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Characterization of Gentisate 1,2-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and Its Stabilization by Immobilization on Nickel-Functionalized Magnetic Nanoparticles. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of this study was the biochemical and kinetic characterization of the gentisate 1,2-dioxygenase (GDO) from Pseudarthrobacter phenanthrenivorans Sphe3 and the development of a nanobiocatalyst by its immobilization on Ni2+-functionalized Fe3O4-polydopamine magnetic nanoparticles (Ni2+-PDA-MNPs). This is the first GDO to be immobilized. The gene encoding the GDO was cloned with an N-terminal His-tag and overexpressed in E. coli. The nanoparticles showed a high purification efficiency of GDO from crude cell lysates with a maximum activity recovery of 97%. The immobilized enzyme was characterized by Fourier transform infrared spectroscopy (FTIR). The reaction product was identified by 1H NMR. Both free and immobilized GDO exhibited Michaelis–Menten kinetics with Km values of 25.9 ± 4.4 and 82.5 ± 14.2 μM and Vmax values of 1.2 ± 0.1 and 0.03 ± 0.002 mM*s−1, respectively. The thermal stability of the immobilized GDO was enhanced at 30 °C, 40 °C, and 50 °C, compared to the free GDO. Stored at −20 °C, immobilized GDO retained more than 60% of its initial activity after 30 d, while the free enzyme completely lost its activity after 10 d. Furthermore, the immobilized nanoparticle–enzyme conjugate retained more than 50% enzyme activity up to the fifth cycle.
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2
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Chen X, Wang W, Hu H, Tang H, Liu Y, Xu P, Lin K, Cui C. Insights from comparative proteomic analysis into degradation of phenanthrene and salt tolerance by the halophilic Martelella strain AD-3. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1499-1510. [PMID: 33244677 DOI: 10.1007/s10646-020-02310-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
A halophilic PAHs-degrading strain, Martelella AD-3, was previously isolated from highly saline petroleum-contaminated soil. In this study, label-free proteomics were performed to identify differentially expressed proteins (DEPs) under Group P (phenanthrene +5% salinity) and Group G (glycerol +1% salinity), which would help to reveal the mechanism of phenanthrene degradation and salt tolerance. A total of 307 up-regulated DEPs were found in Group P, including 17 phenanthrene degradation proteins. Among these phenanthrene-degrading proteins, the ferredoxin of aromatic ring-hydroxylating dioxygenase (RHD) was up-regulated by 110-fold and gentisate 1,2-dioxygenases (GDOs) were only expressed in Group P. Besides, we also found nine high salt stress response proteins, including ectoine synthase and transport protein of compatible (osmoprotectant) solutes, were differentially up-regulated. These results indicate that strain AD-3 mainly relied on RHD and dihydrodiol dehydrogenase to degrade phenanthrene, and accumulated compatible solutes for resistance to salt stress. This study provides strong theoretical guidance for understanding the degradation of phenanthrene by strain AD-3 in high salt environments.
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Affiliation(s)
- Xin Chen
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Yongdi Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Gentisate 1,2-dioxygenase from the gram-positive bacteria Rhodococcus opacus 1CP: Identical active sites vs. different substrate selectivities. Biochimie 2020; 180:90-103. [PMID: 33122105 DOI: 10.1016/j.biochi.2020.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/10/2020] [Accepted: 10/25/2020] [Indexed: 11/20/2022]
Abstract
Gentisate 1,2-dioxygenases belong to the class III ring-cleaving dioxygenases catalyzing key reactions of aromatic compounds degradation by aerobic microorganisms. In the present work, the results of complete molecular, structural, and functional investigations of the gentisate 1,2-dioxygenase (rho-GDO) from a gram-positive bacterium Rhodococcus opacus 1CP growing on 3-hydroxybenzoate as a sole source of carbon and energy are presented. The purified enzyme showed a narrow substrate specificity. Among fourteen investigated substrate analogues only gentisate was oxidized by the enzyme, what can be potentially applied in biosensor technologies. The rho-GDO encoding gene was identified in the genomic DNA of the R. opacus 1CP. According to phylogenetic analysis, the rho-GDO belongs to the group of apparently most recently acquired activities in bacterial genera Rhodococcus, Arthrobacter, Corynebacterium, Nocardia, Amycolatopsis, Comamonas, and Streptomyces. Homology modeling the rho-GDO 3D-structure demonstrates the composition identity of the first-sphere residues of the active site of rho-GDO and salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans (RCSB PDB: 2PHD), despite of their different substrate specificities. The phenomenon described for the first time for this family of enzymes supposes a more complicated mechanism of substrate specificity than previously imagined, and makes the rho-GDO a convenient model for a novel direction of structure-function relationship studies.
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Marín P, Martirani‐Von Abercron SM, Urbina L, Pacheco‐Sánchez D, Castañeda‐Cataña MA, Retegi A, Eceiza A, Marqués S. Bacterial nanocellulose production from naphthalene. Microb Biotechnol 2019; 12:662-676. [PMID: 31087504 PMCID: PMC6559018 DOI: 10.1111/1751-7915.13399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 11/29/2022] Open
Abstract
Polycyclic aromatic compounds (PAHs) are toxic compounds that are released in the environment as a consequence of industrial activities. The restoration of PAH-polluted sites considers the use of bacteria capable of degrading aromatic compounds to carbon dioxide and water. Here we characterize a new Xanthobacteraceae strain, Starkeya sp. strain N1B, previously isolated during enrichment under microaerophilic conditions, which is capable of using naphthalene crystals as the sole carbon source. The strain produced a structured biofilm when grown on naphthalene crystals, which had the shape of a half-sphere organized over the crystal. Scanning electron microscopy (SEM) and GC-MS analysis indicated that the biofilm was essentially made of cellulose, composed of several micron-long nanofibrils of 60 nm diameter. A cellulosic biofilm was also formed when the cells grew with glucose as the carbon source. Fourier transformed infrared spectroscopy (FTIR) confirmed that the polymer was type I cellulose in both cases, although the crystallinity of the material greatly depended on the carbon source used for growth. Using genome mining and mutant analysis, we identified the genetic complements required for the transformation of naphthalene into cellulose, which seemed to have been successively acquired through horizontal gene transfer. The capacity to develop the biofilm around the crystal was found to be dispensable for growth when naphthalene was used as the carbon source, suggesting that the function of this structure is more intricate than initially thought. This is the first example of the use of toxic aromatic hydrocarbons as the carbon source for bacterial cellulose production. Application of this capacity would allow the remediation of a PAH into such a value-added polymer with multiple biotechnological usages.
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Affiliation(s)
- Patricia Marín
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Sophie Marie Martirani‐Von Abercron
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Leire Urbina
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Daniel Pacheco‐Sánchez
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Mayra Alejandra Castañeda‐Cataña
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
| | - Aloña Retegi
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Arantxa Eceiza
- Materials + Technologies Research Group (GMT)Department of Chemical and Environmental EngineeringFaculty of Engineering of GipuzkoaUniversity of the Basque CountryPza Europa 1Donostia‐San Sebastian20018Spain
| | - Silvia Marqués
- Estación Experimental del ZaidínDepartment of Environmental ProtectionConsejo Superior de Investigaciones CientíficasCalle Profesor Albareda, 1Granada18008Spain
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Rahaman R, Munshi S, Banerjee S, Chakraborty B, Bhunia S, Paine TK. Dioxygen reactivity of iron( ii)–gentisate/1,4-dihydroxy-2-naphthoate complexes of N4 ligands: oxidative coupling of 1,4-dihydroxy-2-naphthoate. Dalton Trans 2019; 48:16993-17004. [DOI: 10.1039/c9dt03493e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidative C–C coupling of iron-coordinated co-ligand: Iron(ii)-1,4-dihydroxy-2-naphthoate complexes of neutral N4 ligands react with dioxygen to display C–C coupling of 1,4-dihydroxy-2-naphthoate.
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Affiliation(s)
- Rubina Rahaman
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Sandip Munshi
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Sridhar Banerjee
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Biswarup Chakraborty
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Sarmistha Bhunia
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Tapan Kanti Paine
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
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Martirani-Von Abercron SM, Marín P, Solsona-Ferraz M, Castañeda-Cataña MA, Marqués S. Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity. Microb Biotechnol 2017; 10:1781-1796. [PMID: 28840968 PMCID: PMC5658598 DOI: 10.1111/1751-7915.12842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.
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Affiliation(s)
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Marta Solsona-Ferraz
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mayra-Alejandra Castañeda-Cataña
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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7
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Rahaman R, Chakraborty B, Paine TK. Mimicking the Aromatic-Ring-Cleavage Activity of Gentisate-1,2-Dioxygenase by a Nonheme Iron Complex. Angew Chem Int Ed Engl 2016; 55:13838-13842. [DOI: 10.1002/anie.201607044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Rubina Rahaman
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
| | - Biswarup Chakraborty
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
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8
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Rahaman R, Chakraborty B, Paine TK. Mimicking the Aromatic-Ring-Cleavage Activity of Gentisate-1,2-Dioxygenase by a Nonheme Iron Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rubina Rahaman
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
| | - Biswarup Chakraborty
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
| | - Tapan Kanti Paine
- Department of Inorganic Chemistry; Indian Association for the Cultivation of Science; 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata- 700032 India
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9
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Huang L, Hu H, Tang H, Liu Y, Xu P, Shi J, Lin K, Luo Q, Cui C. Identification and Characterization of a Novel Gentisate 1,2-Dioxygenase Gene from a Halophilic Martelella Strain. Sci Rep 2015; 5:14307. [PMID: 26394696 PMCID: PMC4585797 DOI: 10.1038/srep14307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/24/2015] [Indexed: 01/27/2023] Open
Abstract
Halophilic Martelella strain AD-3, isolated from highly saline petroleum-contaminated soil, can efficiently degrade polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene and anthracene, in 3-5% salinity. Gentisic acid is a key intermediate in the microbial degradation of PAH compounds. However, there is little information on PAH degradation by moderately halophilic bacteria. In this study, a 1,077-bp long gene encoding gentisate 1,2-dioxygenase (GDO) from a halophilic Martelella strain AD-3 was cloned, sequenced, and expressed in Escherichia coli. The recombinant enzyme GDO was purified and characterized in detail. By using the (18)O isotope experiment and LC-MS analysis, the sources of the two oxygen atoms added onto maleylpyruvate were identified as H2O and O2, respectively. The Km and kcat values for gentisic acid were determined to be 26.64 μM and 161.29 s(-1), respectively. In addition, optimal GDO activity was observed at 30 °C, pH 7.0, and at 12% salinity. Site-directed mutagenesis demonstrated the importance of four highly conserved His residues at positions 155, 157, 167, and 169 for enzyme activity. This finding provides new insights into mechanism and variety of gentisate 1,2-dioxygenase for PAH degradation in high saline conditions.
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Affiliation(s)
- Ling Huang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yongdi Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Jie Shi
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Qishi Luo
- Shanghai Engineering Research Center of Contaminated Sites Remediation, Shanghai Institute for Design & Research in Environmental Engineering Co. Ltd., Shanghai 200232, People’s Republic of China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
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10
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Eppinger E, Ferraroni M, Bürger S, Steimer L, Peng G, Briganti F, Stolz A. Function of different amino acid residues in the reaction mechanism of gentisate 1,2-dioxygenases deduced from the analysis of mutants of the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1425-37. [PMID: 26093111 DOI: 10.1016/j.bbapap.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022]
Abstract
The genome of the α-proteobacterium Pseudaminobacter salicylatoxidans codes for a ferrous iron containing ring-fission dioxygenase which catalyzes the 1,2-cleavage of (substituted) salicylate(s), gentisate (2,5-dihydroxybenzoate), and 1-hydroxy-2-naphthoate. Sequence alignments suggested that the "salicylate 1,2-dioxygenase" (SDO) from this strain is homologous to gentisate 1,2-dioxygenases found in bacteria, archaea and fungi. In the present study the catalytic mechanism of the SDO and gentisate 1,2-dioxygenases in general was analyzed based on sequence alignments, mutational and previously performed crystallographic studies and mechanistic comparisons with "extradiol- dioxygenases" which cleave aromatic nuclei in the 2,3-position. Different highly conserved amino acid residues that were supposed to take part in binding and activation of the organic substrates were modified in the SDO by site-specific mutagenesis and the enzyme variants subsequently analyzed for the conversion of salicylate, gentisate and 1-hydroxy-2-naphthoate. The analysis of enzyme variants which carried exchanges in the positions Arg83, Trp104, Gly106, Gln108, Arg127, His162 and Asp174 demonstrated that Arg83 and Arg127 were indispensable for enzymatic activity. In contrast, residual activities were found for variants carrying mutations in the residues Trp104, Gly106, Gln108, His162, and Asp174 and some of these mutants still could oxidize gentisate, but lost the ability to convert salicylate. The results were used to suggest a general reaction mechanism for gentisate-1,2-dioxygenases and to assign to certain amino acid residues in the active site specific functions in the cleavage of (substituted) salicylate(s).
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Affiliation(s)
- Erik Eppinger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Marta Ferraroni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Sibylle Bürger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Lenz Steimer
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Grace Peng
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Fabrizio Briganti
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany.
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11
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dos Santos DFK, Istvan P, Noronha EF, Quirino BF, Krüger RH. New dioxygenase from metagenomic library from Brazilian soil: insights into antibiotic resistance and bioremediation. Biotechnol Lett 2015; 37:1809-17. [DOI: 10.1007/s10529-015-1861-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
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12
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Ferraroni M, Matera I, Bürger S, Reichert S, Steimer L, Scozzafava A, Stolz A, Briganti F. The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate. FEBS J 2013; 280:1643-52. [DOI: 10.1111/febs.12173] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/02/2013] [Accepted: 01/30/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Marta Ferraroni
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Irene Matera
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Sibylle Bürger
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Sabrina Reichert
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Lenz Steimer
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Andrea Scozzafava
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Andreas Stolz
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Fabrizio Briganti
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
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13
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Shiri M, Heravi MM, Soleymanifard B. Arylidene pyruvic acids (APAs) in the synthesis of organic compounds. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Subbotina NM, Kolomytseva MP, Golovleva LA. Metabolism of 3-hydroxybenzoate and gentisate by strain Rhodococcus opacus 1CP. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712030137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans. Appl Environ Microbiol 2011; 78:621-7. [PMID: 22101055 DOI: 10.1128/aem.07137-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A protein fraction exhibiting 1-hydroxy-2-naphthoic acid (1-H2NA) dioxygenase activity was purified via ion exchange, hydrophobic interactions, and gel filtration chromatography from Arthrobacter phenanthrenivorans sp. nov. strain Sphe3 isolated from a Greek creosote-oil-polluted site. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and tandem MS (MS-MS) analysis revealed that the amino acid sequences of oligopeptides of the major 45-kDa protein species, as analyzed by SDS-PAGE and silver staining, comprising 29% of the whole sequence, exhibited strong homology with 1-H2NA dioxygenase of Nocardioides sp. strain KP7. A BLAST search of the recently sequenced Sphe3 genome revealed two putative open reading frames, named diox1 and diox2, showing 90% nucleotide identity to each other and 85% identity at the amino acid level with the Nocardia sp. homologue. diox1 was found on an indigenous Sphe3 plasmid, whereas diox2 was located on the chromosome. Both genes were induced by the presence of phenanthrene used as a sole carbon and energy source, and as expected, both were subject to carbon catabolite repression. The relative RNA transcription level of the chromosomal (diox2) gene was significantly higher than that of its plasmid (diox1) homologue. Both diox1 and diox2 putative genes were PCR amplified, cloned, and overexpressed in Escherichia coli. Recombinant E. coli cells expressed 1-H2NA dioxygenase activity. Recombinant enzymes exhibited Michaelis-Menten kinetics with an apparent K(m) of 35 μM for Diox1 and 29 μM for Diox2, whereas they showed similar kinetic turnover characteristics with K(cat)/K(m) values of 11 × 10(6) M(-1) s(-1) and 12 × 10(6) M(-1) s(-1), respectively. Occurrence of two diox1 and diox2 homologues in the Sphe3 genome implies that a replicative transposition event has contributed to the evolution of 1-H2NA dioxygenase in A. phenanthrenivorans.
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Lee HJ, Kim JM, Lee SH, Park M, Lee K, Madsen EL, Jeon CO. Gentisate 1,2-dioxygenase, in the third naphthalene catabolic gene cluster of Polaromonas naphthalenivorans CJ2, has a role in naphthalene degradation. Microbiology (Reading) 2011; 157:2891-2903. [DOI: 10.1099/mic.0.049387-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polaromonas naphthalenivorans strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by nagI3, within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially nagI3) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that nagI3 was expressed at a relatively high level. Individual knockout mutants of all three nagI genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2ΔnagI3 showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that nagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three nagI genes from strain CJ2 were cloned into Escherichia coli: the nagI2 and nagI3 genes were successfully overexpressed. The subunit mass of the GDOs were ~36–39 kDa, and their structures were deduced to be dimeric. The K
m values of NagI2 and NagI3 were 31 and 10 µM, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the nagI3 gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in Polaromonas sp. JS666 and Leptothrix cholodnii SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the nagI3 allele of strain CJ2 did not share high sequence identity with its homologues in Polaromonas sp. JS666 and L. cholodnii SP-6.
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Affiliation(s)
- Hyo Jung Lee
- Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jeong Myeong Kim
- Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Se Hee Lee
- Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Minjeong Park
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Kangseok Lee
- Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Eugene L. Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Che Ok Jeon
- Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
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Mallick S, Chakraborty J, Dutta TK. Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review. Crit Rev Microbiol 2010; 37:64-90. [PMID: 20846026 DOI: 10.3109/1040841x.2010.512268] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.
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Affiliation(s)
- Somnath Mallick
- Department of Chemistry, Saldiha College, Bankura, West Bengal, India
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Dioxygen activation responsible for oxidation of aliphatic and aromatic hydrocarbon compounds: current state and variants. Appl Microbiol Biotechnol 2010; 87:1595-603. [DOI: 10.1007/s00253-010-2715-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/03/2010] [Accepted: 06/05/2010] [Indexed: 10/19/2022]
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Chen J, Li W, Wang M, Zhu G, Liu D, Sun F, Hao N, Li X, Rao Z, Zhang XC. Crystal structure and mutagenic analysis of GDOsp, a gentisate 1,2-dioxygenase from Silicibacter pomeroyi. Protein Sci 2008; 17:1362-73. [PMID: 18505738 DOI: 10.1110/ps.035881.108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. Here we report the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) at a 2.8 A resolution. The enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. However, each subunit of GDOsp unusually contained two ferrous centers that were located in its two homologous cupin domains, respectively. Further mutagenic analysis indicated that the enzyme activity of GDOsp depends on the microenvironment in both metal-binding sites. Moreover, homologous structural comparison and functional study on GDOsp variants unveiled a group of functionally essential residues and suggested that the active site of the enzyme is located in the amino-terminal domain, but could be influenced by changes in the carboxyl domain. Therefore, GDOsp may provide a working model for studying long-distance communication within a protein (or its complex).
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Affiliation(s)
- Jia Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities. Microbiol Mol Biol Rev 2008; 72:13-53, table of contents. [PMID: 18322033 DOI: 10.1128/mmbr.00026-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.
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Husain S. Literature overview: Microbial metabolism of high molecular weight polycyclic aromatic hydrocarbons. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/rem.20165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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