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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Luna-Flores CH, Weng Y, Wang A, Chen X, Peng B, Zhao CX, Navone L, von Hellens J, Speight RE. Improving phytase production in Pichia pastoris fermentations through de-repression and methanol induction optimization. Biotechnol Bioeng 2023; 120:3276-3287. [PMID: 37489850 DOI: 10.1002/bit.28510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 04/10/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023]
Abstract
Pichia pastoris (Komagataella phaffii) is a fast-growing methylotrophic yeast with the ability to assimilate several carbon sources such as methanol, glucose, or glycerol. It has been shown to have outstanding secretion capability with a variety of heterologous proteins. In previous studies, we engineered P. pastoris to co-express Escherichia coli AppA phytase and the HAC1 transcriptional activator using a bidirectional promoter. Phytase production was characterized in shake flasks and did not reflect industrial conditions. In the present study, phytase expression was explored and optimized using instrumented fermenters in continuous and fed-batch modes. First, the production of phytase was investigated under glucose de-repression in continuous culture at three dilution factors, 0.5 d-1 , 1 d-1 , and 1.5 d-1 . The fermenter parameters of these cultures were used to inform a kinetic model in batch and fed-batch modes for growth and phytase production. The kinetic model developed aided to design the glucose-feeding profile of a fed-batch culture. Kinetic model simulations under glucose de-repression and fed-batch conditions identified optimal phytase productivity at the specific growth rate of 0.041 h-1 . Validation of the model simulation with experimental data confirmed the feasibility of the model to predict phytase production in our newly engineered strain. Methanol was used only to induce the expression of phytase at high cell densities. Our results showed that high phytase production required two stages, the first stage used glucose under de-repression conditions to generate biomass while expressing phytase, and stage two used methanol to induce phytase expression. The production of phytase was improved 3.5-fold by methanol induction compared to the expression with glucose alone under de-repression conditions to a final phytase activity of 12.65 MU/L. This final volumetric phytase production represented an approximate 36-fold change compared to the flask fermentations. Finally, the phytase protein produced was assayed to confirm its molecular weight, and pH and temperature profiles. This study highlights the importance of optimizing protein production in P. pastoris when using novel promoters and presents a general approach to performing bioprocess optimization in this important production host.
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Affiliation(s)
- Carlos H Luna-Flores
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Yilun Weng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland (UQ), Brisbane, Queensland, Australia
| | | | | | - Bingyin Peng
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland (UQ), Brisbane, Queensland, Australia
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia, Australia
| | - Laura Navone
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | | | - Robert E Speight
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
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Navone L, Moffitt K, Behrendorff J, Sadowski P, Hartley C, Speight R. Biosensor-guided rapid screening for improved recombinant protein secretion in Pichia pastoris. Microb Cell Fact 2023; 22:92. [PMID: 37138331 PMCID: PMC10155391 DOI: 10.1186/s12934-023-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023] Open
Abstract
Pichia pastoris (Komagataella phaffii) is widely used for industrial production of heterologous proteins due to high secretory capabilities but selection of highly productive engineered strains remains a limiting step. Despite availability of a comprehensive molecular toolbox for construct design and gene integration, there is high clonal variability among transformants due to frequent multi-copy and off-target random integration. Therefore, functional screening of several hundreds of transformant clones is essential to identify the best protein production strains. Screening methods are commonly based on deep-well plate cultures with analysis by immunoblotting or enzyme activity assays of post-induction samples, and each heterologous protein produced may require development of bespoke assays with multiple sample processing steps. In this work, we developed a generic system based on a P. pastoris strain that uses a protein-based biosensor to identify highly productive protein secretion clones from a heterogeneous set of transformants. The biosensor uses a split green fluorescent protein where the large GFP fragment (GFP1-10) is fused to a sequence-specific protease from Tobacco Etch Virus (TEV) and is targeted to the endoplasmic reticulum. Recombinant proteins targeted for secretion are tagged with the small fragment of the split GFP (GFP11). Recombinant protein production can be measured by monitoring GFP fluorescence, which is dependent on interaction between the large and small GFP fragments. The reconstituted GFP is cleaved from the target protein by TEV protease, allowing for secretion of the untagged protein of interest and intracellular retention of the mature GFP. We demonstrate this technology with four recombinant proteins (phytase, laccase, β-casein and β-lactoglobulin) and show that the biosensor directly reports protein production levels that correlate with traditional assays. Our results confirm that the split GFP biosensor can be used for facile, generic, and rapid screening of P. pastoris clones to identify those with the highest production levels.
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Affiliation(s)
- Laura Navone
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.
| | - Kaylee Moffitt
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - James Behrendorff
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | | | - Robert Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
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Niu T, Cui Y, Shan X, Qin S, Zhou X, Wang R, Chang A, Ma N, Jing J, He J. Comparative transcriptomic analysis-based identification of the regulation of foreign proteins with different stabilities expressed in Pichia pastoris. Front Microbiol 2022; 13:1074398. [PMID: 36620045 PMCID: PMC9814716 DOI: 10.3389/fmicb.2022.1074398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction The industrial yeast Pichia pastoris is widely used as a cell factory to produce proteins, chemicals and advanced biofuels. We have previously constructed P. pastoris strains that overexpress protein disulfide isomerase (PDI), which is a kind of molecular chaperone that can improve the expression of an exogenous protein when they are co-expressed. Chicken cystatin (cC) is a highly thermostable cysteine protease inhibitor and a homologous protein of human cystatin C (HCC). Wild-type cC and the two mutants, I66Q and ΔW (a truncated cC lacking the á-helix 2) represent proteins with different degrees of stability. Methods Wild-type cC, I66Q and ΔW were each overexpressed in P. pastoris without and with the coexpression of PDI and their extracellular levels were determined and compared. Transcriptomic profiling was performed to compare the changes in the main signaling pathways and cell components (other than endoplasmic reticulum quality control system represented by molecular chaperones) in P. pastoris in response to intracellular folding stress caused by the expression of exogenous proteins with different stabilities. Finally, hub genes hunting was also performed. Results and discussion The coexpression of PDI was able to increase the extracellular levels of both wild-type cC and the two mutants, indicating that overexpression of PDI could prevent the misfolding of unstable proteins or promote the degradation of the misfolded proteins to some extent. For P. pastoris cells that expressed the I66Q or ΔW mutant, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the common DEGs in these cells revealed a significant upregulation of the genes involved in protein processing, but a significant downregulation of the genes enriched in the Ribosome, TCA and Glycolysis/Gluconeogenesis pathways. Hub genes hunting indicated that the most downregulated ribosome protein, C4QXU7 in this case, might be an important target protein that could be manipulated to increase the expression of foreign proteins, especially proteins with a certain degree of instability. Conclusion These findings should shed new light on our understanding of the regulatory mechanism in yeast cells that responds to intracellular folding stress, providing valuable information for the development of a convenient platform that could improve the efficiency of heterologous protein expression in P. pastoris.
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Affiliation(s)
- Tingting Niu
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Yi Cui
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xu Shan
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Shuzhen Qin
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Xuejie Zhou
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Rui Wang
- School of Life Sciences, Liaoning University, Shenyang, China
| | - Alan Chang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Nan Ma
- China Academy of Transportation Sciences, Beijing, China,Nan Ma,
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China,Jingjing Jing,
| | - Jianwei He
- School of Life Sciences, Liaoning University, Shenyang, China,*Correspondence: Jianwei He,
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Zhou Y, Anoopkumar AN, Tarafdar A, Madhavan A, Binoop M, Lakshmi NM, B AK, Sindhu R, Binod P, Sirohi R, Pandey A, Zhang Z, Awasthi MK. Microbial engineering for the production and application of phytases to the treatment of the toxic pollutants: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119703. [PMID: 35787420 DOI: 10.1016/j.envpol.2022.119703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Phytases are a group of digestive enzymes which are commonly used as feed enzymes. These enzymes are used exogenously in the feeds of monogastric animals thereby it improves the digestibility of phosphorous and thus reduces the negative impact of inorganic P excretion on the environment. Even though these enzymes are widely distributed in many life forms, microorganisms are the most preferred and potential source of phytase. Despite the extensive availability of the phytase-producing microbial consortia, only a few microorganisms have been known to be exploited at industrial level. The high costs of the enzyme along with the incapability to survive high temperatures followed by the poor storage stability are noted to be the bottleneck in the commercialization of enzymes. For this reason, besides the conventional fermentation approaches, the applicability of cloning, expression studies and genetic engineering has been implemented for the past few years to accomplish the abovesaid benefits. The site-directed mutagenesis as well as knocking out have also validated their prominent role in microbe-based phytase production with enhanced levels. The present review provides detailed information on recent insights on the modification of phytases through heterologous expression and protein engineering to make thermostable and protease-resistant phytases.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - A N Anoopkumar
- Centre for Research in Emerging Tropical Diseases, Department of Zoology, University of Calicut, Kerala, India
| | - Ayon Tarafdar
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243 122, Uttar Pradesh, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, Kerala, India
| | - Mohan Binoop
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, Kerala, India
| | - Nair M Lakshmi
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, Kerala, India
| | - Arun K B
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, Kerala, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, Kerala, India; Department of Food Technology, T K M Institute of Technology, Kollam, 691 505, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, Kerala, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, Uttarakhand, India; Centre for Energy and Environmental Sustainability, Lucknow, 226029, Uttar Pradesh, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Navone L, Moffitt K, Johnston WA, Mercer T, Cooper C, Spann K, Speight RE. Bioengineered textiles with peptide binders that capture SARS-CoV-2 viral particles. COMMUNICATIONS MATERIALS 2022; 3:54. [PMID: 35991518 PMCID: PMC9376897 DOI: 10.1038/s43246-022-00278-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/01/2022] [Indexed: 05/28/2023]
Abstract
The use of personal protective equipment (PPE), face masks and ventilation are key strategies to control the transmission of respiratory viruses. However, most PPE provides physical protection that only partially prevents the transmission of viral particles. Here, we develop textiles with integrated peptide binders that capture viral particles. We fuse peptides capable of binding the receptor domain of the spike protein on the SARS-CoV-2 capsid to the cellulose-binding domain from the Trichoderma reesei cellobiohydrolase II protein. The hybrid peptides can be attached to the cellulose fibres in cotton and capture SARS-CoV-2 viral particles with high affinity. The resulting bioengineered cotton captures 114,000 infective virus particles per cm2 and reduces onwards SARS-CoV-2 infection of cells by 500-fold. The hybrid peptides could be easily modified to capture and control the spread of other infectious pathogens or for attachment to different materials. We anticipate the use of bioengineered protective textiles in PPE, facemasks, ventilation, and furnishings will provide additional protection to the airborne or fomite transmission of viruses.
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Affiliation(s)
- Laura Navone
- School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
| | - Kaylee Moffitt
- School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
| | - Wayne A. Johnston
- School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
| | - Tim Mercer
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland (UQ), Brisbane, QLD 4072 Australia
- Garvan Institute of Medical Research, Sydney, NSW 2010 Australia
| | - Crystal Cooper
- Central Analytical Research Facility (CARF), Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
| | - Kirsten Spann
- Centre for Immunology and Infection Control, School of Biomedical Science, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
| | - Robert E. Speight
- School of Biology and Environmental Sciences, Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, QLD 4000 Australia
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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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Speight RE, Navone L, Gebbie LK, Blinco JAL, Bryden WL. Platforms to accelerate biomanufacturing of enzyme and probiotic animal feed supplements: discovery considerations and manufacturing implications. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Xu Y, Liu K, Han Y, Xing Y, Zhang Y, Yang Q, Zhou M. Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris. Microb Cell Fact 2021; 20:91. [PMID: 33902585 PMCID: PMC8077831 DOI: 10.1186/s12934-021-01580-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background Protein synthesis is one of the extremely important anabolic pathways in the yeast expression system Pichia pastoris. Codon optimization is a commonly adopted strategy for improved protein expression, although unexpected failures did appear sometimes waiting for further exploration. Recently codon bias has been studied to regulate protein folding and activity in many other organisms. Results Here the codon bias profile of P. pastoris genome was examined first and a direct correlation between codon translation efficiency and usage frequency was identified. By manipulating the codon choices of both endogenous and heterologous signal peptides, secretion abilities of N-terminal signal peptides were shown to be tolerant towards codon changes. Then two gene candidates with different levels of structural disorder were studied, and full-length codon optimization was found to affect their expression profiles differentially. Finally, more evidences were provided to support possible protein conformation change brought by codon optimization in structurally disordered proteins. Conclusion Our results suggest that codon bias regulates gene expression by modulating several factors including transcription and translation efficiency, protein folding and activity. Because of sequences difference, the extent of affection may be gene specific. For some genes, special codon optimization strategy should be adopted to ensure appropriate expression and conformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01580-9.
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Affiliation(s)
- Yichun Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yanzi Xing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qiuying Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, 430062, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Navone L, Vogl T, Luangthongkam P, Blinco JA, Luna-Flores CH, Chen X, von Hellens J, Mahler S, Speight R. Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:80. [PMID: 33789740 PMCID: PMC8010977 DOI: 10.1186/s13068-021-01936-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/20/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market. RESULTS In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in kcat and KM for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme. CONCLUSIONS Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.
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Affiliation(s)
- Laura Navone
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Jo-Anne Blinco
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Carlos H Luna-Flores
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- Bioproton Pty Ltd, Brisbane, QLD, Australia
| | | | | | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Robert Speight
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
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