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Koul D, Chander D, Manhas RS, Hossain MM, Dar MJ, Chaubey A. Purification, functional characterization and enhanced production of serratiopeptidase from Serratia marcescens MES-4: An endophyte isolated from Morus rubra. J Biotechnol 2024; 387:58-68. [PMID: 38582407 DOI: 10.1016/j.jbiotec.2024.04.002] [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: 11/25/2023] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Serratiopeptidase, a proteolytic enzyme serves as an important anti-inflammatory and analgesic medication. Present study reports the production and purification of extracellular serratiopeptidase from an endophyte, Serratia marcescens MES-4, isolated from Morus rubra. Purification of the enzyme by Ion exchange chromatography led to the specific activity of 13,030 U/mg protein of serratiopeptidase, showcasing about 3.1 fold enhanced activity. The catalytic domain of the purified serratiopeptidase, composed of Zn coordinated with three histidine residues (His 209, His 213, and His 219), along with glutamate (Glu 210) and tyrosine (Tyr 249). The molecular mass, as determined by SDS-PAGE was ∼51 kDa. The purified serratiopeptidase displayed optimal activity at pH 9.0, temperature 50°C. Kinetic studies revealed Vmax and Km values of 33,333 U/mL and 1.66 mg/mL, respectively. Further, optimized conditions for the production of serratiopeptidase by Taguchi design led to the productivity of 87 U/mL/h with 87.9 fold enhanced production as compared to the previous conditions.
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Affiliation(s)
- Diksha Koul
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Devtulya Chander
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Ravi S Manhas
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Md Mehedi Hossain
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Mohd Jamal Dar
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Asha Chaubey
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India.
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Hosseini SB, Azizi M, Nojoumi SA, Valizadeh V. An up-to-date review of biomedical applications of serratiopeptidase and its biobetter derivatives as a multi-potential metalloprotease. Arch Microbiol 2024; 206:180. [PMID: 38502196 DOI: 10.1007/s00203-024-03889-6] [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: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Serratiopeptidase is a bacterial metalloprotease used in a variety of medical applications. The multidimensional properties of serratiopeptidase make it noticeable as a miraculous enzyme. Anti-coagulant, anti-inflammatory and anti-biofilm activity of serratiopeptidase making it useful in reducing pain and swelling associated with various conditions including arthritis, diabetes, cancer, swelling, pain and also thrombolytic disorders. It breaks down fibrin, thins the fluids formed during inflammation and due to its anti-biofilm activity, can be used in the combination of antibiotics to reduce development of antibiotic resistance. However, some drawbacks like sensitivity to environmental conditions and low penetration into cells due to its large size have limited its usage as a potent pharmaceutical agent. To overcome such limitations, improved versions of the enzyme were introduced using protein engineering in our previous studies. Novel functional serratiopeptidases with shorter length and higher stability have seemingly created a hope for using this enzyme as a more effective therapeutic enzyme. This review explains the structural properties and functional aspects of serratiopeptidase, its main characteristics and properties, pre-clinical and clinical applications of the enzyme, improved qualities of the modified forms, different formulations of the enzyme, and the potential future developments.
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Affiliation(s)
- Seyedeh Bahareh Hosseini
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Azizi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Vahideh Valizadeh
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran.
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Nguyen HT, Kim HG, Yu NH, Hwang IM, Kim H, Kim YC, Kim JC. In Vitro and In Vivo Antibacterial Activity of Serratamid, a Novel Peptide-Polyketide Antibiotic Isolated from Serratia plymuthica C1, against Phytopathogenic Bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5471-5480. [PMID: 33914513 DOI: 10.1021/acs.jafc.1c01162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A new hybrid non-ribosomal peptide-polyketide antibiotic (serratamid) for phytoprotection was isolated from the ethyl acetate layer of tryptic soy agar culture of the soil bacterium Serratia plymuthica C1 through bioassay-guided fractionation. Its chemical structure was elucidated using instrumental analyses, such as mass and nuclear magnetic resonance spectrometry. Serratamid showed antibacterial activity against 15 phytopathogenic bacteria, with minimum inhibitory concentration (MIC) values ranging from 0.244 to 31.25 μg/mL. In vitro, it displayed strong antibacterial activity against Ralstonia solanacearum and four Xanthomonas spp., with MIC values (0.244-0.488 μg/mL) superior to those of streptomycin sulfate, oxolinic acid, and oxytetracycline. Further, serratamid and the ethyl acetate layer of S. plymuthica C1 effectively reduced bacterial wilt caused by R. solanacearum on tomato seedlings and fire blight caused by Erwinia on apple fruits in a dose-dependent manner. These results suggest that serratamid is a promising candidate as a potent bactericide for controlling bacterial diseases.
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Affiliation(s)
- Hoa Thi Nguyen
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyoung-Geun Kim
- Natural Product Chemistry Lab, Graduate School of Biotechnology, Kyung Hee University, Yongin, Gyeonggi 17104, Republic of Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - In Min Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Hun Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
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Chander D, Khosla JK, Koul D, Hossain MM, Dar MJ, Chaubey A. Purification and characterization of thermoactive serratiopeptidase from Serratia marcescens AD-W2. AMB Express 2021; 11:53. [PMID: 33835269 PMCID: PMC8035408 DOI: 10.1186/s13568-021-01215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Serratiopeptidase is a proteolytic enzyme extensively used as an anti-inflammatory and analgesic drug. Present work reports a thermoactive serratiopeptidase from Serratia marcescens AD-W2, a soil isolate from the North-Western Himalayan region of India. The extracellular metalloprotease has been purified by a simple two-step procedure resulting in a specific activity of 20,492 Units/mg protein with 5.28-fold purification. The molecular mass of the metalloprotease, as determined by SDS-PAGE was ~ 51 kDa. The purified serratiopeptidase presented optimum activity at pH 9.0, temperature 50 °C and stability in wide pH and temperature range. Critical temperature of 50 °C confirmed the thermoactivity of the purified serratiopeptidase. The kinetic studies of the purified serratiopeptidase revealed Vmax and Km of 57,256 Units/mL and 1.57 mg/mL, respectively, for casein. The purified serratiopeptidase from S. marcescens AD-W2 was found to be 100% identical to serralysin from Serratia marcescens ATCC 21074/E-15. The catalytic domain comprising of Zn coordinated with three histidine residues (His192, His196, His202), along with glutamate (Glu193) and tyrosine (Tyr232) residues, further confirmed that the purified protein is identical to serralysin.
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ROUHANI M, VALIZADEH V, MOLASALEHI S, NOROUZIAN D. Production and Expression Optimization of Heterologous Serratiopeptidase. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:931-939. [PMID: 32953681 PMCID: PMC7475616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Serratiopeptidase is a bacterial metalloprotease, which is useful for the treatment of pain and inflammation. It breaks down fibrin, thins the fluids formed during inflammation and acts as an anti-biofilm agent. Because of medicinally important role of the enzyme, we aimed to study the cloning and the expression optimization of serratiopeptidase. METHODS The heat-stable serratiopeptidase (5d7w) was selected as the template. Cloning into pET28a expression vector was performed and confirmed by colony PCR and double restriction enzyme digestion. The recombinant protein was expressed in Esherichia coli BL21 and confirmed by SDS-PAGE and Western blot analysis. Different parameters such as expression vector, culture media, post-induction incubation temperature, inducer concentration, and post-induction incubation time were altered to obtain the highest amount of the recombinant protein. RESULTS Serratiopeptidase was successfully cloned and expressed under optimized conditions in E. coli which confirmed by western blot analysis. The optimal conditions of expression were determined using pQE30 as vector, cultivating the host bacteria in Terrific Broth (TB) medium, at 37° C, induction by IPTG concentration equal to 0.5 mM, and cells were harvested 4 h after induction. CONCLUSION As serratiopeptidase is a multi-potent enzyme, the expressed recombinant protein can be considered as a valuable agent for pharmaceutical applications in further studies.
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Denesyuk AI, Permyakov SE, Johnson MS, Denessiouk K, Permyakov EA. System Approach for Building of Calcium-Binding Sites in Proteins. Biomolecules 2020; 10:biom10040588. [PMID: 32290360 PMCID: PMC7226230 DOI: 10.3390/biom10040588] [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: 02/28/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
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Affiliation(s)
- Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Correspondence: ; Tel.: +358-2-215-4006
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
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Baumann U. Structure-Function Relationships of the Repeat Domains of RTX Toxins. Toxins (Basel) 2019; 11:toxins11110657. [PMID: 31718085 PMCID: PMC6891781 DOI: 10.3390/toxins11110657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 01/08/2023] Open
Abstract
RTX proteins are a large family of polypeptides of mainly Gram-negative origin that are secreted into the extracellular medium by a type I secretion system featuring a non-cleavable C-terminal secretion signal, which is preceded by a variable number of nine-residue tandem repeats. The three-dimensional structure forms a parallel β-roll, where β-strands of two parallel sheets are connected by calcium-binding linkers in such a way that a right-handed spiral is built. The Ca2+ ions are an integral part of the structure, which cannot form without them. The structural determinants of this unique architecture will be reviewed with its conservations and variations together with the implication for secretion and folding of these proteins. The general purpose of the RTX domains appears to act as an internal chaperone that keeps the polypeptide unfolded in the calcium-deprived cytosol and triggers folding in the calcium-rich extracellular medium. A rather recent addition to the structural biology of the RTX toxin is a variant occurring in a large RTX adhesin, where this non-canonical β-roll binds to ice and diatoms.
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Affiliation(s)
- Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicherstrasse 47, D-50674 Cologne, Germany
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Nageswara S, Guntuku G, Yakkali BL. Purification, characterization, and structural elucidation of serralysin-like alkaline metalloprotease from a novel source. J Genet Eng Biotechnol 2019; 17:1. [PMID: 31659553 PMCID: PMC6821148 DOI: 10.1186/s43141-019-0002-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 11/15/2022]
Abstract
Background Serratiopeptidase is an alkaline metalloendopeptidase, which acquired wide significance because of its therapeutic applications. The present study was undertaken for purification, characterization, and structural elucidation of serratiopeptidase produced from Streptomyces hydrogenans var. MGS13. Result The crude enzyme was purified by precipitating with ammonium sulfate, dialysis, and Sephadex gel filtration, resulting in 34% recovery with a 12% purification fold. The purified enzyme S.AMP13 was spotted as a single clear hydrolytic band on casein zymogram and whose molecular weight was found to be 32 kDa by SDS-PAGE. The inhibitor and stability studies revealed that this enzyme is metalloprotease, thermostable, and alkaline in nature. The maximum serratiopeptidase activity was observed at 37 °C and pH 9.0. The partial amino acid sequence of the purified enzyme S.AMP13 by LC-MS/MS analysis shows the closest sequence similarities with previously reported alkaline metalloendopeptidases. The amino acid sequence alignment of S.AMP13 shared a conserved C-terminus region with peptidase-M10 serralysin superfamily at amino acid positions 128–147, i.e., ANLSTRATDTVYGFNSTAGR revealed that this enzyme is a serralysin-like protease. The kinetic studies of the purified enzyme revealed a Km of 1 mg/mL for its substrate casein and Vmax of 319 U/mL/min. The 3D structure of the purified enzyme was modeled by using SWISS-MODEL, and the quality of the structure was authenticated by assessing the Ramachandran plot using PROCHECK server, which suggested that the enzyme was stable with good quality. Conclusion Inhibitor, stability, electrophoretic, and bioinformatic studies suggested that the purified enzyme obtained from S. hydrogenans var. MGS13 is a serralysin-like protease. Electronic supplementary material The online version of this article (10.1186/s43141-019-0002-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swathi Nageswara
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India. .,, Srikakulam, India.
| | - Girijasankar Guntuku
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| | - Bhagya Lakshmi Yakkali
- A.U. College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
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Abd Latip MA, Abdul Hamid AA, Nordin NFH. Microbial hydrolytic enzymes: In silico studies between polar and tropical regions. POLAR SCIENCE 2019; 20:9-18. [DOI: 10.1016/j.polar.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Vélez-Gómez JM, Melchor-Moncada JJ, Veloza LA, Sepúlveda-Arias JC. Purification and characterization of a metalloprotease produced by the C8 isolate of Serratia marcescens using silkworm pupae or casein as a protein source. Int J Biol Macromol 2019; 135:97-105. [PMID: 31125647 DOI: 10.1016/j.ijbiomac.2019.05.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022]
Abstract
Serratiopeptidase, a metalloprotease produced by Serratia marcescens, is produced through a fermentation process using carbohydrates and proteins as carbon and nitrogen sources. However, some byproducts of the silk industry could be an alternative source for serratiopeptidase production. Therefore, the present work is focused on the purification and characterization of a serratiopeptidase produced from the C8 isolate of Serratia marcescens and obtained from a Colombian silkworm hybrid using casein or silkworm pupae. The protease was purified using ultrafiltration, anion-exchange, and size-exclusion chromatography. The purified enzyme showed a molecular weight of ~50 kDa with a purity above 96%, an isoelectric point of ~4.6, optimum pH and temperature of 6 and 50 °C, and stability at 4 °C for one month. The kinetic constants using azocasein as substrate were 0.63 mM (Km), 2,016 μM/min (Vmax), 41.41 s-1 (Kcat), and 6.56 × 107 M-1 s-1 (Kcat/Km). Inhibition by 5 mM EDTA or 1,10-phenanthroline was recovered by adding Zn2+ at the same concentration. Mass spectrometry analysis indicated 94% homology with the sequence of serratiopeptidase produced by the E-15 strain. We purified and characterized a serratiopeptidase produced by the C8 isolate of S. marcescens in a culture medium based on a renewable source from the silk industry.
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Affiliation(s)
- Jenny Marcela Vélez-Gómez
- Facultad de Tecnologías, Escuela de Tecnología Química, Grupo Polifenoles, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Jhon Jairo Melchor-Moncada
- Facultad de Ciencias de la Salud, Grupo Infección e Inmunidad, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Luz Angela Veloza
- Facultad de Tecnologías, Escuela de Tecnología Química, Grupo Polifenoles, Universidad Tecnológica de Pereira, Pereira, Colombia
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Qin Y, Wang J, Wang F, Shen L, Zhou H, Sun H, Hao K, Song L, Zhou Z, Zhang C, Wu Y, Yang J. Purification and Characterization of a Secretory Alkaline Metalloprotease with Highly Potent Antiviral Activity from Serratia marcescens Strain S3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3168-3178. [PMID: 30799619 DOI: 10.1021/acs.jafc.8b06909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In this study we report a secretory protein that was purified from Serratia marcescens strain S3 isolated from soil from the tobacco rhizosphere. Subsequent mass spectrometry and annotation characterized the protein as secretory alkaline metalloprotease (SAMP). SAMP plays a crucial role in inhibiting Tobacco mosaic virus (TMV). Transmission electron microscopy (TEM), dynamic light scattering (DLS), confocal microscopy, and microscale thermophoresis (MST) were employed to investigate the anti-TMV mechanism of SAMP. Our results demonstrated that SAMP, as a hydrolytic metal protease, combined and hydrolyzed TMV coat proteins to destroy the virus particles. This study is the first to investigate the antiviral effects of a S. marcescens metalloprotease, and our finding suggests that S. marcescens-S3 may be agronomically useful as a disease-controlling factor active against Tobacco mosaic virus.
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Affiliation(s)
- Yuanxia Qin
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Jie Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Haixiang Zhou
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Hangjun Sun
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Kaiqiang Hao
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Liyun Song
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
| | - Zhicheng Zhou
- Hunan Tobacco Science Institute , Changsha 410004 , P. R. China
| | - Chaoqun Zhang
- Jiangxi Institute of Tobacco Leaf Science , Nanchang 330025 , P. R. China
| | - Yuanhua Wu
- College of Plant Protection , Shenyang Agricultural University , Shenyang 110866 , P. R. China
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management , Tobacco Research Institute of Chinese Academy of Agricultural Sciences , Qingdao 266101 , P. R. China
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Rouhani M, Valizadeh V, Ahangari Cohan R, Norouzian D. Computational design, structure refinement and molecular dynamics simulation of novel engineered serratiopeptidase analogs. J Biomol Struct Dyn 2018; 37:4171-4180. [PMID: 30451085 DOI: 10.1080/07391102.2018.1540361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maryam Rouhani
- Nano-Biotechnology Department, New Technologies Research Group, Pasteur Institute of Iran , Tehran , Iran
| | - Vahideh Valizadeh
- Nano-Biotechnology Department, New Technologies Research Group, Pasteur Institute of Iran , Tehran , Iran
| | - Reza Ahangari Cohan
- Nano-Biotechnology Department, New Technologies Research Group, Pasteur Institute of Iran , Tehran , Iran
| | - Dariush Norouzian
- Nano-Biotechnology Department, New Technologies Research Group, Pasteur Institute of Iran , Tehran , Iran
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Garcia CJ, Pericleous A, Elsayed M, Tran M, Gupta S, Callaghan JD, Stella NA, Franks JM, Thibodeau PH, Shanks RMQ, Kadouri DE. Serralysin family metalloproteases protects Serratia marcescens from predation by the predatory bacteria Micavibrio aeruginosavorus. Sci Rep 2018; 8:14025. [PMID: 30232396 PMCID: PMC6145908 DOI: 10.1038/s41598-018-32330-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 09/03/2018] [Indexed: 12/16/2022] Open
Abstract
Micavibrio aeruginosavorus is an obligate Gram-negative predatory bacterial species that feeds on other Gram-negative bacteria by attaching to the surface of its prey and feeding on the prey's cellular contents. In this study, Serratia marcescens with defined mutations in genes for extracellular cell structural components and secreted factors were used in predation experiments to identify structures that influence predation. No change was measured in the ability of the predator to prey on S. marcescens flagella, fimbria, surface layer, prodigiosin and phospholipase-A mutants. However, higher predation was measured on S. marcescens metalloprotease mutants. Complementation of the metalloprotease gene, prtS, into the protease mutant, as well as exogenous addition of purified serralysin metalloprotease, restored predation to wild type levels. Addition of purified serralysin also reduced the ability of M. aeruginosavorus to prey on Escherichia coli. Incubating M. aeruginosavorus with purified metalloprotease was found to not impact predator viability; however, pre-incubating prey, but not the predator, with purified metalloprotease was able to block predation. Finally, using flow cytometry and fluorescent microscopy, we were able to confirm that the ability of the predator to bind to the metalloprotease mutant was higher than that of the metalloprotease producing wild-type. The work presented in this study shows that metalloproteases from S. marcescens could offer elevated protection from predation.
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Affiliation(s)
- Carlos J Garcia
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Androulla Pericleous
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Mennat Elsayed
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Michael Tran
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Jake D Callaghan
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Nicholas A Stella
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jonathan M Franks
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Patrick H Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15221, USA
| | - Robert M Q Shanks
- Department of Ophthalmology, Charles T. Campbell Laboratory of Ophthalmic Microbiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
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14
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Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Denessiouk K. Building kit for metal cation binding sites in proteins. Biochem Biophys Res Commun 2017; 494:311-317. [PMID: 29017922 DOI: 10.1016/j.bbrc.2017.10.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 11/17/2022]
Abstract
Starting with conformations of calcium-binding sites in parvalbumin and integrin (representative structures of EF-hand and calcium blade zones, respectively) we introduce four new different local Ca2+-recognition units in proteins: a one-residue unit type I (ORI); a three-residue unit type I (TRI); a one-residue unit type II (ORII) and a three-residue unit type II (TRII). Based on the amount and nature of variable atoms, the type I and II units theoretically can have four and twelve variants, respectively. Analysis of known "Ca2+-bound functional niches" in proteins revealed presence of almost all possible variants of Ca2+-recognition units in actual structures. Parvalbumin, integrin alpha-IIb and sixteen other proteins with different Ca2+-bound functional niches contain various consecutively joined combinations of OR(I/II) and TR(I/II) units. Such a OR(I/II)+TR(I/II) joint unit forms a tripeptide, which uses three main-chain atoms for metal binding: nitrogenn (Donor), oxygenn (Acceptor) and nitrogenn+2 (Donor). Thus, taken together, the described ORI, TRI, ORII and TRII units can serve as elementary blocks to construct more complex calcium recognizing substructures in a variety of calcium binding sites of unrelated proteins.
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Affiliation(s)
- Alexander I Denesyuk
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mark S Johnson
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
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15
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Production, purification and characterization of fibrinolytic enzyme from Serratia sp. KG-2-1 using optimized media. 3 Biotech 2017; 7:184. [PMID: 28664371 DOI: 10.1007/s13205-017-0808-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022] Open
Abstract
Intravascular thrombosis is one of the major causes of variety of cardiovascular disorders leading to high mortality worldwide. Fibrinolytic enzymes from microbial sources possess ability to dissolve these clots and help to circumvent these problems in more efficient and safer way. In the present study, fibrinolytic protease with higher fibrinolytic activity than plasmin was obtained from Serratia sp. KG-2-1 isolated from garbage dump soil. Response surface methodology was used to study the interactive effect of concentration of maltose, yeast extract + peptone (1:1), incubation time, and pH on enzyme production and biomass. Maximum enzyme production was achieved at 33 °C after 24 h at neutral pH in media containing 1.5% Maltose, 4.0% yeast extract + peptone and other trace elements resulting in 1.82 folds increased production. The enzyme was purified from crude extract using ammonium sulfate precipitation and DEAE-Sephadex chromatography resulting in 12.9 fold purification with 14.9% yield. The purified enzyme belongs to metalloprotease class and had optimal activity in conditions similar to physiological environment with temperature optima of 40 °C and pH optima of 8. The enzyme was found to be stable in various solvents and its activity was enhanced in presence of Na+, K+, Ba2+, Cu2+, Mn2+, Hg2+ but inhibited by Ca2+ and Fe3+. Hence, the obtained enzyme may be used as potential therapeutic agent in combating various thrombolytic disorders.
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16
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Xu D, Zhou J, Lou X, He J, Ran T, Wang W. Myroilysin Is a New Bacterial Member of the M12A Family of Metzincin Metallopeptidases and Is Activated by a Cysteine Switch Mechanism. J Biol Chem 2017; 292:5195-5206. [PMID: 28188295 DOI: 10.1074/jbc.m116.758110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/01/2017] [Indexed: 11/06/2022] Open
Abstract
Proteases play important roles in all living organisms and also have important industrial applications. Family M12A metalloproteases, mainly found throughout the animal kingdom, belong to the metzincin protease family and are synthesized as inactive precursors. So far, only flavastacin and myroilysin, isolated from bacteria, were reported to be M12A proteases, whereas the classification of myroilysin is still unclear due to the lack of structural information. Here, we report the crystal structures of pro-myroilysin from bacterium Myroides sp. cslb8. The catalytic zinc ion of pro-myroilysin, at the bottom of a deep active site, is coordinated by three histidine residues in the conserved motif HEXXHXXGXXH; the cysteine residue in the pro-peptide coordinates the catalytic zinc ion and inhibits myroilysin activity. Structure comparisons revealed that myroilysin shares high similarity with the members of the M12A, M10A, and M10B families of metalloproteases. However, a unique "cap" structure tops the active site cleft in the structure of pro-myroilysin, and this "cap" structure does not exist in the above structure-reported subfamilies. Further structure-based sequence analysis revealed that myroilysin appears to belong to the M12A family, but pro-myroilysin uses a "cysteine switch" activation mechanism with a unique segment, including the conserved cysteine residue, whereas other reported M12A family proteases use an "aspartate switch" activation mechanism. Thus, our results suggest that myroilysin is a new bacterial member of the M12A family with an exceptional cysteine switch activation mechanism. Our results shed new light on the classification of the M12A family and may suggest a divergent evolution of the M12 family.
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Affiliation(s)
- Dongqing Xu
- From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and
| | - Jiale Zhou
- From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and
| | - Xiangdi Lou
- From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and
| | - Jianhua He
- the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, China
| | - Tingting Ran
- From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and
| | - Weiwu Wang
- From the Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China and
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17
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DO TT, NGUYEN TT, NGUYEN TLS, LE HT. Optimization, purification, and characterization of an extracellular antifungal protein from Serratia marcescens DT3 isolated from soil in Vietnam. Turk J Biol 2017. [DOI: 10.3906/biy-1607-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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