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Rajak N, Dey T, Sharma Y, Bellad V, Rangarajan PN. Unlocking Nature's Toolbox: glutamate-inducible recombinant protein production from the Komagatella phaffii PEPCK promoter. Microb Cell Fact 2024; 23:66. [PMID: 38402195 PMCID: PMC10893637 DOI: 10.1186/s12934-024-02340-1] [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: 11/30/2023] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Komagataella phaffii (a.k.a. Pichia pastoris) harbors a glutamate utilization pathway in which synthesis of glutamate dehydrogenase 2 and phosphoenolpyruvate carboxykinase (PEPCK) is induced by glutamate. Glutamate-inducible synthesis of these enzymes is regulated by Rtg1p, a cytosolic, basic helix-loop-helix protein. Here, we report food-grade monosodium glutamate (MSG)-inducible recombinant protein production from K. phaffii PEPCK promoter (PPEPCK) using green fluorescent protein (GFP) and receptor binding domain of SARS-CoV-2 virus (RBD) as model proteins. RESULTS PPEPCK-RBD/GFP expression cassette was integrated at two different sites in the genome to improve recombinant protein yield from PPEPCK. The traditional, methanol-inducible alcohol oxidase 1 promoter (PAOX1) was used as the benchmark. Initial studies carried out with MSG as the inducer resulted in low recombinant protein yield. A new strategy employing MSG/ethanol mixed feeding improved biomass generation as well as recombinant protein yield. Cell density of 100-120 A600 units/ml was achieved after 72 h of induction in shake flask cultivations, resulting in recombinant protein yield from PPEPCK that is comparable or even higher than that from PAOX1. CONCLUSIONS We have designed an induction medium for recombinant protein production from K. phaffii PPEPCK in shake flask cultivations. It consists of 1.0% yeast extract, 2.0% peptone, 0.17% yeast nitrogen base with ammonium sulfate, 100 mM potassium phosphate (pH 6.0), 0.4 mg/L biotin, 2.0% MSG, and 2% ethanol. Substitution of ammonium sulphate with 0.5% urea is optional. Carbon source was replenished every 24 h during 72 h induction period. Under these conditions, GFP and RBD yields from PPEPCK equaled and even surpassed those from PAOX1. Compared to the traditional methanol-inducible expression system, the inducers of glutamate-inducible expression system are non-toxic and their metabolism does not generate toxic metabolites such as formaldehyde and hydrogen peroxide. This study sets the stage for MSG-inducible, industrial scale recombinant protein production from K. phaffii PPEPCK in bioreactors.
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Affiliation(s)
- Neetu Rajak
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Trishna Dey
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Yash Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Vedanth Bellad
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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Silva AJD, de Jesus ALS, Leal LRS, de Macêdo LS, da Silva Barros BR, de Sousa GF, da Paz Leôncio Alves S, Pena LJ, de Melo CML, de Freitas AC. Whole Yeast Vaccine Displaying ZIKV B and T Cell Epitopes Induces Cellular Immune Responses in the Murine Model. Pharmaceutics 2023; 15:1898. [PMID: 37514084 PMCID: PMC10385271 DOI: 10.3390/pharmaceutics15071898] [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: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Improving antigen presentation is crucial for the success of immunization strategies. Yeasts are classically used as biofactories to produce recombinant proteins and are efficient vehicles for antigen delivery, in addition to their adjuvant properties. Despite the absence of epidemic outbreaks, several vaccine approaches continue to be developed for Zika virus infection. The development of these prophylactic strategies is fundamental given the severity of clinical manifestations, mainly due to viral neurotropism. The present study aimed to evaluate in vivo the immune response induced by P. pastoris recombinant strains displaying epitopes of the envelope (ENV) and NS1 ZIKV proteins. Intramuscular immunization with heat-attenuated yeast enhanced the secretion of IL-6, TNF-α, and IFN-γ, in addition to the activation of CD4+ and CD8+ T cells, in BALB/c mice. P. pastoris displaying ENV epitopes induced a more robust immune response, increasing immunoglobulin production, especially IgG isotypes. Both proposed vaccines showed the potential to induce immune responses without adverse effects, confirming the safety of administering P. pastoris as a vaccine vehicle. Here, we demonstrated, for the first time, the evaluation of a vaccine against ZIKV based on a multiepitope construct using yeast as a delivery system and reinforcing the applicability of P. pastoris as a whole-cell vaccine.
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Affiliation(s)
- Anna Jéssica Duarte Silva
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | | | - Lígia Rosa Sales Leal
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Larissa Silva de Macêdo
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | | | | | | | - Lindomar José Pena
- Department of Virology and Experimental Therapy, Instituto Aggeu Magalhães, Oswaldo Cruz Foundation, Recife 50670-901, Brazil
| | | | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
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Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins. FERMENTATION 2022. [DOI: 10.3390/fermentation8110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.
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Expanding the promoter toolbox for metabolic engineering of methylotrophic yeasts. Appl Microbiol Biotechnol 2022; 106:3449-3464. [PMID: 35538374 DOI: 10.1007/s00253-022-11948-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/31/2023]
Abstract
Methylotrophic yeasts have been widely recognized as a promising host for production of recombinant proteins and value-added chemicals. Promoters for controlled gene expression are critical for construction of efficient methylotrophic yeasts cell factories. Here, we summarized recent advances in characterizing and engineering promoters in methylotrophic yeasts, such as Komagataella phaffii and Ogataea polymorpha. Constitutive and inducible promoters controlled by methanol or other inducers/repressors were introduced to demonstrate their applications in production of proteins and chemicals. Furthermore, efforts of promoter engineering, including site-directed mutagenesis, hybrid promoter, and transcription factor regulation to expand the promoter toolbox were also summarized. This mini-review also provides useful information on promoters for the application of metabolic engineering in methylotrophic yeasts. KEY POINTS: • The characteristics of six methylotrophic yeasts and their promoters are described. • The applications of Komagataella phaffii and Ogataea polymorpha in metabolic engineeringare expounded. • Three promoter engineering strategies are introduced in order to expand the promoter toolbox.
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Rinnofner C, Felber M, Pichler H. Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris. Methods Mol Biol 2022; 2513:79-112. [PMID: 35781201 DOI: 10.1007/978-1-0716-2399-2_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] [Indexed: 06/15/2023]
Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Affiliation(s)
- Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.
- Bisy GmbH, Hofstaetten/Raab, Austria.
| | - Michael Felber
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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Abstract
The availability of exceptionally strong and tightly regulated promoters is a key feature of Komagataella phaffii (syn. Pichia pastoris), a widely applied yeast expression system for heterologous protein production. Most commonly, the methanol-inducible promoter of the alcohol oxidase 1 gene (PAOX1) and the constitutive promoter of the glyceraldehyde 3 phosphate dehydrogenase gene (PGAP) have been used. Recently, also promising novel constitutive (PGCW14), regulated (PGTH1, PCAT1), and bidirectional promoters (histone promoters and synthetic hybrid variants) have been reported.As natural promoters showed so far limited tunability of expression levels and regulatory profiles, various promoter engineering efforts have been undertaken for P. pastoris . PAOX1, PDAS2, PGAP, and PGCW14 have been engineered by systematic deletion studies or random mutagenesis of upstream regulatory sequences. New engineering strategies have focused on PAOX1 core promoter modifications by random or rational approaches and transcriptional regulatory circuits to render PAOX1 independent of methanol induction. These promoter engineering efforts in P. pastoris have resulted in improved, sequence-diversified synthetic promoter variants allowing coordinated fine-tuning of gene expression for a multitude of biotechnological applications.
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Affiliation(s)
- Thomas Vogl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria.
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Silva AJD, Jesus ALS, Leal LRS, Silva GAS, Melo CML, Freitas AC. Pichia pastoris displaying ZIKV protein epitopes from the Envelope and NS1 induce in vitro immune activation. Vaccine 2021; 39:2545-2554. [PMID: 33814233 DOI: 10.1016/j.vaccine.2021.03.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/26/2021] [Accepted: 03/19/2021] [Indexed: 02/08/2023]
Abstract
The severe consequences of ZIKV infection and its emergence and re-emergence in several countries have boosted vaccines' development. Yeasts such as Pichia pastoris has been widely employed as antigen carriers for immunization against infectious agents. Components of the yeast cell wall have immunostimulatory properties, and recombinant antigens can be anchored to the cell surface to enhance the presentation to the immune system. Here we aimed at producing and anchoring ZIKV proteins in the P. pastoris surface as a vaccine approach. Expression cassettes were designed with epitopes of the Envelope and NS1 proteins. Immunofluorescence microscopy confirmed the anchoring of recombinant proteins. Yeasts' ability to stimulate immune cells was evaluated in vitro by incubation with lymphocytes and monocytes isolated from mouse spleen. P. pastoris expressing EnvNS1 epitopes promoted increased levels of IL-6, IL-10, and TNF-α cytokines and an increase in the number of CD4+, CD8+, and CD16+ lymphocytes, similarly to ZIKV. This profile is indicative of the activation of immunological cells and suggests an immunogenic potential of the proposed yeast vaccines against ZIKV, reinforcing the possibility of P. pastoris as adjuvant and carrier of antigens.
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Affiliation(s)
- Anna Jéssica D Silva
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - André Luiz S Jesus
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Lígia Rosa S Leal
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Guilherme Antonio S Silva
- Laboratório de Análises Imunológicas e Antitumorais, Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, Brazil
| | - Cristiane Moutinho L Melo
- Laboratório de Análises Imunológicas e Antitumorais, Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, Brazil
| | - Antonio C Freitas
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil.
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Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
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Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is used as an expression system for recombinant protein production for a variety of applications. It grows rapidly on inexpensive media containing methanol, glucose, glycerol, or ethanol as a sole carbon source. P. pastoris makes many posttranslational modifications and produces recombinant proteins either intracellularly or extracellularly. Because of these properties, P. pastoris has become a highly preferred host organism for biotechnology, pharmaceutical industry, and researchers.Recombinant protein production is usually performed under the control of the promoter of the alcohol oxidase gene I (AOX1). The AOX1 promoter is induced by methanol and repressed by glucose and ethanol. The regulation mechanisms of the AOX1 promoter have been studied in recent years. Another promoter used in recombinant protein production is derived from glyceraldehyde 3-phosphate dehydrogenase (GAP). It is a constitutive promoter. Recent literature showed that newly identified promoters of P. pastoris are promising as well, in addition to pAOX1 and pGAP.In this chapter, the regulation mechanisms of inducible pAOX1 and constitutive pGAP promoters are discussed. In addition, here we present an overview about the novel ADH3 promoter and alternative promoters of P. pastoris.
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Affiliation(s)
| | - Semiramis Yılmaz
- Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Mehmet Inan
- Food Safety and Agricultural Research Center, Akdeniz University, Antalya, Turkey.
- Department of Food Engineering, Akdeniz University, Antalya, Turkey.
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Transcriptome and metabolome analyses reveal global behaviour of a genetically engineered methanol-independent Pichia pastoris strain. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Valero F. Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review. Methods Mol Biol 2018; 1835:205-216. [PMID: 30109654 DOI: 10.1007/978-1-4939-8672-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.
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Affiliation(s)
- Francisco Valero
- Departament d'Enginyeria Química, Biològica i Ambiental. EE, Universitat Autònoma de Barcelona, Barcelona, Spain.
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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Piva LC, Bentacur MO, Reis VCB, De Marco JL, Moraes LMPD, Torres FAG. Molecular strategies to increase the levels of heterologous transcripts in Komagataella phaffii for protein production. Bioengineered 2017; 8:441-445. [PMID: 28399696 DOI: 10.1080/21655979.2017.1296613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Komagataella phaffii (formerly Pichia pastoris) is a well-known fungal system for heterologous protein production in the context of modern biotechnology. To obtain higher protein titers in this system many researchers have sought to optimize gene expression by increasing the levels of transcription of the heterologous gene. This has been typically achieved by manipulating promoter sequences or by generating clones bearing multiple copies of the desired gene. The aim of this work is to describe how these different molecular strategies have been applied in K. phaffii presenting their advantages and drawbacks.
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Affiliation(s)
- Luiza Cesca Piva
- a Laboratório de Biologia Molecular, Instituto de Ciências Biológicas , Universidade de Brasília , Brasília , DF , Brazil
| | - Maritza Ocampo Bentacur
- a Laboratório de Biologia Molecular, Instituto de Ciências Biológicas , Universidade de Brasília , Brasília , DF , Brazil
| | - Viviane Castelo Branco Reis
- a Laboratório de Biologia Molecular, Instituto de Ciências Biológicas , Universidade de Brasília , Brasília , DF , Brazil
| | - Janice Lisboa De Marco
- a Laboratório de Biologia Molecular, Instituto de Ciências Biológicas , Universidade de Brasília , Brasília , DF , Brazil
| | - Lidia Maria Pepe de Moraes
- a Laboratório de Biologia Molecular, Instituto de Ciências Biológicas , Universidade de Brasília , Brasília , DF , Brazil
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Production of recombinant lipase B from Candida antarctica in Pichia pastoris under control of the promoter PGK using crude glycerol from biodiesel production as carbon source. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Wang M, Jiang S, Wang Y. Recent advances in the production of recombinant subunit vaccines in Pichia pastoris. Bioengineered 2017; 7:155-65. [PMID: 27246656 DOI: 10.1080/21655979.2016.1191707] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recombinant protein subunit vaccines are formulated using defined protein antigens that can be produced in heterologous expression systems. The methylotrophic yeast Pichia pastoris has become an important host system for the production of recombinant subunit vaccines. Although many basic elements of P. pastoris expression system are now well developed, there is still room for further optimization of protein production. Codon bias, gene dosage, endoplasmic reticulum protein folding and culture condition are important considerations for improved production of recombinant vaccine antigens. Here we comment on current advances in the application of P. pastoris for the synthesis of recombinant subunit vaccines.
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Affiliation(s)
- Man Wang
- a Institute for Translational Medicine, Medical College of Qingdao University , Qingdao , China
| | - Shuai Jiang
- b State Key Laboratory of Virology , College of Life Sciences, Wuhan University , Wuhan , China
| | - Yefu Wang
- b State Key Laboratory of Virology , College of Life Sciences, Wuhan University , Wuhan , China
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Combinatorial library strategy for strong overexpression of the lipase from Geobacillus thermocatenulatus on the cell surface of yeast Pichia pastoris. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Amores GR, Guazzaroni ME, Arruda LM, Silva-Rocha R. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories. Curr Genomics 2016; 17:85-98. [PMID: 27226765 PMCID: PMC4864837 DOI: 10.2174/1389202917666151116212255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/23/2015] [Accepted: 06/01/2015] [Indexed: 01/03/2023] Open
Abstract
Filamentous fungi are remarkable organisms naturally specialized in deconstructing plant
biomass and this feature has a tremendous potential for biofuel production from renewable sources.
The past decades have been marked by a remarkable progress in the genetic engineering of fungi to
generate industry-compatible strains needed for some biotech applications. In this sense, progress in
this field has been marked by the utilization of high-throughput techniques to gain deep understanding
of the molecular machinery controlling the physiology of these organisms, starting thus the Systems
Biology era of fungi. Additionally, genetic engineering has been extensively applied to modify wellcharacterized
promoters in order to construct new expression systems with enhanced performance under the conditions of
interest. In this review, we discuss some aspects related to significant progress in the understating and engineering of
fungi for biotechnological applications, with special focus on the construction of synthetic promoters and circuits in organisms
relevant for industry. Different engineering approaches are shown, and their potential and limitations for the construction
of complex synthetic circuits in these organisms are examined. Finally, we discuss the impact of engineered
promoter architecture in the single-cell behavior of the system, an often-neglected relationship with a tremendous impact
in the final performance of the process of interest. We expect to provide here some new directions to drive future research
directed to the construction of high-performance, engineered fungal strains working as microbial cell factories.
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A constitutive expression system for Pichia pastoris based on the PGK1 promoter. Biotechnol Lett 2015; 38:509-17. [PMID: 26585331 DOI: 10.1007/s10529-015-2002-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/09/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVES To develop a new vector for constitutive expression in Pichia pastoris based on the endogenous glycolytic PGK1 promoter. RESULTS P. pastoris plasmids bearing at least 415 bp of PGK1 promoter sequences can be used to drive plasmid integration by addition at this locus without affecting cell growth. Based on this result, a new P. pastoris integrative vector, pPICK2, was constructed bearing some features that facilitate protein production in this yeast: a ~620 bp PGK1 promoter fragment with three options of restriction sites for plasmid linearization prior to yeast transformation: a codon-optimized α-factor secretion signal, a new polylinker, and the kan marker for vector propagation in bacteria and selection of yeast transformants. CONCLUSIONS A new constitutive vector for P. pastoris represents an alternative platform for recombinant protein production and metabolic engineering purposes.
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Development of an IP-Free Biotechnology Platform for Constitutive Production of HPV16 L1 Capsid Protein Using the Pichia pastoris PGK1 Promoter. BIOMED RESEARCH INTERNATIONAL 2015; 2015:594120. [PMID: 26090426 PMCID: PMC4450287 DOI: 10.1155/2015/594120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/18/2014] [Accepted: 01/05/2015] [Indexed: 01/07/2023]
Abstract
The human papillomavirus (HPV) L1 major capsid protein, which forms the basis of the currently available vaccines against cervical cancer, self-assembles into virus-like particles (VLPs) when expressed heterologously. We report the development of a biotechnology platform for HPV16 L1 protein expression based on the constitutive PGK1 promoter (PPGK1) from the methylotrophic yeast Pichia pastoris. The L1 gene was cloned under regulation of PPGK1 into pPGKΔ3 expression vector to achieve intracellular expression. In parallel, secretion of the L1 protein was obtained through the use of an alternative vector called pPGKΔ3α, in which a codon optimized α-factor signal sequence was inserted. We devised a work-flow based on the detection of the L1 protein by dot blot, colony blot, and western blot to classify the positive clones. Finally, intracellular HPV VLPs assembly was demonstrated for the first time in yeast cells. This study opens up perspectives for the establishment of an innovative platform for the production of HPV VLPs or other viral antigens for vaccination purposes, based on constitutive expression in P. pastoris.
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Spohner SC, Müller H, Quitmann H, Czermak P. Expression of enzymes for the usage in food and feed industry with Pichia pastoris. J Biotechnol 2015; 202:118-34. [DOI: 10.1016/j.jbiotec.2015.01.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/28/2014] [Accepted: 01/07/2015] [Indexed: 12/29/2022]
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Çalık P, Ata Ö, Güneş H, Massahi A, Boy E, Keskin A, Öztürk S, Zerze GH, Özdamar TH. Recombinant protein production in Pichia pastoris under glyceraldehyde-3-phosphate dehydrogenase promoter: From carbon source metabolism to bioreactor operation parameters. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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de Assunçao EN, Cristina dos SM, Araripe TF, Spartaco AF. Recombinant human proinsulin expression in Pichiapastoris using PGK promoter. BMC Proc 2014. [PMCID: PMC4204360 DOI: 10.1186/1753-6561-8-s4-p88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl Microbiol Biotechnol 2014; 98:5301-17. [PMID: 24743983 PMCID: PMC4047484 DOI: 10.1007/s00253-014-5732-5] [Citation(s) in RCA: 602] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/29/2022]
Abstract
Pichia pastoris is an established protein expression host mainly applied for the production of biopharmaceuticals and industrial enzymes. This methylotrophic yeast is a distinguished production system for its growth to very high cell densities, for the available strong and tightly regulated promoters, and for the options to produce gram amounts of recombinant protein per litre of culture both intracellularly and in secretory fashion. However, not every protein of interest is produced in or secreted by P. pastoris to such high titres. Frequently, protein yields are clearly lower, particularly if complex proteins are expressed that are hetero-oligomers, membrane-attached or prone to proteolytic degradation. The last few years have been particularly fruitful because of numerous activities in improving the expression of such complex proteins with a focus on either protein engineering or on engineering the protein expression host P. pastoris. This review refers to established tools in protein expression in P. pastoris and highlights novel developments in the areas of expression vector design, host strain engineering and screening for high-level expression strains. Breakthroughs in membrane protein expression are discussed alongside numerous commercial applications of P. pastoris derived proteins.
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Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Anastácio GS, Santos KO, Suarez PAZ, Torres FAG, De Marco JL, Parachin NS. Utilization of glycerin byproduct derived from soybean oil biodiesel as a carbon source for heterologous protein production in Pichia pastoris. BIORESOURCE TECHNOLOGY 2013; 152:505-510. [PMID: 24342909 DOI: 10.1016/j.biortech.2013.11.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/16/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Crude glycerol, also known as glycerin, is the main byproduct of the biodiesel industry. It has been estimated that up to 40,000 tons of glycerin will be produced each year by 2020. This study evaluated the value-added use of crude glycerol derived from soybean biodiesel preparation as a carbon source for heterologous protein production using the yeast Pichia pastoris. Eleven glycerin samples were obtained by methanolysis of soybean oil using different acids or bases as catalysts. Cell growth experiments showed that crude glycerol containing either potassium or sodium hydroxide resulted in 1.5-2 times higher final cell densities when compared to glycerol P.A. Finally, crude glycerol containing sodium hydroxide was successfully utilized for constitutive heterologous α-amylase production in P. pastoris. This study demonstrated that crude glycerol without any purification steps may be directly used as carbon source for protein production in P. pastoris.
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Affiliation(s)
- G S Anastácio
- Centro de Biotecnologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - K O Santos
- Laboratório de Materiais e Combustíveis, Instituto de Química, Universidade de Brasília, Brasília, DF 70910-000, Brazil
| | - P A Z Suarez
- Laboratório de Materiais e Combustíveis, Instituto de Química, Universidade de Brasília, Brasília, DF 70910-000, Brazil
| | - F A G Torres
- Centro de Biotecnologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - J L De Marco
- Laboratório de Materiais e Combustíveis, Instituto de Química, Universidade de Brasília, Brasília, DF 70910-000, Brazil
| | - N S Parachin
- Centro de Biotecnologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil; Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
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Regulation of Pichia pastoris promoters and its consequences for protein production. N Biotechnol 2013; 30:385-404. [DOI: 10.1016/j.nbt.2012.11.010] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Accepted: 11/05/2012] [Indexed: 12/18/2022]
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Potvin G, Ahmad A, Zhang Z. Bioprocess engineering aspects of heterologous protein production in Pichia pastoris: A review. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2010.07.017] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stadlmayr G, Mecklenbräuker A, Rothmüller M, Maurer M, Sauer M, Mattanovich D, Gasser B. Identification and characterisation of novel Pichia pastoris promoters for heterologous protein production. J Biotechnol 2010; 150:519-29. [DOI: 10.1016/j.jbiotec.2010.09.957] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 09/28/2010] [Accepted: 09/30/2010] [Indexed: 10/19/2022]
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Zhang P, Zhang W, Zhou X, Bai P, Cregg JM, Zhang Y. Catabolite repression of Aox in Pichia pastoris is dependent on hexose transporter PpHxt1 and pexophagy. Appl Environ Microbiol 2010; 76:6108-18. [PMID: 20656869 PMCID: PMC2937511 DOI: 10.1128/aem.00607-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/14/2010] [Indexed: 11/20/2022] Open
Abstract
In this work, the identification and characterization of two hexose transporter homologs in the methylotrophic yeast Pichia pastoris, P. pastoris Hxt1 (PpHxt1) and PpHxt2, are described. When expressed in a Saccharomyces cerevisiae hxt-null mutant strain that is unable to take up monosaccharides, either protein restored growth on glucose or fructose. Both PpHXT genes are transcriptionally regulated by glucose. Transcript levels of PpHXT1 are induced by high levels of glucose, whereas transcript levels of PpHXT2 are relatively lower and are fully induced by low levels of glucose. In addition, PpHxt2 plays an important role in glycolysis-dependent fermentative growth, since PpHxt2 is essential for growth on glucose or fructose when respiration is inhibited. Notably, we firstly found that the deletion of PpHXT1, but not PpHXT2, leads to the induced expression of the alcohol oxidase I gene (AOX1) in response to glucose or fructose. We also elucidated that a sharp dropping of the sugar-induced expression level of Aox at a later growth phase is caused mainly by pexophagy, a degradation pathway in methylotrophic yeast. The sugar-inducible AOX1 promoter in an Deltahxt1 strain may be promising as a host for the expression of heterologous proteins. The functional analysis of these two hexose transporters is the first step in elucidating the mechanisms of sugar metabolism and catabolite repression in P. pastoris.
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Affiliation(s)
- Ping Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Wenwen Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Peng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - James M. Cregg
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
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Hartner FS, Ruth C, Langenegger D, Johnson SN, Hyka P, Lin-Cereghino GP, Lin-Cereghino J, Kovar K, Cregg JM, Glieder A. Promoter library designed for fine-tuned gene expression in Pichia pastoris. Nucleic Acids Res 2008; 36:e76. [PMID: 18539608 PMCID: PMC2475614 DOI: 10.1093/nar/gkn369] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (PAOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing a green fluorescent protein (GFP) variant, the new regulatory toolbox was successfully utilized in a ‘real case’, i.e. the expression of industrial enzymes. Characterization of the library under repressing, derepressing and inducing conditions displayed at least 12 cis-acting elements involved in PAOX1-driven high-level expression. Based on this deletion analysis, novel short artificial promoter variants were constructed by combining cis-acting elements with basal promoter. In addition to improving yields and quality of heterologous protein production, the new PAOX1 synthetic promoter library constitutes a basic toolbox to fine-tune gene expression in metabolic engineering and sequential induction of protein expression in synthetic biology.
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Affiliation(s)
- Franz S Hartner
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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Current awareness on yeast. Yeast 2005; 22:1249-56. [PMID: 16320446 DOI: 10.1002/yea.1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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