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Stohr AM, Ma D, Chen W, Blenner M. Engineering conditional protein-protein interactions for dynamic cellular control. Biotechnol Adv 2024; 77:108457. [PMID: 39343083 DOI: 10.1016/j.biotechadv.2024.108457] [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: 06/13/2024] [Revised: 08/28/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
Conditional protein-protein interactions enable dynamic regulation of cellular activity and are an attractive approach to probe native protein interactions, improve metabolic engineering of microbial factories, and develop smart therapeutics. Conditional protein-protein interactions have been engineered to respond to various chemical, light, and nucleic acid-based stimuli. These interactions have been applied to assemble protein fragments, build protein scaffolds, and spatially organize proteins in many microbial and higher-order hosts. To foster the development of novel conditional protein-protein interactions that respond to new inputs or can be utilized in alternative settings, we provide an overview of the process of designing new engineered protein interactions while showcasing many recently developed computational tools that may accelerate protein engineering in this space.
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Affiliation(s)
- Anthony M Stohr
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Derron Ma
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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Mičúchová A, Kyslík J, Korytář T, Piačková V, Frébort I. Barley as a production platform for oral vaccines in sustainable fish aquaculture. N Biotechnol 2024; 84:37-52. [PMID: 39332672 DOI: 10.1016/j.nbt.2024.09.004] [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: 08/01/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/29/2024]
Abstract
Vaccination is the most effective measure to prevent disease outbreaks in fish aquaculture, with oral vaccine administration emerging as the most practical approach. However, oral vaccines face a notable limitation due to insufficient stimulation of the complex gut-associated lymphoid tissue caused by factors such as vaccine degradation, poor absorption, and recognition by the immune cells. An innovative solution to these limitations lies in the plant-based production of recombinant vaccines. Plant cells enable the production and targeted storage of recombinant vaccines in specific cell organelles which ensure superior protection from degradation and contain natural compounds acting as adjuvants. Our study explores the potential of barley (Hordeum vulgare), a globally significant cereal crop, for producing orally administered subunit vaccines against viral infections affecting economically important fish species in the Salmonidae and Cyprinidae families. Through Agrobacterium-mediated transformation of immature barley embryos, we have generated homozygous T2 generation of transgenic barley expressing recombinant antigens of spring viremia of carp virus and infectious salmon anaemia virus. The expression of these plant-based recombinant vaccines was confirmed by immunodetection, which was supported by fluorescence observation, specifically in the seed endosperm. The antigenicity of transgenic plant material containing recombinant antigens was evaluated using an intubation model of common carp (Cyprinus carpio), revealing a substantial upregulation of the immunoglobulin transcripts in both systemic and mucosal tissues over a period of 28 days following a single dose of transgenic antigens. Collectively, these results underscore the potential of barley-based recombinant vaccines for disease prevention in fish aquaculture.
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Affiliation(s)
- Alžbeta Mičúchová
- Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czech Republic; Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jiří Kyslík
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic
| | - Tomáš Korytář
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic; University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Vodňany, Czech Republic
| | - Veronika Piačková
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, Vodňany, Czech Republic
| | - Ivo Frébort
- Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czech Republic.
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Gomes JGDS, Brandão LC, Pinheiro DP, Pontes LQ, Carneiro RF, Quintela BCSF, Marinho ACM, Furtado GP, Rocha BAM. Kinetics characterization of a low immunogenic recombinant l-asparaginase from Phaseolus vulgaris with cytotoxic activity against leukemia cells. Int J Biol Macromol 2024; 275:133731. [PMID: 38986978 DOI: 10.1016/j.ijbiomac.2024.133731] [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: 04/18/2024] [Revised: 06/15/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
l-asparaginases play a crucial role in the treatment of acute lymphoblastic leukemia (ALL), a type of cancer that mostly affects children and teenagers. However, it is common for these molecules to cause adverse reactions during treatment. These downsides ignite the search for novel asparaginases to mitigate these problems. Thus, this work aimed to produce and characterize a recombinant asparaginase from Phaseolus vulgaris (Asp-P). In this study, Asp-P was expressed in Escherichia coli with high yields and optimum activity at 40 °C, pH 9.0. The enzyme Km and Vmax values were 7.05 mM and 1027 U/mg, respectively. Asp-P is specific for l-asparagine, showing no activity against l-glutamine and other amino acids. The enzyme showed a higher cytotoxic effect against Raji than K562 cell lines, but only at high concentrations. In silico analysis indicated that Asp-P has lower immunogenicity than a commercial enzyme. Asp-P induced biofilm formation by Candida sp. due to sublethal dose, showing an underexplored potential of asparaginases. The absence of glutaminase activity, lower immunogenicity and optimal activity similar to physiological temperature conditions are characteristics that indicate Asp-P as a potential new commercial enzyme in the treatment of ALL and its underexplored application in the treatment of other diseases.
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Affiliation(s)
| | - Larisse Cadeira Brandão
- Departament of Fishing Engineering, Federal University of Ceara, Fortaleza, Brazil; Oswaldo Cruz Foundation - Fiocruz Ceara, Eusebio, Ceara, Brazil
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Tang J, Yang DZ, Lu C, Zheng W, Hu ZM, Xu YF, Li K, Wei JF, Xu ZQ. A Novel Quality Control Strategy for the Preparation of High-Quality Recombinant Allergens in Escherichia coli: A Case Study of Der f 2. Int Arch Allergy Immunol 2024:1-13. [PMID: 39047720 DOI: 10.1159/000539835] [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: 04/25/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024] Open
Abstract
INTRODUCTION Recombinant allergens produced by Escherichia coli (E. coli) system play an important role in the component-resolved diagnostics of allergy and vaccine development. However, incorrect folding of recombinant allergens may affect their application. Therefore, it is very important to monitor the correct folding of recombinant allergens. Currently, there is still a lack of a quality control strategy to solve this problem. In this study, a mite allergen, Der f 2, was taken as an example to establish a novel quality control strategy, which was based on chromatography to isolate the allergen, and on enzyme-linked immunosorbent assay to verify the IgE reactivity of the isolated allergen. METHODS The nucleotide sequence encoding Der f 2 was codon-optimized and cloned into pET-28a (+) plasmid. Best conditions for the expression of Der f 2 in E. coli were sought. The inclusion body of Der f 2 was denatured and purified by nickel affinity chromatography. Refolding processes were compared using glutathione redox system. The fully and partially folded proteins were separated by anion exchange chromatography, and the IgE reactivity of the isolated proteins was verified by indirect enzyme-linked immunosorbent assay. RESULTS An optimized 387 bp segment of the Der f 2 coding gene was successfully expressed in E. coli. Best induction conditions included preinduction bacterial density with absorbance value at 600 nm was 0.6, 1 mM isopropyl beta-d-thiogalactopyranoside at 28°C for 4 h. The Der f 2 protein after refolding was separated by chromatography and two fractions were obtained. The first fraction was identified as monomer protein and the second as aggregate by size-exclusion chromatography. Indirect enzyme-linked immunosorbent assay also confirmed that the first fraction showed higher IgE reactivity. CONCLUSION In this study, a novel quality control strategy based on chromatographic separation and IgE reactivity monitoring was established in the case of mite Der f 2, which systematically evaluated the effectiveness of multiple preparation methods for the first time. It is faster and more convenient when compared with the existing methods such as size-exclusion chromatography. This strategy laid a foundation for the stable application of recombinant allergens produced by E. coli in component-resolved diagnostics and the development of molecular vaccines in the future.
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Affiliation(s)
- Jian Tang
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - De-Zheng Yang
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Chen Lu
- Precision Medicine Center, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Wei Zheng
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Zhi-Ming Hu
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Yi-Fei Xu
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Ke Li
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Ji-Fu Wei
- Department of Pharmacy, The Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- National Vaccine Innovation Platform, Nanjing Medical University, Nanjing, China
| | - Zhi-Qiang Xu
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Zhang Y, Wang Y, Lu J, Huang Z, Hua H, Li Y, Xu J, Feng J. High-yield and cost-effective biosynthesis process for producing antimicrobial peptide AA139. Protein Expr Purif 2024; 219:106475. [PMID: 38552891 DOI: 10.1016/j.pep.2024.106475] [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: 12/12/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
AA139, a variant of natural antimicrobial peptide (AMP) arenicin-3, displayed potent activity against multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria. Nevertheless, there were currently few reports on the bioprocess of AA139, and the yields were less than 5 mg/L. Additionally, it was difficult and expensive to prepare AA139 through chemical synthesis due to its complex structure. These factors have impeded the further research and following clinical application of AA139. Here, we reported a bioprocess for the preparation of AA139, which was expressed in Escherichia coli (E. coli) BL21 (DE3) intracellularly in a soluble form via SUMO (small ubiquitin-related modifier) fusion technology. Then, recombinant AA139 (rAA139, refer to AA139 obtained by recombinant expression in this study) was obtained through the simplified downstream process, which was rationally designed in accordance with the physicochemical characteristics. Subsequently, the expression level of the interest protein was increased by 54% after optimization of high cell density fermentation (HCDF). Finally, we obtained a yield of 56 mg of rAA139 from 1 L culture with a purity of 98%, which represented the highest reported yield of AA139 to date. Furthermore, various characterizations were conducted to confirm the molecular mass, disulfide bonds, and antimicrobial activity of rAA139.
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Affiliation(s)
- Ying Zhang
- School of Pharmacy, Fudan University, Shanghai, 201203, People's Republic of China; Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China
| | - Yapeng Wang
- School of Pharmacy, Fudan University, Shanghai, 201203, People's Republic of China; Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China
| | - Jianguang Lu
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China; Shanghai Duomirui Bio-Technology Co. Ltd., Shanghai, 201203, People's Republic of China
| | - Zongqing Huang
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China; Shanghai Duomirui Bio-Technology Co. Ltd., Shanghai, 201203, People's Republic of China
| | - Haoju Hua
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China; Shanghai Duomirui Bio-Technology Co. Ltd., Shanghai, 201203, People's Republic of China
| | - Yanan Li
- School of Pharmacy, Fudan University, Shanghai, 201203, People's Republic of China; Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China
| | - Jun Xu
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China; Shanghai Duomirui Bio-Technology Co. Ltd., Shanghai, 201203, People's Republic of China
| | - Jun Feng
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, People's Republic of China; Shanghai Duomirui Bio-Technology Co. Ltd., Shanghai, 201203, People's Republic of China.
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Suyash S, Jha A, Maitra P, Punia P, Mishra A. Differentiating stable and unstable protein using convolution neural network and molecular dynamics simulations. Comput Biol Chem 2024; 110:108081. [PMID: 38677012 DOI: 10.1016/j.compbiolchem.2024.108081] [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: 01/17/2024] [Revised: 03/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Protein stability is a critical aspect of molecular biology and biochemistry, hinges on an intricate balance of thermodynamic and structural factors. Determining protein stability is crucial for understanding and manipulating biological machineries, as it directly correlated with the protein function. Thus, this study delves into the intricacies of protein stability, highlighting its dependence on various factors, including thermodynamics, thermal conditions, and structural properties. Moreover, a notable focus is placed on the free energy change of unfolding (ΔGunfolding), change in heat capacity (ΔCp) with protein structural transition, melting temperature (Tm) and number of disulfide bonds, which are critical parameters in understanding protein stability. In this study, a machine learning (ML) predictive model was developed to estimate these four parameters using the primary sequence of the protein. The shortfall of available tools for protein stability prediction based on multiple parameters propelled the completion of this study. Convolutional Neural Network (CNN) with multiple layers was adopted to develop a more reliable ML model. Individual predictive models were prepared for each property, and all the prepared models showed results with high accuracy. The R2 (coefficient of determination) of these models were 0.79, 0.78, 0.92 and 0.92, respectively, for ΔG, ΔCp, Tm and disulfide bonds. A case study on stability analysis of two homologous proteins was presented to validate the results predicted through the developed model. The case study included in silico analysis of protein stability using molecular docking and molecular dynamic simulations. This validation study assured the accuracy of each model in predicting the stability associated properties. The alignment of physics-based principles with ML models has provided an opportunity to develop a fast machine learning solution to replace the computationally demanding physics-based calculations used to determine protein stability. Furthermore, this work provided valuable insights into the impact of mutation on protein stability, which has implications for the field of protein engineering. The source codes are available at https://github.com/Growdeatechnology.
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Affiliation(s)
| | - Akshat Jha
- Growdea Technologies Pvt. Ltd., Gurugram, Haryana 122004, India
| | - Priyasha Maitra
- Growdea Technologies Pvt. Ltd., Gurugram, Haryana 122004, India
| | - Parveen Punia
- Pt. Neki Ram Sharma Government College, Rohtak, Haryana 124001, India
| | - Avinash Mishra
- Growdea Technologies Pvt. Ltd., Gurugram, Haryana 122004, India.
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Yamazaki S, Takahashi K, Matsuda Y. Tag-free protein modification by lipoate ligase A: exploring substrate tolerance. ANAL SCI 2024; 40:1111-1119. [PMID: 38504072 DOI: 10.1007/s44211-024-00534-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/10/2024] [Indexed: 03/21/2024]
Abstract
This study delves into the functional intricacies of lipoate ligase A (LplA), an enzyme showing great promise in bioconjugation due to its unique capacity for introducing azido groups into proteins without requiring a genetic tag. We aimed to enhance the understanding of LplA's functionality, particularly its substrate tolerance and the reliability of various analytical techniques. A pivotal aspect of our approach was incorporating azido groups into a range of proteins, followed by the addition of the fluorescent molecule Cy3 via click chemistry. Analysis of fluorescent intensity in the altered proteins indicated varying degrees of conjugation. Additionally, phenyl resin-based RP-HPLC facilitated effective separation of modified proteins, unmodified proteins, and remaining fluorescent tags post-separation. SASA analysis provided insights into conjugation trends, guiding the identification of proteins amenable to LplA's tag-free modification. Our findings demonstrate LplA's broad substrate tolerability for protein modification.
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Affiliation(s)
- Shunsuke Yamazaki
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki, Kanagawa, 210-8681, Japan.
| | | | - Yutaka Matsuda
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki, Kanagawa, 210-8681, Japan.
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Gonçalves AAM, Ribeiro AJ, Resende CAA, Couto CAP, Gandra IB, Dos Santos Barcelos IC, da Silva JO, Machado JM, Silva KA, Silva LS, Dos Santos M, da Silva Lopes L, de Faria MT, Pereira SP, Xavier SR, Aragão MM, Candida-Puma MA, de Oliveira ICM, Souza AA, Nogueira LM, da Paz MC, Coelho EAF, Giunchetti RC, de Freitas SM, Chávez-Fumagalli MA, Nagem RAP, Galdino AS. Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis. Microb Cell Fact 2024; 23:145. [PMID: 38778337 PMCID: PMC11110257 DOI: 10.1186/s12934-024-02418-w] [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: 01/31/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.
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Affiliation(s)
- Ana Alice Maia Gonçalves
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Anna Julia Ribeiro
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carlos Ananias Aparecido Resende
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Carolina Alves Petit Couto
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isadora Braga Gandra
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Isabelle Caroline Dos Santos Barcelos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Jonatas Oliveira da Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Juliana Martins Machado
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Kamila Alves Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Líria Souza Silva
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Michelli Dos Santos
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Lucas da Silva Lopes
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Teixeira de Faria
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sabrina Paula Pereira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Sandra Rodrigues Xavier
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Matheus Motta Aragão
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Mayron Antonio Candida-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | | | - Amanda Araujo Souza
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Lais Moreira Nogueira
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Mariana Campos da Paz
- Bioactives and Nanobiotechnology Laboratory, Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil
| | - Eduardo Antônio Ferraz Coelho
- Postgraduate Program in Health Sciences, Infectious Diseases and Tropical Medicine, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, 30130-100, Brazil
| | - Rodolfo Cordeiro Giunchetti
- Laboratory of Biology of Cell Interactions, National Institute of Science and Technology on Tropical Diseases (INCT-DT), Department of Morphology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sonia Maria de Freitas
- Biophysics Laboratory, Institute of Biological Sciences, Department of Cell Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, 04000, Peru
| | - Ronaldo Alves Pinto Nagem
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Alexsandro Sobreira Galdino
- Microorganism Biotechnology Laboratory, National Institute of Science and Technology on Industrial Biotechnology (INCT-BI), Federal University of São João Del-Rei, Midwest Campus, Divinópolis, 35501-296, Brazil.
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Nakahara Y, Kawaguchi T, Matsuda Y, Endo Y, Date M, Takahashi K, Kato K, Okasora T, Ejima D, Nagaki A. Spatiotemporal Control of Protein Refolding through Flash-Change Reaction Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8483-8492. [PMID: 38618876 DOI: 10.1021/acs.langmuir.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Recombinant protein production is an essential aspect of biopharmaceutical manufacturing, with Escherichia coli serving as a primary host organism. Protein refolding is vital for protein production; however, conventional refolding methods face challenges such as scale-up limitations and difficulties in controlling protein conformational changes on a millisecond scale. In this study, we demonstrate the novel application of flow microreactors (FMR) in controlling protein conformational changes on a millisecond scale, enabling efficient refolding processes and opening up new avenues in the science of FMR technology. FMR technology has been primarily employed for small-molecule synthesis, but our novel approach successfully expands its application to protein refolding, offering precise control of the buffer pH and solvent content. Using interleukin-6 as a model, the system yielded an impressive 96% pure refolded protein and allowed for gram-scale production. This FMR system allows flash changes in the reaction conditions, effectively circumventing protein aggregation during refolding. To the best of our knowledge, this is the first study to use FMR for protein refolding, which offers a more efficient and scalable method for protein production. The study results highlight the utility of the FMR as a high-throughput screening tool for streamlined scale-up and emphasize the importance of understanding and controlling intermediates in the refolding process. The FMR technique offers a promising approach for enhancing protein refolding efficiency and has demonstrated its potential in streamlining the process from laboratory-scale research to industrial-scale production, making it a game-changing technology in the field.
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Affiliation(s)
- Yuichi Nakahara
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Tomoko Kawaguchi
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Yutaka Matsuda
- Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, California 92121, United States
| | - Yuta Endo
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Masayo Date
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Kazutoshi Takahashi
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Keisuke Kato
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Takahiro Okasora
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Daisuke Ejima
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Aiichiro Nagaki
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
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Xu JB, Guan WJ, Zhang YL, Qiu ZE, Chen L, Hou XC, Yue J, Zhou YY, Sheng J, Zhao L, Zhu YX, Sun J, Zhao J, Zhou WL, Zhong NS. SARS-CoV-2 envelope protein impairs airway epithelial barrier function and exacerbates airway inflammation via increased intracellular Cl - concentration. Signal Transduct Target Ther 2024; 9:74. [PMID: 38528022 DOI: 10.1038/s41392-024-01753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 03/27/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection disrupts the epithelial barrier and triggers airway inflammation. The envelope (E) protein, a core virulence structural component of coronaviruses, may play a role in this process. Pathogens could interfere with transepithelial Cl- transport via impairment of the cystic fibrosis transmembrane conductance regulator (CFTR), which modulates nuclear factor κB (NF-κB) signaling. However, the pathological effects of SARS-CoV-2 E protein on airway epithelial barrier function, Cl- transport and the robust inflammatory response remain to be elucidated. Here, we have demonstrated that E protein down-regulated the expression of tight junctional proteins, leading to the disruption of the airway epithelial barrier. In addition, E protein triggered the activation of Toll-like receptor (TLR) 2/4 and downstream c-Jun N-terminal kinase (JNK) signaling, resulting in an increased intracellular Cl- concentration ([Cl-]i) via up-regulating phosphodiesterase 4D (PDE4D) expression in airway epithelial cells. This elevated [Cl-]i contributed to the heightened airway inflammation through promoting the phosphorylation of serum/glucocorticoid regulated kinase 1 (SGK1). Moreover, blockade of SGK1 or PDE4 alleviated the robust inflammatory response induced by E protein. Overall, these findings provide novel insights into the pathogenic role of SARS-CoV-2 E protein in airway epithelial damage and the ongoing airway inflammation during SARS-CoV-2 infection.
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Affiliation(s)
- Jian-Bang Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangzhou National Laboratory, Guangzhou, P. R. China.
| | - Yi-Lin Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Guangdong Provincial Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhuo-Er Qiu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lei Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiao-Chun Hou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Junqing Yue
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangzhou National Laboratory, Guangzhou, P. R. China
| | - Yu-Yun Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jie Sheng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Lei Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Department of Physiology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, P. R. China
| | - Yun-Xin Zhu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangzhou National Laboratory, Guangzhou, P. R. China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
- Guangzhou National Laboratory, Guangzhou, P. R. China
| | - Wen-Liang Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China.
- Guangzhou National Laboratory, Guangzhou, P. R. China.
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Essential factors, advanced strategies, challenges, and approaches involved for efficient expression of recombinant proteins in Escherichia coli. Arch Microbiol 2024; 206:152. [PMID: 38472371 DOI: 10.1007/s00203-024-03871-2] [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: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Producing recombinant proteins is a major accomplishment of biotechnology in the past century. Heterologous hosts, either eukaryotic or prokaryotic, are used for the production of these proteins. The utilization of microbial host systems continues to dominate as the most efficient and affordable method for biotherapeutics and food industry productions. Hence, it is crucial to analyze the limitations and advantages of microbial hosts to enhance the efficient production of recombinant proteins on a large scale. E. coli is widely used as a host for the production of recombinant proteins. Researchers have identified certain obstacles with this host, and given the growing demand for recombinant protein production, there is an immediate requirement to enhance this host. The following review discusses the elements contributing to the manifestation of recombinant protein. Subsequently, it sheds light on innovative approaches aimed at improving the expression of recombinant protein. Lastly, it delves into the obstacles and optimization methods associated with translation, mentioning both cis-optimization and trans-optimization, producing soluble recombinant protein, and engineering the metal ion transportation. In this context, a comprehensive description of the distinct features will be provided, and this knowledge could potentially enhance the expression of recombinant proteins in E. coli.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Biochemistry, FacultyofBiotechnologyand BiomolecularSciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Wang J, Xu Y, Wang X, Li J, Hua Z. Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study. Molecules 2024; 29:1071. [PMID: 38474583 DOI: 10.3390/molecules29051071] [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: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp's ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design.
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Affiliation(s)
- Jingyao Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yicong Xu
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xujian Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
| | - Zichun Hua
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing 210023, China
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Xu K, Yu S, Wang K, Tan Y, Zhao X, Liu S, Zhou J, Wang X. AI and Knowledge-Based Method for Rational Design of Escherichia coli Sigma70 Promoters. ACS Synth Biol 2024; 13:402-407. [PMID: 38176073 DOI: 10.1021/acssynbio.3c00578] [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: 01/06/2024]
Abstract
Expanding sigma70 promoter libraries can support the engineering of metabolic pathways and enhance recombinant protein expression. Herein, we developed an artificial intelligence (AI) and knowledge-based method for the rational design of sigma70 promoters. Strong sigma70 promoters were identified by using high-throughput screening (HTS) with enhanced green fluorescent protein (eGFP) as a reporter gene. The features of these strong promoters were adopted to guide promoter design based on our previous reported deep learning model. In the following case study, the obtained strong promoters were used to express collagen and microbial transglutaminase (mTG), resulting in increased expression levels by 81.4% and 33.4%, respectively. Moreover, these constitutive promoters achieved soluble expression of mTG-activating protease and contributed to active mTG expression in Escherichia coli. The results suggested that the combined method may be effective for promoter engineering.
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Affiliation(s)
- Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shangyang Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kun Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinyi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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14
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Shawky H, Tabll AA, Elshenawy RM, Helmy NM, Moustafa RI, Elesnawy YK, Abdelghany MM, El-Abd YS. Glycylglycine promotes the solubility and antigenic utility of recombinant HCV structural proteins in a point-of-care immunoassay for detection of active viremia. Microb Cell Fact 2024; 23:25. [PMID: 38238770 PMCID: PMC10795219 DOI: 10.1186/s12934-024-02297-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although E. coli is generally a well-opted platform for the overproduction of recombinant antigens as heterologous proteins, the optimization of expression conditions to maximize the yield of functional proteins remains empirical. Herein, we developed an optimized E. coli (BL21)-based system for the overproduction of soluble immunoreactive HCV core/envelope proteins that were utilized to establish a novel immunoassay for discrimination of active HCV infection. METHODS The core/E1-E2 genes were amplified and expressed in E. coli BL21 (DE3) in the absence/presence of glycylglycine. The antigenic performance of soluble proteins was assessed against 63 HCV-seronegative (Ab-) sera that included normal and interferent sera (HBV and/or chronic renal failure), and 383 HCV-seropositive (Ab+) samples that included viremic (chronic/relapsers) and recovered patients' sera. The color intensity (OD450) and S/Co values were estimated. RESULTS The integration of 0.1-0.4M glycylglycine in the growth media significantly enhanced the solubility/yield of recombinant core and envelope proteins by ~ 225 and 242 fold, respectively. This was reflected in their immunoreactivity and antigenic performance in the developed immunoassay, where the soluble core/E1/E2 antigen mixture showed 100% accuracy in identifying HCV viremic sera with a viral RNA load as low as 3800 IU/mL, without cross-reactivity against normal/interferent HCV-Ab-sera. The ideal S/Co threshold predicting active viremia (> 2.75) showed an AUC value of 0.9362 (95% CI: 0.9132 to 0.9593), with 87.64, 91.23% sensitivity and specificity, and 94.14, 82.11% positive and negative predictive values, respectively. The different panels of samples assayed with our EIA showed a good concordance with the viral loads and also significant correlations with the golden standards of HCV diagnosis in viremic patients. The performance of the EIA was not affected by the immunocompromised conditions or HBV co-infection. CONCLUSION The applicability of the proposed platform would extend beyond the reported approach, where glycylglycine, low inducer concentration and post-induction temperature, combined with the moderately-strong constitutive promoter enables the stable production of soluble/active proteins, even those with reported toxicity. Also, the newly developed immunoassay provides a cost-effective point-of-care diagnostic tool for active HCV viremia that could be useful in resource-limited settings.
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Affiliation(s)
- Heba Shawky
- Therapeutic Chemistry Department, Pharmaceutical Industries and Drug Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Ashraf A Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Reem M Elshenawy
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Naiera M Helmy
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Rehab I Moustafa
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | | | - Marwa M Abdelghany
- National Committee for Control of Viral Hepatitis (NCCVH), Ministry of Health and Population, Cairo, Egypt
| | - Yasmine S El-Abd
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt.
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Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [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: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
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Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
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Rahban M, Ahmad F, Piatyszek MA, Haertlé T, Saso L, Saboury AA. Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry. RSC Adv 2023; 13:35947-35963. [PMID: 38090079 PMCID: PMC10711991 DOI: 10.1039/d3ra06476j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/30/2023] [Indexed: 04/26/2024] Open
Abstract
Protein-based therapeutics have revolutionized the pharmaceutical industry and become vital components in the development of future therapeutics. They offer several advantages over traditional small molecule drugs, including high affinity, potency and specificity, while demonstrating low toxicity and minimal adverse effects. However, the development and manufacturing processes of protein-based therapeutics presents challenges related to protein folding, purification, stability and immunogenicity that should be addressed. These proteins, like other biological molecules, are prone to chemical and physical instabilities. The stability of protein-based drugs throughout the entire manufacturing, storage and delivery process is essential. The occurrence of structural instability resulting from misfolding, unfolding, and modifications, as well as aggregation, poses a significant risk to the efficacy of these drugs, overshadowing their promising attributes. Gaining insight into structural alterations caused by aggregation and their impact on immunogenicity is vital for the advancement and refinement of protein therapeutics. Hence, in this review, we have discussed some features of protein aggregation during production, formulation and storage as well as stabilization strategies in protein engineering and computational methods to prevent aggregation.
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Affiliation(s)
- Mahdie Rahban
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences Kerman Iran
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard New Delhi-110062 India
| | | | | | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University Rome Italy
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran Tehran 1417614335 Iran +9821 66404680 +9821 66956984
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Nguyen TS, Park JH, Nguyen TK, Nguyen TV, Lee SK, Na SH, Han JH, Park WS, Chun W, Lu F, Han ET. Plasmodium vivax merozoite-specific thrombospondin-related anonymous protein (PvMTRAP) interacts with human CD36, suggesting a novel ligand-receptor interaction for reticulocyte invasion. Parasit Vectors 2023; 16:426. [PMID: 37981686 PMCID: PMC10658926 DOI: 10.1186/s13071-023-06031-5] [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: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND The Plasmodium vivax merozoite restrictively invades immature erythrocytes, suggesting that its ligand(s) might interact with corresponding receptor(s) that are selectively abundant on reticulocytes to complete the invasion. Finding the ligand‒receptor interaction involved in P. vivax invasion is critical to vivax malaria management; nevertheless, it remains to be unraveled. METHODS A library of reticulocyte receptors and P. vivax ligands were expressed by a HEK293E mammalian cell expression system and were then used to screen the interaction using enzyme-linked immunosorbent assay (ELISA). A flow cytometry-based erythrocyte binding assay and bio-layer interferometry experiment were further utilized to cellularly and quantitatively identify the ligand‒receptor interaction, respectively. RESULTS Plasmodium vivax merozoite-specific thrombospondin-related anonymous protein (PvMTRAP) was found to interact with human CD36 using systematic screening. This interaction was specific at a molecular level from in vitro analysis and comparable to that of P. vivax Duffy binding protein (PvDBP) and Duffy antigen receptor for chemokines (DARC) (KD: 37.0 ± 1.4 nM and 7.7 ± 0.5 nM, respectively). Flow cytometry indicated that PvMTRAP preferentially binds to reticulocytes, on which CD36 is selectively present. CONCLUSIONS Human CD36 is selectively abundant on reticulocytes and is able to interact specifically with PvMTRAP, suggesting that it may function as a ligand and receptor during the invasion of reticulocytes by P. vivax.
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Affiliation(s)
- Thau Sy Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-Si, 13488, Republic of Korea
| | - Tuyet-Kha Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Truong Van Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Sung-Hun Na
- Department of Obstetrics and Gynecology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Won-Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Wanjoo Chun
- Department of Pharmacology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea
| | - Feng Lu
- Department of Pathogen Biology and Immunology, School of Medicine, Yangzhou University, Yangzhou, China
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-Do, 24341, Republic of Korea.
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Ganjave SD, O'Niel RA, Wangikar PP. Rate of dilution and redox ratio influence the refolding efficiency of recombinant fungal dehydrogenases. Int J Biol Macromol 2023; 250:126163. [PMID: 37549766 DOI: 10.1016/j.ijbiomac.2023.126163] [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: 05/06/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Dehydrogenases from fungi are attracting attention as industrial biocatalysts due to their high activity and chiral selectivity. However, these enzymes form insoluble aggregates when overexpressed in E. coli, limiting their industrial application. In the present study, we report the systematic development of a refolding process for selected, industrially relevant fungal dehydrogenases, viz., formate dehydrogenase from Candida boidinii (CbFDH) and formate and alcohol dehydrogenases from Geotrichum candium (GcFDH and GcADH, respectively). We first employed a screen to evaluate the effects of different variables on refolding including the buffer system, additives, and rate of dilution. The extent of refolding was determined by enzyme assays, circular dichroism, and tryptophan fluorescence. Our results showed that glycerol and reducing environment are essential for refolding of these dehydrogenases. Further, slow dilution of solubilized protein over 16 h dramatically improved the recovery of refolded enzymes compared to rapid dilution. The importance of slow dilution was further confirmed in a 10-fold scaled-up refolding trial. Overall, we demonstrate a robust method for refolding of fungal dehydrogenases, thus improving their availability for various biocatalytic applications.
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Affiliation(s)
- Snehal D Ganjave
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchika Annie O'Niel
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Rana D, Desai N, Salave S, Karunakaran B, Giri J, Benival D, Gorantla S, Kommineni N. Collagen-Based Hydrogels for the Eye: A Comprehensive Review. Gels 2023; 9:643. [PMID: 37623098 PMCID: PMC10454301 DOI: 10.3390/gels9080643] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Collagen-based hydrogels have emerged as a highly promising platform for diverse applications in ophthalmology, spanning from drug delivery systems to biomedical interventions. This review explores the diverse sources of collagen, which give rise to different types of collagen protein. The critical isolation and purification steps are discussed, emphasizing their pivotal role in preparing collagen for biomedical use. To ensure collagen quality and purity, and the suitability of collagen for targeted applications, a comprehensive characterization and quality control are essential, encompassing assessments of its physical, chemical, and biological properties. Also, various cross-linking collagen methods have been examined for providing insight into this crucial process. This comprehensive review delves into every facet of collagen and explores the wide-ranging applications of collagen-based hydrogels, with a particular emphasis on their use in drug delivery systems and their potential in diverse biomedical interventions. By consolidating current knowledge and advancements in the field, this review aims to provide a detailed overview of the utilization of engineered collagen-based hydrogels in ocular therapeutics.
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Affiliation(s)
- Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (B.K.); (D.B.)
| | - Nimeet Desai
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India; (N.D.); (J.G.)
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (B.K.); (D.B.)
| | - Bharathi Karunakaran
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (B.K.); (D.B.)
| | - Jyotsnendu Giri
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India; (N.D.); (J.G.)
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (B.K.); (D.B.)
| | - Srividya Gorantla
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA;
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Niazi SK. A Proposed Global Medicines Agency (GMA) to Make Biological Drugs Accessible: Starting with the League of Arab States. Healthcare (Basel) 2023; 11:2075. [PMID: 37510516 PMCID: PMC10379659 DOI: 10.3390/healthcare11142075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Medical anthropology teaches us of historical disparity in the accessibility of medicines in the developing world due to their lack of availability and affordability, more particularly of biological drugs, including therapeutic proteins, gene therapy, CRISPR-Cas9, mRNA therapeutics, CART therapy, and many more. This challenge can be resolved by establishing an independent regulatory agency, proposed as the Global Medicines Agency (GMA), with a charter to allow originators from the Stringent Regulatory Agency (SRA) countries to receive immediate registrations applicable to all member states, expanding the market potential as an incentive. For non-SRA countries, it will be limited to biological drugs that are allowed their copies to be made, only biosimilars. A transparent approval process will involve using a rapporteur, a third-party product-related current Good Manufacturing Practice (cGMP), and assurance of the integrity of samples tested for analytical similarity and clinical pharmacology testing. GMA membership will be open to all countries. Still, it is suggested that the League of Arab States, representing 22 states with a population of 400 million, takes the lead due to their cultural and language homogeneity, which is likely to provide a concurrence among the member states. However, some states, like the Gulf Cooperative Council, are already accustomed to this approach, albeit with a different perspective. The target drugs are biotechnology and gene therapy pharmaceuticals, and their scope can be expanded to any drug.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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