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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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Zhang Q, Cai Z, Lin H, Han L, Yan J, Wang J, Ke P, Zhuang J, Huang X. Expression, purification and identification of isotope-labeled recombinant cystatin C protein in Escheichia coli intended for absolute quantification using isotope dilution mass spectrometry. Protein Expr Purif 2020; 178:105785. [PMID: 33152458 DOI: 10.1016/j.pep.2020.105785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 10/23/2022]
Abstract
Isotope-labeled proteins are expected to be used as internal standard proteins in the field of protein quantification by isotope dilution mass spectrometry (ID/MS). To achieve the absolute quantification of Cystatin C (Cys C) based on ID/MS, we aims to obtain 15N isotope-labeled recombinant Cys C (15N-Cys C) protein. Firstly, the Cys C gene was optimized based on the preferred codons of Escherichia coli, and inserted into the pET-28a(+) expression plasmid. Then, the plasmid was transformed into TOP10 and BL21 strains, and 15N-Cys C was expressed in M9 medium using 15N as the only nitrogen source. 15N-Cys C was detected by SDS-PAGE, protein immunoblotting and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The characteristic peptides obtained from 15N-Cys C were analyzed by a Q Exactive Plus MS system. Results showed that 53.06% of the codons were optimized. The codon adaptation index of the Cys C genes increased from 0.31 to 0.95, and the GC content was adjusted from 64.85% to 54.88%. The purity of 15N-Cys C was higher than 95%. MALDI-TOF MS analysis showed that the m/z of 15N-Cys C had changed from 13 449 to 14 850. The characteristic peptides showed that 619.79 m/z (M+2H)2+ was the parent ion of 15N-Cys C and that the secondary ions of 15N-labeled peptides from y+5 to y+9 were 616.27 m/z, 716.33 m/z, 788.39 m/z, 936.43 m/z, and 1052.46 m/z, respectively. In conclusion, we successfully expressed, purified and identified of 15N-Cys C protein in Escheichia coli intended for absolute quantification using ID/MS.
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Affiliation(s)
- Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhiliang Cai
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Haibiao Lin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liqiao Han
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jun Yan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianbing Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junhua Zhuang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Zhang Y, Zhao J, He S, Cao X. Soluble Expression of Recombinant Human Cystatin C and Comparison of the Ni Column and Magnetic Bead Purification. Protein J 2019; 39:85-95. [PMID: 31625059 DOI: 10.1007/s10930-019-09873-0] [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] [Indexed: 02/02/2023]
Abstract
Cystatin C, also known as γ-trace or post-γ-globulin, is a cysteine protease inhibitor from the cystatin superfamily. It is usually used as a marker of the glomerular filtration rate owing to its low molecular weight and constant secretion. The recently available methods for cystatin C preparation have low outputs. Hence, a productive preparation system is urgently required. In this study, a 6 × His-tag coupled with a thrombin cleavage site was fused to the C-terminus of cystatin C, and the protein was well expressed in Escherichia coli after optimization. Then, two different systems were used to obtain no-tag cystatin C: a traditional nickel (Ni)-column system and a subtly Ni magnetic bead system. The column system was more commonly used, and the magnetic bead system was more convenient. Cystatin C (purity > 97%) was successfully obtained, and the yields in both the systems were higher than those in previous studies. Further, the proper folding status and bioactivity of recombinant cystatin C were confirmed using the papain inhibition assay, dynamic light scattering, and circular dichroism spectroscopy.
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Affiliation(s)
- Yibin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jian Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Shiyu He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xuni Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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Abstract
The remarkable growth of therapeutic peptide development in the past decade has led to a large number of market approvals and the market value is expected to hit $25 billion by 2018. This significant market increase is driven by the increasing incidences of metabolic and cardiovascular diseases and technological advancements in peptide synthesis. For this reason, the search for bioactive peptides has also increased exponentially. Many bioactive peptides from food and nonfood sources have shown positive health effects yet, obstacles such as the need to implement efficient and cost-effective strategies for industrial scale production, good manufacturing practices as well as well-designed clinical trials to provide robust evidence for supporting health claims continue to exist. Several other factors such as the possibility of allergenicity, toxicity and the stability of biological functions of the peptides during gastrointestinal digestion would need to be addressed.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea
| | - Byong H Lee
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea.,b Department of Microbiology/Immunology , McGill University , Montreal , QC , H3A 2B4 , Canada
| | - Deog H Oh
- a Department of Food Science and Biotechnology , Kangwon National University , Chuncheon , South Korea
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Chen T, Xu W. A purification method for tag-free human cystatin C recombinant protein expressed in Escherichia coli. Prep Biochem Biotechnol 2017; 47:123-128. [PMID: 27143404 DOI: 10.1080/10826068.2016.1181087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To obtain recombinant cystatin C (CysC) protein, which can be used in immunological diagnostic kits, we focused on the preparation of tag-free CysC. The 6 × His-TF-CysC fusion protein was found to overexpress in soluble form in cells of BL21-Gold (DE3)/pCold TF-CysC, which had been induced with isopropyl-D-1-thiogalactopyranoside. Subsequently, we established a protein purification method for tag-free CysC using immobilized metal-affinity chromatography and size-exclusion chromatography. In this method, glutathione-S-transferase-human rhinovirus 3C proteases were used to remove the protein tags. High homogeneity of the purified CysC was determined by SDS-PAGE, while the purity of the tag-free CysC was ascertained to be above 95%. With a yield of 25 mg/L from bacterial culture, the biological activity of the tag-free CysC was evaluated as inhibitors like natural CysC. The performance of this purification method was successfully evaluated in the preparation of other low molecular weight heterologous proteins in Escherichia coli.
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Affiliation(s)
- Te Chen
- a Department of Laboratory Medicine , The First Affiliated Hospital of Chongqing Medical University , Chongqing , China
| | - Wenchun Xu
- b Laboratory of Medical Diagnostics (Ministry of Education of China) , Department of Key Laboratory Medicine, Chongqing Medical University , Chongqing , China
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Tang X, Chen J, Wang Y, Wang X. Gene cloning, expression and polyclonal antibody preparation of Rab3A for protein interaction analysis. SPRINGERPLUS 2016; 5:1705. [PMID: 27795879 PMCID: PMC5052235 DOI: 10.1186/s40064-016-3330-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 11/29/2022]
Abstract
Background Rab3A is a GTP-binding protein and plays critical roles in the regulation of synaptic vesicle exocytosis. Up to date, how Rab3A participates in such a regulatory process is not completely clear. Results In this report the Rab3A gene from Rattus norvegicus was cloned and heterologously expressed in E. coli using pCold-TF expression vector with folding capacity. Due to the presence of His-tag sequence on the N-terminal side, Rab3A fusion protein was purified to greater than 95 % purity with a single Ni-affinity purification step. After the Rab3A fusion protein was used to immunize mice, an anti-serum against Rab3A with a titer of about 6000 was generated. Western blot analysis indicated that the prepared polyclonal antibody could recognize both Rab3A fusion protein and native Rab3A protein. To remove the tag sequence, thrombin was used to cleave the Rab3A fusion protein, followed by SDS-PAGE to separate the cleavage products. Using the gel protein recovery strategy with a Micro Protein PAGE Recovery Kit, the de-tagged Rab3A protein of electrophoretic purity was prepared. Conclusions The present work not only prepared the ground for the study on Rab3A-mediated protein interactions, but also provided systematic experimental methods referable for the similar studies.
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Affiliation(s)
- Xia Tang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
| | - Jia Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
| | - Ying Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
| | - Xianchun Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan China
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Chauhan S, Tomar RS. Efficient expression and purification of biologically active human cystatin proteins. Protein Expr Purif 2016; 118:10-7. [DOI: 10.1016/j.pep.2015.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
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Perlenfein TJ, Murphy RM. Expression, purification, and characterization of human cystatin C monomers and oligomers. Protein Expr Purif 2015; 117:35-43. [PMID: 26409164 DOI: 10.1016/j.pep.2015.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022]
Abstract
Human cystatin C (cysC) is a soluble basic protein belonging to the cysteine protease inhibitor family. CysC is a potent inhibitor of cathepsins--proteolytic enzymes that degrade intracellular and endocytosed proteins, remodel extracellular matrix, and trigger apoptosis. Inhibition is via tight reversible binding involving the N-terminus as well as two β-hairpin loops of cysC. As a significant component of cerebrospinal fluid, cysC has numerous other functions, including support of neural stem cell growth and differentiation. Several studies suggest that cysC may bind to the Alzheimer-related protein beta-amyloid (Aβ), and inhibit its aggregation and toxicity. Because of an increasing recognition of its important biological roles, there is considerable interest in methods to produce full-length recombinant human cysC. Several researchers have reported success, but with processes that require multiple purification steps. Here we report successful production of human cysC using an intein-based expression system and a simple one-column purification scheme. The recombinant protein so obtained was natively folded and active as an enzyme inhibitor. Unexpectedly, even mild concentration by ultrafiltration caused significant oligomerization. The oligomers are noncovalent and retain the native secondary structure and inhibitory activity of the monomer. The oligomers, but not the monomers, were highly effective at inhibiting aggregation of Aβ. These results demonstrate the critical importance of careful physicochemical characterization of recombinant cysC protein prior to evaluation of its biological functions.
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Affiliation(s)
- Tyler J Perlenfein
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Regina M Murphy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, United States.
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Zhou Y, Zhou Y, Li J, Chen J, Yao Y, Yu L, Peng D, Wang M, Su D, He Y, Gou L. Efficient expression, purification and characterization of native human cystatin C in Escherichia coli periplasm. Protein Expr Purif 2015; 111:18-22. [DOI: 10.1016/j.pep.2015.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 01/06/2023]
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