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Bianchi G, Pessina A, Ami D, Signorelli S, de Divitiis M, Natalello A, Lotti M, Brambilla L, Brocca S, Mangiagalli M. Sustainable production of a biotechnologically relevant β-galactosidase in Escherichia coli cells using crude glycerol and cheese whey permeate. BIORESOURCE TECHNOLOGY 2024; 406:131063. [PMID: 38964512 DOI: 10.1016/j.biortech.2024.131063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024]
Abstract
Responsible use of natural resources and waste reduction are key concepts in bioeconomy. This study demonstrates that agro-food derived-biomasses from the Italian food industry, such as crude glycerol and cheese whey permeate (CWP), can be combined in a high-density fed-batch culture to produce a recombinant β-galactosidase from Marinomonas sp. ef1 (M-βGal). In a small-scale process (1.5 L) using 250 mL of crude glycerol and 300 mL of lactose-rich CWP, approximately 2000 kU of recombinant M-βGal were successfully produced along with 30 g of galactose accumulated in the culture medium. The purified M-βGal exhibited high hydrolysis efficiency in lactose-rich matrices, with hydrolysis yields of 82 % in skimmed milk at 4 °C and 94 % in CWP at 50 °C, highlighting its biotechnological potential. This approach demonstrates the effective use of crude glycerol and CWP in sustainable and cost-effective high-density Escherichia coli cultures, potentially applicable to recombinant production of various proteins.
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Affiliation(s)
- Greta Bianchi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Samuele Signorelli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
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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 2024:10.1007/s00449-024-03045-w. [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] [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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Sales‐Vallverdú A, Gasset A, Requena‐Moreno G, Valero F, Montesinos‐Seguí JL, Garcia‐Ortega X. Synergic kinetic and physiological control to improve the efficiency of Komagataella phaffii recombinant protein production bioprocesses. Microb Biotechnol 2024; 17:e14411. [PMID: 38376073 PMCID: PMC10877992 DOI: 10.1111/1751-7915.14411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/28/2023] [Accepted: 01/07/2024] [Indexed: 02/21/2024] Open
Abstract
The yeast Komagataella phaffii (Pichia pastoris) is currently considered a versatile and highly efficient host for recombinant protein production (RPP). Interestingly, the regulated application of specific stress factors as part of bioprocess engineering strategies has proven potential for increasing the production of recombinant products. This study aims to evaluate the impact of controlled oxygen-limiting conditions on the performance of K. phaffii bioprocesses for RPP in combination with the specific growth rate (μ) in fed-batch cultivations. In this work, Candida rugosa lipase 1 (Crl1) production, regulated by the constitutive GAP promoter, growing at different nominal μ (0.030, 0.065, 0.100 and 0.120 h-1 ) under both normoxic and hypoxic conditions in carbon-limiting fed-batch cultures is analysed. Hypoxic fermentations were controlled at a target respiratory quotient (RQ) of 1.4, with excellent performance, using an innovative automated control based on the stirring rate as the manipulated variable developed during this study. The results conclude that oxygen limitation positively affects bioprocess efficiency under all growing conditions compared. The shift from respiratory to respiro-fermentative metabolism increases bioprocess productivity by up to twofold for the specific growth rates evaluated. Moreover, the specific product generation rate (qp ) increases linearly with μ, regardless of oxygen availability. Furthermore, this hypoxic boosting effect was also observed in the production of Candida antarctica lipase B (CalB) and pro-Rhizopus oryzae lipase (proRol), thus proving the synergic effect of kinetic and physiological stress control. Finally, the Crl1 production scale-up was conducted successfully, confirming the strategy's scalability and the robustness of the results obtained at the bench-scale level.
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Affiliation(s)
- Albert Sales‐Vallverdú
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Arnau Gasset
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Guillermo Requena‐Moreno
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - José Luis Montesinos‐Seguí
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Xavier Garcia‐Ortega
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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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Bernat-Camps N, Ebner K, Schusterbauer V, Fischer JE, Nieto-Taype MA, Valero F, Glieder A, Garcia-Ortega X. Enabling growth-decoupled Komagataella phaffii recombinant protein production based on the methanol-free P DH promoter. Front Bioeng Biotechnol 2023; 11:1130583. [PMID: 37034257 PMCID: PMC10076887 DOI: 10.3389/fbioe.2023.1130583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
The current transition towards the circular bioeconomy requires a rational development of biorefineries to sustainably fulfill the present demands. The use of Komagataella phaffii (Pichia pastoris) can meet this challenge, since it has the capability to use crude glycerol as a carbon-source, a by-product from the biodiesel industry, while producing high- and low-added value products. Recombinant protein production (RPP) using K. phaffii has often been driven either by the methanol induced AOX1 promoter (PAOX1) and/or the constitutive GAP promoter (PGAP). In the last years, strong efforts have been focused on developing novel expression systems that expand the toolbox variety of K. phaffii to efficiently produce diverse proteins that requires different strategies. In this work, a study was conducted towards the development of methanol-free expression system based on a heat-shock gene promoter (PDH) using glycerol as sole carbon source. Using this promoter, the recombinant expression is strongly induced in carbon-starving conditions. The classical PGAP was used as a benchmark, taking for both strains the lipase B from Candida antarctica (CalB) as model protein. Titer of CalB expressed under PDH outperformed PGAP controlled expression in shake-flask cultivations when using a slow-release continuous feeding technology, confirming that PDH is induced under pseudo-starving conditions. This increase was also confirmed in fed-batch cultivations. Several optimization rounds were carried out for PDH under different feeding and osmolarity conditions. In all of them the PDH controlled process outperformed the PGAP one in regard to CalB titer. The best PDH approach reached 3.6-fold more specific productivity than PGAP fed-batch at low μ. Compared to the optimum approach for PGAP-based process, the best PDH fed-batch strategy resulted in 2.3-fold higher titer, while the specific productivity was very similar. To summarize, PDH is an inducible promoter that exhibited a non-coupled growth regulation showing high performance, which provides a methanol-free additional solution to the usual growth-coupled systems for RPP. Thus, this novel system emerges as a potential alternative for K. phaffii RPP bioprocess and for revaluing crude glycerol, promoting the transition towards a circular economy.
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Affiliation(s)
- Núria Bernat-Camps
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | | | | | - Miguel Angel Nieto-Taype
- 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
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | - Xavier Garcia-Ortega
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- *Correspondence: Xavier Garcia-Ortega,
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de Divitiis M, Ami D, Pessina A, Palmioli A, Sciandrone B, Airoldi C, Regonesi ME, Brambilla L, Lotti M, Natalello A, Brocca S, Mangiagalli M. Cheese-whey permeate improves the fitness of Escherichia coli cells during recombinant protein production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:30. [PMID: 36823649 PMCID: PMC9948444 DOI: 10.1186/s13068-023-02281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Escherichia coli cells are the most frequently used hosts in recombinant protein production processes and mainly require molecules such as IPTG or pure lactose as inducers of heterologous expression. A possible way to reduce the production costs is to replace traditional inducers with waste materials such as cheese whey permeate (CWP). CWP is a secondary by-product generated from the production of the valuable whey proteins, which are obtained from ultrafiltration of cheese whey, a main by-product of the dairy industry, which is rich in lactose. RESULTS The effects of CWP collected from an Italian plant were compared with those of traditional inducers on the production of two model proteins (i.e., green fluorescent protein and the toxic Q55 variant of ataxin-3), in E. coli BL21 (DE3) cells. It was found that the high lactose content of CWP (165 g/L) and the antioxidant properties of its micronutrients (vitamins, cofactors and osmolytes) sustain production yields similar to those obtained with traditional inducers, accompanied by the improvement of cell fitness. CONCLUSIONS CWP has proven to be an effective and low-cost alternative inducer to produce recombinant proteins. Its use thus combines the advantage of exploiting a waste product with that of reducing the production costs of recombinant proteins.
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Affiliation(s)
- Marcella de Divitiis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Luca Brambilla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells. J Genet Eng Biotechnol 2022; 20:173. [PMID: 36580173 PMCID: PMC9800685 DOI: 10.1186/s43141-022-00455-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Low-temperature expression of recombinant proteins may be advantageous to support their proper folding and preserve bioactivity. The generation of expression vectors regulated under cold conditions can improve the expression of some target proteins that are difficult to express in different expression systems. The cspA encodes the major cold-shock protein from Escherichia coli (CspA). The promoter of cspA has been widely used to develop cold shock-inducible expression platforms in E. coli. Moreover, it is often necessary to employ expression systems other than bacteria, particularly when recombinant proteins require complex post-translational modifications. Currently, there are no commercial platforms available for expressing target genes by cold shock in eukaryotic cells. Consequently, genetic elements that respond to cold shock offer the possibility of developing novel cold-inducible expression platforms, particularly suitable for yeasts, and mammalian cells. CONCLUSIONS This review covers the importance of the cellular response to low temperatures and the prospective use of cold-sensitive promoters to direct the expression of recombinant proteins. This concept may contribute to renewing interest in applying white technologies to produce recombinant proteins that are difficult to express.
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Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins. FERMENTATION 2022. [DOI: 10.3390/fermentation8110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.
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