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Zheng Y, Lao Z, Liu R, Xu J, Guo L, Lin Z, Yang X. Customizable Click Biochemistry Strategy for the Design and Preparation of Glucagon-like Peptide-1 Conjugates and Coagonists. Bioconjug Chem 2024; 35:693-702. [PMID: 38700695 DOI: 10.1021/acs.bioconjchem.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The development of oligomeric glucagon-like peptide-1 (GLP-1) and GLP-1-containing coagonists holds promise for enhancing the therapeutic potential of the GLP-1-based drugs for treating type 2 diabetes mellitus (T2DM). Here, we report a facile, efficient, and customizable strategy based on genetically encoded SpyCatcher-SpyTag chemistry and an inducible, cleavable self-aggregating tag (icSAT) scheme. icSAT-tagged SpyTag-fused GLP-1 and the dimeric or trimeric SpyCatcher scaffold were designed for dimeric or trimeric GLP-1, while icSAT-tagged SpyCatcher-fused GLP-1 and the icSAT-tagged SpyTag-fused GIP were designed for dual GLP-1/GIP (glucose-dependent insulinotropic polypeptide) receptor agonist. These SpyCatcher- and SpyTag-fused protein pairs were spontaneously ligated directly from the cell lysates. The subsequent icSAT scheme, coupled with a two-step standard column purification, resulted in target proteins with authentic N-termini, with yields ranging from 35 to 65 mg/L and purities exceeding 99%. In vitro assays revealed 3.0- to 4.1-fold increased activities for dimeric and trimeric GLP-1 compared to mono-GLP-1. The dual GLP-1/GIP receptor agonist exhibited balanced activity toward the GLP-1 receptor or the GIP receptor. All the proteins exhibited 1.8- to 3.0-fold prolonged half-lives in human serum compared to mono-GLP-1 or GIP. This study provides a generally applicable click biochemistry strategy for developing oligomeric or dual peptide/protein-based drug candidates.
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Affiliation(s)
- Yunchun Zheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zisha Lao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Run Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jun Xu
- Dongguan HEC Biopharmaceutical R&D Co., Ltd., 368 Middle Zhenan Road, Changan, Dongguan 523871, China
| | - Linfeng Guo
- Dongguan HEC Biopharmaceutical R&D Co., Ltd., 368 Middle Zhenan Road, Changan, Dongguan 523871, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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2
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Komolov AS, Sannikova EP, Gorbunov AA, Gubaidullin II, Plokhikh KS, Konstantinova GE, Bulushova NV, Kuchin SV, Kozlov DG. Synthesis of biologically active proteins as L6KD-SUMO fusions forming inclusion bodies in Escherichia coli. Biotechnol Bioeng 2024; 121:535-550. [PMID: 37927002 DOI: 10.1002/bit.28587] [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: 05/27/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023]
Abstract
A new platform has been developed to facilitate the production of biologically active proteins and peptides in Escherichia coli. The platform includes an N-terminal self-associating L6 KD peptide fused to the SUMO protein (small ubiquitin-like protein modifier) from the yeast Saccharomyces cerevisiae, which is known for its chaperone activity. The target proteins are fused at the C termini of the L6 KD-SUMO fusions, and the resulting three-component fusion proteins are synthesized and self-assembled in E. coli into so-called active inclusion bodies (AIBs). In vivo, the L6 KD-SUMO platform facilitates the correct folding of the target proteins and directs them into AIBs, greatly simplifying their purification. In vitro, the platform facilitates the effective separation of AIBs by centrifugation and subsequent target protein release using SUMO-specific protease. The properties of the AIBs were determined using five proteins with different sizes, folding efficiencies, quaternary structure, and disulfide modifications. Electron microscopy shows that AIBs are synthesized in the form of complex fibrillar structures resembling "loofah sponges" with unusually thick filaments. The obtained results indicate that the new platform has promising features and could be developed to facilitate the synthesis and purification of target proteins and protein complexes without the use of renaturation.
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Affiliation(s)
| | | | | | - Irek I Gubaidullin
- National Research Center "Kurchatov Institute", Moscow, Russia
- Kurchatov Genomic Center, National Research Center "Kurchatov Institute"-GOSNIIGENETIKA, Moscow, Russia
| | | | | | | | - Sergei V Kuchin
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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4
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Zeng G, Zheng Y, Xiang Y, Liu R, Yang X, Lin Z. A novel protein purification scheme based on salt inducible self-assembling peptides. Microb Cell Fact 2023; 22:224. [PMID: 37899435 PMCID: PMC10614350 DOI: 10.1186/s12934-023-02229-5] [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: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND Protein purification remains a critical need for biosciences and biotechnology. It frequently requires multiple rounds of chromatographic steps that are expensive and time-consuming. Our lab previously reported a cleavable self-aggregating tag (cSAT) scheme for streamlined protein expression and purification. The tag consists of a self-assembling peptide (SAP) and a controllable self-cleaving intein. The SAP drives the target protein into an active aggregate, then by intein-mediated cleavage, the target protein is released. Here we report a novel cSAT scheme in which the self-assembling peptide is replaced with a salt inducible self-assembling peptide. This allows a target protein to be expressed first in the soluble form, and the addition of salt then drives the target protein into the aggregated form, followed by cleavage and release. RESULTS In this study, we used MpA (MKQLEDKIEELLSKAAMKQLEDKIEELLSK) as a second class of self-assembling peptide in the cSAT scheme. This scheme utilizes low salt concentration to keep the fusion protein soluble, while eliminating insoluble cellular matters by centrifugation. Salt then triggers MpA-mediated self-aggregation of the fusion, removing soluble background host cell proteins. Finally, intein-mediated cleavage releases the target protein into solution. As a proof-of-concept, we successfully purified four proteins and peptides (human growth hormone, 22.1 kDa; LCB3, 7.7 kDa; SpyCatcherΔN-ELP-SpyCatcherΔN, 26.2 kDa; and xylanase, 45.3 kDa) with yields ranging from 12 to 87 mg/L. This was comparable to the classical His-tag method both in yield and purity (72-97%), but without the His-tag. By using a further two-step column purification process that included ion-exchange chromatography and size-exclusion chromatography, the purity was increased to over 99%. CONCLUSION Our results demonstrate that a salt-inducible self-assembling peptide can serve as a controllable aggregating tag, which might be advantageous in applications where soluble expression of the target protein is preferred. This work also demonstrates the potential and advantages of utilizing salt inducible self-assembling peptides for protein separation.
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Affiliation(s)
- Guang Zeng
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Yinzhen Zheng
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Ya Xiang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Run Liu
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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Lin Z, Jing Y, Huang Y, Yang S, Chen S, Ou Y, Pistolozzi M, Yang X. A cleavable self-aggregating tag scheme for the expression and purification of disulfide bonded proteins and peptides. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Gorbunov AA, Sannikova EP, Gubaidullin II, Serobyan GA, Gorbunova AY, Serkina AV, Plokhikh KS, Kamyshinsky RA, Vorovitch MF, Bulushova NV, Kuchin S, Kozlov DG. Vaccine building ‘kit’: combining peptide bricks to elicit a desired immune response without adding an adjuvant. Nanomedicine (Lond) 2022; 17:461-475. [DOI: 10.2217/nnm-2021-0424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protein nanoparticles (NPs) can be used as vaccine platforms for target antigen presentation. Aim: To conduct a proof-of-concept study to demonstrate that an effective NP platform can be built based on a short self-assembling peptide (SAP) rather than a large self-assembling protein. Materials & methods: SUMO-based protein fusions (SFs) containing an N-terminal SAP and a C-terminal antigen were designed, expressed in Escherichia coli and purified. The structure was investigated by electron microscopy. The antibody response was tested in mice after two adjuvant-free immunizations. Results: Renatured SFs form fiber-like NPs with the antigen exposed on the surface and induce a significant antibody response with a remarkably high target-to-platform ratio. Conclusion: The platform is effective and has considerable potential for modification toward various applications, including vaccine development.
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Affiliation(s)
| | | | - Irek I Gubaidullin
- National Research Center ‘Kurchatov Institute’, Moscow, 123182, Russia
- National Research Center ‘Kurchatov Institute' - GOSNIIGENETIKA, Kurchatov Genomic Center, Moscow, 117545, Russia
| | - Gayane A Serobyan
- National Research Center ‘Kurchatov Institute’, Moscow, 123182, Russia
| | | | - Anna V Serkina
- National Research Center ‘Kurchatov Institute’, Moscow, 123182, Russia
| | | | | | - Mikhail F Vorovitch
- FSBSI ‘Chumakov FSC R&D IBP RAS’, Moscow, 108819, Russia
- Institute of Translational Medicine & Biotechnology, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | | | - Sergei Kuchin
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Dmitry G Kozlov
- National Research Center ‘Kurchatov Institute’, Moscow, 123182, Russia
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7
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Yang X, Lin Z, Jing Y. Cleavable Self-Aggregating Tags (cSAT) for Therapeutic Peptide Expression and Purification. Methods Mol Biol 2022; 2406:131-143. [PMID: 35089554 DOI: 10.1007/978-1-0716-1859-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Efficient protein and peptide expression and purification technologies are highly needed in biotechnology, especially in light of the increasing number of proteins and peptides that are being exploited for therapeutic use, which are inherently difficult to produce via biological means. In this chapter, we describe a facile, reliable, and cost-effective peptide production and purification strategy based on short self-assembling peptides (e.g., L6KD (LLLLLLKD)) and a C-terminal cleavage intein (e.g., Mtu ΔI-CM). This cleavable self-aggregating tag (cSAT) scheme depends on the in vivo formation of aggregates of the fusion protein containing the target peptide, which is induced during the expression by the presence of the self-assembling peptide in the construct. After a simple separation of the aggregates by centrifugation, the purified target peptide with authentic N-terminus is released in solution by pH-induced intein self-cleavage. As an example, a yield of about 4.4 μg/mg wet cell pellet was obtained when the cSAT scheme was used for the expression and purification of the therapeutic peptide GLP-1. This strategy provides a viable approach for preparing peptides with authentic N-termini, especially those in the range of 30 ~ 100 amino acids in size that are typically unstable or susceptible to degradation in Escherichia coli.
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Affiliation(s)
- Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Yanyun Jing
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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8
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Lin Z, Amesso Ndengue PP, Jing Y, Zhao L, Yang X. Facile expression and purification of active human growth hormone in E. coli by a cleavable self-aggregating tag scheme. Protein Expr Purif 2021; 188:105974. [PMID: 34520839 DOI: 10.1016/j.pep.2021.105974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 02/06/2023]
Abstract
Human growth hormone (hGH) plays an important role in growth control, growth promotion, cell development, and regulation of numerous metabolic pathways in the human body and has been approved by the U.S. FDA for the treatment of several human dysfunctions. Over-expression of recombinant hGH (rhGH) affords a misfolded form in cytoplasm of Escherichia coli, and the refolding step required to obtain active rhGH greatly affects its production costs. Herein, the cleavable self-aggregating tag (cSAT) scheme was used for the expression and purification of rhGH in E. coli. Four aggregating tags (L6KD/α3-peptide/EFK8/ELK16) successfully drove rhGH into active protein aggregates. After the Mxe GyrA intein-mediated cleavage, 2.8-21.4 μg rhGH/mg wet cell weight was obtained at laboratory scale, of which the L6KD fusion achieved the highest rhGH yield. The further refined rhGH maintained 92% of the bioactivity compared to commercial rhGH. The self-assembling of the aggregating tag might physically separate the hGH polypeptide chains, which in turn was beneficial to its folding into the active form. This study provided a simple and cost-effective approach for active rhGH production, and suggested an opportunity for improve folding of recombinant proteins in E. coli.
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Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
| | - Peguy Paulie Amesso Ndengue
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Yanyun Jing
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Lei Zhao
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou, 510006, China.
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9
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Hu J, Chen Y, Ren Y, Xiao W, Hu Y, Yu X, Fan J. Combination of the mutations for improving activity of TEV protease in inclusion bodies. Bioprocess Biosyst Eng 2021; 44:2129-2139. [PMID: 34036441 DOI: 10.1007/s00449-021-02589-5] [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: 01/22/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
Tobacco etch virus protease (TEVp) is an enzymatic reagent to remove fusion tag, but additional purification steps are required for removing the TEVp after cleavage reaction is finished. Use of carrier-free and dependent TEVp immobilizates can eliminate protease contamination. In this work, we identified that, among the four constructed missense variants, the insoluble variant with the highest activity was correspondent with the soluble one tested formerly. The activities of the insoluble 15 codon variants were assayed and the variant with highest activity was selected. The K45F and/or E106G mutations have been reported on slightly improving protein stability of the wild-type TEVp, but only E106G mutation enhanced soluble production and activity of the selected TEVp variant, and it increased soluble amounts of two codon variants with the impaired folding. The decreased activity and use efficiency of the optimized TEVp variant in inclusion bodies was balanced by the determined high level production, lower leaking amounts of the protein, the enhanced resistance to the limited proteolysis mediated by protease K and trypsin, and the increased inhibition of auto-cleavage, as comparison to those of the immobilized soluble one. Thus, the TEVp construct is a potential alternate for simplifying protein purification protocols after tag-removal.
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Affiliation(s)
- Jiong Hu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yinghua Chen
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yuanyuan Ren
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Wenjun Xiao
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xuelian Yu
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, 130, Changjiang West Road, Hefei, 230036, Anhui Province, People's Republic of China.
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10
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Sannikova EP, Klebanov FA, Cheperegin SE, Kozlov DG. Properties and Biotechnological Application of Mutant Derivatives of the Mini-Intein PRP8 from Penicillium chrysogenum with Improved Control of C-Terminal Processing. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820080098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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12
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Lin Z, Lin Q, Li J, Pistolozzi M, Zhao L, Yang X, Ye Y. Spy chemistry-enabled protein directional immobilization and protein purification. Biotechnol Bioeng 2020; 117:2923-2932. [PMID: 32543719 DOI: 10.1002/bit.27460] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/10/2020] [Accepted: 06/14/2020] [Indexed: 12/15/2022]
Abstract
Site-directed protein immobilization allows the homogeneous orientation of proteins with high retention of activity, which is advantageous for many applications. Here, we report a facile, specific, and efficient strategy based on the SpyTag-SpyCatcher chemistry. Two SpyTag-fused model proteins, that is, the monomeric red fluorescent protein (RFP) and the oligomeric glutaryl-7-aminocephalosporanic acid acylase, were easily immobilized onto a SpyCatcher-modified resin directly from cell lysates, with activity recoveries in the range of 85-91%. This strategy was further adapted to protein purification, which proceeded through the selective capture of the SpyCatcher-fused target proteins by a SpyTag-modified resin, with the aid of an intein to generate authentic N-termini. For two model proteins, that is, RFP and a variable domain of a heavy chain antibody, the yields were ∼3-7 mg/L culture with >90% purities. This approach could provide a versatile tool for producing high-performance immobilized protein devices and proteins for industrial and therapeutic uses.
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Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Qiao Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Jiahui Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Marco Pistolozzi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Lei Zhao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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13
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Jäger VD, Lamm R, Küsters K, Ölçücü G, Oldiges M, Jaeger KE, Büchs J, Krauss U. Catalytically-active inclusion bodies for biotechnology-general concepts, optimization, and application. Appl Microbiol Biotechnol 2020; 104:7313-7329. [PMID: 32651598 PMCID: PMC7413871 DOI: 10.1007/s00253-020-10760-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022]
Abstract
Bacterial inclusion bodies (IBs) have long been considered as inactive, unfolded waste material produced by heterologous overexpression of recombinant genes. In industrial applications, they are occasionally used as an alternative in cases where a protein cannot be expressed in soluble form and in high enough amounts. Then, however, refolding approaches are needed to transform inactive IBs into active soluble protein. While anecdotal reports about IBs themselves showing catalytic functionality/activity (CatIB) are found throughout literature, only recently, the use of protein engineering methods has facilitated the on-demand production of CatIBs. CatIB formation is induced usually by fusing short peptide tags or aggregation-inducing protein domains to a target protein. The resulting proteinaceous particles formed by heterologous expression of the respective genes can be regarded as a biologically produced bionanomaterial or, if enzymes are used as target protein, carrier-free enzyme immobilizates. In the present contribution, we review general concepts important for CatIB production, processing, and application. KEY POINTS: • Catalytically active inclusion bodies (CatIBs) are promising bionanomaterials. • Potential applications in biocatalysis, synthetic chemistry, and biotechnology. • CatIB formation represents a generic approach for enzyme immobilization. • CatIB formation efficiency depends on construct design and expression conditions.
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Affiliation(s)
- Vera D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, Espoo, 02150, Finland
| | - Robin Lamm
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Gizem Ölçücü
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jochen Büchs
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
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14
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Han H, Zeng W, Zhang G, Zhou J. Active tyrosine phenol-lyase aggregates induced by terminally attached functional peptides in Escherichia coli. J Ind Microbiol Biotechnol 2020; 47:563-571. [PMID: 32737623 PMCID: PMC7508748 DOI: 10.1007/s10295-020-02294-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
The formation of inclusion bodies (IBs) without enzyme activity in bacterial research is generally undesirable. Researchers have attempted to recovery the enzyme activities of IBs, which are commonly known as active IBs. Tyrosine phenol-lyase (TPL) is an important enzyme that can convert pyruvate and phenol into 3,4-dihydroxyphenyl-L-alanine (L-DOPA) and IBs of TPL can commonly occur. To induce the correct folding and recover the enzyme activity of the IBs, peptides, such as ELK16, DKL6, L6KD, ELP10, ELP20, L6K2, EAK16, 18A, and GFIL16, were fused to the carboxyl terminus of TPL. The results showed that aggregate particles of TPL-DKL6, TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16 improved the enzyme activity by 40.9%, 50.7%, 48.9%, 86.6%, and 97.9%, respectively. The peptides TPL-DKL6, TPL-EAK16, TPL-18A, and TPL-GFIL16 displayed significantly improved thermostability compared with TPL. L-DOPA titer of TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16, with cells reaching 37.8 g/L, 53.8 g/L, 37.5 g/L, and 29.1 g/L, had an improvement of 111%, 201%, 109%, and 63%, respectively. A higher activity and L-DOPA titer of the TPL-EAK16 could be valuable for its industrial application to biosynthesize L-DOPA.
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Affiliation(s)
- Hongmei Han
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guoqiang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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15
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Lin Z, Zhao Q, Wang X, Zhou B, Xing L, Wang J, Pistolozzi M, Zhao L, Wang T. Engineered pH‐inducible intein
Mtu
ΔI‐CM variants with markedly reduced premature cleavage activity. AIChE J 2019. [DOI: 10.1002/aic.16806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhanglin Lin
- School of Biology and Biological EngineeringSouth China University of Technology Guangzhou China
- Department of Chemical EngineeringTsinghua University Beijing China
| | - Qing Zhao
- Department of Chemical EngineeringTsinghua University Beijing China
| | - Xu Wang
- Department of Chemical EngineeringTsinghua University Beijing China
| | - Bihong Zhou
- Department of Chemical EngineeringTsinghua University Beijing China
| | - Lei Xing
- Department of Chemical EngineeringTsinghua University Beijing China
| | - Jiangyun Wang
- Institute of BiophysicsChinese Academy of Sciences Beijing China
| | - Marco Pistolozzi
- School of Biology and Biological EngineeringSouth China University of Technology Guangzhou China
| | - Lei Zhao
- School of Biology and Biological EngineeringSouth China University of Technology Guangzhou China
| | - Tingting Wang
- School of Biology and Biological EngineeringSouth China University of Technology Guangzhou China
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16
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A novel protein purification strategy mediated by the combination of CipA and Ssp DnaB intein. J Biotechnol 2019; 301:97-104. [PMID: 31181238 DOI: 10.1016/j.jbiotec.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
Protein purification is an indispensable step in diverse fields of biological research or production process. Conventional purification methods including the affinity purification or the usage of self-aggregating tags suffered from many drawbacks such as the complicated steps, high cost and low efficiency. Moreover, the fusion tag usually had negative effects on the activity of the target protein. To address the above issues, here we propose a novel protein purification method which needs simple operation steps, and this method is mediated by the combination of CipA protein and a mini-intein (Synechocystis sp. PCC6803 DnaB, Ssp DnaB), depending on the assembly function of CipA and the self-cleavage function of Ssp DnaB. To realize the purification, CipA-DnaB-eGFP protein was expressed and assembled into protein crystalline inclusions (PCIs) in E. coli. Then, only cell lysis, cleavage and centrifugation steps were required to purify eGFP. Purified eGFP was in the supernatant with a purity of over 90%. The cleavage efficiency and the yield of eGFP reached 51.96% and 13.99 ± 0.88 mg/L fermentation broth, respectively. Furthermore, to broaden the application of this approach, three other proteins which were maltose binding protein (MBP), ketoisovalerate decarboxylase (Kivd) and alcohol dehydrogenase (AdhP) were purified with high cleavage efficiency. The purified Kivd and AdhP remained high specific activities. This work demonstrated an effective and convenient protein purification method.
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17
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Luo H, Hu L, Ma B, Zhao M, Luo M, Deng Q, Deng S, Ye H, Lin T, Chen J, Wang T, Zhu J, Lu H. Molecular dynamics based improvement of the solubilizing self-cleavable tag Z basic-ΔI-CM application in the preparation of recombinant proteins in Escherichia coli. Biochem Biophys Res Commun 2019; 513:412-418. [PMID: 30967267 DOI: 10.1016/j.bbrc.2019.03.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
Abstract
Zbasic-ΔI-CM is a novel intein-based self-cleavable tag we developed to accelerate the soluble expression of recombinant proteins in Escherichia coli (E. coli). Previously we found that intein activity could be interfered by its flanking exteins, and thus reducing the production efficiency and final yield. In this work, we used CXC-chemokine 9 (CXCL9) as a model C-extein, which fusion with Zbasic-ΔI-CM showed high intein activity. When the fusion protein got soluble expression, CXCL9 was released immediately and purified directly from cell lysis supernatant. The results demonstrated that Zbasic-ΔI-CM tag had successfully mediated the efficient production of high-quality CXCL9 with reduced time and resources consumption in comparison with inclusion bodies expression. Molecular dynamics simulations suggested that the improved cleavage activity of Zbasic-ΔI-CM upon fusion with CXCL9 may be due to the higher dynamics of the first half loop and stabilization of the second half loop of intein. Our results proved that the self-cleavable Zbasic-ΔI-CM mediated soluble expression could be a feasible process for cytokines like CXCL9, thus of attractive potentials for production of therapeutic proteins using E. coli expression system.
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Affiliation(s)
- Han Luo
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lifu Hu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Research Institute at Frederick, Frederick, MD, 21702, USA
| | - Meiqi Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Manyu Luo
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qing Deng
- Regeneromics Laboratory, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shaorong Deng
- Regeneromics Laboratory, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Ye
- Regeneromics Laboratory, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Tong Lin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Junsheng Chen
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Tao Wang
- Jecho Biopharmaceuticals Co. Ltd., 2633 Zhongbin Road, Sino-Singapore Tianjin Eco-City, Tianjin, 300467, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China; Jecho Biopharmaceuticals Co. Ltd., 2633 Zhongbin Road, Sino-Singapore Tianjin Eco-City, Tianjin, 300467, China; Jecho Laboratories, Inc., 7320 Executive Way, Frederick, MD, 21704, USA.
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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18
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Fan Y, Miozzi JM, Stimple SD, Han TC, Wood DW. Column-Free Purification Methods for Recombinant Proteins Using Self-Cleaving Aggregating Tags. Polymers (Basel) 2018; 10:polym10050468. [PMID: 30966502 PMCID: PMC6415421 DOI: 10.3390/polym10050468] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
Conventional column chromatography processes to purify recombinant proteins are associated with high production costs and slow volumetric throughput at both laboratory and large scale. Non-chromatographic purifications based on selective aggregating tags have the potential to reduce costs with acceptable protein yields. A significant drawback, however, is that current proteolytic approaches for post-purification tag removal after are expensive and non-scalable. To address this problem, we have developed two non-chromatographic purification strategies that use either the elastin-like polypeptide (ELP) tag or the β-roll tag (BRT17) in combination with an engineered split intein for tag removal. The use of the split intein eliminates premature cleavage during expression and provides controlled cleavage under mild conditions after purification. These self-cleaving aggregating tags were used to efficiently purify β-lactamase (β-lac), super-folder green fluorescent protein (sfGFP), streptokinase (SK) and maltose binding protein (MBP), resulting in increased yields compared to previous ELP and BRT17-based methods. Observed yields of purified targets for both systems typically ranged from approximately 200 to 300 micrograms per milliliter of cell culture, while overall recoveries ranged from 10 to 85 percent and were highly dependent on the target protein.
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Affiliation(s)
- Yamin Fan
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Jackelyn M Miozzi
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Samuel D Stimple
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Tzu-Chiang Han
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - David W Wood
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
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19
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New trends in aggregating tags for therapeutic protein purification. Biotechnol Lett 2018; 40:745-753. [PMID: 29605942 DOI: 10.1007/s10529-018-2543-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
Abstract
The rapid growth of the therapeutic protein market calls for more efficient purification methods. Various aggregating tags have recently emerged as simple, fast, cost-effective and column-free technologies for protein (and peptide) purification. In general, these column-free protein purification technologies involve the use of aggregating tags that induce the target protein into insoluble aggregates. These aggregates can be easily separated from soluble impurities and the target protein or peptide is then liberated by a cleavage process. This review summarizes the current state-of-the-art in using aggregating tags for protein purification. The methods are here categorized as follows: (1) tags that allow soluble expression of target protein in vivo and induce aggregation in vitro; (2) tags that induce soluble expression and self-assembling of target protein on insoluble biological polyester beads in vivo; (3) tags that induce formation of inactive aggregates in vivo; (4) tags that induce formation of active aggregates in vivo.
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