological strain characterization using dynamic experiments proved to be beneficial. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0292-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Capone
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Jernej Horvat
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Oliver Spadiut
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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High-Level Extracellular Production of Glucose Oxidase by Recombinant Pichia Pastoris Using a Combined Strategy. Appl Biochem Biotechnol 2014; 175:1429-47. [DOI: 10.1007/s12010-014-1387-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
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Enhanced production of Thermomyces lanuginosus lipase in Pichia pastoris via genetic and fermentation strategies. ACTA ACUST UNITED AC 2014; 41:1541-51. [DOI: 10.1007/s10295-014-1491-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/10/2014] [Indexed: 11/27/2022]
Abstract
Abstract
This study attempted to enhance the expression level of Thermomyces lanuginosus lipase (TLL) in Pichia pastoris using a series of strategies. The tll gene was first inserted into the expression vector pPIC9 K and transformed into P. pastoris strain GS115. The maximum hydrolytic activity of TLL reached 4,350 U/mL under the optimal culture conditions of a 500 mL shaking flask containing 20 mL culture medium with the addition of 1.2 % (w/v) methanol, cultivation for 144 h at pH 7.0 and 27 °C. To further increase the TLL expression and copy number, strains containing two plasmids were obtained by sequential electroporation into GS115/9k-TLL #3 with a second vector, either pGAPZαA-TLL, pFZα-TLL, or pPICZαA-TLL. The maximum activity of the resultant strains GS115/9KTLL-ZαATLL #40, GS115/9KTLL-FZαATLL #46 and GS115/9KTLL-GAPTLL #45 was 6,600 U/mL, 6,000 U/mL and 4,800 U/mL, respectively. The tll copy number in these strains, as assessed by real-time quantitative PCR, was demonstrated to be seven, five, and three, respectively, versus two copies in GS115/9k-TLL #3. When a co-feeding strategy of sorbitol/methanol was adopted in a 3-L fermenter, the maximum TLL activity of GS115/9k-TLL #3 increased to 27,000 U/mL after 130 h of fed-batch fermentation, whereas, the maximum TLL activity was 19,500 U/mL after 145 h incubation when methanol was used as the sole carbon source.
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Impacts of high β-galactosidase expression on central metabolism of recombinant Pichia pastoris GS115 using glucose as sole carbon source via (13)C metabolic flux analysis. J Biotechnol 2014; 187:124-34. [PMID: 25058396 DOI: 10.1016/j.jbiotec.2014.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/20/2014] [Accepted: 07/08/2014] [Indexed: 11/22/2022]
Abstract
The yeast Pichia pastoris GS115 is a widely used microbial cell factory for the production of heterologous protein. In order to reveal the impacts of high heterologous protein expression on the central metabolism of Pichia pastoris GS115 using glucose as sole carbon source, we engineered a high β-galactosidase expression strain P. pastoris G1HL and a low expression control strain P. pastoris GHL through controlling the initiation strength of constitutive promoter pGAP. The carbon flux distributions in these two strains were quantified via (13)C metabolic flux analysis. Compared to the control strain, G1HL showed a lower growth rate, a higher flux through glycolysis pathway, a higher flux through pentose phosphate pathway, and a lower flux through by-products secretion pathway. The metabolic flux redistribution in G1HL was thought to compensate the increased redox cofactors and energy demands caused by the high protein expression. Although the fluxes through Krebs cycle in two engineered strains were almost the same, they were significantly lower than those in wild strain. The enhanced expression of β-galactosidase by glutamate supplementation demonstrated the potential of P. pastoris GS115 to catabolize more carbon through the Krebs cycle for even higher protein expression. In conclusion, our work indicates that P. pastoris GS115 can readjusts the central metabolism for higher heterologous protein expression and provides strategies for strain development or process optimization for enhancing production of heterologous protein.
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Panula-Perälä J, Vasala A, Karhunen J, Ojamo H, Neubauer P, Mursula A. Small-scale slow glucose feed cultivation of Pichia pastoris without repression of AOX1 promoter: towards high throughput cultivations. Bioprocess Biosyst Eng 2013; 37:1261-9. [DOI: 10.1007/s00449-013-1098-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/15/2013] [Indexed: 01/24/2023]
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