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Tian T, Wu X, Wu P, Lu X, Wang Q, Lin Y, Liu C, Zhou J, Yu Y, Lu H. High-level expression of leghemoglobin in Kluyveromyces marxianus by remodeling the heme metabolism pathway. Front Bioeng Biotechnol 2024; 11:1329016. [PMID: 38264583 PMCID: PMC10804453 DOI: 10.3389/fbioe.2023.1329016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024] Open
Abstract
Soy leghemoglobin, when bound to heme, imparts a meat-like color and flavor and can serve as a substitute for animal-derived proteins. Enhancing cellular heme synthesis improves the recombinant expression of leghemoglobin in yeast. To achieve high-level expression of leghemoglobin A (LBA) in Kluyveromyces marxianus, a food-safe yeast, large-scale heme synthesis modules were transferred into K. marxianus using yeast artificial chromosomes (KmYACs). These modules contained up to 8 native and heterologous genes to promote the supply of heme precursors and downstream synthesis. Next, eight genes inhibiting heme or LBA synthesis were individually or combinatorially deleted, with the lsc1Δssn3Δ mutant yielding the best results. Subsequently, heme synthesis modules were combined with the lsc1Δssn3Δ mutant. In the resulting strains, the module genes were all actively expressed. Among these module genes, heterologous S. cerevisiae genes in the downstream heme synthesis pathway significantly enhanced the expression of their counterparts in K. marxianus, resulting in high heme content and LBA yield. After optimizing the medium recipe by adjusting the concentrations of glucose, glycine, and FeSO4·7H2O, a heme content of 66.32 mg/L and an intracellular LBA titer of 7.27 g/L were achieved in the engineered strain in a 5 L fermentor. This represents the highest intracellular expression of leghemoglobin in microorganisms to date. The leghemoglobin produced by K. marxianus can be utilized as a safe ingredient for plant-based protein products.
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Affiliation(s)
- Tian Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Xinwei Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Xinyi Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Qi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yifan Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Canjie Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
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2
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Wang X, Li Y, Jin Z, Liu X, Gao X, Guo S, Yu T. A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris. Synth Syst Biotechnol 2023; 8:445-451. [PMID: 37448527 PMCID: PMC10336193 DOI: 10.1016/j.synbio.2023.06.003] [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: 03/27/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The methylotrophic budding yeast Pichia pastoris has been utilized to the production of a variety of heterologous recombinant proteins owing to the strong inducible alcohol oxidase promoter (pAOX1). However, it is difficult to use P. pastoris as the chassis cell factory for high-valuable metabolite biosynthesis due to the low homologous recombination (HR) efficiency and the limitation of handy selective markers, especially in the condition of multistep biosynthetic pathways. Hence, we developed a novel CRISPR/Cas9 system with highly editing efficiencies and recyclable auxotrophic selective marker (HiEE-ReSM) to facilitate cell factory in P. pastoris. Firstly, we improved the HR rates of P. pastoris through knocking out the non-homologous-end-joining gene (Δku70) and overexpressing HR-related proteins (RAD52 and RAD59), resulting in higher positive rate compared to the basal strain, achieved 97%. Then, we used the uracil biosynthetic genes PpURA3 as the reverse screening marker, which can improve the recycling efficiency of marker. Meanwhile, the HR rate is still 100% in uracil auxotrophic yeast. Specially, we improved the growth rate of uracil auxotrophic yeast strains by overexpressing the uracil transporter (scFUR4) to increase the uptake of exogenous uracil from medium. Meanwhile, we explored the optimal concentration of uracil (90 mg/L) for strain growth. In the end, the HiEE-ReSM system has been applied for the inositol production (250 mg/L) derived from methanol in P. pastoris. The systems will contribute to P. pastoris as an attractive cell factory for the complex compound biosynthesis through multistep metabolic pathway engineering and will be a useful tool to improve one carbon (C1) bio-utilization.
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Affiliation(s)
- Xiang Wang
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Li
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhehao Jin
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiangjian Liu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Xiang Gao
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology of CAS, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academic of Science, Shenzhen, 518055, China
| | - Shuyuan Guo
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Tao Yu
- Center for Synthetic Biochemistry, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
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3
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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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4
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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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5
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Naumann TA, Sollenberger KG, Hao G. Production of selenomethionine labeled polyglycine hydrolases in Pichia pastoris. Protein Expr Purif 2022; 194:106076. [PMID: 35240278 DOI: 10.1016/j.pep.2022.106076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023]
Abstract
Producing recombinant proteins with incorporated selenomethionine (SeMet) facilitates solving X-ray crystallographic structures of novel proteins. Production of SeMet labeled proteins in the yeast Pichia pastoris (syn. Komagataella phaffii) is difficult because SeMet is mildly toxic, reducing protein expression levels. To counteract this yield loss for a novel protease, Epicoccum sorghi chitinase modifying protein (Es-cmp), a novel disease promoting protease secreted by these plant pathogenic fungi, we isolated a yeast strain that secreted more protein. By comparing the expression level of 48 strains we isolated one that produced significantly more protein. This strain was found to be gene dosed, having four copies of the expression cassette. After optimization the strain produced Es-cmp in defined media with SeMet at levels nearly equal to that of the original strain in complex media. Also, we produced SeMet labeled protein for a homologous protease from the fungus Fusarium vanettenii, Fvan-cmp, by directly selecting a gene dosed strain on agar plates with increased zeocin. Linearization of plasmid with PmeI before electroporation led to high numbers of 1 mg/mL zeocin resistant clones with significantly increased expression compared to those selected on 0.1 mg/mL. The gene dosed strains expressing Es-cmp and Fvan-cmp allowed production of 8.5 and 16.8 mg of SeMet labeled protein from 500 mL shake flask cultures. The results demonstrate that selection of P. pastoris expression strains by plating after transformation on agar with 1 mg/mL zeocin rather than the standard 0.1 mg/mL directly selects gene dosed strains that can facilitate production of selenomethionine labeled proteins.
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Affiliation(s)
- Todd A Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA.
| | - Kurt G Sollenberger
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA
| | - Guixia Hao
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL, 61604, USA
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6
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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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7
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Liao X, Li L, Jameel A, Xing XH, Zhang C. A versatile toolbox for CRISPR-based genome engineering in Pichia pastoris. Appl Microbiol Biotechnol 2021; 105:9211-9218. [PMID: 34773154 DOI: 10.1007/s00253-021-11688-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/26/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2022]
Abstract
Pichia pastoris has gained much attention as a popular microbial cell factory for the production of recombinant proteins and high-value chemicals from laboratory to industrial scale. However, the lack of convenient and efficient genome engineering tools has impeded further applications of Pichia pastoris towards metabolic engineering and synthetic biology. Here, we report a CRISPR-based toolbox for gene editing and transcriptional regulation in P. pastoris. Based on the previous attempts in P. pastoris, we constructed a CRISPR/Cas9 system for gene editing using the RNA Pol-III-driven expression of sgRNA. The system was used to rapidly recycle the selectable marker with an eliminable episomal plasmid and achieved up to 100% knockout efficiency. Via dCas9 fused with transcriptional repressor (Mix1/RD1152) or activator (VPR), a flexible toolbox for regulation of gene expression was developed. The reporter gene eGFP driven by yeast pGAP or pCYC1 promoter showed strong inhibition (above 70%) and up to ~ 3.5-fold activation. To implement the combinatorial genetic engineering strategy, the CRISPR system contained a single Cas9-VPR protein, and engineered gRNA was introduced in P. pastoris for simultaneous gene activation, repression, and editing (CRISPR-ARE). We demonstrated that CRISPR-ARE was highly efficient for eGFP activation, mCherry repression, and ADE2 disruption, individually or in a combinatorial manner with a stable expression of multiplex sgRNAs. The simple and multifunctional toolkit demonstrated in this study will accelerate the application of P. pastoris in metabolic engineering and synthetic biology. KEY POINTS: • An eliminable CRISPR/Cas9 system yielded a highly efficient knockout of genes. • Simplified CRISPR/dCas9-based tools enabled transcriptional regulation of targeted genes. • CRISPR-ARE system achieved simultaneous gene activation, repression, and editing in P. pastoris.
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Affiliation(s)
- Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Lu Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Aysha Jameel
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China. .,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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8
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Kielkopf CL, Bauer W, Urbatsch IL. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc 2021; 2021:pdb.top102129. [PMID: 33272973 DOI: 10.1101/pdb.top102129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.
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9
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Aw R, De Wachter C, Laukens B, De Rycke R, De Bruyne M, Bell D, Callewaert N, Polizzi KM. Knockout of RSN1, TVP18 or CSC1-2 causes perturbation of Golgi cisternae in Pichia pastoris. Traffic 2020; 22:48-63. [PMID: 33263222 DOI: 10.1111/tra.12773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022]
Abstract
The structural organization of the Golgi stacks in mammalian cells is intrinsically linked to function, including glycosylation, but the role of morphology is less clear in lower eukaryotes. Here we investigated the link between the structural organization of the Golgi and secretory pathway function using Pichia pastoris as a model system. To unstack the Golgi cisternae, we disrupted 18 genes encoding proteins in the secretory pathway without loss of viability. Using biosensors, confocal microscopy and transmission electron microscopy we identified three strains with irreversible perturbations in the stacking of the Golgi cisternae, all of which had disruption in genes that encode proteins with annotated function as or homology to calcium/calcium permeable ion channels. Despite this, no variation in the secretory pathway for ER size, whole cell glycomics or recombinant protein glycans was observed. Our investigations showed the robust nature of the secretory pathway in P. pastoris and suggest that Ca2+ concentration, homeostasis or signalling may play a significant role for Golgi stacking in this organism and should be investigated in other organisms.
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Affiliation(s)
- Rochelle Aw
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Charlot De Wachter
- VIB-UGent, Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bram Laukens
- VIB-UGent, Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,VIB Center for Inflammation Research and BioImaging Core, Ghent, Belgium
| | - Michiel De Bruyne
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,VIB Center for Inflammation Research and BioImaging Core, Ghent, Belgium
| | - David Bell
- Section for Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,London Biofoundry, Imperial College London, London, United Kingdom
| | - Nico Callewaert
- VIB-UGent, Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
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10
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Banoth S, Tangutur AD, Anthappagudem A, Ramaiah J, Bhukya B. Cloning and in vivo metabolizing activity study of CYP3A4 on amiodarone drug residues: A possible probiotic and therapeutic option. Pharmacotherapy 2020; 127:110128. [DOI: 10.1016/j.biopha.2020.110128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
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11
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Role of BGS13 in the Secretory Mechanism of Pichia pastoris. Appl Environ Microbiol 2019; 85:AEM.01615-19. [PMID: 31585990 DOI: 10.1128/aem.01615-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/22/2019] [Indexed: 02/08/2023] Open
Abstract
The methylotrophic yeast Pichia pastoris has been utilized for heterologous protein expression for over 30 years. Because P. pastoris secretes few of its own proteins, the exported recombinant protein is the major polypeptide in the extracellular medium, making purification relatively easy. Unfortunately, some recombinant proteins intended for secretion are retained within the cell. A mutant strain isolated in our laboratory, containing a disruption of the BGS13 gene, displayed elevated levels of secretion for a variety of reporter proteins. The Bgs13 peptide (Bgs13p) is similar to the Saccharomyces cerevisiae protein kinase C 1 protein (Pkc1p), but its specific mode of action is currently unclear. To illuminate differences in the secretion mechanism between the wild-type (wt) strain and the bgs13 strain, we determined that the disrupted bgs13 gene expressed a truncated protein that had reduced protein kinase C activity and a different location in the cell, compared to the wt protein. Because the Pkc1p of baker's yeast plays a significant role in cell wall integrity, we investigated the sensitivity of the mutant strain's cell wall to growth antagonists and extraction by dithiothreitol, determining that the bgs13 strain cell wall suffered from inherent structural problems although its porosity was normal. A proteomic investigation of the bgs13 strain secretome and cell wall-extracted peptides demonstrated that, compared to its wt parent, the bgs13 strain also displayed increased release of an array of normally secreted, endogenous proteins, as well as endoplasmic reticulum-resident chaperone proteins, suggesting that Bgs13p helps regulate the unfolded protein response and protein sorting on a global scale.IMPORTANCE The yeast Pichia pastoris is used as a host system for the expression of recombinant proteins. Many of these products, including antibodies, vaccine antigens, and therapeutic proteins such as insulin, are currently on the market or in late stages of development. However, one major weakness is that sometimes these proteins are not secreted from the yeast cell efficiently, which impedes and raises the cost of purification of these vital proteins. Our laboratory has isolated a mutant strain of Pichia pastoris that shows enhanced secretion of many proteins. The mutant produces a modified version of Bgs13p. Our goal is to understand how the change in the Bgs13p function leads to improved secretion. Once the Bgs13p mechanism is illuminated, we should be able to apply this understanding to engineer new P. pastoris strains that efficiently produce and secrete life-saving recombinant proteins, providing medical and economic benefits.
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12
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Ahmad M, Winkler CM, Kolmbauer M, Pichler H, Schwab H, Emmerstorfer‐Augustin A. Pichia pastoris protease-deficient and auxotrophic strains generated by a novel, user-friendly vector toolbox for gene deletion. Yeast 2019; 36:557-570. [PMID: 31148217 PMCID: PMC6771850 DOI: 10.1002/yea.3426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/28/2019] [Accepted: 05/26/2019] [Indexed: 01/24/2023] Open
Abstract
Targeted gene knockouts play an important role in the study of gene function. For the generation of knockouts in the industrially important yeast Pichia pastoris, several protocols have been published to date. Nevertheless, creating a targeted knockout in P. pastoris still is a time-consuming process, as the existing protocols are labour intensive and/or prone to accumulate nucleotide mutations. In this study, we introduce a novel, user-friendly vector-based system for the generation of targeted knockouts in P. pastoris. Upon confirming the successful knockout, respective selection markers can easily be recycled. Excision of the marker is mediated by Flippase (Flp) recombinase and occurs at high frequency (≥95%). We validated our knockout system by deleting 20 (confirmed and putative) protease genes and five genes involved in biosynthetic pathways. For the first time, we describe gene deletions of PRO3 and PHA2 in P. pastoris, genes involved in proline, and phenylalanine biosynthesis, respectively. Unexpectedly, knockout strains of PHA2 did not display the anticipated auxotrophy for phenylalanine but rather showed a bradytroph phenotype on minimal medium hinting at an alternative but less efficient pathway for production of phenylalanine exists in P. pastoris. Overall, all knockout vectors can easily be adapted to the gene of interest and strain background by efficient exchange of target homology regions and selection markers in single cloning steps. Average knockout efficiencies for all 25 genes were shown to be 40%, which is comparably high.
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Affiliation(s)
- Mudassar Ahmad
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | | | - Markus Kolmbauer
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | - Harald Pichler
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria,Austrian Centre of Industrial Biotechnology (ACIB)GrazAustria
| | - Helmut Schwab
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria,Austrian Centre of Industrial Biotechnology (ACIB)GrazAustria
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13
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Aw R, Polizzi KM. Biosensor‐assisted engineering of a high‐yield
Pichia pastoris
cell‐free protein synthesis platform. Biotechnol Bioeng 2019; 116:656-666. [DOI: 10.1002/bit.26901] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/12/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rochelle Aw
- Department of Chemical EngineeringImperial College LondonLondon UK
- Imperial College Centre for Synthetic Biology, Imperial College LondonLondon UK
| | - Karen M. Polizzi
- Department of Chemical EngineeringImperial College LondonLondon UK
- Imperial College Centre for Synthetic Biology, Imperial College LondonLondon UK
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Aw R, McKay PF, Shattock RJ, Polizzi KM. A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization. Protein Expr Purif 2018; 149:43-50. [PMID: 29601964 PMCID: PMC5982643 DOI: 10.1016/j.pep.2018.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/27/2018] [Accepted: 03/26/2018] [Indexed: 01/10/2023]
Abstract
Pichia pastoris (Komagataella phaffi) has been used for recombinant protein production for over 30 years with over 5000 proteins reported to date. However, yields of antibody are generally low. We have evaluated the effect of secretion signal peptides on the production of a broadly neutralizing antibody (VRC01) to increase yield. Eleven different signal peptides, including the murine IgG1 signal peptide, were combinatorially evaluated for their effect on antibody titer. Strains using different combinations of signal peptides were identified that secreted approximately 2-7 fold higher levels of VRC01 than the previous best secretor, with the highest yield of 6.50 mg L-1 in shake flask expression. Interestingly it was determined that the highest yields were achieved when the murine IgG1 signal peptide was fused to the light chain, with several different signal peptides leading to high yield when fused to the heavy chain. Finally, we have evaluated the effect of using a 2A signal peptide to create a bicistronic vector in the attempt to reduce burden and increase transformation efficiency, but found it to give reduced yields compared to using two independent vectors.
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Affiliation(s)
- Rochelle Aw
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK; Centre for Synthetic Biology and Innovation, Imperial College London, SW7 2AZ, UK
| | - Paul F McKay
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - Robin J Shattock
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK; Centre for Synthetic Biology and Innovation, Imperial College London, SW7 2AZ, UK.
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Betancur MO, Reis VCB, Nicola AM, De Marco JL, de Moraes LMP, Torres FAG. Multicopy plasmid integration in Komagataella phaffii mediated by a defective auxotrophic marker. Microb Cell Fact 2017; 16:99. [PMID: 28595601 PMCID: PMC5465527 DOI: 10.1186/s12934-017-0715-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background A commonly used approach to improve recombinant protein production is to increase the levels of expression by providing extra-copies of a heterologous gene. In Komagataella phaffii (Pichia pastoris) this is usually accomplished by transforming cells with an expression vector carrying a drug-resistance marker following a screening for multicopy clones on plates with increasingly higher concentrations of an antibiotic. Alternatively, defective auxotrophic markers can be used for the same purpose. These markers are generally transcriptionally impaired genes lacking most of the promoter region. Among the defective markers commonly used in Saccharomyces cerevisiae is leu2-d, an allele of LEU2 which is involved in leucine metabolism. Cells transformed with this marker can recover prototrophy when they carry multiple copies of leu2-d in order to compensate the poor transcription from this defective allele. Results A K. phaffii strain auxotrophic for leucine (M12) was constructed by disrupting endogenous LEU2. The resulting strain was successfully transformed with a vector carrying leu2-d and an EGFP (enhanced green fluorescent protein) reporter gene. Vector copy numbers were determined from selected clones which grew to different colony sizes on transformation plates. A direct correlation was observed between colony size, number of integrated vectors and EGFP production. By using this approach we were able to isolate genetically stable clones bearing as many as 20 integrated copies of the vector and with no significant effects on cell growth. Conclusions In this work we have successfully developed a genetic system based on a defective auxotrophic which can be applied to improve heterologous protein production in K. phaffii. The system comprises a K. phaffii leu2 strain and an expression vector carrying the defective leu2-d marker which allowed the isolation of multicopy clones after a single transformation step. Because a linear correlation was observed between copy number and heterologous protein production, this system may provide a simple approach to improve recombinant protein productivity in K. phaffii. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0715-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maritza Ocampo Betancur
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Viviane Castelo Branco Reis
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - André Moraes Nicola
- Faculdade de Medicina, Laboratório de Imunologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Janice Lisboa De Marco
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Lídia Maria Pepe de Moraes
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Fernando Araripe Gonçalves Torres
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
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Plackett-Burman Design for rGILCC1 Laccase Activity Enhancement in Pichia pastoris: Concentrated Enzyme Kinetic Characterization. Enzyme Res 2017; 2017:5947581. [PMID: 28421142 PMCID: PMC5379127 DOI: 10.1155/2017/5947581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/27/2017] [Accepted: 03/09/2017] [Indexed: 01/09/2023] Open
Abstract
Laccases are multicopper oxidases that catalyze aromatic and nonaromatic compounds with concomitant reduction of molecular oxygen to water. They are of great interest due to their potential biotechnological applications. In this work we statistically improved culture media for recombinant GILCC1 (rGILCC1) laccase production at low scale from Ganoderma lucidum containing the construct pGAPZαA-GlucPost-Stop in Pichia pastoris. Temperature, pH stability, and kinetic parameter characterizations were determined by monitoring concentrate enzyme oxidation at different ABTS substrate concentrations. Plackett-Burman Design allowed improving enzyme activity from previous work 36.08-fold, with a laccase activity of 4.69 ± 0.39 UL−1 at 168 h of culture in a 500 mL shake-flask. Concentrated rGILCC1 remained stable between 10 and 50°C and retained a residual enzymatic activity greater than 70% at 60°C and 50% at 70°C. In regard to pH stability, concentrated enzyme was more stable at pH 4.0 ± 0.2 with a residual activity greater than 90%. The lowest residual activity greater than 55% was obtained at pH 10.0 ± 0.2. Furthermore, calculated apparent enzyme kinetic parameters were a Vmax of 6.87 × 10−5 mM s−1, with an apparent Km of 5.36 × 10−2 mM. Collectively, these important stability findings open possibilities for applications involving a wide pH and temperature ranges.
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Paul R, Saha G, Selvaraja V, Kaliraj P. Cloning, expression and characterization of Brugia malayi abundant larval protein transcript-2 (BmALT-2) expressed in Pichia pastoris. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1264274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Rajkumar Paul
- Centre for Biotechnology, Anna University, Chennai, India
| | - Gundappa Saha
- Centre for Biotechnology, Anna University, Chennai, India
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Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications. World J Microbiol Biotechnol 2016; 33:19. [PMID: 27905091 DOI: 10.1007/s11274-016-2185-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.
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Enhancing the production of recombinant acidic α-amylase and phytase in Pichia pastoris under dual promoters [constitutive ( GAP ) and inducible ( AOX )] in mixed fed batch high cell density cultivation. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.07.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Moua PS, Gonzalez A, Oshiro KT, Tam V, Li ZH, Chang J, Leung W, Yon A, Thor D, Venkatram S, Franz AH, Risser DD, Lin-Cereghino J, Lin-Cereghino GP. Differential secretion pathways of proteins fused to the Escherichia coli maltose binding protein (MBP) in Pichia pastoris. Protein Expr Purif 2016; 124:1-9. [PMID: 27079175 DOI: 10.1016/j.pep.2016.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/13/2023]
Abstract
The Escherichia coli maltose binding protein (MBP) is an N-terminal fusion partner that was shown to enhance the secretion of some heterologous proteins from the yeast Pichia pastoris, a popular host for recombinant protein expression. The amount of increase in secretion was dependent on the identity of the cargo protein, and the fusions were proteolyzed prior to secretion, limiting its use as a purification tag. In order to overcome these obstacles, we used the MBP as C-terminal partner for several cargo peptides. While the Cargo-MBP proteins were no longer proteolyzed in between these two moieties when the MBP was in this relative position, the secretion efficiency of several fusions was lower than when MBP was located at the opposite end of the cargo protein (MBP-Cargo). Furthermore, fluorescence analysis suggested that the MBP-EGFP and EGFP-MBP proteins followed different routes within the cell. The effect of several Pichia pastoris beta-galactosidase supersecretion (bgs) strains, mutants showing enhanced secretion of select reporters, was also investigated on both MBP-EGFP and EGFP-MBP. While the secretion efficiency, proteolysis and localization of the MBP-EGFP was influenced by the modified function of Bgs13, EGFP-MBP behavior was not affected in the bgs strain. Taken together, these results indicate that the location of the MBP in a fusion affects the pathway and trans-acting factors regulating secretion in P. pastoris.
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Affiliation(s)
- Pachai S Moua
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Alfonso Gonzalez
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Kristin T Oshiro
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Vivian Tam
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Zhiguo Harry Li
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Jennifer Chang
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Wilson Leung
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Amy Yon
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Der Thor
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, United States
| | - Sri Venkatram
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Douglas D Risser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Joan Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States
| | - Geoff P Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, United States.
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Spohner SC, Schaum V, Quitmann H, Czermak P. Kluyveromyces lactis: An emerging tool in biotechnology. J Biotechnol 2016; 222:104-16. [DOI: 10.1016/j.jbiotec.2016.02.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 02/04/2023]
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Liquid PTVA: a faster and cheaper alternative for generating multi-copy clones in Pichia pastoris. Microb Cell Fact 2016; 15:29. [PMID: 26849882 PMCID: PMC4744420 DOI: 10.1186/s12934-016-0432-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/25/2016] [Indexed: 01/06/2023] Open
Abstract
Background Multiple cognate gene copy clones have often been used in order to increase the yield of recombinant protein expression in the yeast Pichia pastoris. The method of posttransformational vector amplification (PTVA) has allowed for the efficient generation of multi-copy clones in P. pastoris. However, despite its relative ease and success, this process can be expensive and time consuming. Results We have developed a modified version of PTVA, called Liquid PTVA, which allows for faster and cheaper selection of multi-copy clones. Cultures are grown in liquid medium with only a final selection carried out on agar plates, reducing overall antibiotic usage and increasing the speed of clone amplification. In addition, it was established that starting PTVA with a single copy clone resulted in higher copy number strains for both traditional plate PTVA and liquid PTVA. Furthermore, using the Zeocin selection marker in liquid PTVA results in strains with higher growth rates, which could be beneficial for recombinant protein production processes. Conclusions We present a methodology for creating multi-copy clones that can be achieved over 12 days instead of the traditional 45 and at approximately half the cost. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0432-8) contains supplementary material, which is available to authorized users.
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24
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Liu H, Cheng Y, Du B, Tong C, Liang S, Han S, Zheng S, Lin Y. Overexpression of a novel thermostable and chloride-tolerant laccase from Thermus thermophilus SG0.5JP17-16 in Pichia pastoris and its application in synthetic dye decolorization. PLoS One 2015; 10:e0119833. [PMID: 25790466 PMCID: PMC4366370 DOI: 10.1371/journal.pone.0119833] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Abstract
Laccases have been used for the decolorization and detoxification of synthetic dyes due to their ability to oxidize a wide variety of dyes with water as the sole byproduct. A putative laccase gene (LacTT) from Thermus thermophilus SG0.5JP17-16 was screened using the genome mining approach, and it was highly expressed in Pichia pastoris, yielding a high laccase activity of 6130 U/L in a 10-L fermentor. The LacTT open reading frame encoded a protein of 466 amino acid residues with four putative Cu-binding regions. The optimal pH of the recombinant LacTT was 4.5, 6.0, 7.5 and 8.0 with 2,2'-azino-bis(3-ethylbenzothazoline-6-sulfonic acid) (ABTS), syringaldazine (SGZ), guaiacol, and 2,6-dimethoxyphenol (2,6-DMP) as the substrate, respectively. The optimal temperature of LacTT was 90°C with guaiacol as the substrate. LacTT was highly stable at pH 4.0-11.0 and thermostable at 40°C-90°C, confirming that it is a pH-stable and thermostable laccase. Furthermore, LacTT also exhibited high tolerance to halides such as NaCl, NaBr and NaF, and decolorized 100%, 94%, 94% and 73% of Congo Red, Reactive Black B and Reactive Black WNN, and Remazol Brilliant Blue R, respectively. Interestingly, addition of high concentration of NaCl increased the RBBR decolorization efficiency of LacTT. These results suggest that LacTT is a good candidate for industrial applications such as dyestuff processing and degradation of dyes in textile wastewaters.
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Affiliation(s)
- Huiping Liu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Cheng
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Bing Du
- College of Food Science and Engineering, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Chaofan Tong
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Shuli Liang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Shuangyan Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Suiping Zheng
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Ying Lin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
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Zheng J, Guo N, Zhou HB. A simple strategy for the generation of multi-copyPichia pastoriswith the efficient expression of mannanase. J Basic Microbiol 2014; 54:1410-6. [DOI: 10.1002/jobm.201400208] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 05/26/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Jia Zheng
- School of Minerals Processing and Bioengineering; Central South University; Changsha P. R. China
| | - Ning Guo
- School of Minerals Processing and Bioengineering; Central South University; Changsha P. R. China
| | - Hong-Bo Zhou
- School of Minerals Processing and Bioengineering; Central South University; Changsha P. R. China
- Key Laboratory of Biometallurgy of Ministry of Education; Central South University; Changsha P. R. China
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Yang J, Nie L, Chen B, Liu Y, Kong Y, Wang H, Diao L. Hygromycin-resistance vectors for gene expression inPichia pastoris. Yeast 2014; 31:115-25. [DOI: 10.1002/yea.3001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Junjie Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai People's Republic of China
- Shanghai Research Centre of Industrial Biotechnology; Shanghai People's Republic of China
| | - Lei Nie
- Zhejiang Hisun Pharmaceutical Co. Ltd; Taizhou Zhejiang People's Republic of China
| | - Biao Chen
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai People's Republic of China
- Shanghai Research Centre of Industrial Biotechnology; Shanghai People's Republic of China
| | - Yingmiao Liu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai People's Republic of China
- Shanghai Research Centre of Industrial Biotechnology; Shanghai People's Republic of China
| | - Yimeng Kong
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai People's Republic of China
- University of the Chinese Academy of Sciences; Beijing People's Republic of China
| | - Haibin Wang
- Zhejiang Hisun Pharmaceutical Co. Ltd; Taizhou Zhejiang People's Republic of China
| | - Liuyang Diao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai People's Republic of China
- Shanghai Research Centre of Industrial Biotechnology; Shanghai People's Republic of China
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Sherwood RK, Scaduto CM, Torres SE, Bennett RJ. Convergent evolution of a fused sexual cycle promotes the haploid lifestyle. Nature 2014; 506:387-390. [PMID: 24390351 PMCID: PMC4051440 DOI: 10.1038/nature12891] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/18/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Racquel Kim Sherwood
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Christine M Scaduto
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Sandra E Torres
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
| | - Richard J Bennett
- Department of Microbiology and Immunology, Brown University, 171 Meeting St, Providence, RI, 02912
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Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Aw R, Polizzi KM. Can too many copies spoil the broth? Microb Cell Fact 2013; 12:128. [PMID: 24354594 PMCID: PMC3878197 DOI: 10.1186/1475-2859-12-128] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/16/2013] [Indexed: 02/02/2023] Open
Abstract
The success of Pichia pastoris as a heterologous expression system lies predominantly in the impressive yields that can be achieved due to high volumetric productivity. However, low specific productivity still inhibits the potential success of this platform. Multi-(gene) copy clones are potentially a quick and convenient method to increase recombinant protein titer, yet they are not without their pitfalls. It has been more than twenty years since the first reported use of multi-copy clones and it is still an active area of research to find the fastest and most efficient method for generating these strains. It has also become apparent that there is not always a linear correlation between copy number and protein titer, leading to in-depth investigations into how to minimize the negative impact of secretory stress and achieve clonal stability.
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Affiliation(s)
- Rochelle Aw
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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Larsen S, Weaver J, de Sa Campos K, Bulahan R, Nguyen J, Grove H, Huang A, Low L, Tran N, Gomez S, Yau J, Ilustrisimo T, Kawilarang J, Lau J, Tranphung M, Chen I, Tran C, Fox M, Lin-Cereghino J, Lin-Cereghino GP. Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins. Biotechnol Lett 2013; 35:1925-35. [PMID: 23881328 PMCID: PMC3814129 DOI: 10.1007/s10529-013-1290-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
Abstract
Although Pichia pastoris is a popular protein expression system, it exhibits limitations in its ability to secrete heterologous proteins. Therefore, a REMI (restriction enzyme mediated insertion) strategy was utilized to select mutant beta-g alactosidase s upersecretion (bgs) strains that secreted increased levels of a β-galactosidase reporter. Many of the twelve BGS genes may have functions in intracellular signaling or vesicle transport. Several of these strains also appeared to contain a more permeable cell wall. Preliminary characterization of four bgs mutants showed that they differed in the ability to enhance the export of other reporter proteins. bgs13, which has a disruption in a gene homologous to Saccharomyces cerevisiae protein kinase C (PKC1), gave enhanced secretion of most recombinant proteins that were tested, raising the possibility that it has the universal super-secreter phenotype needed in an industrial production strain of P. pastoris.
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Affiliation(s)
- Sasha Larsen
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Jun Weaver
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Katherine de Sa Campos
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Rhobe Bulahan
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Jackson Nguyen
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Heather Grove
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Amy Huang
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Lauren Low
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Namphuong Tran
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Seth Gomez
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Jennifer Yau
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Thomas Ilustrisimo
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Jessica Kawilarang
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Jonathan Lau
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Maivi Tranphung
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Irene Chen
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Christina Tran
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Marcia Fox
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Joan Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Geoff P. Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
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Screening of multi-copy mannanase recombinants of Pichia pastoris based on colony size. World J Microbiol Biotechnol 2013; 30:579-84. [PMID: 24002577 DOI: 10.1007/s11274-013-1479-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 08/29/2013] [Indexed: 02/04/2023]
Abstract
Pichia pastoris pGAP (glyceraldehyde dehydrogenase promoter) expression system was widely used for the expression and production of heterologous proteins. Screening multi-copy recombinants was an effective strategy to improve the heterologous protein production in P. pastoris. Because multiple gene insertion events occurred with a low frequency, hundreds to thousands of antibiotic-resistance recombinants need to be screened. The common way of improving screening efficiency was to increase antibiotic concentration in screening plates. Here we developed a screening method by selecting small colonies from low-concentration antibiotic screening plates. This strategy greatly improved the probability of obtaining multi-copy mannanase gene (man) recombinants and it could replace the common strategy by increasing antibiotic concentration in screening plates. The further study in liquid shake flask cultures revealed that cell concentrations, growth rates and substrate consumption rates of recombinants gradually decreased with the increase in man copy number. This indicated that such a screening strategy was effective to screen multi-copy recombinants based on colony size.
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The effect of α-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris. Gene 2013; 519:311-7. [PMID: 23454485 DOI: 10.1016/j.gene.2013.01.062] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/16/2013] [Accepted: 01/23/2013] [Indexed: 11/21/2022]
Abstract
The methylotrophic yeast, Pichia pastoris, has been genetically engineered to produce many heterologous proteins for industrial and research purposes. In order to secrete proteins for easier purification from the extracellular medium, the coding sequence of recombinant proteins is initially fused to the Saccharomyces cerevisiae α-mating factor secretion signal leader. Extensive site-directed mutagenesis of the prepro-region of the α-mating factor secretion signal sequence was performed in order to determine the effects of various deletions and substitutions on expression. Though some mutations clearly dampened protein expression, deletion of amino acids 57-70, corresponding to the predicted 3rd alpha helix of α-mating factor secretion signal, increased secretion of reporter proteins horseradish peroxidase and lipase at least 50% in small-scale cultures. These findings raise the possibility that the secretory efficiency of the leader can be further enhanced in the future.
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Qian Y, Xu X, Qian NX, Dhar V, You L, Xing Z, Huang C, Pan SH, Li ZJ. WITHDRAWN: Aminoglycoside phosphotransferase II gene as primary selection marker for Pichia pastoris producing full-length monoclonal antibody. Protein Expr Purif 2012:S1046-5928(12)00238-0. [PMID: 22982086 DOI: 10.1016/j.pep.2012.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/08/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Yueming Qian
- Biologics Process Sciences, Global Manufacturing and Supply, Bristol-Myers Squibb, 6000 Thompson Road, East Syracuse, NY 13057, United States
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34
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Staley CA, Huang A, Nattestad M, Oshiro KT, Ray LE, Mulye T, Li ZH, Le T, Stephens JJ, Gomez SR, Moy AD, Nguyen JC, Franz AH, Lin-Cereghino J, Lin-Cereghino GP. Analysis of the 5' untranslated region (5'UTR) of the alcohol oxidase 1 (AOX1) gene in recombinant protein expression in Pichia pastoris. Gene 2012; 496:118-27. [PMID: 22285974 DOI: 10.1016/j.gene.2012.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 12/31/2011] [Accepted: 01/05/2012] [Indexed: 11/17/2022]
Abstract
Pichia pastoris is a methylotrophic yeast that has been genetically engineered to express over one thousand heterologous proteins valued for industrial, pharmaceutical and basic research purposes. In most cases, the 5' untranslated region (UTR) of the alcohol oxidase 1 (AOX1) gene is fused to the coding sequence of the recombinant gene for protein expression in this yeast. Because the effect of the AOX1 5'UTR on protein expression is not known, site-directed mutagenesis was performed in order to decrease or increase the length of this region. Both of these types of changes were shown to affect translational efficiency, not transcript stability. While increasing the length of the 5'UTR clearly decreased expression of a β-galactosidase reporter in a proportional manner, a deletion analysis demonstrated that the AOX1 5'UTR contains a complex mixture of both positive and negative cis-acting elements, suggesting that the construction of a synthetic 5'UTR optimized for a higher level of expression may be challenging.
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Affiliation(s)
- Chris A Staley
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
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35
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Improved expression of Rhizopus oryzae α-amylase in the methylotrophic yeast Pichia pastoris. Protein Expr Purif 2011; 79:142-8. [DOI: 10.1016/j.pep.2011.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/05/2011] [Accepted: 05/09/2011] [Indexed: 11/20/2022]
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36
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Li Z, Moy A, Gomez SR, Franz AH, Lin-Cereghino J, Lin-Cereghino GP. An improved method for enhanced production and biological activity of human secretory leukocyte protease inhibitor (SLPI) in Pichia pastoris. Biochem Biophys Res Commun 2010; 402:519-24. [PMID: 20971072 DOI: 10.1016/j.bbrc.2010.10.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 10/17/2010] [Indexed: 10/18/2022]
Abstract
The human secretory leukocyte protease inhibitor (SLPI) is an 11.7 kD cysteine-rich protein that has been shown to possess anti-protease, anti-inflammatory, and antimicrobial properties. By using a Pichia pastoris strain that overproduces protein disulfide isomerase (PDI), we obtained greater than fivefold higher levels of SLPI than in strains expressing normal levels of PDI and containing multiple copies of the SLPI gene. Elevated levels of PDI also enhanced the specific activity of the secreted SLPI by helping it achieve a proper tertiary structure. Mass spectrometry analysis indicated a greater number of disulfide bonds in the SLPI produced by the PDI overexpression strain compared to the SLPI produced in strains with normal PDI levels. Although others have utilized a similar strategy to increase yield, we believe that this is the first example of PDI overexpression being demonstrated to enhance the folding and thus increase the biological activity of a protein produced in the yeast P. pastoris.
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Affiliation(s)
- Zhiguo Li
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA
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37
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Fernández L, Jiao N, Soni P, Gumulya Y, de Oliveira LG, Reetz MT. An efficient method for mutant library creation inPichia pastorisuseful in directed evolution. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.3109/10242420903505834] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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38
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Papakonstantinou T, Harris S, Hearn MTW. Expression of GFP using Pichia pastoris vectors with zeocin or G-418 sulphate as the primary selectable marker. Yeast 2009; 26:311-21. [PMID: 19399907 DOI: 10.1002/yea.1666] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pichia pastoris is a popular host organism for expressing heterologous proteins, and various expression vectors for this yeast are currently available. Recently, vectors containing novel dominant antibiotic resistance markers have become a strong and developing field of research for this methylotropic yeast strain. We have developed new P. pastoris expression vectors, the pPICKanMX6 and pPICKanMX6alpha series. These vectors were constructed by replacing the zeocin resistance gene of the pPICZA, B, C and pPICZalphaA, B and C vectors with the Tn903 kan(R) marker from pFA6a KanMX6, which confers G-418 sulphate resistance in P. pastoris. The limits of antibiotic resistance in two transformant yeast strains were investigated, and the selection marker was shown to be stably retained. To demonstrate their usefulness, a gene encoding hexa-histidine-tagged green fluorescent protein (GFPH6) was cloned into one of the new vectors and GFP expression examined in P. pastoris cells. The protein expression levels using the pPICKanMX6B vector were comparable with that using the original plasmid, based on zeocin resistance as seen by yeast cell fluorescence. Moreover, GFPH6 was able to be isolated by immobilized metal ion affinity chromatography (IMAC) from lysates of both yeast strains. A model reporter construct has been used to demonstrate successful recombinant protein expression and its subsequent purification using these new vectors. Corresponding vectors can now also be engineered with foreign gene expression under the control of various different promoters, to increase the flexibility of P. pastoris as a cellular factory for heterologous protein production.
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Affiliation(s)
- Theo Papakonstantinou
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria 3800, Australia
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39
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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