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Zhang J, Li J, Gong J, Liu J, Wang Y, Zhao F, Sun S, Wang W. A novel highly thermostable and stress resistant ROS scavenging metalloprotein from Paenibacillus. Arch Biochem Biophys 2024; 751:109837. [PMID: 38007074 DOI: 10.1016/j.abb.2023.109837] [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: 08/08/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Reactive oxygen species (ROS) are unstable metabolites produced during cellular respiration that can cause extensive damage to the body. Here we report a unique structural metalloprotein called RSAPp for the first time, which exhibits robust ROS-scavenging activity, high thermostability, and stress resistance. RSAPp is a previously uncharacterized DUF2935 (domain of unknown function, accession number: cl12705) family protein from Paenibacillus, containing a highly conserved four-helix bundle with binding sites for variable-valence metal ions (Mn2+/Fe2+/Zn2+). Enzymatic characterization results indicated that RSAPp displays the functionality of three different antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD). In particular, RSAPp exhibits a significant SOD-like activity that is remarkably effective in eliminating superoxide radicals (up to kcat/KM = 2.27 × 1011 mol-1 s-1), and maintains the catalytical active in a wide range of temperatures (25-100 °C) and pH (pH 2.0-9.0), as well as resistant to high temperature, alkali and acidic pH, and 55 different concentrations of detergent agents, chemical solvents, and inhibitors. These properties make RSAPp an attractive candidate for various industrial applications, including cosmetics, food, and pharmaceuticals.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jiabin Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jingbo Gong
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Jingjing Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Yijia Wang
- Laboratory of Oncologic Molecular Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300121, PR China
| | - Fang Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Shenmei Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, PR China.
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Kang JW, Kim WJ, Kang DH. Synergistic effect of 222-nm krypton-chlorine excilamp and mild heating combined treatment on inactivation of Escherichia coli O157:H7 and Salmonella Typhimurium in apple juice. Int J Food Microbiol 2020; 329:108665. [PMID: 32497789 DOI: 10.1016/j.ijfoodmicro.2020.108665] [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] [Received: 11/26/2019] [Revised: 03/20/2020] [Accepted: 05/16/2020] [Indexed: 10/24/2022]
Abstract
Simultaneous treatment with 222-nm KrCl excilamp and mild heating (EX-MH) at 45, 50 and 55 °C showed synergistic bactericidal effects on non-acid and acid adapted cells of Escherichia coli O157:H7 and Salmonella Typhimurium in apple juice. In particular, acid-adapted pathogens exhibited increased resistance to EX-MH compared to pathogenic bacteria that were not acid-adapted. Also, elucidation of the synergistic bactericidal mechanism of EX-MH was performed through several assays and this mechanism was described as follows: (i) when KrCl excilamp (EX) and mild heating (MH) are applied simultaneously, MH reversibly inactivates the antioxidant enzyme, superoxide dismutase (SOD), thereby increasing accumulation of reactive oxygen species (ROS) generated by EX and thus inducing synergistic ROS generation, (ii) ROS production induces lipid peroxidation occurrence in the cell membrane, (iii) this lipid peroxidation occurrence in the cell membrane induces synergistic destruction of cell membrane, resulting in synergistic cell death. While EX-MH of 45, 50, or 55 °C reduced E. coli O157:H7 (the pathogen most resistant to EX-MH) in apple juice by 5-log, the qualities such as color (L*, a*, and b*), total phenolic compounds (TPC), and DPPH free radical scavenging activity of apple juice did not change significantly (P > 0.05). This study not only suggests the applicability of EX-MH to the apple juice industry, but also can be used as baseline data for future relevant research.
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Affiliation(s)
- Jun-Won Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woo-Ju Kim
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe road, Columbus, OH 43210, USA
| | - Dong-Hyun Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Republic of Korea.
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3
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Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72. Catalysts 2020. [DOI: 10.3390/catal10080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability.
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Park C, Park W. Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential. Front Microbiol 2018; 9:1081. [PMID: 29910779 PMCID: PMC5992423 DOI: 10.3389/fmicb.2018.01081] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Li M, Guo S, Li X, Wang Q, Zhu L, Yin C, Wang W. Engineering a highly thermostable and stress tolerant superoxide dismutase by N-terminal modification and metal incorporation. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Retnoningrum DS, Yoshida H, Arumsari S, Kamitori S, Ismaya WT. The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus. Acta Crystallogr F Struct Biol Commun 2018; 74:135-142. [PMID: 29497016 PMCID: PMC5947698 DOI: 10.1107/s2053230x18001036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/17/2018] [Indexed: 11/10/2022] Open
Abstract
A recombinant Staphylococcus equorum manganese superoxide dismutase (MnSOD) with an Asp13Arg substitution displays activity over a wide range of pH, at high temperature and in the presence of chaotropic agents, and retains 50% of its activity after irradiation with UVC for up to 45 min. Interestingly, Bacillus subtilis MnSOD does not have the same stability, despite having a closely similar primary structure and thus presumably also tertiary structure. Here, the crystal structure of S. equorum MnSOD at 1.4 Å resolution is reported that may explain these differences. The crystal belonged to space group P3221, with unit-cell parameters a = 57.36, b = 57.36, c = 105.76 Å, and contained one molecule in the asymmetric unit. The symmetry operation indicates that the enzyme has a dimeric structure, as found in nature and in B. subtilis MnSOD. As expected, their overall structures are nearly identical. However, the loop connecting the helical and α/β domains of S. equorum MnSOD is shorter than that in B. subtilis MnSOD, and adopts a conformation that allows more direct water-mediated hydrogen-bond interactions between the amino-acid side chains of the first and last α-helices in the latter domain. Furthermore, S. equorum MnSOD has a slightly larger buried area compared with the dimer surface area than that in B. subtilis MnSOD, while the residues that form the interaction in the dimer-interface region are highly conserved. Thus, the stability of S. equorum MnSOD may not originate from the dimeric form alone. Furthermore, an additional water molecule was found in the active site. This allows an alternative geometry for the coordination of the Mn atom in the active site of the apo form. This is the first structure of MnSOD from the genus Staphylococcus and may provide a template for the structural study of other MnSODs from this genus.
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Affiliation(s)
- Debbie S. Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Sekar Arumsari
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Wangsa T. Ismaya
- Dexa Laboratories of Biomolecular Sciences, Jl. Industri Selatan V Blok PP No. 7, Kawasan Industri Jababeka II, Cikarang 17550, Indonesia
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Murata H, Carmali S, Baker SL, Matyjaszewski K, Russell AJ. Solid-phase synthesis of protein-polymers on reversible immobilization supports. Nat Commun 2018; 9:845. [PMID: 29487296 PMCID: PMC5829226 DOI: 10.1038/s41467-018-03153-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/24/2018] [Indexed: 11/28/2022] Open
Abstract
Facile automated biomacromolecule synthesis is at the heart of blending synthetic and biologic worlds. Full access to abiotic/biotic synthetic diversity first occurred when chemistry was developed to grow nucleic acids and peptides from reversibly immobilized precursors. Protein-polymer conjugates, however, have always been synthesized in solution in multi-step, multi-day processes that couple innovative chemistry with challenging purification. Here we report the generation of protein-polymer hybrids synthesized by protein-ATRP on reversible immobilization supports (PARIS). We utilized modified agarose beads to covalently and reversibly couple to proteins in amino-specific reactions. We then modified reversibly immobilized proteins with protein-reactive ATRP initiators and, after ATRP, we released and analyzed the protein polymers. The activity and stability of PARIS-synthesized and solution-synthesized conjugates demonstrated that PARIS was an effective, rapid, and simple method to generate protein-polymer conjugates. Automation of PARIS significantly reduced synthesis/purification timelines, thereby opening a path to changing how to generate protein-polymer conjugates.
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Affiliation(s)
- Hironobu Murata
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Sheiliza Carmali
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Stefanie L Baker
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
- Department of Biomedical Engineering, Scott Hall 4N201, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Krzysztof Matyjaszewski
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Alan J Russell
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
- Department of Biomedical Engineering, Scott Hall 4N201, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
- Disruptive Health Technology Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA.
- Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.
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Geobacillus and Anoxybacillus spp. from Terrestrial Geothermal Springs Worldwide: Diversity and Biotechnological Applications. EXTREMOPHILES IN EURASIAN ECOSYSTEMS: ECOLOGY, DIVERSITY, AND APPLICATIONS 2018. [DOI: 10.1007/978-981-13-0329-6_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Roy C, Alam M, Mandal S, Haldar PK, Bhattacharya S, Mukherjee T, Roy R, Rameez MJ, Misra AK, Chakraborty R, Nanda AK, Mukhopadhyay SK, Ghosh W. Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria. Front Microbiol 2016; 7:412. [PMID: 27065976 PMCID: PMC4814524 DOI: 10.3389/fmicb.2016.00412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
Exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 pH) mid-temperature (55-85°C) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of Gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media with 50 μg ml(-1) vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic bacteria present in the tested hot water inocula. Moreover, it also killed all the Gram-negative hot-spring isolates that were obtained in vancomycin-free media. Concurrent literature search for the description of Gram-negative thermophilic bacteria revealed that at least 16 of them were reportedly vancomycin-susceptible. While these data suggested that vancomycin-susceptibility could be a global trait of thermophilic bacteria (irrespective of their taxonomy, biogeography and Gram-character), MALDI Mass Spectroscopy of the peptidoglycans of a few Gram-negative thermophilic bacteria revealed that tandem alanines were present in the fourth and fifth positions of their muropeptide precursors (MPPs). Subsequent phylogenetic analyses revealed a close affinity between the D-alanine-D-alanine ligases (Ddl) of taxonomically-diverse Gram-negative thermophiles and the thermostable Ddl protein of Thermotoga maritima, which is well-known for its high specificity for alanine over other amino acids. The Ddl tree further illustrated a divergence between the homologs of Gram-negative thermophiles and mesophiles, which broadly coincided with vancomycin-susceptibility and vancomycin-resistance respectively. It was thus hypothesized that thermophilic Ddls have been evolutionarily selected to favor a D-ala-D-ala bonding. However, preference for D-ala-D-ala-terminated MPPs does not singlehandedly guarantee vancomycin susceptibility of thermophilic bacteria as the large and relatively-hydrophilic vancomycin molecule has to cross the outer membrane before it can inhibit peptidoglycan biosynthesis. Literature shows that many mesophilic Gram-negative bacteria also have D-ala-D-ala-terminated MPPs, but they still remain resistant to vancomycin due to the relative impermeability of their membranes. But the global vancomycin-susceptibility phenotype of thermophilic bacteria itself testifies that the drug crosses the membrane in all these cases. As a corollary, it seems quite likely that the outer membranes of thermophilic bacteria have some yet-unknown characteristic feature(s) that invariably ensures the entry of vancomycin.
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Affiliation(s)
- Chayan Roy
- Department of Microbiology, Bose Institute Kolkata, India
| | - Masrure Alam
- Department of Microbiology, Bose Institute Kolkata, India
| | | | | | | | | | - Rimi Roy
- Department of Microbiology, Bose Institute Kolkata, India
| | - Moidu J Rameez
- Department of Microbiology, Bose Institute Kolkata, India
| | - Anup K Misra
- Division of Molecular Medicine, Bose Institute Kolkata, India
| | | | - Ashish K Nanda
- Department of Chemistry, University of North Bengal Siliguri, India
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Li M, Zhu L, Wang W. Improving the thermostability and stress tolerance of an archaeon hyperthermophilic superoxide dismutase by fusion with a unique N-terminal domain. SPRINGERPLUS 2016; 5:241. [PMID: 27026935 PMCID: PMC4771647 DOI: 10.1186/s40064-016-1854-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 02/15/2016] [Indexed: 11/10/2022]
Abstract
The superoxide dismutase from the archaeon Sulfolobus solfataricus (SOD Ss ) is a well-studied hyperthermophilic SOD with crystal structure and possible thermostability factors characterized. Previously, we discovered an N-terminal domain (NTD) in a thermophilic SOD from Geobacillus thermodenitrificans NG80-2 which confers heat resistance on homologous mesophilic SODs. The present study therefore aimed to further improve the thermostability and stress tolerance of SOD Ss via fusion with this NTD. The recombinant protein, rSOD Ss , exhibited improved thermophilicity, higher working temperature, improved thermostability, broader pH stability, and enhanced tolerance to inhibitors and organic media than SOD Ss without any alterations in its oligomerization state. These results suggest that the NTD is an excellent candidate for improving stability of both mesophilic and thermophilic SOD from either bacteria or archaea via simple genetic manipulation. Therefore, this study provides a general, feasible and highly useful strategy for generating extremely thermostable SODs for industrial applications.
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Affiliation(s)
- Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457 People's Republic of China
| | - Lin Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457 People's Republic of China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457 People's Republic of China ; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin, 300457 People's Republic of China
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