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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [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: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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2
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Zhang MJ, Yun ST, Wang XC, Peng LY, Dou C, Zhou YX. Insights into the Influence of Signal Peptide on the Enzymatic Properties of Alginate Lyase AlyI1 with Removal Effect on Pseudomonas aeruginosa Biofilm. Mar Drugs 2022; 20:md20120753. [PMID: 36547900 PMCID: PMC9787728 DOI: 10.3390/md20120753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Most reports on signal peptides focus on their ability to affect the normal folding of proteins, thereby affecting their secreted expression, while few studies on its effects on enzymatic properties were published. Therefore, biochemical characterization and comparison of alginate lyase rALYI1/rALYI1-1 (rALYI1: without signal peptides; rALYI1-1:with signal peptides) were conducted in our study, and the results showed that the signal peptide affected the biochemical properties, especially in temperature and pH. rALYI1 (32.15 kDa) belonging to polysaccharide lyase family 7 was cloned from sea-cucumber-gut bacterium Tamlana sp. I1. The optimum temperature of both rALYI1 and rALYI1-1 was 40 °C, but the former had a wider optimum temperature range and better thermal stability. The optimum pH of rALYI1 and rALYI1-1 were 7.6 and 8.6, respectively. The former was more stable and acid resistant. Noticeably, rALYI1 was a salt-activated enzyme and displayed remarkable salt tolerance. Alginate, an essential polysaccharide in algae and Pseudomonas aeruginosa biofilms, is composed of α-L-guluronate and β-D-mannuronate. It is also found in our study that rALYI1 is also effective in removing mature biofilms compared with controls. In conclusion, the signal peptide affects several biochemical properties of the enzyme, and alginate lyase rALYI1 may be an effective method for inhibiting biofilm formation of Pseudomonas aeruginosa.
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Affiliation(s)
| | - Shuai-Ting Yun
- Marine College, Shandong University, Weihai 264209, China
| | - Xiao-Chen Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Li-Yang Peng
- Marine College, Shandong University, Weihai 264209, China
| | - Chuan Dou
- Shangdong Kelun Pharmaceutical Co., Ltd., Bingzhou 256600, China
| | - Yan-Xia Zhou
- Marine College, Shandong University, Weihai 264209, China
- Correspondence:
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De Farias Silva CE, Costa GYSCM, Ferro JV, de Oliveira Carvalho F, da Gama BMV, Meili L, dos Santos Silva MC, Almeida RMRG, Tonholo J. Application of machine learning to predict the yield of alginate lyase solid-state fermentation by Cunninghamella echinulata: artificial neural networks and support vector machine. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02293-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:md20060341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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Li M, Wang Z, Zhou M, Zhang C, Zhi K, Liu S, Sun X, Wang Z, Liu J, Liu D. Continuous Production of Human Epidermal Growth Factor Using Escherichia coli Biofilm. Front Microbiol 2022; 13:855059. [PMID: 35495696 PMCID: PMC9039743 DOI: 10.3389/fmicb.2022.855059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing demand for recombinant proteins necessitates efficient protein production processes. In this study, a continuous process for human epidermal growth factor (hEGF) secretion by Escherichia coli was developed by taking advantage of biofilm formation. Genes bcsB, fimH, and csgAcsgB that have proved to facilitate biofilm formation and some genes moaE, yceA, ychJ, and gshB potentially involved in biofilm formation were examined for their effects on hEGF secretion as well as biofilm formation. Finally, biofilm-based fermentation processes were established, which demonstrated the feasibility of continuous production of hEGF with improved efficiency. The best result was obtained from ychJ-disruption that showed a 28% increase in hEGF secretion over the BL21(DE3) wild strain, from 24 to 32 mg/L. Overexpression of bcsB also showed great potential in continuous immobilized fermentation. Overall, the biofilm engineering here represents an effective strategy to improve hEGF production and can be adapted to produce more recombinant proteins in future.
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Affiliation(s)
- Mengting Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenyu Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Miao Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chong Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Kaiqi Zhi
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Shuli Liu
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Xiujuan Sun
- Institute of Industrial Biotechnology, Jiangsu Industrial Technology Research Institute (JITRI), Nanjing, China
| | - Zhi Wang
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Jinle Liu
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China.,Institute of Industrial Biotechnology, Jiangsu Industrial Technology Research Institute (JITRI), Nanjing, China
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6
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Tang L, Guo E, Zhang L, Wang Y, Gao S, Bao M, Han F, Yu W. The Function of CBM32 in Alginate Lyase VxAly7B on the Activity on Both Soluble Sodium Alginate and Alginate Gel. Front Microbiol 2022; 12:798819. [PMID: 35069502 PMCID: PMC8776709 DOI: 10.3389/fmicb.2021.798819] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Carbohydrate-binding modules (CBMs), as an important auxiliary module, play a key role in degrading soluble alginate by alginate lyase, but the function on alginate gel has not been elucidated. Recently, we reported alginate lyase VxAly7B containing a CBM32 and a polysaccharide lyase family 7 (PL7). To investigate the specific function of CBM32, we characterized the full-length alginate lyase VxAly7B (VxAly7B-FL) and truncated mutants VxAly7B-CM (PL7) and VxAly7B-CBM (CBM32). Both VxAly7B-FL and native VxAly7B can spontaneously cleavage between CBM32 and PL7. The substrate-binding capacity and activity of VxAly7B-CM to soluble alginate were 0.86- and 1.97-fold those of VxAly7B-FL, respectively. Moreover, CBM32 could accelerate the expansion and cleavage of alginate gel beads, and the degradation rate of VxAly7B-FL to alginate gel beads was threefold that of VxAly7B-CM. Results showed that CBM32 is not conducive to the degradation of soluble alginate by VxAly7B but is helpful for binding and degradation of insoluble alginate gel. This study provides new insights into the function of CBM32 on alginate gel, which may inspire the application strategy of CBMs in insoluble substrates.
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Affiliation(s)
- Luyao Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Enwen Guo
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lan Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shan Gao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mengmeng Bao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Drugs, Ministry of Education, Qingdao, China.,Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol 2021; 23:3130-3148. [PMID: 33876546 DOI: 10.1111/1462-2920.15536] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.
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Affiliation(s)
- Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Dharani SR, Srinivasan R, Sarath R, Ramya M. Recent progress on engineering microbial alginate lyases towards their versatile role in biotechnological applications. Folia Microbiol (Praha) 2020; 65:937-954. [DOI: 10.1007/s12223-020-00802-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
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9
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Ilamaran M, Sriram Raghavan S, Karthik S, Sanjay Nalawade K, Samvedna S, Routray W, Kamini NR, Saravanan P, Ayyadurai N. A facile method for high level dual expression of recombinant and congener protein in a single expression system. Protein Expr Purif 2018; 156:1-7. [PMID: 30562573 DOI: 10.1016/j.pep.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Protein engineering is an emerging field for developing novel therapeutic proteins and commercial enzymes, along with a major impact on the global market. In recent decades, advanced methods employing protein modification through expansion of the genetic code have led to the development of proteins with new biochemical and physical properties. These techniques have produced engineered proteins with improved attribute comprising substrate relaxation, protein drug conjugation and high stability under extreme conditions of high temperatures, pH and organic solvents. Furthermore, residue specific incorporation is the simplest method for the global incorporation of non-canonical amino acid (NCAA) for protein modification; however it has the major drawbacks of high production cost and manpower requirement. In the present study, we developed a method for the incorporation of single NCAA in two different proteins by using Escherichia coli (E. coli) expression system. For that, the dual protein expressing Escherichia coli JW2581 strain was constructed by transforming pQE80L and pD881-PpiBT vectors with different promoters, selectable markers and AnnexinV, GFPHS gene. To modify the protein, the 3,4 dihydroxy phenyl alanine (DOPA) was globally incorporated into the GFPHS and Annexin V protein using dual protein expression system. The incorporation efficiency during the dual protein expression was achieved through optimized concentrations of amino acids, carbohydrate and inducers in minimal medium. This method for the incorporation of single NCAA into two different proteins using a single expression host system saves the production cost, manpower and time substantially.
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Affiliation(s)
- M Ilamaran
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - S Sriram Raghavan
- Department of Crystallography and Biophysics, Madras University, Chennai, India
| | - S Karthik
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | | | - S Samvedna
- Department of Biotechnology, Rajalakshmi Engineering Collage, Chennai, India
| | - W Routray
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - N R Kamini
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - P Saravanan
- Department of Biotechnology, Rajalakshmi Engineering Collage, Chennai, India
| | - N Ayyadurai
- Department of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India.
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