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Sanyasi C, Balakrishnan SS, Chinnasamy T, Venugopalan N, Kandavelu P, Batra-Safferling R, Muthuvel SK. Insights on the dynamic behavior of protein disulfide isomerase in the solution environment through the SAXS technique. In Silico Pharmacol 2024; 12:23. [PMID: 38584776 PMCID: PMC10997565 DOI: 10.1007/s40203-024-00198-0] [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: 10/25/2023] [Accepted: 02/17/2024] [Indexed: 04/09/2024] Open
Abstract
The dynamic behavior of Protein Disulfide Isomerase (PDI) in an aqueous solution environment under physiologically active pH has been experimentally verified in this study using Small Angle X-ray Scattering (SAXS) technique. The structural mechanism of dimerization for full-length PDI molecules and co-complex with two renowned substrates has been comprehensively discussed. The structure models obtained from the SAXS data of PDI purified from bovine liver display behavior duality between unaccompanied-enzyme and after engaged with substrates. The analysis of SAXS data revealed that PDI exists as a homo-dimer in the solution environment, and substrate induction provoked its segregation into monomer to enable the enzyme to interact systematically with incoming clients. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00198-0.
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Affiliation(s)
- Chandrasekar Sanyasi
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Susmida Seni Balakrishnan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Thirunavukkarasu Chinnasamy
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
| | - Nagarajan Venugopalan
- GMCA Structural Biology Facility, X-Ray Science Division, Argonne National Laboratory, Argonne, IL USA
| | - Palani Kandavelu
- SER-CAT and The Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30601 USA
| | - Renu Batra-Safferling
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Suresh Kumar Muthuvel
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, 605014 India
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Zhang J, Wang J, Feng T, Du R, Tian X, Wang Y, Zhang XH. Heterologous Expression of the Marine-Derived Quorum Quenching Enzyme MomL Can Expand the Antibacterial Spectrum of Bacillus brevis. Mar Drugs 2019; 17:E128. [PMID: 30795579 PMCID: PMC6409708 DOI: 10.3390/md17020128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 12/28/2022] Open
Abstract
Quorum sensing (QS) is closely associated with the production of multiple virulence factors in bacterial pathogens. N-acyl homoserine lactones (AHLs) are important QS signal molecules that modulate the virulence of gram-negative pathogenic bacteria. Enzymatic degradation of AHLs to interrupt QS, termed quorum quenching (QQ), has been considered a novel strategy for reduction of pathogenicity and prevention of bacterial disease. However, the low expression levels of QQ proteins in the original host bacteria has affected the applications of these proteins. Previously, we identified a novel marine QQ enzyme, named MomL, with high activity and promising biocontrol function. In this study, we linked the target fragment momL to pNCMO2, which provided a basis for the first heterologous expression of MomL in the antifungal and anti-gram-positive-bacteria biocontrol strain Bacillus brevis, and obtaining the recombinant strain named BbMomL. The QQ activity of BbMomL was confirmed using a series of bioassays. BbMomL could not only degrade the exogenous signal molecule C6-HSL, but also the AHL signal molecules produced by the gram-negative pathogens Pectobacterium carotovorum subsp. carotovorum (Pcc) and Pseudomonas aeruginosa PAO1. In addition, BbMomL significantly reduced the secretion of pathogenic factors and the pathogenicity of Pcc and P. aeruginosa PAO1. We tested the biocontrol function of BbMomL for prevention of plant diseases in vitro. The result indicates that BbMomL has a broad antibacterial spectrum. Compared with wild-type B. brevis, BbMomL not only inhibited fungi and gram-positive bacterial pathogens but also considerably inhibited gram-negative bacterial pathogens. Moreover, the Bacillus brevis expression system has good application prospects and is an ideal host for expression and secretion of foreign proteins.
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Affiliation(s)
- Jingjing Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiayi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Tao Feng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Rui Du
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xiaorong Tian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Yamamoto T, Hoshikawa K, Ezura K, Okazawa R, Fujita S, Takaoka M, Mason HS, Ezura H, Miura K. Improvement of the transient expression system for production of recombinant proteins in plants. Sci Rep 2018; 8:4755. [PMID: 29555968 PMCID: PMC5859073 DOI: 10.1038/s41598-018-23024-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/30/2018] [Indexed: 01/24/2023] Open
Abstract
An efficient and high yielding expression system is required to produce recombinant proteins. Furthermore, the transient expression system can be used to identify the localization of proteins in plant cells. In this study, we demonstrated that combination of a geminiviral replication and a double terminator dramatically enhanced the transient protein expression level in plants. The GFP protein was expressed transiently in lettuce, Nicotiana benthamiana, tomatoes, eggplants, hot peppers, melons, and orchids with agroinfiltration. Compared to a single terminator, a double terminator enhanced the expression level. A heat shock protein terminator combined with an extensin terminator resulted in the highest protein expression. Transiently expressed GFP was confirmed by immunoblot analysis with anti-GFP antibodies. Quantitative analysis revealed that the geminiviral vector with a double terminator resulted in the expression of at least 3.7 mg/g fresh weight of GFP in Nicotiana benthamiana, approximately 2-fold that of the geminiviral vector with a single terminator. These results indicated that combination of the geminiviral replication and a double terminator is a useful tool for transient expression of the gene of interest in plant cells.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Ken Hoshikawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kentaro Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Risa Okazawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Satoshi Fujita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Miyo Takaoka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hugh S Mason
- Center for Immunotherapy, Vaccines and Virotherapy (CIVV), The Biodesign Institute at Arizona State University, Tempe, AZ, 85287, USA
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
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Human pancreas-specific protein disulfide isomerase homolog (PDIp) is redox-regulated through formation of an inter-subunit disulfide bond. Arch Biochem Biophys 2009; 485:1-9. [DOI: 10.1016/j.abb.2008.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 12/24/2008] [Accepted: 12/25/2008] [Indexed: 11/23/2022]
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Li SJ, Hong XG, Shi YY, Li H, Wang CC. Annular arrangement and collaborative actions of four domains of protein-disulfide isomerase: a small angle X-ray scattering study in solution. J Biol Chem 2005; 281:6581-8. [PMID: 16407203 DOI: 10.1074/jbc.m508422200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We presented for the first time a small angle x-ray scattering study of intact protein-disulfide isomerase (PDI) in solution. The restored model revealed that PDI is a short and roughly elliptical cylinder with a molecular mass of 69 kDa and dimensions of 105 x 65 x 40 A, and the four thioredoxin-fold domains in the order a-b-b'-a' are arranged in an annular fashion. Atomic force microscope imaging also supported the finding that PDI appears as an approximately flat elliptical cylinder. A PDI species with apparent molecular mass of 116 kDa measured by using size-exclusion chromatography, previously assumed to be a dimer, was determined to exist mainly as a monomer by using analytical ultracentrifugation. The C-terminal fragment 441-491 contributed to the anomalous molecular mass determination of PDI by size-exclusion chromatography. The annular model of PDI accounted for the cooperative properties of the four domains in both the isomerase and chaperone functions of PDI.
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Affiliation(s)
- Sheng-jian Li
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
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Niemitalo O, Neubauer A, Liebal U, Myllyharju J, Juffer AH, Neubauer P. Modelling of translation of human protein disulfide isomerase in Escherichia coli—A case study of gene optimisation. J Biotechnol 2005; 120:11-24. [PMID: 16111781 DOI: 10.1016/j.jbiotec.2005.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 04/21/2005] [Accepted: 05/04/2005] [Indexed: 11/30/2022]
Abstract
Recombinant human protein disulfide isomerase (PDI) was expressed in vivo in Escherichia coli using a non-optimised gene sequence and an optimised sequence with four 5' codons substituted by synonymous codons that take less time to translate. The optimisation resulted in a 2-fold increase of total PDI concentration and by successive optimisation with expression at low temperature in a 10-fold increase of the amount of soluble PDI in comparison with the original wild-type construct. The improvement can be due to a faster clearing of the ribosome binding site on the mRNA, elevating the translation initiation rate and resulting in higher ribosome loading and better ribosome protection of the PDI mRNA against endonucleolytic cleavage by RNase. This hypothesis was supported by a novel computer simulation model of E. coli translational ribosome traffic based upon the stochastic Gillespie algorithm. The study indicates the applicability of such models in optimisation of recombinant protein sequences.
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Affiliation(s)
- Olli Niemitalo
- Bioprocess Engineering Laboratory, Department of Process and Environmental Engineering, University of Oulu, Oulu, Finland
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Asano Y, Akaishi E, Tajima K, Shinozawa T. Establishment of monoclonal antibodies specific for Bacillus subtilis DB9011. Biosci Biotechnol Biochem 2000; 64:652-6. [PMID: 10803975 DOI: 10.1271/bbb.64.652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacillus subtilis DB9011 is a strain with useful functions for agriculture. To establish a method for the discrimination of this strain from others, monoclonal antibodies (MAbs) were prepared. Although two established MAbs (MAb9B6 and MAb14D2) cross-react with some other Bacillus strains in ELISA, only B. subtilis DB9011 vegetative cells are recognized by both MAbs. MAb14D2 recognizes flagellin, a 34-kDa unit protein of flagella. The two MAbs established will provide powerful tools with which detailed analysis of this bacterial strain can be obtained under environmental conditions.
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Affiliation(s)
- Y Asano
- Department of Biological and Chemical Engineering, Faculty of Engineering, Gunma University, Kiryu, Japan
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Gao Y, Quan H, Jiang M, Dai Y, Wang CC. Mutant human protein disulfide isomerase assists protein folding in a chaperone-like fashion. J Biotechnol 1997; 54:105-12. [PMID: 9195754 DOI: 10.1016/s0168-1656(97)01695-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human protein disulfide isomerase with an extra 10 amino acid residues of AEITRIDPAM at the N-terminal was expressed in E. coli as a soluble protein comprising 20% of total cell proteins, and was purified to near homogeneity through one step of DEAE-Sephacel chromatography. The mutant enzyme, which had the same CD spectrum and comparable disulfide isomerase and thiol-protein oxidoreductase activities with that of the wild type human and bovine protein disulfide isomerases, also showed chaperone-like activity in stimulating the refolding of proteins containing no disulfide bond. The overall yield of the active product is about 20 mg 1-1 culture.
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Affiliation(s)
- Y Gao
- National Laboratory of Biomacromolecules, Academia Sinica, Beijing, People's Republic of China
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