1
|
Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [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: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
Collapse
Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
| |
Collapse
|
2
|
Karaoğlan M. Alternative secretory signal sequences for recombinant protein production in Pichia pastoris. Enzyme Microb Technol 2023; 168:110256. [PMID: 37196384 DOI: 10.1016/j.enzmictec.2023.110256] [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: 02/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Extracellular protein production is primarily preferred to facilitate the downstream processes in recombinant protein production. Secretion of recombinant proteins is mediated by the processing of signal peptides in their N-terminal portion by the secretory mechanism of host expression systems. These molecular elements involved in secretion are functionally interchangeable between different species and secretion sequence screening is one of the widely used approaches to improve extracellular protein production. In this study, α-mating and protein internal repeats (PIR) secretion sequences isolated from different yeasts (Kluyveromyces lactis, Kluyveromyces marxianus and Hansenula polymorpha) were tested in Pichia pastoris for the production of two different proteins (α-amylase and xylanase) and compared with the well-known secretory signals, S. cerevisiae α-mating factor (Sc-MF) and P. pastoris protein internal repeats PIR (PpPIR). The results obtained showed the potential of signal sequences tested. Among the tested peptides, the highest yields were achieved with H. polymorpha protein internal repeats (HpPIR) and K. lactis α-mating factor (Kl-MF) for xylanase and K. marxianus protein internal repeats (KmPIR) and K. lactis α-mating factor (Kl-MF) for amylase. In further studies, these sequences can be evaluated as alternatives in the production of different proteins in P. pastoris and in the production of recombinant proteins in different expression systems.
Collapse
Affiliation(s)
- Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Türkiye.
| |
Collapse
|
3
|
Jiang M, Liu Y, Xue H, Wang Y, Wang C, Yang F, Li X. Expression and biochemical characterization of a Bacillus subtilis catalase in Pichia pastoris X-33. Protein Expr Purif 2023; 208-209:106277. [PMID: 37100104 DOI: 10.1016/j.pep.2023.106277] [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: 12/13/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023]
Abstract
Catalase, which catalyzes the decomposition of H2O2 to H2O and O2, is widely used to reduce H2O2 in industrial applications, such as in food processing, textile dyeing and wastewater treatment. In this study, the catalase (KatA) from Bacillus subtilis was cloned and expressed in the yeast Pichia pastoris X-33. The effect of the promoter in the expression plasmid on the activity level of the secreted KatA protein was also studied. First, the gene encoding KatA was cloned and inserted into a plasmid containing an inducible alcohol oxidase 1 promoter (pAOX1) or a constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (pGAP). The recombinant plasmids were validated by colony PCR and sequencing and then linearized and transformed into the yeast P. pastoris X-33 for expression. With the promoter pAOX1, the maximum yield of KatA in the culture medium reached 338.8 ± 9.6 U/mL in 2 days of shake flask cultivation, which was approximately 2.1-fold greater than the maximum yield obtained with the promoter pGAP. The expressed KatA was then purified from the culture medium by anion exchange chromatography, and its specific activity was determined to be 14826.58 U/mg. Finally, the purified KatA exhibited optimum activity at 25 °C and pH 11.0. Its Km for hydrogen peroxide was 10.9 ± 0.5 mM, and its kcat/Km was 5788.1 ± 25.6 s-1 mM-1. Through the work presented in this article, we have therefore demonstrated efficient expression and purification of KatA in P. pastoris, which might be advantageous for scaling up the production of KatA for use in a variety of biotechnological applications.
Collapse
Affiliation(s)
- Mengtong Jiang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yuxin Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Hongjian Xue
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Yiqi Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Conggang Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| |
Collapse
|
4
|
Potential of the Signal Peptide Derived from the PAS_chr3_0030 Gene Product for Secretory Expression of Valuable Enzymes in Pichia pastoris. Appl Environ Microbiol 2022; 88:e0029622. [PMID: 35435711 DOI: 10.1128/aem.00296-22] [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] [Indexed: 11/20/2022] Open
Abstract
Pichia pastoris is widely used for the production of valuable recombinant proteins. An advantage of P. pastoris over other expression systems is that it secretes low levels of endogenous proteins, which facilitates the purification processes if the desired recombinant proteins are efficiently secreted into the culture medium. However, not all recombinant proteins can be successfully secreted by P. pastoris, especially enzymes that are located in intracellular compartments in their native hosts. Few studies have reported strategies for releasing recombinant proteins which cannot be secreted by standard protocols. Here, we investigated whether this challenge can be addressed using novel secretion leaders. Analysis of the secretome and transcriptome of P. pastoris indicated that the four genes with the highest protein-to-transcript ratios were EPX1, PAS_chr3_0030, SCW10, and UTH1, suggesting that their gene products contain efficient secretion leaders. Our data revealed that the signal peptide derived from the PAS_chr3_0030 gene product conferred secretion competence to certain industrial enzymes, e.g., a nitrilase of Alcaligenes faecalis ZJUTB10, a ribosylnicotinamide kinase of P. pastoris, and a glucose dehydrogenase of Exiguobacterium sibiricum. Therefore, the signal peptide derived from the PAS_chr3_0030 gene product represents a novel secretion sequence for the secretory expression of recombinant enzymes in P. pastoris. IMPORTANCE Although P. pastoris is widely used for the secretory production of pharmaceutical proteins, its successful applications in the secretory production of industrial enzymes are limited. The α-mating factor pre-pro leader is the most widely used secretion signal in P. pastoris, but numerous industrial enzymes cannot be secreted using it. The importance of this study is that we identified a signal peptide derived from the PAS_chr3_0030 gene product which conferred secretion competence to three-quarters of the enzymes tested. This signal peptide derived from the PAS_chr3_0030 gene product may facilitate the application of P. pastoris in industrial biocatalysis.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Ahn SO, Lim HD, You SH, Cheong DE, Kim GJ. Soluble Expression and Efficient Purification of Recombinant Class I Hydrophobin DewA. Int J Mol Sci 2021; 22:ijms22157843. [PMID: 34360609 PMCID: PMC8345945 DOI: 10.3390/ijms22157843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Hydrophobins are small proteins (<20 kDa) with an amphipathic tertiary structure that are secreted by various filamentous fungi. Their amphipathic properties provide surfactant-like activity, leading to the formation of robust amphipathic layers at hydrophilic–hydrophobic interfaces, which make them useful for a wide variety of industrial fields spanning protein immobilization to surface functionalization. However, the industrial use of recombinant hydrophobins has been hampered due to low yield from inclusion bodies owing to the complicated process, including an auxiliary refolding step. Herein, we report the soluble expression of a recombinant class I hydrophobin DewA originating from Aspergillus nidulans, and its efficient purification from recombinant Escherichia coli. Soluble expression of the recombinant hydrophobin DewA was achieved by a tagging strategy using a systematically designed expression tag (ramp tag) that was fused to the N-terminus of DewA lacking the innate signal sequence. Highly expressed recombinant hydrophobin DewA in a soluble form was efficiently purified by a modified aqueous two-phase separation technique using isopropyl alcohol. Our approach for expression and purification of the recombinant hydrophobin DewA in E. coli shed light on the industrial production of hydrophobins from prokaryotic hosts.
Collapse
Affiliation(s)
- Sang-Oh Ahn
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Korea; (S.-O.A.); (D.-E.C.)
| | - Ho-Dong Lim
- Center for Industrialization of Agricultural and Livestock Microorganisms, 241 Cheomdangwahak-ro, Jeongeup-si 56212, Jeollabuk-do, Korea;
| | - Sung-Hwan You
- Biomedical Research Center, Chonnam National University, Convergence Science Building (M2), Suite 301-1 264, Seoyang-ro, Hwasun-eup, Hwasun-gun 58128, Jeollanam-do, Korea;
| | - Dae-Eun Cheong
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Korea; (S.-O.A.); (D.-E.C.)
| | - Geun-Joong Kim
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju 61186, Korea; (S.-O.A.); (D.-E.C.)
- Correspondence: ; Tel.: +82-62-530-3403
| |
Collapse
|
7
|
Zhao Z, Cai F, Gao R, Ding M, Jiang S, Chen P, Pang G, Chenthamara K, Shen Q, Bayram Akcapinar G, Druzhinina IS. At least three families of hyphosphere small secreted cysteine-rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment. Environ Microbiol 2021; 23:5750-5768. [PMID: 33538393 PMCID: PMC8596622 DOI: 10.1111/1462-2920.15413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022]
Abstract
The secretomes of filamentous fungi contain a diversity of small secreted cysteine‐rich proteins (SSCPs) that have a variety of properties ranging from toxicity to surface activity. Some SSCPs are recognized by other organisms as indicators of fungal presence, but their function in fungi is not fully understood. We detected a new family of fungal surface‐active SSCPs (saSSCPs), here named hyphosphere proteins (HFSs). An evolutionary analysis of the HFSs in Pezizomycotina revealed a unique pattern of eight single cysteine residues (C‐CXXXC‐C‐C‐C‐C‐C) and a long evolutionary history of multiple gene duplications and ancient interfungal lateral gene transfers, suggesting their functional significance for fungi with different lifestyles. Interestingly, recombinantly produced saSSCPs from three families (HFSs, hydrophobins and cerato‐platanins) showed convergent surface‐modulating activity on glass and on poly(ethylene‐terephthalate), transforming their surfaces to a moderately hydrophilic state, which significantly favoured subsequent hyphal attachment. The addition of purified saSSCPs to the tomato rhizosphere had mixed effects on hyphal attachment to roots, while all tested saSSCPs had an adverse effect on plant growth in vitro. We propose that the exceptionally high diversity of saSSCPs in Trichoderma and other fungi evolved to efficiently condition various surfaces in the hyphosphere to a fungal‐beneficial state.
Collapse
Affiliation(s)
- Zheng Zhao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Feng Cai
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China.,Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Renwei Gao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Mingyue Ding
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Siqi Jiang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Peijie Chen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Guan Pang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Komal Chenthamara
- Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| | - Qirong Shen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Günseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irina S Druzhinina
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China.,Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China.,Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
| |
Collapse
|
8
|
de Paula RG, Antoniêto ACC, Nogueira KMV, Ribeiro LFC, Rocha MC, Malavazi I, Almeida F, Silva RN. Extracellular vesicles carry cellulases in the industrial fungus Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:146. [PMID: 31223336 PMCID: PMC6570945 DOI: 10.1186/s13068-019-1487-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Trichoderma reesei is the most important industrial producer of lignocellulolytic enzymes. These enzymes play an important role in biomass degradation leading to novel applications of this fungus in the biotechnology industry, specifically biofuel production. The secretory pathway of fungi is responsible for transporting proteins addressed to different cellular locations involving some cellular endomembrane systems. Although protein secretion is an extremely efficient process in T. reesei, the mechanisms underlying protein secretion have remained largely uncharacterized in this organism. RESULTS Here, we report for the first time the isolation and characterization of T. reesei extracellular vesicles (EVs). Using proteomic analysis under cellulose culture condition, we have confidently identified 188 vesicular proteins belonging to different functional categories. Also, we characterized EVs production using transmission electron microscopy in combination with light scattering analysis. Biochemical assays revealed that T. reesei extracellular vesicles have an enrichment of filter paper (FPase) and β-glucosidase activities in purified vesicles from 24, 72 and 96, and 72 and 96 h, respectively. Furthermore, our results showed that there is a slight enrichment of small RNAs inside the vesicles after 96 h and 120 h, and presence of hsp proteins inside the vesicles purified from T. reesei grown in the presence of cellulose. CONCLUSIONS This work points to important insights into a better understanding of the cellular mechanisms underlying the regulation of cellulolytic enzyme secretion in this fungus.
Collapse
Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| |
Collapse
|
9
|
Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
Collapse
Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
| |
Collapse
|
10
|
Vieira Gomes AM, Souza Carmo T, Silva Carvalho L, Mendonça Bahia F, Parachin NS. Comparison of Yeasts as Hosts for Recombinant Protein Production. Microorganisms 2018; 6:microorganisms6020038. [PMID: 29710826 PMCID: PMC6027275 DOI: 10.3390/microorganisms6020038] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis, and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.
Collapse
Affiliation(s)
- Antonio Milton Vieira Gomes
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Talita Souza Carmo
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Lucas Silva Carvalho
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Frederico Mendonça Bahia
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| |
Collapse
|
11
|
Cao L, Ren G, Qin Z, Huang X, Kong W, Wang Z, Liang W, Bi X, Liu Y. Improving the Secretion Yield of the β-Galactosidase Bgal1-3 in Pichia pastoris for Use as a Potential Catalyst in the Production of Prebiotic-Enriched Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10757-10766. [PMID: 29181978 DOI: 10.1021/acs.jafc.7b04694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, three kinds of milk were treated with the β-galactosidase Bgal1-3 (4 U/mL), resulting in 7.2-9.5 g/L galactooligosaccharides (GOS) at a lactose conversion of 90-95%. Then, Bgal1-3 was secreted from Pichia pastoris X33 under the direction of an α-factor signal peptide. After cultivation for 144 h in a flask culture with shaking, the extracellular activity of Bgal1-3 was 4.4 U/mL. Five more signal peptides (HFBI, apre, INU1A, MF4I, and W1) were employed to direct the secretion, giving rise to a more efficient signal peptide, W1 (11.2 U/mL). To further improve the secretion yield, recombinant strains harboring two copies of the bgal1-3 gene were constructed, improving the extracellular activity to 22.6 U/mL (about 440 mg/L). This study successfully constructed an engineered strain for the production of the β-galactosidase Bgal1-3, which is a promising catalyst in the preparation of prebiotic-enriched milk.
Collapse
Affiliation(s)
- Lichuang Cao
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Guanghui Ren
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Zongmin Qin
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Xin Huang
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Wei Kong
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Zhijun Wang
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| | - Weiqu Liang
- Dongguan Agricultural Research Center , Dongguan, Guangdong 523086, P. R. China
| | - Xiaogang Bi
- The Third Affiliated Hospital of Sun Yat-Sen University , Guangzhou, Guangdong 510630, P. R. China
| | - Yuhuan Liu
- School of Life Sciences, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, National Engineering Center for Marine Biotechnology of South China Sea, Sun Yat-Sen University , Guangzhou, Guangdong 510275, P. R. China
| |
Collapse
|
12
|
High-level expression and purification of a molluskan endoglucanase from Ampullaria crossean in Pichia pastoris. Protein Expr Purif 2017; 139:8-13. [DOI: 10.1016/j.pep.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/29/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022]
|
13
|
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.
Collapse
|
14
|
Camattari A, Goh A, Yip LY, Tan AHM, Ng SW, Tran A, Liu G, Liachko I, Dunham MJ, Rancati G. Characterization of a panARS-based episomal vector in the methylotrophic yeast Pichia pastoris for recombinant protein production and synthetic biology applications. Microb Cell Fact 2016; 15:139. [PMID: 27515025 PMCID: PMC4981965 DOI: 10.1186/s12934-016-0540-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022] Open
Abstract
Background Recombinant protein production in the methylotrophic yeast Pichia pastoris largely relies on integrative vectors. Although the stability of integrated expression cassettes is well appreciated for most applications, the availability of reliable episomal vectors for this host would represent a useful tool to expedite cloning and high-throughput screening, ameliorating also the relatively high clonal variability reported in transformants from integrative vectors caused by off-target integration in the P. pastoris genome. Recently, heterologous and endogenous autonomously replicating sequences (ARS) were identified in P. pastoris by genome mining, opening the possibility of expanding the available toolbox to include efficient episomal plasmids. The aim of this technical report is to validate a 452-bp sequence (“panARS”) in context of P. pastoris expression vectors, and to compare their performance to classical integrative plasmids. Moreover, we aimed to test if such episomal vectors would be suitable to sustain in vivo recombination, using fragments for transformation, directly in P. pastoris cells. Results A panARS-based episomal vector was evaluated using blue fluorescent protein (BFP) as a reporter gene. Normalized fluorescence from colonies carrying panARS-BFP outperformed the level of signal obtained from integrative controls by several-fold, whereas endogenous sequences, identified from the P. pastoris genome, were not as efficient in terms of protein production. At the single cell level, panARS-BFP clones showed lower interclonal variability but higher intraclonal variation compared to their integrative counterparts, supporting the idea that heterologous protein production could benefit from episomal plasmids. Finally, efficiency of 2-fragment and 3-fragment in vivo recombination was tested using varying lengths of overlapping regions and molar ratios between fragments. Upon optimization, minimal background was obtained for in vivo assembled vectors, suggesting this could be a quick and efficient method to generate of episomal plasmids of interest. Conclusions An expression vector based on the panARS sequence was shown to outperform its integrative counterparts in terms of protein productivity and interclonal variability, facilitating recombinant protein expression and screening. Using optimized fragment lengths and ratios, it was possible to perform reliable in vivo recombination of fragments in P. pastoris. Taken together, these results support the applicability of panARS episomal vectors for synthetic biology approaches.
Collapse
Affiliation(s)
- Andrea Camattari
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore.
| | - Amelia Goh
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Lian Yee Yip
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Andy Hee Meng Tan
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Sze Wai Ng
- Bioprocessing Technology Institute (A-STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668, Singapore
| | - Anthony Tran
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
| | - Gaowen Liu
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Giulia Rancati
- Institute of Medical Biology (A-STAR), 8a Biomedical Grove, #06-06, Singapore, 138648, Singapore
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Fungal Biotechnology for Industrial Enzyme Production: Focus on (Hemi)cellulase Production Strategies, Advances and Challenges. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
17
|
Madhavan A, Sukumaran RK. Signal peptides from filamentous fungi efficiently mediate the secretion of recombinant proteins in Kluyveromyces lactis. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
18
|
Vogl T, Ahmad M, Krainer FW, Schwab H, Glieder A. Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. Microb Cell Fact 2015; 14:103. [PMID: 26169367 PMCID: PMC4501187 DOI: 10.1186/s12934-015-0293-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Tagging proteins is a standard method facilitating protein detection, purification or targeting. When tagging a certain protein of interest, it is challenging to predict which tag will give optimal results and will not interfere with protein folding, activity or yields. Ideally, multiple tags and positions are tested which however complicates molecular cloning and expression vector generation. In conventional cloning, tags are either added on PCR primers (requiring a distinct primer and PCR product per tag) or provided on the vector (typically leaving a restriction site scar). RESULTS Here we report a vector family of 40 plasmids allowing simple, seamless fusions of a single PCR product with various N- and C-terminal tags, signal sequences and promoters. The restriction site free cloning (RSFC) strategy presented in this paper relies on seamless cloning using type IIS restriction endonucleases. After cutting out a stuffer (placeholder) fragment from the vectors, a single PCR product can be directly inserted in frame into all 40 plasmids using blunt end or TA ligations, requiring only verification of the orientation. We have established a RSFC vector family for the commonly used protein expression host Pichia pastoris and demonstrated the system with the secretory expression of horseradish peroxidase (HRP). HRP fusions to four tags (Myc, FLAG, His, Strep) and two fusion proteins (GFP and MBP) showed a 31-fold difference in volumetric activities. C-terminal tagging caused in some cases almost a complete loss of function, whereas N-terminal tags showed moderate differences. CONCLUSIONS The RSFC vectors provide an unprecedented toolbox for expression optimization in P. pastoris. The results obtained with HRP underline the importance of comparing different tags to maximize activities of fusion proteins. In a similar fashion the RSFC strategy can be applied in other expression hosts to screen for optimal promoters, signal sequences or to facilitate the evaluation of (iso-) enzyme families.
Collapse
Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria. .,Queensland University of Technology, 2 George St., Brisbane, QLD, 4000, Australia.
| | - Mudassar Ahmad
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Florian W Krainer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Helmut Schwab
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| |
Collapse
|
19
|
Heiss S, Puxbaum V, Gruber C, Altmann F, Gasser B, Mattanovich D. Multistep processing of the secretion leader of the extracellular protein Epx1 in Pichia pastoris and implications for protein localization. Microbiology (Reading) 2015; 161:1356-68. [DOI: 10.1099/mic.0.000105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
20
|
Yarimizu T, Nakamura M, Hoshida H, Akada R. Synthetic signal sequences that enable efficient secretory protein production in the yeast Kluyveromyces marxianus. Microb Cell Fact 2015; 14:20. [PMID: 25889890 PMCID: PMC4347551 DOI: 10.1186/s12934-015-0203-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/27/2015] [Indexed: 02/02/2023] Open
Abstract
Background Targeting of cellular proteins to the extracellular environment is directed by a secretory signal sequence located at the N-terminus of a secretory protein. These signal sequences usually contain an N-terminal basic amino acid followed by a stretch containing hydrophobic residues, although no consensus signal sequence has been identified. In this study, simple modeling of signal sequences was attempted using Gaussia princeps secretory luciferase (GLuc) in the yeast Kluyveromyces marxianus, which allowed comprehensive recombinant gene construction to substitute synthetic signal sequences. Results Mutational analysis of the GLuc signal sequence revealed that the GLuc hydrophobic peptide length was lower limit for effective secretion and that the N-terminal basic residue was indispensable. Deletion of the 16th Glu caused enhanced levels of secreted protein, suggesting that this hydrophilic residue defined the boundary of a hydrophobic peptide stretch. Consequently, we redesigned this domain as a repeat of a single hydrophobic amino acid between the N-terminal Lys and C-terminal Glu. Stretches consisting of Phe, Leu, Ile, or Met were effective for secretion but the number of residues affected secretory activity. A stretch containing sixteen consecutive methionine residues (M16) showed the highest activity; the M16 sequence was therefore utilized for the secretory production of human leukemia inhibitory factor protein in yeast, resulting in enhanced secreted protein yield. Conclusions We present a new concept for the provision of secretory signal sequence ability in the yeast K. marxianus, determined by the number of residues of a single hydrophobic residue located between N-terminal basic and C-terminal acidic amino acid boundaries. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0203-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tohru Yarimizu
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, 2-16-1 Tokiwadai, Ube, 755-8611, Japan. .,Present address: Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kan-nondai, Tsukuba, Ibaraki, 305-8604, Japan.
| | - Mikiko Nakamura
- Innovation Center, Yamaguchi University, 2-16-1 Tokiwadai, Ube, 755-8611, Japan.
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, 2-16-1 Tokiwadai, Ube, 755-8611, Japan.
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, 2-16-1 Tokiwadai, Ube, 755-8611, Japan.
| |
Collapse
|
21
|
Massahi A, Çalık P. In-silico determination of Pichia pastoris signal peptides for extracellular recombinant protein production. J Theor Biol 2015; 364:179-88. [DOI: 10.1016/j.jtbi.2014.08.048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/13/2014] [Accepted: 08/27/2014] [Indexed: 11/29/2022]
|
22
|
Zhan R, Mu W, Jiang B, Zhou L, Zhang T. Efficient secretion of inulin fructotransferase in Pichia pastoris using the formaldehyde dehydrogenase 1 promoter. ACTA ACUST UNITED AC 2014; 41:1783-91. [DOI: 10.1007/s10295-014-1516-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 09/19/2014] [Indexed: 10/24/2022]
Abstract
Abstract
Inulin fructotransferase (IFTase) has received considerable attention due to its ability to catalyse inulin hydrolysis to difructose anhydride (DFA III), a natural low-calorie functional sweetener. In the present study, for the first time, we describe the expression of IFTase in Pichia pastoris under the control of the formaldehyde dehydrogenase 1 promoter (PFLD1). Using this system, we achieved efficient secretion with four substrate fed-batch strategies in a 3-L fermenter. The co-feeding induction strategy with methylamine hydrochloride and methanol achieved the maximum extracellular IFTase activity of 62.72 U mL−1, which was 3.2-fold higher than that obtained with the wild-type strain. In addition to methanol, carbon sources such as glucose and glycerol could also be utilised by PFLD1-controlled P. pastoris for IFTase production using methylamine hydrochloride induction. However, we found that glycerol and glucose should be strictly controlled at low concentrations of 0.5–1.5 % (v/v) and 1–1.5 % (w/v), respectively. The use of glycerol and glucose demonstrated that P. pastoris was also attractive for IFTase production via methanol-free cultivation strategies. This study may provide the basis for the industrial use of this recombinant IFTase for the production of DFA III.
Collapse
Affiliation(s)
- Rongrong Zhan
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University 1800 Lihu Avenue 214122 Wuxi Jiangsu China
| | - Wanmeng Mu
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University 1800 Lihu Avenue 214122 Wuxi Jiangsu China
| | - Bo Jiang
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University 1800 Lihu Avenue 214122 Wuxi Jiangsu China
| | - Liuming Zhou
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University 1800 Lihu Avenue 214122 Wuxi Jiangsu China
- Roquette America 52632 Keokuk IA USA
| | - Tao Zhang
- grid.258151.a 0000000107081323 State Key Laboratory of Food Science and Technology Jiangnan University 1800 Lihu Avenue 214122 Wuxi Jiangsu China
| |
Collapse
|
23
|
Madhavan A, Sukumaran RK. Promoter and signal sequence from filamentous fungus can drive recombinant protein production in the yeast Kluyveromyces lactis. BIORESOURCE TECHNOLOGY 2014; 165:302-308. [PMID: 24661814 DOI: 10.1016/j.biortech.2014.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/26/2014] [Accepted: 03/01/2014] [Indexed: 06/03/2023]
Abstract
Cross-recognition of promoters from filamentous fungi in yeast can have important consequences towards developing fungal expression systems, especially for the rapid evaluation of their efficacy. A truncated 510bp inducible Trichoderma reesei cellobiohydrolase I (cbh1) promoter was tested for the expression of green fluorescent protein (GFP) in Kluyveromyces lactis after disrupting its native β-galactosidase (lac4) promoter. The efficiency of the CBH1 secretion signal was also evaluated by fusing it to the lac4 promoter of the yeast, which significantly increased the secretion of recombinant protein in K. lactis compared to the native α-mating factor secretion signal. The fungal promoter is demonstrated to have potential to drive heterologous protein production in K. lactis; and the small sized T. reesei cbh1 secretion signal can mediate the protein secretion in K. lactis with high efficiency.
Collapse
Affiliation(s)
- Aravind Madhavan
- Centre for Biofuels, Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate PO, Trivandrum 695 019, India
| | - Rajeev K Sukumaran
- Centre for Biofuels, Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate PO, Trivandrum 695 019, India.
| |
Collapse
|
24
|
Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl Microbiol Biotechnol 2014; 98:5301-17. [PMID: 24743983 PMCID: PMC4047484 DOI: 10.1007/s00253-014-5732-5] [Citation(s) in RCA: 602] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/29/2022]
Abstract
Pichia pastoris is an established protein expression host mainly applied for the production of biopharmaceuticals and industrial enzymes. This methylotrophic yeast is a distinguished production system for its growth to very high cell densities, for the available strong and tightly regulated promoters, and for the options to produce gram amounts of recombinant protein per litre of culture both intracellularly and in secretory fashion. However, not every protein of interest is produced in or secreted by P. pastoris to such high titres. Frequently, protein yields are clearly lower, particularly if complex proteins are expressed that are hetero-oligomers, membrane-attached or prone to proteolytic degradation. The last few years have been particularly fruitful because of numerous activities in improving the expression of such complex proteins with a focus on either protein engineering or on engineering the protein expression host P. pastoris. This review refers to established tools in protein expression in P. pastoris and highlights novel developments in the areas of expression vector design, host strain engineering and screening for high-level expression strains. Breakthroughs in membrane protein expression are discussed alongside numerous commercial applications of P. pastoris derived proteins.
Collapse
|
25
|
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.
Collapse
|
26
|
Gasser B, Prielhofer R, Marx H, Maurer M, Nocon J, Steiger M, Puxbaum V, Sauer M, Mattanovich D. Pichia pastoris: protein production host and model organism for biomedical research. Future Microbiol 2013; 8:191-208. [DOI: 10.2217/fmb.12.133] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pichia pastoris is the most frequently used yeast system for heterologous protein production today. The last few years have seen several products based on this platform reach approval as biopharmaceutical drugs. Successful glycoengineering to humanize N-glycans is further fuelling this development. However, detailed understanding of the yeast’s physiology, genetics and regulation has only developed rapidly in the last few years since published genome sequences have become available. An expanding toolbox of genetic elements and strains for the improvement of protein production is being generated, including promoters, gene copy-number enhancement, gene knockout and high-throughput methods. Protein folding and secretion have been identified as significant bottlenecks in yeast expression systems, pinpointing a major target for strain optimization. At the same time, it has become obvious that P. pastoris, as an evolutionarily more ‘ancient’ yeast, may in some cases be a better model for human cell biology and disease than Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Brigitte Gasser
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Roland Prielhofer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Hans Marx
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Michael Maurer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
- University of Applied Sciences FH-Campus Vienna, School of Bioengineering, 1190 Vienna, Austria
| | - Justyna Nocon
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| | - Matthias Steiger
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Verena Puxbaum
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Michael Sauer
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), 1190 Vienna, Austria
| | - Diethard Mattanovich
- University of Natural Resources & Life Sciences (BOKU), Department of Biotechnology, 1190 Vienna, Austria
| |
Collapse
|
27
|
Han SJ, Cho S, Lowehhaupt K, Park SY, Sim SJ, Kim YG. Recombinant tagging system using ribosomal frameshifting to monitor protein expression. Biotechnol Bioeng 2012; 110:898-904. [PMID: 23042497 DOI: 10.1002/bit.24740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/27/2012] [Accepted: 09/27/2012] [Indexed: 01/20/2023]
Abstract
For rapid and accurate quantitation of recombinant proteins during expression and after purification, we introduce a new tagging strategy that expresses both target proteins and limitedly tagged target proteins together in a single cell at a constant ratio by utilizing cis-elements of programmed -1 ribosomal frameshifting (-1RFS) as an embedded device. -1RFS is an alternative reading mechanism that effectively controls protein expression by many viruses. When a target gene is fused to the enhanced green fluorescent protein (EGFP) gene with a -1RFS element implanted between them, the unfused target and the target-GFP fusion proteins are expressed at a fixed ratio. The expression ratio between these two protein products is adjustable simply by changing -1RFS signals. This limited-tagging system would be valuable for the real-time monitoring of protein expression when optimizing expression condition for a new protein, and in monitoring large-scale bioprocesses without a large metabolic burden on host cells. Furthermore, this strategy allows for the direct measurement of the quantity of a protein on a chip surface and easy application to proteomewide study of gene products.
Collapse
Affiliation(s)
- Se Jong Han
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | | | | | | | | | | |
Collapse
|
28
|
Liang S, Li C, Ye Y, Lin Y. Endogenous signal peptides efficiently mediate the secretion of recombinant proteins in Pichia pastoris. Biotechnol Lett 2012; 35:97-105. [PMID: 23160737 DOI: 10.1007/s10529-012-1055-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/14/2012] [Indexed: 11/30/2022]
Abstract
By predicting the potential signal peptides from proteins that are naturally secreted by Pichia pastoris, we identified three possible endogenous signal peptides: Scw, Dse and Exg. We compared their capability to mediate the secretion of enhanced green fluorescent protein (EGFP) and Candida antarctica lipase B (CALB) with that of the Saccharomyces cerevisiae α-factor prepro-signal. EGFP entered the secretory pathway of P. pastoris and was efficiently secreted into the culture medium by all three endogenous peptides. Further, these three putative endogenous signal peptides were also effective in secreting CALB. These endogenous signal peptides thus have the potential to mediate the efficient secretion of heterologous proteins in P. pastoris.
Collapse
Affiliation(s)
- Shuli Liang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.
| | | | | | | |
Collapse
|
29
|
Kottmeier K, Günther TJ, Weber J, Kurtz S, Ostermann K, Rödel G, Bley T. Constitutive expression of hydrophobin HFB1 from Trichoderma reesei in Pichia pastoris and its pre-purification by foam separation during cultivation. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Tobias Jan Günther
- Institute of Radiochemistry; Helmholtz-Zentrum Dresden-Rossendorf; Dresden; Germany
| | - Jost Weber
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden; Germany
| | - Susann Kurtz
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Kai Ostermann
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Gerhard Rödel
- Technische Universität Dresden; Institute of Genetics; Dresden; Germany
| | - Thomas Bley
- Institute of Food Technology and Bioprocess Engineering; Technische Universität Dresden; Dresden; Germany
| |
Collapse
|