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Bonczidai-Kelemen D, Tóth K, Fábián I, Lihi N. The role of the terminal cysteine moiety in a metallopeptide mimicking the active site of the NiSOD enzyme. Dalton Trans 2024; 53:1648-1656. [PMID: 38168682 DOI: 10.1039/d3dt03638c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Superoxide dismutase (SOD) enzymes are pivotal in regulating oxidative stress. In order to model Ni containing SOD enzymes, the results of the thermodynamic, spectroscopic and SOD activity studies on the complexes formed between nickel(II) and a NiSOD related peptide, CysCysAspLeuProCysGlyValTyr-NH2 (wtCC), are reported. Cysteine was introduced to replace the first histidine residue in the amino acid sequence of the active site of the NiSOD enzyme. The novel peptide exhibits 3 times higher metal binding affinity compared to the native NiSOD fragment. This is due to the presence of the first cysteine in the coordination sphere of nickel(II). At physiological pH, the (NH2,S-,S-,S-) coordinated complex is the major species. This coordination mode is altered when one thiolate group is replaced by an amide nitrogen of the peptide backbone above pH 7.5. The nickel complexes of wtCC exhibit similar SOD activity to that of the complex formed with the active site fragment of the native NiSOD. The reaction between the complexes and the superoxide anion was studied by the sequential stopped-flow method. These studies revealed that the nickel(II) complex is always in excess over the nickel(III) complex during the dismutation process. However, the nickel(III) species is also involved in a relatively fast degradation process. This unambiguously proves that a protective mechanism must be operative in the NiSOD enzyme which prevents the oxidation of the sulfur atom of cysteine in the presence of O2-. The results provide new possibilities for the use of NiSOD mimics in bio- and industrial catalytic processes.
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Affiliation(s)
- Dóra Bonczidai-Kelemen
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
- Doctoral School of Chemistry, University of Debrecen, Debrecen H-4032, Hungary
| | - Klaudia Tóth
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - István Fábián
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
| | - Norbert Lihi
- HUN-REN-UD Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, H-4032 Debrecen, Hungary.
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2
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Nakane D, Akiyama Y, Suzuki S, Miyazaki R, Akitsu T. Improvement of the SOD activity of the Cu 2+ complexes by hybridization with lysozyme and its hydrogen bond effect on the activity enhancement. Front Chem 2024; 11:1330833. [PMID: 38304569 PMCID: PMC10830756 DOI: 10.3389/fchem.2023.1330833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
We prepared L-amino acids (L-valine and L-serine, respectively) based on the Schiff base Cu2+ complexes CuSV and CuSS in the absence/presence of hydroxyl groups and their imidazole-bound compounds CuSV-Imi and CuSS-Imi to reveal the effects of hydroxyl groups on SOD activity. The structural and spectroscopic features of the Cu2+ complexes were evaluated using X-ray crystallography, UV-vis spectroscopy, and EPR spectroscopy. The spectroscopic behavior upon addition of lysozyme indicated that both CuSV and CuSS were coordinated by the imidazole group of His15 in lysozyme at their equatorial position, leading to the formation of hybrid proteins with lysozyme. CuSS-Imi showed a higher SOD activity than CuSV-Imi, indicating that the hydroxyl group of CuSS-Imi played an important role in the disproportionation of O2 - ion. Hybridization of the Cu2+ complexes CuSV and CuSS with lysozyme resulted in higher SOD activity than that of CuSV-Imi and CuSS-Imi. The improvements in SOD activity suggest that there are cooperative effects between Cu2+ complexes and lysozyme.
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Affiliation(s)
- Daisuke Nakane
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
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3
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Ni J, Wood JL, White MY, Lihi N, Markham TE, Wang J, Chivers PT, Codd R. Reduction-cleavable desferrioxamine B pulldown system enriches Ni(ii)-superoxide dismutase from a Streptomyces proteome. RSC Chem Biol 2023; 4:1064-1072. [PMID: 38033724 PMCID: PMC10685849 DOI: 10.1039/d3cb00097d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023] Open
Abstract
Two resins with the hydroxamic acid siderophore desferrioxamine B (DFOB) immobilised as a free ligand or its Fe(iii) complex were prepared to screen the Streptomyces pilosus proteome for proteins involved in siderophore-mediated Fe(iii) uptake. The resin design included a disulfide bond to enable the release of bound proteins under mild reducing conditions. Proteomics analysis of the bound fractions did not identify proteins associated with siderophore-mediated Fe(iii) uptake, but identified nickel superoxide dismutase (NiSOD), which was enriched on the apo-DFOB-resin but not the Fe(iii)-DFOB-resin or the control resin. While DFOB is unable to sequester Fe(iii) from sites deeply buried in metalloproteins, the coordinatively unsaturated Ni(ii) ion in NiSOD is present in a surface-exposed loop region at the N-terminus, which might enable partial chelation. The results were consistent with the notion that the apo-DFOB-resin formed a ternary complex with NiSOD, which was not possible for either the coordinatively saturated Fe(iii)-DFOB-resin or the non-coordinating control resin systems. In support, ESI-TOF-MS measurements from a solution of a model Ni(ii)-SOD peptide and DFOB showed signals that correlated with a ternary Ni(ii)-SOD peptide-DFOB complex. Although any biological implications of a DFOB-NiSOD complex are unclear, the work shows that the metal coordination properties of siderophores might influence an array of metal-dependent biological processes beyond those established in iron uptake.
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Affiliation(s)
- Jenny Ni
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - James L Wood
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Melanie Y White
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
- Charles Perkins Centre, The University of Sydney New South Wales 2006 Australia
| | - Norbert Lihi
- ELKH-DE Mechanisms of Complex Homogeneous and Heterogeneous Chemical Reactions Research Group, Department of Inorganic and Analytical Chemistry, University of Debrecen Debrecen H-4032 Hungary
| | - Todd E Markham
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Joseph Wang
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
| | - Peter T Chivers
- Department of Chemistry, Durham University Durham DH1 3LE UK
- Department of Biosciences, Durham University Durham DH1 3LE UK
| | - Rachel Codd
- School of Medical Sciences, The University of Sydney New South Wales 2006 Australia
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4
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Basak P, Cabelli DE, Chivers PT, Farquhar ER, Maroney MJ. In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation. Metallomics 2023; 15:mfad054. [PMID: 37723610 PMCID: PMC10628968 DOI: 10.1093/mtomcs/mfad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
The importance of cellular low molecular weight ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of nickel-dependent superoxide dismutase (NiSOD) from Streptomyces coelicolor. In vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.
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Affiliation(s)
- Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Diane E Cabelli
- Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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5
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Zhang P, Shen L, Chen J, Li Z, Zhao W, Wen Y, Liu H. Comparative study of the toxicity mechanisms of quinolone antibiotics on soybean seedlings: Insights from molecular docking and transcriptomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165254. [PMID: 37394075 DOI: 10.1016/j.scitotenv.2023.165254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
The ecological effects of quinolone antibiotics (QNs) on non-target organisms have received widespread attention. The toxicological mechanisms of three common QNs, that is, enrofloxacin, levofloxacin, and ciprofloxacin, on soybean seedlings were investigated in this study. Enrofloxacin and levofloxacin caused significant growth inhibition, ultrastructural alterations, photosynthetic suppression, and stimulation of the antioxidant system, with levofloxacin exhibiting the strongest toxic effects. Ciprofloxacin (<1 mg·L-1) did not have a significant effect on the soybean seedlings. As the concentrations of enrofloxacin and levofloxacin increased, antioxidant enzyme activities, malondialdehyde content, and hydrogen peroxide levels also increased. Meanwhile, the chlorophyll content and chlorophyll fluorescence parameters decreased, indicating that the plants underwent oxidative stress and photosynthesis was suppressed. The cellular ultrastructure was also disrupted, which was manifested by swollen chloroplasts, increased starch granules, disintegration of plastoglobules, and mitochondrial degradation. The molecular docking results suggested that the QNs have an affinity for soybean target protein receptors (4TOP, 2IUJ, and 1FHF), with levofloxacin having the highest binding energy (-4.97, -3.08, -3.8, respectively). Transcriptomic analysis has shown that genes were upregulated under the enrofloxacin and levofloxacin treatments were mainly involved in ribosome metabolism and processes to synthesize oxidative stress-related proteins. Downregulated genes in the levofloxacin treatment were primarily enriched in photosynthesis-related pathways, indicating that levofloxacin significantly inhibited gene expression for photosynthesis. Genes expression level by quantitative real-time PCR analysis was consistent with the transcriptomic results. This study confirmed the toxic effect of QNs on soybean seedlings, and provided new insights into the environmental risks of antibiotics.
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Affiliation(s)
- Ping Zhang
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Luoqin Shen
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Jiayao Chen
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Zhiheng Li
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Wenlu Zhao
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China
| | - Yuezhong Wen
- MOE Key Laboratory of Environmental Remediation & Ecosystem Health, Institute of Environmental Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Huijun Liu
- School of Environmental Science and Engineering, Key Laboratory of Solid Waste Treatment and Recycling of Zhejiang Province, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang Province, China.
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6
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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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7
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Pinmanee P, Sompinit K, Jantimaporn A, Khongkow M, Haltrich D, Nimchua T, Sukyai P. Purification and Immobilization of Superoxide Dismutase Obtained from Saccharomyces cerevisiae TBRC657 on Bacterial Cellulose and Its Protective Effect against Oxidative Damage in Fibroblasts. Biomolecules 2023; 13:1156. [PMID: 37509191 PMCID: PMC10377281 DOI: 10.3390/biom13071156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential enzyme that eliminates harmful reactive oxygen species (ROS) generating inside living cells. Due to its efficacities, SOD is widely applied in many applications. In this study, the purification of SOD produced from Saccharomyces cerevisiae TBRC657 was conducted to obtain the purified SOD that exhibited specific activity of 513.74 U/mg with a purification factor of 10.36-fold. The inhibitory test revealed that the purified SOD was classified as Mn-SOD with an estimated molecular weight of 25 kDa on SDS-PAGE. After investigating the biochemical characterization, the purified SOD exhibited optimal activity under conditions of pH 7.0 and 35 °C, which are suitable for various applications. The stability test showed that the purified SOD rapidly decreased in activity under high temperatures. To overcome this, SOD was successfully immobilized on bacterial cellulose (BC), resulting in enhanced stability under those conditions. The immobilized SOD was investigated for its ability to eliminate ROS in fibroblasts. The results indicated that the immobilized SOD released and retained its function to regulate the ROS level inside the cells. Thus, the immobilized SOD on BC could be a promising candidate for application in many industries that require antioxidant functionality under operating conditions.
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Affiliation(s)
- Phitsanu Pinmanee
- Biotechnology of Biopolymers and Bioactive Compounds Special Research Unit, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Kamonwan Sompinit
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Angkana Jantimaporn
- Nanomedicine and Veterinary Research Team, National Center of Nanotechnology (NANOTEC), Pathum Thani 12120, Thailand
| | - Mattaka Khongkow
- Nanomedicine and Veterinary Research Team, National Center of Nanotechnology (NANOTEC), Pathum Thani 12120, Thailand
| | - Dietmar Haltrich
- Department for Food Science and Food Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Thidarat Nimchua
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Prakit Sukyai
- Biotechnology of Biopolymers and Bioactive Compounds Special Research Unit, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
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8
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Domergue J, Guinard P, Douillard M, Pécaut J, Hostachy S, Proux O, Lebrun C, Le Goff A, Maldivi P, Duboc C, Delangle P. A Series of Ni Complexes Based on a Versatile ATCUN-Like Tripeptide Scaffold to Decipher Key Parameters for Superoxide Dismutase Activity. Inorg Chem 2023. [PMID: 37247425 DOI: 10.1021/acs.inorgchem.3c00766] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The cellular level of reactive oxygen species (ROS) has to be controlled to avoid some pathologies, especially those linked to oxidative stress. One strategy for designing antioxidants consists of modeling natural enzymes involved in ROS degradation. Among them, nickel superoxide dismutase (NiSOD) catalyzes the dismutation of the superoxide radical anion, O2•-, into O2 and H2O2. We report here Ni complexes with tripeptides derived from the amino-terminal CuII- and NiII-binding (ATCUN) motif that mimics some structural features found in the active site of the NiSOD. A series of six mononuclear NiII complexes were investigated in water at physiological pH with different first coordination spheres, from compounds with a N3S to N2S2 set, and also complexes that are in equilibrium between the N-coordination (N3S) and S-coordination (N2S2). They were fully characterized by a combination of spectroscopic techniques, including 1H NMR, UV-vis, circular dichroism, and X-ray absorption spectroscopy, together with theoretical calculations and their redox properties studied by cyclic voltammetry. They all display SOD-like activity, with a kcat ranging between 0.5 and 2.0 × 106 M-1 s-1. The complexes in which the two coordination modes are in equilibrium are the most efficient, suggesting a beneficial effect of a nearby proton relay.
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Affiliation(s)
- Jérémy Domergue
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Pawel Guinard
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Magali Douillard
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Jacques Pécaut
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Sarah Hostachy
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Olivier Proux
- CNRS, OSUG, Université Grenoble Alpes, 38000 Grenoble, France
| | - Colette Lebrun
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Alan Le Goff
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
| | - Pascale Maldivi
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France
| | - Pascale Delangle
- IRIG, SyMMES, Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, 38000 Grenoble, France
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9
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Furuya T, Nakane D, Kitanishi K, Katsuumi N, Tsaturyan A, Shcherbakov IN, Unno M, Akitsu T. A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme. Sci Rep 2023; 13:6892. [PMID: 37106030 PMCID: PMC10140267 DOI: 10.1038/s41598-023-33926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O2- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.
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Affiliation(s)
- Tetsundo Furuya
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Daisuke Nakane
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
| | - Kenichi Kitanishi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Natsuki Katsuumi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Arshak Tsaturyan
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Étienne, France
- Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-On-Don, 344090, Russia
| | - Igor N Shcherbakov
- Department of Chemistry, Southern Federal University, 7 Zorge Str., Rostov-On-Don, 344090, Russia
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki, 316-8511, Japan
| | - Takashiro Akitsu
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
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10
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Chen D, Ai X, Li Y, Li Y, Ao Y, Rong J, Li G. Protective effects of Cu/Zn-SOD and Mn-SOD on UVC radiation-induced damage in NIH/3T3 cells and murine skin. Acta Histochem 2023; 125:152030. [PMID: 37099996 DOI: 10.1016/j.acthis.2023.152030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023]
Abstract
Superoxide dismutase (SOD) is an antioxidant enzyme with multiple metal cofactors that can specifically clear reactive oxygen species (ROS), which plays an important role in a variety of ultraviolet-induced lesions. Therefore, SOD has the anti-ultraviolet radiation effect. The objective of this study was to compare the differences in the anti-ultraviolet radiation effect of SOD with distinct metal cofactors: Cu/Zn-SOD and Mn-SOD. SOD was first purified using hydrophobic interaction chromatography and ion-exchange chromatography. Second, the Methylthiazolyldiphenyl-tetrazolium bromide method and cell senescence kits were used to study the protective effect of SOD on ultraviolet-induced cell damage. Finally, the protective effect of SOD on ultraviolet -induced skin damage was histopathologically evaluated, and the expression levels of malondialdehyde (MDA) and matrix metalloproteinases (MMPs) in tissues were detected. The results showed that Cu/Zn-SOD was superior to Mn-SOD in promoting cell proliferation, alleviating cell damage, protecting skin structure, and regulating the expression levels of MDA and MMPs, and it has no side effects. In conclusion, Cu/Zn-SOD had a better anti-ultraviolet radiation effect than Mn-SOD, and it can be used in anti-aging and anti-ultraviolet skin-care products.
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Affiliation(s)
- Disi Chen
- College of Life Science, Yangtze University, Jingzhou 434000, PR China
| | - Xiaoyang Ai
- College of Life Science, Yangtze University, Jingzhou 434000, PR China
| | - Yang Li
- College of Life Science, Yangtze University, Jingzhou 434000, PR China
| | - Yue Li
- College of Life Science, Yangtze University, Jingzhou 434000, PR China
| | - Yunfan Ao
- College of Life Science, Yangtze University, Jingzhou 434000, PR China
| | - Jun Rong
- College of Life Science, Yangtze University, Jingzhou 434000, PR China; Jingzhou Changxin Biotechnology Co., Ltd., Jingzhou 434000, PR China.
| | - Guopan Li
- College of Life Science, Yangtze University, Jingzhou 434000, PR China; Jingzhou Changxin Biotechnology Co., Ltd., Jingzhou 434000, PR China.
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11
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Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
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Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
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12
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Qamar AY, Naveed MI, Raza S, Fang X, Roy PK, Bang S, Tanga BM, Saadeldin IM, Lee S, Cho J. Role of antioxidants in fertility preservation of sperm - A narrative review. Anim Biosci 2023; 36:385-403. [PMID: 36397685 PMCID: PMC9996255 DOI: 10.5713/ab.22.0325] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022] Open
Abstract
Male fertility is affected by multiple endogenous stressors, including reactive oxygen species (ROS), which greatly deteriorate the fertility. However, physiological levels of ROS are required by sperm for the proper accomplishment of different cellular functions including proliferation, maturation, capacitation, acrosomal reaction, and fertilization. Excessive ROS production creates an imbalance between ROS production and neutralization resulting in oxidative stress (OS). OS causes male infertility by impairing sperm functions including reduced motility, deoxyribonucleic acid damage, morphological defects, and enhanced apoptosis. Several in-vivo and in-vitro studies have reported improvement in quality-related parameters of sperm following the use of different natural and synthetic antioxidants. In this review, we focus on the causes of OS, ROS production sources, mechanisms responsible for sperm damage, and the role of antioxidants in preserving sperm fertility.
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Affiliation(s)
- Ahmad Yar Qamar
- College of Veterinary and Animal Sciences, Jhang 35200, Sub-campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Muhammad Ilyas Naveed
- College of Veterinary and Animal Sciences, Jhang 35200, Sub-campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Sanan Raza
- College of Veterinary and Animal Sciences, Jhang 35200, Sub-campus of University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Xun Fang
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Pantu Kumar Roy
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Seonggyu Bang
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Bereket Molla Tanga
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Islam M Saadeldin
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Sanghoon Lee
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Jongki Cho
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea.,Daejeon Wildlife Rescue Center, Chungnam National University, Daejeon 34134, Korea
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13
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Fierro CM, Smith PD, Light ME. Structure of a dinickel(II)-dithiolate bridged macrocyclic complex synthesised via a novel solvent-assisted disulfide cleavage reaction. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Valenti R, Jabłońska J, Tawfik DS. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin. Protein Sci 2022; 31:e4423. [PMID: 36173172 PMCID: PMC9490801 DOI: 10.1002/pro.4423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the “ancestors” are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
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Affiliation(s)
- Rosario Valenti
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
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15
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Bag J, Pal K. The access of {NiIV(OH)2} intermediate in Ni(II) mediated oxygen atom transfer to coordinated Phosphine: Combined experimental and computational studies. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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In Silico Identification of Novel Inhibitors Targeting the Homodimeric Interface of Superoxide Dismutase from the Dental Pathogen Streptococcus mutans. Antioxidants (Basel) 2022; 11:antiox11040785. [PMID: 35453470 PMCID: PMC9029323 DOI: 10.3390/antiox11040785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
The microaerophile Streptococcus mutans, the main microaerophile responsible for the development of dental plaque, has a single cambialistic superoxide dismutase (SmSOD) for its protection against reactive oxygen species. In order to discover novel inhibitors of SmSOD, possibly interfering with the biofilm formation by this pathogen, a virtual screening study was realised using the available 3D-structure of SmSOD. Among the selected molecules, compound ALS-31 was capable of inhibiting SmSOD with an IC50 value of 159 µM. Its inhibition power was affected by the Fe/Mn ratio in the active site of SmSOD. Furthermore, ALS-31 also inhibited the activity of other SODs. Gel-filtration of SmSOD in the presence of ALS-31 showed that the compound provoked the dissociation of the SmSOD homodimer in two monomers, thus compromising the catalytic activity of the enzyme. A docking model, showing the binding mode of ALS-31 at the dimer interface of SmSOD, is presented. Cell viability of the fibroblast cell line BJ5-ta was not affected up to 100 µM ALS-31. A preliminary lead optimization program allowed the identification of one derivative, ALS-31-9, endowed with a 2.5-fold improved inhibition power. Interestingly, below this concentration, planktonic growth and biofilm formation of S. mutans cultures were inhibited by ALS-31, and even more by its derivative, thus opening the perspective of future drug design studies to fight against dental caries.
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17
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Functional Conversion of Acetyl-Coenzyme a Synthase to a Nickel Superoxide Dismutase via Rational Design of Coordination Microenvironment for the Ni d-Site. Int J Mol Sci 2022; 23:ijms23052652. [PMID: 35269794 PMCID: PMC8910529 DOI: 10.3390/ijms23052652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The Nid site coordination microenvironment of a truncated acetyl-coenzyme A synthase has been designed systematically for functional conversion to a Ni-SOD-like enzyme. To this end, the first strategy is to introduce an axial histidine ligand, using mutations F598H, S594H and S594H-GP individually. The resulting three mutants obtained Ni-SOD-like activity successfully, although the catalytic activity was about 10-fold lower than in native Ni-SOD. The second strategy is to mimic the H-bond network in the second sphere coordination microenvironment of the native Ni-SOD. Two mutations based on F598H (EFG-F598H and YGP-F598H) were designed. The successful EFG-F598H exhibited ~3-fold Ni-SOD-like activity of F598H. These designed Ni-SOD-like metalloproteins were characterized by UV/Vis, EPR and Cyclic voltammetry while F598H was also characterized by X-ray protein crystallography. The pH titrations were performed to reveal the source of the two protons required for forming H2O2 in the SOD catalytic reaction. Based on all of the results, a proposed catalytic mechanism for the Ni-SOD-like metalloproteins is presented.
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18
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Rehman S, Rashid A, Manzoor MA, Li L, Sun W, Riaz MW, Li D, Zhuge Q. Genome-Wide Evolution and Comparative Analysis of Superoxide Dismutase Gene Family in Cucurbitaceae and Expression Analysis of Lagenaria siceraria Under Multiple Abiotic Stresses. Front Genet 2022; 12:784878. [PMID: 35211150 PMCID: PMC8861505 DOI: 10.3389/fgene.2021.784878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Superoxide dismutase (SOD) is an important enzyme that serves as the first line of defense in the plant antioxidant system and removes reactive oxygen species (ROS) under adverse conditions. The SOD protein family is widely distributed in the plant kingdom and plays a significant role in plant growth and development. However, the comprehensive analysis of the SOD gene family has not been conducted in Cucurbitaceae. Subsequently, 43 SOD genes were identified from Cucurbitaceae species [Citrullus lanatus (watermelon), Cucurbita pepo (zucchini), Cucumis sativus (cucumber), Lagenaria siceraria (bottle gourd), Cucumis melo (melon)]. According to evolutionary analysis, SOD genes were divided into eight subfamilies (I, II, III, IV, V, VI, VII, VIII). The gene structure analysis exhibited that the SOD gene family had comparatively preserved exon/intron assembly and motif as well. Phylogenetic and structural analysis revealed the functional divergence of Cucurbitaceae SOD gene family. Furthermore, microRNAs 6 miRNAs were predicted targeting 3 LsiSOD genes. Gene ontology annotation outcomes confirm the role of LsiSODs under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Promoter regions of the SOD family revealed that most cis-elements were involved in plant development, stress response, and plant hormones. Evaluation of the gene expression showed that most SOD genes were expressed in different tissues (root, flower, fruit, stem, and leaf). Finally, the expression profiles of eight LsiSOD genes analyzed by qRT-PCR suggested that these genetic reserves responded to drought, saline, heat, and cold stress. These findings laid the foundation for further study of the role of the SOD gene family in Cucurbitaceae. Also, they provided the potential for its use in the genetic improvement of Cucurbitaceae.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Arif Rashid
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | | | - Lingling Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Weibo Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
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19
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Frye KA, Sendra KM, Waldron KJ, Kehl-Fie TE. Old dogs, new tricks: New insights into the iron/manganese superoxide dismutase family. J Inorg Biochem 2022; 230:111748. [PMID: 35151099 PMCID: PMC9112591 DOI: 10.1016/j.jinorgbio.2022.111748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/14/2022] [Accepted: 01/30/2022] [Indexed: 12/21/2022]
Abstract
Superoxide dismutases (SODs) are ancient enzymes of widespread importance present in all domains of life. Many insights have been gained into these important enzymes over the 50 years since their initial description, but recent studies in the context of microbial pathogenesis have resulted in findings that challenge long established dogmas. The repertoire of SODs that bacterial pathogens encode is diverse both in number and in metal dependencies, including copper, copper and zinc, manganese, iron, and cambialistic enzymes. Other bacteria also possess nickel dependent SODs. Compartmentalization of SODs only partially explains their diversity. The need for pathogens to maintain SOD activity across distinct hostile environments encountered during infection, including those limited for essential metals, is also a driver of repertoire diversity. SOD research using pathogenic microbes has also revealed the apparent biochemical ease with which metal specificity can change within the most common family of SODs. Collectively, these studies are revealing the dynamic nature of SOD evolution, both that of individual SOD enzymes that can change their metal specificity to adapt to fluctuating cellular metal availability, and of a cell's repertoire of SOD isozymes that can be differentially expressed to adapt to fluctuating environmental metal availability in a niche.
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20
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LIMA IGORG, BISPO JAMESR, AGOSTINHO ADSONY, QUEIROZ ALINECDE, MOREIRA MAGNASUZANAA, PASSARINI MICHELRODRIGOZ, OLIVEIRA VALÉRIAMDE, SETTE LARAD, ROSA LUIZHENRIQUE, DUARTE ALYSSONWAGNERF. Antarctic environments as a source of bacterial and fungal therapeutic enzymes. AN ACAD BRAS CIENC 2022; 94:e20210452. [DOI: 10.1590/0001-3765202220210452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/20/2021] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - LARA D. SETTE
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
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21
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Bonczidai-Kelemen D, Sciortino G, May NV, Garribba E, Fábián I, Lihi N. Introducing the penicillamine moiety into a metallopeptide mimicking the NiSOD enzyme: electronic and kinetic effects. Inorg Chem Front 2022. [DOI: 10.1039/d1qi01025e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel NiSOD related metallopeptide incorporates penicillamine moiety in the active center which alters both the electronic and kinetic features.
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Affiliation(s)
- Dóra Bonczidai-Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Giuseppe Sciortino
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Technology, 43007 Tarragona, Spain
| | - Nóra V. May
- Centre for Structural Science, Research Centre for Natural Sciences, H-1117, Budapest, Hungary
| | - Eugenio Garribba
- Dipartimento di Scienze Mediche, Chirurgiche e Sperimentali, Università di Sassari, I-07100 Sassari, Italy
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032, Debrecen, Hungary
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22
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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23
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Domergue J, Guinard P, Douillard M, Pécaut J, Proux O, Lebrun C, Le Goff A, Maldivi P, Delangle P, Duboc C. A Bioinspired Ni II Superoxide Dismutase Catalyst Designed on an ATCUN-like Binding Motif. Inorg Chem 2021; 60:12772-12780. [PMID: 34416109 DOI: 10.1021/acs.inorgchem.1c00899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nickel superoxide dismutase (NiSOD) is an enzyme that protects cells against O2·-. While the structure of its active site is known, the mechanism of the catalytic cycle is still not elucidated. Its active site displays a square planar NiII center with two thiolates, the terminal amine and an amidate. We report here a bioinspired NiII complex built on an ATCUN-like binding motif modulated with one cysteine, which demonstrates catalytic SOD activity in water (kcat = 8.4(2) × 105 M-1 s-1 at pH = 8.1). Its reactivity with O2·- was also studied in acetonitrile allowing trapping two different short-lived species that were characterized by electron paramagnetic resonance or spectroelectrochemistry and a combination of density functional theory (DFT) and time-dependent DFT calculations. Based on these observations, we propose that O2·- interacts first with the complex outer sphere through a H-bond with the peptide scaffold in a [NiIIO2·-] species. This first species could then evolve into a NiIII hydroperoxo inner sphere species through a reaction driven by protonation that is thermodynamically highly favored according to DFT calculations.
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Affiliation(s)
- Jérémy Domergue
- Universite Grenoble Alpes, CNRS, DCM, Grenoble 38000, France.,Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Pawel Guinard
- Universite Grenoble Alpes, CNRS, DCM, Grenoble 38000, France.,Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Magali Douillard
- Universite Grenoble Alpes, CNRS, DCM, Grenoble 38000, France.,Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Jacques Pécaut
- Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Olivier Proux
- Universite Grenoble Alpes, CNRS, OSUG, Grenoble 38000, France
| | - Colette Lebrun
- Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Alan Le Goff
- Universite Grenoble Alpes, CNRS, DCM, Grenoble 38000, France
| | - Pascale Maldivi
- Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Pascale Delangle
- Universite Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble 38000, France
| | - Carole Duboc
- Universite Grenoble Alpes, CNRS, DCM, Grenoble 38000, France
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24
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Sutherland KM, Ward LM, Colombero CR, Johnston DT. Inter-domain horizontal gene transfer of nickel-binding superoxide dismutase. GEOBIOLOGY 2021; 19:450-459. [PMID: 33989454 DOI: 10.1111/gbi.12448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/22/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The ability of aerobic microorganisms to regulate internal and external concentrations of the reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous enzymes that perform the same function. Thus, the evolutionary history of genes encoding for different SOD enzymes is one of convergent evolution, which reflects environmental selection brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic horizontal gene transfer (HGT). In this study, we examine the phylogenetic history of the protein sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). The genomic potential to produce SodN is widespread among bacteria, including Actinobacteriota (Actinobacteria), Chloroflexota (Chloroflexi), Cyanobacteria, Proteobacteria, Patescibacteria, and others. The gene is also present in many archaea, with Thermoplasmatota and Nanoarchaeota representing the vast majority of archaeal sodN diversity. A comparison of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. Nearly half of the archaeal members with sodN live in the photic zone of the marine water column. The sodN gene is widespread and characterized by apparent vertical gene transfer in some sediment- or soil-associated lineages within the Actinobacteriota and Chloroflexota phyla, suggesting the ancestral sodN likely originated in one of these clades before expanding its taxonomic and biogeographic distribution to additional microbial groups in the surface ocean in response to decreasing iron availability. In addition to decreasing iron quotas, nickel-binding SOD has the added benefit of withstanding high reactant and product ROS concentrations without damaging the enzyme, making it particularly well suited for the modern surface ocean.
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Affiliation(s)
- K M Sutherland
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - L M Ward
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - C-R Colombero
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - D T Johnston
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
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25
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Zhang L, Tian W, Huang G, Liu B, Wang A, Zhu J, Guo X. The SikCuZnSOD3 gene improves abiotic stress resistance in transgenic cotton. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:26. [PMID: 37309423 PMCID: PMC10236091 DOI: 10.1007/s11032-021-01217-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/15/2021] [Indexed: 06/14/2023]
Abstract
The expression of a gene encoding peroxisomal Cu-Zn superoxide dismutase from Saussurea involucrata Kar. et Kir. was induced by low temperature, PEG6000 treatment, and NaCl stress. To investigate the role of SikCuZnSOD3 in the mitigation of abiotic stress, we used Agrobacterium-mediated transformation to create transgenic cotton that overexpressed SikCuZnSOD3. Phenotypic analysis of T4 generation transgenic lines showed that they generally grew better than wild-type cotton under low temperature, PEG6000 treatment, and NaCl stress. Although there were no significant differences under control conditions, transgenic plants exhibited greater survival, fresh weight, and dry weight than wild-type plants under all three stress treatments. Additional physiological analyses demonstrated that the transgenic cotton had higher relative water content, proline and soluble sugar contents, and activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidase), as well as lower relative conductivity, malondialdehyde content, and H2O2 and O2- accumulation. More importantly, overexpression of SikCuZnSOD3 increased the yield of cotton fiber. Our results confirm that the overexpression of SikCuZnSOD3 can improve the abiotic stress resistance of cotton by increasing the activity of antioxidant enzymes, maintaining ROS homeostasis, and reducing cell membrane damage. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01217-0.
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Affiliation(s)
- Li Zhang
- Department of Preventive Medicine, School of Medicine, Key laboratory of Preventive Medicine, Shihezi University, Shihezi, 832000 China
| | - Wenhui Tian
- College of Life Science, Shihezi University, Shihezi, 832000 China
| | - Gang Huang
- College of Life Science, Shihezi University, Shihezi, 832000 China
| | - Bucang Liu
- College of Life Science, Shihezi University, Shihezi, 832000 China
| | - Aiying Wang
- College of Life Science, Shihezi University, Shihezi, 832000 China
| | - Jianbo Zhu
- College of Life Science, Shihezi University, Shihezi, 832000 China
| | - Xinyong Guo
- College of Life Science, Shihezi University, Shihezi, 832000 China
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26
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Kelemen D, May NV, Andrási M, Gáspár A, Fábián I, Lihi N. High Enzyme Activity of a Binuclear Nickel Complex Formed with the Binding Loops of the NiSOD Enzyme*. Chemistry 2020; 26:16767-16773. [PMID: 32744741 PMCID: PMC7756883 DOI: 10.1002/chem.202002706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 11/08/2022]
Abstract
Detailed equilibrium, spectroscopic and superoxide dismutase (SOD) activity studies are reported on a nickel complex formed with a new metallopeptide bearing two nickel binding loops of NiSOD. The metallopeptide exhibits unique nickel binding ability and the binuclear complex is a major species with 2×(NH2 ,Namide ,S- ,S- ) donor set even in an equimolar solution of the metal ion and the ligand. Nickel(III) species were generated by oxidizing the NiII complexes with KO2 and the coordination modes were identified by EPR spectroscopy. The binuclear complex formed with the binding motifs exhibits superior SOD activity, in this respect it is an excellent model of the native NiSOD enzyme. A detailed kinetic model is postulated that incorporates spontaneous decomposition of the superoxide ion, the dismutation cycle and fast redox degradation of the binuclear complex. The latter process leads to the elimination of the SOD activity. A unique feature of this system is that the NiIII form of the catalyst rapidly accumulates in the dismutation cycle and simultaneously the NiII form becomes a minor species.
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Affiliation(s)
- Dóra Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4032, Debrecen, Hungary
| | - Nóra V May
- Research Centre for Natural Sciences, 1117, Budapest, Hungary
| | - Melinda Andrási
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4032, Debrecen, Hungary
| | - Attila Gáspár
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4032, Debrecen, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.,MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms, Research Group, University of Debrecen, 4032, Debrecen, Hungary
| | - Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.,MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms, Research Group, University of Debrecen, 4032, Debrecen, Hungary
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Zheng P, Chen L, Zhong S, Wei X, Zhao Q, Pan Q, Kang Z, Liu J. A Cu-only superoxide dismutase from stripe rust fungi functions as a virulence factor deployed for counter defense against host-derived oxidative stress. Environ Microbiol 2020; 22:5309-5326. [PMID: 32985748 DOI: 10.1111/1462-2920.15236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 12/13/2022]
Abstract
Plants quickly accumulate reactive oxygen species (ROS) to resist against pathogen invasion, while pathogens strive to escape host immune surveillance by degrading ROS. However, the nature of the strategies that fungal pathogens adopt to counteract host-derived oxidative stress is manifold and requires deep investigation. In this study, a superoxide dismutase (SOD) from Puccinia striiformis f. sp. tritici (Pst) PsSOD2 with a signal peptide (SP) and the glycophosphatidyl inositol (GPI) anchor, strongly induced during infection, was analysed for its biological characteristics and potential role in wheat-Pst interactions. The results showed that PsSOD2 encodes a Cu-only SOD and responded to ROS treatment. Heterologous complementation assays in Saccharomyces cerevisiae suggest that the SP of PsSOD2 is functional for its secretion. Transient expression in Nicotiana benthamiana leaves revealed that PsSOD2 is localized to the plasma membrane. In addition, knockdown of PsSOD2 by host-induced gene silencing reduced Pst virulence and resulted in restricted hyphal development and increased ROS accumulation. In contrast, heterologous transient assays of PsSOD2 suppressed flg22-elicited ROS production. Taken together, our data indicate that PsSOD2, as a virulence factor, was induced and localized to the plasma membrane where it may function to scavenge host-derived ROS for promoting fungal infection.
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Affiliation(s)
- Peijing Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Liyang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Suye Zhong
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaobo Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qi Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinglin Pan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,College of Plant Scicence, Tarim University, Alaer, Xinjiang, 843300, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Pedone E, Fiorentino G, Bartolucci S, Limauro D. Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea. Antioxidants (Basel) 2020; 9:antiox9080703. [PMID: 32756530 PMCID: PMC7465337 DOI: 10.3390/antiox9080703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2-.) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
- Correspondence:
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Molecular characterization, purification, and antioxidant activity of recombinant superoxide dismutase from the Pacific abalone Haliotis discus hannai Ino. World J Microbiol Biotechnol 2020; 36:115. [PMID: 32661581 PMCID: PMC7359182 DOI: 10.1007/s11274-020-02892-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
Superoxide dismutase (SOD) is an acidic metalloenzyme that scavenges free radicals produced by endogenous and exogenous substances. In the present study, the tissue distribution of the superoxide dismutase HdhCu/Zn-SOD was investigated in Haliotis discus hannai Ino. The expression profile after lipopolysaccharide (LPS) challenge was determined using quantitative real-time polymerase chain reaction (qPCR). To study the antioxidant activity of a recombinant HdhCu/Zn-SOD protein, the HdhCu/Zn-SOD gene was cloned into the pPIC9K vector and transformed into the Pichia pastoris GS115 strain by electroporation. After induction by methanol, the recombinant product was purified using immobilized metal affinity chromatography and confirmed using mass spectrometry. The optimal expression conditions were determined to be incubation with 0.5% methanol at pH 6.0, resulting in a stable expressed product with the molecular weight of approximately 17 kDa and 21 kDa. The enzymatic activity of HdhCu/Zn-SOD consistently increased with increasing Cu2+ concentrations and showed good thermal stability. Recombinant HdhCu/Zn-SOD showed a strong ability to scavenge superoxide anions and hydroxyl radicals and protected L929 cells against the toxicity caused by H2O2 through its in vitro antioxidant activity. The heterologous expression of HdhCu/Zn-SOD in P. pastoris and the antioxidant activity of this enzyme are reported for the first time.
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Lihi N, Kelemen D, May NV, Fábián I. The Role of the Cysteine Fragments of the Nickel Binding Loop in the Activity of the Ni(II)-Containing SOD Enzyme. Inorg Chem 2020; 59:4772-4780. [DOI: 10.1021/acs.inorgchem.0c00057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norbert Lihi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
| | - Dóra Kelemen
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Nóra V. May
- Research Centre of Natural Sciences, H-1117 Budapest, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
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Alfano M, Cavazza C. Structure, function, and biosynthesis of nickel-dependent enzymes. Protein Sci 2020; 29:1071-1089. [PMID: 32022353 DOI: 10.1002/pro.3836] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022]
Abstract
Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.
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Affiliation(s)
- Marila Alfano
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
| | - Christine Cavazza
- University of Grenoble Alpes, CEA, CNRS, IRIG, CBM, Grenoble, France
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32
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Adams JJ, Morton CJ, Parker MW. The Crystal Structure of the Manganese Superoxide Dismutase from Geobacillus stearothermophilus: Parker and Blake (1988) Revisited. Aust J Chem 2020. [DOI: 10.1071/ch19346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Superoxide dismutase (SOD) is an almost ubiquitous metalloenzyme in aerobic organisms that catalyses the disproportionation of superoxide. Geobacillus stearothermophilus MnSOD is the only published MnSOD structure that does not have its coordinates publicly available, yet it is one of the more cited structures in the SOD literature. The structure has now been refined with modern programs, yielding a significantly improved structure which has been deposited in the Protein Data Bank. Importantly, the further refined structure reveals the presence of a catalytically important fifth ligand, water, to the metal centre, as observed in other SOD structures.
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Shi J, Zhao D, Li X, Ding F, Tang X, Liu N, Huang H, Liu C. The conjugation of rhodamine B enables carrier-free mitochondrial delivery of functional proteins. Org Biomol Chem 2020; 18:6829-6839. [DOI: 10.1039/d0ob01305f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Small molecule-guided mitochondrial carrier-free delivery and tumor suppression of functional proteins.
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Affiliation(s)
- Jiayuan Shi
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Dan Zhao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Xiang Li
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Feng Ding
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Xuemei Tang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Nian Liu
- Department of Biomedical Engineering
- School of Basic Medical Sciences
- Wuhan University
- Wuhan
- 430071 China
| | - Hua Huang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
| | - Changlin Liu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education
- International Joint Research Center for Intelligent Biosensing Technology and Health
- School of Chemistry
- Central China Normal University
- Wuhan
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SrnR from Streptomyces griseus is a nickel-binding transcriptional activator. J Biol Inorg Chem 2019; 25:187-198. [PMID: 31853648 DOI: 10.1007/s00775-019-01751-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023]
Abstract
Nickel ions are crucial components for the catalysis of biological reactions in prokaryotic organisms. As an uncontrolled nickel trafficking is toxic for living organisms, nickel-dependent bacteria have developed tightly regulated strategies to maintain the correct intracellular metal ion quota. These mechanisms require transcriptional regulator proteins that respond to nickel concentration, activating or repressing the expression of specific proteins related to Ni(II) metabolism. In Streptomyces griseus, a Gram-positive bacterium used for antibiotic production, SgSrnR and SgSrnQ regulate the nickel-dependent antagonistic expression of two superoxide dismutase (SOD) enzymes, a Ni-SOD and a FeZn-SOD. According to a previously proposed model, SgSrnR and SgSrnQ form a protein complex in which SgSrnR works as repressor, binding directly to the promoter of the gene coding for FeZn-SOD, while SgSrnQ is the Ni(II)-dependent co-repressor. The present work focuses on the determination of the biophysical and functional properties of SgSrnR. The protein was heterologously expressed and purified from Escherichia coli. The structural and metal-binding analysis, carried out by circular dichroism, light scattering, fluorescence and isothermal titration calorimetry, showed that the protein is a well-structured homodimer, able to bind nickel with moderate affinity. DNase I footprinting and β-galactosidase gene reporter assays revealed that apo-SgSrnR is able to bind its DNA operator and activates a transcriptional response. The structural and functional properties of this protein are discussed relatively to its role as a Ni(II)-dependent sensor.
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Wang B, Liu G, Wang C, Ruan Z, Wang Q, Wang B, Qiu L, Zou S, Zhang X, Zhang L. Molecular cloning and functional characterization of a Cu/Zn superoxide dismutase from jellyfish Cyanea capillata. Int J Biol Macromol 2019; 144:1-8. [PMID: 31836391 DOI: 10.1016/j.ijbiomac.2019.12.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/22/2019] [Accepted: 12/09/2019] [Indexed: 12/22/2022]
Abstract
We identified and characterized a novel superoxide dismutase (SOD), designated as CcSOD1, from the cDNA library from the tentacle tissue of the jellyfish Cyanea capillata. The full-length cDNA sequence of CcSOD1 consists of 745 nucleotides with an open reading frame encoding a mature protein of 154 amino acids, sharing a predicted structure similar to the typical Cu/Zn-SODs. The CcSOD1 coding sequence was cloned into the expression vector pET-24a and successfully expressed in Escherichia coli Rosetta (DE3) pLysS. The recombinant protein rCcSOD1 was purified by HisTrap High Performance chelating column chromatography and analyzed for its biological function. Our results showed that the purified rCcSOD1 could inhibit superoxide anion and keep active in a pH interval of 4.5-9 and a temperature interval of 10-70°C. Even when heated at 70°C for 60 min, rCcSOD1 retained 100% activity, indicating a relatively high thermostability. These results suggest that CcSOD1 protein may play an important role in protecting jellyfish from oxidative damage and can serve as a new resource for antioxidant products.
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Affiliation(s)
- Bo Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Guoyan Liu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Chao Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Zengliang Ruan
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Zhongshan Road 2 No.74, Guangzhou 510080, China
| | - Qianqian Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Beilei Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Leilei Qiu
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Shuaijun Zou
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China
| | - Xiping Zhang
- Department of Traumatic Orthopaedics, the Affiliated Zhuzhou Hospital, Xiangya Medical College CSU, South Changjiang Road No.116, Changsha 412007, China.
| | - Liming Zhang
- Department of Marine Biomedicine and Polar Medicine, Naval Characteristic Medical Center, Naval Medical University, Xiangyin Road No.800, Shanghai 200433, China.
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Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase. Genes Genomics 2019; 42:273-281. [PMID: 31797314 DOI: 10.1007/s13258-019-00878-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain. OBJECTIVE To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes. METHODS DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio long-reads with the HGAP3 pipeline. RESULTS We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel-iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds. CONCLUSION We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.
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Abstract
Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The possibility of reduced structural integrity was suggested by the first crystal structures of human SOD1 even before deleterious mutations in the sod1 gene were linked to the ALS. This concept evolved in the intervening years as an impressive array of biophysical studies examined the characteristics of mutant SOD1 in great detail. We now recognise how ALS-related mutations perturb the SOD1 maturation processes, reduce its ability to fold and reduce its thermal stability and half-life. Mutant SOD1 is therefore predisposed to monomerisation, non-canonical self-interactions, the formation of small misfolded oligomers and ultimately accumulation in the tell-tale insoluble inclusions found within the neurons of ALS patients. We have also seen that several post-translational modifications could push wild-type SOD1 down this toxic pathway. Recently we have come to view ALS as a prion-like disease where both the symptoms, and indeed SOD1 misfolding itself, are transmitted to neighbouring cells. This raises the possibility of intervention after the initial disease presentation. Several small-molecule and biologic-based strategies have been devised which directly target the SOD1 molecule to change the behaviour thought to be responsible for ALS. Here we provide a comprehensive review of the many biophysical advances that sculpted our view of SOD1 biology and the recent work that aims to apply this knowledge for therapeutic outcomes in ALS.
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Jiang W, Yang L, He Y, Zhang H, Li W, Chen H, Ma D, Yin J. Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat ( Triticum aestivum). PeerJ 2019; 7:e8062. [PMID: 31763072 PMCID: PMC6873880 DOI: 10.7717/peerj.8062] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/20/2019] [Indexed: 12/17/2022] Open
Abstract
Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.
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Affiliation(s)
- Wenqiang Jiang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China.,Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Lei Yang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yiqin He
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Haotian Zhang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
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Domergue J, Pécaut J, Proux O, Lebrun C, Gateau C, Le Goff A, Maldivi P, Duboc C, Delangle P. Mononuclear Ni(II) Complexes with a S3O Coordination Sphere Based on a Tripodal Cysteine-Rich Ligand: pH Tuning of the Superoxide Dismutase Activity. Inorg Chem 2019; 58:12775-12785. [PMID: 31545024 DOI: 10.1021/acs.inorgchem.9b01686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The superoxide dismutase (SOD) activity of mononuclear NiII complexes, whose structures are inspired by the NiSOD, has been investigated. They have been designed with a sulfur-rich pseudopeptide ligand, derived from nitrilotriacetic acid (NTA), where the three acid functions are grafted with cysteines (L3S). Two mononuclear complexes, which exist in pH-dependent proportions, have been fully characterized by a combination of spectroscopic techniques including 1H NMR, UV-vis, circular dichroism, and X-ray absorption spectroscopy, together with theoretical calculations. They display similar square-planar S3O coordination, with the three thiolates of the three cysteine moieties from L3S coordinated to the NiII ion, together with either a water molecule at physiological pH, as [NiL3S(OH2)]-, or a hydroxo ion in more basic conditions, as [NiL3S(OH)]2-. The 1H NMR study has revealed that contrary to the hydroxo ligand, the bound water molecule is labile. The cyclic voltammogram of both complexes displays an irreversible one-electron oxidation process assigned to the NiII/NiIII redox system with Epa = 0.48 and 0.31 V versus SCE for NiL3S(OH2) and NiL3S(OH), respectively. The SOD activity of both complexes has been tested. On the basis of the xanthine oxidase assay, an IC50 of about 1 μM has been measured at pH 7.4, where NiL3S(OH2) is mainly present (93% of the NiII species), while the IC50 is larger than 100 μM at pH 9.6, where NiL3S(OH) is the major species (92% of the NiII species). Interestingly, only NiL3S(OH2) displays SOD activity, suggesting that the presence of a labile ligand is required. The SOD activity has been also evaluated under catalytic conditions at pH 7.75, where the ratio between NiL3S(OH2)/ NiL3S(OH) is about (86:14), and a rate constant, kcat = 1.8 × 105 M-1 s-1, has been measured. NiL3S(OH2) is thus the first low-molecular weight, synthetic, bioinspired Ni complex that displays catalytic SOD activity in water at physiological pH, although it does not contain any N-donor ligand in its first coordination sphere, as in the NiSOD. Overall, the data show that a key structural feature is the presence of a labile ligand in the coordination sphere of the NiII ion.
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Affiliation(s)
- Jérémy Domergue
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France.,Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Jacques Pécaut
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Olivier Proux
- Univ. Grenoble Alpes, CNRS, OSUG , 38000 Grenoble , France
| | - Colette Lebrun
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Christelle Gateau
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Alan Le Goff
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - Pascale Maldivi
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SYMMES , 38000 Grenoble , France
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Abstract
Nickel is an essential cofactor for some pathogen virulence factors. Due to its low availability in hosts, pathogens must efficiently transport the metal and then balance its ready intracellular availability for enzyme maturation with metal toxicity concerns. The most notable virulence-associated components are the Ni-enzymes hydrogenase and urease. Both enzymes, along with their associated nickel transporters, storage reservoirs, and maturation enzymes have been best-studied in the gastric pathogen Helicobacter pylori, a bacterium which depends heavily on nickel. Molecular hydrogen utilization is associated with efficient host colonization by the Helicobacters, which include both gastric and liver pathogens. Translocation of a H. pylori carcinogenic toxin into host epithelial cells is powered by H2 use. The multiple [NiFe] hydrogenases of Salmonella enterica Typhimurium are important in host colonization, while ureases play important roles in both prokaryotic (Proteus mirabilis and Staphylococcus spp.) and eukaryotic (Cryptoccoccus genus) pathogens associated with urinary tract infections. Other Ni-requiring enzymes, such as Ni-acireductone dioxygenase (ARD), Ni-superoxide dismutase (SOD), and Ni-glyoxalase I (GloI) play important metabolic or detoxifying roles in other pathogens. Nickel-requiring enzymes are likely important for virulence of at least 40 prokaryotic and nine eukaryotic pathogenic species, as described herein. The potential for pathogenic roles of many new Ni-binding components exists, based on recent experimental data and on the key roles that Ni enzymes play in a diverse array of pathogens.
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41
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Csire G, Kolozsi A, Gajda T, Pappalardo G, Várnagy K, Sóvágó I, Fábián I, Lihi N. The ability of the NiSOD binding loop to chelate zinc(ii): the role of the terminal amino group in the enzymatic functions. Dalton Trans 2019; 48:6217-6227. [PMID: 30984950 DOI: 10.1039/c9dt01015g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Equilibrium and detailed spectroscopic characterization of zinc(ii) complexes with NiSOD binding loop and their related model fragments are reported in the whole investigated pH-range. The zinc(ii) complexes of L1 (HCDLPCGVY-NH2), L2 (Ac-HCDLPCGVY-NH2) and L3 (HCDLACGVY-NH2) and the nickel(ii) and zinc(ii) complexes of L4 (HCDLPCG-NH2) were studied by pH-potentiometric and several spectroscopic methods. The results indicated that the macrochelate coordinated zinc(ii) complexes are dominant in a whole pH-range and the side chain donors of the peptides are involved in the metal binding. Therefore, the deprotonation and coordination of the peptide backbone occur only in a strongly alkaline solution. The acetylation of the peptide amino terminus (L2) significantly enhances the zinc(ii) binding ability compared to the corresponding nickel(ii) complexes. L2 complexes of zinc(ii) are 2 or 3 orders of magnitude more stable than the corresponding nickel(ii) complexes. This effect clearly shows the crucial role of the terminal amino group in the nickel binding for the NiSOD enzyme.
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Affiliation(s)
- Gizella Csire
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
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42
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Raje S, Mani K, Kandasamy P, Butcher RJ, Angamuthu R. Bioinspired Oxidative Cleavage of Aliphatic C–C Bonds Utilizing Aerial Oxygen by Nickel Acireductone Dioxygenase Mimics. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sakthi Raje
- Laboratory of Inorganic Synthesis and Bioinspired Catalysis (LISBIC) Department of Chemistry Indian Institute of Technology Kanpur 208016 Kanpur India
| | - Kalaikodikumaran Mani
- Laboratory of Inorganic Synthesis and Bioinspired Catalysis (LISBIC) Department of Chemistry Indian Institute of Technology Kanpur 208016 Kanpur India
| | - Parameswaran Kandasamy
- Laboratory of Inorganic Synthesis and Bioinspired Catalysis (LISBIC) Department of Chemistry Indian Institute of Technology Kanpur 208016 Kanpur India
| | - Ray J. Butcher
- Department of Chemistry Howard University 20059 Washington, D.C. United States
| | - Raja Angamuthu
- Laboratory of Inorganic Synthesis and Bioinspired Catalysis (LISBIC) Department of Chemistry Indian Institute of Technology Kanpur 208016 Kanpur India
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Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family. Int J Genomics 2019; 2019:7350414. [PMID: 30923713 PMCID: PMC6409070 DOI: 10.1155/2019/7350414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/01/2018] [Accepted: 12/20/2018] [Indexed: 01/23/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.
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Lihi N, Csire G, Szakács B, May NV, Várnagy K, Sóvágó I, Fábián I. Stabilization of the Nickel Binding Loop in NiSOD and Related Model Complexes: Thermodynamic and Structural Features. Inorg Chem 2019; 58:1414-1424. [DOI: 10.1021/acs.inorgchem.8b02952] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norbert Lihi
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Gizella Csire
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Bence Szakács
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Nóra V. May
- Research Centre of Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Katalin Várnagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Imre Sóvágó
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - István Fábián
- MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, H-4032 Debrecen, Hungary
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
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Larosa V, Remacle C. Insights into the respiratory chain and oxidative stress. Biosci Rep 2018; 38:BSR20171492. [PMID: 30201689 PMCID: PMC6167499 DOI: 10.1042/bsr20171492] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 01/13/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive reduced oxygen molecules that result from aerobic metabolism. The common forms are the superoxide anion (O2∙-) and hydrogen peroxide (H2O2) and their derived forms, hydroxyl radical (HO∙) and hydroperoxyl radical (HOO∙). Their production sites in mitochondria are reviewed. Even though being highly toxic products, ROS seem important in transducing information from dysfunctional mitochondria. Evidences of signal transduction mediated by ROS in mitochondrial deficiency contexts are then presented in different organisms such as yeast, mammals or photosynthetic organisms.
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Affiliation(s)
- Véronique Larosa
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
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46
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Pischedda A, Ramasamy KP, Mangiagalli M, Chiappori F, Milanesi L, Miceli C, Pucciarelli S, Lotti M. Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Sci Rep 2018; 8:14721. [PMID: 30283056 PMCID: PMC6170424 DOI: 10.1038/s41598-018-33127-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/20/2018] [Indexed: 11/09/2022] Open
Abstract
Oxidative stress is a particularly severe threat to Antarctic marine polar organisms because they are exposed to high dissolved oxygen and to intense UV radiation. This paper reports the features of three superoxide dismutases from the Antarctic psychrophilic ciliate Euplotes focardii that faces two environmental challenges, oxidative stress and low temperature. Two out of these are Cu,Zn superoxide dismutases (named Ef-SOD1a and Ef-SOD1b) and one belongs to the Mn-containing group (Ef-SOD2). Ef-SOD1s and Ef-SOD2 differ in their evolutionary history, expression and overall structural features. Ef-SOD1 genes are expressed at different levels, with Ef-SOD1b mRNA 20-fold higher at the ciliate optimal temperature of growth (4 °C). All Ef-SOD enzymes are active at 4 °C, consistent with the definition of cold-adapted enzymes. At the same time, they display temperatures of melting in the range 50-70 °C and retain residual activity after incubation at 65-75 °C. Supported by data of molecular dynamics simulation, we conclude that the E. focardii SODs combine cold activity, local molecular flexibility and thermo tolerance.
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Affiliation(s)
- Alessandro Pischedda
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Kesava Priyan Ramasamy
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | | | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy.
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
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47
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Tietze D, Koley Seth B, Brauser M, Tietze AA, Buntkowsky G. NiII
Complex Formation and Protonation States at the Active Site of a Nickel Superoxide Dismutase-Derived Metallopeptide: Implications for the Mechanism of Superoxide Degradation. Chemistry 2018; 24:15879-15888. [DOI: 10.1002/chem.201803042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel Tietze
- Eduard-Zintl Institute for Physical and Inorganic Chemistry; Darmstadt University of Technology; Alarich-Weiss-Str. 8 64287 Darmstadt Germany), -darmstadt
| | - Banabithi Koley Seth
- Eduard-Zintl Institute for Physical and Inorganic Chemistry; Darmstadt University of Technology; Alarich-Weiss-Str. 8 64287 Darmstadt Germany), -darmstadt
- current address: Department of Chemistry; Durham University; Lower Mountjoy, Stockton Road Durham DH1 3LE United Kingdom
| | - Matthias Brauser
- Eduard-Zintl Institute for Physical and Inorganic Chemistry; Darmstadt University of Technology; Alarich-Weiss-Str. 8 64287 Darmstadt Germany), -darmstadt
| | - Alesia A. Tietze
- Clemens-Schöpf Institute for Organic Chemistry and Biochemistry; Darmstadt University of Technology; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Gerd Buntkowsky
- Eduard-Zintl Institute for Physical and Inorganic Chemistry; Darmstadt University of Technology; Alarich-Weiss-Str. 8 64287 Darmstadt Germany), -darmstadt
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48
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Perera NCN, Godahewa GI, Nam BH, Park JY, Lee J. Two metalloenzymes from rockfish (Sebastes schligellii): Deciphering their potential involvement in redox homeostasis against oxidative stress. FISH & SHELLFISH IMMUNOLOGY 2018; 80:31-45. [PMID: 29859306 DOI: 10.1016/j.fsi.2018.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Disturbance in the balance between pro-oxidants and anti-oxidants result oxidative stress in aerobic organisms. However, oxidative stress can be inhibited by enzymatic and non-enzymatic defense mechanisms. Superoxide dismutases (SODs) are well-known scavengers of superoxide radicals, and they protect cells by detoxifying hazardous reactive oxygen species. Here, we have identified and characterized two different SODs, CuZnSOD and MnSOD, from black rockfish (RfCuZnSOD and RfMnSOD, respectively). In silico analysis revealed the well-conserved molecular structures comprising all essential properties of CuZnSOD and MnSOD. Phylogenetic analysis revealed that both RfCuZnSOD and RfMnSOD cladded with their fish counterparts. The recombinant RfSOD proteins demonstrated their potential superoxide scavenging abilities through a xanthine oxidase assay. The optimum temperature and pH conditions for both rRfSODs were 25 °C and pH 8, respectively. Moreover, the potential peroxidation function of rRfCuZnSOD was observed in the presence of HCO3-. The highest peroxidation activity was observed at 100 μg/mL of rRfCuZnSOD using the MTT cell viability assay and flow cytometry. The analogous tissue-specific expression profile indicated ubiquitous expression of both RfCuZnSOD and RfMnSOD in selected tissues of healthy juvenile rockfish. An immune challenge experiment illustrated the altered expression profiles of both RfCuZnSOD and RfMnSOD against lipopolysaccharide, Streptococcus iniae, and polyinosinic-polycytidylic acid (poly I:C). Collectively, these results strengthen the general understanding of the structural and functional characteristics of SODs within the host defense system.
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Affiliation(s)
- N C N Perera
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - G I Godahewa
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan, 46083, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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49
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Pandey B, Ray K, Rajaraman G. Structure, Bonding, Reactivity and Spectral Features of Putative NiIII
=O Species: A Theoretical Perspective. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bhawana Pandey
- Department of Chemistry; Indian Institute of Technology Bombay; 400 076 Powai India
| | - Kallol Ray
- Institut fár Chemie; Humboldt-Universität zu Berlin; Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Gopalan Rajaraman
- Department of Chemistry; Indian Institute of Technology Bombay; 400 076 Powai India
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50
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Schatzman SS, Culotta VC. Chemical Warfare at the Microorganismal Level: A Closer Look at the Superoxide Dismutase Enzymes of Pathogens. ACS Infect Dis 2018. [PMID: 29517910 DOI: 10.1021/acsinfecdis.8b00026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Superoxide anion radical is generated as a natural byproduct of aerobic metabolism but is also produced as part of the oxidative burst of the innate immune response design to kill pathogens. In living systems, superoxide is largely managed through superoxide dismutases (SODs), families of metalloenzymes that use Fe, Mn, Ni, or Cu cofactors to catalyze the disproportionation of superoxide to oxygen and hydrogen peroxide. Given the bursts of superoxide faced by microbial pathogens, it comes as no surprise that SOD enzymes play important roles in microbial survival and virulence. Interestingly, microbial SOD enzymes not only detoxify host superoxide but also may participate in signaling pathways that involve reactive oxygen species derived from the microbe itself, particularly in the case of eukaryotic pathogens. In this Review, we will discuss the chemistry of superoxide radicals and the role of diverse SOD metalloenzymes in bacterial, fungal, and protozoan pathogens. We will highlight the unique features of microbial SOD enzymes that have evolved to accommodate the harsh lifestyle at the host-pathogen interface. Lastly, we will discuss key non-SOD superoxide scavengers that specific pathogens employ for defense against host superoxide.
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Affiliation(s)
- Sabrina S. Schatzman
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Pubic Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland 21205, United States
| | - Valeria C. Culotta
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Pubic Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland 21205, United States
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