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Cumming A, Khananisho D, Balka M, Liljestrand N, Daley DO. Biosensor that Detects Stress Caused by Periplasmic Proteins. ACS Synth Biol 2024; 13:1477-1491. [PMID: 38676700 PMCID: PMC11106774 DOI: 10.1021/acssynbio.3c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Escherichia coli is often used as a factory to produce recombinant proteins. In many cases, the recombinant protein needs disulfide bonds to fold and function correctly. These proteins are genetically fused to a signal peptide so that they are secreted to the oxidizing environment of the periplasm (where the enzymes required for disulfide bond formation exist). Currently, it is difficult to determine in vivo whether a recombinant protein is efficiently secreted from the cytoplasm and folded in the periplasm or if there is a bottleneck in one of these steps because cellular capacity has been exceeded. To address this problem, we have developed a biosensor that detects cellular stress caused by (1) inefficient secretion of proteins from the cytoplasm and (2) aggregation of proteins in the periplasm. We demonstrate how the fluorescence fingerprint obtained from the biosensor can be used to identify induction conditions that do not exceed the capacity of the cell and therefore do not cause cellular stress. These induction conditions result in more effective biomass and in some cases higher titers of soluble recombinant proteins.
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Affiliation(s)
- Alister
J. Cumming
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Mateusz Balka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Nicklas Liljestrand
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Daniel O. Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
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2
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Sharma N, Patel SN, Rai AK, Singh SP. Biochemical characterization of a novel acid-active endopolygalacturonase for pectin depolymerization, pectic-oligomer production, and fruit juice clarification. Int J Biol Macromol 2024; 267:131565. [PMID: 38614184 DOI: 10.1016/j.ijbiomac.2024.131565] [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: 01/03/2024] [Revised: 03/18/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Endopolygalacturonases are crucial pectinases known for their efficient and sustainable pectin depolymerization activities. The present study identified a novel gene encoding endopolygalacturonase from an acidic mine tailing metagenome. The putative gene showed a maximum identity of 67.55 % with an uncharacterized peptide sequence from Flavobacterium fluvii. The gene was cloned and expressed in a heterologous host, E. coli. Biochemical characterization of the novel endopolygalacturonase enzyme variant (EPHM) showed maximum activity at 60 °C and at 5.0 pH, while retaining 50 % activity under the temperature and pH range of 20 °C to 70 °C for 6 h, and 3.0 to 10.0 for 3 h, respectively. The enzyme exhibited tolerance to different metal ions. EPHM was characterized for the depolymerization of methylated pectin into pectic oligosaccharides. Further, its utility was established for fruit juice clarification, as endorsed by high transmittance, significant viscosity reduction, and release of reducing sugars in the treated fruit juice samples.
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Affiliation(s)
- Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India
| | - Satya N Patel
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India
| | - Amit Kumar Rai
- National Agri-Food Biotechnology Institute, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), SAS Nagar, Sector 81, Mohali, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Biotechnology Research and Innovation Council (Department of Biotechnology, Government of India), NABI, SAS Nagar, Sector 81, Mohali, India.
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3
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Sarasa-Buisan C, Ochoa de Alda JAG, Velázquez-Suárez C, Rubio MÁ, Gómez-Baena G, Fillat MF, Luque I. An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome. PLoS Biol 2024; 22:e3002546. [PMID: 38466754 PMCID: PMC10957091 DOI: 10.1371/journal.pbio.3002546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/21/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Bacteria have developed fine-tuned responses to cope with potential zinc limitation. The Zur protein is a key player in coordinating this response in most species. Comparative proteomics conducted on the cyanobacterium Anabaena highlighted the more abundant proteins in a zur mutant compared to the wild type. Experimental evidence showed that the exoprotein ZepA mediates zinc uptake. Genomic context of the zepA gene and protein structure prediction provided additional insights on the regulation and putative function of ZepA homologs. Phylogenetic analysis suggests that ZepA represents a primordial system for zinc acquisition that has been conserved for billions of years in a handful of species from distant bacterial lineages. Furthermore, these results show that Zur may have been one of the first regulators of the FUR family to evolve, consistent with the scarcity of zinc in the ecosystems of the Archean eon.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús A. G. Ochoa de Alda
- Didáctica de las Ciencias Experimentales y la Matemáticas, Universidad de Extremadura, Cáceres, Spain
| | | | - Miguel Ángel Rubio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular e Instituto de Biocomputación y Física de Sistemas Complejos (Bifi), Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Seville, Spain
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Osgerby A, Overton TW. Approaches for high-throughput quantification of periplasmic recombinant proteins. N Biotechnol 2023; 77:149-160. [PMID: 37708933 DOI: 10.1016/j.nbt.2023.09.003] [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: 05/03/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The Gram-negative periplasm is a convenient location for the accumulation of many recombinant proteins including biopharmaceutical products. It is the site of disulphide bond formation, required by some proteins (such as antibody fragments) for correct folding and function. It also permits simpler protein release and downstream processing than cytoplasmic accumulation. As such, targeting of recombinant proteins to the E. coli periplasm is a key strategy in biologic manufacture. However, expression and translocation of each recombinant protein requires optimisation including selection of the best signal peptide and growth and production conditions. Traditional methods require separation and analysis of protein compositions of periplasmic and cytoplasmic fractions, a time- and labour-intensive method that is difficult to parallelise. Therefore, approaches for high throughput quantification of periplasmic protein accumulation offer advantages in rapid process development.
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Affiliation(s)
- Alexander Osgerby
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering and Institute of Microbiology and Infection, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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5
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Pouresmaeil M, Azizi-Dargahlou S. Factors involved in heterologous expression of proteins in E. coli host. Arch Microbiol 2023; 205:212. [PMID: 37120438 PMCID: PMC10148705 DOI: 10.1007/s00203-023-03541-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
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Affiliation(s)
- Mahin Pouresmaeil
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran.
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6
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Renaud S, Dussutour A, Daboussi F, Pompon D. Characterization of chitinases from the GH18 gene family in the myxomycete Physarum polycephalum. Biochim Biophys Acta Gen Subj 2023; 1867:130343. [PMID: 36933625 DOI: 10.1016/j.bbagen.2023.130343] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Physarum polycephalum is an unusual macroscopic myxomycete expressing a large range of glycosyl hydrolases. Among them, enzymes from the GH18 family can hydrolyze chitin, an important structural component of the cell walls in fungi and in the exoskeleton of insects and crustaceans. METHODS Low stringency sequence signature search in transcriptomes was used to identify GH18 sequences related to chitinases. Identified sequences were expressed in E. coli and corresponding structures modelled. Synthetic substrates and in some cases colloidal chitin were used to characterize activities. RESULTS Catalytically functional hits were sorted and their predicted structures compared. All share the TIM barrel structure of the GH18 chitinase catalytic domain, optionally fused to binding motifs, such as CBM50, CBM18, and CBM14, involved in sugar recognition. Assessment of the enzymatic activities following deletion of the C-terminal CBM14 domain of the most active clone evidenced a significant contribution of this extension to the chitinase activity. A classification based on module organization, functional and structural criteria of characterized enzymes was proposed. CONCLUSIONS Physarum polycephalum sequences encompassing a chitinase like GH18 signature share a modular structure involving a structurally conserved catalytic TIM barrels decorated or not by a chitin insertion domain and optionally surrounded by additional sugar binding domains. One of them plays a clear role in enhancing activities toward natural chitin. GENERAL SIGNIFICANCE Myxomycete enzymes are currently poorly characterized and constitute a potential source for new catalysts. Among them glycosyl hydrolases have a strong potential for valorization of industrial waste as well as in therapeutic field.
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Affiliation(s)
| | - Audrey Dussutour
- Centre de Recherche en Cognition Animale, UMR 5169 CNRS, Université Toulouse III, Toulouse, France
| | | | - Denis Pompon
- Toulouse Biotechnology Institute, UMR CNRS / INRAE / INSA, Université de Toulouse, Toulouse, France.
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7
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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8
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Yaghoobizadeh F, Ardakani MR, Ranjbar MM, Galehdari H, Khosravi M. Expression, purification, and study on the efficiency of a new potent recombinant scFv antibody against the SARS-CoV-2 spike RBD in E. coli BL21. Protein Expr Purif 2023; 203:106210. [PMID: 36473692 PMCID: PMC9719605 DOI: 10.1016/j.pep.2022.106210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022]
Abstract
Many efforts have been made around the world to combat SARS-CoV-2. Among these are recombinant antibodies considered to be suitable as an alternative for some diagnostics/therapeutics. Based on their importance, this study aimed to investigate the expression, purification, and efficiency of a new potent recombinant scFv in the E. coli BL21 (DE3) system. The expression studies were performed after confirming the scFv cloning into the pET28a vector using specific PCRs. After comprehensive expression studies, a suitable strategy was adopted to extract and purify periplasmic proteins using Ni2+-NTA resin. Besides the purified scFv, the crude bacterial lysate was also used to develop a sandwich ELISA (S-ELISA) for the detection of SARS-CoV-2. The use of PCR, E. coli expression system, western blotting (WB), and S-ELISA confirmed the functionality of this potent scFv. Moreover, the crude bacterial lysate also showed good potential for detecting SARS-CoV-2. This could be decreasing the costs and ease its utilization for large-scale applications. The production of high-quality recombinant proteins is essential for humankind. Moreover, with attention to the more aggressive nature of SARS-CoV-2 than other coronaviruses, the development of an effective detection method is urgent. Based on our knowledge, this study is one of the limited investigations in two fields: (1) The production of anti-SARS-CoV-2 scFv using E. coli [as a cheap heterologous host] in relatively high amounts and with good stability, and (2) Designing a sensitive S-ELISA for its detection. It may also be utilized as potent therapeutics after further investigations.
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Affiliation(s)
| | | | | | - Hamid Galehdari
- Department of Biology, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Mohammad Khosravi
- Department of Pathobiology, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
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9
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Ni W, Wang Z, Zheng A, Zhao Y. Preparation and self-cleavage of fusion soluble farnesyl diphosphate synthase in E. coli. Prep Biochem Biotechnol 2023; 53:988-994. [PMID: 36639146 DOI: 10.1080/10826068.2022.2164591] [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: 01/15/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is a crucial protein in terpenoid production. However, its industrial application is limited owing to its low solubility in Escherichia coli. In this study, we focused on ispA encoding FPPS and designed a fusion expression system to reduce inclusion body (IB) formation. Among the chosen fusion tags, the GB1-domain (GB1) exhibited the highest ability to solubilize the recombinant protein. Increased rare tRNA abundance not only improved the GB1-FPPS yield but also increased its soluble level. A "one-step" method for the acquisition of soluble FPPS was also considered. By combining GB1-FPPS expression and Tobacco Etch Virus protease (TEVp) cleavage in vivo, a controllable GB1-FPPS "self-cleavage" system was constructed. Overall, this study provides an efficient approach for obtaining soluble forms of FPPS, which show great potential for use in the soluble expression of other homologous diphosphate synthase.
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Affiliation(s)
- Wenfeng Ni
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Zixuan Wang
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Aifang Zheng
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Ying Zhao
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
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10
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Loughran ST, Bree RT, Walls D. Poly-Histidine-Tagged Protein Purification Using Immobilized Metal Affinity Chromatography (IMAC). Methods Mol Biol 2023; 2699:193-223. [PMID: 37647000 DOI: 10.1007/978-1-0716-3362-5_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: 09/01/2023]
Abstract
His-tagging is the most widespread and versatile strategy used to purify recombinant proteins for biochemical and structural studies. Recombinant DNA methods are first used to engineer the addition of a short tract of poly-histidine tag (His-tag) to the N-terminus or C-terminus of a target protein. The His-tag is then exploited to enable purification of the "tagged" protein by immobilized metal affinity chromatography (IMAC). In this chapter, we describe efficient procedures for the isolation of highly purified His-tagged target proteins from an Escherichia coli host using IMAC in a bind-wash-elute strategy that can be performed under both native and denaturing conditions.
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Affiliation(s)
- Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland.
| | - Ronan T Bree
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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11
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Rettenbacher LA, von der Haar T. A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microb Cell Fact 2022; 21:268. [PMID: 36550495 PMCID: PMC9773447 DOI: 10.1186/s12934-022-01982-3] [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: 10/24/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Escherichia coli is of central interest to biotechnological research and a widely used organism for producing proteins at both lab and industrial scales. However, many proteins remain difficult to produce efficiently in E. coli. This is particularly true for proteins that require post translational modifications such as disulfide bonds. RESULTS In this study we develop a novel approach for quantitatively investigating the ability of E. coli to produce disulfide bonds in its own proteome. We summarise the existing knowledge of the E. coli disulfide proteome and use this information to investigate the demand on this organism's quantitative oxidative folding apparatus under different growth conditions. Furthermore, we built an ordinary differential equation-based model describing the cells oxidative folding capabilities. We use the model to infer the kinetic parameters required by the cell to achieve the observed oxidative folding requirements. We find that the cellular requirement for disulfide bonded proteins changes significantly between growth conditions. Fast growing cells require most of their oxidative folding capabilities to keep up their proteome while cells growing in chemostats appear limited by their disulfide bond isomerisation capacities. CONCLUSION This study establishes a novel approach for investigating the oxidative folding capacities of an organism. We show the capabilities and limitations of E. coli for producing disulfide bonds under different growth conditions and predict under what conditions excess capability is available for recombinant protein production.
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Affiliation(s)
- Lukas A. Rettenbacher
- grid.9759.20000 0001 2232 2818Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, UK
| | - Tobias von der Haar
- grid.9759.20000 0001 2232 2818Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, UK
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12
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Tang D, Gunson J, Tran E, Lam C, Shen A, Snedecor B, Barnard G, Misaghi S. Expressing antigen binding fragments with high titers in a targeted integration CHO host by optimizing expression vector gene copy numbers and position: A case study. Biotechnol Prog 2022; 38:e3290. [PMID: 36537257 DOI: 10.1002/btpr.3290] [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: 05/16/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022]
Abstract
Antigen binding fragments (Fab) are a promising class of therapeutics as they maintain high potency while having significantly smaller size relative to full-length antibodies. Because Fab molecules are aglycosylated, many expression platforms, including prokaryotic, yeast, and mammalian cells, have been developed for their expression, with Escherichia coli being the most commonly used Fab expression system. In this study, we have examined production of a difficult to express Fab molecule in a targeted integration (TI) Chinese Hamster Ovary (CHO) host. Without a need for extensive host or process optimization, as is usually required for E. coli, by simply using different vector configurations, clones with very high Fab expression titers were obtained. In this case, by increasing heavy chain (HC) gene copy numbers, clones with titers of up to 7.4 g/L in the standard fed-batch production culture were obtained. Our findings suggest that having a predetermined transgene integration site, as well as the option to optimize gene copy number/dosage, makes CHO TI hosts an effective system for expression of Fab molecules, allowing Fab expression using platform process and without significant process development efforts.
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Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA.,Protein Sciences, Proteologix US Inc., Redwood Shores, California, USA
| | - Jane Gunson
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Eric Tran
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Amy Shen
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Gavin Barnard
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, California, USA
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13
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Microbial protein cell factories fight back? Trends Biotechnol 2021; 40:576-590. [PMID: 34924209 DOI: 10.1016/j.tibtech.2021.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 01/26/2023]
Abstract
The biopharmaceutical market is growing faster than ever, with two production systems competing for market dominance: mammalian cells and microorganisms. In recent years, based on the rise of antibody-based therapies, new biotherapeutic approvals have favored mammalian hosts. However, not only has extensive research elevated our understanding of microbes to new levels, but emerging therapeutic molecules also facilitate their use; thus, is it time for microbes to fight back? In this review, we answer this timely question by cross-comparing four microbial production hosts and examining the innovations made to both their secretion and post-translational modification (PTM) capabilities. Furthermore, we discuss the impact of tools, such as omics and systems biology, as well as alternative production systems and emerging biotherapeutics.
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14
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Karyolaimos A, de Gier JW. Strategies to Enhance Periplasmic Recombinant Protein Production Yields in Escherichia coli. Front Bioeng Biotechnol 2021; 9:797334. [PMID: 34970535 PMCID: PMC8712718 DOI: 10.3389/fbioe.2021.797334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
Main reasons to produce recombinant proteins in the periplasm of E. coli rather than in its cytoplasm are to -i- enable disulfide bond formation, -ii- facilitate protein isolation, -iii- control the nature of the N-terminus of the mature protein, and -iv- minimize exposure to cytoplasmic proteases. However, hampered protein targeting, translocation and folding as well as protein instability can all negatively affect periplasmic protein production yields. Strategies to enhance periplasmic protein production yields have focused on harmonizing secretory recombinant protein production rates with the capacity of the secretory apparatus by transcriptional and translational tuning, signal peptide selection and engineering, increasing the targeting, translocation and periplasmic folding capacity of the production host, preventing proteolysis, and, finally, the natural and engineered adaptation of the production host to periplasmic protein production. Here, we discuss these strategies using notable examples as a thread.
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Affiliation(s)
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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15
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Zalai D, Kopp J, Kozma B, Küchler M, Herwig C, Kager J. Microbial technologies for biotherapeutics production: Key tools for advanced biopharmaceutical process development and control. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 38:9-24. [PMID: 34895644 DOI: 10.1016/j.ddtec.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022]
Abstract
Current trends in the biopharmaceutical market such as the diversification of therapies as well as the increasing time-to-market pressure will trigger the rethinking of bioprocess development and production approaches. Thereby, the importance of development time and manufacturing costs will increase, especially for microbial production. In the present review, we investigate three technological approaches which, to our opinion, will play a key role in the future of biopharmaceutical production. The first cornerstone of process development is the generation and effective utilization of platform knowledge. Building processes on well understood microbial and technological platforms allows to accelerate early-stage bioprocess development and to better condense this knowledge into multi-purpose technologies and applicable mathematical models. Second, the application of verified scale down systems and in silico models for process design and characterization will reduce the required number of large scale batches before dossier submission. Third, the broader availability of mathematical process models and the improvement of process analytical technologies will increase the applicability and acceptance of advanced control and process automation in the manufacturing scale. This will reduce process failure rates and subsequently cost of goods. Along these three aspects we give an overview of recently developed key tools and their potential integration into bioprocess development strategies.
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Affiliation(s)
- Denes Zalai
- Richter-Helm BioLogics GmbH & Co. KG, Suhrenkamp 59, 22335 Hamburg, Germany.
| | - Julian Kopp
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Bence Kozma
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Michael Küchler
- Richter-Helm BioLogics GmbH & Co. KG, Suhrenkamp 59, 22335 Hamburg, Germany
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria; Competence Center CHASE GmbH, Altenbergerstraße 69, 4040 Linz, Austria
| | - Julian Kager
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
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16
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Kavousipour S, Mohammadi S, Eftekhar E, Barazesh M, Morowvat MH. In Silico Investigation of Signal Peptide Sequences to Enhance Secretion of CD44 Nanobodies Expressed in Escherichia coli. Curr Pharm Biotechnol 2021; 22:1192-1205. [PMID: 33045964 DOI: 10.2174/1389201021666201012162904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/01/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The selection of a suitable signal peptide that can direct recombinant proteins from the cytoplasm to the extracellular space is an important criterion affecting the production of recombinant proteins in Escherichia coli, a widely used host. Nanobodies are currently attracting the attention of scientists as antibody alternatives due to their specific properties and feasibility of production in E. coli. OBJECTIVE CD44 nanobodies constitute a potent therapeutic agent that can block CD44/HA interaction in cancer and inflammatory diseases. This molecule may also function as a drug against cancer cells and has been produced previously in E. coli without a signal peptide sequence. The goal of this project was to find a suitable signal peptide to direct CD44 nanobody extracellular secretion in E. coli that will potentially lead to optimization of experimental methods and facilitate downstream steps such as purification. METHODS We analyzed 40 E. coli derived signal peptides retrieved from the Signal Peptide database and selected the best candidate signal peptides according to relevant criteria including signal peptide probability, stability, and physicochemical features, which were evaluated using signalP software version 4.1 and the ProtParam tool, respectively. RESULTS In this in silico study, suitable candidate signal peptide(s) for CD44 nanobody secretory expression were identified. CSGA, TRBC, YTFQ, NIKA, and DGAL were selected as appropriate signal peptides with acceptable D-scores, and appropriate physicochemical and structural properties. Following further analysis, TRBC was selected as the best signal peptide to direct CD44 nanobody expression to the extracellular space of E. coli. CONCLUSION The selected signal peptide, TRBC is the most suitable to promote high-level secretory production of CD44 nanobodies in E. coli and potentially will be useful for scaling up CD44 nanobody production in experimental research as well as in other CD44 nanobody applications. However, experimental work is needed to confirm the data.
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Affiliation(s)
- Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Shiva Mohammadi
- Department of Biotechnology, School of Advanced Medical Science and Technologies, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahdi Barazesh
- School of Paramedical, Gerash University of Medical Sciences, Gerash, Iran
| | - Mohammad H Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran P.O. Box 71468-64685, Shiraz, Iran
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17
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Harkness RW, Toyama Y, Ripstein ZA, Zhao H, Sever AIM, Luan Q, Brady JP, Clark PL, Schuck P, Kay LE. Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP. Proc Natl Acad Sci U S A 2021. [PMID: 34362850 DOI: proc/self/fd/32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.
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Affiliation(s)
- Robert W Harkness
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Yuki Toyama
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Zev A Ripstein
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Huaying Zhao
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
| | - Alexander I M Sever
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Qing Luan
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jacob P Brady
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Patricia L Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Peter Schuck
- National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
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18
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Competing stress-dependent oligomerization pathways regulate self-assembly of the periplasmic protease-chaperone DegP. Proc Natl Acad Sci U S A 2021; 118:2109732118. [PMID: 34362850 DOI: 10.1073/pnas.2109732118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DegP is an oligomeric protein with dual protease and chaperone activity that regulates protein homeostasis and virulence factor trafficking in the periplasm of gram-negative bacteria. A number of oligomeric architectures adopted by DegP are thought to facilitate its function. For example, DegP can form a "resting" hexamer when not engaged to substrates, mitigating undesired proteolysis of cellular proteins. When bound to substrate proteins or lipid membranes, DegP has been shown to populate a variety of cage- or bowl-like oligomeric states that have increased proteolytic activity. Though a number of DegP's substrate-engaged structures have been robustly characterized, detailed mechanistic information underpinning its remarkable oligomeric plasticity and the corresponding interplay between these dynamics and biological function has remained elusive. Here, we have used a combination of hydrodynamics and NMR spectroscopy methodologies in combination with cryogenic electron microscopy to shed light on the apo-DegP self-assembly mechanism. We find that, in the absence of bound substrates, DegP populates an ensemble of oligomeric states, mediated by self-assembly of trimers, that are distinct from those observed in the presence of substrate. The oligomeric distribution is sensitive to solution ionic strength and temperature and is shifted toward larger oligomeric assemblies under physiological conditions. Substrate proteins may guide DegP toward canonical cage-like structures by binding to these preorganized oligomers, leading to changes in conformation. The properties of DegP self-assembly identified here suggest that apo-DegP can rapidly shift its oligomeric distribution in order to respond to a variety of biological insults.
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19
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Lv L, Lin J, Feng Y, Wang W, Li S. Coated recombinant Escherichia coli for delayed release of β-mannanase in the water-based fracturing fluid. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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A scalable and reproducible preparation for the antitumor protein TLC, a human-derived telomerase inhibitor. Protein Expr Purif 2021; 187:105942. [PMID: 34284069 DOI: 10.1016/j.pep.2021.105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/13/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022]
Abstract
Telomerase, which is overexpressed in approximately 90% of liver cancer cells, is an ideal target for anti-liver cancer therapy. LPTS, a putative liver tumor suppressor, is the only human-derived protein that can bind telomerase directly and inhibit the extension of telomere activity. Our previous studies demonstrated that TAT-LPTS-LC (TLC), a recombinant protein fused by the C-terminal 133-328 fragment of LPTS and TAT peptides, could be delivered into cells to inhibit telomerase-positive hepatoma cell growth in vitro and in vivo with very low toxicity. In the present study, E. coli strains which expressed TLC in abundance were screened and cultured in a laboratory bioreactor. A reproducible protein separation process was built, and this process was suitable for industrial amplification. The yields of TLC protein were up to 184 mg in one batch with a purity of approximately 95%. The purified TLC protein had a similar inhibitory effect on telomerase activity in vitro compared with those purified by Ni-affinity chromatography. Furthermore, TLC protein could be delivered into the cell nucleus to increase the doubling time of the cell and suppress cell growth in telomerase-positive liver cancer cell lines. Cell growth inhibition was negatively correlated with telomere length, suggesting that TLC is a highly targeted telomerase-telomere anticancer agent. These results will contribute to future preclinical studies of the TLC protein.
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21
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Kastenhofer J, Rajamanickam V, Libiseller-Egger J, Spadiut O. Monitoring and control of E. coli cell integrity. J Biotechnol 2021; 329:1-12. [PMID: 33485861 DOI: 10.1016/j.jbiotec.2021.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/15/2022]
Abstract
Soluble expression of recombinant proteins in E. coli is often done by translocation of the product across the inner membrane (IM) into the periplasm, where it is retained by the outer membrane (OM). While the integrity of the IM is strongly coupled to viability and impurity release, a decrease in OM integrity (corresponding to increased "leakiness") leads to accumulation of product in the extracellular space, strongly impacting the downstream process. Whether leakiness is desired or not, differential monitoring and control of IM and OM integrity are necessary for an efficient E. coli bioprocess in compliance with the guidelines of Quality by Design and Process Analytical Technology. In this review, we give an overview of relevant monitoring tools, summarize the research on factors affecting E. coli membrane integrity and provide a brief discussion on how the available monitoring technology can be implemented in real-time control of E. coli cultivations.
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Affiliation(s)
- Jens Kastenhofer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Vignesh Rajamanickam
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Julian Libiseller-Egger
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
| | - Oliver Spadiut
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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22
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Ling WL, Su CTT, Lua WH, Poh JJ, Ng YL, Wipat A, Gan SKE. Essentially Leading Antibody Production: An Investigation of Amino Acids, Myeloma, and Natural V-Region Signal Peptides in Producing Pertuzumab and Trastuzumab Variants. Front Immunol 2020; 11:604318. [PMID: 33365032 PMCID: PMC7750424 DOI: 10.3389/fimmu.2020.604318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022] Open
Abstract
Boosting the production of recombinant therapeutic antibodies is crucial in both academic and industry settings. In this work, we investigated the usage of varying signal peptides by antibody V-genes and their roles in recombinant transient production, systematically comparing myeloma and the native signal peptides of both heavy and light chains in 168 antibody permutation variants. We found that amino acids count and types (essential or non-essential) were important factors in a logistic regression equation model for predicting transient co-transfection protein production rates. Deeper analysis revealed that the culture media were often incomplete and that the supplementation of essential amino acids can improve the recombinant protein yield. While these findings are derived from transient HEK293 expression, they also provide insights to the usage of the large repertoire of antibody signal peptides, where by varying the number of specific amino acids in the signal peptides attached to the variable regions, bottlenecks in amino acid availability can be mitigated.
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Affiliation(s)
- Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Newcastle Research and Innovation Institute (NewRIIS), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuen-Ling Ng
- Newcastle Research and Innovation Institute (NewRIIS), Singapore, Singapore
| | - Anil Wipat
- School of Computing, Newcastle University, Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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23
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Kopp J, Kittler S, Slouka C, Herwig C, Spadiut O, Wurm DJ. Repetitive Fed-Batch: A Promising Process Mode for Biomanufacturing With E. coli. Front Bioeng Biotechnol 2020; 8:573607. [PMID: 33240864 PMCID: PMC7683717 DOI: 10.3389/fbioe.2020.573607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production with Escherichia coli is usually carried out in fed-batch mode in industry. As set-up and cleaning of equipment are time- and cost-intensive, it would be economically and environmentally favorable to reduce the number of these procedures. Switching from fed-batch to continuous biomanufacturing with microbials is not yet applied as these cultivations still suffer from time-dependent variations in productivity. Repetitive fed-batch process technology facilitates critical equipment usage, reduces the environmental fingerprint and potentially increases the overall space-time yield. Surprisingly, studies on repetitive fed-batch processes for recombinant protein production can be found for yeasts only. Knowledge on repetitive fed-batch cultivation technology for recombinant protein production in E. coli is not available until now. In this study, a mixed feed approach, enabling repetitive fed-batch technology for recombinant protein production in E. coli, was developed. Effects of the cultivation mode on the space-time yield for a single-cycle fed-batch, a two-cycle repetitive fed-batch, a three-cycle repetitive fed batch and a chemostat cultivation were investigated. For that purpose, we used two different E. coli strains, expressing a model protein in the cytoplasm or in the periplasm, respectively. Our results demonstrate that a repetitive fed-batch for E. coli leads to a higher space-time yield compared to a single-cycle fed-batch and can potentially outperform continuous biomanufacturing. For the first time, we were able to show that repetitive fed-batch technology is highly suitable for recombinant protein production in E. coli using our mixed feeding approach, as it potentially (i) improves product throughput by using critical equipment to its full capacity and (ii) allows implementation of a more economic process by reducing cleaning and set-up times.
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Affiliation(s)
| | | | | | | | | | - David J. Wurm
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
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24
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Lénon M, Ke N, Szady C, Sakhtah H, Ren G, Manta B, Causey B, Berkmen M. Improved production of Humira antibody in the genetically engineered Escherichia coli SHuffle, by co-expression of human PDI-GPx7 fusions. Appl Microbiol Biotechnol 2020; 104:9693-9706. [PMID: 32997203 PMCID: PMC7595990 DOI: 10.1007/s00253-020-10920-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
Abstract Microbial production of antibodies offers the promise of cheap, fast, and efficient production of antibodies at an industrial scale. Limiting this capacity in prokaryotes is the absence of the post-translational machinery, present in dedicated antibody producing eukaryotic cell lines, such as B cells. There has been few and limited success in producing full-length, correctly folded, and assembled IgG in the cytoplasm of prokaryotic cell lines. One such success was achieved by utilizing the genetically engineered Escherichia coli strain SHuffle with an oxidative cytoplasm. Due to the genetic disruption of reductive pathways, SHuffle cells are under constant oxidative stress, including increased levels of hydrogen peroxide (H2O2). The oxidizing capacity of H2O2 was linked to improved disulfide bond formation, by expressing a fusion of two endoplasmic reticulum-resident proteins, the thiol peroxidase GPx7 and the protein disulfide isomerase, PDI. In concert, these proteins mediate disulfide transfer from H2O2 to target proteins via PDI-Gpx7 fusions. The potential of this new strain was tested with Humira, a blockbuster antibody usually produced in eukaryotic cells. Expression results demonstrate that the new engineered SHuffle strain (SHuffle2) could produce Humira IgG four-fold better than the parental strain, both in shake-flask and in high-density fermentation. These preliminary studies guide the field in genetically engineering eukaryotic redox pathways in prokaryotes for the production of complex macromolecules. Key points • A eukaryotic redox pathway was engineered into the E. coli strain SHuffle in order to improve the yield of the blockbuster antibody Humira. • The best peroxidase-PDI fusion was selected using bioinformatics and in vivo studies. • Improved yields of Humira were demonstrated at shake-flask and high-density fermenters. Electronic supplementary material The online version of this article (10.1007/s00253-020-10920-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marine Lénon
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, UMR CNRS 2001, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Na Ke
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Cecily Szady
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Hassan Sakhtah
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
- Boston Institute of Biotechnology, LLC., Upstream Process Development, 225 Turnpike Road, Southborough, MA, 01772, USA
| | - Guoping Ren
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Bruno Manta
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
- Facultad de Medicina, Departamento de Bioquímica and Centro de Investigaciones Biomédicas, Universidad de la República, CP 11800, Montevideo, Uruguay
| | - Bryce Causey
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Mehmet Berkmen
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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26
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Sandomenico A, Sivaccumar JP, Ruvo M. Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments. Int J Mol Sci 2020; 21:ijms21176324. [PMID: 32878291 PMCID: PMC7504322 DOI: 10.3390/ijms21176324] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. While full-length antibodies require mammalian expression systems due to the occurrence of functionally and structurally important glycosylations, most antibody fragments and antibody-like molecules are non-glycosylated and can be more conveniently prepared in E. coli-based expression platforms. We propose here an updated survey of the most effective and appropriate methods of preparation of antibody fragments that exploit E. coli as an expression background and review the pros and cons of the different platforms available today. Around 250 references accompany and complete the review together with some lists of the most important new antibody-like molecules that are on the market or are being developed as new biotherapeutics or diagnostic agents.
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27
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Zhu J, Ruan Y, Fu X, Zhang L, Ge G, Wall JG, Zou T, Zheng Y, Ding N, Hu X. An Engineered Pathway for Production of Terminally Sialylated N-glycoproteins in the Periplasm of Escherichia coli. Front Bioeng Biotechnol 2020; 8:313. [PMID: 32351949 PMCID: PMC7174548 DOI: 10.3389/fbioe.2020.00313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/23/2020] [Indexed: 12/16/2022] Open
Abstract
Terminally sialylated N-glycoproteins are of great interest in therapeutic applications. Due to the inability of prokaryotes to carry out this post-translational modification, they are currently predominantly produced in eukaryotic host cells. In this study, we report a synthetic pathway to produce a terminally sialylated N-glycoprotein in the periplasm of Escherichia coli, mimicking the sialylated moiety (Neu5Ac-α-2,6-Gal-β-1,4-GlcNAc-) of human glycans. A sialylated pentasaccharide, Neu5Ac-α-2,6-Gal-β-1,4-GlcNAc-β-1,3-Gal-β-1,3-GlcNAc-, was synthesized through the activity of co-expressed glycosyltransferases LsgCDEF from Haemophilus influenzae, Campylobacter jejuni NeuBCA enzymes, and Photobacterium leiognathi α-2,6-sialyltransferase in an engineered E. coli strain which produces CMP-Neu5Ac. C. jejuni oligosaccharyltransferase PglB was used to transfer the terminally sialylated glycan onto a glyco-recognition sequence in the tenth type III cell adhesion module of human fibronectin. Sialylation of the target protein was confirmed by lectin blotting and mass spectrometry. This proof-of-concept study demonstrates the successful production of terminally sialylated, homogeneous N-glycoproteins with α-2,6-linkages in the periplasm of E. coli and will facilitate the construction of E. coli strains capable of producing terminally sialylated N-glycoproteins in high yield.
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Affiliation(s)
- Jing Zhu
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Yao Ruan
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Xin Fu
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Lichao Zhang
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Gaoshun Ge
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - J Gerard Wall
- Centre for Research in Medical Devices (CÚRAM) and Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Teng Zou
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Yang Zheng
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Ning Ding
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Xuejun Hu
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
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Functional mononuclear molybdenum enzymes: challenges and triumphs in molecular cloning, expression, and isolation. J Biol Inorg Chem 2020; 25:547-569. [PMID: 32279136 DOI: 10.1007/s00775-020-01787-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022]
Abstract
Mononuclear molybdenum enzymes catalyze a variety of reactions that are essential in the cycling of nitrogen, carbon, arsenic, and sulfur. For decades, the structure and function of these crucial enzymes have been investigated to develop a fundamental knowledge for this vast family of enzymes and the chemistries they carry out. Therefore, obtaining abundant quantities of active enzyme is necessary for exploring this family's biochemical capability. This mini-review summarizes the methods for overexpressing mononuclear molybdenum enzymes in the context of the challenges encountered in the process. Effective methods for molybdenum cofactor synthesis and incorporation, optimization of expression conditions, improving isolation of active vs. inactive enzyme, incorporation of additional prosthetic groups, and inclusion of redox enzyme maturation protein chaperones are discussed in relation to the current molybdenum enzyme literature. This article summarizes the heterologous and homologous expression studies providing underlying patterns and potential future directions.
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29
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Mirzadeh K, Shilling PJ, Elfageih R, Cumming AJ, Cui HL, Rennig M, Nørholm MHH, Daley DO. Increased production of periplasmic proteins in Escherichia coli by directed evolution of the translation initiation region. Microb Cell Fact 2020; 19:85. [PMID: 32264894 PMCID: PMC7137448 DOI: 10.1186/s12934-020-01339-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
Background Recombinant proteins are often engineered with an N-terminal signal peptide, which facilitates their secretion to the oxidising environment of the periplasm (gram-negative bacteria) or the culture supernatant (gram-positive bacteria). A commonly encountered problem is that the signal peptide influences the synthesis and secretion of the recombinant protein in an unpredictable manner. A molecular understanding of this phenomenon is highly sought after, as it could lead to improved methods for producing recombinant proteins in bacterial cell factories. Results Herein we demonstrate that signal peptides contribute to an unpredictable translation initiation region. A directed evolution approach that selects a new translation initiation region, whilst leaving the amino acid sequence of the signal peptide unchanged, can increase production levels of secreted recombinant proteins. The approach can increase production of single chain antibody fragments, hormones and other recombinant proteins in the periplasm of E. coli. Conclusions The study demonstrates that signal peptide performance is coupled to the efficiency of the translation initiation region.
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Affiliation(s)
- Kiavash Mirzadeh
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,CloneOpt AB, Stockholm, Sweden
| | - Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rageia Elfageih
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alister J Cumming
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Huanhuan L Cui
- Department of Medicine (Solna), Division of Microbial Pathogenesis, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- CloneOpt AB, Stockholm, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. .,CloneOpt AB, Stockholm, Sweden.
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30
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Karyolaimos A, Dolata KM, Antelo-Varela M, Mestre Borras A, Elfageih R, Sievers S, Becher D, Riedel K, de Gier JW. Escherichia coli Can Adapt Its Protein Translocation Machinery for Enhanced Periplasmic Recombinant Protein Production. Front Bioeng Biotechnol 2020; 7:465. [PMID: 32064253 PMCID: PMC7000420 DOI: 10.3389/fbioe.2019.00465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
Recently, we engineered a tunable rhamnose promoter-based setup for the production of recombinant proteins in E. coli. This setup enabled us to show that being able to precisely set the production rate of a secretory recombinant protein is critical to enhance protein production yields in the periplasm. It is assumed that precisely setting the production rate of a secretory recombinant protein is required to harmonize its production rate with the protein translocation capacity of the cell. Here, using proteome analysis we show that enhancing periplasmic production of human Growth Hormone (hGH) using the tunable rhamnose promoter-based setup is accompanied by increased accumulation levels of at least three key players in protein translocation; the peripheral motor of the Sec-translocon (SecA), leader peptidase (LepB), and the cytoplasmic membrane protein integrase/chaperone (YidC). Thus, enhancing periplasmic hGH production leads to increased Sec-translocon capacity, increased capacity to cleave signal peptides from secretory proteins and an increased capacity of an alternative membrane protein biogenesis pathway, which frees up Sec-translocon capacity for protein secretion. When cells with enhanced periplasmic hGH production yields were harvested and subsequently cultured in the absence of inducer, SecA, LepB, and YidC levels went down again. This indicates that when using the tunable rhamnose-promoter system to enhance the production of a protein in the periplasm, E. coli can adapt its protein translocation machinery for enhanced recombinant protein production in the periplasm.
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Affiliation(s)
- Alexandros Karyolaimos
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | | | | | - Anna Mestre Borras
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Rageia Elfageih
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Susanne Sievers
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
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31
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Tripathi NK, Shrivastava A. Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development. Front Bioeng Biotechnol 2019; 7:420. [PMID: 31921823 PMCID: PMC6932962 DOI: 10.3389/fbioe.2019.00420] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.
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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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