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Majumder D, Dey A, Ray S, Bhattacharya D, Nag M, Lahiri D. Use of genomics & proteomics in studying lipase producing microorganisms & its application. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 9:100218. [PMID: 39281291 PMCID: PMC11402113 DOI: 10.1016/j.fochms.2024.100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/08/2024] [Accepted: 08/17/2024] [Indexed: 09/18/2024]
Abstract
In biotechnological applications, lipases are recognized as the most widely utilized and versatile enzymes, pivotal in biocatalytic processes, predominantly produced by various microbial species. Utilizing omics technology, natural sources can be meticulously screened to find microbial flora which are responsible for oil production. Lipases are versatile biocatalysts. They are used in a variety of bioconversion reactions and are receiving a lot of attention because of the quick development of enzyme technology and its usefulness in industrial operations. This article offers recent insights into microbial lipase sources, including fungi, bacteria, and yeast, alongside traditional and modern methods of purification such as precipitation, immunopurification and chromatographic separation. Additionally, it explores innovative methods like the reversed micellar system, aqueous two-phase system (ATPS), and aqueous two-phase flotation (ATPF). The article deals with the use of microbial lipases in a variety of sectors, including the food, textile, leather, cosmetics, paper, detergent, while also critically analyzing lipase-producing microbes. Moreover, it highlights the role of lipases in biosensors, biodiesel production, tea processing, bioremediation, and racemization. This review provides the concept of the use of omics technique in the mechanism of screening of microbial species those are capable of producing lipase and also find the potential applications.
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Affiliation(s)
- Debashrita Majumder
- Department of Biotechnology, Institute of Engineering and Management, Kolkata, University of Engineering and Management, Kolkata, West Bengal, India
| | - Ankita Dey
- Department of Chemical Engineering, National Institute of Technology, Agartala, India
| | - Srimanta Ray
- Department of Chemical Engineering, National Institute of Technology, Agartala, India
| | - Debasmita Bhattacharya
- Department of Basic Science and Humanities, Institute of Engineering and Management, Kolkata, University of Engineering and Management, Kolkata, West Bengal, India
| | - Moupriya Nag
- Department of Biotechnology, Institute of Engineering and Management, Kolkata, University of Engineering and Management, Kolkata, West Bengal, India
| | - Dibyajit Lahiri
- Department of Biotechnology, Institute of Engineering and Management, Kolkata, University of Engineering and Management, Kolkata, West Bengal, India
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Bechtel A, Seitl I, Pross E, Hetzel F, Keutgen M, Fischer L. Recombinant production of Paenibacillus wynnii β-galactosidase with Komagataella phaffii. Microb Cell Fact 2024; 23:263. [PMID: 39367390 PMCID: PMC11452983 DOI: 10.1186/s12934-024-02544-5] [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: 07/19/2024] [Accepted: 09/28/2024] [Indexed: 10/06/2024] Open
Abstract
BACKGROUND The β-galactosidase from Paenibacillus wynnii (β-gal-Pw) is a promising candidate for lactose hydrolysis in milk and dairy products, as it has a higher affinity for the substrate lactose (low KM value) compared to industrially used β-galactosidases and is not inhibited by the hydrolysis-generated product D-galactose. However, β-gal-Pw must firstly be produced cost-effectively for any potential industrial application. Accordingly, the yeast Komagataella phaffii was chosen to investigate its feasibility to recombinantly produce β-gal-Pw since it is approved for the regulated production of food enzymes. The aim of this study was to find the most suitable way to produce the β-gal-Pw in K. phaffii either extracellularly or intracellularly. RESULTS Firstly, 11 different signal peptides were tested for extracellular production of β-gal-Pw by K. phaffii under the control of the constitutive GAP promoter. None of the signal peptides resulted in a secretion of β-gal-Pw, indicating problems within the secretory pathway of this enzyme. Therefore, intracellular β-gal-Pw production was investigated using the GAP or methanol-inducible AOX1 promoter. A four-fold higher volumetric β-galactosidase activity of 7537 ± 66 µkatoNPGal/Lculture was achieved by the K. phaffii clone 27 using the AOX1 promoter in fed-batch bioreactor cultivations, compared to the clone 5 using the GAP promoter. However, a two-fold higher specific productivity of 3.14 ± 0.05 µkatoNPGal/gDCW/h was achieved when using the GAP promoter for β-gal-Pw production compared to the AOX1 promoter. After partial purification, a β-gal-Pw enzyme preparation with a total β-galactosidase activity of 3082 ± 98 µkatoNPGal was obtained from 1 L of recombinant K. phaffii culture (using AOX1 promoter). CONCLUSION This study showed that the β-gal-Pw was produced intracellularly by K. phaffii, but the secretion was not achieved with the signal peptides chosen. Nevertheless, a straightforward approach to improve the intracellular β-gal-Pw production with K. phaffii by using either the GAP or AOX1 promoter in bioreactor cultivations was demonstrated, offering insights into alternative production methods for this enzyme.
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Affiliation(s)
- Anna Bechtel
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Ines Seitl
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Eva Pross
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Frank Hetzel
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Mario Keutgen
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Lutz Fischer
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Garbenstr. 25, 70599, Stuttgart, Germany.
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Steimann T, Wegmann J, Espinosa MI, Blank LM, Büchs J, Mann M, Magnus JB. Avoiding overflow metabolite formation in Komagataella phaffii fermentations to enhance recombinant protein production. J Biol Eng 2024; 18:54. [PMID: 39363343 PMCID: PMC11448000 DOI: 10.1186/s13036-024-00453-0] [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: 07/24/2024] [Accepted: 09/21/2024] [Indexed: 10/05/2024] Open
Abstract
BACKGROUND Komagataella phaffii (K. phaffii), formerly known as Pichia pastoris, is a widely utilized yeast for recombinant protein production. However, due to the formation of overflow metabolites, carbon yields may be reduced and product recovery becomes challenging. This study investigates the impact of oxygen availability, different glucose concentrations and feeding strategies on overflow metabolite formation and recombinant protein production in K. phaffii. RESULTS High glucose concentrations in batch fermentation, as applied in literature, lead to substantial ethanol accumulation, adversely affecting biomass yield and product formation. Increasing dissolved oxygen setpoints does not significantly reduce ethanol formation, indicating that glucose surplus, rather than oxygen availability, drives overflow metabolism. Decreasing the initial glucose concentration to 5 g/L and adapting the feeding strategy of the fed-batch phase, effectively mitigates overflow metabolite formation, improving biomass yield by up to 9% and product concentration by 40% without increasing process time. CONCLUSIONS These findings underscore the importance of a suitable glucose-feeding strategy in K. phaffii fermentation processes and highlight the detrimental effects of overflow metabolites on productivity. By optimizing carbon source utilization, it is possible to enhance fermentation efficiency and recombinant protein production with K. phaffii.
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Affiliation(s)
- Thomas Steimann
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Judith Wegmann
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Monica I Espinosa
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Marcel Mann
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany
| | - Jørgen Barsett Magnus
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen, 52074, Germany.
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Unver Y, Ari B, Acar M, Yildiz Arslan S. A self-inducible heterologous protein expression system in Komagataella phaffii ( Pichia pastoris). 3 Biotech 2024; 14:193. [PMID: 39131177 PMCID: PMC11306816 DOI: 10.1007/s13205-024-04039-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024] Open
Abstract
Komagataella phaffii (previously described as Pichia pastoris) is a yeast that produces high-level heterologous proteins with a wide range of applications in medicine and industry. The methanol-induced alcohol oxidase I promoter (PAOX1) is frequently used for protein expression in this yeast. However, limitations on the use of methanol have been observed in large-scale production, including its flammability, toxicity, and need for special handling. Here, we propose to develop a system using recombinant cells constitutively expressing pectinmethyl esterase for expression of two reporter proteins, GFP and azurin, under the control of PAOX1 using pectin in production medium. So, this system is coherent with yeast culture medium containing pectin and heterologous gene inserted downstream of PAOX1 can be successfully expressed without the addition of methanol. Therefore, this novel Self-inducibLe heterologous protein EXpression (SILEX) system, which does not require the addition of methanol, can be used for the production of any protein. It can also be adapted for large-scale production. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04039-x.
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Affiliation(s)
- Yagmur Unver
- Department of Molecular Biology and Genetics, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Betul Ari
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Melek Acar
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
| | - Seyda Yildiz Arslan
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Atatürk University, Erzurum, Turkey
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Adame M, Vázquez H, Juárez-López D, Corzo G, Amezcua M, López D, González Z, Schcolnik-Cabrera A, Morales-Martínez A, Villegas E. Expression and characterization of scFv-6009FV in Pichia pastoris with improved ability to neutralize the neurotoxin Cn2 from Centruroides noxius. Int J Biol Macromol 2024; 275:133461. [PMID: 38945343 DOI: 10.1016/j.ijbiomac.2024.133461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Small single-chain variable fragments (scFv) are promising biomolecules to inhibit and neutralize toxins and to act as antivenoms. In this work, we aimed to produce a functional scFv-6009FV in the yeast Pichia pastoris, which inhibits the pure Cn2 neurotoxin and the whole venom of Centruroides noxius. We were able to achieve yields of up to 31.6 ± 2 mg/L in flasks. Furthermore, the protein showed a structure of 6.1 % α-helix, 49.1 % β-sheet, and 44.8 % of random coil by CD. Mass spectrometry confirmed the amino acid sequence and showed no glycosylation profile for this molecule. Purified scFv-6009FV allowed us to develop anti-scFvs in rabbits, which were then used in affinity columns to purify other scFvs. Determination of its half-maximal inhibitory concentration value (IC50) was 40 % better than the scFvs produced by E. coli as a control. Finally, we found that scFv-6009FV was able to inhibit ex vivo the pure Cn2 toxin and the whole venom from C. noxius in murine rescue experiments. These results demonstrated that under the conditions assayed here, P. pastoris is suited to produce scFv-6009FV that, compared to scFvs produced by E. coli, maintains the characteristics of an antibody and neutralizes the Cn2 toxin more effectively.
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Affiliation(s)
- Mariel Adame
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hilda Vázquez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Juárez-López
- Instituto de Investigaciones Biomédicas, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mónica Amezcua
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Daniela López
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Zuriel González
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | - Adriana Morales-Martínez
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Elba Villegas
- Departamento de Productos Naturales, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
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Ye C, Hong H, Gao J, Li M, Gou Y, Gao D, Dong C, Huang L, Xu Z, Lian J. Characterization and engineering of peroxisome targeting sequences for compartmentalization engineering in Pichia pastoris. Biotechnol Bioeng 2024; 121:2091-2105. [PMID: 38568751 DOI: 10.1002/bit.28706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Peroxisomal compartmentalization has emerged as a highly promising strategy for reconstituting intricate metabolic pathways. In recent years, significant progress has been made in the peroxisomes through harnessing precursor pools, circumventing metabolic crosstalk, and minimizing the cytotoxicity of exogenous pathways. However, it is important to note that in methylotrophic yeasts (e.g. Pichia pastoris), the abundance and protein composition of peroxisomes are highly variable, particularly when peroxisome proliferation is induced by specific carbon sources. The intricate subcellular localization of native proteins, the variability of peroxisomal metabolic pathways, and the lack of systematic characterization of peroxisome targeting signals have limited the applications of peroxisomal compartmentalization in P. pastoris. Accordingly, this study established a high-throughput screening method based on β-carotene biosynthetic pathway to evaluate the targeting efficiency of PTS1s (Peroxisome Targeting Signal Type 1) in P. pastoris. First, 25 putative endogenous PTS1s were characterized and 3 PTS1s with high targeting efficiency were identified. Then, directed evolution of PTS1s was performed by constructing two PTS1 mutant libraries, and a total of 51 PTS1s (29 classical and 22 noncanonical PTS1s) with presumably higher peroxisomal targeting efficiency were identified, part of which were further characterized via confocal microscope. Finally, the newly identified PTS1s were employed for peroxisomal compartmentalization of the geraniol biosynthetic pathway, resulting in more than 30% increase in the titer of monoterpene compared with when the pathway was localized to the cytosol. The present study expands the synthetic biology toolkit and lays a solid foundation for peroxisomal compartmentalization in P. pastoris.
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Affiliation(s)
- Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Haosen Hong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
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Anny CA, Nouaille S, Fauré R, Schulz C, Spriet C, Huvent I, Biot C, Lefebvre T. A Step-by-Step Guide for the Production of Recombinant Fluorescent TAT-HA-Tagged Proteins and their Transduction into Mammalian Cells. Curr Protoc 2024; 4:e1016. [PMID: 38511507 DOI: 10.1002/cpz1.1016] [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: 03/22/2024]
Abstract
Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.
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Affiliation(s)
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Céline Schulz
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | | | | | - Tony Lefebvre
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
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Reis-Claro I, Silva MI, Moutinho A, Garcia BC, Pereira-Castro I, Moreira A. Application of the iPLUS non-coding sequence in improving biopharmaceuticals production. Front Bioeng Biotechnol 2024; 12:1355957. [PMID: 38380261 PMCID: PMC10876878 DOI: 10.3389/fbioe.2024.1355957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
The biotechnological landscape has witnessed significant growth in biological therapeutics particularly in the field of recombinant protein production. Here we investigate the function of 3'UTR cis-regulatory elements in increasing mRNA and protein levels in different biological therapeutics and model systems, spanning from monoclonal antibodies to mRNA vaccines. We explore the regulatory function of iPLUS - a universal sequence capable of consistently augmenting recombinant protein levels. By incorporating iPLUS in a vector to express a monoclonal antibody used in immunotherapy, in a mammalian cell line used by the industry (ExpiCHO), trastuzumab production increases by 2-fold. As yeast Pichia pastoris is widely used in the manufacture of industrial enzymes and pharmaceuticals, we then used iPLUS in tandem (3x) and iPLUSv2 (a variant of iPLUS) to provide proof-of-concept data that it increases the production of a reporter protein more than 100-fold. As iPLUS functions by also increasing mRNA levels, we hypothesize that these sequences could be used as an asset in the mRNA vaccine industry. In fact, by including iPLUSv2 downstream of Spike we were able to double its production. Moreover, the same effect was observed when we introduced iPLUSv2 downstream of MAGEC2, a tumor-specific antigen tested for cancer mRNA vaccines. Taken together, our study provides data (TLR4) showing that iPLUS may be used as a valuable asset in a variety of systems used by the biotech and biopharmaceutical industry. Our results underscore the critical role of non-coding sequences in controlling gene expression, offering a promising avenue to accelerate, enhance, and cost-effectively optimize biopharmaceutical production processes.
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Affiliation(s)
- Inês Reis-Claro
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria Inês Silva
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana Moutinho
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Beatriz C. Garcia
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Sales‐Vallverdú A, Gasset A, Requena‐Moreno G, Valero F, Montesinos‐Seguí JL, Garcia‐Ortega X. Synergic kinetic and physiological control to improve the efficiency of Komagataella phaffii recombinant protein production bioprocesses. Microb Biotechnol 2024; 17:e14411. [PMID: 38376073 PMCID: PMC10877992 DOI: 10.1111/1751-7915.14411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/28/2023] [Accepted: 01/07/2024] [Indexed: 02/21/2024] Open
Abstract
The yeast Komagataella phaffii (Pichia pastoris) is currently considered a versatile and highly efficient host for recombinant protein production (RPP). Interestingly, the regulated application of specific stress factors as part of bioprocess engineering strategies has proven potential for increasing the production of recombinant products. This study aims to evaluate the impact of controlled oxygen-limiting conditions on the performance of K. phaffii bioprocesses for RPP in combination with the specific growth rate (μ) in fed-batch cultivations. In this work, Candida rugosa lipase 1 (Crl1) production, regulated by the constitutive GAP promoter, growing at different nominal μ (0.030, 0.065, 0.100 and 0.120 h-1 ) under both normoxic and hypoxic conditions in carbon-limiting fed-batch cultures is analysed. Hypoxic fermentations were controlled at a target respiratory quotient (RQ) of 1.4, with excellent performance, using an innovative automated control based on the stirring rate as the manipulated variable developed during this study. The results conclude that oxygen limitation positively affects bioprocess efficiency under all growing conditions compared. The shift from respiratory to respiro-fermentative metabolism increases bioprocess productivity by up to twofold for the specific growth rates evaluated. Moreover, the specific product generation rate (qp ) increases linearly with μ, regardless of oxygen availability. Furthermore, this hypoxic boosting effect was also observed in the production of Candida antarctica lipase B (CalB) and pro-Rhizopus oryzae lipase (proRol), thus proving the synergic effect of kinetic and physiological stress control. Finally, the Crl1 production scale-up was conducted successfully, confirming the strategy's scalability and the robustness of the results obtained at the bench-scale level.
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Affiliation(s)
- Albert Sales‐Vallverdú
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Arnau Gasset
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Guillermo Requena‐Moreno
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - José Luis Montesinos‐Seguí
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
| | - Xavier Garcia‐Ortega
- Department of Chemical, Biological and Environmental EngineeringSchool of Engineering, Universitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
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Elsäßer G, Seidl T, Pfannstiel J, Schaller A, Stührwohldt N. Characterization of Prolyl-4-Hydroxylase Substrate Specificity Using Pichia pastoris as an Efficient Eukaryotic Expression System. Methods Mol Biol 2024; 2731:59-80. [PMID: 38019426 DOI: 10.1007/978-1-0716-3511-7_5] [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: 11/30/2023]
Abstract
The use of eukaryotic expression systems facilitates the heterologous expression of complex eukaryotic proteins in their post-translationally modified and biologically active state, as a prerequisite for subsequent biochemical characterization and functional analysis. Here we describe the complete workflow for the expression of Arabidopsis thaliana prolyl-4-hydroxylases (P4Hs) in the methylotrophic yeast Pichia pastoris (renamed as Komagataella phaffii), for the extraction of the recombinant enzymes, purification by affinity chromatography, and characterization of P4H activity and specificity toward oligopeptide substrates by mass spectrometry. We expressed eight of the 13 Arabidopsis P4Hs and show that they are all active against proline-rich extensin-derived peptides. However, three of them differed in substrate specificity and were also able to hydroxylate the CLEL9 signaling peptide, featuring a single proline within its mature peptide sequence.
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Affiliation(s)
- Gerith Elsäßer
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Tim Seidl
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, Stuttgart, Germany
| | - Andreas Schaller
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Nils Stührwohldt
- Department of Plant Physiology and Biochemistry, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
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11
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Coltman BL, Rebnegger C, Gasser B, Zanghellini J. Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii. Microb Biotechnol 2024; 17:e14386. [PMID: 38206275 PMCID: PMC10832545 DOI: 10.1111/1751-7915.14386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024] Open
Abstract
Retentostat cultivations have enabled investigations into substrate-limited near-zero growth for a number of microbes. Quantitative physiology at these near-zero growth conditions has been widely discussed, yet characterisation of the fluxome is relatively under-reported. We investigated the rewiring of metabolism in the transition of a recombinant protein-producing strain of Komagataella phaffii to glucose-limited near-zero growth rates. We used cultivation data from a 200-fold range of growth rates and comprehensive biomass composition data to integrate growth rate dependent biomass equations, generated using a number of different approaches, into a K. phaffii genome-scale metabolic model. Here, we show that a non-growth-associated maintenance value of 0.65 mmol ATP g CDW - 1 h - 1 and a growth-associated maintenance value of 108 mmol ATP g CDW - 1 lead to accurate growth rate predictions. In line with its role as energy source, metabolism is rewired to increase the yield of ATP per glucose. This includes a reduction of flux through the pentose phosphate pathway, and a greater utilisation of glycolysis and the TCA cycle. Interestingly, we observed activity of an external, non-proton translocating NADH dehydrogenase in addition to the malate-aspartate shuttle. Regardless of the method used for the generation of biomass equations, a similar, yet different, growth rate dependent rewiring was predicted. As expected, these differences between the different methods were clearer at higher growth rates, where the biomass equation provides a much greater constraint than at slower growth rates. When placed on an increasingly limited glucose diet, the metabolism of K. phaffii adapts, enabling it to continue to drive critical processes sustaining its high viability at near-zero growth rates.
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Affiliation(s)
- Benjamin Luke Coltman
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Corinna Rebnegger
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Brigitte Gasser
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyViennaAustria
- Department of Analytical ChemistryUniversity of ViennaViennaAustria
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12
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Arjmand S. Promoters in Pichia pastoris: A Toolbox for Fine-Tuned Gene Expression. Methods Mol Biol 2024; 2844:159-178. [PMID: 39068339 DOI: 10.1007/978-1-0716-4063-0_11] [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: 07/30/2024]
Abstract
This chapter reviews the different promoters used to control gene expression in the yeast Pichia pastoris, mainly for recombinant protein production. It covers natural inducible, derepressed, and constitutive promoters, as well as engineered synthetic/hybrid promoters, orthologous promoters from related yeasts, and emerging bidirectional promoters. Key examples, characteristics, and regulatory mechanisms are discussed for each promoter class. Recent efforts in promoter engineering through rational design, mutagenesis, and computational approaches are also highlighted. Looking ahead, we anticipate further developments that will enhance promoter design for Pichia pastoris. Overall, this comprehensive overview underscores the importance of promoter choice and engineering for fully harnessing Pichia pastoris biotechnological potential.
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Affiliation(s)
- Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran.
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13
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Fernandes Fidelis C, Silva de Araújo L, Prates-Patarroyo PA, Martins-Kalks KH, Licursi de Oliveira L, Vargas Viloria MI, Tafur-Gómez GA, Patarroyo Salcedo JH. Immunisation with Neospora caninum subunits rsNcSAG4 and rsNcGRA1 (NcSAG4 and NcGRA1 epitopes construct) in BALB/c mice: the profile of the immune response and controlling the vertical transmission. Parasitol Res 2023; 123:58. [PMID: 38110570 PMCID: PMC10728228 DOI: 10.1007/s00436-023-08020-0] [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: 04/17/2023] [Accepted: 11/21/2023] [Indexed: 12/20/2023]
Abstract
Neospora caninum is an apicomplexan protozoan that causes neosporosis, which has a high economic impact on cattle herds with no available vaccine. During infection, the secretion of dense granules and the expression of surface antigens play an important role in hosting immunomodulation. However, some epitopes of those antigens are immunogenic, and using these fractions could improve the subunit antigens in vaccine design. This study evaluates the recombinant peptides rsNcGRA1 and rsNcSAG4 derived from NcGRA1 and NcSAG4 native antigens as vaccine candidates produced by a fermentative process in the yeast culture system of Komagataella phaffii strain Km71, confirmed by colony PCR, SDS-PAGE, and western blotting. The assay was conducted in BALB/c mice using the peptides at low (25 μg) and standard (50 μg) dosages in monovalent and combined administrations at three time points with saponin as an adjuvant assessing the immunogenicity by antibodies response and cytokine production. We challenge the females after pregnancy confirmation using 2 × 105 NC-1 tachyzoites previously propagated in Vero cells. We assessed the chronic infection in dams and vertical transmission in the offspring by PCR and histopathology. Mice, especially those immunised with combined peptides and monovalent rsNcGRA1 at a standard dose, controlling the chronic infection in dams with the absence of clinical manifestations, showed an immune response with induction of IgG1, a proper balance between Th1/Th2 cytokines and reduced vertical transmission in the pups. In contrast, dams inoculated with a placebo vaccine showed clinical signs, low-scored brain lesions, augmented chronic infection with 80% positivity, 31% mortality in pups, and 81% vertical transmission. These findings indicate that rsNcGRA1 peptides in monovalent and combined with rsNCSAG4 at standard dose are potential vaccine candidates and improve the protective immune response against neosporosis in mice.
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Affiliation(s)
- Cintia Fernandes Fidelis
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Leandro Silva de Araújo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Pablo A Prates-Patarroyo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Karlos H Martins-Kalks
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Leandro Licursi de Oliveira
- Laboratório de Imunoquímica e Glicobiologia, Departamento de Biologia Geral, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Marlene Isabel Vargas Viloria
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil
| | - Gabriel A Tafur-Gómez
- Universidad de Ciencias Aplicadas y Ambientales - U.D.C.A, Bogotá, 111166, Colombia.
| | - Joaquín Hernán Patarroyo Salcedo
- Laboratório de Biologia e Controle de Hematozoários e Vetores, Departamento de Veterinária, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Universidade Federal de Viçosa - UFV, CEP, Viçosa, MG, 36570-900, Brazil.
- Patsos Biotecnologia, Parque tecnológico de Viçosa, CEP, Viçosa, MG, 36570-900, Brazil.
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14
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Verdú-Navarro F, Moreno-Cid JA, Weiss J, Egea-Cortines M. The advent of plant cells in bioreactors. FRONTIERS IN PLANT SCIENCE 2023; 14:1310405. [PMID: 38148861 PMCID: PMC10749943 DOI: 10.3389/fpls.2023.1310405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/01/2023] [Indexed: 12/28/2023]
Abstract
Ever since agriculture started, plants have been bred to obtain better yields, better fruits, or sustainable products under uncertain biotic and abiotic conditions. However, a new way to obtain products from plant cells emerged with the development of recombinant DNA technologies. This led to the possibility of producing exogenous molecules in plants. Furthermore, plant chemodiversity has been the main source of pharmacological molecules, opening a field of plant biotechnology directed to produce high quality plant metabolites. The need for different products by the pharma, cosmetics agriculture and food industry has pushed again to develop new procedures. These include cell production in bioreactors. While plant tissue and cell culture are an established technology, beginning over a hundred years ago, plant cell cultures have shown little impact in biotechnology projects, compared to bacterial, yeasts or animal cells. In this review we address the different types of bioreactors that are currently used for plant cell production and their usage for quality biomolecule production. We make an overview of Nicotiana tabacum, Nicotiana benthamiana, Oryza sativa, Daucus carota, Vitis vinifera and Physcomitrium patens as well-established models for plant cell culture, and some species used to obtain important metabolites, with an insight into the type of bioreactor and production protocols.
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Affiliation(s)
- Fuensanta Verdú-Navarro
- Bioprocessing R&D Department, Bionet, Parque Tecnológico Fuente Álamo, Fuente Álamo, Spain
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Juan A. Moreno-Cid
- Bioprocessing R&D Department, Bionet, Parque Tecnológico Fuente Álamo, Fuente Álamo, Spain
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
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15
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Joseph JA, Akkermans S, Van Impe JF. Macroscopic modeling of the growth and substrate consumption of wild type and genetically modified Pichia pastoris. Biotechnol J 2023; 18:e2300164. [PMID: 37688402 DOI: 10.1002/biot.202300164] [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: 04/13/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Pichia pastoris is a popular yeast platform to generate several industrially relevant products which have applications in a wide range of sectors. The complexities in the processes due to the addition of a foreign gene are not widely explored. Since these complexities can be dependent on the strain characteristics, promoter, and type of protein produced, it is vital to investigate the growth and substrate consumption patterns of the host to facilitate customized process optimization. In this study, the growth rates of P. pastoris GS115 wild type (WT) and genetically modified (GM) strains grown on glycerol and methanol in batch cultivation mode were estimated and the model providing the best representation of the true growth kinetics based on substrate consumption was identified. It was observed that the growth of P. pastoris exhibits Haldane kinetics on glycerol rather than the most commonly used Monod kinetics due to the inability of the latter to describe growth inhibition at high concentrations of glycerol. Whereas, the cardinal parameter model, a newly proposed model for this application, was found to be the best fitting to describe the growth of P. pastoris on methanol due to its ability to describe methanol toxicity. Interestingly, the findings from this study concluded that in both substrates, the genetically engineered strain exhibited a higher growth rate compared to the WT strain. Such an observation has not been established yet in other published works, indicating an opportunity to further optimize the carbon source feeding strategies when the host is grown in fed-batch mode.
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Affiliation(s)
- Jewel Ann Joseph
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Simen Akkermans
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Jan F Van Impe
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
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16
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Hidalgo-Gajardo A, Gutiérrez N, Lamazares E, Espinoza F, Escobar-Riquelme F, Leiva MJ, Villavicencio C, Mena-Ulecia K, Montesino R, Altamirano C, Sánchez O, Rivas CI, Ruíz Á, Toledo JR. Co-Formulation of Recombinant Porcine IL-18 Enhances the Onset of Immune Response in a New Lawsonia intracellularis Vaccine. Vaccines (Basel) 2023; 11:1788. [PMID: 38140192 PMCID: PMC10747595 DOI: 10.3390/vaccines11121788] [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: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Pig is one of the most consumed meats worldwide. One of the main conditions for pig production is Porcine Enteropathy caused by Lawsonia intracellularis. Among the effects of this disease is chronic mild diarrhea, which affects the weight gain of pigs, generating economic losses. Vaccines available to prevent this condition do not have the desired effect, but this limitation can be overcome using adjuvants. Pro-inflammatory cytokines, such as interleukin 18 (IL-18), can improve an immune response, reducing the immune window of protection. In this study, recombinant porcine IL-18 was produced and expressed in Escherichia coli and Pichia pastoris. The protein's biological activity was assessed in vitro and in vivo, and we determined that the P. pastoris protein had better immunostimulatory activity. A vaccine candidate against L. intracellularis, formulated with and without IL-18, was used to determine the pigs' cellular and humoral immune responses. Animals injected with the candidate vaccine co-formulated with IL-18 showed a significant increase of Th1 immune response markers and an earlier increase of antibodies than those vaccinated without the cytokine. This suggests that IL-18 acts as an immunostimulant and vaccine adjuvant to boost the immune response against the antigens, reducing the therapeutic window of recombinant protein-based vaccines.
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Affiliation(s)
- Angela Hidalgo-Gajardo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Nicolás Gutiérrez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Emilio Lamazares
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Felipe Espinoza
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
- Centro de Desarrollo e Innovación Biovacuvet SpA, VIII Región, Concepción 4090838, Chile
| | - Fernanda Escobar-Riquelme
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - María J. Leiva
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Carla Villavicencio
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, IX Región, Temuco 4813302, Chile;
| | - Raquel Montesino
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Claudia Altamirano
- Laboratorio de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, V Región, Valparaíso 2362803, Chile;
| | - Oliberto Sánchez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Coralia I. Rivas
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
| | - Álvaro Ruíz
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, XVI Región, Chillán 3812120, Chile;
| | - Jorge R. Toledo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, VIII Región, Concepción 4070386, Chile; (A.H.-G.); (M.J.L.); (C.V.); (C.I.R.)
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17
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Rosmeita CN, Budiarti S, Mustopa AZ, Novianti E, Swasthikawati S, Chairunnisa S, Hertati A, Nurfatwa M, Ekawati N, Hasan N. Expression, purification, and characterization of self-assembly virus-like particles of capsid protein L1 HPV 52 in Pichia pastoris GS115. J Genet Eng Biotechnol 2023; 21:126. [PMID: 37981617 PMCID: PMC10657913 DOI: 10.1186/s43141-023-00571-0] [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: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Cervical cancer caused by the human papillomavirus (HPV) is one of the most frequent malignances globally. HPV 52 is a high-risk cancer-causing genotype that has been identified as the most prevalent type in Indonesia. Virus-like particles (VLP)-based vaccinations against HPV infection could benefit from self-assembled VLP of L1 capsid protein. RESULT The recombinant HPV 52 L1 was expressed in Pichia pastoris on a shake-flask scale with 0.5% methanol induction in this study. The copy number was used to compare the expression level and stability. The colony that survived on a solid medium containing 2000 μg/ml of Zeocin was selected and cultured to express HPV 52 L1. DNA was extracted from the chosen colony, and the copy was determined using qPCR. HPV 52 L1 protein was then purified through fast performance liquid chromatography. Transmission electron microscopy (TEM) evaluation confirmed the VLP self-assembly. The genomic DNA remained intact after 100 generations of serial cultivation under no selective pressure medium conditions, and the protein produced was relatively stable. However, the band intensity was slightly lower than in the parental colony. In terms of copy number, a low copy transformant resulted in low expression but produced a highly stable recombinant clone. Eventually, the L1 protein expressed in Pichia pastoris can self-assemble into VLP. Therefore, recombinant HPV possesses a stable clone and the ability to self-assemble into VLP. CONCLUSION The recombinant L1 HPV 52 protein is successfully expressed in P. pastoris within a size range of approximately 55 kDa and demonstrated favorable stability. The L1 protein expressed in Pichia pastoris successful self-assembled of HPV VLPs, thereby establishing their potential efficacy as a prophylactic vaccine.
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Affiliation(s)
- Chindy Nur Rosmeita
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
| | - Sri Budiarti
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
- Indonesia Research Center for Bioresources and Biotechnology, IPB University, Bogor, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Ela Novianti
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sri Swasthikawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sheila Chairunnisa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurlaili Ekawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
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18
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Wang YS, Gong MH, Wang JH, Yu JC, Li MJ, Xue YP, Zheng YG. Heterologous expression of a deacetylase and its application in L-glufosinate preparation. Bioprocess Biosyst Eng 2023; 46:1639-1650. [PMID: 37733076 DOI: 10.1007/s00449-023-02925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
With potent herbicidal activity, biocatalysis synthesis of L-glufosinate has drawn attention. In present research, NAP-Das2.3, a deacetylase capable of stereoselectively resolving N-acetyl-L-glufosinate to L-glufosinate mined from Arenimonas malthae, was heterologously expressed and characterized. In Escherichia coli, NAP-Das2.3 activity only reached 0.25 U/L due to the formation of inclusive bodies. Efficient soluble expression of NAP-Das2.3 was achieved in Pichia pastoris. In shake flask and 5 L bioreactor fermentation, NAP-Das2.3 activity by recombinant P. pastoris reached 107.39 U/L and 1287.52 U/L, respectively. The optimum temperature and pH for N-acetyl-glufosinate hydrolysis by NAP-Das2.3 were 45 °C and pH 8.0, respectively. The Km and Vmax of NAP-Das2.3 towards N-acetyl-glufosinate were 25.32 mM and 19.23 μmol mg-1 min-1, respectively. Within 90 min, 92.71% of L-enantiomer in 100 mM racemic N-acetyl-glufosinate was converted by NAP-Das2.3. L-glufosinate with high optical purity (e.e.P above 99.9%) was obtained. Therefore, the recombinant NAP-Das2.3 might be an alternative for L-glufosinate biosynthesis.
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Affiliation(s)
- Yuan-Shan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Mei-Hua Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jin-Hao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Jia-Cheng Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Mei-Jing Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China.
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No. 18, Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- Engineering Research Centre of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, No. 18,Chaowang Road, Hangzhou, 310014, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Centre for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Akentyev P, Sokolova D, Korzhenkov A, Gubaidullin I, Kozlov D. Expression level of SOR1 is a bottleneck for efficient sorbitol utilization by yeast Komagataella kurtzmanii. Yeast 2023; 40:414-424. [PMID: 37272406 DOI: 10.1002/yea.3884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023] Open
Abstract
The yeast strain Komagataella kurtzmanii VKPM Y-727 shows a significant defect in sorbitol utilization compared to closely related yeast K. phaffii (including strains formerly identified as Pichia pastoris). Our aim was to investigate the factors that determine the phenotype of the wild-type strain and to obtain a K. kurtzmanii strain with an improved ability to utilize sorbitol. We sequenced and annotated the genome of K. kurtzmanii VKPM Y-727 and compared it with that of K. phaffii GS115. Five K. phaffii GS115 genes that might be involved in sorbitol metabolism were selected and transferred into K. kurtzmanii Y-727. The transfer of the modified SOR1 gene resulted in an increased growth rate of K. kurtzmanii in sorbitol, despite the fact that Y-727 already contains its own SOR1 gene without any apparent mutations. The enzymes encoded by the SOR1 genes were analyzed in vitro and found to have similar properties. Differences in promoter activity were assessed using lacZ as a reporter gene, and the PSDH727 (promoter of SOR1 (SDH727) from K. kurtzmanii Y-727) promoter was shown to be 1.5-2.0 times weaker than PSDH115 (promoter of SOR1 (SDH115) from K. phaffii GS115). Moreover, both promoters were less active in K. kurtzmanii than in K. phaffii when evaluated in cells grown in synthetic complete media with glucose or sorbitol. Thus, SOR1 gene expression was identified as a bottleneck in sorbitol metabolism in K. kurtzmanii. Also, the positive effect of additional modified SOR1 gene copies was observed in both yeasts, as K. kurtzmanii and K. phaffii could grow on synthetic complete media with sorbitol three times faster than the original K. phaffii GS115 strain.
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Affiliation(s)
- Philipp Akentyev
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - Daria Sokolova
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | | | - Irek Gubaidullin
- National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, Russia
| | - Dmitry Kozlov
- National Research Center "Kurchatov Institute", Moscow, Russia
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20
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Zazulya AZ, Semkiv MV, Stec M, Cyske Z, Gaffke L, Pierzynowska K, Węgrzyn G, Sibirny AA. The Komagatella phaffii ACG1 gene, encoding β-1,6-N-acetylglucosaminyltransferase, is involved in the autophagy of cytosolic and peroxisomal proteins. Yeast 2023; 40:367-376. [PMID: 36814084 DOI: 10.1002/yea.3846] [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: 11/24/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The methylotrophic yeast Komagataella phaffii is considered one of the most effective producers of recombinant proteins of industrial importance. Effective producers should be characterized by the maximal reduction of degradation of the cytosolic recombinant proteins. The mechanisms of degradation of cytosolic proteins in K. phaffii have not been elucidated; however, data suggest that they are partially degraded in the autophagic pathway. To identify factors that influence this process, a developed system for the selection of recombinant strains of K. phaffii with impaired autophagic degradation of the heterologous model cytosolic protein (yeast β-galactosidase) was used for insertional tagging of the genes involved in cytosolic proteins degradation. In one of the obtained strains, the insertion cassette disrupted the open reading frame of the gene encoding β-1,6-N-acetylglucosaminyltransferase. A recombinant strain with deletion of this gene was also obtained. The rate of degradation of the β-galactosidase enzyme was two times slower in the insertion mutant and 1.5 times slower in the deletion strain as compared to the parental strain with native β-1,6-N-acetylglucosaminyltransferase. The rate of degradation of native K. phaffii cytosolic and peroxisomal enzymes, formaldehyde dehydrogenase, formate dehydrogenase, and alcohol oxidase, respectively, showed similar trends to that of β-galactosidase-slower degradation in the deletion and insertional mutants as compared to the wild-type strain, but faster protein degradation relative to the strain completely defective in autophagy. We conclude that K. phaffii gene designated ACG1, encoding β-1,6-N-acetylglucosaminyltransferase, is involved in autophagy of the cytosolic and peroxisomal proteins.
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Affiliation(s)
- Anastasiya Z Zazulya
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Marta V Semkiv
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Maxim Stec
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Zuzanna Cyske
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Karolina Pierzynowska
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Andriy A Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
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21
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De Groeve M, Laukens B, Schotte P. Optimizing expression of Nanobody® molecules in Pichia pastoris through co-expression of auxiliary proteins under methanol and methanol-free conditions. Microb Cell Fact 2023; 22:135. [PMID: 37481525 PMCID: PMC10362571 DOI: 10.1186/s12934-023-02132-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/24/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Ablynx NV, a subsidiary of Sanofi, has a long-standing focus on the development of Nanobody® molecules as biopharmaceuticals (Nanobody® is a registered trademark of Ablynx NV). Nanobody molecules are single variable domains, and they have been met with great success part due to their favorable expression properties in several microbial systems. Nevertheless, the search for the host of the future is an ongoing and challenging process. Komagataella phaffi (Pichia pastoris) is one of the most suitable organisms to produce Nanobody molecules. In addition, genetic engineering of Pichia is easy and an effective approach to improve titers. RESULTS Here we report that P. pastoris engineered to co-express genes encoding four auxiliary proteins (HAC1, KAR2, PDI and RPP0), leads to a marked improvement in the expression of Nanobody molecules using the AOX1 methanol induction system. Titer improvement is mainly attributed to HAC1, and its beneficial effect was also observed in a methanol-free expression system. CONCLUSION Our findings are based on over a thousand fed-batch fermentations and offer a valuable guide to produce Nanobody molecules in P. pastoris. The presented differences in expressability between types of Nanobody molecules will be helpful for researchers to select both the type of Nanobody molecule and Pichia strain and may stimulate further the development of a more ecological methanol-free expression platform.
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Affiliation(s)
- Manu De Groeve
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Bram Laukens
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium
| | - Peter Schotte
- Centre of Excellence in Host creation and Upstream processing at Sanofi R&D, Ghent, Belgium.
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22
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Li C, Cao H, Wu W, Meng G, Zhao C, Cao Y, Yuan J. Expression and characterization of α-L-arabinofuranosidase derived from Aspergillus awamori and its enzymatic degradation of corn byproducts with xylanase. BIORESOURCE TECHNOLOGY 2023:129278. [PMID: 37290707 DOI: 10.1016/j.biortech.2023.129278] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
In this study, α-L-arabinofuranosidase (AF) from Aspergillus awamori was heterologously expressed in Pichia pastoris X33, with a 1-fold increase in AF activity after codon and vector optimization. AF remained stable at 60-65 °C and displayed a broad pH stability range of 2.5-8.0. It also demonstrated considerable resistance to pepsin and trypsin. Furthermore, compared with xylanase alone, AF with xylanase exhibited a marked synergistic effect in the degradation of expanded corn bran, corn bran, and corn distillers' dried grains with solubles, reducing sugars by 3.6-fold, 1.4-fold, and 6.5-fold, respectively, with the degree of synergy increasing to 4.61, 2.44, and 5.4, respectively, while in vitro dry matter digestibility values were 17.6%, 5.2%, and 8.8%, respectively. After enzymatic saccharification, corn byproducts were converted to prebiotic xylo-oligosaccharides and arabinoses, thereby demonstrating the favorable properties of AF in the degradation of corn biomass and its byproducts.
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Affiliation(s)
- Chunyue Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Heng Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Meng
- Ningxia Eppen Biotech Co., Ltd., China Agricultural University, Beijing 100193, China
| | - Chunguang Zhao
- Ningxia Eppen Biotech Co., Ltd., China Agricultural University, Beijing 100193, China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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23
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Enhancing Antimicrobial Peptide Productivity in Pichia pastoris (Muts Strain) by Improving the Fermentation Process Based on Increasing the Volumetric Methanol Consumption Rate. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The instability of the protein expression in Pichia pastoris strains has been an issue for various peptide productions. Some modifications to the traditional fermentation process could potentially solve the problem. Here, we consider a four-stage fermentation process to express the CAP2 (cell-penetrating antimicrobial peptide 2) candidate in P. pastoris KM71H, a slow methanol utilization strain. During the fermentation process, CAP2 productivity is limited (6.15 ± 0.21 mg/L·h) by the low overall methanol consumption (approximately 645 g), which is mainly the result of the slow methanol utilization of the P. pastoris KM71H. To overcome this limitation, we increased the cell concentration two-fold prior to the induction stage. A fed-batch process with exponential and dissolved oxygen tension (DOT) stat feeding strategies was deployed to control the glycerol feed, resulting in an increase in cell concentration and enhancement of the volumetric methanol consumption rate. The improved fermentation process increased the overall methanol consumption (approximately 1070 g) and the CAP2 productivity (13.59 ± 0.24 mg/L·h) by 1.66 and 2.21 times, respectively. In addition, the CAP3 (cell-penetrating antimicrobial peptide 3) candidate could also be produced using this improved fermentation process at a high yield of 3.96 ± 0.02 g/L without any further optimization. Note that there was no oxygen limitation during the improved fermentation process operating at high cell density. This could be due to the controlled substrate addition via the DOT stat system.
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24
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Ni B, Feussner K. Ex vivo metabolomics-A hypothesis-free approach to identify native substrate(s) and product(s) of orphan enzymes. Methods Enzymol 2023; 680:303-323. [PMID: 36710016 DOI: 10.1016/bs.mie.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Over the past decade, the number of fully sequenced genomes has increased at an awe-inspiring pace. Similarly, the quality and scope of tools for the prediction of both protein structure and function has seen vast improvements. However, to pinpoint the exact function of a protein, for instance the exact reaction catalyzed by an enzyme, experimental evidence is crucial. At the same time, this step is the main bottleneck when generating a conclusive model for the function of an enzyme and to interpret its function in a physiological context. Hence, a comprehensive experimental strategy for functional annotation of enzymes that is as efficient as possible is required. Ex vivo metabolomics is a powerful non-targeted approach that overcomes several of the challenges inherent to in vitro characterization of enzymes with unknown functions. By incubating the recombinant enzyme of interest in a quasi-native metabolite extract from its tissue of origin under specific environmental and developmental conditions, the complete native substrate range can be tested in a single assay. This unlocks compounds that are commercially unavailable or otherwise difficult to procure. Coupled with non-targeted metabolomics analysis, ex vivo has the capability to test for and identify even unexpected substrates and assign the respective products of the enzymatic reaction.
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Affiliation(s)
- Benedikt Ni
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany
| | - Kirstin Feussner
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, Goettingen, Germany.
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25
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Ávila-Fernández Á, Montiel S, Rodríguez-Alegría ME, Caspeta L, López Munguía A. Simultaneous enzyme production, Levan-type FOS synthesis and sugar by-products elimination using a recombinant Pichia pastoris strain expressing a levansucrase-endolevanase fusion enzyme. Microb Cell Fact 2023; 22:18. [PMID: 36703199 PMCID: PMC9881289 DOI: 10.1186/s12934-022-02009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Although Levan-type fructooligosaccharides (L-FOS) have been shown to exhibit prebiotic properties, no efficient methods for their large-scale production have been proposed. One alternative relies on the simultaneous levan synthesis from sucrose, followed by endolevanase hydrolysis. For this purpose, several options have been described, particularly through the synthesis of the corresponding enzymes in recombinant Escherichia coli. Major drawbacks still consist in the requirement of GRAS microorganisms for enzyme production, but mainly, the elimination of glucose and fructose, the reaction by-products. RESULTS The expression of a fusion enzyme between Bacillus licheniformis endolevanase (LevB1) and B. subtilis levansucrase (SacB) in Pichia pastoris cultures, coupled with the simultaneous synthesis of L-FOS from sucrose and the elimination of the residual monosaccharides, in a single one-pot process was developed. The proof of concept at 250 mL flask-level, resulted in 8.62 g of monosaccharide-free L-FOS and 12.83 gDCW of biomass, after 3 successive sucrose additions (30 g in total), that is a 28.7% yield (w L-FOS/w sucrose) over a period of 288 h. At a 1.5 L bioreactor-level, growth considerably increased and, after 59 h and two sucrose additions, 72.9 g of monosaccharide-free L-FOS and 22.77 gDCW of biomass were obtained from a total of 160 g of sucrose fed, corresponding to a 45.5% yield (w L-FOS/w sucrose), 1.6 higher than the flask system. The L-FOS obtained at flask-level had a DP lower than 20 fructose units, while at bioreactor-level smaller oligosaccharides were obtained, with a DP lower than 10, as a consequence of the lower endolevanase activity in the flask-level. CONCLUSION We demonstrate here in a novel system, that P. pastoris cultures can simultaneously be used as comprehensive system to produce the enzyme and the enzymatic L-FOS synthesis with growth sustained by sucrose by-products. This system may be now the center of an optimization strategy for an efficient production of glucose and fructose free L-FOS, to make them available for their application as prebiotics. Besides, P. pastoris biomass also constitutes an interesting source of unicellular protein.
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Affiliation(s)
- Ángela Ávila-Fernández
- grid.441115.40000 0001 2293 8305Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulte ´, 86150 Villahermosa, Centro, Tabasco Mexico
| | - Silvia Montiel
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - María Elena Rodríguez-Alegría
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - Luis Caspeta
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
| | - Agustín López Munguía
- grid.9486.30000 0001 2159 0001Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad, 2001 Chamilpa, Cuernavaca, Mor. Mexico
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Govindan P, Manjusha P, Saravanan KM, Natesan V, Salmen SH, Alfarraj S, Wainwright M, Shakila H. RETRACTED ARTICLE: Expression and preliminary characterization of the potential vaccine candidate LipL32 of leptospirosis. APPLIED NANOSCIENCE 2023; 13:1801. [PMID: 34608427 PMCID: PMC8483425 DOI: 10.1007/s13204-021-02097-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Pothiaraj Govindan
- grid.10214.360000 0001 2186 7912Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai-21, Tamil Nadu India
| | - Packiyadass Manjusha
- grid.10214.360000 0001 2186 7912Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai-21, Tamil Nadu India
| | - Konda Mani Saravanan
- Scigen Research and Innovation Pvt Ltd, Periyar Technology Business Incubator, Thanjavur, Tamil Nadu 613403 India
| | - Vijayakumar Natesan
- grid.411408.80000 0001 2369 7742Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar, Chidambaram, Tamil Nadu 608002 India
| | - Saleh H. Salmen
- grid.56302.320000 0004 1773 5396Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451 Saudi Arabia
| | - Saleh Alfarraj
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, 11451 Saudi Arabia
| | - Milton Wainwright
- grid.11835.3e0000 0004 1936 9262Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Harshavardhan Shakila
- grid.10214.360000 0001 2186 7912Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai-21, Tamil Nadu India
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Inoue K, Ohsawa S, Ito S, Yurimoto H, Sakai Y. Phosphoregulation of the transcription factor Mxr1 plays a crucial role in the concentration-regulated methanol induction in Komagataella phaffii. Mol Microbiol 2022; 118:683-697. [PMID: 36268798 DOI: 10.1111/mmi.14994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/26/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023]
Abstract
Methylotrophic yeasts can utilize methanol as the sole carbon and energy source, and the expression of their methanol-induced genes is regulated based on the environmental methanol concentration. Our understanding of the function of transcription factors and Wsc family of proteins in methanol-induced gene expression and methanol sensing is expanding, but the methanol signal transduction mechanism remains undetermined. Our study has revealed that the transcription factor KpMxr1 is involved in the concentration-regulated methanol induction (CRMI) in Komagataella phaffii (Pichia pastoris) and that the phosphorylation state of KpMxr1 changes based on methanol concentration. We identified the functional regions of KpMxr1 and determined its multiple phosphorylation sites. Non-phosphorylatable substitution mutations of these newly identified phosphorylated threonine and serine residues resulted in significant defects in CRMI. We revealed that KpMxr1 receives the methanol signal from Wsc family proteins via KpPkc1 independent of the mitogen-activated protein kinase (MAPK) cascade and speculate that the activity of KpPkc1 influences KpMxr1 phosphorylation state. We propose that the CRMI pathway from Wsc to KpMxr1 diverges from KpPkc1 and that phosphoregulation of KpMxr1 plays a crucial role in CRMI.
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Affiliation(s)
- Koichi Inoue
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shin Ohsawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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28
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Yuan H, Zhou Y, Lin Y, Tu R, Guo Y, Zhang Y, Wang Q. Microfluidic screening and genomic mutation identification for enhancing cellulase production in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:50. [PMID: 35568955 PMCID: PMC9107654 DOI: 10.1186/s13068-022-02150-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Pichia pastoris is a widely used host organism for heterologous production of industrial proteins, such as cellulases. Although great progress has been achieved in improving protein expression in P. pastoris, the potential of the P. pastoris expression system has not been fully explored due to unknown genomic impact factors. Recently, whole-cell directed evolution, employing iterative rounds of genome-wide diversity generation and high-throughput screening (HTS), has been considered to be a promising strategy in strain improvement at the genome level.
Results
In this study, whole-cell directed evolution of P. pastoris, employing atmospheric and room temperature plasma (ARTP) mutagenesis and droplet-based microfluidic HTS, was developed to improve heterogenous cellulase production. The droplet-based microfluidic platform based on a cellulase-catalyzed reaction of releasing fluorescence was established to be suitable for methanol-grown P. pastoris. The validation experiment showed a positive sorting efficiency of 94.4% at a sorting rate of 300 droplets per second. After five rounds of iterative ARTP mutagenesis and microfluidic screening, the best mutant strain was obtained and exhibited the cellulase activity of 11,110 ± 523 U/mL, an approximately twofold increase compared to the starting strain. Whole-genome resequencing analysis further uncovered three accumulated genomic alterations in coding region. The effects of point mutations and mutant genes on cellulase production were verified using reconstruction of point mutations and gene deletions. Intriguingly, the point mutation Rsc1G22V was observed in all the top-performing producers selected from each round, and gene deletion analysis confirmed that Rsc1, a component of the RSC chromatin remodeling complex, might play an important role in cellulase production.
Conclusions
We established a droplet-based microfluidic HTS system, thereby facilitating whole-cell directed evolution of P. pastoris for enhancing cellulase production, and meanwhile identified genomic alterations by whole-genome resequencing and genetic validation. Our approaches and findings would provide guides to accelerate whole-cell directed evolution of host strains and enzymes of high industrial interest.
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Cordeiro FA, Amorim FG, Boldrini-França J, Pinheiro-Júnior EL, Cardoso IA, Zoccal KF, Peigneur S, Faccioli LH, Tytgat J, Arantes EC. Heterologous expression of Ts8, a neurotoxin from Tityus serrulatus venom, evidences its antifungal activity. Toxicon 2022; 218:47-56. [PMID: 36063971 DOI: 10.1016/j.toxicon.2022.08.019] [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: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
In this study we expressed the Ts8, a neurotoxin from Tityus serrulatus scorpion venom, in Pichia pastoris yeast. We evaluated the peptide expression in different conditions, such as pH, temperature, and addition of casamino acids supplement. Analyses of expressed products by mass spectrometry and Edman degradation showed that rTs8 has sites that allow its cleavage by yeast proteases released into the culture medium. The casamino acids addition was favourable for toxin expression, however, was not sufficient to minimize proteolytic degradation. Functional assays with recombinant toxin fragments and native toxins have demonstrated the release of cytokines such as TNF-α and IL-1β in some peptides tested. In addition, the toxins were shown to inhibit the Pichia pastoris growth in antifungal test and were not toxic to alveolar macrophages cells at the concentrations analyzed The electrophysiological screening, by voltage clamp technique, showed that the rTs8 fragment with the highest molecular weight inhibited the Kv1.3 channel, whereas the N-terminal fragment had no activity on the ion channels tested.
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Affiliation(s)
- Francielle Almeida Cordeiro
- Department of BioMolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
| | - Fernanda Gobbi Amorim
- Mass Spectrometry Laboratory, Department of Chemistry, Faculty of Sciences, University of Liège, Bât. B6C Laboratoire de spectrométrie de Masse (L.S.M.), Quartier Agora, Allée du six Août 11, 4000, Liège, Belgium
| | - Johara Boldrini-França
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
| | | | - Iara Aimê Cardoso
- Department of BioMolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Karina Furlani Zoccal
- Center University Barão of Mauá, St. Ramos of Azavedo, N 423, 14090-062, Ribeirão Preto, SP, Brazil
| | - Steve Peigneur
- Toxicology and Pharmacology, KU Leuven, O&N II Herestraat 49 - PO Box 922, 3000, Leuven, Belgium
| | - Lucia Helena Faccioli
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, O&N II Herestraat 49 - PO Box 922, 3000, Leuven, Belgium
| | - Eliane Candiani Arantes
- Department of BioMolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Kavianpour A, Ashjari M, Hosseini SN, Khatami M. Quantitative assessment of LPS-HBsAg interaction by introducing a novel application of immunoaffinity chromatography. Prep Biochem Biotechnol 2022; 53:672-682. [PMID: 36244016 DOI: 10.1080/10826068.2022.2132512] [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: 10/17/2022]
Abstract
Lipopolysaccharide (LPS), as a stubborn contamination, should be monitored and kept in an acceptable level during the pharmaceutical production process. Recombinant hepatitis B surface antigen (r-HBsAg) is one of the recombinant biological products, which is probable to suffer from extrinsic endotoxin due to its long and complex production process. This research aims to assess the potential interaction between LPS and r-HBsAg by recruiting immunoaffinity chromatography (IAC) as a novel tool to quantify the interaction. Molecular modeling was performed on the HBsAg molecule to theoretically predict its potential binding and interaction sites. Then dynamic light scattering (DLS) analysis was implemented on HBsAg, LPS, and mixtures of them to reveal the interaction. The virus-like particle (VLP) structure of HBsAg and the ribbon-like structure of LPS were visualized by transmission electron microscopy (TEM). Finally, the interaction was quantified by applying various LPS/HBsAg ratios ranging from 1.67 to 120 EU/dose in the IAC. Consequently, the LPS/HBsAg ratios in the eluate were measured from 1.67 to a maximum of 92.5 EU/dose. The results indicated that 77 to 100% of total LPS interacted with HBsAg by an inverse relationship to the incubated LPS concentration. The findings implied that the introduced procedure is remarkably practical in the quantification of LPS interaction with a target recombinant protein.
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Affiliation(s)
- Alireza Kavianpour
- Department of Chemical Engineering, Faculty of Engineering, University of Kashan, Kashan, Iran
| | - Mohsen Ashjari
- Nanostructures and Bioresearch Lab, Department of Chemical Engineering, Faculty of Engineering, University of Kashan, Kashan, Iran
| | - Seyed Nezamedin Hosseini
- Department of Hepatitis B Vaccine Production, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Khatami
- Department of Hepatitis B Vaccine Production, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
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Acar M, Unver Y. Constitutive and extracellular expression of pectin methylesterase from Pectobacterium chrysanthemi in Pichia pastoris. 3 Biotech 2022; 12:219. [PMID: 35965660 PMCID: PMC9365906 DOI: 10.1007/s13205-022-03291-3] [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: 01/12/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Pectin methylesterase (PME) which is widely used in the cosmetic, food and pharmaceutical industries catalyses the hydrolysis of the methyl ester of pectin to yield methanol and free carboxyl groups. This study was performed to produce active pectin methylesterase (PME) extracellularly from Pectobacterium chrysanthemi in Pichia pastoris. Firstly, pGKBα was constructed for the secretion of heterologous protein. After it was cloned in Escherichia coli cells and the sequence was affirmed, PME gene was inserted into pGKBα. So, pGKBα-PME carried the PME gene in correct position was cloned in E. coli cells. Then, P. pastoris X-33 cells were transformed with linearized pGKBα-PME and six transformants were cultivated for recombinant PME production. It was observed that one of them had a high-capacity secretion of active PME. The molecular mass of extracellular PME enzyme was found to be about 59 kDa. The PME enzyme from P. chrysanthemi was produced by P. pastoris for the first time in this study. This recombinant enzyme might be produced in a large scale and also purified from the culture medium. Then, the purified enzyme might be used for clarification and increasing yield of juice in food industrial applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03291-3.
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Affiliation(s)
- Melek Acar
- Department of Molecular Biology and Genetics, Atatürk University, 25240 Erzurum, Turkey
| | - Yagmur Unver
- Department of Molecular Biology and Genetics, Atatürk University, 25240 Erzurum, Turkey
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Peng H, Wang M, Wang N, Yang C, Guo W, Li G, Huang S, Wei D, Liu D. Different N-Glycosylation Sites Reduce the Activity of Recombinant DSPAα2. Curr Issues Mol Biol 2022; 44:3930-3947. [PMID: 36135182 PMCID: PMC9497888 DOI: 10.3390/cimb44090270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 12/01/2022] Open
Abstract
Bat plasminogen activators α2 (DSPAα2) has extremely high medicinal value as a powerful natural thrombolytic protein. However, wild-type DSPAα2 has two N-glycosylation sites (N185 and N398) and its non-human classes of high-mannose-type N-glycans may cause immune responses in vivo. By mutating the N-glycosylation sites, we aimed to study the effect of its N-glycan chain on plasminogen activation, fibrin sensitivity, and to observe the physicochemical properties of DSPAα2. A logical structure design was performed in this study. Four single mutants and one double mutant were constructed and expressed in Pichia pastoris. When the N398 site was eliminated, the plasminogen activator in the mutants had their activities reduced to ~40%. When the N185 site was inactivated, there was a weak decrease in the plasminogen activation of its mutant, while the fibrin sensitivity significantly decreased by ~10-fold. Neither N-glycosylation nor deglycosylation mutations changed the pH resistance or heat resistance of DSPAα2. This study confirms that N-glycosylation affects the biochemical function of DSPAα2, which provides a reference for subsequent applications of DSPAα2.
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Affiliation(s)
- Huakang Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengqi Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caifeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfang Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gangqiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sumei Huang
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dehu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence:
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Gätjen D, Tomszak F, Dettmann JC, Droste M, Nölle V, Wieczorek M. Design of a novel switchable antibody display system in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:6209-6224. [PMID: 35953606 DOI: 10.1007/s00253-022-12108-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Yeast surface display (YSD) has been shown to represent a powerful tool in the field of antibody discovery and engineering as well as for selection of high producer clones. However, YSD is predominantly applied in Saccharomyces cerevisiae, whereas expression of heterologous proteins is generally favored in the non-canonical yeast Pichia pastoris (Komagataella phaffii). Establishment of surface display in P. pastoris would therefore enable antibody selection and expression in a single host. Here we describe the generation of a Pichia surface display (PSD) system based on antibody expression from episomal plasmids. By screening a diverse set of expression vectors using Design of Experiments (DoE), the effect of different genetic elements on the surface expression of antibody fragments was analyzed. Among the tested genetic elements, we found that the combination of P. pastoris formaldehyde dehydrogenase (FLD1) promoter, S. cerevisiae invertase 2 signal peptide (SUC2), and α-agglutinin cell wall protein (SAG1) including an autonomously replicating sequence of Kluyveromyces lactis (panARS) were contributing most strongly to higher display levels of three tested antibody fragments. Employing this combination resulted in the display of antibody fragments for up to 25% of cells. Despite significantly reduced expression levels in PSD compared to well-established YSD in S. cerevisiae, similar fractions of antigen binding single-chain variable fragments (scFvs) were observed (80% vs. 84%). In addition, plasmid stability assays and flow cytometric analysis demonstrated the efficient plasmid clearance of cells and associated loss of antibody fragment display after removal of selective pressure. KEY POINTS: • First report of antibody display in P. pastoris using episomal plasmids. • Identification of genetic elements conferring highest levels of antibody display. • Comparable antigen binding capacity of displayed scFvs for PSD compared to YSD.
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Affiliation(s)
- Dominic Gätjen
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Florian Tomszak
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | | | - Miriam Droste
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Volker Nölle
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Marek Wieczorek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany.
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High-level production of recombinant HBcAg virus-like particles in a mathematically modelled P. pastoris GS115 Mut + bioreactor process under controlled residual methanol concentration. Bioprocess Biosyst Eng 2022; 45:1447-1463. [PMID: 35939139 PMCID: PMC9358087 DOI: 10.1007/s00449-022-02754-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/04/2022] [Indexed: 11/08/2022]
Abstract
Recombinant hepatitis B core antigen (HBcAg) molecules, produced in heterologous expression systems, self-assemble into highly homogenous and non-infectious virus-like particles (VLPs) that are under extensive research for biomedical applications. HBcAg production in the methylotrophic yeast P. pastoris has been well documented; however, productivity screening under various residual methanol levels has not been reported for bioreactor processes. HBcAg production under various excess methanol levels of 0.1, 1.0 and 2.0 g L−1 was investigated in this research. Results indicate that, under these particular conditions, the total process and specific protein yields of 876–1308 mg L−1 and 7.9–11.2 mg gDCW−1, respectively, were achieved after 67–75 h of cultivation. Produced HBcAg molecules were efficiently purified and the presence of highly immunogenic, correctly formed and homogenous HBcAg-VLPs with an estimated purity of 90% was confirmed by electron microscopy. The highest reported HBcAg yield of 1308 mg L−1 and 11.2 mg gDCW−1 was achieved under limiting residual methanol concentration, which is about 2.5 times higher than the next highest reported result. A PI-algorithm-based residual methanol concentration feed rate controller was employed to maintain a set residual methanol concentration. Finally, mathematical process models to characterise the vegetative, dead and total cell biomass (Xv, Xd and X), substrate (Glycerol and Methanol) concentration, reactor volume (V), and product (HBcAg) dynamics during cultivation, were identified. A rare attempt to model the residual methanol concentration during induction is also presented.
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Heterologous (Over) Expression of Human SoLute Carrier (SLC) in Yeast: A Well-Recognized Tool for Human Transporter Function/Structure Studies. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081206. [PMID: 36013385 PMCID: PMC9410066 DOI: 10.3390/life12081206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022]
Abstract
For more than 20 years, yeast has been a widely used system for the expression of human membrane transporters. Among them, more than 400 are members of the largest transporter family, the SLC superfamily. SLCs play critical roles in maintaining cellular homeostasis by transporting nutrients, ions, and waste products. Based on their involvement in drug absorption and in several human diseases, they are considered emerging therapeutic targets. Despite their critical role in human health, a large part of SLCs' is 'orphans' for substrate specificity or function. Moreover, very few data are available concerning their 3D structure. On the basis of the human health benefits of filling these knowledge gaps, an understanding of protein expression in systems that allow functional production of these proteins is essential. Among the 500 known yeast species, S. cerevisiae and P. pastoris represent those most employed for this purpose. This review aims to provide a comprehensive state-of-the-art on the attempts of human SLC expression performed by exploiting yeast. The collected data will hopefully be useful for guiding new attempts in SLCs expression with the aim to reveal new fundamental data that could lead to potential effects on human health.
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Auto-induction Screening Protocol for Ranking Clonal Libraries of Pichia pastoris MutS Strains. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0006-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Zuo Y, Xiao F, Gao J, Ye C, Jiang L, Dong C, Lian J. Establishing Komagataella phaffii as a Cell Factory for Efficient Production of Sesquiterpenoid α-Santalene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8024-8031. [PMID: 35729733 DOI: 10.1021/acs.jafc.2c02353] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Santalene, a major component of the sandalwood essential oil, is a typical representative of sesquiterpenes and has important applications in medicine, food, flavors, and other fields. Due to the limited supply of natural sandalwood resources, there is a growing interest in engineering microbial cell factories for the mass production of santalene. In the present study, Komagataella phaffii (also known as Pichia pastoris) was established as a cell factory for high-level production of α-santalene for the first time. The metabolic fluxes were rewired toward α-santalene biosynthesis through the optimization of promoters to drive the expression of the α-santalene synthase (SAS) gene, overexpression of the key mevalonate pathway genes (i.e., tHMG1, IDI1, and ERG20), and multi-copy integration of the SAS expression cassette. In combination with medium optimization and bioprocess engineering, the optimal strain (STE-9) was able to produce α-santalene with a titer as high as 829.8 ± 70.6 mg/L, 4.4 ± 0.3 g/L, and 21.5 ± 1.6 g/L in a shake flask, batch fermenter, and fed-batch fermenter, respectively. These represented the highest production of α-santalene ever reported, highlighting the advantages of K. phaffii cell factories for the production of terpenoids and other natural products.
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Affiliation(s)
- Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Feng Xiao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou 310027, China
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Wollborn D, Munkler LP, Horstmann R, Germer A, Blank LM, Büchs J. Predicting high recombinant protein producer strains of Pichia pastoris Mut S using the oxygen transfer rate as an indicator of metabolic burden. Sci Rep 2022; 12:11225. [PMID: 35780248 PMCID: PMC9250517 DOI: 10.1038/s41598-022-15086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is a widely used host for recombinant protein production. In this study, a clonal library of P. pastoris MutS strains (S indicates slow methanol utilization) was screened for high green fluorescent protein (GFP) production. The expression cassette was under the control of the methanol inducible AOX promoter. The growth behavior was online-monitored in 48-well and 96-well microtiter plates by measuring the oxygen transfer rate (OTR). By comparing the different GFP producing strains, a correlation was established between the slope of the cumulative oxygen transfer during the methanol metabolization phase and the strain’s production performance. The correlation corresponds to metabolic burden during methanol induction. The findings were validated using a pre-selected strain library (7 strains) of high, medium, and low GFP producers. For those strains, the gene copy number was determined via Whole Genome Sequencing. The results were consistent with the described OTR correlation. Additionally, a larger clone library (45 strains) was tested to validate the applicability of the proposed method. The results from this study suggest that the cumulative oxygen transfer can be used as a screening criterion for protein production performance that allows for a simple primary screening process, facilitating the pre-selection of high producing strains.
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Affiliation(s)
- David Wollborn
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Lara Pauline Munkler
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Rebekka Horstmann
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany.
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Krayem N, Sidhoum R, Cherif S, Karray A. Efficient heterologous expression in Pichia pastoris, immobilization and functional characterization of a scorpion venom secreted phospholipase A 2. Toxicon 2022; 216:1-10. [PMID: 35660627 DOI: 10.1016/j.toxicon.2022.05.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 11/26/2022]
Abstract
Industrial processes have expanded with the ability to clone and express recombinant immobilized enzymes in microorganisms such as Pichia pastoris that have commercially attractive amounts of the appropriate genes. This report describes the overexpression in Pichia pastoris, immobilization, and functional characterization of a secreted phospholipase A2 from scorpion venom Scorpio maurus: rPLA2(-5). After 48 h of culture, the recombinant rPLA2(-5) was secreted into the culture medium and expressed at about 9 mg/L. Comparative analyses of the kinetics and hydrolysis of rPLA2(-5) monolayers at various surface pressures were conducted with the same form produced in Escherichia coli. As a second part of the study, rPLA2(-5) overexpressed in Pichia pastoris was immobilized by adsorption on CaCO3, with about 78 percent of the activity. In comparison to the free enzyme, rPLA2(-5) was studied for stability. Immobilization improved the thermal stability of rPLA2(-5) and even the stability at acidic pH. Moreover, we found that the immobilization improved the stability of rPLA2(-5) towards bile salts, Tween 80, Triton X-100, and SDS, as well as its stability towards many organic solvents. Until now, this is the first study to describe the overexpression and immobilization of a scorpion venom phospholipase A2 that possesses an interesting stability characteristic that makes it useful for a wide range of biotechnological applications.
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Affiliation(s)
- Najeh Krayem
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, route de Soukra 3038, BP 1173, Sfax, Tunisia.
| | - Rim Sidhoum
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, route de Soukra 3038, BP 1173, Sfax, Tunisia
| | - Slim Cherif
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, route de Soukra 3038, BP 1173, Sfax, Tunisia
| | - Aida Karray
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, route de Soukra 3038, BP 1173, Sfax, Tunisia
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Identification of a New Endo-β-1,4-xylanase Prospected from the Microbiota of the Termite Heterotermes tenuis. Microorganisms 2022; 10:microorganisms10050906. [PMID: 35630351 PMCID: PMC9143652 DOI: 10.3390/microorganisms10050906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Xylanases are hemicellulases that break down xylan to soluble pentoses. They are used for industrial purposes, such as paper whitening, beverage clarification, and biofuel production. The second-generation bioethanol production is hindered by the enzymatic hydrolysis step of the lignocellulosic biomass, due to the complex arrangement established among its constituents. Xylanases can potentially increase the production yield by improving the action of the cellulolytic enzyme complex. We prospected endo-β-1,4-xylanases from meta-transcriptomes of the termite Heterotermes tenuis. In silico structural characterization and functional analysis of an endo-β-1,4-xylanase from a symbiotic protist of H. tenuis indicate two active sites and a substrate-binding groove needed for the catalytic activity. No N-glycosylation sites were found. This endo-β-1,4-xylanase was recombinantly expressed in Pichia pastoris and Escherichia coli cells, presenting a molecular mass of approximately 20 kDa. Enzymatic activity assay using recombinant endo-β-1,4-xylanase was also performed on 1% xylan agar stained with Congo red at 30 °C and 40 °C. The enzyme expressed in both systems was able to hydrolyze the substrate xylan, becoming a promising candidate for further analysis aiming to determine its potential for application in industrial xylan degradation processes.
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Heistinger L, Dohm JC, Paes BG, Koizar D, Troyer C, Ata Ö, Steininger-Mairinger T, Mattanovich D. Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization. Microb Cell Fact 2022; 21:70. [PMID: 35468837 PMCID: PMC9036795 DOI: 10.1186/s12934-022-01796-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The yeast genus Komagataella currently consists of seven methylotrophic species isolated from tree environments. Well-characterized strains of K. phaffii and K. pastoris are important hosts for biotechnological applications, but the potential of other species from the genus remains largely unexplored. In this study, we characterized 25 natural isolates from all seven described Komagataella species to identify interesting traits and provide a comprehensive overview of the genotypic and phenotypic diversity available within this genus. RESULTS Growth tests on different carbon sources and in the presence of stressors at two different temperatures allowed us to identify strains with differences in tolerance to high pH, high temperature, and growth on xylose. As Komagataella species are generally not considered xylose-utilizing yeasts, xylose assimilation was characterized in detail. Growth assays, enzyme activity measurements and 13C labeling confirmed the ability of K. phaffii to utilize D-xylose via the oxidoreductase pathway. In addition, we performed long-read whole-genome sequencing to generate genome assemblies of all Komagataella species type strains and additional K. phaffii and K. pastoris isolates for comparative analysis. All sequenced genomes have a similar size and share 83-99% average sequence identity. Genome structure analysis showed that K. pastoris and K. ulmi share the same rearrangements in difference to K. phaffii, while the genome structure of K. kurtzmanii is similar to K. phaffii. The genomes of the other, more distant species showed a larger number of structural differences. Moreover, we used the newly assembled genomes to identify putative orthologs of important xylose-related genes in the different Komagataella species. CONCLUSIONS By characterizing the phenotypes of 25 natural Komagataella isolates, we could identify strains with improved growth on different relevant carbon sources and stress conditions. Our data on the phenotypic and genotypic diversity will provide the basis for the use of so-far neglected Komagataella strains with interesting characteristics and the elucidation of the genetic determinants of improved growth and stress tolerance for targeted strain improvement.
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Affiliation(s)
- Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria.
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Barbara G Paes
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia (UnB), Brasilia, Brazil
| | - Daniel Koizar
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
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Gao M, Zhou Y, Yan J, Zhu L, Li Z, Hu X, Zhan X. Efficient precious metal Rh(III) adsorption by waste P. pastoris and P. pastoris surface display from high-density culture. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128140. [PMID: 34979391 DOI: 10.1016/j.jhazmat.2021.128140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Rhodium is one of the most used precious metals in catalysis both in laboratory reactions and industrial processes. However, the adsorption of Rh(III) by microorganisms has been seldomly reported. In this work, waste P. pastoris and recombinant P. pastoris with surface-displayed Rh metal peptides (P. pastoris GS-R) from high-density culture were used as novel adsorbents to study Rh(III) adsorption. Under the optimal adsorption conditions of biomass of 0.25 g L-1, pH of 1.2, temperature of 30 °C, and adsorption time of 2 h in simulated wastewater, the maximum adsorption ratios of 55.69% (110.1 mg g-1) and 75.03% (142.11 mg g-1) were achieved for waste P. pastoris and P. pastoris GS-R, respectively. Using the two adsorbents, the adsorption kinetic models fit the quasi-second-order equation, and isotherm models followed the Langmuir and Temkin equations, respectively. P. pastoris GS-R showed high adsorption capacity (48.49%) and selectivity (65.86%) in electroplating wastewater, and the desorption ratio reached 34.49% after treatment with 2 M HNO3 and ultrasonic wave. Therefore, an environmental-friendly strategy was developed for the recovery of Rh(III) and other precious metals by using P. pastoris.
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Affiliation(s)
- Minjie Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Yuchen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Jiajun Yan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Li Zhu
- Wuxi Galaxy Biotech Co. Ltd., Wuxi 214125, PR China
| | - Zhitao Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Xiuyu Hu
- China Biotech Fermentation Industry Association, Beijing 100833, PR China
| | - Xiaobei Zhan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China.
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Kashyap A, Saini K, Saini M, Khasa YP, Gupta R. Development of a novel Pichia pastoris expression platform via genomic integration of lipase gene for sustained release of methanol from methyloleate. Prep Biochem Biotechnol 2022; 53:64-75. [PMID: 35238717 DOI: 10.1080/10826068.2022.2039941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A novel Lip+ Pichia pastoris expression platform was developed by integrating lipase Lip2 from Yarrowia lipolytica under constitutive Glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter. Effective expression of reporter protein amylase from Bacillus licheniformis was achieved utilizing methyloleate in Lip+Amy+host. Lipase hydrolyzed methyloleate into methanol that sustained PAOX1 induction, and oleic acid, which was readily utilized as a carbon source. The protein expression achieved in presence of methyloleate was comparable to methanol-induced cells, along with an increase in productive biomass. In Lip+Amy+ host, total amylase production of 220.9 ± 13 U/mg biomass was achieved at 96 h using methyloleate supplemented every 24 h. While 206.0 ± 17 U/mg biomass was obtained at 108 h in an Amy+ host induced with methanol every 12 h. Further, lipase expression neither affected growth nor added additional burden on the cellular machinery and no oleic acid accumulation was observed at any time point due to its emulsification and efficient utilization by lipase positive host. Similar results obtained with the second reporter protein γ-cyclodextrin glycosyltransferase (CGTase) from Evansella caseinilytica validated the platform. An alternate lipase Lip11 from Y. lipolytica was also employed in developing a Lip+ host to validate disparity between lipase background and PAOX1 induction in presence of methyloleate.
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Affiliation(s)
- Amuliya Kashyap
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Kuldeep Saini
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Meenu Saini
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Yogender Pal Khasa
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rani Gupta
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
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Gao J, Xu J, Zuo Y, Ye C, Jiang L, Feng L, Huang L, Xu Z, Lian J. Synthetic Biology Toolkit for Marker-Less Integration of Multigene Pathways into Pichia pastoris via CRISPR/Cas9. ACS Synth Biol 2022; 11:623-633. [PMID: 35080853 DOI: 10.1021/acssynbio.1c00307] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pichia pastoris, an important methylotrophic yeast, is currently mainly used for the expression of recombinant proteins and has great potential applications in the production of value-added compounds (e.g., chemical and natural products). However, the construction of P. pastoris cell factories is largely hindered by the lack of genetic tools for the manipulation of multigene biosynthetic pathways. Therefore, the present study aimed to establish a CRISPR-based synthetic biology toolkit for the integration and assembly of multigene biosynthetic pathways into the chromosome of P. pastoris. First, 23 intergenic regions were selected and characterized as potential integration sites, with a focus on the integration efficiency and heterologous gene expression levels. In addition, a panel of constitutive and methanol-inducible promoters with different strengths (weak, medium, and strong promoters) were characterized to control the expression of biosynthetic pathway genes to the desirable levels. With a series of gRNA plasmids (for single-locus, two-loci, and three-loci integration) and donor plasmids (containing homology arms for integration and promoters and terminators for driving heterologous gene expression) as major components, a CRISPR-based synthetic biology toolkit was established, which enabled the integration of one locus, two loci, and three loci with efficiencies as high as ∼100, ∼93, and ∼75%, respectively, in P. pastoris GS115 strain. Finally, the application of the toolkit was demonstrated by the construction of a series of P. pastoris cell factories, which could produce 2,3-butanediol, β-carotene, zeaxanthin, and astaxanthin with methanol as the sole carbon and energy source. The P. pastoris synthetic biology toolkit is highly standardized and can be employed to construct P. pastoris cell factories with high efficiency.
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Affiliation(s)
- Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Junhao Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Yimeng Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Leijie Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Linjuan Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
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Enespa, Chandra P, Singh DP. Sources, purification, immobilization and industrial applications of microbial lipases: An overview. Crit Rev Food Sci Nutr 2022; 63:6653-6686. [PMID: 35179093 DOI: 10.1080/10408398.2022.2038076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Microbial lipase is looking for better attention with the fast growth of enzyme proficiency and other benefits like easy, cost-effective, and reliable manufacturing. Immobilized enzymes can be used repetitively and are incapable to catalyze the reactions in the system continuously. Hydrophobic supports are utilized to immobilize enzymes when the ionic strength is low. This approach allows for the immobilization, purification, stability, and hyperactivation of lipases in a single step. The diffusion of the substrate is more advantageous on hydrophobic supports than on hydrophilic supports in the carrier. These approaches are critical to the immobilization performance of the enzyme. For enzyme immobilization, synthesis provides a higher pH value as well as greater heat stability. Using a mixture of immobilization methods, the binding force between enzymes and the support rises, reducing enzyme leakage. Lipase adsorption produces interfacial activation when it is immobilized on hydrophobic support. As a result, in the immobilization process, this procedure is primarily used for a variety of industrial applications. Microbial sources, immobilization techniques, and industrial applications in the fields of food, flavor, detergent, paper and pulp, pharmaceuticals, biodiesel, derivatives of esters and amino groups, agrochemicals, biosensor applications, cosmetics, perfumery, and bioremediation are all discussed in this review.
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Affiliation(s)
- Enespa
- School for Agriculture, Sri Mahesh Prasad Post Graduate College, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Prem Chandra
- Food Microbiology & Toxicology Laboratory, Department of Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
| | - Devendra Pratap Singh
- Department of Environmental Science, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh, India
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Wang Y, Jiang S, Jiang X, Sun X, Guan X, Han Y, Zhong L, Song H, Xu Y. Cloning and codon optimization of a novel feline interferon omega gene for production by Pichia pastoris and its antiviral efficacy in polyethylene glycol-modified form. Virulence 2022; 13:297-309. [PMID: 35068319 PMCID: PMC8788361 DOI: 10.1080/21505594.2022.2029330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Feline viral diseases, such as feline panleukopenia, feline infectious peritonitis, and feline coronaviral enteritis, seriously endanger the health of cats, and restrict the development of pet industry. Meanwhile, there is a current lack of effective vaccines to protect against feline viral diseases. Thus, effective therapeutic agents are highly desirable. Interferons (IFNs) are important mediators of the antiviral host defense in animals, particularly type I IFNs. In this study, a novel feline IFN omega (feIFN-ω) gene was extracted from the cat stimulated with feline parvovirus (FPV) combined with poly(I:C), and following codon optimization encoding the feIFN-ω, the desired gene (feIFN-ω’) fragment was inserted into plasmid pPICZαA, and transformed into Pichia pastoris GS115, generating a recombinant P. pastoris GS115 strain expressing the feIFN-ω’. After induction, we found that the expression level of the feIFN-ω’ was two times more than that of feIFN-ω (p < 0.01). Subsequently, the feIFN-ω’ was purified and modified with polyethylene glycol, and its antiviral efficacy was evaluated in vitro and in vivo, using vesicular stomatitis virus (VSV) and FPV as model virus. Our results clearly demonstrated that the feIFN-ω’ had significant antiviral activities on both homologous and heterologous animal cells in vitro. Importantly, the feIFN-ω’ can effectively promote the expression of antiviral proteins IFIT3, ISG15, Mx1, and ISG56, and further enhance host defense to eliminate FPV infection in vivo, suggesting a potential candidate for the development of therapeutic agent against feline viral diseases.
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Affiliation(s)
- Yixin Wang
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Sheng Jiang
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Xiaoxia Jiang
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Xiaobo Sun
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Xueting Guan
- College of Animal Science & Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Yanyan Han
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Linhan Zhong
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China.,Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China.,Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
| | - Yigang Xu
- Key Laboratory of Applied Technology on Green-eco-healthy Animal Husbandry of Zhejiang Province, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China.,Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China.,Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, College of Animal Science & Technology College of Veterinary Medicine, Zhejiang A&f University, Hangzhou, P.R. China
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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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Pekarsky A, Spadiut O. Dynamic Feeding for Pichia pastoris. Methods Mol Biol 2022; 2513:243-254. [PMID: 35781209 DOI: 10.1007/978-1-0716-2399-2_14] [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
The knowledge of certain strain-specific parameters of recombinant Pichia pastoris strains is required to be able to set up a feeding regime for fed-batch cultivations. These parameters are commonly determined either by time-consuming and labor-intensive continuous cultivations or by several, consecutive fed-batch cultivations. Here, we describe a fast method based on batch experiments with substrate pulses to extract certain strain characteristic parameters, which are required to set up a dynamic feeding strategy for P. pastoris strains based on the specific substrate uptake rate. We further describe in detail the course of actions, which have to be taken to obtain the desired dynamics during feeding.
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Affiliation(s)
- Alexander Pekarsky
- Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria
| | - Oliver Spadiut
- Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Vienna, Austria.
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