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Krappinger JC, Aguilar Gomez CM, Hoenikl A, Schusterbauer V, Hatzl AM, Feichtinger J, Glieder A. dMAD7 is a promising tool for targeted gene regulation in the methylotrophic yeast Komagataella phaffii. N Biotechnol 2024; 83:110-120. [PMID: 38960022 DOI: 10.1016/j.nbt.2024.06.008] [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: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The methylotrophic yeast Komagataella phaffii is a popular host system for the pharmaceutical and biotechnological production of recombinant proteins. CRISPR-Cas9 and its derivative CRISPR interference (CRISPRi) offer a promising avenue to further enhance and exploit the full capabilities of this host. MAD7 and its catalytically inactive variant "dead" MAD7 (dMAD7) represent an interesting alternative to established CRISPR-Cas9 systems and are free to use for industrial and academic research. CRISPRi utilizing dMAD7 does not introduce double-strand breaks but only binds to the DNA to regulate gene expression. Here, we report the first use of dMAD7 in K. phaffii to regulate the expression of the enhanced green fluorescent protein (eGFP). A reduction of eGFP fluorescence level (up to 88 %) was achieved in random integration experiments using dMAD7 plasmids. Integration loci/events of investigated strains were assessed through whole genome sequencing. Additionally, RNA-sequencing experiments corroborated the whole genome sequencing results and showed a significantly reduced expression of eGFP in strains containing a dMAD7 plasmid, among others. Our findings conclusively demonstrate the utility of dMAD7 in K. phaffii through successfully regulating eGFP expression.
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Affiliation(s)
- Julian C Krappinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Carla M Aguilar Gomez
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Andrea Hoenikl
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Anna-Maria Hatzl
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Julia Feichtinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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2
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Weiss F, Requena-Moreno G, Pichler C, Valero F, Glieder A, Garcia-Ortega X. Scalable protein production by Komagataella phaffii enabled by ARS plasmids and carbon source-based selection. Microb Cell Fact 2024; 23:116. [PMID: 38643119 PMCID: PMC11031860 DOI: 10.1186/s12934-024-02368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Most recombinant Komagataella phaffii (Pichia pastoris) strains for protein production are generated by genomic integration of expression cassettes. The clonal variability in gene copy numbers, integration loci and consequently product titers limit the aptitude for high throughput applications in drug discovery, enzyme engineering or most comparative analyses of genetic elements such as promoters or secretion signals. Circular episomal plasmids with an autonomously replicating sequence (ARS), an alternative which would alleviate some of these limitations, are inherently unstable in K. phaffii. Permanent selection pressure, mostly enabled by antibiotic resistance or auxotrophy markers, is crucial for plasmid maintenance and hardly scalable for production. The establishment and use of extrachromosomal ARS plasmids with key genes of the glycerol metabolism (glycerol kinase 1, GUT1, and triosephosphate isomerase 1, TPI1) as selection markers was investigated to obtain a system with high transformation rates that can be directly used for scalable production processes in lab scale bioreactors. RESULTS In micro-scale deep-well plate experiments, ARS plasmids employing the Ashbya gossypii TEF1 (transcription elongation factor 1) promoter to regulate transcription of the marker gene were found to deliver high transformation efficiencies and the best performances with the reporter protein (CalB, lipase B of Candida antarctica) for both, the GUT1- and TPI1-based, marker systems. The GUT1 marker-bearing strain surpassed the reference strain with integrated expression cassette by 46% upon re-evaluation in shake flask cultures regarding CalB production, while the TPI1 system was slightly less productive compared to the control. In 5 L bioreactor methanol-free fed-batch cultivations, the episomal production system employing the GUT1 marker led to 100% increased CalB activity in the culture supernatant compared to integration construct. CONCLUSIONS For the first time, a scalable and methanol-independent expression system for recombinant protein production for K. phaffii using episomal expression vectors was demonstrated. Expression of the GUT1 selection marker gene of the new ARS plasmids was refined by employing the TEF1 promoter of A. gossypii. Additionally, the antibiotic-free marker toolbox for K. phaffii was expanded by the TPI1 marker system, which proved to be similarly suited for the use in episomal plasmids as well as integrative expression constructs for the purpose of recombinant protein production.
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Affiliation(s)
- Florian Weiss
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Guillermo Requena-Moreno
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Carsten Pichler
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Francisco Valero
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria.
| | - Xavier Garcia-Ortega
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
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3
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Kastberg LLB, Petrov MS, Strucko T, Jensen MK, Workman CT. Codon-tRNA Coadaptation Bias for Identifying Strong Native Promoters in Komagataella phaffii. ACS Synth Biol 2024; 13:714-720. [PMID: 38381624 DOI: 10.1021/acssynbio.3c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Promoters are crucial elements for engineering microbial production strains used in bioprocesses. For the increasingly popular chassis Komagataella phaffii (formerly Pichia pastoris), a limited number of well-characterized promoters constrain the data-driven engineering of production strains. Here, we present an in silico approach for condition-independent de novo identification of strong native promoters. The method relies on tRNA-codon coadaptation of coding sequences in the K. phaffii genome and is based on two complementary scores: the number of effective codons and the tRNA adaptation index. Genes with high codon bias are expected to be translated efficiently and, thus, also be under control of strong promoters. Using this approach, we identified promising strong promoter candidates and experimentally assessed their activity using fluorescent reporter assays characterizing 50 promoters spanning a 76-fold difference in expression levels in a glucose medium. Overall, we report several promoters that should be added to the molecular toolbox for engineering of K. phaffii and present an approach for identifying promoters in microbial genomes.
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Affiliation(s)
- Louise La Barbera Kastberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, 2800 Kgs. Lyngby, Denmark
| | - Mykhaylo S Petrov
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, 2800 Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, 2800 Kgs. Lyngby, Denmark
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4
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Yen CC, Wu PY, Ou-Yang H, Chen HL, Chong KY, Chang RL, Chen CM. Production of Bioactive Porcine Lactoferrin through a Novel Glucose-Inducible Expression System in Pichia pastoris: Unveiling Antimicrobial and Anticancer Functionalities. Int J Mol Sci 2024; 25:1818. [PMID: 38339093 PMCID: PMC10855427 DOI: 10.3390/ijms25031818] [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: 12/19/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Lactoferrin (LF) stands as one of the extensively investigated iron-binding glycoproteins within milk, exhibiting diverse biological functionalities. The global demand for LF has experienced consistent growth. Biotechnological strategies aimed at enhancing LF productivity through microbial expression systems offer substantial cost-effective advantages and exhibit fewer constraints compared to traditional animal bioreactor technologies. This study devised a novel recombinant plasmid, wherein the AOX1 promoter was replaced with a glucose-inducible G1 promoter (PG1) to govern the expression of recombinant porcine LF (rpLF) in Pichia pastoris GS115. High-copy-number PG1-rpLF yeast clones were meticulously selected, and subsequent induction with 0.05 g/L glucose demonstrated robust secretion of rpLF. Scaling up production transpired in a 5 L fermenter, yielding an estimated rpLF productivity of approximately 2.8 g/L by the conclusion of glycerol-fed fermentation. A three-step purification process involving tangential-flow ultrafiltration yielded approximately 6.55 g of rpLF crude (approximately 85% purity). Notably, exceptional purity of rpLF was achieved through sequential heparin and size-exclusion column purification. Comparatively, the present glucose-inducible system outperformed our previous methanol-induced system, which yielded a level of 87 mg/L of extracellular rpLF secretion. Furthermore, yeast-produced rpLF demonstrated affinity for ferric ions (Fe3+) and exhibited growth inhibition against various pathogenic microbes (E. coli, S. aureus, and C. albicans) and human cancer cells (A549, MDA-MB-231, and Hep3B), similar to commercial bovine LF (bLF). Intriguingly, the hydrolysate of rpLF (rpLFH) manifested heightened antimicrobial and anticancer effects compared to its intact form. In conclusion, this study presents an efficient glucose-inducible yeast expression system for large-scale production and purification of active rpLF protein with the potential for veterinary or medical applications.
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Affiliation(s)
- Chih-Ching Yen
- Department of Internal Medicine, China Medical University Hospital, College of Health Care, China Medical University, Taichung 404, Taiwan;
- Department of Life Sciences, Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan; (P.-Y.W.); (H.O.-Y.)
| | - Pei-Ying Wu
- Department of Life Sciences, Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan; (P.-Y.W.); (H.O.-Y.)
| | - Huan Ou-Yang
- Department of Life Sciences, Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan; (P.-Y.W.); (H.O.-Y.)
| | - Hsiao-Ling Chen
- Department of Biomedical Science, Da-Yeh University, Changhua 515, Taiwan;
| | - Kowit-Yu Chong
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ro-Lin Chang
- Department of Life Sciences, Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan; (P.-Y.W.); (H.O.-Y.)
| | - Chuan-Mu Chen
- Department of Life Sciences, Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan; (P.-Y.W.); (H.O.-Y.)
- The iEGG and Animal Biotechnology Center, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
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5
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Schütz A, Bernhard F, Berrow N, Buyel JF, Ferreira-da-Silva F, Haustraete J, van den Heuvel J, Hoffmann JE, de Marco A, Peleg Y, Suppmann S, Unger T, Vanhoucke M, Witt S, Remans K. A concise guide to choosing suitable gene expression systems for recombinant protein production. STAR Protoc 2023; 4:102572. [PMID: 37917580 PMCID: PMC10643540 DOI: 10.1016/j.xpro.2023.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
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Affiliation(s)
- Anja Schütz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform for Protein Production & Characterization, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Goethe-University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Nick Berrow
- Protein Expression Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Johannes F Buyel
- Univeristy of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Muthgasse 18, 1190 Vienna, Austria
| | - Frederico Ferreira-da-Silva
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Jurgen Haustraete
- VIB, Center for Inflammation Research & Ugent, Department of Biomedical Molecular Biology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Joop van den Heuvel
- Helmholtz Centre for Infection Research (HZI), Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sabine Suppmann
- Protein Expression and Purification Core Facility, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tamar Unger
- Structural Proteomics Unit (SPU), Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martine Vanhoucke
- BCCM/GeneCorner Plasmid Collection, Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Gent, Belgium
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Notkestr. 85, 22607 Hamburg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Zha J, Liu D, Ren J, Liu Z, Wu X. Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories. J Fungi (Basel) 2023; 9:1027. [PMID: 37888283 PMCID: PMC10608127 DOI: 10.3390/jof9101027] [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: 08/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
| | | | | | | | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (D.L.); (J.R.); (Z.L.)
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7
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Incze DJ, Poppe L, Bata Z. Optimization Workflow of Fumonisin Esterase Production for Biocatalytic Degradation of Fumonisin B 1. Life (Basel) 2023; 13:1885. [PMID: 37763289 PMCID: PMC10533188 DOI: 10.3390/life13091885] [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: 08/13/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Industrial enzyme production with the Pichia pastoris expression system requires a well-characterized production strain and a competitively priced fermentation medium to meet the expectations of the industry. The present work shows a workflow that allows the rapid and reliable screening of transformants of single copy insertion of the target production cassette. A constitutive expression system with the glyceraldehyde-3-phosphate dehydrogenase promoter (pGAP) with homology arms for the glycerol kinase 1 (GUT1) was constructed for the targeted integration of the expression plasmid in a KU70 deficient Pichia pastoris and the production of a bacterial fumonisin esterase enzyme (CFE). A robust colony qPCR method was developed for the copy number estimation of the expression cassette. Optimization of the protein production medium and the scale-up ability was aided by design of experiments (DOE) approach resulting in optimized production conditions at a semi-industrial scale. A novel fermentation medium containing 3% inactivated yeast and 2% dextrose in an ammonium-citrate buffer (IYD) was shown to be a promising alternative to YPD media (containing yeast extract, peptone, and dextrose), as similar protein titers could be obtained, while the cost of the medium was reduced 20-fold. In a demonstration-scale 48 h long fed-batch fermentation, the IYD media outperformed the small-scale YPD cultivation by 471.5 ± 22.6%.
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Affiliation(s)
- Dániel János Incze
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem Rakpart 3, H-1111 Budapest, Hungary;
- Research and Development Laboratory, Dr. Bata Ltd., Bajcsy-Zsilinszky utca 139, H-2364 Ócsa, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem Rakpart 3, H-1111 Budapest, Hungary;
- Biocatalysis and Biotransformation Research Center, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University of Cluj-Napoca, Strada Arany János 11, RO-400028 Cluj-Napoca, Romania
| | - Zsófia Bata
- Research and Development Laboratory, Dr. Bata Ltd., Bajcsy-Zsilinszky utca 139, H-2364 Ócsa, Hungary
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8
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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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9
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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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10
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Efficient expression of heterologous protein by engineered Komagataella phaffii by harnessing a bioelectrical CO2 reduction system. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Schusterbauer V, Fischer JE, Gangl S, Schenzle L, Rinnofner C, Geier M, Sailer C, Glieder A, Thallinger GG. Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in Komagataella phaffii: A Budding Yeast in Distress. J Fungi (Basel) 2022; 8:jof8100992. [PMID: 36294556 PMCID: PMC9605565 DOI: 10.3390/jof8100992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies. We compared the outcomes of single target CRISPR transformations to double target experiments. Furthermore, we examined the extent of possible large deletions by targeting a large genomic region, which is likely to be non-essential. The analysis of on-target mutations showed an unexpectedly high number of large deletions and chromosomal rearrangements at the CRISPR target loci. We also observed an increase of on-target structural variants in double target experiments as compared to single target experiments. Targeting of two loci within a putatively non-essential region led to a truncation of chromosome 3 at the target locus in multiple cases, causing the deletion of 20 genes and several ribosomal DNA repeats. The identified de novo off-target mutations were rare and randomly distributed, with no apparent connection to unspecific CRISPR/Cas9 off-target binding sites.
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Affiliation(s)
- Veronika Schusterbauer
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
- Institute of Biomedical Imaging, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | | | - Sarah Gangl
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Lisa Schenzle
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | | | - Martina Geier
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Christian Sailer
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | - Anton Glieder
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Gerhard G. Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-873-5343
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Joseph J, Akkermans S, Van Impe JFM. Processing Method for the Quantification of Methanol and Ethanol from Bioreactor Samples Using Gas Chromatography-Flame Ionization Detection. ACS OMEGA 2022; 7:24121-24133. [PMID: 35874265 PMCID: PMC9301692 DOI: 10.1021/acsomega.2c00055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Methanol, a simple polar solvent, has been widely identified as an attractive carbon source to produce chemicals and fuels in bioprocesses. Specifically, to achieve recombinant protein production from methylotrophic yeasts, such as Pichia pastoris, this organic solvent can be used as a sole carbon source for growth and maintenance as well as an inducer for protein expression. However, if methanol feeding is not controlled well in such a fermentation process, accumulation of the solvent in the growth media will have a detrimental effect on the cells. Hence, monitoring the levels of methanol in these fermentation processes is a crucial step to ensure a healthy culture and maximum protein production. There are various techniques elaborated in the literature for monitoring methanol in cell cultures, but often, they appear to be expensive methods that are less affordable for many laboratories. This is because, in addition to the sophisticated equipment that is required for the analysis, the complexity of the samples retrieved from the bioprocesses necessitates laborious processing steps often involving expensive tools. In this study, a fast, simple, and sensitive method is developed to process biological samples by using the salting-out-assisted liquid-liquid extraction technique to quantify the concentration of methanol and ethanol using gas chromatography. On comparing the combinations of widely available salts and solvents, it was noticed that salting out using potassium carbonate followed by the liquid-liquid extraction of the analyte using ethyl acetate showed the best recovery. Followed by this, a validation test for the developed method was performed, which resulted in good peak resolution, linearity, and limit of detection for the quantitation of methanol and ethanol. By further assessing the tested combination, it was confirmed that its application could be extended to other matrices. Such an approach facilitates the possibility to monitor and control the methanol levels in fermentation and aids in bioprocess optimization.
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Kastberg LLB, Ard R, Jensen MK, Workman CT. Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:827704. [PMID: 37746199 PMCID: PMC10512257 DOI: 10.3389/ffunb.2022.827704] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.
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Affiliation(s)
| | - Ryan Ard
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T. Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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14
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Gasset A, Garcia-Ortega X, Garrigós-Martínez J, Valero F, Montesinos-Seguí JL. Innovative Bioprocess Strategies Combining Physiological Control and Strain Engineering of Pichia pastoris to Improve Recombinant Protein Production. Front Bioeng Biotechnol 2022; 10:818434. [PMID: 35155391 PMCID: PMC8826567 DOI: 10.3389/fbioe.2022.818434] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
The combination of strain and bioprocess engineering strategies should be considered to obtain the highest levels of recombinant protein production (RPP) while assuring product quality and process reproducibility of heterologous products. In this work, two complementary approaches were investigated to improve bioprocess efficiency based on the yeast P. pastoris. Firstly, the performance of two Candida rugosa lipase 1 producer clones with different gene dosage under the regulation of the constitutive PGAP were compared in chemostat cultures with different oxygen-limiting conditions. Secondly, hypoxic conditions in carbon-limited fed-batch cultures were applied by means of a physiological control based on the respiratory quotient (RQ). Stirring rate was selected to maintain RQ between 1.4 and 1.6, since it was found to be the most favorable in chemostat. As the major outcome, between 2-fold and 4-fold higher specific production rate (qP) values were observed when comparing multicopy clone (MCC) and single-copy clone (SCC), both in chemostat and fed-batch. Additionally, when applying oxygen limitation, between 1.5-fold and 3-fold higher qP values were obtained compared with normoxic conditions. Thus, notable increases of up to 9-fold in the production rates were reached. Furthermore, transcriptional analysis of certain key genes related to RPP and central carbon metabolism were performed. Results seem to indicate the presence of a limitation in post-transcriptional protein processing steps and a possible transcription attenuation of the target gene in the strains with high gene dosage. The entire approach, including both strain and bioprocess engineering, represents a relevant novelty involving physiological control in Pichia cell factory and is of crucial interest in bioprocess optimization, boosting RPP, allowing bioproducts to be economically competitive in the market, and helping develop the bioeconomy.
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Affiliation(s)
- Arnau Gasset
- 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
- QuBi Lab, Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Javier Garrigós-Martínez
- 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
- *Correspondence: Francisco Valero,
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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15
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Eto Y, Saubi N, Ferrer P, Joseph-Munné J. Expression of Chimeric HPV-HIV Protein L1P18 in Pichia pastoris; Purification and Characterization of the Virus-like Particles. Pharmaceutics 2021; 13:pharmaceutics13111967. [PMID: 34834382 PMCID: PMC8622379 DOI: 10.3390/pharmaceutics13111967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Currently, three human papillomavirus (HPV) vaccines are already licensed and all of them are based on virus-like particles (VLPs) of HPV L1 capsid protein but not worldwide accessible. While about 38.0 million people were living with HIV in 2019, only 68% of HIV-infected individuals were accessing antiretroviral therapy as of the end of June 2020 and there is no HIV vaccine yet. Therefore, safe, effective, and affordable vaccines against those two viruses are immediately needed. Both HPV and HIV are sexually transmitted infections and one of the main access routes is the mucosal genital tract. Thus, the development of a combined vaccine that would protect against HPV and HIV infections is a logical effort in the fight against these two major global pathogens. In this study, a recombinant Pichia pastoris producing chimeric HPV-HIV L1P18 protein intracellularly was constructed. After cell disruption, the supernatant was collected, and the VLPs were purified by a combination of ammonium sulfate precipitation, size exclusion chromatography, ultracentrifugation, and ultrafiltration. At the end of purification process, the chimeric VLPs were recovered with 96% purity and 9.23% overall yield, and the morphology of VLPs were confirmed by transmission electron microscopy. This work contributes towards the development of an alternative platform for production of a bivalent vaccine against HPV and HIV in P. pastoris.
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Affiliation(s)
- Yoshiki Eto
- Department of Microbiology, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (Y.E.); (N.S.)
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- AIDS Research Unit, Infectious Diseases Department, Hospital Clínic/IDIBAPS, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Narcís Saubi
- Department of Microbiology, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (Y.E.); (N.S.)
- Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- AIDS Research Unit, Infectious Diseases Department, Hospital Clínic/IDIBAPS, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Joan Joseph-Munné
- Department of Microbiology, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain; (Y.E.); (N.S.)
- Correspondence:
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Constitutive Expression in Komagataella phaffii of Mature Rhizopus oryzae Lipase Jointly with Its Truncated Prosequence Improves Production and the Biocatalyst Operational Stability. Catalysts 2021. [DOI: 10.3390/catal11101192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Rhizopus oryzae lipase (ROL) containing 28 C-terminal amino acids of the prosequence fused to the N-terminal mature sequence in ROL (proROL) was successfully expressed in the methylotrophic yeast Komagataella phaffii (Pichia pastoris) under the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (PGAP). Although the sequence encoding the mature lipase (rROL) was also transformed, no clones were obtained after three transformation cycles, which highlights the importance of the truncated prosequence to obtain viable transformed clones. Batch cultures of the K. phaffii strain constitutively expressing proROL scarcely influenced growth rate and exhibited a final activity and volumetric productivity more than six times higher than those obtained with proROL from K. phaffii under the methanol-inducible alcohol oxidase 1 promoter (PAOX1). The previous differences were less marked in fed-batch cultures. N-terminal analysis confirmed the presence of the 28 amino acids in proROL. In addition, immobilized proROL exhibited increased tolerance of organic solvents and an operational stability 0.25 and 3 times higher than that of immobilized rROL in biodiesel and ethyl butyrate production, respectively. Therefore, the truncated prosequence enables constitutive proROL production, boosts bioprocess performance and provides a more stable biocatalyst in two reactions in which lipases are mostly used at industrial level, esterification (ethyl butyrate) and transesterification (biodiesel).
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