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Yang Y, Ahmad E, Premkumar V, Liu A, Ashikur Rahman SM, Nikolovska‐Coleska Z. Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. Protein Sci 2024; 33:e5019. [PMID: 38747396 PMCID: PMC11094776 DOI: 10.1002/pro.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
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Affiliation(s)
- Yuting Yang
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Ejaz Ahmad
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Vidhya Premkumar
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Alicen Liu
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - S. M. Ashikur Rahman
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Zaneta Nikolovska‐Coleska
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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2
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Arumapperuma T, Snow AJD, Lee M, Sharma M, Zhang Y, Lingford JP, Goddard-Borger ED, Davies GJ, Williams SJ. Capture-and-release of a sulfoquinovose-binding protein on sulfoquinovose-modified agarose. Org Biomol Chem 2024; 22:3237-3244. [PMID: 38567495 DOI: 10.1039/d4ob00307a] [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: 04/04/2024]
Abstract
The solute-binding protein (SBP) components of periplasmic binding protein-dependent ATP-binding cassette (ABC)-type transporters often possess exquisite selectivity for their cognate ligands. Maltose binding protein (MBP), the best studied of these SBPs, has been extensively used as a fusion partner to enable the affinity purification of recombinant proteins. However, other SBPs and SBP-ligand based affinity systems remain underexplored. The sulfoquinovose-binding protein SmoF, is a substrate-binding protein component of the ABC transporter cassette in Agrobacterium tumefaciens involved in importing sulfoquinovose (SQ) and its derivatives for SQ catabolism. Here, we show that SmoF binds with high affinity to the octyl glycoside of SQ (octyl-SQ), demonstrating remarkable tolerance to extension of the anomeric substituent. The 3D X-ray structure of the SmoF·octyl-SQ complex reveals accommodation of the octyl chain, which projects to the protein surface, providing impetus for the synthesis of a linker-equipped SQ-amine using a thiol-ene reaction as a key step, and its conjugation to cyanogen bromide modified agarose. We demonstrate the successful capture and release of SmoF from SQ-agarose resin using SQ as competitive eluant, and selectivity for release versus other organosulfonates. We show that SmoF can be captured and purified from a cell lysate, demonstrating the utility of SQ-agarose in capturing SQ binding proteins from complex mixtures. The present work provides a pathway for development of 'capture-and-release' affinity resins for the discovery and study of SBPs.
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Affiliation(s)
- Thimali Arumapperuma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Alexander J D Snow
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, UK.
| | - Mihwa Lee
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, UK.
| | - Yunyang Zhang
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - James P Lingford
- Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia.
| | - Ethan D Goddard-Borger
- Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, UK.
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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3
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Patra A, Kandasamy T, Ghosh SS, Saini GK. In vitro anticancer effects of recombinant anisoplin through activation of SAPK/JNK and downregulation of NFκB. Toxicol In Vitro 2024; 94:105737. [PMID: 37984481 DOI: 10.1016/j.tiv.2023.105737] [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: 03/25/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Emerging chemotherapeutic resistance is considered as one of the major obstacles in breast cancer therapy. Fungal ribotoxins possess promising therapeutic potential against cancer owing to their ribosome-targeted protein synthesis inhibitory action. Though the entomopathogenic ribotoxin anisoplin was characterized in the earlier study, its therapeutic efficacy against cancer cells remained unexplored. In the current study, recombinant anisoplin has been successfully produced in Escherichia coli BL21(DE3) expression system and further purified and validated by in silico, biophysical and functional characterizations. Recombinant anisoplin significantly reduced the viability of MCF-7 breast cancer cells in a dose-dependent manner. It exhibited an IC50 value of 4 μM with concurrent 3.5 fold elevation in the intracellular reactive oxygen species. Anisoplin also resulted in depolarization of the mitochondrial membrane and subsequently induced apoptosis, as evident from flow cytometric analyses. In addition, MCF-7 cells significantly lost their self-renewal capability for clonal expansion and regeneration upon treatment. Immunoblotting experiments further confirmed activation of downstream JNK-dependent MAP kinase signaling pathway due to ribotoxic stress response generated by anisoplin through upregulation of phospho-SAPK/JNK expression. This upregulation was further correlated with the NFκB expression profile, leading to cell death, highlighting therapeutic potential of the recombinant anisoplin.
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Affiliation(s)
- Arupam Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Thirukumaran Kandasamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Gurvinder Kaur Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India.
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4
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Wang Y, Li S, Zhou Z, Sun L, Sun J, Shen C, Gao R, Song J, Pu X. The Functional Characteristics and Soluble Expression of Saffron CsCCD2. Int J Mol Sci 2023; 24:15090. [PMID: 37894770 PMCID: PMC10606151 DOI: 10.3390/ijms242015090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Crocins are important natural products predominantly obtained from the stigma of saffron, and that can be utilized as a medicinal compound, spice, and colorant with significant promise in the pharmaceutical, food, and cosmetic industries. Carotenoid cleavage dioxygenase 2 (CsCCD2) is a crucial limiting enzyme that has been reported to be responsible for the cleavage of zeaxanthin in the crocin biosynthetic pathway. However, the catalytic activity of CsCCD2 on β-carotene/lycopene remains elusive, and the soluble expression of CsCCD2 remains a big challenge. In this study, we reported the functional characteristics of CsCCD2, that can catalyze not only zeaxanthin cleavage but also β-carotene and lycopene cleavage. The molecular basis of the divergent functionality of CsCCD2 was elucidated using bioinformatic analysis and truncation studies. The protein expression optimization results demonstrated that the use of a maltose-binding protein (MBP) tag and the optimization of the induction conditions resulted in the production of more soluble protein. Correspondingly, the catalytic efficiency of soluble CsCCD2 was higher than that of the insoluble one, and the results further validated its functional verification. This study not only broadened the substrate profile of CsCCD2, but also achieved the soluble expression of CsCCD2. It provides a firm platform for CsCCD2 crystal structure resolution and facilitates the synthesis of crocetin and crocins.
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Affiliation(s)
- Ying Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Siqi Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Ze Zhou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Lifen Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Jing Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Chuanpu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Ranran Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
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5
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Wang B, Zhao X, Fu T, Chen X, Guo X, Li X, Yang F. Glucose Starvation Stimulates the Promoting Strength of a Novel Evolved Suc2 Promoter. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13838-13847. [PMID: 37669532 DOI: 10.1021/acs.jafc.3c03699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Promoters are essential for designing Saccharomyces cerevisiae cell factories. Identifying novel promoters tuned to produce specific metabolites under increasingly diverse industrial stresses is required to improve the economic feasibility of whole fermentation processes. In this study, a positively evolved Suc2 promoter (SUC 2p) with promoter activity stronger than that of the wild-type Suc2 promoter (SUC 2wtp) was obtained. Quantitative real-time PCR, fluorescence analysis, Western blotting, and a β-galactosidase activity assay revealed that SUC 2p is a medium-strength promoter compared with eight reported promoters at a medium glucose concentration (2% (w/v)). Different glucose concentrations modulated the strength of SUC 2p. Low glucose concentrations (0.05 and 0.5% (w/v)) enhanced the promoter strength of SUC 2p dramatically, with promoter activity higher than that of reported strong promoters. Glucose starvation resulted in the formation of a new Msn2/4 binding site on SUC 2p. Our work should facilitate the development of promoters with novel fine-tuning properties and the construction of S. cerevisiae cell factories suitable for the industrial production of essential chemicals under glucose-deprived conditions.
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Affiliation(s)
- Biying Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoya Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Tong Fu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyu Guo
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
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6
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Loughran ST, Walls D. Tagging Recombinant Proteins to Enhance Solubility and Aid Purification. Methods Mol Biol 2023; 2699:97-123. [PMID: 37646996 DOI: 10.1007/978-1-0716-3362-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has a long history, and there is a considerable repertoire of these that can be used to address issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. In this chapter, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
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Affiliation(s)
- Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland.
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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7
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Zhang Z, Su W, Bao Y, Huang Q, Ye K, Liu P, Chu X. Modular reconstruction and optimization of the trans-4-hydroxy-L-proline synthesis pathway in Escherichia coli. Microb Cell Fact 2022; 21:159. [PMID: 35953819 PMCID: PMC9367115 DOI: 10.1186/s12934-022-01884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background In recent years, there has been a growing demand for microbial production of trans-4-hydroxy-L-proline (t4Hyp), which is a value-added amino acid and has been widely used in the fields of medicine, food, and cosmetics. In this study, a multivariate modular metabolic engineering approach was used to remove the bottleneck in the synthesis pathway of t4Hyp. Results Escherichia coli t4Hyp synthesis was performed using two modules: a α-ketoglutarate (α-KG) synthesis module (K module) and L-proline synthesis with hydroxylation module (H module). First, α-KG attrition was reduced, and then, L-proline consumption was inhibited. Subsequently, to improve the contribution to proline synthesis with hydroxylation, optimization of gene overexpression, promotor, copy number, and the fusion system was performed. Finally, optimization of the H and K modules was performed in combination to balance metabolic flow. Using the final module H1K4 in a shaking flask culture, 8.80 g/L t4Hyp was produced, which was threefold higher than that produced by the W0 strain. Conclusions These strategies demonstrate that a microbial cell factory can be systematically optimized by modular engineering for efficient production of t4Hyp. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01884-4.
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Affiliation(s)
- Zhenyu Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.,School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yunyun Bao
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Qianqian Huang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Kai Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
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8
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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9
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Kronqvist N, Rising A, Johansson J. A Novel Approach for the Production of Aggregation-Prone Proteins Using the Spidroin-Derived NT* Tag. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2406:113-130. [PMID: 35089553 DOI: 10.1007/978-1-0716-1859-2_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Spiders have evolved proteins that can be kept in a highly concentrated soluble form in the silk gland yet rapidly assemble into stable silk fibers under certain environmental conditions. The transition between soluble and fibrillar states is partly regulated by the pH-sensitive N-terminal (NT) domain which has emerged as nature's own solubility-enhancing domain. NT has an inherent capacity to keep the silk proteins' partly hydrophobic and very aggregation-prone regions from premature fibrillation in spite of storage at enormous concentrations. The genetically engineered double-mutant NT* shows increased solubility and stability and has arisen as a powerful tool for the production of aggregation-prone as well as other recombinant proteins. Here we describe a robust and highly efficient protocol for improved soluble expression of peptides and proteins by fusion to the NT* tag.
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Affiliation(s)
- Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.
| | - Anna Rising
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
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10
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A Method for Evaluation of the Level of Circulating Mitochondrial DNA by ND1 and ND2 Genes. Bull Exp Biol Med 2022; 172:495-498. [PMID: 35175481 PMCID: PMC8853029 DOI: 10.1007/s10517-022-05421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 11/20/2022]
Abstract
The measurement of the level of mitochondrial DNA (mtDNA) in the blood is a difficult problem due to high variability of mitochondrial genes, deletions in the mitochondrial genome in some pathological conditions, different sources of mtDNA into the bloodstream (mtDNA from tissues, from blood cells, etc.). We designed primers and TaqMan probes for highly conserved regions of the ND1 and ND2 genes outside the mitochondrial deletions “hot zones”. For standardizing the technique, the true concentration of low-molecular-weight mtDNA was determined by real-time PCR for two targets: a fragment of the ND2 gene (122 bp) and the ND1 and ND2 genes (1198 bp). The sensitivity and specificity of the developed approach were verified on a DNA pool isolated from the blood plasma of healthy donors of various nationalities. The concentration of low-molecular-weight mtDNA in the blood plasma of two patients with COVID-19 was monitored over two weeks of inpatient treatment. A significant increase in the content of low-molecular-weight mtDNA was observed during the first 5 days after hospitalization, followed by a drop to the level of healthy donors. The developed technique makes it possible to assess the blood level of low-molecular-weight mtDNA regardless of the quality of sampling and makes it possible to standardize this biological marker in a wide range of infectious and non-infectious pathologies.
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11
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Kamma E, Lasisi W, Libner C, Ng HS, Plemel JR. Central nervous system macrophages in progressive multiple sclerosis: relationship to neurodegeneration and therapeutics. J Neuroinflammation 2022; 19:45. [PMID: 35144628 PMCID: PMC8830034 DOI: 10.1186/s12974-022-02408-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 01/31/2022] [Indexed: 02/08/2023] Open
Abstract
There are over 15 disease-modifying drugs that have been approved over the last 20 years for the treatment of relapsing–remitting multiple sclerosis (MS), but there are limited treatment options available for progressive MS. The development of new drugs for the treatment of progressive MS remains challenging as the pathophysiology of progressive MS is poorly understood. The progressive phase of MS is dominated by neurodegeneration and a heightened innate immune response with trapped immune cells behind a closed blood–brain barrier in the central nervous system. Here we review microglia and border-associated macrophages, which include perivascular, meningeal, and choroid plexus macrophages, during the progressive phase of MS. These cells are vital and are largely the basis to define lesion types in MS. We will review the evidence that reactive microglia and macrophages upregulate pro-inflammatory genes and downregulate homeostatic genes, that may promote neurodegeneration in progressive MS. We will also review the factors that regulate microglia and macrophage function during progressive MS, as well as potential toxic functions of these cells. Disease-modifying drugs that solely target microglia and macrophage in progressive MS are lacking. The recent treatment successes for progressive MS include include B-cell depletion therapies and sphingosine-1-phosphate receptor modulators. We will describe several therapies being evaluated as a potential treatment option for progressive MS, such as immunomodulatory therapies that can target myeloid cells or as a potential neuroprotective agent.
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Affiliation(s)
- Emily Kamma
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wendy Lasisi
- Recovery and Performance Laboratory, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, Canada
| | - Cole Libner
- Department of Health Sciences and the Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Huah Shin Ng
- Division of Neurology and the Djavad Mowafaghian Centre for Brain Health, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jason R Plemel
- Division of Neurology, Department of Medicine, University of Alberta, Edmonton, AB, Canada. .,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada. .,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada. .,University of Alberta, 5-64 Heritage Medical Research Centre, Edmonton, AB, T6G2S2, Canada.
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12
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Wan X, Link AJ, Brynildsen MP. Translational Fusion to Hmp Improves Heterologous Protein Expression. Microorganisms 2022; 10:microorganisms10020358. [PMID: 35208816 PMCID: PMC8879370 DOI: 10.3390/microorganisms10020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/16/2022] Open
Abstract
Flavohemoglobins, which are widely distributed in prokaryotes and eukaryotes, play key roles in oxygen (O2) transport and nitric oxide (·NO) defense. Hmp is the flavohemoglobin of Escherichia coli, and here we report that the translational fusion of Hmp to the N-terminus of heterologous proteins increases their expression in E. coli. The effect required the fusion of the proteins, and was independent of both the O2-binding and catalytic activity of Hmp. Increased expression was at the translational level, likely to be downstream of initiation, and we observed that as little as the first 100 amino acids of Hmp were sufficient to boost protein production. These data demonstrate the potential of Hmp as an N-terminal fusion tag to increase protein yield, and suggest that the utility of bacterial hemoglobins to biotechnology goes beyond their O2 transport and ·NO detoxification capabilities.
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A combination strategy of solubility enhancers for effective production of soluble and bioactive human enterokinase. J Biotechnol 2021; 340:57-63. [PMID: 34506803 DOI: 10.1016/j.jbiotec.2021.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/23/2022]
Abstract
Enterokinase is one of the hydrolases that catalyze hydrolysis to regulate biological processes in intestinal visceral mucosa. Enterokinase plays an essential role in accelerating the process of protein digestion as it converts trypsinogen into active trypsin by accurately recognizing and cleaving a specific peptide sequence, (Asp)4-Lys. Due to its exceptional substrate specificity, enterokinase is widely used as a versatile molecular tool in various bioprocessing, especially in removing fusion tags from recombinant proteins. Despite its biotechnological importance, mass production of soluble enterokinase in bacteria still remains an unsolved challenge. Here, we present an effective production strategy of human enterokinase using tandemly linked solubility enhancers consisting of thioredoxin, phosphoglycerate kinase or maltose-binding protein. The resulting enterokinases exhibited significantly enhanced solubility and bacterial expression level while retaining enzymatic activity, which demonstrates that combinatorial design of fusion proteins has the potential to provide an efficient way to produce recombinant proteins in bacteria.
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14
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Antimicrobial Peptides from Plants: A cDNA-Library Based Isolation, Purification, Characterization Approach and Elucidating Their Modes of Action. Int J Mol Sci 2021; 22:ijms22168712. [PMID: 34445412 PMCID: PMC8395713 DOI: 10.3390/ijms22168712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022] Open
Abstract
Even in a natural ecosystem, plants are continuously threatened by various microbial diseases. To save themselves from these diverse infections, plants build a robust, multilayered immune system through their natural chemical compounds. Among the several crucial bioactive compounds possessed by plants’ immune systems, antimicrobial peptides (AMPs) rank in the first tier. These AMPs are environmentally friendly, anti-pathogenic, and do not bring harm to humans. Antimicrobial peptides can be isolated in several ways, but recombinant protein production has become increasingly popular in recent years, with the Escherichia coli expression system being the most widely used. However, the efficacy of this expression system is compromised due to the difficulty of removing endotoxin from its system. Therefore, this review suggests a high-throughput cDNA library-based plant-derived AMP isolation technique using the Bacillus subtilis expression system. This method can be performed for large-scale screening of plant sources to classify unique or homologous AMPs for the agronomic and applied field of plant studies. Furthermore, this review also focuses on the efficacy of plant AMPs, which are dependent on their numerous modes of action and exceptional structural stability to function against a wide range of invaders. To conclude, the findings from this study will be useful in investigating how novel AMPs are distributed among plants and provide detailed guidelines for an effective screening strategy of AMPs.
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15
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Nemergut M, Škrabana R, Berta M, Plückthun A, Sedlák E. Purification of MBP fusion proteins using engineered DARPin affinity matrix. Int J Biol Macromol 2021; 187:105-112. [PMID: 34298044 DOI: 10.1016/j.ijbiomac.2021.07.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/20/2021] [Accepted: 07/18/2021] [Indexed: 11/15/2022]
Abstract
Maltose binding protein (MBP) has a long history as an expression tag with the ability to increase the solubility of fused proteins. A critical step for obtaining a sufficient amount of the MBP fusion protein is purification. Commercially available amylose matrix for the affinity purification of MBP fusion proteins has two main issues: (i) low (micromolar) affinity and (ii) the limited number of uses due to the cleavage of polysaccharide matrix by the amylases, present in the crude cell extract. Here, we present a new affinity purification approach based on the protein-protein interaction. We developed the affinity matrix which contains immobilized Designed Ankyrin Repeat Protein off7 (DARPin off7) - previously identified MBP binder with nanomolar affinity. The functionality of the DARPin affinity matrix was tested on the purification of MBP-tagged green fluorescent protein and flavodoxin. The affinity purification of the MBP fusion proteins, based on the MBP-DARPin off7 interaction, enables the purification of the fusion proteins in a simple two-steps procedure. The DARPin affinity matrix - easy to construct, resistant to amylase, insensitive to maltose contamination, and reusable for multiple purification cycles - provides an alternative approach to commercially available affinity matrices for purification of proteins containing the MBP tag.
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Affiliation(s)
- Michal Nemergut
- Center for Interdisciplinary Biosciences, Technology and Innovation Park of P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Rostislav Škrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10 Bratislava, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park of P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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16
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Shim J, Zhou C, Gong T, Iserlis DA, Linjawi HA, Wong M, Pan T, Tan C. Building protein networks in synthetic systems from the bottom-up. Biotechnol Adv 2021; 49:107753. [PMID: 33857631 PMCID: PMC9558565 DOI: 10.1016/j.biotechadv.2021.107753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023]
Abstract
The recent development of synthetic biology has expanded the capability to design and construct protein networks outside of living cells from the bottom-up. The new capability has enabled us to assemble protein networks for the basic study of cellular pathways, expression of proteins outside cells, and building tissue materials. Furthermore, the integration of natural and synthetic protein networks has enabled new functions of synthetic or artificial cells. Here, we review the underlying technologies for assembling protein networks in liposomes, water-in-oil droplets, and biomaterials from the bottom-up. We cover the recent applications of protein networks in biological transduction pathways, energy self-supplying systems, cellular environmental sensors, and cell-free protein scaffolds. We also review new technologies for assembling protein networks, including multiprotein purification methods, high-throughput assay screen platforms, and controllable fusion of liposomes. Finally, we present existing challenges towards building protein networks that rival the complexity and dynamic response akin to natural systems. This review addresses the gap in our understanding of synthetic and natural protein networks. It presents a vision towards developing smart and resilient protein networks for various biomedical applications.
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Affiliation(s)
- Jiyoung Shim
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Chuqing Zhou
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Ting Gong
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Dasha Aleksandra Iserlis
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Hamad Abdullah Linjawi
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Matthew Wong
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America
| | - Tingrui Pan
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America; Suzhou Institute for Advanced Research, University of Science and Technology, Suzhou, China.
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, United States of America.
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17
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Itoh N, Hayashi Y, Honda S, Yamamoto Y, Tanaka D, Toda H. Construction and characterization of a functional chimeric laccase from metagenomes suitable as a biocatalyst. AMB Express 2021; 11:90. [PMID: 34146179 PMCID: PMC8214651 DOI: 10.1186/s13568-021-01248-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
Screening of gene-specific amplicons from metagenomes (S-GAM) is an efficient technique for the isolation of homologous genes from metagenomes. Using the S-GAM approach, we targeted multi-copper oxidase (MCO) genes including laccase and bilirubin oxidase (BOX) in soil and compost metagenomes, and successfully isolated novel MCO core regions. These core enzyme genes shared approximately 70% identity with that of the putative MCO from Micromonospora sp. MP36. According to the principle of S-GAM, the N- and C-terminal regions of the deduced products of the mature gene come from the known parent gene, which should be homologous and compatible with the target gene. We constructed two different MCO hybrid genes using Bacillus subtilis BOX and Micromonospora sp. MP36 MCO, to give Bs-mg-mco and Mic-mg-mco, respectively. The constructed chimeric MCO genes were fused with the maltose-binding protein (MBP) gene at the N-terminus for expression in Escherichia coli cells. We found that MBP-Mic-mg-MCO/Mic-mg-MCO possessed the characteristic properties of laccase, although MBP-Bs-mg-MCO had no activity. This novel laccase (Mic-mg-MCO) demonstrated unique substrate specificity, sufficient activity at neutral pH, and high thermal stability, which are suitable properties for its use as a laccase biocatalyst.
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18
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Kielkopf CL, Bauer W, Urbatsch IL. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc 2021; 2021:pdb.top102129. [PMID: 33272973 DOI: 10.1101/pdb.top102129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.
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19
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Kobashigawa Y, Namikawa M, Sekiguchi M, Inada Y, Yamauchi S, Kimoto Y, Okazaki K, Toyota Y, Sato T, Morioka H. Expression, Purification and Characterization of CAR/NCOA-1 Tethered Protein in E. coli Using Maltose-Binding Protein Fusion Tag and Gelatinized Corn Starch. Biol Pharm Bull 2021; 44:125-130. [PMID: 33390539 DOI: 10.1248/bpb.b20-00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The constitutive active/androstane receptor (CAR) is a nuclear receptor that functions as a xenobiotic sensor, which regulates the expression of enzymes involved in drug metabolism and of efflux transporters. Evaluation of the binding properties between CAR and a drug was assumed to facilitate the prediction of drug-drug interaction, thereby contributing to drug discovery. The purpose of this study is to construct a system for the rapid evaluation of interactions between CAR and drugs. We prepared recombinant CAR protein using the Escherichia coli expression system. Since isolated CAR protein is known to be unstable, we designed a fusion protein with the CAR binding sequence of the nuclear receptor coactivator 1 (NCOA1), which was expressed as a fusion protein with maltose binding protein (MBP), and purified it by several chromatography steps. The thus-obtained CAR/NCOA1 tethered protein (CAR-NCOA1) was used to evaluate the interactions of CAR with agonists and inverse agonists by a thermal denaturation experiment using differential scanning fluorometry (DSF) in the presence and absence of drugs. An increase in the melting temperature was observed with the addition of the drugs, confirming the direct interaction between them and CAR. DSF is easy to set up and compatible with multiwell plate devices (such as 96-well plates). The use of DSF and the CAR-NCOA1 fusion protein together allows for the rapid evaluation of the interaction between a drug and CAR, and is thereby considered to be useful in drug discovery.
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Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Mana Namikawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Mitsuhiro Sekiguchi
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University
| | - Yuki Inada
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Soichiro Yamauchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Yuu Kimoto
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University
| | - Kyo Okazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Yuya Toyota
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
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20
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Abstract
The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific toward particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications in proteins and peptides widen the application of affinity ligand-tag receptors pairs toward universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely the affinity tags and receptors employed on the production of recombinant fusion proteins, and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.
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21
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Zanker AA, Ahmad N, Son TH, Schwaminger SP, Berensmeier S. Selective ene-reductase immobilization to magnetic nanoparticles through a novel affinity tag. Biotechnol J 2020; 16:e2000366. [PMID: 33245633 DOI: 10.1002/biot.202000366] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/05/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND Magnetic nanoparticles (MNPs) are becoming more important as carriers, because of their large specific surface area and easy separability. They are increasingly used in enzyme technology, diagnostics, and drug delivery. MAJOR RESULTS For the directed and almost irreversible immobilization of proteins on MNPs, we have developed a new selective (His-Arg)4 peptide-tag, that binds fusion proteins directly from an E. coli cell lysate to non-functionalized, low-cost MNPs. Using the immobilization of an ene-reductase as an example, we could demonstrate that the fusion with this tag increases thermostability without reducing overall activity (ER w/o tag: t1/2 = 3.7 h, (HR)4 -ER: t1/2 = 9.9 h). Immobilization by adsorption in Tris buffer resulted in very high enzyme loads with approx. 380 mg g-1 and 67% residual activity. The immobilization on the MNPs allowed a fast concentration, buffer exchange, and reuse. While about 50% of the activity was lost after the first reuse, we were able to show that the activity did not decrease further and was stable for another nine cycles. CONCLUSION According to our studies, our tag highly works for any kind of immobilization on MNPs and holds the potential for enzyme immobilizations as well as for drug delivery and sensors.
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Affiliation(s)
- Alexander A Zanker
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Nadim Ahmad
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Tuan Hoang Son
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Sebastian P Schwaminger
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Sonja Berensmeier
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Garching, Germany
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22
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Wang Y, Li Z, Yu H. Aptamer-Based Western Blot for Selective Protein Recognition. Front Chem 2020; 8:570528. [PMID: 33195056 PMCID: PMC7658645 DOI: 10.3389/fchem.2020.570528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/21/2020] [Indexed: 11/13/2022] Open
Abstract
Selective protein recognition is critical in molecular biology techniques such as Western blotting and ELISA. Successful detection of the target proteins in these methods relies on the specific interaction of the antibodies, which often bring a high production cost and require a long incubation time. Aptamers represent an alternative class of simple and affordable affinity reagents for protein recognition, and replacing antibodies with aptamers in Western blotting would potentially be more time- and cost-effective. In this work, multiple fluorescent DNA aptamers were isolated by in vitro selection to selectively label commonly used tag proteins including GST, MBP, and His-tag. The generated aptamers G1, M1, and H1 specifically bound to their cognate target proteins with nanomolar affinities, respectively. Compared with conventional antibody-based immunoblotting, such aptamer-based procedure gave a cleaner background and was able to selectively label target protein in a complex mixture. Lastly, the identified aptamers were also effective in recognition of different fusion proteins with the same tag, thus greatly expanding the scope of the potential applications of these aptamers. This work provided aptamers as useful molecular tools for selective protein recognition in Western blotting analysis.
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Affiliation(s)
- Yao Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China.,State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China.,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China.,State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
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23
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Expression and Purification of Recombinant Proteins in Escherichia coli Tagged with the Metal-Binding Proteins SmbP and CusF3H. Methods Mol Biol 2020. [PMID: 33128759 DOI: 10.1007/978-1-0716-0775-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The bacterium Escherichia coli is still considered the first option as a microbial cell factory for recombinant protein production, and affinity chromatography is by far the preferred technique for initial purification after protein expression and cell lysis. In this chapter, we describe the methodology to express and purify recombinant proteins in E. coli tagged with the first two metal-binding proteins proposed as fusion partners. They are the small metal-binding protein SmbP and a mutant of the copper resistance protein CusF3H+. There are several advantages of using them as protein tags: they prevent the formation of inclusion bodies by increasing solubility of the target proteins, they enable purification by immobilized metal-affinity chromatography using Ni(II) ions with high purity, and because of their low molecular weights, excellent final yields are obtained for the target proteins after cleavage and removal of the protein tag. Here we also describe the protocol for the production of proteins in the periplasm of E. coli tagged with two SmbP variants that include the PelB or the TorA signal sequences for transport via the Sec or the Tat pathway, respectively. Based on these methods, we consider CusF3H+ and SmbP excellent alternatives as fusion proteins for the production of recombinant proteins in E. coli.
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24
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Gong Y, Yi M, Zhang L, Feng S, Deng H. Characterization of the Fc-III-4C-based recombinant protein expression system by using carbonic anhydrase as the model protein. Protein Expr Purif 2020; 177:105761. [PMID: 32956801 DOI: 10.1016/j.pep.2020.105761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/25/2022]
Abstract
Development of new affinity tags is important for recombinant protein expression and purification. Based on our earlier work, we devised an affinity tag by addition of two cysteine residues onto the N- and C-termini of the Fc-III peptide and designated as the Fc-III-4C tag, in which four cysteine residues form two disulfide linkages. The binding affinity of Fc-III-4C tag to human IgG is measured as 2.28 nM (Kd) and is 100 times higher than that of the Fc-III tag to IgG. Fc-III-4C tagged carbonic anhydrase (CA) can be effectively purified with IgG-immobilized beads, and Fc-III-4C tag does not possess adverse effects on the structure and stability of CA. Furthermore, the Fc-III-4C tagged protein binds to multiple transition metal ions, which enhances activities of enzymes that use metal ions as co-factors. These results suggest that Fc-III-4C tag is a useful tool for expression and purification of recombinant proteins and enhances the activities of some fusion proteins that use Zn2+ or Cu2+ as cofactors.
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Affiliation(s)
- Yiyi Gong
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China; MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meiqi Yi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lin Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, 100084, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China; Mass Spectrometry Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, 100084, China.
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25
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins. Curr Res Struct Biol 2020; 2:180-190. [PMID: 34235478 PMCID: PMC8244415 DOI: 10.1016/j.crstbi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities. MBP operates by induced fit, HisJ by the conformational selection mechanism. Dual structure based models (dSBMs) encode two structures of a protein. MD simulations of dSBMs can identify the mechanism of conformational transitions. Locks, absent in HisJ, hold MBP open with ligand contacts required for closing. Binding mechanisms can be modified by altering such structural locks.
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Key Words
- BI, Balancing interface
- CS, conformational selection
- CTD, C-terminal domain
- Conformational selection
- Dual structure based models
- FEP, free energy profile
- HisJ, histidine binding protein
- IF, induced fit
- Induced fit
- MBP, maltose binding protein
- MD simulations
- MD, molecular dynamics
- NTD, N-terminal domain
- PBP, periplasmic binding protein
- Periplasmic binding proteins
- SH, spine helix
- Structural restraints
- WT, wild-type
- dSBM, dual structure-based model
- sSBM, single structure-based model
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26
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Parisi K, Poon S, Renda RF, Sahota G, English J, Yalpani N, Bleackley MR, Anderson MA, van der Weerden NL. Improving the Digestibility of Plant Defensins to Meet Regulatory Requirements for Transgene Products in Crop Protection. FRONTIERS IN PLANT SCIENCE 2020; 11:1227. [PMID: 32922418 PMCID: PMC7456892 DOI: 10.3389/fpls.2020.01227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/27/2020] [Indexed: 06/01/2023]
Abstract
Despite the use of chemical fungicides, fungal diseases have a major impact on the yield and quality of plant produce globally and hence there is a need for new approaches for disease control. Several groups have examined the potential use of antifungal plant defensins for plant protection and have produced transgenic plants expressing plant defensins with enhanced resistance to fungal disease. However, before they can be developed commercially, transgenic plants must pass a series of strict regulations to ensure that they are safe for human and animal consumption as well as the environment. One of the requirements is rapid digestion of the transgene protein in the gastrointestinal tract to minimize the risk of any potential allergic response. Here, we examine the digestibility of two plant defensins, NaD1 from Nicotiana alata and SBI6 from soybean, which have potent antifungal activity against major cereal pathogens. The native defensins were not digestible in simulated gastrointestinal fluid assays. Several modifications to the sequences enhanced the digestibility of the two small proteins without severely impacting their antifungal activity. However, these modified proteins did not accumulate as well as the native proteins when transiently expressed in planta, suggesting that the protease-resistant structure of plant defensins facilitates their stability in planta.
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Affiliation(s)
- Kathy Parisi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Rosemary F. Renda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Gurinder Sahota
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - James English
- Maxygen LLC, Sunnyvale, CA, United States
- Corteva Agriscience, Agriculture Division of DowDuPont, Johnston, IA, United States
| | - Nasser Yalpani
- Corteva Agriscience, Agriculture Division of DowDuPont, Johnston, IA, United States
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Mark R. Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
| | - Nicole L. van der Weerden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC, Australia
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Asano T, Kaneko MK, Kato Y. RIEDL tag: A novel pentapeptide tagging system for transmembrane protein purification. Biochem Biophys Rep 2020; 23:100780. [PMID: 32715101 PMCID: PMC7369347 DOI: 10.1016/j.bbrep.2020.100780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Affinity tag systems are an essential tool in biochemistry, biophysics, and molecular biology. Although several different tag systems have been developed, the epitope tag system, composed of a polypeptide “tag” and an anti-tag antibody, is especially useful for protein purification. However, almost all tag sequences, such as the FLAG tag, are added to the N- or C-termini of target proteins, as tags inserted in loops tend to disrupt the functional structure of multi-pass transmembrane proteins. In this study, we developed a novel “RIEDL tag system,” which is composed of a peptide with only five amino acids (RIEDL) and an anti-RIEDL monoclonal antibody (mAb), LpMab-7. To investigate whether the RIEDL tag system is applicable for protein purification, we conducted the purification of two kinds of RIEDL-tagged proteins using affinity column chromatography: whale podoplanin (wPDPN) with an N-terminal RIEDL tag (RIEDL-wPDPN) and human CD20 with an internal RIEDL tag insertion (CD20-169RIEDL170). Using an LpMab-7-Sepharose column, RIEDL-wPDPN and CD20-169RIEDL170 were efficiently purified in one-step purification procedures, and were strongly detected by LpMab-7 using Western blot and flow cytometry. These results show that the RIEDL tag system can be useful for the detection and one-step purification of membrane proteins when inserted at either the N-terminus or inserted in an internal loop structure of multi-pass transmembrane proteins. We established a novel RIEDL tag system, composed of RIEDL peptide and LpMab-7 mAb. The RIEDL tag system is applicable for protein purification, as well as FCM and WB. The RIEDL tag, inserted into a loop structure of CD20, was detected by LpMab-7. RIEDL-tagged proteins were efficiently purified using 2 × RIEDL peptide.
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Affiliation(s)
- Teizo Asano
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.,New Industry Creation Hatchery Center, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
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O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability. Int J Mol Sci 2020; 21:ijms21082878. [PMID: 32326075 PMCID: PMC7216122 DOI: 10.3390/ijms21082878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.
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Zhang J, Wang Y, Chai B, Wang J, Li L, Liu M, Zhao G, Yao L, Gao X, Yin Y, Xu J. Efficient and Low-Cost Error Removal in DNA Synthesis by a High-Durability MutS. ACS Synth Biol 2020; 9:940-952. [PMID: 32135061 DOI: 10.1021/acssynbio.0c00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzyme-based error correction is a key step in de novo DNA synthesis, yet the inherent instability of error-correction enzymes such as MutS has hindered the throughput and efficiency of DNA synthesis workflows. Here we introduce a process called Improved MICC (iMICC), in which all error-correction steps of oligos and fragments within a complete gene-synthesis cycle are completed in a simple, efficient, and low-cost manner via a MutS protein engineered for high durability. By establishing a disulfide bond of L157C-G233C, full-activity shelf life of E. coli MutS (eMutS) was prolonged from 7 to 49 days and was further extended to 63 days via cellulose-bound 4 °C storage. In synthesis of 10 Cas9 homologues in-solution and 10 xylose reductase (XR) homologues on-chip, iMICC reduced error frequency to 0.64/Kb and 0.41/Kb, respectively, with 72.1% and 86.4% of assembled fragments being error-free. By elevating base accuracy by 37.6-fold while avoiding repetitive preparation of fresh enzymes, iMICC is more efficient and robust than the wild-type eMutS, and it is 6.6-fold more accurate and 26.7-fold cheaper than CorrectASE. These advantages promise its broad applications in industrial DNA synthesis.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Baihui Chai
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichao Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Li
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
| | - Min Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolian Gao
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004-5001, United States
| | - Yifeng Yin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Otandault A, Abraham JD, Al Amir Dache Z, Khalyfa A, Jariel-Encontre I, Forné T, Prévostel C, Chouaib S, Gozal D, Thierry AR. Hypoxia differently modulates the release of mitochondrial and nuclear DNA. Br J Cancer 2020; 122:715-725. [PMID: 31929518 PMCID: PMC7054557 DOI: 10.1038/s41416-019-0716-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/29/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We investigated the influence of hypoxia on the concentration of mitochondrial and nuclear cell-free DNA (McfDNA and NcfDNA, respectively). METHOD By an ultra-sensitive quantitative PCR-based assay, McfDNA and NcfDNA were measured in the supernatants of different colorectal cell lines, and in the plasma of C57/Bl6 mice engrafted with TC1 tumour cells, in normoxic or hypoxic conditions. RESULTS Our data when setting cell culture conditions highlighted the higher stability of McfDNA as compared to NcfDNA and revealed that cancer cells released amounts of nuclear DNA equivalent to the mass of a chromosome over a 6-h duration of incubation. In cell model, hypoxia induced a great increase in NcfDNA and McfDNA concentrations within the first 24 h. After this period, cfDNA total concentrations remained stable in hypoxia consecutive to a decrease of nuclear DNA release, and noteworthy, to a complete inhibition of daily mitochondrial DNA release. In TC1-engrafted mice submitted to intermittent hypoxia, plasma NcfDNA levels are much higher than in mice bred in normoxia, unlike plasma McfDNA concentration that is not impacted by hypoxia. CONCLUSION This study suggests that hypoxia negatively modulates nuclear and, particularly, mitochondrial DNA releases in long-term hypoxia, and revealed that the underlying mechanisms are differently regulated.
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Affiliation(s)
- Amaelle Otandault
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Jean-Daniel Abraham
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Zahra Al Amir Dache
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Abdelnaby Khalyfa
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Corinne Prévostel
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France
- Université de Montpellier, Montpellier, 34090, France
- Institut régional du cancer de Montpellier, Montpellier, 34298, France
| | - Salem Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Fac. de médecine-Univ. Paris-Sud, University Paris-Saclay, Villejuif, 94805, France
- TRIPM, Gulf Medical University, Ajman, UAE
| | - David Gozal
- Department of Child Health and Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, 65201, USA
| | - Alain R Thierry
- IRCM, Inserm U1194, Institut de recherche en cancérologie de Montpellier, 208, avenue des Apothicaires, Montpellier, 34298, France.
- Université de Montpellier, Montpellier, 34090, France.
- Institut régional du cancer de Montpellier, Montpellier, 34298, France.
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31
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Lee TH, Kim KS, Kim JH, Jeong JH, Woo HR, Park SR, Sohn MH, Lee HJ, Rhee JH, Cha SS, Hwang JH, Chung KM. Novel short peptide tag from a bacterial toxin for versatile applications. J Immunol Methods 2020; 479:112750. [PMID: 31981564 DOI: 10.1016/j.jim.2020.112750] [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: 06/24/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 11/26/2022]
Abstract
The specific recognition between a monoclonal antibody (mAb) and its epitope can be used in a tag system that has proved valuable in a wide range of biological applications. Herein, we describe a novel tag called RA-tag that is composed of a seven amino acid sequence (DIDLSRI) and recognized by a highly specific mAb, 47RA, against the bacterial toxin Vibrio vulnificus RtxA1/MARTXVv. By using recombinant proteins with the RA-tag at the N-terminal, C-terminal, or an internal site, we demonstrated that the tag system could be an excellent biological system for both protein purification and protein detection in enzyme-linked immunosorbent, Western blot, flow cytometry, and immunofluorescence staining analyses in Escherichia coli, mammalian cell lines, yeast, and plant. In addition, our RA-tag/47RA mAb combination showed high sensitivity and reliable affinity (KD = 5.90 × 10-8 M) when compared with conventional tags. Overall, our results suggest that the RA-tag system could facilitate the development of a broadly applicable tag system for biological research.
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Affiliation(s)
- Tae Hee Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Kwang Soo Kim
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Republic of Korea; Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - So Ra Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Myung-Ho Sohn
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Hyeon Ju Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Joon Haeng Rhee
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Clinical Vaccine R&D Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Vaxcell-Bio Therapeutics, Hwasun-gun 58141, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joo-Hee Hwang
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
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32
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Huo L, Zhao X, Acedo JZ, Estrada P, Nair SK, van der Donk WA. Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae. Chembiochem 2020; 21:190-199. [PMID: 31532570 PMCID: PMC6980331 DOI: 10.1002/cbic.201900483] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 12/15/2022]
Abstract
As a result of the exponential increase in genomic data, discovery of novel ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has progressed rapidly in the past decade. The lanthipeptides are a major subset of RiPPs. Through genome mining we identified a novel lanthipeptide biosynthetic gene cluster (lah) from Lachnospiraceae bacterium C6A11, an anaerobic bacterium that is a member of the human microbiota and which is implicated in the development of host disease states such as type 2 diabetes and resistance to Clostridium difficile colonization. The lah cluster encodes at least seven putative precursor peptides and multiple post-translational modification (PTM) enzymes. Two unusual class II lanthipeptide synthetases LahM1/M2 and a substrate-tolerant S-adenosyl-l-methionine (SAM)-dependent methyltransferase LahSB are biochemically characterized in this study. We also present the crystal structure of LahSB in complex with product S-adenosylhomocysteine. This study sets the stage for further exploration of the final products of the lah pathway as well as their potential physiological functions in human/animal gut microbiota.
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Affiliation(s)
- Liujie Huo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- State Key Laboratory for Microbial Technology (SKLMT), Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao, 266237, P. R. China
| | - Xiling Zhao
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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Khatiwada B, Purslow JA, Underbakke ES, Venditti V. N-terminal fusion of the N-terminal domain of bacterial enzyme I facilitates recombinant expression and purification of the human RNA demethylases FTO and Alkbh5. Protein Expr Purif 2019; 167:105540. [PMID: 31740367 DOI: 10.1016/j.pep.2019.105540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 01/20/2023]
Abstract
Various fusion tags are commonly employed to increase the heterologous expression and solubility of aggregation-prone proteins within Escherichia coli. Herein, we present a protocol for efficient recombinant expression and purification of the human RNA demethylases Alkbh5 and FTO. Our method incorporates a novel fusion tag (the N-terminal domain of bacterial enzyme I, EIN) that dramatically increases the solubility of its fusion partner and is promptly removed upon digestion with a protease. The presented protocol allows for the production of mg amounts of Alkbh5 and FTO in 1L of both rich and minimal media. We developed a liquid chromatography-mass spectrometry (LC-MS)-based assay to confirm that both proteins are enzymatically active. Furthermore, the LC-MS method developed here is applicable to other members of the AlkB family of Fe(II)/α-ketoglutarate-dependent dioxygenases. The superior protein yield, afforded by our expression and purification method, will facilitate biochemical investigations into the biological function of the human RNA demethylases and endorse employment of EIN as a broadly applicable fusion tag for recombinant expression projects.
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Affiliation(s)
| | - Jeffrey A Purslow
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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Stevens LM, Zhang Y, Volnov Y, Chen G, Stein DS. Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation. PLoS One 2019; 14:e0219878. [PMID: 31658274 PMCID: PMC6816556 DOI: 10.1371/journal.pone.0219878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
The extraordinarily strong non-covalent interaction between biotin and avidin (kD = 10-14-10-16) has permitted this interaction to be used in a wide variety of experimental contexts. The Biotin Acceptor Peptide (BAP), a 15 amino acid motif that can be biotinylated by the E. coli BirA protein, has been fused to proteins-of-interest, making them substrates for in vivo biotinylation. Here we report on the construction and characterization of a modified BirA bearing signals for secretion and endoplasmic reticulum (ER) retention, for use in experimental contexts requiring biotinylation of secreted proteins. When expressed in the Drosophila female germline or ovarian follicle cells under Gal4-mediated transcriptional control, the modified BirA protein could be detected and shown to be enzymatically active in ovaries and progeny embryos. Surprisingly, however, it was not efficiently retained in the ER, and instead appeared to be secreted. To determine whether this secreted protein, now designated secBirA, could biotinylate secreted proteins, we generated BAP-tagged versions of two secreted Drosophila proteins, Torsolike (Tsl) and Gastrulation Defective (GD), which are normally expressed maternally and participate in embryonic pattern formation. Both Tsl-BAP and GD-BAP were shown to exhibit normal patterning activity. Co-expression of Tsl-BAP together with secBirA in ovarian follicle cells resulted in its biotinylation, which permitted its isolation from both ovaries and progeny embryos using Avidin-coupled affinity matrix. In contrast, co-expression with secBirA in the female germline did not result in detectable biotinylation of GD-BAP, possibly because the C-terminal location of the BAP tag made it inaccessible to BirA in vivo. Our results indicate that secBirA directs biotinylation of proteins bound for secretion in vivo, providing access to powerful experimental approaches for secreted proteins-of-interest. However, efficient biotinylation of target proteins may vary depending upon the location of the BAP tag or other structural features of the protein.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuan Zhang
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuri Volnov
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Geng Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - David S. Stein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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35
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Osei-Owusu P, Charlton TM, Kim HK, Missiakas D, Schneewind O. FPR1 is the plague receptor on host immune cells. Nature 2019; 574:57-62. [PMID: 31534221 PMCID: PMC6776691 DOI: 10.1038/s41586-019-1570-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/14/2019] [Indexed: 01/07/2023]
Abstract
The plague agent, Yersinia pestis, employs a type III secretion system (T3SS) to selectively destroy human immune cells, thereby enabling its replication in the bloodstream and transmission to new hosts via fleabite. The host factors responsible for the selective destruction of immune cells by plague bacteria were not known. Here we show that LcrV, the needle cap protein of the Y. pestis T3SS, binds N-formylpeptide receptor (FPR1) on human immune cells to promote the translocation of bacterial effectors. Plague infection in mice is characterized by high mortality, however N-formylpeptide receptor deficient animals exhibit increased survival and plague-protective antibody responses. We identified FPR1 p.R190W as a candidate human resistance allele that protects neutrophils from Y. pestis T3SS. These findings reveal the plague receptor on immune cells and show that FPR1 mutations provide for plague survival, which appears to have shaped human immune responses towards other infectious diseases and malignant neoplasms.
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Affiliation(s)
- Patrick Osei-Owusu
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL, USA.,Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Thomas M Charlton
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL, USA.,Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Hwan Keun Kim
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL, USA.,Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL, USA. .,Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, IL, USA.,Department of Microbiology, University of Chicago, Chicago, IL, USA
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Culham DE, Marom D, Boutin R, Garner J, Ozturk TN, Sahtout N, Tempelhagen L, Lamoureux G, Wood JM. Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. Biophys J 2018; 115:2152-2166. [PMID: 30448037 PMCID: PMC6289098 DOI: 10.1016/j.bpj.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/23/2022] Open
Abstract
ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.g., ProPEc, from Escherichia coli). Group B orthologs lack that feature (e.g., ProPXc, from Xanthomonas campestris). ProPXc was expressed and characterized in E. coli to further elucidate the role of the coiled coil in osmosensing. The activity of ProPXc was a sigmoid function of the osmolality in cells and proteoliposomes. ProPEc and ProPXc attained similar activities at the same expression level in E. coli. ProPEc transports proline and glycine betaine with comparable high affinities at low osmolality. In contrast, proline weakly inhibited high-affinity glycine-betaine uptake via ProPXc. The KM for proline uptake via ProPEc increases dramatically with the osmolality. The KM for glycine-betaine uptake via ProPXc did not. Thus, ProPXc is an osmosensing transporter, and the C-terminal coiled coil is not essential for osmosensing. The role of CTD-membrane interaction in osmosensing was examined further. As for ProPEc, the ProPXc CTD co-sedimented with liposomes comprising E. coli phospholipid. Molecular dynamics simulations illustrated association of the monomeric ProPEc CTD with the membrane surface. Comparison with the available NMR structure for the homodimeric coiled coil formed by the ProPEc-CTD suggested that membrane association and homodimeric coiled-coil formation by that peptide are mutually exclusive. The membrane fluidity in liposomes comprising E. coli phospholipid decreased with increasing osmolality in the range relevant for ProP activation. These data support the proposal that ProP activates as cellular dehydration increases cytoplasmic cation concentration, releasing the CTD from the membrane surface. For group A orthologs, this also favors α-helical coiled-coil formation that stabilizes the transporter in an active form.
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Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David Marom
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rebecca Boutin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jennifer Garner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada; Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada
| | - Tugba Nur Ozturk
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada
| | - Naheda Sahtout
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Guillaume Lamoureux
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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37
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Bernier SC, Cantin L, Salesse C. Systematic analysis of the expression, solubility and purification of a passenger protein in fusion with different tags. Protein Expr Purif 2018; 152:92-106. [DOI: 10.1016/j.pep.2018.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022]
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38
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Zhang M, Wang Z, Chi L, Sun J, Shen Y. Enhanced production of soluble tumor necrosis factor-related apoptosis-inducing ligand in Escherichia coli using a novel self-cleavable tag system Fh8-ΔI-CM. Protein Expr Purif 2018; 148:16-23. [PMID: 29555311 DOI: 10.1016/j.pep.2018.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 11/29/2022]
Abstract
Escherichia coli is an essential host for large-scale expression of heterologous polypeptides. However, further applications are limited by the formation of potential protein aggregates. In this work, we developed a novel on-column tag removal and purification system based on Fh8 hydrophobic interaction chromatography purification and ΔI-CM self-cleavage to obtain soluble tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). We evaluated several methods to improve TRAIL solubility and finally demonstrated that the Fh8 tag was a powerful solubility enhancer. Finally, we replaced the tobacco etch virus (TEV) protease site with a ΔI-CM self-cleavage intein to simplify the purification process. The released soluble TRAIL purity and yield reached 98.4% and 82.1 mg/L in shake flasks, respectively. Thus, the Fh8-ΔI-CM system enhanced target protein solubility by Fh8, enabled on-column tag removal and purification based on Fh8 calcium-binding properties and ΔI-CM self-cleavage properties, and promoted the release of highly active protein with high yield and purity. Overall, our findings suggest that this Fh8-ΔI-CM system could be used as a novel solubility-inducing and purification fusion tag for protein production in E. coli.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Zhanqing Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lili Chi
- Department of Gastroenterolog, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Shandong, People's Republic of China
| | - Jing Sun
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, People's Republic of China; Shanghai Gebaide Biotechnical Co., Ltd., Shanghai, People's Republic of China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, People's Republic of China.
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39
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Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides containing thioether cross-links formed through addition of a cysteine to a dehydroalanine (to form lanthionine) or to a dehydrobutyrine (to form 3-methyllanthionine). Genome sequencing of marine cyanobacteria lead to the discovery of 1.6 million open reading frames encoding lanthipeptides. In many cases, a genome encodes a single lanthipeptide synthetase, but a large number of substrates. The enzymatic modification process in Prochlorococcus MIT9313 has been reconstituted in vitro, and a variety of experimental approaches have been used to try and understand how one enzyme is capable of modifying 30 different substrates. The methods used to characterize this system will be described along with a brief genomic description of the lanthipeptide landscape found in Prochlorococcus and Synechococcus.
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40
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Abstract
Heavy isotope labeling of enzymes slows protein motions without disturbing the electrostatics and can therefore be used to probe the role of dynamics in enzyme catalysis. To identify the structural elements responsible for dynamic effects, individual segments of an enzyme can be labeled and the resulting effect on the kinetics of the reaction can be measured. Such hybrid isotopomers can be constructed by expressed protein ligation, in which complementary labeled and unlabeled peptide segments are prepared by recombinant gene expression and linked by means of chemical ligation. The construction of such hybrid isotopomers is exemplified here with the paradigmatic enzyme dihydrofolate reductase (DHFR) from Escherichia coli.
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41
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His-FLAG Tag as a Fusion Partner of Glycosylated Human Interferon-Gamma and Its Mutant: Gain or Loss? BIOMED RESEARCH INTERNATIONAL 2017; 2017:3018608. [PMID: 28685146 PMCID: PMC5480026 DOI: 10.1155/2017/3018608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/23/2017] [Indexed: 11/17/2022]
Abstract
In order to obtain glycosylated human interferon-gamma (hIFNγ) and its highly prone to aggregation mutant K88Q, a secretory expression in insect cells was employed. To facilitate recombinant proteins purification, detection, and stability the baculovirus expression vectors were constructed to bear N-terminal His6-FLAG tag. Although the obtained proteins were glycosylated, we found that their biological activity was 100 times lower than expected. Our attempts to recover the biological properties of both proteins by tag removal failed due to enterokinase resistance of the tag. Surprisingly, the tag was easily cleaved when the proteins were expressed in E. coli cells and the tag-free proteins showed fully restored activity. To shed light on this phenomenon we performed molecular dynamics simulations. The latter showed that the tags interact with the receptor binding domains and the flexible C-termini of the fusion proteins thus suppressing their complex formation with the hIFNγ receptor. We hypothesize that in the case of glycosylated proteins the tag/C-terminal interaction positions the FLAG peptide in close proximity to the glycans thus sterically impeding the enterokinase access to its recognition site.
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42
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Kottom TJ, Hebrink DM, Jenson PE, Ramirez-Prado JH, Limper AH. Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy. Am J Respir Cell Mol Biol 2017; 56:213-222. [PMID: 27632412 DOI: 10.1165/rcmb.2016-0155oc] [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: 01/02/2023] Open
Abstract
N-acetylglucosamine (GlcNAc) serves as an essential structural sugar on the cell surface of organisms. For example, GlcNAc is a major component of bacterial peptidoglycan, it is an important building block of fungal cell walls, including a major constituent of chitin and mannoproteins, and it is also required for extracellular matrix generation by animal cells. Herein, we provide evidence for a uridine diphospho (UDP)-GlcNAc pathway in Pneumocystis species. Using an in silico search of the Pneumocystis jirovecii and P. murina (Pm) genomic databases, we determined the presence of at least four proteins implicated in the Saccharomyces cerevisiae UDP-GlcNAc biosynthetic pathway. These genes, termed GFA1, GNA1, AGM1, and UDP-GlcNAc pyrophosphorylase (UAP1), were either confirmed to be present in the Pneumocystis genomes by PCR, or, in the case of Pm uap1 (Pmuap1), functionally confirmed by direct enzymatic activity assay. Expression analysis using quantitative PCR of Pneumocystis pneumonia in mice demonstrated abundant expression of the Pm uap1 transcript. A GlcNAc-binding recombinant protein and a novel GlcNAc-binding immune detection method both verified the presence of GlcNAc in P. carinii (Pc) lysates. Studies of Pc cell wall fractions using high-performance gas chromatography/mass spectrometry documented the presence of GlcNAc glycosyl residues. Pc was shown to synthesize GlcNAc in vitro. The competitive UDP-GlcNAc substrate synthetic inhibitor, nikkomycin Z, suppressed incorporation of GlcNAc by Pc preparations. Finally, treatment of rats with Pneumocystis pneumonia using nikkomycin Z significantly reduced organism burdens. Taken together, these data support an important role for GlcNAc generation in the cell surface of Pneumocystis organisms.
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Affiliation(s)
- Theodore J Kottom
- 1 Thoracic Diseases Research Unit, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota; and
| | - Deanne M Hebrink
- 1 Thoracic Diseases Research Unit, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota; and
| | - Paige E Jenson
- 1 Thoracic Diseases Research Unit, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota; and
| | - Jorge H Ramirez-Prado
- 2 Unidad de Biotecnologia, Centro de Investigacion Cientifica de Yucatan, Asociación Civil, Merida, Yucatan, Mexico
| | - Andrew H Limper
- 1 Thoracic Diseases Research Unit, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota; and
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43
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Fujii Y, Kaneko MK, Ogasawara S, Yamada S, Yanaka M, Nakamura T, Saidoh N, Yoshida K, Honma R, Kato Y. Development of RAP Tag, a Novel Tagging System for Protein Detection and Purification. Monoclon Antib Immunodiagn Immunother 2017; 36:68-71. [PMID: 28339303 PMCID: PMC5404252 DOI: 10.1089/mab.2016.0052] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Affinity tag systems, possessing high affinity and specificity, are useful for protein detection and purification. The most suitable tag for a particular purpose should be selected from many available affinity tag systems. In this study, we developed a novel affinity tag called the “RAP tag” system, which comprises a mouse antirat podoplanin monoclonal antibody (clone PMab-2) and the RAP tag (DMVNPGLEDRIE). This system is useful not only for protein detection in Western blotting, flow cytometry, and sandwich enzyme-linked immunosorbent assay, but also for protein purification.
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Affiliation(s)
- Yuki Fujii
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Mika K Kaneko
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Satoshi Ogasawara
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Shinji Yamada
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Miyuki Yanaka
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Takuro Nakamura
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Noriko Saidoh
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Kanae Yoshida
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Ryusuke Honma
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan
| | - Yukinari Kato
- 1 Department of Regional Innovation, Tohoku University Graduate School of Medicine , Sendai, Japan .,2 New Industry Creation Hatchery Center, Tohoku University , Sendai, Japan
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44
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Abstract
Determining protein partners is an essential step toward understanding protein function and identifying relevant biological pathways. Many methods exist for investigating protein-protein interactions. The pull-down assay is an in vitro technique used to detect physical interactions between two or more proteins and an invaluable tool for confirming a predicted protein-protein interaction or identifying novel interacting partners. This method typically involves the use of affinity purification with various wash and elution steps. In this chapter, we describe how an interaction between two purified bacterial proteins or between bacterial and eukaryotic proteins can be detected by pull-down experiments.
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Affiliation(s)
- Arthur Louche
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France
| | - Suzana P Salcedo
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Lyon 1, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France.
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45
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Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
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Affiliation(s)
- Sinéad T Loughran
- Department of Applied Sciences, Dundalk Institute of Technology, Dundalk, Ireland
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
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46
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Yadav DK, Yadav N, Yadav S, Haque S, Tuteja N. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics. Arch Biochem Biophys 2016; 612:57-77. [DOI: 10.1016/j.abb.2016.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
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47
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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48
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Fujii Y, Kaneko MK, Kato Y. MAP Tag: A Novel Tagging System for Protein Purification and Detection. Monoclon Antib Immunodiagn Immunother 2016; 35:293-299. [PMID: 27801621 PMCID: PMC5206699 DOI: 10.1089/mab.2016.0039] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protein purification is an essential procedure in fields such as biochemistry, molecular biology, and biophysics. Acquiring target proteins with high quality and purity is still difficult, although several tag systems have been established for protein purification. Affinity tag systems are excellent because they possess high affinity and specificity for acquiring the target proteins. Nevertheless, further affinity tag systems are needed to compensate for several disadvantages of the presently available affinity tag systems. Herein, we developed a novel affinity tag system designated as the MAP tag system. This system is composed of a rat anti-mouse podoplanin monoclonal antibody (clone PMab-1) and MAP tag (GDGMVPPGIEDK) derived from the platelet aggregation-stimulating domain of mouse podoplanin. PMab-1 possesses high affinity and specificity for the MAP tag, and the PMab-1/MAP tag complex dissociates in the presence of the epitope peptide, indicating that the MAP tag system is suitable for protein purification. We successfully purified several proteins, including a nuclear protein, soluble proteins, and a membrane protein using the MAP tag system. The MAP tag system is very useful not only for protein purification but also in protein detection systems such as western blot and flow cytometric analyses. Taken together, these findings indicate that the MAP tag system could be a powerful tool for protein purification and detection.
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Affiliation(s)
- Yuki Fujii
- Department of Regional Innovation, Tohoku University Graduate School of Medicine , Miyagi, Japan
| | - Mika K Kaneko
- Department of Regional Innovation, Tohoku University Graduate School of Medicine , Miyagi, Japan
| | - Yukinari Kato
- Department of Regional Innovation, Tohoku University Graduate School of Medicine , Miyagi, Japan
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49
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Haustant J, Sil A, Maillo-Rius C, Hocquellet A, Costaglioli P, Garbay B, Dieryck W. Use of the human hepcidin gene to build a positive-selection vector for periplasmic expression in Escherichia coli. Anal Biochem 2016; 500:35-7. [PMID: 26873403 DOI: 10.1016/j.ab.2016.02.002] [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] [Received: 12/10/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 12/01/2022]
Abstract
Recombinant proteins are often produced in the periplasm of Escherichia coli because this facilitates the purification process. The oxidizing environment favors the formation of disulfide bridges. We showed that the periplasmic expression of the human hormone hepcidin 25 (Hep25) fused to the maltose-binding protein (MBP) resulted in cell death. This toxicity was not observed when MBP-Hep25 accumulated in the bacterial cytoplasm, or when Hep25 was addressed to the periplasm without the MBP tag. We then modified the periplasmic expression vector pMALp2E to create pMALp2EH, a positive-selection vector with Hep25 as counterselection gene.
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Affiliation(s)
- Jérome Haustant
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Annesha Sil
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Christopher Maillo-Rius
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Agnès Hocquellet
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Patricia Costaglioli
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Bertrand Garbay
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France
| | - Wilfrid Dieryck
- Université de Bordeaux, EA 4135, F-33000 Bordeaux, France; Bordeaux-INP, EA4135, F-33000 Bordeaux, France.
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50
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Expression and purification of recombinant proteins in Escherichia coli tagged with the metal-binding protein CusF. Protein Expr Purif 2016; 121:61-5. [DOI: 10.1016/j.pep.2016.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/07/2015] [Accepted: 01/08/2016] [Indexed: 11/23/2022]
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