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Ersöz F, İnan M. The combined effect of the gene copy number and chaperone overexpression on the recombinant bovine chymosin production in Pichia pastoris, with mutant ADH2 promoter. Protein Expr Purif 2025; 227:106636. [PMID: 39617310 DOI: 10.1016/j.pep.2024.106636] [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: 09/27/2024] [Revised: 11/15/2024] [Accepted: 11/28/2024] [Indexed: 12/06/2024]
Abstract
Chymosin is an enzyme used to coagulate milk, in the cheese industry. This study aimed to increase recombinant production of the chymosin in Pichia pastoris by determining the optimum copy number and overproduction of a Protein Disulfide Isomerase (PpPDI) chaperon protein. Bos taurus chymosin was expressed under the control of a mutant ADH2 promoter. The clones containing 1-4 gene copy numbers of the chymosin were constructed using the in vitro cloning method, and the effect of chaperone protein on chymosin secretion was investigated. The enzyme production levels are 4, 6.3, 4.5, and 3 IMCU/mL for 1, 2, 3, and 4-copy clones. The secreted chymosin levels increased up to two copies, and increasing the number of copies decreased the secretion level. Therefore, PpPDI was over-expressed in the clones regulated with the ADH2 promoter. The over-expression of PDI gene increased chymosin secretion in clones compared to the counterpart host. However, the highest chymosin level was obtained with C2 (2-copy chymosin containing clone; 6.3 IMCU/mL) and C2P2 (2-copy chymosin/2-copy PDI containing clone; 8.2 IMCU/mL). The maximum production was 39 IMCU/mL with the clone C2P2 in the fermenter scale production. The enzyme activity increased approximately 2-fold by adding two copies of the chaperone protein. The combined effect of gene copy number and chaperone overexpression on chymosin production was investigated. Two copies of the chymosin and PpPDI genes were the optimum among the tested clones.
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Affiliation(s)
- Fatma Ersöz
- Ardahan University, Engineering Faculty, Department of Food Engineering, Turkiye; Akdeniz University, Engineering Faculty, Department of Food Engineering, Turkiye.
| | - Mehmet İnan
- Akdeniz University, Engineering Faculty, Department of Food Engineering, Turkiye; İzmir Biomedicine and Genome Center, Turkiye
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2
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Villada-Troncoso SM, Arévalo-Romero JA, Hernández Rivera V, Pedraza-Escalona M, Pérez-Tapia SM, Espejo-Mojica AJ, Alméciga-Díaz CJ. Study of Potential Blocking Peptides Targeting the SARS-CoV-2 RBD/hACE2 Interaction. Pharmaceuticals (Basel) 2024; 17:1240. [PMID: 39338402 PMCID: PMC11435355 DOI: 10.3390/ph17091240] [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: 09/02/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND/OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, was declared a public health emergency in early 2020. The infection initiates when the receptor-binding domain (RBD) of the viral spike protein binds to human angiotensin-converting enzyme 2 (ACE2). Despite the success of vaccination efforts, the emergence of new variants highlights the ongoing need for treatments targeting these evolving strains. In silico methods previously identified peptides BP2, BP9, and BP11 as being capable of disrupting the RBD-ACE2 interaction, though their efficacy has not been experimentally validated until now. METHODS In this study, these peptides were recombinantly produced in the yeast Komagataella phaffii, and the activity was assessed in vitro using binding assays with multiple RBD variants and the inhibition of the RBD-ACE2 interaction. RESULTS The production yield for BP2, BP9, and BP11 was 14.34, 4.01, and 1.35 mg per culture liter, respectively. Noteworthy, the three BPs interacted with the RBD of SARS-CoV-2 variants of concern, with BP2 showing higher recognition. Finally, the BPs showed an RBD/hACE2 interaction blocking capacity with IC50 values between 1.03 and 5.35 nM, with BP2 showing the lowest values among the evaluated peptides. CONCLUSIONS These results demonstrate that BP2, specifically, is a promising candidate for the development of novel therapeutic interventions targeting SARS-CoV-2 and other coronaviruses that use hACE2 for cellular entry.
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Affiliation(s)
- Sara M. Villada-Troncoso
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
| | - Jenny Andrea Arévalo-Romero
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
- Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud—IDCBIS, Bogotá 111611, Colombia
| | - Vanessa Hernández Rivera
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico; (V.H.R.); (S.M.P.-T.)
| | - Martha Pedraza-Escalona
- CONAHCyT-Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico;
| | - Sonia M. Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico; (V.H.R.); (S.M.P.-T.)
| | - Angela Johana Espejo-Mojica
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
| | - Carlos Javier Alméciga-Díaz
- Institute for the Study in Inborn Errors of Metabolism—IEIM, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (S.M.V.-T.); (J.A.A.-R.); (A.J.E.-M.)
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Werin B, Hansson Wennersten W, Olsson R, Kołodziejczyk O, Andersson MN, Carlquist M, Johanson U. Evaluation of heterologous expression in Pichia pastoris of Pine Weevil TRPA1 by GFP and flow cytometry. Microb Cell Fact 2024; 23:110. [PMID: 38609906 PMCID: PMC11015645 DOI: 10.1186/s12934-024-02382-5] [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: 01/31/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND The wasabi receptor, also known as the Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel, is a potential target for development of repellents for insects, like the pine weevil (Hylobius abietis) feeding on conifer seedlings and causing damage in forestry. Heterologous expression of TRPA1 from pine weevil in the yeast Pichia pastoris can potentially provide protein for structural and functional studies. Here we take advantage of the Green Fluorescent Protein (GFP) tag to examine the various steps of heterologous expression, to get more insight in clone selection, expression and isolation of the intact purified protein. RESULTS The sequence of HaTRPA1 is reported and GFP-tagged constructs were made of the full-length protein and a truncated version (Δ1-708 HaTRPA1), lacking the N-terminal ankyrin repeat domain. Clones were screened on GFP expression plates, induced in small liquid cultures and in fed-batch cultures, and evaluated by flow cytometry and fluorescence microscopy. The screening on plates successfully identifies low-expression clones, but fails to predict the ranking of the best performing clones in small-scale liquid cultures. The two constructs differ in their cellular localization. Δ1-708 HaTRPA1 is found in a ring at the perimeter of cell, whereas HaTRPA1 is forming highly fluorescent speckles in interior regions of the cell. The pattern is consistent in different clones of the same construct and persists in fed-batch culture. The expression of Δ1-708 HaTRPA1 decreases the viability more than HaTRPA1, and in fed-batch culture it is clear that intact cells first express Δ1-708 HaTRPA1 and then become damaged. Purifications show that both constructs suffer from degradation of the expressed protein, but especially the HaTRPA1 construct. CONCLUSIONS The GFP tag makes it possible to follow expression by flow cytometry and fluorescence microscopy. Analyses of localization, cell viability and expression show that the former two parameters are specific for each of the two evaluated constructs, whereas the relative expression of the constructs varies with the cultivation method. High expression is not all that matters, so taking damaged cells into account, something that may be linked to protein degradation, is important when picking the most suitable construct, clone, and expression scheme.
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Affiliation(s)
- Balder Werin
- Center for Molecular Protein Science, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | | | - Robin Olsson
- Center for Molecular Protein Science, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Oliwia Kołodziejczyk
- Center for Molecular Protein Science, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | | | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Urban Johanson
- Center for Molecular Protein Science, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden.
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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [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: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Current achievements, strategies, obstacles, and overcoming the challenges of the protein engineering in Pichia pastoris expression system. World J Microbiol Biotechnol 2023; 40:39. [PMID: 38062216 DOI: 10.1007/s11274-023-03851-6] [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: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Yeasts serve as exceptional hosts in the manufacturing of functional protein engineering and possess industrial or medical utilities. Considerable focus has been directed towards yeast owing to its inherent benefits and recent advancements in this particular cellular host. The Pichia pastoris expression system is widely recognized as a prominent and widely accepted instrument in molecular biology for the purpose of generating recombinant proteins. The advantages of utilizing the P. pastoris system for protein production encompass the proper folding process occurring within the endoplasmic reticulum (ER), as well as the subsequent secretion mediated by Kex2 as a signal peptidase, ultimately leading to the release of recombinant proteins into the extracellular environment of the cell. In addition, within the P. pastoris expression system, the ease of purifying recombinant protein arises from its restricted synthesis of endogenous secretory proteins. Despite its achievements, scientists often encounter persistent challenges when attempting to utilize yeast for the production of recombinant proteins. This review is dedicated to discussing the current achievements in the usage of P. pastoris as an expression host. Furthermore, it sheds light on the strategies employed in the expression system and the optimization and development of the fermentative process of this yeast. Finally, the impediments (such as identifying high expression strains, improving secretion efficiency, and decreasing hyperglycosylation) and successful resolution of certain difficulties are put forth and deliberated upon in order to assist and promote the expression of complex proteins in this prevalent recombinant host.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
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Pan Y, Yang J, Wu J, Yang L, Fang H. Current advances of Pichia pastoris as cell factories for production of recombinant proteins. Front Microbiol 2022; 13:1059777. [PMID: 36504810 PMCID: PMC9730254 DOI: 10.3389/fmicb.2022.1059777] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Pichia pastoris (syn. Komagataella spp.) has attracted extensive attention as an efficient platform for recombinant protein (RP) production. For obtaining a higher protein titer, many researchers have put lots of effort into different areas and made some progress. Here, we summarized the most recent advances of the last 5 years to get a better understanding of its future direction of development. The appearance of innovative genetic tools and methodologies like the CRISPR/Cas9 gene-editing system eases the manipulation of gene expression systems and greatly improves the efficiency of exploring gene functions. The integration of novel pathways in microorganisms has raised more ideas of metabolic engineering for enhancing RP production. In addition, some new opportunities for the manufacture of proteins have been created by the application of novel mathematical models coupled with high-throughput screening to have a better overview of bottlenecks in the biosynthetic process.
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Affiliation(s)
- Yingjie Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiao Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianping Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lirong Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, Zhejiang, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi, China
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7
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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: 2.7] [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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8
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Buyel JF, Stöger E, Bortesi L. Targeted genome editing of plants and plant cells for biomanufacturing. Transgenic Res 2021; 30:401-426. [PMID: 33646510 PMCID: PMC8316201 DOI: 10.1007/s11248-021-00236-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Plants have provided humans with useful products since antiquity, but in the last 30 years they have also been developed as production platforms for small molecules and recombinant proteins. This initially niche area has blossomed with the growth of the global bioeconomy, and now includes chemical building blocks, polymers and renewable energy. All these applications can be described as "plant molecular farming" (PMF). Despite its potential to increase the sustainability of biologics manufacturing, PMF has yet to be embraced broadly by industry. This reflects a combination of regulatory uncertainty, limited information on process cost structures, and the absence of trained staff and suitable manufacturing capacity. However, the limited adaptation of plants and plant cells to the requirements of industry-scale manufacturing is an equally important hurdle. For example, the targeted genetic manipulation of yeast has been common practice since the 1980s, whereas reliable site-directed mutagenesis in most plants has only become available with the advent of CRISPR/Cas9 and similar genome editing technologies since around 2010. Here we summarize the applications of new genetic engineering technologies to improve plants as biomanufacturing platforms. We start by identifying current bottlenecks in manufacturing, then illustrate the progress that has already been made and discuss the potential for improvement at the molecular, cellular and organism levels. We discuss the effects of metabolic optimization, adaptation of the endomembrane system, modified glycosylation profiles, programmable growth and senescence, protease inactivation, and the expression of enzymes that promote biodegradation. We outline strategies to achieve these modifications by targeted gene modification, considering case-by-case examples of individual improvements and the combined modifications needed to generate a new general-purpose "chassis" for PMF.
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Affiliation(s)
- J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074, Aachen, Germany.
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - E Stöger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - L Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
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Raschmanová H, Weninger A, Knejzlík Z, Melzoch K, Kovar K. Engineering of the unfolded protein response pathway in Pichia pastoris: enhancing production of secreted recombinant proteins. Appl Microbiol Biotechnol 2021; 105:4397-4414. [PMID: 34037840 PMCID: PMC8195892 DOI: 10.1007/s00253-021-11336-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Folding and processing of proteins in the endoplasmic reticulum (ER) are major impediments in the production and secretion of proteins from Pichia pastoris (Komagataella sp.). Overexpression of recombinant genes can overwhelm the innate secretory machinery of the P. pastoris cell, and incorrectly folded proteins may accumulate inside the ER. To restore proper protein folding, the cell naturally triggers an unfolded protein response (UPR) pathway, which upregulates the expression of genes coding for chaperones and other folding-assisting proteins (e.g., Kar2p, Pdi1, Ero1p) via the transcription activator Hac1p. Unfolded/misfolded proteins that cannot be repaired are degraded via the ER-associated degradation (ERAD) pathway, which decreases productivity. Co-expression of selected UPR genes, along with the recombinant gene of interest, is a common approach to enhance the production of properly folded, secreted proteins. Such an approach, however, is not always successful and sometimes, protein productivity decreases because of an unbalanced UPR. This review summarizes successful chaperone co-expression strategies in P. pastoris that are specifically related to overproduction of foreign proteins and the UPR. In addition, it illustrates possible negative effects on the cell's physiology and productivity resulting from genetic engineering of the UPR pathway. We have focused on Pichia's potential for commercial production of valuable proteins and we aim to optimize molecular designs so that production strains can be tailored to suit a specific heterologous product. KEY POINTS: • Chaperones co-expressed with recombinant genes affect productivity in P. pastoris. • Enhanced UPR may impair strain physiology and promote protein degradation. • Gene copy number of the target gene and the chaperone determine the secretion rate.
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Affiliation(s)
- Hana Raschmanová
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic.
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Astrid Weninger
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karel Melzoch
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karin Kovar
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
- daspool Association, Wädenswil, Switzerland
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Bioprocess performance analysis of novel methanol-independent promoters for recombinant protein production with Pichia pastoris. Microb Cell Fact 2021; 20:74. [PMID: 33757505 PMCID: PMC7986505 DOI: 10.1186/s12934-021-01564-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/12/2021] [Indexed: 11/30/2022] Open
Abstract
Background Pichia pastoris is a powerful and broadly used host for recombinant protein production (RPP), where past bioprocess performance has often been directed with the methanol regulated AOX1 promoter (PAOX1), and the constitutive GAP promoter (PGAP). Since promoters play a crucial role in an expression system and the bioprocess efficiency, innovative alternatives are constantly developed and implemented. Here, a thorough comparative kinetic characterization of two expression systems based on the commercial PDF and UPP promoters (PPDF, PUPP) was first conducted in chemostat cultures. Most promising conditions were subsequently tested in fed-batch cultivations. These new alternatives were compared with the classical strong promoter PGAP, using the Candida antarctica lipase B (CalB) as model protein for expression system performance. Results Both the PPDF and PUPP-based expression systems outperformed similar PGAP-based expression in chemostat cultivations, reaching ninefold higher specific production rates (qp). CALB transcription levels were drastically higher when employing the novel expression systems. This higher expression was also correlated with a marked upregulation of unfolded protein response (UPR) related genes, likely from an increased protein burden in the endoplasmic reticulum (ER). Based on the chemostat results obtained, best culture strategies for both PPDF and PUPP expression systems were also successfully implemented in 15 L fed-batch cultivations where qp and product to biomass yield (YP/X*) values were similar than those obtained in chemostat cultivations. Conclusions As an outcome of the macrokinetic characterization presented, the novel PPDF and PUPP were observed to offer much higher efficiency for CalB production than the widely used PGAP-based methanol-free alternative. Thus, both systems arise as highly productive alternatives for P. pastoris-based RPP bioprocesses. Furthermore, the different expression regulation patterns observed indicate the level of gene expression can be adjusted, or tuned, which is interesting when using Pichia pastoris as a cell factory for different products of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01564-9.
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Grigs O, Bolmanis E, Galvanauskas V. Application of In-Situ and Soft-Sensors for Estimation of Recombinant P. pastoris GS115 Biomass Concentration: A Case Analysis of HBcAg (Mut +) and HBsAg (Mut S) Production Processes under Varying Conditions. SENSORS 2021; 21:s21041268. [PMID: 33578904 PMCID: PMC7916731 DOI: 10.3390/s21041268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/30/2021] [Accepted: 02/04/2021] [Indexed: 12/27/2022]
Abstract
Microbial biomass concentration is a key bioprocess parameter, estimated using various labor, operator and process cross-sensitive techniques, analyzed in a broad context and therefore the subject of correct interpretation. In this paper, the authors present the results of P. pastoris cell density estimation based on off-line (optical density, wet/dry cell weight concentration), in-situ (turbidity, permittivity), and soft-sensor (off-gas O2/CO2, alkali consumption) techniques. Cultivations were performed in a 5 L oxygen-enriched stirred tank bioreactor. The experimental plan determined varying aeration rates/levels, glycerol or methanol substrates, residual methanol levels, and temperature. In total, results from 13 up to 150 g (dry cell weight)/L cultivation runs were analyzed. Linear and exponential correlation models were identified for the turbidity sensor signal and dry cell weight concentration (DCW). Evaluated linear correlation between permittivity and DCW in the glycerol consumption phase (<60 g/L) and medium (for Mut+ strain) to significant (for MutS strain) linearity decline for methanol consumption phase. DCW and permittivity-based biomass estimates used for soft-sensor parameters identification. Dataset consisting from 4 Mut+ strain cultivation experiments used for estimation quality (expressed in NRMSE) comparison for turbidity-based (8%), permittivity-based (11%), O2 uptake-based (10%), CO2 production-based (13%), and alkali consumption-based (8%) biomass estimates. Additionally, the authors present a novel solution (algorithm) for uncommon in-situ turbidity and permittivity sensor signal shift (caused by the intensive stirrer rate change and antifoam agent addition) on-line identification and minimization. The sensor signal filtering method leads to about 5-fold and 2-fold minimized biomass estimate drifts for turbidity- and permittivity-based biomass estimates, respectively.
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Affiliation(s)
- Oskars Grigs
- Laboratory of Bioprocess Engineering, Latvian State Institute of Wood Chemistry, LV-1006 Riga, Latvia;
- Correspondence: ; Tel.: +371-6755-3063
| | - Emils Bolmanis
- Laboratory of Bioprocess Engineering, Latvian State Institute of Wood Chemistry, LV-1006 Riga, Latvia;
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Vytautas Galvanauskas
- Department of Automation, Kaunas University of Technology, LT-51367 Kaunas, Lithuania;
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Evolution of Pichia pastoris as a model organism for vaccines production in healthcare industry. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Prattipati M, Ramakrishnan K, Sankaranarayanan M. Pichia pastoris Protein Disulfide Isomerase (PDI1) promoter for heterologous protein production and its sequence characterization. Enzyme Microb Technol 2020; 140:109633. [PMID: 32912692 DOI: 10.1016/j.enzmictec.2020.109633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Pichia pastoris (syn. Komagataella phaffii) expression system has been widely used in heterologous protein production. PDI1 is the structural gene for Protein Disulfide Isomerase (PDI) and one of the main proteins in the endoplasmic reticulum (ER). It serves as a chaperone and helps in the formation, restoration and isomerization of disulfide bonds in nascent proteins. Overexpression of chaperone genes like PDI1, is one of the approaches to alleviate unfolded protein response (UPR) in multicopy clones of P. pastoris. However, it is not in a general scheme and these approaches are protein specific. The complete understanding of promoter region of PDI1 can give insights for better regulation of UPR. The aim of our work was to characterize promoter region of PDI1 gene and evaluate the possibility of their use for efficient expression of heterologous proteins. For this purpose, we used a reporter system based on the Candida antarctica lipase B (CalB) gene. The efficiency of PDI1 promoter was also compared with that of inducible promoter, AOX1, and the constitutive promoter, GAP, under different carbon sources like glucose, glycerol and methanol. The results appear that the PDI1 promoter may act as an UPR inducible promoter at high copy numbers of target gene. Therefore, we propose that the PDI1 promoter can be used for moderate expression of heterologous proteins in pathway engineering applications and also for overexpression of molecular chaperones.
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Role of BGS13 in the Secretory Mechanism of Pichia pastoris. Appl Environ Microbiol 2019; 85:AEM.01615-19. [PMID: 31585990 DOI: 10.1128/aem.01615-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/22/2019] [Indexed: 02/08/2023] Open
Abstract
The methylotrophic yeast Pichia pastoris has been utilized for heterologous protein expression for over 30 years. Because P. pastoris secretes few of its own proteins, the exported recombinant protein is the major polypeptide in the extracellular medium, making purification relatively easy. Unfortunately, some recombinant proteins intended for secretion are retained within the cell. A mutant strain isolated in our laboratory, containing a disruption of the BGS13 gene, displayed elevated levels of secretion for a variety of reporter proteins. The Bgs13 peptide (Bgs13p) is similar to the Saccharomyces cerevisiae protein kinase C 1 protein (Pkc1p), but its specific mode of action is currently unclear. To illuminate differences in the secretion mechanism between the wild-type (wt) strain and the bgs13 strain, we determined that the disrupted bgs13 gene expressed a truncated protein that had reduced protein kinase C activity and a different location in the cell, compared to the wt protein. Because the Pkc1p of baker's yeast plays a significant role in cell wall integrity, we investigated the sensitivity of the mutant strain's cell wall to growth antagonists and extraction by dithiothreitol, determining that the bgs13 strain cell wall suffered from inherent structural problems although its porosity was normal. A proteomic investigation of the bgs13 strain secretome and cell wall-extracted peptides demonstrated that, compared to its wt parent, the bgs13 strain also displayed increased release of an array of normally secreted, endogenous proteins, as well as endoplasmic reticulum-resident chaperone proteins, suggesting that Bgs13p helps regulate the unfolded protein response and protein sorting on a global scale.IMPORTANCE The yeast Pichia pastoris is used as a host system for the expression of recombinant proteins. Many of these products, including antibodies, vaccine antigens, and therapeutic proteins such as insulin, are currently on the market or in late stages of development. However, one major weakness is that sometimes these proteins are not secreted from the yeast cell efficiently, which impedes and raises the cost of purification of these vital proteins. Our laboratory has isolated a mutant strain of Pichia pastoris that shows enhanced secretion of many proteins. The mutant produces a modified version of Bgs13p. Our goal is to understand how the change in the Bgs13p function leads to improved secretion. Once the Bgs13p mechanism is illuminated, we should be able to apply this understanding to engineer new P. pastoris strains that efficiently produce and secrete life-saving recombinant proteins, providing medical and economic benefits.
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