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Birchfield AS, McIntosh CA. Expression and Purification of Cp3GT: Structural Analysis and Modeling of a Key Plant Flavonol-3-O Glucosyltransferase from Citrus paradisi. BIOTECH 2024; 13:4. [PMID: 38390907 PMCID: PMC10885057 DOI: 10.3390/biotech13010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024] Open
Abstract
Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated with recombinant protein production in Pichia pastoris, such as proteolytic degradation, were addressed through the optimization of culture conditions and purification processes. The purification strategy employed affinity, anion exchange, and size exclusion chromatography, leading to greater than 95% homogeneity for Cp3GT. In silico modeling, using D-I-TASSER and COFACTOR integrated with the AlphaFold2 pipeline, provided insights into the structural dynamics of Cp3GT and its ligand binding sites, offering predictions for enzyme-substrate interactions. These models were compared to experimentally derived structures, enhancing understanding of the enzyme's functional mechanisms. The findings present a comprehensive approach to produce a highly purified Cp3GT which is suitable for crystallographic studies and to shed light on the structural basis of flavonol specificity in plant GTs. The significant implications of these results for synthetic biology and enzyme engineering in pharmaceutical applications are also considered.
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Affiliation(s)
- Aaron S Birchfield
- Department of Biological Sciences, East Tennessee State University, P.O. Box 70703, Johnson City, TN 37614, USA
| | - Cecilia A McIntosh
- Department of Biological Sciences, East Tennessee State University, P.O. Box 70703, Johnson City, TN 37614, USA
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Boldrini-França J, Santos Rodrigues R, Santos-Silva LK, de Souza DLN, Gomes MSR, Cologna CT, de Pauw E, Quinton L, Henrique-Silva F, de Melo Rodrigues V, Arantes EC. Expression of a new serine protease from Crotalus durissus collilineatus venom in Pichia pastoris and functional comparison with the native enzyme. Appl Microbiol Biotechnol 2015; 99:9971-86. [PMID: 26227411 DOI: 10.1007/s00253-015-6836-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/07/2015] [Accepted: 07/11/2015] [Indexed: 11/28/2022]
Abstract
Snake venom serine proteases (SVSPs) act primarily on plasma proteins related to blood clotting and are considered promising for the treatment of several hemostatic disorders. We report the heterologous expression of a serine protease from Crotalus durissus collilineatus, named collinein-1, in Pichia pastoris, as well as the enzymatic comparative characterization of the toxin in native and recombinant forms. The complementary DNA (cDNA) encoding collinein-1 was amplified from cDNA library of C. d. collilineatus venom gland and cloned into the pPICZαA vector. The recombinant plasmid was used to transform cells of KM71H P. pastoris. Heterologous expression was induced by methanol and yielded 56 mg of recombinant collinein-1 (rCollinein-1) per liter of culture. The native collinein-1 was purified from C. d. collilineatus venom, and its identity was confirmed by amino acid sequencing. The native and recombinant enzymes showed similar effects upon bovine fibrinogen by releasing preferentially fibrinopeptide A. Although both enzymes have induced plasma coagulation, native Colinein-1 has shown higher coagulant activity. The serine proteases were able to hydrolyze the chromogenic substrates S-2222, S-2238, and S2302. Both enzymes showed high stability on different pH and temperature, and their esterase activities were inhibited in the presence of Zn2+ and Cu2+. The serine proteases showed similar k cat/K m values in enzyme kinetics assays, suggesting no significant differences in efficiency of these proteins to hydrolyze the substrate. These results demonstrated that rCollinein-1 was expressed with functional integrity on the evaluated parameters. The success in producing a functionally active recombinant SVSP may generate perspectives to their future therapeutic applications.
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Affiliation(s)
- Johara Boldrini-França
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Física e Química, Universidade de São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Renata Santos Rodrigues
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Brazil.,INCT, Instituto Nacional de Ciência e Tecnologia em Nano-Biofarmacêutica, Belo Horizonte, MG, Brazil
| | | | - Dayane Lorena Naves de Souza
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Brazil.,INCT, Instituto Nacional de Ciência e Tecnologia em Nano-Biofarmacêutica, Belo Horizonte, MG, Brazil
| | - Mário Sérgio Rocha Gomes
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Brazil.,INCT, Instituto Nacional de Ciência e Tecnologia em Nano-Biofarmacêutica, Belo Horizonte, MG, Brazil
| | | | - Edwin de Pauw
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Loïc Quinton
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Flávio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Veridiana de Melo Rodrigues
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Brazil.,INCT, Instituto Nacional de Ciência e Tecnologia em Nano-Biofarmacêutica, Belo Horizonte, MG, Brazil
| | - Eliane Candiani Arantes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Física e Química, Universidade de São Paulo, Av. do Café s/n, Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Minde DP, Halff EF, Tans S. Designing disorder: Tales of the unexpected tails. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26790. [PMID: 28516025 PMCID: PMC5424805 DOI: 10.4161/idp.26790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/24/2022]
Abstract
Protein tags of various sizes and shapes catalyze progress in biosciences. Well-folded tags can serve to solubilize proteins. Small, unfolded, peptide-like tags have become invaluable tools for protein purification as well as protein-protein interaction studies. Intrinsically Disordered Proteins (IDPs), which lack unique 3D structures, received exponentially increasing attention during the last decade. Recently, large ID tags have been developed to solubilize proteins and to engineer the pharmacological properties of protein and peptide pharmaceuticals. Here, we contrast the complementary benefits and applications of both folded and ID tags based on predictions of ID. Less structure often means more function in a shorter tag.
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Affiliation(s)
| | - Els F Halff
- Crystal and Structural Chemistry; Bijvoet Center for Biomolecular Research; Utrecht University; Utrecht, The Netherlands
| | - Sander Tans
- FOM Institute AMOLF; Amsterdam, The Netherlands
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Jariyachawalid K, Laowanapiban P, Meevootisom V, Wiyakrutta S. Effective enhancement of Pseudomonas stutzeri D-phenylglycine aminotransferase functional expression in Pichia pastoris by co-expressing Escherichia coli GroEL-GroES. Microb Cell Fact 2012; 11:47. [PMID: 22515657 PMCID: PMC3503884 DOI: 10.1186/1475-2859-11-47] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 03/26/2012] [Indexed: 12/02/2022] Open
Abstract
Background D-phenylglycine aminotransferase (D-PhgAT) of Pseudomonas stutzeri ST-201 catalyzes the reversible stereo-inverting transamination potentially useful in the application for synthesis of D-phenylglycine and D-4-hydroxyphenylglycine using L-glutamate as a low cost amino donor substrate in one single step. The enzyme is a relatively hydrophobic homodimeric intracellular protein difficult to express in the soluble functionally active form. Over-expression of the dpgA gene in E. coli resulted in the majority of the D-PhgAT aggregated into insoluble inclusion bodies that failed to be re-natured. Expression in Pichia pastoris was explored as an alternative route for high level production of the D-PhgAT. Results Intracellular expression of the codon-optimized synthetic dpgA gene under the PAOX1 promoter in P. pastoris resulted in inactive D-PhgAT associated with insoluble cellular fraction and very low level of D-PhgAT activity in the soluble fraction. Manipulation of culture conditions such as addition of sorbitol to induce intracellular accumulation of osmolytes, addition of benzyl alcohol to induce chaperone expression, or lowering incubation temperature to slow down protein expression and folding rates all failed to increase the active D-PhgAT yield. Co-expression of E. coli chaperonins GroEL-GroES with the D-PhgAT dramatically improved the soluble active enzyme production. Increasing gene dosage of both the dpgA and those of the chaperones further increased functional D-PhgAT yield up to 14400-fold higher than when the dpgA was expressed alone. Optimization of cultivation condition further increased D-PhgAT activity yield from the best co-expressing strain by 1.2-fold. Conclusions This is the first report on the use of bacterial chaperones co-expressions to enhance functional intracellular expression of bacterial enzyme in P. pastoris. Only two bacterial chaperone genes groEL and groES were sufficient for dramatic enhancement of functionally active D-PhgAT expression in this yeast. With the optimized gene dosage and chaperone combinations, P. pastoris can be attractive for intracellular expression of bacterial proteins since it can grow to a very high cell density which is translated into the higher volumetric product yield than the E. coli or other bacterial systems.
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Affiliation(s)
- Kanidtha Jariyachawalid
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
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Li Z, Leung W, Yon A, Nguyen J, Perez VC, Vu J, Giang W, Luong LT, Phan T, Salazar KA, Gomez SR, Au C, Xiang F, Thomas DW, Franz AH, Lin-Cereghino J, Lin-Cereghino GP. Secretion and proteolysis of heterologous proteins fused to the Escherichia coli maltose binding protein in Pichia pastoris. Protein Expr Purif 2010; 72:113-24. [PMID: 20230898 PMCID: PMC2860017 DOI: 10.1016/j.pep.2010.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 03/09/2010] [Accepted: 03/10/2010] [Indexed: 11/19/2022]
Abstract
The Escherichia coli maltose binding protein (MBP) has been utilized as a translational fusion partner to improve the expression of foreign proteins made in E. coli. When located N-terminal to its cargo protein, MBP increases the solubility of intracellular proteins and improves the export of secreted proteins in bacterial systems. We initially explored whether MBP would have the same effect in the methylotrophic yeast Pichia pastoris, a popular eukaryotic host for heterologous protein expression. When MBP was fused as an N-terminal partner to several C-terminal cargo proteins expressed in this yeast, proteolysis occurred between the two peptides, and MBP reached the extracellular region unattached to its cargo. However, in two of three instances, the cargo protein reached the extracellular region as well, and its initial attachment to MBP enhanced its secretion from the cell. Extensive mutagenesis of the spacer region between MBP and its C-terminal cargo protein could not inhibit the cleavage although it did cause changes in the protease target sites in the fusion proteins, as determined by mass spectrometry. Taken together, these results suggested that an uncharacterized P. pastoris protease attacked at different locations in the region C-terminal of the MBP domain, including the spacer and cargo regions, but the MBP domain could still act to enhance the secretion of certain cargo proteins.
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Affiliation(s)
- Zhiguo Li
- Department of Chemistry, University of the Pacific, Stockton, California 95211
| | - Wilson Leung
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Amy Yon
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - John Nguyen
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Vincent C. Perez
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Jane Vu
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - William Giang
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Linda T. Luong
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Tracy Phan
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Katherine A. Salazar
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Seth R. Gomez
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Colin Au
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Fan Xiang
- Shimadzu Biotech Corporation, 7060 Koll Center Parkway, Suite 328, Pleasanton, California 94566
| | - David W. Thomas
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA 95211
| | - Andreas H. Franz
- Department of Chemistry, University of the Pacific, Stockton, California 95211
| | - Joan Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Geoff P. Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
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