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Xie J, Xiao C, Pan Y, Xue S, Huang M. ER stress-induced transcriptional response reveals tolerance genes in yeast. Biotechnol J 2024; 19:e2400082. [PMID: 38896412 DOI: 10.1002/biot.202400082] [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: 02/12/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 06/21/2024]
Abstract
Saccharomyces cerevisiae is important for protein secretion studies, yet the complexities of protein synthesis and secretion under endoplasmic reticulum (ER) stress conditions remain not fully understood. ER stress, triggered by alterations in the ER protein folding environment, poses substantial challenges to cells, especially during heterologous protein production. In this study, we used RNA-seq to analyze the transcriptional responses of yeast strains to ER stress induced by reagents such as tunicamycin (Tm) or dithiothreitol (DTT). Our gene expression analysis revealed several crucial genes, such as HMO1 and BIO5, that are involved in ER-stress tolerance. Through metabolic engineering, the best engineered strain R23 with HMO1 overexpression and BIO5 deletion, showed enhanced ER stress tolerance and improved protein folding efficiency, leading to a 2.14-fold increase in α-amylase production under Tm treatment and a 2.04-fold increase in cell density under DTT treatment. Our findings contribute to the understanding of cellular responses to ER stress and provide a basis for further investigations into the mechanisms of ER stress at the cellular level.
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Affiliation(s)
- Jingrong Xie
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Songlyu Xue
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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Ren H, Lan Q, Zhou S, Lyu Y, Yu Y, Zhou J, Mo W, Lu H. Coupling thermotolerance and high production of recombinant protein by CYR1 N1546K mutation via cAMP signaling cascades. Commun Biol 2024; 7:627. [PMID: 38789513 PMCID: PMC11126729 DOI: 10.1038/s42003-024-06341-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
In recombinant protein-producing yeast strains, cells experience high production-related stresses similar to high temperatures. It is possible to increase recombinant protein production by enhancing thermotolerance, but few studies have focused on this topic. Here we aim to identify cellular regulators that can simultaneously activate thermotolerance and high yield of recombinant protein. Through screening at 46 °C, a heat-resistant Kluyveromyces marxianus (K. marxianus) strain FDHY23 is isolated. It also exhibits enhanced recombinant protein productivity at both 30 °C and high temperatures. The CYR1N1546K mutation is identified as responsible for FDHY23's improved phenotype, characterized by weakened adenylate cyclase activity and reduced cAMP production. Introducing this mutation into the wild-type strain greatly enhances both thermotolerance and recombinant protein yields. RNA-seq analysis reveals that under high temperature and recombinant protein production conditions, CYR1 mutation-induced reduction in cAMP levels can stimulate cells to improve its energy supply system and optimize material synthesis, meanwhile enhance stress resistance, based on the altered cAMP signaling cascades. Our study provides CYR1 mutation as a novel target to overcome the bottleneck in achieving high production of recombinant proteins under high temperature conditions, and also offers a convenient approach for high-throughput screening of recombinant proteins with high yields.
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Affiliation(s)
- Haiyan Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Qing Lan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Shihao Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yilin Lyu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Wenjuan Mo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
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Weiss F, Requena-Moreno G, Pichler C, Valero F, Glieder A, Garcia-Ortega X. Scalable protein production by Komagataella phaffii enabled by ARS plasmids and carbon source-based selection. Microb Cell Fact 2024; 23:116. [PMID: 38643119 PMCID: PMC11031860 DOI: 10.1186/s12934-024-02368-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Most recombinant Komagataella phaffii (Pichia pastoris) strains for protein production are generated by genomic integration of expression cassettes. The clonal variability in gene copy numbers, integration loci and consequently product titers limit the aptitude for high throughput applications in drug discovery, enzyme engineering or most comparative analyses of genetic elements such as promoters or secretion signals. Circular episomal plasmids with an autonomously replicating sequence (ARS), an alternative which would alleviate some of these limitations, are inherently unstable in K. phaffii. Permanent selection pressure, mostly enabled by antibiotic resistance or auxotrophy markers, is crucial for plasmid maintenance and hardly scalable for production. The establishment and use of extrachromosomal ARS plasmids with key genes of the glycerol metabolism (glycerol kinase 1, GUT1, and triosephosphate isomerase 1, TPI1) as selection markers was investigated to obtain a system with high transformation rates that can be directly used for scalable production processes in lab scale bioreactors. RESULTS In micro-scale deep-well plate experiments, ARS plasmids employing the Ashbya gossypii TEF1 (transcription elongation factor 1) promoter to regulate transcription of the marker gene were found to deliver high transformation efficiencies and the best performances with the reporter protein (CalB, lipase B of Candida antarctica) for both, the GUT1- and TPI1-based, marker systems. The GUT1 marker-bearing strain surpassed the reference strain with integrated expression cassette by 46% upon re-evaluation in shake flask cultures regarding CalB production, while the TPI1 system was slightly less productive compared to the control. In 5 L bioreactor methanol-free fed-batch cultivations, the episomal production system employing the GUT1 marker led to 100% increased CalB activity in the culture supernatant compared to integration construct. CONCLUSIONS For the first time, a scalable and methanol-independent expression system for recombinant protein production for K. phaffii using episomal expression vectors was demonstrated. Expression of the GUT1 selection marker gene of the new ARS plasmids was refined by employing the TEF1 promoter of A. gossypii. Additionally, the antibiotic-free marker toolbox for K. phaffii was expanded by the TPI1 marker system, which proved to be similarly suited for the use in episomal plasmids as well as integrative expression constructs for the purpose of recombinant protein production.
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Affiliation(s)
- Florian Weiss
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Guillermo Requena-Moreno
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Carsten Pichler
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria
| | - Francisco Valero
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris host and vector systems, Institute of Molecular Biotechnology, Graz University of Technology, Graz, A-8010, Austria.
| | - Xavier Garcia-Ortega
- Christian Doppler Laboratory for Innovative Pichia Pastoris Host and Vector Systems, Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, 08193, Spain
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Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
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Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
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Gorczyca M, Nicaud JM, Celińska E. Transcription factors enhancing synthesis of recombinant proteins and resistance to stress in Yarrowia lipolytica. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12607-z. [PMID: 37318637 DOI: 10.1007/s00253-023-12607-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Resistance to environmental stress and synthesis of recombinant proteins (r-Prots) are both complex, strongly interconnected biological traits relying on orchestrated contribution of multiple genes. This, in turn, makes their engineering a challenging task. One of the possible strategies is to modify the operation of transcription factors (TFs) associated with these complex traits. The aim of this study was to examine the potential implications of selected five TFs (HSF1-YALI0E13948g, GZF1-YALI0D20482g, CRF1-YALI0B08206g, SKN7-YALI0D14520g, and YAP-like-YALI0D07744g) in stress resistance and/or r-Prot synthesis in Yarrowia lipolytica. The selected TFs were over-expressed or deleted (OE/KO) in a host strain synthesizing a reporter r-Prot. The strains were subjected to phenotype screening under different environmental conditions (pH, oxygen availability, temperature, and osmolality), and the obtained data processing was assisted by mathematical modeling. The results demonstrated that growth and the r-Prot yields under specific conditions can be significantly increased or decreased due to the TFs' engineering. Environmental factors "awakening" individual TFs were indicated, and their contribution was mathematically described. For example, OE of Yap-like TF was proven to alleviate growth retardation under high pH, while Gzf1 and Hsf1 were shown to serve as universal enhancers of r-Prot production in Y. lipolytica. On the other hand, KO of SKN7 and HSF1 disabled growth under hyperosmotic stress. This research demonstrates the usefulness of the TFs engineering approach in the manipulation of complex traits and evidences newly identified functions of the studied TFs. KEY POINTS: • Function and implication in complex traits of 5 TFs in Y. lipolytica were studied. • Gzf1 and Hsf1 are the universal r-Prots synthesis enhancers in Y. lipolytica. • Yap-like TF's activity is pH-dependent; Skn7 and Hsf1 act in osmostress response.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland.
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Korpys-Woźniak P, Celińska E. Molecular background of HAC1-driven improvement in the secretion of recombinant protein in Yarrowia lipolytica based on comparative transcriptomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 38:e00801. [PMID: 37234569 PMCID: PMC10206436 DOI: 10.1016/j.btre.2023.e00801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023]
Abstract
While the unfolded protein response (UPR) and its major regulator - transcription factor Hac1 are well-conserved across Eukarya, species-specific variations are repeatedly reported. Here we investigated molecular mechanisms by which co-over-expression of HAC1 improves secretion of a recombinant protein (r-Prot) in Yarrowia lipolytica, using comparative transcriptomics. Co-over-expression of HAC1 caused an >2-fold increase in secreted r-Prot, but its intracellular levels were decreased. The unconventional splicing rate of the HAC1 mRNA was counted through transcript sequencing. Multiple biological processes were affected in the HAC1-and-r-Prot co-over-expressing strain, including ribosome biogenesis, nuclear and mitochondrial events, cell cycle arrest, attenuation of gene expression by RNA polymerase III and II, as well as modulation of proteolysis and RNA metabolism; but whether the HAC1 co-over-expression/induction was the actual causative agent for these changes, was not always clear. We settled that the expression of the "conventional" HAC1 targets (KAR2 and PDI1) is not affected by its over-expression.
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Minden S, Aniolek M, Noorman H, Takors R. Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts. Genes (Basel) 2023; 14:genes14050997. [PMID: 37239357 DOI: 10.3390/genes14050997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
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Tamošiūnas PL, Pērkons I, Kukk K. Yeast-based system for in vivo evaluation of alleles of the anthocyanin production pathway. World J Microbiol Biotechnol 2023; 39:156. [PMID: 37039815 DOI: 10.1007/s11274-023-03593-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
Plants produce anthocyanins to incite the pollination and seed dispersion performed by pigment-attracted animals. These natural blue-to-red-coloured pigments can be used as food colourants and antioxidants. For this purpose, microbial bioproduction of anthocyanins has become of industrial interest in recent years. 20 new alleles of anthocyanin production pathway genes were extracted and characterised for protein expression level and stability using a developed single-PCR product gene-entry system for tagged protein synthesis in yeast S. cerevisiae. Enzymatic activities of these proteins in the episomally complemented in vivo systems were compared by HPLC-MS analysis. Results show that the codon optimisation of the anthocyanin pathway genes is not essential for the effective heterologous expression in yeast. Elevating the cellular abundance of CHS and F3H enzymes can increase anthocyanidin production from supplemented precursors. New alleles VmF3Hv1 and VuCHS were shown to have the best performance in the analysed system. System complementation with flavonoid 3',5'-hydroxylase substantially increases total anthocyanidin production. The described single-entry yeast episomal complementation system is a convenient and rapid tool for the complex evaluation of new alleles in vivo.
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Affiliation(s)
| | - Ingus Pērkons
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes st. 3, Riga, LV-1076, Latvia
| | - Kaia Kukk
- Latvian Biomedical Research and Study Centre, Ratsupites st. 1, Riga, LV-1067, Latvia
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So KK, Le NMT, Nguyen NL, Kim DH. Improving expression and assembly of difficult-to-express heterologous proteins in Saccharomyces cerevisiae by culturing at a sub-physiological temperature. Microb Cell Fact 2023; 22:55. [PMID: 36959657 PMCID: PMC10035479 DOI: 10.1186/s12934-023-02065-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Escherichia coli heat labile toxin B subunit (LTB) is one of the most popular oral vaccine adjuvants and intestine adsorption enhancers. It is often expressed as a fusion partner with target antigens to enhance their immunogenicity as well as gut absorbability. However, high expression levels of a fusion protein are critical to the outcome of immunization experiments and the success of subsequent vaccine development efforts. In order to improve the expression and functional assembly of LTB-fusion proteins using Saccharomyces cerevisiae, we compared their expression under culture conditions at a sub-physiological temperature 20 °C with their expression under a standard 30 °C. RESULTS The assembled expression of LTB-EDIII2 (LTB fused to the envelope domain III (EDIII) of Dengue virus serotype 2), which was expressed at the level of 20 µg/L in our previous study, was higher when the expression temperature was 20 °C as opposed to 30 °C. We also tested whether the expression and functional assembly of a difficult-to-express LTB fusion protein could be increased. The assembled expression of the difficult-to-express LTB-VP1 fusion protein (LTB fused to VP1 antigen of Foot-and-Mouth Disease Virus) dramatically increased, although the total amount of expressed protein was still lower than that of LTB-EDIII2. Slight but significant increase in the expression of well-known reporter protein eGFP, which has previously been shown to be increased by cultivation at 20 °C, was also observed in our expression system. As no significant changes in corresponding transcripts levels and cell growth were observed between 20 °C and 30 °C, we infer that translation and post-translational assembly are responsible for these enhancements. CONCLUSIONS The effects of lowering the expression temperature from 30 °C to 20 °C on protein expression and folding levels in S. cerevisiae, using several proteins as models, are reported. When heterologous proteins are expressed at 20 °C, a greater amount of (specially, more assembled) functional proteins accumulated than at 30 °C. Although further studies are required to understand the molecular mechanisms, our results suggest that lowering the expression temperature is a convenient strategy for improving the expression of relatively complexly structured and difficult-to-express proteins in S. cerevisiae.
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Affiliation(s)
- Kum-Kang So
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc My Tieu Le
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc-Luong Nguyen
- Department of Biology, College of Sciences, Hue University, Hue, 530000, Vietnam.
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
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10
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Macauyag EA, Kajiura H, Ohashi T, Misaki R, Fujiyama K. High-level transient production of a protease-resistant mutant form of human basic fibroblast growth factor in Nicotiana benthamiana leaves. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:291-301. [PMID: 36349230 PMCID: PMC9592933 DOI: 10.5511/plantbiotechnology.22.0628a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/28/2022] [Indexed: 06/16/2023]
Abstract
The human basic fibroblast growth factor (bFGF) is a protein that plays a pivotal role in cellular processes like cell proliferation and development. As a result, it has become an important component in cell culture systems, with applications in biomedical engineering, cosmetics, and research. Alternative production techniques, such as transient production in plants, are becoming a feasible option as the demand continues to grow. High-level bFGF production was achieved in this study employing an optimized Agrobacterium-mediated transient expression system, which yielded about a 3-fold increase in production over a conventional system. This yield was further doubled at about 185 µg g-1 FW using a mutant protease-resistant version that degraded/aggregated at a three-fold slower rate in leaf crude extracts. To achieve a pure product, a two-step purification technique was applied. The capacity of the pure protease-resistant bFGF (PRbFGF) to stimulate cell proliferation was tested and was found to be comparable to that of E. coli-produced bFGF in HepG2 and CHO-K1 cells. Overall, this study demonstrates a high-level transient production system of functional PRbFGF in N. benthamiana leaves as well as an efficient tag-less purification technique of leaf crude extracts.
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Affiliation(s)
- Edjohn Aaron Macauyag
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroyuki Kajiura
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Takao Ohashi
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
- Cooperative Research Station in Southeast Asia (OU: CRS), Faculty of Science, Mahidol University, Bangkok, Thailand
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Lai WY, Wong Z, Chang CH, Samian MR, Watanabe N, Teh AH, Noordin R, Ong EBB. Identifying Leptospira interrogans putative virulence factors with a yeast protein expression screen. Appl Microbiol Biotechnol 2022; 106:6567-6581. [DOI: 10.1007/s00253-022-12160-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
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12
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Yang ZK, Li DW, Peng L, Liu CF, Wang ZY. Transcriptomic responses of the zearalenone (ZEN)-detoxifying yeast Apiotrichum mycotoxinivorans to ZEN exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113756. [PMID: 35691196 DOI: 10.1016/j.ecoenv.2022.113756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Zearalenone (ZEN) is a potent oestrogenic mycotoxin that is mainly produced by Fusarium species and is a serious environmental pollutant in animal feeds. Apiotrichum mycotoxinivorans has been widely used as a feed additive to detoxify ZEN. However, the effects of ZEN on A. mycotoxinivorans and its detoxification mechanisms remain unclear. In this study, transcriptomic and bioinformatic analyses were used to investigate the molecular responses of A. mycotoxinivorans to ZEN exposure and the genetic basis of ZEN detoxification. We detected 1424 significantly differentially expressed genes (DEGs), of which 446 were upregulated and 978 were downregulated. Functional and enrichment analyses showed that ZEN-induced genes were significantly associated with xenobiotic metabolism, oxidative stress response, and active transport systems. However, ZEN-inhibited genes were mainly related to cell division, cell cycle, and fungal development. Subsequently, bioinformatic analysis identified candidate ZEN-detoxification enzymes. The Baeyer-Villiger monooxygenases and carboxylesterases, which are responsible for the formation and subsequent hydrolysis of a new ZEN lactone, respectively, were significantly upregulated. In addition, the expression levels of genes related to conjugation and transport involved in the xenobiotic detoxification pathway were significantly upregulated. Moreover, the expression levels of genes encoding enzymatic antioxidants and those related to growth and apoptosis were significantly upregulated and downregulated, respectively, which made it possible for A. mycotoxinivorans to survive in a highly toxic environment and efficiently detoxify ZEN. This is the first systematic report of ZEN tolerance and detoxification in A. mycotoxinivorans. We identified the metabolic enzymes that were potentially involved in detoxifying ZEN in the GMU1709 strain and found that ZEN-induced transcriptional regulation of genes is key to withstanding highly toxic environments. Hence, our results provide valuable information for developing enzymatic detoxification systems or engineering this detoxification pathway in other species.
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Affiliation(s)
- Zhi-Kai Yang
- Innovation centre for Advanced Interdisciplinary Medicine, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Guangzhou Key Laboratory of Enhanced Recovery after Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Da-Wei Li
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liang Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chen-Fei Liu
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yuan Wang
- Innovation Centre for Translational Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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13
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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14
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Effects of Temperature and pH on Recombinant Thaumatin II Production by Pichia pastoris. Foods 2022; 11:foods11101438. [PMID: 35627007 PMCID: PMC9141780 DOI: 10.3390/foods11101438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
The sweet protein thaumatin is emerging as a promising sugar replacer in the market today, especially in the food and beverage sector. Rising demand for its production necessitates the large-scale extraction of this protein from its natural plant source, which can be limited in terms of raw material availability and production costs. Using a recombinant production technique via a yeast platform, specifically, Pichia pastoris, is more promising to achieve the product economically while maintaining batch-to-batch consistency. However, the bioproduction of recombinant proteins requires the identification of optimal process variables, constituting the maximal yield of the product of interest. These variables have a direct effect on the growth of the host organism and the secretion levels of the recombinant protein. In this study, two important environmental factors, pH, and temperature were assessed by cultivating P. pastoris in shake flasks to understand their influence on growth and the production levels of thaumatin II protein. The results from the pH study indicate that P. pastoris attained a higher viable cell density and secretion of protein at pH 6.0 compared to 5.0 when grown at 30 °C. Furthermore, within the three levels of temperatures investigated when grown at pH 6.0, the protein levels were the highest at 30 °C compared to 20 and 25 °C, whereas 25 °C exhibited the highest viable cell density. Interestingly, the trend observed from the qualitative effects of temperature and pH occurred in all the media that was investigated. These results broaden our understanding of how pH and temperature adjustment during P. pastoris cultivation aid in enhancing the production yields of thaumatin II prior to optimising the fed batch bioreactor operation.
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15
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Celińska E. "Fight-flight-or-freeze" - how Yarrowia lipolytica responds to stress at molecular level? Appl Microbiol Biotechnol 2022; 106:3369-3395. [PMID: 35488934 PMCID: PMC9151528 DOI: 10.1007/s00253-022-11934-x] [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: 03/02/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Yarrowia lipolytica is a popular yeast species employed in multiple biotechnological production processes. High resistance to extreme environmental conditions or metabolic burden triggered by synthetically forced over-synthesis of a target metabolite has its practical consequences. The proud status of an “industrial workhorse” that Y. lipolytica has gained is directly related to such a quality of this species. With the increasing amount of knowledge coming from detailed functional studies and comprehensive omics analyses, it is now possible to start painting the landscape of the molecular background behind stress response and adaptation in Y. lipolytica. This review summarizes the current state-of-art of a global effort in revealing how Y. lipolytica responds to both environmental threats and the intrinsic burden caused by the overproduction of recombinant secretory proteins at the molecular level. Detailed lists of genes, proteins, molecules, and biological processes deregulated upon exposure to external stress factors or affected by over-synthesis of heterologous proteins are provided. Specificities and universalities of Y. lipolytica cellular response to different extrinsic and intrinsic threats are highlighted. Key points • Y. lipolytica as an industrial workhorse is subjected to multiple stress factors. • Cellular responses together with involved genes, proteins, and molecules are reviewed. • Native stress response mechanisms are studied and inspire engineering strategies.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627, Poznan, Poland.
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16
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Zinkevičiūtė R, Ražanskas R, Kaupinis A, Macijauskaitė N, Čiplys E, Houen G, Slibinskas R. Yeast Secretes High Amounts of Human Calreticulin without Cellular Stress. Curr Issues Mol Biol 2022; 44:1768-1787. [PMID: 35678651 PMCID: PMC9164041 DOI: 10.3390/cimb44050122] [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: 01/16/2022] [Revised: 03/25/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
The ER chaperone calreticulin (CALR) also has extracellular functions and can exit the mammalian cell in response to various factors, although the mechanism by which this takes place is unknown. The yeast Saccharomyces cerevisiae efficiently secretes human CALR, and the analysis of this process in yeast could help to clarify how it gets out of eukaryotic cells. We have achieved a secretion titer of about 140 mg/L CALR in our S. cerevisiae system. Here, we present a comparative quantitative whole proteome study in CALR-secreting yeast using non-equilibrium pH gradient electrophoresis (NEPHGE)-based two-dimensional gel electrophoresis (2DE) as well as liquid chromatography mass spectrometry in data-independent analysis mode (LC-MSE). A reconstructed carrier ampholyte (CA) composition of NEPHGE-based first-dimension separation for 2DE could be used instead of formerly commercially available gels. Using LC-MSE, we identified 1574 proteins, 20 of which exhibited differential expression. The largest group of differentially expressed proteins were structural ribosomal proteins involved in translation. Interestingly, we did not find any signs of cellular stress which is usually observed in recombinant protein-producing yeast, and we did not identify any secretory pathway proteins that exhibited changes in expression. Taken together, high-level secretion of human recombinant CALR protein in S. cerevisiae does not induce cellular stress and does not burden the cellular secretory machinery. There are only small changes in the cellular proteome of yeast secreting CALR at a high level.
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Affiliation(s)
- Rūta Zinkevičiūtė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (R.R.); (N.M.); (E.Č.); (R.S.)
| | - Raimundas Ražanskas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (R.R.); (N.M.); (E.Č.); (R.S.)
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania;
| | - Neringa Macijauskaitė
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (R.R.); (N.M.); (E.Č.); (R.S.)
| | - Evaldas Čiplys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (R.R.); (N.M.); (E.Č.); (R.S.)
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark;
| | - Rimantas Slibinskas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (R.R.); (N.M.); (E.Č.); (R.S.)
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17
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Spice AJ, Aw R, Polizzi KM. Cell-Free Protein Synthesis Using Pichia pastoris. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:75-88. [PMID: 34985738 DOI: 10.1007/978-1-0716-1998-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pichia pastoris (syn. Komagataella phaffii) is an industrially relevant recombinant protein platform that has been used to produce over 5000 proteins to date. Cell-free protein synthesis can be used as a screening tool before strain development or for the production of proteins that are difficult or toxic to make in vivo. Here we describe the methods for generating an active cell lysate from P. pastoris using high pressure homogenization and an improved reaction mix which results in high yields of reporter proteins such as luciferase, and complex proteins such as human serum albumin and virus-like particles.
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Affiliation(s)
- Alex J Spice
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rochelle Aw
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK.
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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18
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Zou S, Jia Y, He Q, Zhang K, Ban R, Hong J, Zhang M. Comparison of the Unfolded Protein Response in Cellobiose Utilization of Recombinant Angel- and W303-1A-Derived Yeast Expressing β-Glucosidase. Front Bioeng Biotechnol 2022; 10:837720. [PMID: 35433667 PMCID: PMC9008459 DOI: 10.3389/fbioe.2022.837720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The unfolded protein response (UPR) is one of the most important protein quality control mechanisms in cells. At least, three factors are predicted to activate the UPR in yeast cells during fermentation. Using UPRE-lacZ as a reporter, we constructed two indicator strains, KZ and WZ, based on Angel-derived K-a and W303-1A strains, respectively, and investigated their UPR response to tunicamycin, ethanol, and acetic acid. Then, four strains carrying plasmids BG-cwp2 and BG were obtained to realize the displaying and secretion of β-glucosidase, respectively. The results of cellobiose utilization assays indicated interactions between the UPR and the metabolic burden between the strain source, anchoring moiety, oxygen supply, and cellobiose concentration. Meanwhile, as expected, growth (OD600), β-glucosidase, and β-galactosidase activities were shown to have a positive inter-relationship, in which the values of the KZ-derived strains were far lower than those of the WZ-derived strains. Additionally, extra metabolic burden by displaying over secreting was also much more serious in strain KZ than in strain WZ. The maximum ethanol titer of the four strains (KZ (BG-cwp2), KZ (BG), WZ (BG-cwp2), and WZ (BG)) in oxygen-limited 10% cellobiose fermentation was 3.173, 5.307, 5.495, and 5.486% (v/v), respectively, and the acetic acid titer ranged from 0.038 to 0.060% (v/v). The corresponding maximum values of the ratio of β-galactosidase activity to that of the control were 3.30, 5.29, 6.45, and 8.72, respectively. Under aerobic conditions with 2% cellobiose, those values were 3.79, 4.97, 6.99, and 7.67, respectively. A comparison of the results implied that β-glucosidase expression durably induced the UPR, and the effect of ethanol and acetic acid depended on the titer produced. Further study is necessary to identify ethanol- or acid-specific target gene expression. Taken together, our results indicated that the host strain W303-1A is a better secretory protein producer, and the first step to modify strain K-a for cellulosic ethanol fermentation would be to relieve the bottleneck of UPR capacity. The results of the present study will help to identify candidate host strains and optimize expression and fermentation by quantifying UPR induction.
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Affiliation(s)
- Shaolan Zou
- Tianjin R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory for Green Chemical Technology of Ministry of Education, Tianjin University, Tianjin, China
- *Correspondence: Shaolan Zou, ; Jiefang Hong,
| | - Yudie Jia
- Tianjin R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qing He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Kun Zhang
- Tianjin R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Rui Ban
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jiefang Hong
- Tianjin R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory for Green Chemical Technology of Ministry of Education, Tianjin University, Tianjin, China
- *Correspondence: Shaolan Zou, ; Jiefang Hong,
| | - Minhua Zhang
- Tianjin R&D Center for Petrochemical Technology, Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory for Green Chemical Technology of Ministry of Education, Tianjin University, Tianjin, China
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19
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Kastberg LLB, Ard R, Jensen MK, Workman CT. Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:827704. [PMID: 37746199 PMCID: PMC10512257 DOI: 10.3389/ffunb.2022.827704] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.
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Affiliation(s)
| | - Ryan Ard
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T. Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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20
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Abstract
The availability of exceptionally strong and tightly regulated promoters is a key feature of Komagataella phaffii (syn. Pichia pastoris), a widely applied yeast expression system for heterologous protein production. Most commonly, the methanol-inducible promoter of the alcohol oxidase 1 gene (PAOX1) and the constitutive promoter of the glyceraldehyde 3 phosphate dehydrogenase gene (PGAP) have been used. Recently, also promising novel constitutive (PGCW14), regulated (PGTH1, PCAT1), and bidirectional promoters (histone promoters and synthetic hybrid variants) have been reported.As natural promoters showed so far limited tunability of expression levels and regulatory profiles, various promoter engineering efforts have been undertaken for P. pastoris . PAOX1, PDAS2, PGAP, and PGCW14 have been engineered by systematic deletion studies or random mutagenesis of upstream regulatory sequences. New engineering strategies have focused on PAOX1 core promoter modifications by random or rational approaches and transcriptional regulatory circuits to render PAOX1 independent of methanol induction. These promoter engineering efforts in P. pastoris have resulted in improved, sequence-diversified synthetic promoter variants allowing coordinated fine-tuning of gene expression for a multitude of biotechnological applications.
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Affiliation(s)
- Thomas Vogl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria.
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21
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Kubiak M, Białas W, Celińska E. Thermal treatment improves a process of crude glycerol valorization for the production of a heterologous enzyme by Yarrowia lipolytica. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 31:e00648. [PMID: 34221911 PMCID: PMC8243353 DOI: 10.1016/j.btre.2021.e00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022]
Abstract
A crude glycerol valorization process to enzymatic preparation was developed. Impact of thermal treatment on the protein production by Y. lipolytica is studied. Pilot-scale processes with laboratory and technical substrates were simulated. Techno-economic analysis of a pilot-scale waste-free process was conducted. Comprehensive stream analysis and identification of bottlenecks is provided.
Valorization of crude glycerol requires a potent bifunctional biocatalyst, such as Yarrowia lipolytica, capable of high-density growth on this substrate, and having i.a. high propensity for heterologous protein synthesis. Increasing evidence suggests that controlled administration of stress, i.a. thermal treatment, has a positive impact on bioprocess performance. In this study, we systematically adjusted thermal treatment conditions (20 to 42 °C) in order to maximize heterologous protein production by Y. lipolytica growing in crude glycerol-based medium. Our results showed nearly 30% enhancement in the enzyme production triggered by temporary exposure to decreased temperature. Here developed mathematical model indicated optimal treatment conditions (20 °C, 153′) that were later applied to a process with biodiesel-derived glycerol and technical substrates. Techno-economic analysis of a pilot-scale-waste-free process was conducted. Quantitative description of the associated costs and economic gain due to exploitation of industrial substrates, as well as indication of current bottlenecks of the process, are also provided.
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Affiliation(s)
- Monika Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-637 Poznań, Poland
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22
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Swift CL, Malinov NG, Mondo SJ, Salamov A, Grigoriev IV, O'Malley MA. A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708358. [PMID: 37744151 PMCID: PMC10512342 DOI: 10.3389/ffunb.2021.708358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi are a potential biotechnology platform to produce biomass-degrading enzymes. Unlike model fungi such as yeasts, stress responses that are relevant during bioprocessing have not yet been established for anaerobic fungi. In this work, we characterize both the heat shock and unfolded protein responses of four strains of anaerobic fungi (Anaeromyces robustus, Caecomyces churrovis, Neocallimastix californiae, and Piromyces finnis). The inositol-requiring 1 (Ire1) stress sensor, which typically initiates the fungal UPR, was conserved in all four genomes. However, these genomes also encode putative transmembrane kinases with catalytic domains that are similar to the metazoan stress-sensing enzyme PKR-like endoplasmic reticulum kinase (PERK), although whether they function in the UPR of anaerobic fungi remains unclear. Furthermore, we characterized the global transcriptional responses of Anaeromyces robustus and Neocallimastix californiae to a transient heat shock. Both fungi exhibited the hallmarks of ER stress, including upregulation of genes with functions in protein folding, ER-associated degradation, and intracellular protein trafficking. Relative to other fungi, the genomes of Neocallimastigomycetes contained the greatest gene percentage of HSP20 and HSP70 chaperones, which may serve to stabilize their asparagine-rich genomes. Taken together, these results delineate the unique stress response of anaerobic fungi, which is an important step toward their development as a biotechnology platform to produce enzymes and valuable biomolecules.
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Affiliation(s)
- Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nikola G. Malinov
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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23
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Wang Y, Li X, Chen X, Nielsen J, Petranovic D, Siewers V. Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion. Microb Cell Fact 2021; 20:134. [PMID: 34261490 PMCID: PMC8278646 DOI: 10.1186/s12934-021-01624-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
Monoclonal antibodies, antibody fragments and fusion proteins derived thereof have revolutionized the practice of medicine. Major challenges faced by the biopharmaceutical industry are however high production costs, long processing times and low productivities associated with their production in mammalian cell lines. The yeast Saccharomyces cerevisiae, a well-characterized eukaryotic cell factory possessing the capacity of post-translational modifications, has been industrially exploited as a secretion host for production of a range of products, including pharmaceuticals. However, due to the incompatible surface glycosylation, few antibody molecules have been functionally expressed in S. cerevisiae. Here, three non-glycosylated antibody fragments from human and the Camelidae family were chosen for expression in a S. cerevisiae strain (HA) previously evolved for high α-amylase secretion. These included the Fab fragment Ranibizumab (Ran), the scFv peptide Pexelizumab (Pex), and a nanobody consisting of a single V-type domain (Nan). Both secretion and biological activities of the antibody fragments were confirmed. In addition, the secretion level of each protein was compared in the wild type (LA) and two evolved strains (HA and MA) with different secretory capacities. We found that the secretion of Ran and Nan was positively correlated with the strains' secretory capacity, while Pex was most efficiently secreted in the parental strain. To investigate the mechanisms for different secretion abilities in these selected yeast strains for the different antibody fragments, RNA-seq analysis was performed. The results showed that several bioprocesses were significantly enriched for differentially expressed genes when comparing the enriched terms between HA.Nan vs. LA.Nan and HA.Pex vs. LA.Pex, including amino acid metabolism, protein synthesis, cell cycle and others, which indicates that there are unique physiological needs for each antibody fragment secretion.
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Affiliation(s)
- Yanyan Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xin Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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24
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Chen X, Li C, Liu H. Enhanced Recombinant Protein Production Under Special Environmental Stress. Front Microbiol 2021; 12:630814. [PMID: 33935992 PMCID: PMC8084102 DOI: 10.3389/fmicb.2021.630814] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 01/09/2023] Open
Abstract
Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.
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Affiliation(s)
- Xinyi Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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25
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Rosenbergová Z, Kántorová K, Šimkovič M, Breier A, Rebroš M. Optimisation of Recombinant Myrosinase Production in Pichia pastoris. Int J Mol Sci 2021; 22:ijms22073677. [PMID: 33916093 PMCID: PMC8037066 DOI: 10.3390/ijms22073677] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022] Open
Abstract
Myrosinase is a plant defence enzyme catalysing the hydrolysis of glucosinolates, a group of plant secondary metabolites, to a range of volatile compounds. One of the products, isothiocyanates, proved to have neuroprotective and chemo-preventive properties, making myrosinase a pharmaceutically interesting enzyme. In this work, extracellular expression of TGG1 myrosinase from Arabidopsis thaliana in the Pichia pastoris KM71H (MutS) strain was upscaled to a 3 L laboratory fermenter for the first time. Fermentation conditions (temperature and pH) were optimised, which resulted in a threefold increase in myrosinase productivity compared to unoptimised fermentation conditions. Dry cell weight increased 1.5-fold, reaching 100.5 g/L without additional glycerol feeding. Overall, a specific productivity of 4.1 U/Lmedium/h was achieved, which was 102.5-fold higher compared to flask cultivations.
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Affiliation(s)
- Zuzana Rosenbergová
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (Z.R.); (K.K.)
| | - Kristína Kántorová
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (Z.R.); (K.K.)
| | - Martin Šimkovič
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.Š.); (A.B.)
| | - Albert Breier
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (M.Š.); (A.B.)
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (Z.R.); (K.K.)
- Correspondence:
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26
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Mokdadi M, Abdelkrim YZ, Banroques J, Huvelle E, Oualha R, Yeter-Alat H, Guizani I, Barhoumi M, Tanner NK. The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. Genes (Basel) 2021; 12:212. [PMID: 33535521 PMCID: PMC7912733 DOI: 10.3390/genes12020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs.
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Affiliation(s)
- Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, CEDEX, Tunis 1080, Tunisia
| | - Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Rafeh Oualha
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
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Battaglino B, Arduino A, Pagliano C. Mathematical modeling for the design of evolution experiments to study the genetic instability of metabolically engineered photosynthetic microorganisms. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Aponte-Ubillus JJ, Barajas D, Sterling H, Aghajanirefah A, Bardliving C, Peltier J, Shamlou P, Roy M, Gold D. Proteome profiling and vector yield optimization in a recombinant adeno-associated virus-producing yeast model. Microbiologyopen 2020; 9:e1136. [PMID: 33166081 PMCID: PMC7755776 DOI: 10.1002/mbo3.1136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/03/2022] Open
Abstract
Recent studies on recombinant adeno‐associated viral (rAAV) vector production demonstrated the generation of infectious viral particles in Saccharomyces cerevisiae. Proof‐of‐concept results showed low vector yields that correlated with low AAV DNA encapsidation rates. In an attempt to understand the host cell response to rAAV production, we profiled proteomic changes throughout the fermentation process by mass spectrometry. By comparing an rAAV‐producing yeast strain with a respective non‐producer control, we identified a subset of yeast host proteins with significantly different expression patterns during the rAAV induction period. Gene ontology enrichment and network interaction analyses identified changes in expression patterns associated mainly with protein folding, as well as amino acid metabolism, gluconeogenesis, and stress response. Specific fold change patterns of heat shock proteins and other stress protein markers suggested the occurrence of a cytosolic unfolded protein response during rAAV protein expression. Also, a correlative increase in proteins involved in response to oxidative stress suggested cellular activities to ameliorate the effects of reactive oxygen species or other oxidants. We tested the functional relevance of the identified host proteins by overexpressing selected protein leads using low‐ and high‐copy number plasmids. Increased vector yields up to threefold were observed in clones where proteins SSA1, SSE1, SSE2, CCP1, GTT1, and RVB2 were overexpressed. Recombinant expression of SSA1 and YDJ insect homologues (HSP40 and HSC70, respectively) in Sf9 cells led to a volumetric vector yield increase of 50% relative to control, which validated the importance of chaperone proteins in rAAV‐producing systems. Overall, these results highlight the utility of proteomic‐based tools for the understanding and optimization of rAAV‐producing recombinant strains.
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Affiliation(s)
- Juan Jose Aponte-Ubillus
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA.,Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, USA
| | - Daniel Barajas
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Harry Sterling
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Ali Aghajanirefah
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | | | - Joseph Peltier
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Parviz Shamlou
- Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, USA
| | - Mimi Roy
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
| | - Daniel Gold
- Process Sciences Department, Biomarin Pharmaceutical Inc., Novato, CA, USA
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29
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Panting M, Holme IB, Björnsson JM, Brinch-Pedersen H. Modulation of Barley (Hordeum vulgare L.) Grain Protein Sink-Source Relations Towards Human Epidermal Growth Factor Instead of B-hordein Storage Protein. Mol Biotechnol 2020; 63:13-23. [PMID: 33051823 DOI: 10.1007/s12033-020-00279-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
Seeds have evolutionarily developed to store protein without immediately degrading it and constitute ideal tissues for recombinant protein storage. Unfortunately, the production of recombinant protein in seeds is compromised by low yield as compared to other heterologous expression systems. In order to improve the yield of the human epidermal growth factor (EGF) in barley, protein sink-source relations in the developing grain were modulated towards EGF instead of the barley storage protein. The EGF gene, under the control of a B-hordein and a seed-specific oat globulin promoter, was introduced by crossing EGF lines into the Risø 56 mutant deficient in B-hordein storage protein synthesis. Offspring plants were analysed for EGF and Hordein expression and for expression of the unfolded protein response (UPR) genes PDI and CRT to monitor changes in ER stress levels. EGF content was increased significantly in the mature grain of homozygous offspring and PDI and CRT gene expressions were upregulated. We demonstrate, for the first time in barley, that replacement of an abundant seed storage protein with a specific heterologous protein driven by the promoter of the removed gene can accelerate the production of a specific heterologous protein in barley grains.
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Affiliation(s)
- Michael Panting
- Department of AgroEcology, Research Center Flakkebjerg, Aarhus University, 4200, Slagelse, Denmark
| | - Inger Bæksted Holme
- Department of AgroEcology, Research Center Flakkebjerg, Aarhus University, 4200, Slagelse, Denmark
| | | | - Henrik Brinch-Pedersen
- Department of AgroEcology, Research Center Flakkebjerg, Aarhus University, 4200, Slagelse, Denmark.
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Martins M, Ávila PF, Paim de Andrade CC, Goldbeck R. Synergic recombinant enzyme association to optimize xylo-oligosaccharides production from agricultural waste. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Factors affecting yeast ethanol tolerance and fermentation efficiency. World J Microbiol Biotechnol 2020; 36:114. [DOI: 10.1007/s11274-020-02881-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
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32
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Lamour J, Wan C, Zhang M, Zhao X, Den Haan R. Overexpression of endogenous stress-tolerance related genes in Saccharomyces cerevisiae improved strain robustness and production of heterologous cellobiohydrolase. FEMS Yeast Res 2020; 19:5479884. [PMID: 31073597 DOI: 10.1093/femsyr/foz035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
To enable Saccharomyces cerevisiae to produce renewable fuels from lignocellulose in a consolidated bioprocess, a heterologous cellulase system must be engineered into this yeast. In addition, inherently low secretion titers and sensitivity to adverse environmental conditions must be overcome. Here, two native S. cerevisiae genes related to yeast stress tolerance, YHB1 and SET5, were overexpressed under transcriptional control of the constitutive PGK1 promoter and their effects on heterologous secretion of Talaromyces emersonii cel7A cellobiohydrolase was investigated. Transformants showed increased secreted enzyme activity that ranged from 22% to 55% higher compared to the parental strains and this did not lead to deleterious growth effects. The recombinant strains overexpressing either YHB1 or SET5 also demonstrated multi-tolerant characteristics desirable in bioethanol production, i.e. improved tolerance to osmotic and heat stress. Quantitative reverse transcriptase PCR analysis in these strains showed decreased transcription of secretion pathway genes. However, decreased unfolded protein response was also observed, suggesting novel mechanisms for enhancing enzyme production through stress modulation. Overexpression of YHB1 in an unrelated diploid strain also enhanced stress tolerance and improved ethanol productivity in medium containing acetic acid. To our knowledge, this is the first demonstration that improved heterologous secretion and environmental stress tolerance could be engineered into yeast simultaneously.
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Affiliation(s)
- Jarryd Lamour
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
| | - Chun Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Riaan Den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa
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Improved cellulase expression in diploid yeast strains enhanced consolidated bioprocessing of pretreated corn residues. Enzyme Microb Technol 2019; 131:109382. [DOI: 10.1016/j.enzmictec.2019.109382] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/27/2019] [Accepted: 07/12/2019] [Indexed: 01/12/2023]
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Davison SA, den Haan R, van Zyl WH. Identification of superior cellulase secretion phenotypes in haploids derived from natural Saccharomyces cerevisiae isolates. FEMS Yeast Res 2019; 19:5154912. [PMID: 30388213 DOI: 10.1093/femsyr/foy117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is considered an important host for consolidated bioprocessing and the production of high titres of recombinant cellulases is required for efficient hydrolysis of lignocellulosic substrates to fermentable sugars. Since recombinant protein secretion profiles vary highly among different strain backgrounds, careful selection of robust strains with optimal secretion profiles is of crucial importance. Here, we construct and screen sets of haploid derivatives, derived from natural strain isolates YI13, FINI and YI59, for improved general cellulase secretion. This report details a novel approach that combines secretion profiles of strains and phenotypic responses to stresses known to influence the secretion pathway for the development of a phenotypic screen to isolate strains with improved secretory capacities. A clear distinction was observed between the YI13 haploid derivatives and industrial and laboratory counterparts, Ethanol Red and S288c, respectively. By using sub-lethal concentrations of the secretion stressor tunicamycin and cell wall stressor Congo Red, YI13 haploid derivative strains demonstrated tolerance profiles related to their heterologous secretion profiles. Our results demonstrated that a new screening technique combined with a targeted mating approach could produce a pool of novel strains capable of high cellulase secretion.
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Affiliation(s)
- Steffi A Davison
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Willem Heber van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Sallada ND, Harkins LE, Berger BW. Effect of gene copy number and chaperone coexpression on recombinant hydrophobin HFBI biosurfactant production in Pichia pastoris. Biotechnol Bioeng 2019; 116:2029-2040. [PMID: 30934110 DOI: 10.1002/bit.26982] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/07/2019] [Accepted: 03/28/2019] [Indexed: 11/07/2022]
Abstract
Hydrophobins are small highly surface-active fungal proteins with potential as biosurfactants in a wide array of applications. However, practical implementation of hydrophobins at large scale has been hindered by low recombinant yields. In this study, the effects of increasing hydrophobin gene copy number and overexpressing endoplasmic reticulum resident chaperone proteins Kar2p, Pdi1p, and Ero1p were explored as a means to enhance recombinant yields of the class II hydrophobin HFBI in the eukaryotic expression host Pichia pastoris. One-, 2-, and 3-copy-HFBI strains were attained using an in vitro multimer ligation approach, with strains displaying copy number stability following subsequent transformations as measured by quantitative polymerase chain reaction. Increasing HFBI copy number alone had no effect on increasing HFBI secretion, but increasing copy number in concert with chaperone overexpression synergistically increased HFBI secretion. Overexpression of PDI1 or ERO1 caused insignificant changes in HFBI secretion in 1- and 2-copy strains, but a statistically significant HFBI secretion increase in 3-copy strain. KAR2 overexpression consistently resulted in enhanced HFBI secretion in all copy number strains, with 3-copy-HFBI secreting 22±1.6 fold more than the 1-copy-HFBI/no chaperone strain. The highest increase was seen in 3-copy-HFBI/Ero1p overexpressing strain with 30±4.0 fold increase in HFBI secretion over 1-copy-HFBI/no chaperone strain. This corresponded to an expression level of approximately 330 mg/L HFBI in the 5 ml small-scale format used in this study.
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Affiliation(s)
- Nathanael D Sallada
- Department of Biomedical Engineering, University of Virginia, Thornton Hall, Charlottesville, Virginia
| | - Lauren E Harkins
- Department of Biomedical Engineering, University of Virginia, Thornton Hall, Charlottesville, Virginia
| | - Bryan W Berger
- Department of Biomedical Engineering, University of Virginia, Thornton Hall, Charlottesville, Virginia.,Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia
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Kubiak M, Borkowska M, Białas W, Korpys P, Celińska E. Feeding strategy impacts heterologous protein production in
Yarrowia lipolytica
fed‐batch cultures—Insight into the role of osmolarity. Yeast 2019; 36:305-318. [DOI: 10.1002/yea.3384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/28/2019] [Accepted: 02/05/2019] [Indexed: 01/30/2023] Open
Affiliation(s)
- Monika Kubiak
- Department of Biotechnology and Food MicrobiologyPoznan University of Life Sciences Poznań Poland
| | - Monika Borkowska
- Department of Biotechnology and Food MicrobiologyPoznan University of Life Sciences Poznań Poland
| | - Wojciech Białas
- Department of Biotechnology and Food MicrobiologyPoznan University of Life Sciences Poznań Poland
| | - Paulina Korpys
- Department of Biotechnology and Food MicrobiologyPoznan University of Life Sciences Poznań Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food MicrobiologyPoznan University of Life Sciences Poznań Poland
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Raschmanová H, Zamora I, Borčinová M, Meier P, Weninger A, Mächler D, Glieder A, Melzoch K, Knejzlík Z, Kovar K. Single-Cell Approach to Monitor the Unfolded Protein Response During Biotechnological Processes With Pichia pastoris. Front Microbiol 2019; 10:335. [PMID: 30873140 PMCID: PMC6404689 DOI: 10.3389/fmicb.2019.00335] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
Pichia pastoris (Komagataella sp.) is broadly used for the production of secreted recombinant proteins. Due to the high rate of protein production, incorrectly folded proteins may accumulate in the endoplasmic reticulum (ER). To restore their proper folding, the cell triggers the unfolded protein response (UPR); however, if the proteins cannot be repaired, they are degraded, which impairs process productivity. Moreover, a non-producing/non-secreting subpopulation of cells might occur, which also decreases overall productivity. Therefore, an in depth understanding of intracellular protein fluxes and population heterogeneity is needed to improve productivity. Under industrially relevant cultivation conditions in bioreactors, we cultured P. pastoris strains producing three different recombinant proteins: penicillin G acylase from Escherichia coli (EcPGA), lipase B from Candida antarctica (CaLB) and xylanase A from Thermomyces lanuginosus (TlXynA). Extracellular and intracellular product concentrations were determined, along with flow cytometry-based single-cell measurements of cell viability and the up-regulation of UPR. The cell population was distributed into four clusters, two of which were viable cells with no UPR up-regulation, differing in cell size and complexity. The other two clusters were cells with impaired viability, and cells with up-regulated UPR. Over the time course of cultivation, the distribution of the population into these four clusters changed. After 30 h of production, 60% of the cells producing EcPGA, which accumulated in the cells (50-70% of the product), had up-regulated UPR, but only 13% of the cells had impaired viability. A higher proportion of cells with decreased viability was observed in strains producing CaLB (20%) and TlXynA (27%). The proportion of cells with up-regulated UPR in CaLB-producing (35%) and TlXynA-producing (30%) strains was lower in comparison to the EcPGA-producing strain, and a smaller proportion of CaLB and TlXynA (<10%) accumulated in the cells. These data provide an insight into the development of heterogeneity in a recombinant P. pastoris population during a biotechnological process. A deeper understanding of the relationship between protein production/secretion and the regulation of the UPR might be utilized in bioprocess control and optimization with respect to secretion and population heterogeneity.
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Affiliation(s)
- Hana Raschmanová
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia.,Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Iwo Zamora
- Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Martina Borčinová
- Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.,Department of Genetics and Microbiology, Charles University, Prague, Czechia
| | - Patrick Meier
- Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Astrid Weninger
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Dominik Mächler
- Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Karel Melzoch
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
| | - Karin Kovar
- Institute of Chemistry and Biotechnology, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
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Production Optimization of an Active β-Galactosidase of Bifidobacterium animalis in Heterologous Expression Systems. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8010635. [PMID: 30915359 PMCID: PMC6402204 DOI: 10.1155/2019/8010635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/31/2018] [Accepted: 01/25/2019] [Indexed: 02/06/2023]
Abstract
β-Galactosidase (E.C.3.2.1.23) catalyzes the hydrolysis of lactose into glucose and galactose and the synthesis of galacto-oligosaccharides as well. The β-galactosidases from bacteria, especially lactobacilli, and yeast have neutral pH and are much more likely to be developed as food additives. However, the challenges of cumbersome purification, product toxicity, and low yield in protein production have limited the commercialization of many excellent candidates. In this study, we identified a β-galactosidase gene (bg42-106) in Bifidobacterium animalis ACCC05790 and expressed the gene product in Escherichia coli BL21(DE3) and Pichia pastoris GS115, respectively. The recombinant bG42-106 purified from E. coli cells was found to be optimally active at pH 6.0 and 60°C and had excellent stability over a wide pH range (5.0–8.0) and at high temperature (60°C). The specific activity of bG42-106 reached up to 2351 U/mg under optimal conditions. The galacto-oligosaccharide yield was 24.45 g/L after incubation with bG42-106 at 60°C for 2 h. When recombinant bG42-106 was expressed in Pichia pastoris GS115, it was found in the culture medium but only at a concentration of 1.73 U/ml. To increase its production, three strategies were employed, including codon optimization, disulfide formation, and fusion with a Cherry tag, with Cherry-tag fusion being most effective. The culture medium of P. pastoris that expressed Cherry-tagged bG42-106 contained 24.4 U/mL of β-galactosidase activity, which is 14-fold greater than that produced by culture of P. pastoris harboring wild-type bG42-106.
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40
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Wu D, Zhu H, Chu J, Wu J. N-acetyltransferase co-expression increases α-glucosidase expression level in Pichia pastoris. J Biotechnol 2019; 289:26-30. [PMID: 30428383 DOI: 10.1016/j.jbiotec.2018.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 10/08/2018] [Accepted: 11/07/2018] [Indexed: 11/27/2022]
Abstract
Pichia pastoris is subjected to strong oxidative stress in the methanol induction phase. The oxidative stress inflicts severe injury to yeast cells, which causes cell death and reduces protein expression ability. N-acetyltransferase in Saccharomyces cerevisiae can protect yeast cells from damage caused by decreasing reactive oxygen species (ROS) in oxidative pressure environments such as ethanol treatment, freeze-thawing, or heat shock. In this study, N-acetyltransferase from P. pastoris (PpMpr1) was overexpressed for the first time to improve the anti-oxidative stress ability to protect cells from strong ROS damage during the methanol induction phase. Cell viability of the PpMpr1 overexpression strain increased significantly, while biomass was increased by 22.7% at high dissolved oxygen (DO). At the same time, the heterologous α-glucosidase (AGL) expression level at 25% DO was increased by 21.5%. The AGL degradation was greatly relieved in the fermentation supernatant of the PpMpr1 overexpression strain. This study shows that PpMpr1 has a great potential for improvement of anti-oxidative stress ability in P. pastoris and provides a promising recombinant microorganism for industrial production of proteins.
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Affiliation(s)
- Dan Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Haifeng Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
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41
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Zahrl RJ, Gasser B, Mattanovich D, Ferrer P. Detection and Elimination of Cellular Bottlenecks in Protein-Producing Yeasts. Methods Mol Biol 2019; 1923:75-95. [PMID: 30737735 DOI: 10.1007/978-1-4939-9024-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Yeasts are efficient cell factories and are commonly used for the production of recombinant proteins for biopharmaceutical and industrial purposes. For such products high levels of correctly folded proteins are needed, which sometimes requires improvement and engineering of the expression system. The article summarizes major breakthroughs that led to the efficient use of yeasts as production platforms and reviews bottlenecks occurring during protein production. Special focus is given to the metabolic impact of protein production. Furthermore, strategies that were shown to enhance secretion of recombinant proteins in different yeast species are presented.
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Affiliation(s)
- Richard J Zahrl
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Pau Ferrer
- Luxembourg Institute of Science and Technology, Belvaux, Luxembourg. .,Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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42
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Sawatzki A, Hans S, Narayanan H, Haby B, Krausch N, Sokolov M, Glauche F, Riedel SL, Neubauer P, Cruz Bournazou MN. Accelerated Bioprocess Development of Endopolygalacturonase-Production with Saccharomyces cerevisiae Using Multivariate Prediction in a 48 Mini-Bioreactor Automated Platform. Bioengineering (Basel) 2018; 5:E101. [PMID: 30469407 PMCID: PMC6316240 DOI: 10.3390/bioengineering5040101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/04/2023] Open
Abstract
Mini-bioreactor systems enabling automatized operation of numerous parallel cultivations are a promising alternative to accelerate and optimize bioprocess development allowing for sophisticated cultivation experiments in high throughput. These include fed-batch and continuous cultivations with multiple options of process control and sample analysis which deliver valuable screening tools for industrial production. However, the model-based methods needed to operate these robotic facilities efficiently considering the complexity of biological processes are missing. We present an automated experiment facility that integrates online data handling, visualization and treatment using multivariate analysis approaches to design and operate dynamical experimental campaigns in up to 48 mini-bioreactors (8⁻12 mL) in parallel. In this study, the characterization of Saccharomyces cerevisiae AH22 secreting recombinant endopolygalacturonase is performed, running and comparing 16 experimental conditions in triplicate. Data-driven multivariate methods were developed to allow for fast, automated decision making as well as online predictive data analysis regarding endopolygalacturonase production. Using dynamic process information, a cultivation with abnormal behavior could be detected by principal component analysis as well as two clusters of similarly behaving cultivations, later classified according to the feeding rate. By decision tree analysis, cultivation conditions leading to an optimal recombinant product formation could be identified automatically. The developed method is easily adaptable to different strains and cultivation strategies, and suitable for automatized process development reducing the experimental times and costs.
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Affiliation(s)
- Annina Sawatzki
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Sebastian Hans
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | | | - Benjamin Haby
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Niels Krausch
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Michael Sokolov
- ETH Zürich, Rämistrasse 101, CH-8092 Zurich, Switzerland.
- DataHow AG, c/o ETH Zürich, HCl, F137, Vladimir-Prelog-Weg 1, CH-8093 Zurich, Switzerland.
| | - Florian Glauche
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Sebastian L Riedel
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Peter Neubauer
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
| | - Mariano Nicolas Cruz Bournazou
- Department of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr. 71-76, ACK24, D-13355 Berlin, Germany.
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43
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Celińska E, Nicaud JM. Filamentous fungi-like secretory pathway strayed in a yeast system: peculiarities of Yarrowia lipolytica secretory pathway underlying its extraordinary performance. Appl Microbiol Biotechnol 2018; 103:39-52. [PMID: 30353423 PMCID: PMC6311201 DOI: 10.1007/s00253-018-9450-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
Abstract
Microbial production of secretory proteins constitutes one of the key branches of current industrial biotechnology, earning billion dollar (USD) revenues each year. That industrial branch strongly relies on fluent operation of the secretory machinery within a microbial cell. The secretory machinery, directing the nascent polypeptide to its final destination, constitutes a highly complex system located across the eukaryotic cell. Numerous molecular identities of diverse structure and function not only build the advanced network assisting folding, maturation and secretion of polypeptides but also serve as sensors and effectors of quality control points. All these events must be harmoniously orchestrated to enable fluent processing of the protein traffic. Availability of these elements is considered to be the limiting factor determining capacity of protein traffic, which is of crucial importance upon biotechnological production of secretory proteins. The main purpose of this work is to review and discuss findings concerning secretory machinery operating in a non-conventional yeast species, Yarrowia lipolytica, and to highlight peculiarities of this system prompting its use as the production host. The reviewed literature supports the thesis that secretory machinery in Y. lipolytica is characterized by significantly higher complexity than a canonical yeast protein secretion pathway, making it more similar to filamentous fungi-like systems in this regard.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France
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44
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de Paiva DP, Rocha TB, Rubini MR, Nicola AM, Reis VCB, Torres FAG, de Moraes LMP. A study on the use of strain-specific and homologous promoters for heterologous expression in industrial Saccharomyces cerevisiae strains. AMB Express 2018; 8:82. [PMID: 29785587 PMCID: PMC5962522 DOI: 10.1186/s13568-018-0613-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/12/2018] [Indexed: 02/08/2023] Open
Abstract
Polymorphism is well known in Saccharomyces cerevisiae strains used for different industrial applications, however little is known about its effects on promoter efficiency. In order to test this, five different promoters derived from an industrial and a laboratory (S288c) strain were used to drive the expression of eGFP reporter gene in both cells. The ADH1 promoter (PADH1) in particular, which showed more polymorphism among the promoters analyzed, also exhibited the highest differences in intracellular fluorescence production. This was further confirmed by Northern blot analysis. The same behavior was also observed when the gene coding for secreted α-amylase from Cryptococcus flavus was placed under the control of either PADH1. These results underline the importance of the careful choice of the source of the promoter to be used in industrial yeast strains for heterologous expression.
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45
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Chen L, Mohsin A, Chu J, Zhuang Y, Liu Y, Guo M. Enhanced protein production by sorbitol co-feeding with methanol in recombinant Pichia pastoris strains. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0011-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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46
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Improved microscale cultivation of Pichia pastoris for clonal screening. Fungal Biol Biotechnol 2018; 5:8. [PMID: 29750118 PMCID: PMC5932850 DOI: 10.1186/s40694-018-0053-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development. Results Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode. Conclusion The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes. Electronic supplementary material The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.
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47
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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: 138] [Impact Index Per Article: 23.0] [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.
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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.
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48
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Zepeda AB, Figueroa CA, Pessoa A, Farías JG. Free fatty acids reduce metabolic stress and favor a stable production of heterologous proteins in Pichia pastoris. Braz J Microbiol 2018; 49:856-864. [PMID: 29705163 PMCID: PMC6175731 DOI: 10.1016/j.bjm.2018.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 02/19/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
The growth of yeasts in culture media can be affected by many factors. For example, methanol can be metabolized by other pathways to produce ethanol, which acts as an inhibitor of the heterologous protein production pathway; oxygen concentration can generate aerobic or anaerobic environments and affects the fermentation rate; and temperature affects the central carbon metabolism and stress response protein folding. The main goal of this study was determine the implication of free fatty acids on the production of heterologous proteins in different culture conditions in cultures of Pichia pastoris. We evaluated cell viability using propidium iodide by flow cytometry and thiobarbituric acid reactive substances to measure cell membrane damage. The results indicate that the use of low temperatures and low methanol concentrations favors the decrease in lipid peroxidation in the transition phase from glycerol to methanol. In addition, a temperature of 14 °C + 1%M provided the most stable viability. By contrast, the temperature of 18 °C + 1.5%M favored the production of a higher antibody fragment concentration. In summary, these results demonstrate that the decrease in lipid peroxidation is related to an increased production of free fatty acids.
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Affiliation(s)
- Andrea B Zepeda
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile; Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Carolina A Figueroa
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile; Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Adalberto Pessoa
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas, Departamento de Tecnologia Bioquímico-Farmacêutica, São Paulo, SP, Brazil
| | - Jorge G Farías
- Universidad de La Frontera, Facultad de Ingeniería, Ciencias y Administración, Departamento de Ingeniería Química, Temuco, Chile.
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Aw R, McKay PF, Shattock RJ, Polizzi KM. Expressing anti-HIV VRC01 antibody using the murine IgG1 secretion signal in Pichia pastoris. AMB Express 2017; 7:70. [PMID: 28342171 PMCID: PMC5366992 DOI: 10.1186/s13568-017-0372-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/20/2017] [Indexed: 12/25/2022] Open
Abstract
The use of the recombinant expression platform Pichia pastoris to produce pharmaceutically important proteins has been investigated over the past 30 years. Compared to mammalian cultures, expression in P. pastoris is cheaper and faster, potentially leading to decreased costs and process development times. Product yields depend on a number of factors including the secretion signal chosen for expression, which can influence the host cell response to recombinant protein production. VRC01, a broadly neutralising anti-HIV antibody, was expressed in P. pastoris, using the methanol inducible AOX1 promoter for both the heavy and light chains. Titre reached up to 3.05 μg mL−1 in small scale expression. VRC01 was expressed using both the α-mating factor signal peptide from Saccharomyces cerevisiae and the murine IgG1 signal peptide. Surprisingly, using the murine IgG1 signal peptide resulted in higher yield of antibody capable of binding gp140 antigen. Furthermore, we evaluated levels of secretory stress compared to the untransformed wild-type strain and show a reduced level of secretory stress in the murine IgG1 signal peptide strains versus those containing the α-MF signal peptide. As bottlenecks in the secretory pathway are often the limiting factor in protein secretion, reduced levels of secretory stress and the higher yield of functional antibody suggest the murine IgG1 signal peptide may lead to better protein folding and secretion. This work indicates the possibilities for utilising the murine IgG1 signal peptide for a range of antibodies, resulting in high yields and reduced cellular stress.
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Theron CW, Berrios J, Delvigne F, Fickers P. Integrating metabolic modeling and population heterogeneity analysis into optimizing recombinant protein production by Komagataella (Pichia) pastoris. Appl Microbiol Biotechnol 2017; 102:63-80. [PMID: 29138907 DOI: 10.1007/s00253-017-8612-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 12/24/2022]
Abstract
The methylotrophic yeast Komagataella (Pichia) pastoris has become one of the most utilized cell factories for the production of recombinant proteins over the last three decades. This success story is linked to its specific physiological traits, i.e., the ability to grow at high cell density in inexpensive culture medium and to secrete proteins at high yield. Exploiting methanol metabolism is at the core of most P. pastoris-based processes but comes with its own challenges. Co-feeding cultures with glycerol/sorbitol and methanol is a promising approach, which can benefit from improved understanding and prediction of metabolic response. The development of profitable processes relies on the construction and selection of efficient producing strains from less efficient ones but also depends on the ability to master the bioreactor process itself. More specifically, how a bioreactor processes could be monitored and controlled to obtain high yield of production. In this review, new perspectives are detailed regarding a multi-faceted approach to recombinant protein production processes by P. pastoris; including gaining improved understanding of the metabolic pathways involved, accounting for variations in transcriptional and translational efficiency at the single cell level and efficient monitoring and control of methanol levels at the bioreactor level.
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Affiliation(s)
- Chrispian W Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Avenue de la Faculté, 2B, B-5030, Gembloux, Belgium.
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