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Fedorovych DV, Tsyrulnyk AO, Ruchala J, Sobchuk SM, Dmytruk KV, Fayura LR, Sibirny AA. Construction of the advanced flavin mononucleotide producers in the flavinogenic yeast Candida famata. Yeast 2023; 40:360-366. [PMID: 36751139 DOI: 10.1002/yea.3843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Flavin mononucleotide (FMN, riboflavin-5'-phosphate) is flavin coenzyme synthesized in all living organisms from riboflavin (vitamin B2 ) after phosphorylation in the reaction catalyzed by riboflavin kinase. FMN has several applications mostly as yellow colorant in food industry due to 200 times better water solubility as compared to riboflavin. Currently, FMN is produced by chemical phosphorylation of riboflavin, however, final product contains up to 25% of flavin impurities. Microbial overproducers of FMN are known, however, they accumulate this coenzyme in glucose medium. Current work shows that the recombinant strains of the flavinogenic yeast Candida famata with overexpressed FMN1 gene coding for riboflavin kinase in the recently isolated by us advanced riboflavin producers due to overexpression of the structural and regulatory genes of riboflavin synthesis and of the putative exporter of riboflavin from the cell, synthesized elevated amounts of FMN in the media not only with glucose but also in lactose and cheese whey. Activation of FMN accumulation on lactose and cheese whey was especially strong in the strains which expressed the gene of transcription activator SEF1 under control of the lactose-induced LAC4 promoter. The accumulation of this coenzyme by the washed cells of the best recombinant strain achieved 540 mg/L in the cheese whey supplemented only with ammonium sulfate during 48 h in shake flask experiments.
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Affiliation(s)
- Dariya V Fedorovych
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Andriy O Tsyrulnyk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Justyna Ruchala
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
| | - Svitlana M Sobchuk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Lyubov R Fayura
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
| | - Andriy A Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Science of Ukraine, Lviv, Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
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Improvement of Fusel Alcohol Production by Engineering of the Yeast Branched-Chain Amino Acid Aminotransaminase. Appl Environ Microbiol 2022; 88:e0055722. [PMID: 35699439 PMCID: PMC9275217 DOI: 10.1128/aem.00557-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Branched-chain higher alcohols (BCHAs), or fusel alcohols, including isobutanol, isoamyl alcohol, and active amyl alcohol, are useful compounds in several industries. The yeast Saccharomyces cerevisiae can synthesize these compounds via the metabolic pathways of branched-chain amino acids (BCAAs). Branched-chain amino acid aminotransaminases (BCATs) are the key enzymes for BCHA production via the Ehrlich pathway of BCAAs. BCATs catalyze a bidirectional transamination reaction between branched-chain α-keto acids (BCKAs) and BCAAs. In S. cerevisiae, there are two BCAT isoforms, Bat1 and Bat2, which are encoded by the genes BAT1 and BAT2. Although many studies have shown the effects of deletion or overexpression of BAT1 and BAT2 on BCHA production, there have been no reports on the enhancement of BCHA production by functional variants of BCATs. Here, to improve BCHA productivity, we designed variants of Bat1 and Bat2 with altered enzyme activity by using in silico computational analysis: the Gly333Ser and Gly333Trp Bat1 and corresponding Gly316Ser and Gly316Trp Bat2 variants, respectively. When expressed in S. cerevisiae cells, most of these variants caused a growth defect in minimal medium. Interestingly, the Gly333Trp Bat1 and Gly316Ser Bat2 variants achieved 18.7-fold and 17.4-fold increases in isobutanol above that for the wild-type enzyme, respectively. The enzyme assay revealed that the catalytic activities of all four BCAT variants were lower than that of the wild-type enzyme. Our results indicate that the decreased BCAT activity enhanced BCHA production by reducing BCAA biosynthesis, which occurs via a pathway that directly competes with BCHA production. IMPORTANCE Recently, several studies have attempted to increase the production of branched-chain higher alcohols (BCHAs) in the yeast Saccharomyces cerevisiae. The key enzymes for BCHA biosynthesis in S. cerevisiae are the branched-chain amino acid aminotransaminases (BCATs) Bat1 and Bat2. Deletion or overexpression of the genes encoding BCATs has an impact on the production of BCHAs; however, amino acid substitution variants of Bat1 and Bat2 that could affect enzymatic properties—and ultimately BCHA productivity—have not been fully studied. By using in silico analysis, we designed variants of Bat1 and Bat2 and expressed them in yeast cells. We found that the engineered BCATs decreased catalytic activities and increased BCHA production. Our approach provides new insight into the functions of BCATs and will be useful in the future construction of enzymes optimized for high-level production of BCHAs.
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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: 8] [Impact Index Per Article: 4.0] [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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Branduardi P, Barroso L, Dato L, Louis EJ, Porro D. Molecular Tools for Leveraging the Potential of the Acid-Tolerant Yeast Zygosaccharomyces bailii as Cell Factory. Methods Mol Biol 2022; 2513:179-204. [PMID: 35781206 DOI: 10.1007/978-1-0716-2399-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycete budding yeast, is widely known for its peculiar tolerance to different stresses, among which are organic acids. Moreover, the recent reclassification of the species, including diverse hybrids, is further expanding both fundamental and applied interests. It is therefore reasonable that despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here we describe in detail the methods for determining chromosome number, size, and aneuploidy, transformation, classical target gene disruption or gene integration, and designing of episomal expression plasmids helpful for engineering the yeast Z. bailii .
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
| | - Liliane Barroso
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Laura Dato
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Edward J Louis
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Verdecia M, Kokai-Kun JF, Kibbey M, Acharya S, Venema J, Atouf F. COVID-19 vaccine platforms: Delivering on a promise? Hum Vaccin Immunother 2021; 17:2873-2893. [PMID: 34033528 PMCID: PMC8381795 DOI: 10.1080/21645515.2021.1911204] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The emergence of the novel SARS-CoV-2 and COVID-19 has brought into sharp focus the need for a vaccine to prevent this disease. Vaccines have saved millions of lives since their introduction to the public over 200 years ago. The potential for vaccination reached new heights in the mid-20th century with the development of technologies that expanded the ability to create novel vaccines. Since then, there has been continued technological advancement in vaccine development. The resulting platforms provide the promise for solutions for many infectious diseases, including those that have been with us for decades as well as those just now emerging. Each vaccine platform represents a different technology with a unique set of advantages and challenges, especially when considering manufacturing. Therefore, it is essential to understand each platform as a separate product and process with its specific quality considerations. This review outlines the relevant platforms for developing a vaccine for SARS-CoV-2 and discusses the advantages and disadvantages of each.
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Affiliation(s)
- Mark Verdecia
- United States Pharmacopeial Convention, Rockville, MD, USA
| | | | - Maura Kibbey
- United States Pharmacopeial Convention, Rockville, MD, USA
| | - Sarita Acharya
- United States Pharmacopeial Convention, Rockville, MD, USA
| | - Jaap Venema
- United States Pharmacopeial Convention, Rockville, MD, USA
| | - Fouad Atouf
- United States Pharmacopeial Convention, Rockville, MD, USA
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Ajingi YS, Rukying N, Aroonsri A, Jongruja N. Recombinant active Peptides and their Therapeutic functions. Curr Pharm Biotechnol 2021; 23:645-663. [PMID: 34225618 DOI: 10.2174/1389201022666210702123934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 11/22/2022]
Abstract
Recombinant active peptides are utilized as diagnostic and biotherapeutics in various maladies and as bacterial growth inhibitors in the food industry. This consequently stimulated the need for recombinant peptides' production, which resulted in about 19 approved biotech peptides of 1-100 amino acids commercially available. While most peptides have been produced by chemical synthesis, the production of lengthy and complicated peptides comprising natural amino acids has been problematic with low quantity. Recombinant peptide production has become very vital, cost-effective, simple, environmentally friendly with satisfactory yields. Several reviews have focused on discussing expression systems, advantages, disadvantages, and alternatives strategies. Additionally, the information on the antimicrobial activities and other functions of multiple recombinant peptides is challenging to access and is scattered in literature apart from the food and drug administration (FDA) approved ones. From the reports that come to our knowledge, there is no existing review that offers substantial information on recombinant active peptides developed by researchers and their functions. This review provides an overview of some successfully produced recombinant active peptides of ≤100 amino acids by focusing on their antibacterial, antifungal, antiviral, anticancer, antioxidant, antimalarial, and immune-modulatory functions. It also elucidates their modes of expression that could be adopted and applied in future investigations. We expect that the knowledge available in this review would help researchers involved in recombinant active peptide development for therapeutic uses and other applications.
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Affiliation(s)
- Ya'u Sabo Ajingi
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok. Thailand
| | - Neeranuch Rukying
- Department of Biology, Faculty of Science, Kano University of Science and Technology (KUST), Wudil. Nigeria
| | - Aiyada Aroonsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani. Thailand
| | - Nujarin Jongruja
- Department of Biology, Faculty of Science, Kano University of Science and Technology (KUST), Wudil. Nigeria
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Machhi J, Shahjin F, Das S, Patel M, Abdelmoaty MM, Cohen JD, Singh PA, Baldi A, Bajwa N, Kumar R, Vora LK, Patel TA, Oleynikov MD, Soni D, Yeapuri P, Mukadam I, Chakraborty R, Saksena CG, Herskovitz J, Hasan M, Oupicky D, Das S, Donnelly RF, Hettie KS, Chang L, Gendelman HE, Kevadiya BD. Nanocarrier vaccines for SARS-CoV-2. Adv Drug Deliv Rev 2021; 171:215-239. [PMID: 33428995 PMCID: PMC7794055 DOI: 10.1016/j.addr.2021.01.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/18/2020] [Accepted: 01/01/2021] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 global pandemic has seen rapid spread, disease morbidities and death associated with substantive social, economic and societal impacts. Treatments rely on re-purposed antivirals and immune modulatory agents focusing on attenuating the acute respiratory distress syndrome. No curative therapies exist. Vaccines remain the best hope for disease control and the principal global effort to end the pandemic. Herein, we summarize those developments with a focus on the role played by nanocarrier delivery.
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Affiliation(s)
- Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Farah Shahjin
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Srijanee Das
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Mai Mohamed Abdelmoaty
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA; Therapeutic Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Giza, Egypt
| | - Jacob D Cohen
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Preet Amol Singh
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Ashish Baldi
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Neha Bajwa
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Raj Kumar
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Lalit K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Tapan A Patel
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences (PDPIAS), Charotar University of Science and Technology (CHARUSAT), Changa, Anand 388421, Gujarat, India
| | - Maxim D Oleynikov
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Dhruvkumar Soni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
| | - Pravin Yeapuri
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Insiya Mukadam
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
| | - Rajashree Chakraborty
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Caroline G Saksena
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Jonathan Herskovitz
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA
| | - David Oupicky
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Suvarthi Das
- Department of Medicine, Stanford Medical School, Stanford University, Palo Alto, CA 94304, USA
| | - Ryan F Donnelly
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Kenneth S Hettie
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Department of Otolaryngology - Head & Neck Surgery, Stanford University, Palo Alto, CA 94304, USA
| | - Linda Chang
- Departments of Diagnostic Radiology & Nuclear Medicine, and Neurology, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA; Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, NE 68198, USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, NE 68198, USA.
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, NE 68198, USA
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Su Y, Shao W, Zhang A, Zhang W. Improving isobutanol tolerance and titers through EMS mutagenesis in Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6147039. [PMID: 33620449 DOI: 10.1093/femsyr/foab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/20/2021] [Indexed: 11/14/2022] Open
Abstract
Improving yeast tolerance toward isobutanol is a critical issue enabling high-titer industrial production. Here, we used EMS mutagenesis to screen Saccharomyces cerevisiae with greater tolerance toward isobutanol. By this method, we obtained EMS39 with high-viability in medium containing 16 g/L isobutanol. Then, we metabolically engineered isobutanol synthesis in EMS39. About 2μ plasmids carrying PGK1p-ILV2, PGK1p-ILV3 and TDH3p-cox4-ARO10 were used to over-express ILV2, ILV3 and ARO10 genes, respectively, in EMS39 and wild type W303-1A. And the resulting strains were designated as EMS39-20 and W303-1A-20. Our results showed that EMS39-20 increased isobutanol titers by 49.9% compared to W303-1A-20. Whole genome resequencing analysis of EMS39 showed that more than 59 genes had mutations in their open reading frames or regulatory regions. These 59 genes are enriched mainly into cell growth, basal transcription factors, cell integrity signaling, translation initiation and elongation, ribosome assembly and function, oxidative stress response, etc. Additionally, transcriptomic analysis of EMS39-20 was carried out. Finally, reverse engineering tests showed that overexpression of CWP2 and SRP4039 could improve tolerance of S.cerevisiae toward isobutanol. In conclusion, EMS mutagenesis could be used to increase yeast tolerance toward isobutanol. Our study supplied new insights into mechanisms of tolerance toward isobutanol and enhancing isobutanol production in S. cerevisiae.
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Affiliation(s)
- Yide Su
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Wenju Shao
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Aili Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Weiwei Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
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Srivastava S, Kaur S, Verma HK, Rani S, Thakur M, Haldar S, Singh J. Reciprocal relation between reporter gene transcription and translation efficiency in fission yeast. Plasmid 2021; 115:102557. [PMID: 33539828 DOI: 10.1016/j.plasmid.2021.102557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/12/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
The fission yeast, Schizosaccharomyces pombe, is an excellent model for basic research but is not useful for commercial scale protein expression due to lack of strong expression vectors. Earlier, we showed that the lsd90 promoter elicited significantly greater GFP expression level than the adh1 and nmt1 promoters, albeit in different vector backbones. Here, we have systematically investigated the contribution of selectable markers, LEU2 and URA3m to GFP expression: while LEU2 elicited very low expression, the URA3m gene, with truncated promoter, elicited much greater GFP expression level with all promoters. Paradoxically, an inverse correlation was observed between the GFP transcription and translation efficiency. This system can be useful for understanding the factors governing recombinant gene expression and optimization of protein production.
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Affiliation(s)
- Suchita Srivastava
- Central Research Institute, Kasauli, Distt, Solan, Himachal Pradesh 173204, India; Department of Molecular Biology, Institute of Microbial Technology, Sector 39A, Chandigarh-160036. India
| | - Satinderdeep Kaur
- Central Research Institute, Kasauli, Distt, Solan, Himachal Pradesh 173204, India; Pharmacology Department, School of Science and Technology, Nottingham Trent University, Nottingha, NG11 8NS, UK
| | - Hemant K Verma
- Biotech Department, Mankind Research Center, 191-E, Sector 4-11, IMT, Manesar, Haryana 122050, India
| | - Suman Rani
- Department of Molecular Biology, Institute of Microbial Technology, Sector 39A, Chandigarh-160036. India
| | - Manisha Thakur
- Department of Molecular Biology, Institute of Microbial Technology, Sector 39A, Chandigarh-160036. India
| | - Swati Haldar
- Microbiology Division, Patanjali Research Institute, Haridwar, Uttarakhand, India
| | - Jagmohan Singh
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector- 39 A, Chandigarh 160036, India.
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Suhaimi H, Dailin DJ, Malek RA, Hanapi SZ, Ambehabati KK, Keat HC, Prakasham S, Elsayed EA, Misson M, El Enshasy H. Fungal Pectinases: Production and Applications in Food Industries. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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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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Rigo MM, Borges TJ, Lang BJ, Murshid A, Nitika, Wolfgeher D, Calderwood SK, Truman AW, Bonorino C. Host expression system modulates recombinant Hsp70 activity through post-translational modifications. FEBS J 2020; 287:10.1111/febs.15279. [PMID: 32144867 PMCID: PMC7483562 DOI: 10.1111/febs.15279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/22/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022]
Abstract
The use of model organisms for recombinant protein production results in the addition of model-specific post-translational modifications (PTMs) that can affect the structure, charge, and function of the protein. The 70-kDa heat shock proteins (Hsp70) were originally described as intracellular chaperones, with ATPase and foldase activity. More recently, new extracellular activities of Hsp70 proteins (e.g. as immunomodulators) have been identified. While some studies indicate an inflammatory potential for extracellular Hsp70 proteins, others suggest an immunosuppressive activity. We hypothesized that the production of recombinant Hsp70 in different expression systems would result in the addition of different PTMs, perhaps explaining at least some of these opposing immunological outcomes. We produced and purified Mycobacterium tuberculosis DnaK from two different systems, Escherichia coli and Pichia pastoris, and analyzed by mass spectrometry the protein preparations, investigating the impact of PTMs in an in silico and in vitro perspective. The comparisons of DnaK structures in silico highlighted that electrostatic and topographical differences exist that are dependent upon the expression system. Production of DnaK in the eukaryotic system dramatically affected its ATPase activity, and significantly altered its ability to downregulate MHC II and CD86 expression on murine dendritic cells (DCs). Phosphatase treatment of DnaK indicated that some of these differences related specifically to phosphorylation. Altogether, our data indicate that PTMs are an important characteristic of the expression system, with differences that impact interactions of Hsps with their ligands and subsequent functional activities.
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Affiliation(s)
- Mauricio M Rigo
- School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Av. Ipiranga, 6681, Porto Alegre Rio Grande do Sul, Zip Code: 90619-900, Brazil
| | - Thiago J Borges
- Schuster Family Transplantation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA
| | - Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Ayesha Murshid
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, 28223
| | - Donald Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Andrew W Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, 28223
| | - Cristina Bonorino
- Laboratório de Imunoterapia, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Porto Alegre Rio Grande do Sul, Zip Code: 90050-170, Brazil
- Department of Surgery, School of Medicine, University of California at San Diego, La Jolla, CA, 92037
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14
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Statistically Designed Medium Reveals Interactions between Metabolism and Genetic Information Processing for Production of Stable Human Serum Albumin in Pichia pastoris. Biomolecules 2019; 9:biom9100568. [PMID: 31590267 PMCID: PMC6843683 DOI: 10.3390/biom9100568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
Human serum albumin (HSA), sourced from human serum, has been an important therapeutic protein for several decades. Pichia pastoris is strongly considered as an expression platform, but proteolytic degradation of recombinant HSA in the culture filtrate remains a major bottleneck for use of this system. In this study, we have reported the development of a medium that minimized proteolytic degradation across different copy number constructs. A synthetic codon-optimized copy of HSA was cloned downstream of α-factor secretory signal sequence and expressed in P. pastoris under the control of Alcohol oxidase 1 promoter. A two-copy expression cassette was also prepared. Culture conditions and medium components were identified and optimized using statistical tools to develop a medium that supported stable production of HSA. Comparative analysis of transcriptome data obtained by cultivation on optimized and unoptimized medium indicated upregulation of genes involved in methanol metabolism, alternate nitrogen assimilation, and DNA transcription, whereas enzymes of translation and secretion were downregulated. Several new genes were identified that could serve as possible targets for strain engineering of this yeast.
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15
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Park SH, Hahn JS. Development of an efficient cytosolic isobutanol production pathway in Saccharomyces cerevisiae by optimizing copy numbers and expression of the pathway genes based on the toxic effect of α-acetolactate. Sci Rep 2019; 9:3996. [PMID: 30850698 PMCID: PMC6408573 DOI: 10.1038/s41598-019-40631-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 02/18/2019] [Indexed: 11/09/2022] Open
Abstract
Isobutanol production in Saccharomyces cerevisiae is limited by subcellular compartmentalization of the pathway enzymes. In this study, we improved isobutanol production in S. cerevisiae by constructing an artificial cytosolic isobutanol biosynthetic pathway consisting of AlsS, α-acetolactate synthase from Bacillus subtilis, and two endogenous mitochondrial enzymes, ketol-acid reductoisomerase (Ilv5) and dihydroxy-acid dehydratase (Ilv3), targeted to the cytosol. B. subtilis AlsS was more active than Ilv2ΔN54, an endogenous α-acetolactate synthase targeted to the cytosol. However, overexpression of alsS led to a growth inhibition, which was alleviated by overexpressing ILV5ΔN48 and ILV3ΔN19, encoding the downstream enzymes targeted to the cytosol. Therefore, accumulation of the intermediate α-acetolactate might be toxic to the cells. Based on these findings, we improved isobutanol production by expressing alsS under the control of a copper-inducible CUP1 promoter, and by increasing translational efficiency of the ILV5ΔN48 and ILV3ΔN19 genes by adding Kozak sequence. Furthermore, strains with multi-copy integration of alsS into the delta-sequences were screened based on growth inhibition upon copper-dependent induction of alsS. Next, the ILV5ΔN48 and ILV3ΔN19 genes were integrated into the rDNA sites of the alsS-integrated strain, and the strains with multi-copy integration were screened based on the growth recovery. After optimizing the induction conditions of alsS, the final engineered strain JHY43D24 produced 263.2 mg/L isobutanol, exhibiting about 3.3-fold increase in production compared to a control strain constitutively expressing ILV2ΔN54, ILV5ΔN48, and ILV3ΔN19 on plasmids.
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Affiliation(s)
- Seong-Hee Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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16
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Liu J, Basit A, Miao T, Zheng F, Yu H, Wang Y, Jiang W, Cao Y. Secretory expression of β-mannanase in Saccharomyces cerevisiae and its high efficiency for hydrolysis of mannans to mannooligosaccharides. Appl Microbiol Biotechnol 2018; 102:10027-10041. [PMID: 30215129 DOI: 10.1007/s00253-018-9355-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/05/2018] [Accepted: 08/30/2018] [Indexed: 01/23/2023]
Abstract
Degradation of mannans is a key process in the production of foods and prebiotics. β-Mannanase is the key enzyme that hydrolyzes 1,4-β-D-mannosidic linkages in mannans. Heterogeneous expression of β-mannanase in Pichia pastoris systems is widely used; however, Saccharomyces cerevisiae expression systems are more reliable and safer. We optimized β-mannanase gene from Aspergillus sulphureus and expressed it in five S. cerevisiae strains. Haploid and diploid strains, and strains with constitutive promoter TEF1 or inducible promoter GAL1, were tested for enzyme expression in synthetic auxotrophic or complex medium. Highest efficiency expression was observed for haploid strain BY4741 integrated with β-mannanase gene under constitutive promoter TEF1, cultured in complex medium. In fed-batch culture in a fermentor, enzyme activity reached ~ 24 U/mL after 36 h, and production efficiency reached 16 U/mL/day. Optimal enzyme pH was 2.0-7.0, and optimal temperature was 60 °C. In studies of β-mannanase kinetic parameters for two substrates, locust bean gum galactomannan (LBG) gave Km = 24.13 mg/mL and Vmax = 715 U/mg, while konjac glucomannan (KGM) gave Km = 33 mg/mL and Vmax = 625 U/mg. One-hour hydrolysis efficiency values were 57% for 1% LBG, 74% for 1% KGM, 39% for 10% LBG, and 53% for 10% KGM. HPLC analysis revealed that the major hydrolysis products were the oligosaccharides mannose, mannobiose, mannotriose, mannotetraose, mannopentaose, and mannohexaose. Our findings show that this β-mannanase has high efficiency for hydrolysis of mannans to mannooligosaccharides, a type of prebiotic, suggesting strong potential application in food industries.
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Affiliation(s)
- Junquan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Abdul Basit
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Ting Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Fengzhen Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Hang Yu
- Liaoning Union Pharmaceutical Company Limited, Benxi, Liaoning, China
| | - Yan Wang
- Liaoning Union Pharmaceutical Company Limited, Benxi, Liaoning, China
| | - Wei Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China.
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China.
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17
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Tripathi NK, Shrivastava A. Recent Developments in Recombinant Protein-Based Dengue Vaccines. Front Immunol 2018; 9:1919. [PMID: 30190720 PMCID: PMC6115509 DOI: 10.3389/fimmu.2018.01919] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/03/2018] [Indexed: 12/11/2022] Open
Abstract
Recombinant proteins are gaining enormous importance these days due to their wide application as biopharmaceutical products and proven safety record. Various recombinant proteins of therapeutic and prophylactic importance have been successfully produced in microbial and higher expression host systems. Since there is no specific antiviral therapy available against dengue, the prevention by vaccination is the mainstay in reducing the disease burden. Therefore, efficacious vaccines are needed to control the spread of dengue worldwide. Dengue is an emerging viral disease caused by any of dengue virus 1-4 serotypes that affects the human population around the globe. Dengue virus is a single stranded RNA virus encoding three structural proteins (capsid protein, pre-membrane protein, and envelope protein) and seven non-structural proteins (NS1, NS2a, NS2b, NS3, NS4a, NS4b, NS5). As the only licensed dengue vaccine (Dengvaxia) is unable to confer balanced protection against all the serotypes, therefore various approaches for development of dengue vaccines including tetravalent live attenuated, inactivated, plasmid DNA, virus-vectored, virus-like particles, and recombinant subunit vaccines are being explored. These candidates are at different stages of vaccine development and have their own merits and demerits. The promising subunit vaccines are mainly based on envelope or its domain and non-structural proteins of dengue virus. These proteins have been produced in different hosts and are being investigated for development of a successful dengue vaccine. Novel immunogens have been designed employing various strategies like protein engineering and fusion of antigen with various immunostimulatory motif to work as self-adjuvant. Moreover, recombinant proteins can be formulated with novel adjuvants to enhance the immunogenicity and thus conferring better protection to the vaccinees. With the advent of newer and safer host systems, these recombinant proteins can be produced in a cost effective manner at large scale for vaccine studies. In this review, we summarize recent developments in recombinant protein based dengue vaccines that could lead to a good number of efficacious vaccine candidates for future human use and ultimately alternative dengue vaccine candidates.
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Affiliation(s)
- Nagesh K. Tripathi
- Bioprocess Scale Up Facility, Defence Research and Development Establishment, Gwalior, India
| | - Ambuj Shrivastava
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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18
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Li X, Yang Y, Zhan C, Zhang Z, Liu X, Liu H, Bai Z. Transcriptional analysis of impacts of glycerol transporter 1 on methanol and glycerol metabolism in Pichia pastoris. FEMS Yeast Res 2017; 18:4582313. [DOI: 10.1093/femsyr/fox081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/29/2017] [Indexed: 01/13/2023] Open
Affiliation(s)
- Xiang Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhenyang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Hebin Liu
- Department of Biological Science, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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19
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Windram OPF, Rodrigues RTL, Lee S, Haines M, Bayer TS. Engineering microbial phenotypes through rewiring of genetic networks. Nucleic Acids Res 2017; 45:4984-4993. [PMID: 28369627 PMCID: PMC5416768 DOI: 10.1093/nar/gkx197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/13/2017] [Indexed: 11/12/2022] Open
Abstract
The ability to program cellular behaviour is a major goal of synthetic biology, with applications in health, agriculture and chemicals production. Despite efforts to build 'orthogonal' systems, interactions between engineered genetic circuits and the endogenous regulatory network of a host cell can have a significant impact on desired functionality. We have developed a strategy to rewire the endogenous cellular regulatory network of yeast to enhance compatibility with synthetic protein and metabolite production. We found that introducing novel connections in the cellular regulatory network enabled us to increase the production of heterologous proteins and metabolites. This strategy is demonstrated in yeast strains that show significantly enhanced heterologous protein expression and higher titers of terpenoid production. Specifically, we found that the addition of transcriptional regulation between free radical induced signalling and nitrogen regulation provided robust improvement of protein production. Assessment of rewired networks revealed the importance of key topological features such as high betweenness centrality. The generation of rewired transcriptional networks, selection for specific phenotypes, and analysis of resulting library members is a powerful tool for engineering cellular behavior and may enable improved integration of heterologous protein and metabolite pathways.
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Affiliation(s)
- Oliver P F Windram
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rui T L Rodrigues
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sangjin Lee
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Matthew Haines
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Travis S Bayer
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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20
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Berterame NM, Bertagnoli S, Codazzi V, Porro D, Branduardi P. Temperature-induced lipocalin (TIL): a shield against stress-inducing environmental shocks in Saccharomyces cerevisiae. FEMS Yeast Res 2017; 17:4056149. [PMID: 28830085 DOI: 10.1093/femsyr/fox056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 11/14/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a well-established workhorse, either for recombinant or natural products, thanks to its natural traits and easily editable metabolism. However, during a bio-based industrial process it meets multiple stresses generated by operative conditions such as non-optimal temperature, pH, oxygenation and product accumulation. The development of tolerant strains is therefore indispensable for the improvement of production, yield and productivity of fermentative processes. In this regard, plants as resilient organisms are a generous source for fishing genes and/or metabolites that can help the cell factory to counteract environmental constraints. Plants possess proteins named temperature-induced lipocalins, TIL, whose levels in the cells correlates with the tolerance to sudden temperature changes and with the scavenging of reactive oxygen species. In this work, the gene encoding for the Arabidopsis thaliana TIL protein was for the first time expressed in S. cerevisiae. The recombinant strain was compared and analysed against the parental counterpart under heat shock, freezing, exposure to organic acid and oxidative agents. In all the tested conditions, TIL expression conferred a higher tolerance to the stress imposed, making this strain a promising candidate for the development of robust cell factories able to overtake the major impairments of industrial processes.
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Affiliation(s)
- Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Stefano Bertagnoli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Vera Codazzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan 20126, Italy
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21
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Not All Antigens Are Created Equally: Progress, Challenges, and Lessons Associated with Developing a Vaccine for Leishmaniasis. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00108-17. [PMID: 28515135 DOI: 10.1128/cvi.00108-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
From experimental models and the analyses of patients, it is well documented that antigen-specific T cells are critical for protection against Leishmania infection. Effective vaccines require both targeting to the pathogen and an immune stimulant to induce maturation of appropriate immune responses. While a great number of antigens have been examined as vaccine candidates against various Leishmania species, few have advanced to human or canine clinical trials. With emphasis on antigen expression, in this minireview we discuss some of the vaccine platforms that are currently being explored for the development of Leishmania vaccines. It is clear that the vaccine platform of choice can have a significant impact upon the level of protection induced by particular antigens, and we provide and highlight some examples for which the vaccine system used has impacted the protective efficacy imparted.
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22
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Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13C labeled reference lipids for quantification by mass spectrometry. Analyst 2017; 142:1891-1899. [PMID: 28475182 DOI: 10.1039/c7an00107j] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantification is an essential task in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity and their dynamic range of the lipidome. In this work, we introduce lipidome isotope labeling of yeast (LILY) in order to produce (non-radioactive) isotopically labeled eukaryotic lipid standards in yeast for normalization and quantification in mass spectrometric assays. More specifically, LILY is a fast and efficient in vivo labeling strategy in Pichia pastoris for the production of 13C labeled lipid library further paving the way to comprehensive compound-specific internal standardization in quantitative mass spectrometry based assays. More than 200 lipid species (from PA, PC, PE, PG, PI, PS, LysoGP, CL, DAG, TAG, DMPE, Cer, HexCer, IPC, MIPC) were obtained from yeast extracts with an excellent 13C enrichment >99.5%, as determined by complementary high resolution mass spectrometry based shotgun and high resolution LC-MS/MS analysis. In a first proof of principle study we tested the relative and absolute quantification capabilities of the 13C enriched lipids obtained by LILY using a parallel reaction monitoring based LC-MS approach. In relative quantification it could be shown that compound specific internal standardization was essential for the accuracy extending the linear dynamic range to four orders of magnitude. Excellent analytical figures of merit were observed for absolute quantification for a selected panel of 5 investigated glycerophospholipids (e.g. LOQs around 5 fmol absolute; typical concentrations ranging between 1 to 10 nmol per 108 yeast cell starting material; RSDs <10% (N = 4)).
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Affiliation(s)
- Evelyn Rampler
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gerrit Hermann
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and ISOtopic Solutions, Währingerstr. 38, 1090 Vienna, Austria
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany and College of Physical Sciences, University of Aberdeen, Department of Chemistry, AB24 3UE Aberdeen, UK and Medizinische Fakultät, Medizinische Proteom-Center (MCP), Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 38, 1090 Vienna, Austria. and Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria and Chemistry Meets Microbiolgy, Althanstraße 14, 1090 Vienna, Austria
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23
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Møller TSB, Hay J, Saxton MJ, Bunting K, Petersen EI, Kjærulff S, Finnis CJA. Human β-defensin-2 production from S. cerevisiae using the repressible MET17 promoter. Microb Cell Fact 2017; 16:11. [PMID: 28100236 PMCID: PMC5241953 DOI: 10.1186/s12934-017-0627-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/08/2017] [Indexed: 11/25/2022] Open
Abstract
Background Baker’s yeast Saccharomyces cerevisiae is a proven host for the commercial production of recombinant biopharmaceutical proteins. For the manufacture of heterologous proteins with activities deleterious to the host it can be desirable to minimise production during the growth phase and induce production late in the exponential phase. Protein expression by regulated promoter systems offers the possibility of improving productivity in this way by separating the recombinant protein production phase from the yeast growth phase. Commonly used inducible promoters do not always offer convenient solutions for industrial scale biopharmaceutical production with engineered yeast systems. Results Here we show improved secretion of the antimicrobial protein, human β-defensin-2, (hBD2), using the S. cerevisiae MET17 promoter by repressing expression during the growth phase. In shake flask culture, a higher final concentration of human β-defensin-2 was obtained using the repressible MET17 promoter system than when using the strong constitutive promoter from proteinase B (PRB1) in a yeast strain developed for high-level commercial production of recombinant proteins. Furthermore, this was achieved in under half the time using the MET17 promoter compared to the PRB1 promoter. Cell density, plasmid copy-number, transcript level and protein concentration in the culture supernatant were used to study the effects of different initial methionine concentrations in the culture media for the production of human β-defensin-2 secreted from S. cerevisiae. Conclusions The repressible S. cerevisiae MET17 promoter was more efficient than a strong constitutive promoter for the production of human β-defensin-2 from S. cerevisiae in small-scale culture and offers advantages for the commercial production of this and other heterologous proteins which are deleterious to the host organism. Furthermore, the MET17 promoter activity can be modulated by methionine alone, which has a safety profile applicable to biopharmaceutical manufacturing.
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Affiliation(s)
- Thea S B Møller
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.,Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Joanna Hay
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Malcolm J Saxton
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Karen Bunting
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Evamaria I Petersen
- Department of Physics and Nanotechnology, Aalborg University, Skjernvej 4A, Aalborg East, 9220, Aalborg, Denmark
| | - Søren Kjærulff
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK
| | - Christopher J A Finnis
- Novozymes Biopharma UK Limited, Castle Court, 59 Castle Boulevard, Nottingham, NG7 1FD, UK.
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24
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Hung CW, Klein T, Cassidy L, Linke D, Lange S, Anders U, Bureik M, Heinzle E, Schneider K, Tholey A. Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion. Mol Cell Proteomics 2016; 15:3090-3106. [PMID: 27477394 DOI: 10.1074/mcp.m115.051474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 01/09/2023] Open
Abstract
Protein secretion in yeast is a complex process and its efficiency depends on a variety of parameters. We performed a comparative proteome analysis of a set of Schizosaccharomyces pombe strains producing the α-glucosidase maltase in increasing amounts to investigate the overall proteomic response of the cell to the burden of protein production along the various steps of protein production and secretion. Proteome analysis of these strains, utilizing an isobaric labeling/two dimensional LC-MALDI MS approach, revealed complex changes, from chaperones and secretory transport machinery to proteins controlling transcription and translation. We also found an unexpectedly high amount of changes in enzyme levels of the central carbon metabolism and a significant up-regulation of several amino acid biosyntheses. These amino acids were partially underrepresented in the cellular protein compared with the composition of the model protein. Additional feeding of these amino acids resulted in a 1.5-fold increase in protein secretion. Membrane fluidity was identified as a second bottleneck for high-level protein secretion and addition of fluconazole to the culture caused a significant decrease in ergosterol levels, whereas protein secretion could be further increased by a factor of 2.1. In summary, we show that high level protein secretion causes global changes of protein expression levels in the cell and that precursor availability and membrane composition limit protein secretion in this yeast. In this respect, comparative proteome analysis is a powerful tool to identify targets for an efficient increase of protein production and secretion in S. pombe Data are available via ProteomeXchange with identifiers PXD002693 and PXD003016.
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Affiliation(s)
- Chien-Wen Hung
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tobias Klein
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Liam Cassidy
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Dennis Linke
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Sabrina Lange
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Uwe Anders
- ¶Roche Diagnostics GmbH, 68305 Mannheim, Germany
| | - Matthias Bureik
- ‖PomBioTech GmbH, 66123 Saarbrücken, Germany; **School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Elmar Heinzle
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Konstantin Schneider
- §Biochemical Engineering Institute, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Tholey
- From the ‡Institute for Experimental Medicine, Div. Systematic Proteome Research & Bioanalytics, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany;
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Yang B, Liu J, Jiang Y, Chen F. Chlorella species as hosts for genetic engineering and expression of heterologous proteins: Progress, challenge and perspective. Biotechnol J 2016; 11:1244-1261. [PMID: 27465356 DOI: 10.1002/biot.201500617] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 11/08/2022]
Abstract
The species of Chlorella represent a highly specialized group of green microalgae that can produce high levels of protein. Many Chlorella strains can grow rapidly and achieve high cell density under controlled conditions and are thus considered to be promising protein sources. Many advances in the genetic engineering of Chlorella have occurred in recent years, with significant developments in successful expression of heterologous proteins for various applications. Nevertheless, a lot of obstacles remain to be addressed, and a sophisticated and stable Chlorella expression system has yet to emerge. This review provides a brief summary of current knowledge on Chlorella and an overview of recent progress in the genetic engineering of Chlorella, and highlights the advances in the development of a genetic toolbox of Chlorella for heterologous protein expression. Research directions to further exploit the Chlorella expression system with respect to both challenges and perspectives are also discussed. This paper serves as a comprehensive literature review for the Chlorella community and will provide valuable insights into future exploration of Chlorella as a promising host for heterologous protein expression.
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Affiliation(s)
- Bo Yang
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China.,School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China. .,Singapore-Peking University Research Centre for a Sustainable Low-Carbon Future, CREATE Tower, Singapore.
| | - Yue Jiang
- Runke Bioengineering Co., Ltd., Zhangzhou, China.
| | - Feng Chen
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China.,Singapore-Peking University Research Centre for a Sustainable Low-Carbon Future, CREATE Tower, Singapore
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Martínez JL, Meza E, Petranovic D, Nielsen J. The impact of respiration and oxidative stress response on recombinant α-amylase production by Saccharomyces cerevisiae. Metab Eng Commun 2016; 3:205-210. [PMID: 29468124 PMCID: PMC5779723 DOI: 10.1016/j.meteno.2016.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/19/2016] [Accepted: 06/21/2016] [Indexed: 11/29/2022] Open
Abstract
Studying protein production is important for fundamental research on cell biology and applied research for biotechnology. Yeast Saccharomyces cerevisiae is an attractive workhorse for production of recombinant proteins as it does not secrete many endogenous proteins and it is therefore easy to purify a secreted product. However, recombinant production at high rates represents a significant metabolic burden for the yeast cells, which results in oxidative stress and ultimately affects the protein production capacity. Here we describe a method to reduce the overall oxidative stress by overexpressing the endogenous HAP1 gene in a S. cerevisiae strain overproducing recombinant α-amylase. We demonstrate how Hap1p can activate a set of oxidative stress response genes and meanwhile contribute to increase the metabolic rate of the yeast strains, therefore mitigating the negative effect of the ROS accumulation associated to protein folding and hence increasing the production capacity during batch fermentations. Recombinant protein production is a multi-billion dollar market. Heterologous production by yeast generates oxidative stress regardless the target. HAP1 overexpression mitigates oxidative stress while enhancing metabolic capacity. Overexpression of HAP1 allows higher volumetric productivity of recombinant proteins. Strains overexpressing HAP1 may grow in chemostats operated at higher dilution rates.
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Affiliation(s)
- José L Martínez
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Eugenio Meza
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Dina Petranovic
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE41296 Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
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A step forward to improve recombinant protein production in Pichia pastoris : From specific growth rate effect on protein secretion to carbon-starving conditions as advanced strategy. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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28
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Improvement of isobutanol production in Saccharomyces cerevisiae by increasing mitochondrial import of pyruvate through mitochondrial pyruvate carrier. Appl Microbiol Biotechnol 2016; 100:7591-8. [DOI: 10.1007/s00253-016-7636-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/17/2016] [Accepted: 05/14/2016] [Indexed: 12/31/2022]
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29
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Tripathi NK. Production and Purification of Recombinant Proteins fromEscherichia coli. CHEMBIOENG REVIEWS 2016. [DOI: 10.1002/cben.201600002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Guerrero-Torres V, Rios-Lozano M, Badillo-Corona JA, Chairez I, Garibay-Orijel C. Robust Parameter Identification to Perform the Modeling of pta and poxB Genes Deletion Effect on Escherichia Coli. Appl Biochem Biotechnol 2016; 179:1418-34. [PMID: 27093969 DOI: 10.1007/s12010-016-2074-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/03/2016] [Indexed: 11/27/2022]
Abstract
The aim of this study was to design a robust parameter identification algorithm to characterize the effect of gene deletion on Escherichia coli (E. coli) MG1655. Two genes (pta and poxB) in the competitive pathways were deleted from this microorganism to inhibit pyruvate consumption. This condition deviated the E. coli metabolism toward the Krebs cycle. As a consequence, the biomass, substrate (glucose), lactic, and acetate acids as well as ethanol concentrations were modified. A hybrid model was proposed to consider the effect of gene deletion on the metabolism of E. coli. The model parameters were estimated by the application of a least mean square method based on the instrument variable technique. To evaluate the parametric identifier method, a set of robust exact differentiators, based on the super-twisting algorithm, was implemented. The hybrid model was successfully characterized by the parameters obtained from experimental information of E. coli MG1655. The significant difference between parameters obtained with wild-type strain and the modified (with deleted genes) justifies the application of the parametric identification algorithm. This characterization can be used to optimize the production of different byproducts of commercial interest.
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Affiliation(s)
| | - M Rios-Lozano
- SEPI-UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - I Chairez
- Department of Bioprocesses-UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico.
| | - C Garibay-Orijel
- Department of Bioprocesses-UPIBI, Instituto Politécnico Nacional, Mexico City, Mexico
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Berterame NM, Porro D, Ami D, Branduardi P. Protein aggregation and membrane lipid modifications under lactic acid stress in wild type and OPI1 deleted Saccharomyces cerevisiae strains. Microb Cell Fact 2016; 15:39. [PMID: 26887851 PMCID: PMC4756461 DOI: 10.1186/s12934-016-0438-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/02/2016] [Indexed: 11/12/2022] Open
Abstract
Background Lactic acid is a versatile chemical platform with many different industrial applications. Yeasts have been demonstrated as attractive alternative to natural lactic acid producers since they can grow at low pH, allowing the direct purification of the product in the desired acidic form. However, when very high concentrations of organic acids are reached, the major limitation for a viable production is the toxic effect of the product. The accumulation in the cytosol of H+ and of the weak organic counter-anions triggers a cellular reprogramming. Here, the effects of lactic acid exposure on Saccharomycescerevisiae have been evaluated by Fourier transform infrared (FTIR) microspectroscopy. In addition to -omic techniques, describing these responses in terms of systems and networks, FTIR microspectroscopy allows a rapid acquisition of the cellular biochemical fingerprint, providing information on the major classes of macromolecules. Results FTIR analyses on Saccharomyces cerevisiae cells under lactic acid stress at low pH revealed some still uncharacterized traits: (1) a direct correlation between lactic acid exposure and a rearrangement in lipid hydrocarbon tails, together with a decrease in the signals of phosphatidylcholine (PC), one of the main components of cell membrane; (2) a rearrangement in the cell wall carbohydrates, including glucans and mannans (3) a significant yet transient protein aggregation, possibly responsible for the observed transient decrease of the growth rate. When repeated on the isogenic strain deleted in OPI1, encoding for a transcriptional repressor of genes involved in PC biosynthesis, FTIR analysis revealed that not only the PC levels were affected but also the cell membrane/wall composition and the accumulation of protein aggregates, resulting in higher growth rate in the presence of the stressing agent. Conclusions This work revealed novel effects evoked by lactic acid on cell membrane/wall composition and protein aggregation in S. cerevisiae cells. We consequently demonstrated that the targeted deletion of OPI1 resulted in improved lactic acid tolerance. Considering that stress response involves many and different cellular networks and regulations, most of which are still not implemented in modelling, these findings constitute valuable issues for interpreting cellular rewiring and for tailoring ameliorated cell factories for lactic acid production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0438-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia Maria Berterame
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.
| | - Danilo Porro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy. .,SYSBIO - Centre of Systems Biology, Milano and Roma, Italy.
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy. .,Department of Physics, University of Milano-Bicocca, Piazza della Scienza 3, Milan, 20126, Italy. .,Consorzio Nazionale Interuniversitario per le Scienze fisiche della Materia (CNISM) UdR Milano-Bicocca, Milan, 20126, Italy.
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy.
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Anyaogu DC, Mortensen UH. Manipulating the glycosylation pathway in bacterial and lower eukaryotes for production of therapeutic proteins. Curr Opin Biotechnol 2015; 36:122-8. [DOI: 10.1016/j.copbio.2015.08.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/07/2015] [Accepted: 08/09/2015] [Indexed: 11/16/2022]
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Mazzoleni S, Landi C, Cartenì F, de Alteriis E, Giannino F, Paciello L, Parascandola P. A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures. Microb Cell Fact 2015; 14:109. [PMID: 26223307 PMCID: PMC4518646 DOI: 10.1186/s12934-015-0295-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/13/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. RESULTS A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. CONCLUSIONS The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.
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Affiliation(s)
- Stefano Mazzoleni
- Dept. di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055, Portici, NA, Italy.
| | - Carmine Landi
- Dept. di Ingegneria Industriale, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy.
| | - Fabrizio Cartenì
- Dept. di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055, Portici, NA, Italy.
| | - Elisabetta de Alteriis
- Dept. di Biologia, Università degli Studi di Napoli Federico II, Via Cinthia, 80100, Naples, Italy.
| | - Francesco Giannino
- Dept. di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055, Portici, NA, Italy.
| | - Lucia Paciello
- Dept. di Ingegneria Industriale, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy.
| | - Palma Parascandola
- Dept. di Ingegneria Industriale, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy.
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Fidan O, Zhan J. Recent advances in engineering yeast for pharmaceutical protein production. RSC Adv 2015. [DOI: 10.1039/c5ra13003d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Currently available systems and synthetic biology tools can be applied to yeast engineering for improved biopharmaceutical protein production.
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Affiliation(s)
- Ozkan Fidan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
| | - Jixun Zhan
- Department of Biological Engineering
- Utah State University
- Logan
- USA
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Jajesniak P, Seng Wong T. From genetic circuits to industrial-scale biomanufacturing: bacterial promoters as a cornerstone of biotechnology. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Bill RM. Recombinant protein subunit vaccine synthesis in microbes: a role for yeast? J Pharm Pharmacol 2014; 67:319-28. [DOI: 10.1111/jphp.12353] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/18/2014] [Indexed: 12/14/2022]
Abstract
Abstract
Objectives
Recombinant protein subunit vaccines are formulated using protein antigens that have been synthesized in heterologous host cells. Several host cells are available for this purpose, ranging from Escherichia coli to mammalian cell lines. This article highlights the benefits of using yeast as the recombinant host.
Key findings
The yeast species, Saccharomyces cerevisiae and Pichia pastoris, have been used to optimize the functional yields of potential antigens for the development of subunit vaccines against a wide range of diseases caused by bacteria and viruses. Saccharomyces cerevisiae has also been used in the manufacture of 11 approved vaccines against hepatitis B virus and one against human papillomavirus; in both cases, the recombinant protein forms highly immunogenic virus-like particles.
Summary
Advances in our understanding of how a yeast cell responds to the metabolic load of producing recombinant proteins will allow us to identify host strains that have improved yield properties and enable the synthesis of more challenging antigens that cannot be produced in other systems. Yeasts therefore have the potential to become important host organisms for the production of recombinant antigens that can be used in the manufacture of subunit vaccines or in new vaccine development.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham, UK
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Dato L, Berterame NM, Ricci MA, Paganoni P, Palmieri L, Porro D, Branduardi P. Changes in SAM2 expression affect lactic acid tolerance and lactic acid production in Saccharomyces cerevisiae. Microb Cell Fact 2014; 13:147. [PMID: 25359316 PMCID: PMC4230512 DOI: 10.1186/s12934-014-0147-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/08/2014] [Indexed: 01/25/2023] Open
Abstract
Background The great interest in the production of highly pure lactic acid enantiomers comes from the application of polylactic acid (PLA) for the production of biodegradable plastics. Yeasts can be considered as alternative cell factories to lactic acid bacteria for lactic acid production, despite not being natural producers, since they can better tolerate acidic environments. We have previously described metabolically engineered Saccharomyces cerevisiae strains producing high amounts of L-lactic acid (>60 g/L) at low pH. The high product concentration represents the major limiting step of the process, mainly because of its toxic effects. Therefore, our goal was the identification of novel targets for strain improvement possibly involved in the yeast response to lactic acid stress. Results The enzyme S-adenosylmethionine (SAM) synthetase catalyses the only known reaction leading to the biosynthesis of SAM, an important cellular cofactor. SAM is involved in phospholipid biosynthesis and hence in membrane remodelling during acid stress. Since only the enzyme isoform 2 seems to be responsive to membrane related signals (e.g. myo-inositol), Sam2p was tagged with GFP to analyse its abundance and cellular localization under different stress conditions. Western blot analyses showed that lactic acid exposure correlates with an increase in protein levels. The SAM2 gene was then overexpressed and deleted in laboratory strains. Remarkably, in the BY4741 strain its deletion conferred higher resistance to lactic acid, while its overexpression was detrimental. Therefore, SAM2 was deleted in a strain previously engineered and evolved for industrial lactic acid production and tolerance, resulting in higher production. Conclusions Here we demonstrated that the modulation of SAM2 can have different outcomes, from clear effects to no significant phenotypic responses, upon lactic acid stress in different genetic backgrounds, and that at least in one genetic background SAM2 deletion led to an industrially relevant increase in lactic acid production. Further work is needed to elucidate the molecular basis of these observations, which underline once more that strain robustness relies on complex cellular mechanisms, involving regulatory genes and proteins. Our data confirm cofactor engineering as an important tool for cell factory improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Dato
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| | - Nadia Maria Berterame
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| | - Maria Antonietta Ricci
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy.
| | - Paola Paganoni
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| | - Luigi Palmieri
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy.
| | - Danilo Porro
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| | - Paola Branduardi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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Park SH, Kim S, Hahn JS. Metabolic engineering of Saccharomyces cerevisiae for the production of isobutanol and 3-methyl-1-butanol. Appl Microbiol Biotechnol 2014; 98:9139-47. [DOI: 10.1007/s00253-014-6081-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
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41
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Baeshen NA, Baeshen MN, Sheikh A, Bora RS, Ahmed MMM, Ramadan HAI, Saini KS, Redwan EM. Cell factories for insulin production. Microb Cell Fact 2014; 13:141. [PMID: 25270715 PMCID: PMC4203937 DOI: 10.1186/s12934-014-0141-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/16/2014] [Indexed: 12/17/2022] Open
Abstract
The rapid increase in the number of diabetic patients globally and exploration of alternate insulin delivery methods such as inhalation or oral route that rely on higher doses, is bound to escalate the demand for recombinant insulin in near future. Current manufacturing technologies would be unable to meet the growing demand of affordable insulin due to limitation in production capacity and high production cost. Manufacturing of therapeutic recombinant proteins require an appropriate host organism with efficient machinery for posttranslational modifications and protein refolding. Recombinant human insulin has been produced predominantly using E. coli and Saccharomyces cerevisiae for therapeutic use in human. We would focus in this review, on various approaches that can be exploited to increase the production of a biologically active insulin and its analogues in E. coli and yeast. Transgenic plants are also very attractive expression system, which can be exploited to produce insulin in large quantities for therapeutic use in human. Plant-based expression system hold tremendous potential for high-capacity production of insulin in very cost-effective manner. Very high level of expression of biologically active proinsulin in seeds or leaves with long-term stability, offers a low-cost technology for both injectable as well as oral delivery of proinsulin.
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Affiliation(s)
- Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Mohammed N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Abdullah Sheikh
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Roop S Bora
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Mohamed Morsi M Ahmed
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia. .,Nucleic Acids Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City for Scientific Research and Technology Applications, Alexandria, Egypt.
| | - Hassan A I Ramadan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia. .,Cell Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Tahrir St. Dokki, Cairo, 12311, Egypt.
| | - Kulvinder Singh Saini
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia. .,Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Applied Technology, New Borg AL-Arab, Alexandria, Egypt.
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42
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Martínez JL, Liu L, Petranovic D, Nielsen J. Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production bySaccharomyces cerevisiae. Biotechnol Bioeng 2014; 112:181-8. [DOI: 10.1002/bit.25347] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022]
Affiliation(s)
- José L. Martínez
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Lifang Liu
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Dina Petranovic
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Kemivägen 10 SE-41296 Göteborg Sweden
- Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Fremtidsvej 3 DK-2970 Hørsholm Denmark
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43
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Young CL, Robinson AS. Protein folding and secretion: mechanistic insights advancing recombinant protein production in S. cerevisiae. Curr Opin Biotechnol 2014; 30:168-77. [PMID: 25032908 DOI: 10.1016/j.copbio.2014.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 10/25/2022]
Abstract
The emergence of genomic approaches coupled to recombinant DNA technologies have identified the quality control systems that regulate proteostasis - biological pathways that modulate protein biogenesis, maturation, trafficking, and degradation. The elucidation of these pathways has become of growing importance in therapeutics as loss of proteostasis has been suggested to lead to a number of human diseases including Alzheimer's, Parkinson's Disease and Type II Diabetes. We anticipate that the most successful strategies for protein expression and therapeutics development may involve integration of protein engineering strategies with host manipulation, to exploit the cell's native stress response pathways and trafficking mechanisms. This review will highlight recent findings and mechanistic detail correlated to quality control in the early secretory pathway of Saccharomyces cerevisiae.
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Affiliation(s)
- Carissa L Young
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, United States.
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44
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Nocon J, Steiger MG, Pfeffer M, Sohn SB, Kim TY, Maurer M, Rußmayer H, Pflügl S, Ask M, Haberhauer-Troyer C, Ortmayr K, Hann S, Koellensperger G, Gasser B, Lee SY, Mattanovich D. Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab Eng 2014; 24:129-38. [PMID: 24853352 PMCID: PMC4094982 DOI: 10.1016/j.ymben.2014.05.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 01/08/2023]
Abstract
The production of recombinant proteins is frequently enhanced at the levels of transcription, codon usage, protein folding and secretion. Overproduction of heterologous proteins, however, also directly affects the primary metabolism of the producing cells. By incorporation of the production of a heterologous protein into a genome scale metabolic model of the yeast Pichia pastoris, the effects of overproduction were simulated and gene targets for deletion or overexpression for enhanced productivity were predicted. Overexpression targets were localized in the pentose phosphate pathway and the TCA cycle, while knockout targets were found in several branch points of glycolysis. Five out of 9 tested targets led to an enhanced production of cytosolic human superoxide dismutase (hSOD). Expression of bacterial β-glucuronidase could be enhanced as well by most of the same genetic modifications. Beneficial mutations were mainly related to reduction of the NADP/H pool and the deletion of fermentative pathways. Overexpression of the hSOD gene itself had a strong impact on intracellular fluxes, most of which changed in the same direction as predicted by the model. In vivo fluxes changed in the same direction as predicted to improve hSOD production. Genome scale metabolic modeling is shown to predict overexpression and deletion mutants which enhance recombinant protein production with high accuracy. Recombinant protein production in P. pastoris affects the central metabolism. A genome scale metabolic model can predict these metabolic flux changes. Mutations in central metabolic genes enhanced recombinant protein yield up to 40%. These beneficial mutations were predicted by the metabolic model with high accuracy.
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Affiliation(s)
- Justyna Nocon
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria
| | - Matthias G Steiger
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Martin Pfeffer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria
| | - Seung Bum Sohn
- Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Tae Yong Kim
- Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Michael Maurer
- School of Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Hannes Rußmayer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Stefan Pflügl
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Magnus Ask
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Christina Haberhauer-Troyer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karin Ortmayr
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gunda Koellensperger
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Sang Yup Lee
- Bioinformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria.
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45
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Mattanovich D, Sauer M, Gasser B. Yeast biotechnology: teaching the old dog new tricks. Microb Cell Fact 2014; 13:34. [PMID: 24602262 PMCID: PMC3975642 DOI: 10.1186/1475-2859-13-34] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 02/15/2014] [Indexed: 02/07/2023] Open
Abstract
Yeasts are regarded as the first microorganisms used by humans to process food and alcoholic beverages. The technology developed out of these ancient processes has been the basis for modern industrial biotechnology. Yeast biotechnology has gained great interest again in the last decades. Joining the potentials of genomics, metabolic engineering, systems and synthetic biology enables the production of numerous valuable products of primary and secondary metabolism, technical enzymes and biopharmaceutical proteins. An overview of emerging and established substrates and products of yeast biotechnology is provided and discussed in the light of the recent literature.
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Affiliation(s)
- Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
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46
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Bill RM. Playing catch-up with Escherichia coli: using yeast to increase success rates in recombinant protein production experiments. Front Microbiol 2014; 5:85. [PMID: 24634668 PMCID: PMC3942658 DOI: 10.3389/fmicb.2014.00085] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/17/2014] [Indexed: 11/13/2022] Open
Abstract
Several host systems are available for the production of recombinant proteins, ranging from Escherichia coli to mammalian cell-lines. This article highlights the benefits of using yeast, especially for more challenging targets such as membrane proteins. On account of the wide range of molecular, genetic, and microbiological tools available, use of the well-studied model organism, Saccharomyces cerevisiae, provides many opportunities to optimize the functional yields of a target protein. Despite this wealth of resources, it is surprisingly under-used. In contrast, Pichia pastoris, a relative new-comer as a host organism, is already becoming a popular choice, particularly because of the ease with which high biomass (and hence recombinant protein) yields can be achieved. In the last few years, advances have been made in understanding how a yeast cell responds to the stress of producing a recombinant protein and how this information can be used to identify improved host strains in order to increase functional yields. Given these advantages, and their industrial importance in the production of biopharmaceuticals, I argue that S. cerevisiae and P. pastoris should be considered at an early stage in any serious strategy to produce proteins.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University Birmingham, UK
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47
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Branduardi P, Dato L, Porro D. Molecular tools and protocols for engineering the acid-tolerant yeast Zygosaccharomyces bailii as a potential cell factory. Methods Mol Biol 2014; 1152:63-85. [PMID: 24744027 DOI: 10.1007/978-1-4939-0563-8_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycetales budding yeast, is widely known for its peculiar tolerance to various stresses, among which are organic acids. Despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here, we describe in detail protocols for transformation, for target gene disruption or gene integration, and for designing episomal expression plasmids helpful for developing and further studying the yeast Z. bailii.
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Affiliation(s)
- Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2 - 20126, Milan, Italy,
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48
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Camattari A, Weinhandl K, Gudiminchi RK. Methods for efficient high-throughput screening of protein expression in recombinant Pichia pastoris strains. Methods Mol Biol 2014; 1152:113-123. [PMID: 24744029 DOI: 10.1007/978-1-4939-0563-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The methylotrophic yeast Pichia pastoris is becoming one of the favorite industrial workhorses for protein expression. Due to the widespread use of integration vectors, which generates significant clonal variability, screening methods allowing assaying hundreds of individual clones are of particular importance. Here we describe methods to detect and analyze protein expression, developed in a 96-well format for high-throughput screening of recombinant P. pastoris strains. The chapter covers essentially three common scenarios: (1) an enzymatic assay for proteins expressed in the cell cytoplasm, requiring cell lysis; (2) a whole-cell assay for a fungal cytochrome P450; and (3) a nonenzymatic assay for detection and quantification of tagged protein secreted into the supernatant.
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Affiliation(s)
- Andrea Camattari
- Graz University of Technology, Petersgasse 14, 8010, Graz, Austria,
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49
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Liu H, Zhou X, Tian S, Hao X, You J, Zhang Y. Two-step transpeptidation of the insulin precursor expressed in Pichia pastoris to insulin ester via trypsin-catalyzed cleavage and coupling. Biotechnol Appl Biochem 2013; 61:408-17. [PMID: 24325254 DOI: 10.1002/bab.1186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/05/2013] [Indexed: 11/07/2022]
Abstract
Insulin precursor fusion protein expressed in Pichia pastoris is a single-chain protein with a spacer peptide (EEAEAEAEPK) localized at its N-terminal. Currently, the one-step transpeptidation reaction with low yield and high cost is generally employed to convert the insulin precursor fusion protein into human insulin ester. In this study, a two-step transpeptidation reaction was proposed separating the cleavage step from the coupling step so that each reaction was performed under its optimal conditions. Using this method, the total efficiency doubled and the reaction time was shortened compared with the one-step method. In addition, the amount of O-t-butyl-l-threonine t-butyl ester and trypsin dosages were reduced by 50% and 75%, respectively. This two-step transpeptidation strategy was simple and efficient and could be used for the pharmaceutical production of human insulin.
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Affiliation(s)
- Haifeng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China.,Shandong Ehua Biopharmaceutical Co., Ltd., Shandong, People's Republic of China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Shousheng Tian
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China
| | - Xianghui Hao
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China
| | - Jinhua You
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China.,Shandong Ehua Biopharmaceutical Co., Ltd., Shandong, People's Republic of China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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50
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Weinacker D, Rabert C, Zepeda AB, Figueroa CA, Pessoa A, Farías JG. Applications of recombinant Pichia pastoris in the healthcare industry. Braz J Microbiol 2013; 44:1043-8. [PMID: 24688491 PMCID: PMC3958167 DOI: 10.1590/s1517-83822013000400004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/04/2013] [Indexed: 12/16/2022] Open
Abstract
Since the 1970s, the establishment and development of the biotech industry has improved exponentially, allowing the commercial production of biopharmaceutical proteins. Nowadays, new recombinant protein production is considered a multibillion-dollar market, in which about 25% of commercial pharmaceuticals are biopharmaceuticals. But to achieve a competitive production process is not an easy task. Any production process has to be highly productive, efficient and economic. Despite that the perfect host is still not discovered, several research groups have chosen Pichia pastoris as expression system for the production of their protein because of its many features. The attempt of this review is to embrace several research lines that have adopted Pichia pastoris as their expression system to produce a protein on an industrial scale in the health care industry.
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Affiliation(s)
- Daniel Weinacker
- Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
| | - Claudia Rabert
- Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Temuco, Chile
| | - Andrea B. Zepeda
- Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
| | - Carolina A. Figueroa
- Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
| | - Adalberto Pessoa
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jorge G. Farías
- Departamento de Ingeniería Química, Facultad de Ingeniería, Ciencias y Administración, Universidad de La Frontera, Temuco, Chile
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