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Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
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Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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Njiru C, Xue W, De Rouck S, Alba JM, Kant MR, Chruszcz M, Vanholme B, Dermauw W, Wybouw N, Van Leeuwen T. Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals. BMC Biol 2022; 20:131. [PMID: 35658860 PMCID: PMC9167512 DOI: 10.1186/s12915-022-01323-1] [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: 12/15/2021] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
Background Generalist herbivores such as the two-spotted spider mite Tetranychus urticae thrive on a wide variety of plants and can rapidly adapt to novel hosts. What traits enable polyphagous herbivores to cope with the diversity of secondary metabolites in their variable plant diet is unclear. Genome sequencing of T. urticae revealed the presence of 17 genes that code for secreted proteins with strong homology to “intradiol ring cleavage dioxygenases (DOGs)” from bacteria and fungi, and phylogenetic analyses show that they have been acquired by horizontal gene transfer from fungi. In bacteria and fungi, DOGs have been well characterized and cleave aromatic rings in catecholic compounds between adjacent hydroxyl groups. Such compounds are found in high amounts in solanaceous plants like tomato, where they protect against herbivory. To better understand the role of this gene family in spider mites, we used a multi-disciplinary approach to functionally characterize the various T. urticae DOG genes. Results We confirmed that DOG genes were present in the T. urticae genome and performed a phylogenetic reconstruction using transcriptomic and genomic data to advance our understanding of the evolutionary history of spider mite DOG genes. We found that DOG expression differed between mites from different plant hosts and was induced in response to jasmonic acid defense signaling. In consonance with a presumed role in detoxification, expression was localized in the mite’s gut region. Silencing selected DOGs expression by dsRNA injection reduced the mites’ survival rate on tomato, further supporting a role in mitigating the plant defense response. Recombinant purified DOGs displayed a broad substrate promiscuity, cleaving a surprisingly wide array of aromatic plant metabolites, greatly exceeding the metabolic capacity of previously characterized microbial DOGs. Conclusion Our findings suggest that the laterally acquired spider mite DOGs function as detoxification enzymes in the gut, disarming plant metabolites before they reach toxic levels. We provide experimental evidence to support the hypothesis that this proliferated gene family in T. urticae is causally linked to its ability to feed on an extremely wide range of host plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01323-1.
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Shapterhasmi T, Palani N, Velusamy M, Bhuvanesh NS, Sundaravel K, Easwaramoorthi S. Iron(III) Complexes of Pyrrolidine and Piperidine Appended Tridentate 3N Donor Ligands as Models for Catechol Dioxygenase Enzymes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Aravind MK, Varalakshmi P, John SA, Ashokkumar B. Catechol 1,2-Dioxygenase From Paracoccus sp. MKU1-A Greener and Cleaner Bio-Machinery for cis, cis-Muconic Acid Production by Recombinant E. coli. Front Bioeng Biotechnol 2021; 9:703399. [PMID: 34790650 PMCID: PMC8591083 DOI: 10.3389/fbioe.2021.703399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/19/2021] [Indexed: 11/23/2022] Open
Abstract
Cis, cis-muconic acid (ccMA) is known for its industrial importance as a precursor for the synthesis of several biopolymers. Catechol 1,2-dioxygenase (C12O) is involved in aromatic compounds catabolism and ccMA synthesis in a greener and cleaner way. This is the first study on C12O gene from a metabolically versatile Paracoccus sp. MKU1, which was cloned and expressed in E. coli to produce ccMA from catechol. From the E. coli transformant, recombinant C12O enzyme was purified and found to be a homotrimer with a subunit size of 38.6 kDa. The apparent K m and V max for C12O was 12.89 µM and 310.1 U.mg-1, respectively, evidencing high affinity to catechol than previously reported C12Os. The predicted 3D-structure of C12O from MKU1 consisted of five α-helices in N-terminus, one α-helix in C-terminus, and nine β-sheets in C-terminus. Moreover, a unique α-helix signature 'EESIHAN' was identified in C-terminus between 271 and 277 amino acids, however the molecular insight of conservative α-helix remains obscure. Further, fed-batch culture was employed using recombinant E. coli expressing C12O gene from Paracoccus sp. MKU1 to produce ccMA by whole-cells catalyzed bioconversion of catechol. With the successive supply of 120 mM catechol, the transformant produced 91.4 mM (12.99 g/L) of ccMA in 6 h with the purity of 95.7%. This single step conversion of catechol to ccMA using whole-cells reactions of recombinants did not generate any by-products in the reaction mixtures. Thus, the recombinant E. coli expressing high activity C12O from Paracoccus sp. MKU1 holds promise as a potential candidate for yielding high concentrations of ccMA at faster rates in low cost settings.
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Affiliation(s)
- Manikka Kubendran Aravind
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Perumal Varalakshmi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Swamidoss Abraham John
- Centre for Nanoscience and Nanotechnology, Department of Chemistry, Gandhigram Rural Institute, Gandhigram, India
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Design of a Microbial Remediation Inoculation Program for Petroleum Hydrocarbon Contaminated Sites Based on Degradation Pathways. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168794. [PMID: 34444543 PMCID: PMC8395025 DOI: 10.3390/ijerph18168794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
This paper analyzed the degradation pathways of petroleum hydrocarbon degradation bacteria, screened the main degradation pathways, and found the petroleum hydrocarbon degradation enzymes corresponding to each step of the degradation pathway. Through the Copeland method, the best inoculation program of petroleum hydrocarbon degradation bacteria in a polluted site was selected as follows: single oxygenation path was dominated by Streptomyces avermitilis, hydroxylation path was dominated by Methylosinus trichosporium OB3b, secondary oxygenation path was dominated by Pseudomonas aeruginosa, secondary hydroxylation path was dominated by Methylococcus capsulatus, double oxygenation path was dominated by Acinetobacter baylyi ADP1, hydrolysis path was dominated by Rhodococcus erythropolis, and CoA path was dominated by Geobacter metallireducens GS-15 to repair petroleum hydrocarbon contaminated sites. The Copeland method score for this solution is 22, which is the highest among the 375 solutions designed in this paper, indicating that it has the best degradation effect. Meanwhile, we verified its effect by the Cdocker method, and the Cdocker energy of this solution is −285.811 kcal/mol, which has the highest absolute value. Among the inoculation programs of the top 13 petroleum hydrocarbon degradation bacteria, the effect of the best inoculation program of petroleum hydrocarbon degradation bacteria was 18% higher than that of the 13th group, verifying that this solution has the best overall degradation effect. The inoculation program of petroleum hydrocarbon degradation bacteria designed in this paper considered the main pathways of petroleum hydrocarbon pollutant degradation, especially highlighting the degradability of petroleum hydrocarbon intermediate degradation products, and enriching the theoretical program of microbial remediation of petroleum hydrocarbon contaminated sites.
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Rodríguez-Salazar J, Almeida-Juarez AG, Ornelas-Ocampo K, Millán-López S, Raga-Carbajal E, Rodríguez-Mejía JL, Muriel-Millán LF, Godoy-Lozano EE, Rivera-Gómez N, Rudiño-Piñera E, Pardo-López L. Characterization of a Novel Functional Trimeric Catechol 1,2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico. Front Microbiol 2020; 11:1100. [PMID: 32582076 PMCID: PMC7287156 DOI: 10.3389/fmicb.2020.01100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/04/2020] [Indexed: 12/17/2022] Open
Abstract
Catechol 1,2 dioxygenases (C12DOs) have been studied for its ability to cleavage the benzene ring of catechol, the main intermediate in the degradation of aromatic compounds derived from aerobic degradation of hydrocarbons. Here we report the genome sequence of the marine bacterium Pseudomonas stutzeri GOM2, isolated from the southwestern Gulf of Mexico, and the biochemical characterization of its C12DO (PsC12DO). The catA gene, encoding PsC12DO of 312 amino acid residues, was cloned and expressed in Escherichia coli. Many C12DOs have been described as dimeric enzymes including those present in Pseudomonas species. The purified PsC12DO enzyme was found as an active trimer, with a molecular mass of 107 kDa. Increasing NaCl concentration in the enzyme reaction gradually reduced activity; in high salt concentrations (0.7 M NaCl) quaternary structural analysis determined that the enzyme changes to a dimeric arrangement and causes a 51% decrease in specific activity on catechol substrate. In comparison with other C12DOs, our enzyme showed a broad range of action for PsC12DO in solutions with pH values ranging from neutral to alkaline (70%). The enzyme is still active after incubation at 50°C for 30 min and in low temperatures to long term storage after 6 weeks at 4°C (61%). EDTA or Ca2+ inhibitors cause no drastic changes on residual activity; nevertheless, the activity of the enzyme was affected by metal ions Fe3+, Zn2+ and was completely inhibited by Hg2+. Under optimal conditions the k cat and K m values were 16.13 s-1 and 13.2 μM, respectively. To our knowledge, this is the first report describing the characterization of a marine C12DOs from P. stutzeri isolated from the Gulf of Mexico that is active in a trimeric state. We consider that our enzyme has important features to be used in environments in presence of EDTA, metals and salinity conditions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Liliana Pardo-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Todorova Y, Yotinov I, Topalova Y, Benova E, Marinova P, Tsonev I, Bogdanov T. Evaluation of the effect of cold atmospheric plasma on oxygenases' activities for application in water treatment technologies. ENVIRONMENTAL TECHNOLOGY 2019; 40:3783-3792. [PMID: 29923777 DOI: 10.1080/09593330.2018.1491631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Plasma-based technologies take an increasing place in the new conceptions of wastewater management as a promising tool for the treatment of persistent organic pollutants with low biodegradability. Plasma major advantage is the synergy of diverse active components with high oxidative action and additional benefits as disinfection of treated water. But the bactericidal effect of plasma can influence the treatment effectiveness when this technology is used in combination with biological methods for the removal of pollutants. The aim of this paper is to study the effect of non-thermal atmospheric plasma torch on key enzymes from phenol biodegradation pathways in Pseudomonas aureofaciens (chlororaphis) AP-9. The strain was isolated from contaminated soils and had a high potential for biodegradation of aromatic compounds. The used plasma source is surface-wave-sustained discharge operating at 2.45 GHz in argon produced by an electromagnetic wave launcher surfatron type. The enzyme activities of phenol 2-monooxygenase (P2MO), catechol 1,2-dioxygenase (C12DO), catechol 2,3-dioxygenase (C23DO), protocatechuate 3,4-dioxygenase (P34DO) and succinate dehydrogenase (SDH) were measured in control and after plasma treatment of 10, 30 and 60 s. At short-time treatment, the activities of intradiol dioxygenases increased with 26% and 59% for C12DO and P34DO, respectively. Other oxygenases and SDH were inhibited with 35% even at 10 s treatment. Longer treatment times had a clear negative effect but SDH kept the higher activity at 60 s treatment compared to the oxygenases. Our data suggest that plasma-based technologies are a useful approach for post-treatment of aryl-containing wastewater in order to increase the effectiveness of biological removal.
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Affiliation(s)
- Yovana Todorova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivaylo Yotinov
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Yana Topalova
- Department of General and Applied Hydrobiology, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Evgenia Benova
- DLTIS, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Plamena Marinova
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Ivan Tsonev
- Faculty of Physics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Todor Bogdanov
- Faculty of Medicine, Medical University Sofia, Sofia, Bulgaria
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Four Aromatic Intradiol Ring Cleavage Dioxygenases from Aspergillus niger. Appl Environ Microbiol 2019; 85:AEM.01786-19. [PMID: 31540981 DOI: 10.1128/aem.01786-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/13/2019] [Indexed: 11/20/2022] Open
Abstract
Ring cleavage dioxygenases catalyze the critical ring-opening step in the catabolism of aromatic compounds. The archetypal filamentous fungus Aspergillus niger previously has been reported to be able to utilize a range of monocyclic aromatic compounds as sole sources of carbon and energy. The genome of A. niger has been sequenced, and deduced amino acid sequences from a large number of gene models show various levels of similarity to bacterial intradiol ring cleavage dioxygenases, but no corresponding enzyme has been purified and characterized. Here, the cloning, heterologous expression, purification, and biochemical characterization of four nonheme iron(III)-containing intradiol dioxygenases (NRRL3_02644, NRRL3_04787, NRRL3_05330, and NRRL3_01405) from A. niger are reported. Purified enzymes were tested for their ability to cleave model catecholate substrates, and their apparent kinetic parameters were determined. Comparisons of k cat /Km values show that NRRL3_02644 and NRRL3_05330 are specific for hydroxyquinol (1,2,4-trihydroxybenzene), and phylogenetic analysis shows that these two enzymes are related to bacterial hydroxyquinol 1,2-dioxygenases. A high-activity catechol 1,2-dioxygenase (NRRL3_04787), which is phylogenetically related to other characterized and putative fungal catechol 1,2-dioxygenases, was also identified. The fourth enzyme (NRRL3_01405) appears to be a novel homodimeric Fe(III)-containing protocatechuate 3,4-dioxygenase that is phylogenetically distantly related to heterodimeric bacterial protocatechuate 3,4-dioxygenases. These investigations provide experimental evidence for the molecular function of these proteins and open the way to further investigations of the physiological roles for these enzymes in fungal metabolism of aromatic compounds.IMPORTANCE Aromatic ring opening using molecular oxygen is one of the critical steps in the degradation of aromatic compounds by microorganisms. While enzymes catalyzing this step have been well-studied in bacteria, their counterparts from fungi are poorly characterized despite the abundance of genes annotated as ring cleavage dioxygenases in fungal genomes. Aspergillus niger degrades a variety of aromatic compounds, and its genome harbors 5 genes encoding putative intracellular intradiol dioxygenases. The ability to predict the substrate specificities of the encoded enzymes from sequence data are limited. Here, we report the characterization of four purified intradiol ring cleavage dioxygenases from A. niger, revealing two hydroxyquinol-specific dioxygenases, a catechol dioxygenase, and a unique homodimeric protocatechuate dioxygenase. Their characteristics, as well as their phylogenetic relationships to predicted ring cleavage dioxygenases from other fungal species, provide insights into their molecular functions in aromatic compound metabolism by this fungus and other fungi.
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Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L. Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. J Biol Chem 2019; 294:10211-10235. [PMID: 31092555 PMCID: PMC6664185 DOI: 10.1074/jbc.ra119.007595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
A diverse collection of enzymes comprising the protocatechuate dioxygenases (PCADs) has been characterized in several extradiol aromatic compound degradation pathways. Structural studies have shown a relationship between PCADs and the more broadly-distributed, functionally enigmatic Memo domain linked to several human diseases. To better understand the evolution of this PCAD-Memo protein superfamily, we explored their structural and functional determinants to establish a unified evolutionary framework, identifying 15 clearly-delineable families, including a previously-underappreciated diversity in five Memo clade families. We place the superfamily's origin within the greater radiation of the nucleoside phosphorylase/hydrolase-peptide/amidohydrolase fold prior to the last universal common ancestor of all extant organisms. In addition to identifying active-site residues across the superfamily, we describe three distinct, structurally-variable regions emanating from the core scaffold often housing conserved residues specific to individual families. These were predicted to contribute to the active-site pocket, potentially in substrate specificity and allosteric regulation. We also identified several previously-undescribed conserved genome contexts, providing insight into potentially novel substrates in PCAD clade families. We extend known conserved contextual associations for the Memo clade beyond previously-described associations with the AMMECR1 domain and a radical S-adenosylmethionine family domain. These observations point to two distinct yet potentially overlapping contexts wherein the elusive molecular function of the Memo domain could be finally resolved, thereby linking it to nucleotide base and aliphatic isoprenoid modification. In total, this report throws light on the functions of large swaths of the experimentally-uncharacterized PCAD-Memo families.
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Affiliation(s)
- A Maxwell Burroughs
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Margaret E Glasner
- the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, and
| | - Kevin P Barry
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Erika A Taylor
- the Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459
| | - L Aravind
- From the Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894,
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Manipulating intradiol dioxygenases by C-terminus truncation. Enzyme Microb Technol 2019; 125:21-28. [PMID: 30885321 DOI: 10.1016/j.enzmictec.2019.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 11/23/2022]
Abstract
Intradiol dioxygenases (EC 1.13.11.1) are bacterial enzymes that catalyze the ring cleavage of catechols which is a central step in the aerobic degradation of aromatic compounds. Some members of this enzyme group have a C-terminus which is 4-5% longer (an additional 13-18 amino acids) compared to the majority of known sequences. The longer C-terminus itself is not highly conserved and appears to be poorly integrated in the protein structural models developed for representative intradiol dioxygenases. Using a protein engineering approach variant intradiol dioxygenases were produced by truncating the C-terminus to a size comparable to the shorter versions of the enzyme. Three enzymes were selected and were originally described from the model organisms; Burkholderia xenovorans LB400, Pseudomonas putida KT2440 and Acinetobacter baylyi ADP1. The activity of the truncated enzymes were compared to the unmodified enzymes which revealed that truncation of the C-terminus could alter the enzyme activity; increasing the LB400 enzyme activity by as much as five fold, but reducing the activity of the intradiol dioxygenases from KT2440 and ADP1. The difference in effect is explained by the presence of a greater number of amino acid residues that can contribute to forming stable protein structures in the KT2440 and ADP1 enzymes. It is hypothesized that C-terminal truncation could in some cases provide a useful strategy for increasing intradiol dioxygenase activity for biotechnological production of muconic and adipic acids.
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Huang Y, Duan Y, Zhang Y, Fan P, Li Z, Liu W, Cui Z. Crystal structure of hydroxyquinol 1,2-dioxygenase PnpC from Pseudomonas putida DLL-E4 and its role of N-terminal domain for catalysis. Biochem Biophys Res Commun 2018; 507:267-273. [PMID: 30446218 DOI: 10.1016/j.bbrc.2018.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/04/2018] [Indexed: 11/29/2022]
Abstract
Hydroxyquinol 1,2-dioxygenase is a key enzyme in the hydroxyquinol pathway of p-nitrophenol (PNP) degradation, and catalyzes the ring cleavage of benzenetriol to maleylacetate. Here, we report the first structure of a hydroxyquinol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida DLL-E4 (PnpC) at the resolution of 2.1 Å. The tertiary structure of PnpC resembles that of the homologous intradiol dioxygenases. The catalytic Fe(III) is pentacoordinated by the conserved Tyr160, Tyr194, His218 and His220, the citrate anion and one water molecule. Among the residues expected to interact with the substrate, structural comparison with the (chloro)catechol dioxygenases suggested that Asp80, Thr81 and Val248 are responsible for the substrate specificity. Moreover, truncation of the N-terminal α-helix of PnpC suggested the N-terminal domain is required for its soluble expression and enzyme catalysis. Our results might provide insights in the substrate recognition and rational design of this enzyme class to be used in bioremediation.
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Affiliation(s)
- Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yajuan Duan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yajuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Panpan Fan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
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14
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Xu B, Xiong C, Deng M, Li J, Tang X, Wu Q, Zhou J, Yang Y, Ding J, Han N, Huang Z. Genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome. J Basic Microbiol 2017; 57:883-895. [PMID: 28745827 DOI: 10.1002/jobm.201700106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022]
Abstract
Catechol 1,2-dioxygenase is the key enzyme that catalyzes the cleavage of the aromatic ring of catechol. We explored the genetic diversity of catechol 1,2-dioxygenase in the fecal microbial metagenome by PCR with degenerate primers. A total of 35 gene fragments of C12O were retrieved from microbial DNA in the feces of pygmy loris. Based on phylogenetic analysis, most sequences were closely related to C12O sequences from Acinetobacter. A full-length C12O gene was directly cloned, heterologously expressed in Escherichia coli, and biochemically characterized. Purified catPL12 had optimum pH and temperature pH 8.0 and 25 °C and retained 31 and 50% of its maximum activity when assayed at 0 and 35 °C, respectively. The enzyme was stable at 25 and 37 °C, retaining 100% activity after pre-incubation for 1 h. The kinetic parameters of catPL12 were determined. The enzyme had apparent Km of 67 µM, Vmax of 7.3 U/mg, and kcat of 4.2 s-1 for catechol, and the cleavage activities for 3-methylcatechol, 4-methylcatechol, and 4-chlorocatechol were much less than for catechol, and no activity with hydroquinone or protocatechuate was detected. This study is the first to report the molecular and biochemical characterizations of a cold-adapted catechol 1,2-dioxygenase from a fecal microbial metagenome.
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Affiliation(s)
- Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Caiyun Xiong
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Meng Deng
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Yunjuan Yang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan, China
- School of Life Science, Yunnan Normal University, Kunming, Yunnan, China
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15
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Long Y, Yang S, Xie Z, Cheng L. Cloning, expression, and characterization of catechol 1,2-dioxygenase from a phenol-degrading Candida tropicalis JH8 strain. Prep Biochem Biotechnol 2016; 46:673-8. [DOI: 10.1080/10826068.2015.1135449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yan Long
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan University, Wuhan, China
| | - Sheng Yang
- College of Life Sciences, Hubei University, Wuhan, China
| | - Zhixiong Xie
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan University, Wuhan, China
| | - Li Cheng
- College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), State Key Laboratory of Virology, Wuhan University, Wuhan, China
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16
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De A, Garai M, Yadav HR, Choudhury AR, Biswas B. Catalytic promiscuity of an iron(II)-phenanthroline complex. Appl Organomet Chem 2016. [DOI: 10.1002/aoc.3551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Abhranil De
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Mamoni Garai
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research Mohali; Sector 81, S. A. S. Nagar, Manauli PO Mohali 140306 India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723133 India
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17
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Lakshman TR, Chatterjee S, Chakraborty B, Paine TK. Substrate-dependent aromatic ring fission of catechol and 2-aminophenol with O2 catalyzed by a nonheme iron complex of a tripodal N4 ligand. Dalton Trans 2016; 45:8835-44. [PMID: 27148606 DOI: 10.1039/c5dt04541j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic reactivity of an iron(ii) complex [(TPA)Fe(II)(CH3CN)2](2+) (1) (TPA = tris(2-pyridylmethyl)amine) towards oxygenative aromatic C-C bond cleavage of catechol and 2-aminophenol is presented. Complex 1 exhibits catalytic and regioselective C-C bond cleavage of 3,5-di-tert-butylcatechol (H2DBC) to form intradiol products, whereas it catalyzes extradiol-type C-C bond cleavage of 2-amino-4,6-di-tert-butylphenol (H2AP). The catalytic reactions are found to be pH-dependent and the complex exhibits maximum turnovers at pH 5 in acetonitrile-phthalate buffer. An iron(iii)-catecholate complex [(TPA)Fe(III)(DBC)](+) (2) is formed in the ring cleavage of catechol. In the extradiol-type cleavage of H2AP, an iron(iii)-2-iminobenzosemiquinonate complex [(TPA)Fe(III)(ISQ)](2+) (3) (ISQ = 4,6-di-tert-butyl-2-iminobenzosemiquinonate radical anion) is observed in the reaction pathway. This work shows the importance of the nature of 'redox non-innocent' substrates in governing the mode of ring fission reactivity.
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Affiliation(s)
- Triloke Ranjan Lakshman
- 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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18
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Basso LGM, Mendes LFS, Costa-Filho AJ. The two sides of a lipid-protein story. Biophys Rev 2016; 8:179-191. [PMID: 28510056 DOI: 10.1007/s12551-016-0199-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/29/2016] [Indexed: 01/10/2023] Open
Abstract
Protein-membrane interactions play essential roles in a variety of cell functions such as signaling, membrane trafficking, and transport. Membrane-recruited cytosolic proteins that interact transiently and interfacially with lipid bilayers perform several of those functions. Experimental techniques capable of probing changes on the structural dynamics of this weak association are surprisingly limited. Among such techniques, electron spin resonance (ESR) has the enormous advantage of providing valuable local information from both membrane and protein perspectives by using intrinsic paramagnetic probes in metalloproteins or by attaching nitroxide spin labels to proteins and lipids. In this review, we discuss the power of ESR to unravel relevant structural and functional details of lipid-peripheral membrane protein interactions with special emphasis on local changes of specific regions of the protein and/or the lipids. First, we show how ESR can be used to investigate the direct interaction between a protein and a particular lipid, illustrating the case of lipid binding into a hydrophobic pocket of chlorocatechol 1,2-dioxygenase, a non-heme iron enzyme responsible for catabolism of aromatic compounds that are industrially released in the environment. In the second case, we show the effects of GPI-anchored tissue-nonspecific alkaline phosphatase, a protein that plays a crucial role in skeletal mineralization, and on the ordering and dynamics of lipid acyl chains. Then, switching to the protein perspective, we analyze the interaction with model membranes of the brain fatty acid binding protein, the major actor in the reversible binding and transport of hydrophobic ligands such as long-chain, saturated, or unsaturated fatty acids. Finally, we conclude by discussing how both lipid and protein views can be associated to address a common question regarding the molecular mechanism by which dihydroorotate dehydrogenase, an essential enzyme for the de novo synthesis of pyrimidine nucleotides, and how it fishes out membrane-embedded quinones to perform its function.
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Affiliation(s)
- Luis G Mansor Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis F Santos Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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19
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Safaei E, Heidari S, Wojtczak A, Cotič P, Kozakiewicz A. 4-Nitrocatecholato iron(III) complexes of 2-aminomethyl pyridine-based bis(phenol) amine as structural models for catechol-bound 3,4-PCD. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Lakk-Bogáth D, Csonka R, Lorencz N, Giorgi M, Speier G, Kaizer J. Oxidant dependent oxidation of copper bound catecholate: Catecholase versus catechol dioxygenase activity. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Lin J, Milase RN. Purification and Characterization of Catechol 1,2-Dioxygenase from Acinetobacter sp. Y64 Strain and Escherichia coli Transformants. Protein J 2015; 34:421-33. [DOI: 10.1007/s10930-015-9637-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Han L, Liu P, Sun J, Wu Y, Zhang Y, Chen W, Lin J, Wang Q, Ma Y. Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli. Sci Rep 2015; 5:13435. [PMID: 26306712 PMCID: PMC4549619 DOI: 10.1038/srep13435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022] Open
Abstract
Regulating and ameliorating enzyme expression and activity greatly affects the performance of a given synthetic pathway. In this study, a new synthetic pathway for cis, cis-muconic acid (ccMA) production was reconstructed without exogenous induction by regulating the constitutive expression of the important enzyme catechol 1,2-dioxygenase (CatA). Next, new CatAs with significantly improved activities were developed to enhance ccMA production using structure-assisted protein design. Nine mutations were designed, simulated and constructed based on the analysis of the CatA crystal structure. These results showed that mutations at Gly72, Leu73 and/or Pro76 in CatA could improve enzyme activity, and the activity of the most effective mutant was 10-fold greater than that of the wild-type CatA from Acinetobacter sp. ADP1. The most productive synthetic pathway with a mutated CatA increased the titer of ccMA by more than 25%. Molecular dynamic simulation results showed that enlarging the entrance of the substrate-binding pocket in the mutants contributed to their increased enzyme activities and thus improved the performance of the synthetic pathway.
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Affiliation(s)
- Li Han
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Yuanqing Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanyuan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wujiu Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianping Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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23
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Nešvera J, Rucká L, Pátek M. Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:107-60. [PMID: 26505690 DOI: 10.1016/bs.aambs.2015.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.
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Affiliation(s)
- Jan Nešvera
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Lenka Rucká
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
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24
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Jastrzebski R, van den Berg EJ, Weckhuysen BM, Bruijnincx PCA. Sustainable production of dimethyl adipate by non-heme iron(iii) catalysed oxidative cleavage of catechol. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01562b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective catechol cleavage by a non-heme iron(iii) complex followed by hydrogenation and transesterifaction yields dimethyl adipate in a green and sustainable manner.
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Affiliation(s)
- Robin Jastrzebski
- Inorganic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584 CG Utrecht
- The Netherlands
| | - Emily J. van den Berg
- Inorganic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584 CG Utrecht
- The Netherlands
| | - Bert M. Weckhuysen
- Inorganic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584 CG Utrecht
- The Netherlands
| | - Pieter C. A. Bruijnincx
- Inorganic Chemistry and Catalysis
- Debye Institute for Nanomaterials Science
- Utrecht University
- 3584 CG Utrecht
- The Netherlands
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25
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Jastrzebski R, Quesne MG, Weckhuysen BM, de Visser SP, Bruijnincx PCA. Experimental and computational evidence for the mechanism of intradiol catechol dioxygenation by non-heme iron(III) complexes. Chemistry 2014; 20:15686-91. [PMID: 25322920 PMCID: PMC4497327 DOI: 10.1002/chem.201404988] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Indexed: 11/15/2022]
Abstract
Catechol intradiol dioxygenation is a unique reaction catalyzed by iron-dependent enzymes and non-heme iron(III) complexes. The mechanism by which these systems activate dioxygen in this important metabolic process remains controversial. Using a combination of kinetic measurements and computational modelling of multiple iron(III) catecholato complexes, we have elucidated the catechol cleavage mechanism and show that oxygen binds the iron center by partial dissociation of the substrate from the iron complex. The iron(III) superoxide complex that is formed subsequently attacks the carbon atom of the substrate by a rate-determining C-O bond formation step.
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Affiliation(s)
- Robin Jastrzebski
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Matthew G Quesne
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
| | - Sam P de Visser
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Pieter C A Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
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26
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Balamurugan M, Vadivelu P, Palaniandavar M. Iron(iii) complexes of tripodal tetradentate 4N ligands as functional models for catechol dioxygenases: the electronic vs. steric effect on extradiol cleavage. Dalton Trans 2014; 43:14653-68. [DOI: 10.1039/c3dt52145a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Xie NZ, Liang H, Huang RB, Xu P. Biotechnological production of muconic acid: current status and future prospects. Biotechnol Adv 2014; 32:615-22. [PMID: 24751381 DOI: 10.1016/j.biotechadv.2014.04.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/23/2014] [Accepted: 04/07/2014] [Indexed: 11/17/2022]
Abstract
Muconic acid (MA), a high value-added bio-product with reactive dicarboxylic groups and conjugated double bonds, has garnered increasing interest owing to its potential applications in the manufacture of new functional resins, bio-plastics, food additives, agrochemicals, and pharmaceuticals. At the very least, MA can be used to produce commercially important bulk chemicals such as adipic acid, terephthalic acid and trimellitic acid. Recently, great progress has been made in the development of biotechnological routes for MA production. This present review provides a comprehensive and systematic overview of recent advances and challenges in biotechnological production of MA. Various biological methods are summarized and compared, and their constraints and possible solutions are also described. Finally, the future prospects are discussed with respect to the current state, challenges, and trends in this field, and the guidelines to develop high-performance microbial cell factories are also proposed for the MA production by systems metabolic engineering.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, People's Republic of China
| | - Hong Liang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ri-Bo Huang
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, 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.
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28
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Micalella C, Caglio R, Mozzarelli A, Valetti F, Pessione E, Giunta C, Bruno S. Ormosil gels doped with engineered catechol 1,2 dioxygenases for chlorocatechol bioremediation. Biotechnol Appl Biochem 2014; 61:297-303. [PMID: 24571591 DOI: 10.1002/bab.1162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/01/2013] [Indexed: 11/06/2022]
Abstract
Enzymes entrapped in wet, nanoporous silica gel have great potential as bioreactors for bioremediation because of their improved thermal, chemical, and mechanical stability with respect to enzymes in solution. The B isozyme of catechol 1,2 dioxygenase from Acinetobacter radioresistens and its mutants of Leu69 and Ala72, designed for an increased reactivity toward the environmental pollutant chlorocatechols, were encapsulated using alkoxysilanes and alkyl alkoxysilanes as precursors in varying proportions. Encapsulation of the mutants in a hydrophobic tetramethoxysilane/dimethoxydimethylsilane-based matrix yielded a remarkable 10- to 12-fold enhancement in reactivity toward chlorocatechols. These gels also showed a fivefold increase in relative reactivity toward chlorocatechols with respect to the natural substrate catechol, thus compensating for their relatively low activity for these substrates in solution. The encapsulated enzyme, unlike the enzyme in solution, proved resilient in assays carried out in urban wastewater and bacteria-contaminated solutions mimicking environmentally relevant conditions. Overall, the combination of a structure-based rational design of enzyme mutants, and the selection of a suitable encapsulation material, proved to be a powerful approach for the production and optimization of a potential bioremediation device, with increased activity and resistance toward bacterial degradation.
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Sankaralingam M, Saravanan N, Anitha N, Suresh E, Palaniandavar M. Biomimetic iron(iii) complexes of facially and meridionally coordinating tridentate 3N ligands: tuning of regioselective extradiol dioxygenase activity in organized assemblies. Dalton Trans 2014; 43:6828-41. [DOI: 10.1039/c3dt52350k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bianchetti CM, Harmann CH, Takasuka TE, Hura GL, Dyer K, Fox BG. Fusion of dioxygenase and lignin-binding domains in a novel secreted enzyme from cellulolytic Streptomyces sp. SirexAA-E. J Biol Chem 2013; 288:18574-87. [PMID: 23653358 PMCID: PMC3689997 DOI: 10.1074/jbc.m113.475848] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/03/2013] [Indexed: 11/06/2022] Open
Abstract
Streptomyces sp. SirexAA-E is a highly cellulolytic bacterium isolated from an insect/microbe symbiotic community. When grown on lignin-containing biomass, it secretes SACTE_2871, an aromatic ring dioxygenase domain fused to a family 5/12 carbohydrate-binding module (CBM 5/12). Here we present structural and catalytic studies of this novel fusion enzyme, thus providing insight into its function. The dioxygenase domain has the core β-sandwich fold typical of this enzyme family but lacks a dimerization domain observed in other intradiol dioxygenases. Consequently, the x-ray structure shows that the enzyme is monomeric and the Fe(III)-containing active site is exposed to solvent in a shallow depression on a planar surface. Purified SACTE_2871 catalyzes the O2-dependent intradiol cleavage of catechyl compounds from lignin biosynthetic pathways, but not their methylated derivatives. Binding studies show that SACTE_2871 binds synthetic lignin polymers and chitin through the interactions of the CBM 5/12 domain, representing a new binding specificity for this fold-family. Based on its unique structural features and functional properties, we propose that SACTE_2871 contributes to the invasive nature of the insect/microbial community by destroying precursors needed by the plant for de novo lignin biosynthesis as part of its natural wounding response.
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Affiliation(s)
- Christopher M. Bianchetti
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706 and
| | - Connor H. Harmann
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706 and
| | - Taichi E. Takasuka
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706 and
| | - Gregory L. Hura
- the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kevin Dyer
- the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Brian G. Fox
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706 and
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Mesquita NCMR, Dyszy FH, Kumagai PS, Araújo APU, Costa-Filho AJ. Amphipatic molecules affect the kinetic profile of Pseudomonas putida chlorocatechol 1,2-dioxygenase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:655-60. [PMID: 23754625 DOI: 10.1007/s00249-013-0914-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/29/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
Abstract
Dioxygenases are nonheme iron enzymes that biodegrade recalcitrant compounds, such as catechol and derivatives, released into the environment by modern industry. Intradiol dioxygenases have attracted much attention due to the interest in their use for bioremediation, which has demanded efforts towards understanding their action mechanism and also how to control it. The role of unexpected amphipatic molecules, observed in crystal structures of intradiol dioxygenases, during catalysis has been poorly explored. We report results obtained with the intradiol enzyme chlorocatechol 1,2-dioxygenase (1,2-CCD) from Pseudomonas putida subjected to delipidation. The delipidated enzyme is more stable and shows more cooperative thermal denaturation. The kinetics changes from Michaelis-Menten to a cooperative scheme, indicating that conformational changes propagate between monomers in the absence of amphipatic molecules. Furthermore, these molecules inhibit catalysis, yielding lower v(max) values. To the best of our knowledge, this is the first report concerning the effects of amphipatic molecules on 1,2-CCD function.
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Affiliation(s)
- Nathalya C M R Mesquita
- Grupo de Biofísica Molecular Sérgio Mascarenhas, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, C.P. 369 São Carlos, SP 13560-970, Brazil
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Guzik U, Hupert-Kocurek K, Sitnik M, Wojcieszyńska D. High activity catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis,cis-muconic acid production. Antonie van Leeuwenhoek 2013; 103:1297-307. [PMID: 23536173 PMCID: PMC3656225 DOI: 10.1007/s10482-013-9910-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/22/2013] [Indexed: 10/31/2022]
Abstract
This is the first report of a catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 with high activity against catechol and its methyl derivatives. This enzyme was maximally active at pH 8.0 and 40 °C and the half-life of the enzyme at this temperature was 3 h. Kinetic studies showed that the value of K m and V max was 12.8 μM and 1,218.8 U/mg of protein, respectively. During our studies on kinetic properties of the catechol 1,2-dioxygenase we observed substrate inhibition at >80 μM. The nucleotide sequence of the gene encoding the S. maltophilia strain KB2 catechol 1,2-dioxygenase has high identity with other catA genes from members of the genus Pseudomonas. The deduced 314-residue sequence of the enzyme corresponds to a protein of molecular mass 34.5 kDa. This enzyme was inhibited by competitive inhibitors (phenol derivatives) only by ca. 30 %. High tolerance against condition changes is desirable in industrial processes. Our data suggest that this enzyme could be of use as a tool in production of cis,cis-muconic acid and its derivatives.
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Affiliation(s)
- Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland.
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Ferraroni M, Kolomytseva M, Scozzafava A, Golovleva L, Briganti F. X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: New perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity. J Struct Biol 2013; 181:274-82. [DOI: 10.1016/j.jsb.2012.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/28/2022]
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Dermauw W, Wybouw N, Rombauts S, Menten B, Vontas J, Grbić M, Clark RM, Feyereisen R, Van Leeuwen T. A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae. Proc Natl Acad Sci U S A 2013; 110:E113-22. [PMID: 23248300 PMCID: PMC3545796 DOI: 10.1073/pnas.1213214110] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants produce a wide range of allelochemicals to defend against herbivore attack, and generalist herbivores have evolved mechanisms to avoid, sequester, or detoxify a broad spectrum of natural defense compounds. Successful arthropod pests have also developed resistance to diverse classes of pesticides and this adaptation is of critical importance to agriculture. To test whether mechanisms to overcome plant defenses predispose the development of pesticide resistance, we examined adaptation of the generalist two-spotted spider mite, Tetranychus urticae, to host plant transfer and pesticides. T. urticae is an extreme polyphagous pest with more than 1,100 documented hosts and has an extraordinary ability to develop pesticide resistance. When mites from a pesticide-susceptible strain propagated on bean were adapted to a challenging host (tomato), transcriptional responses increased over time with ~7.5% of genes differentially expressed after five generations. Whereas many genes with altered expression belonged to known detoxification families (like P450 monooxygenases), new gene families not previously associated with detoxification in other herbivores showed a striking response, including ring-splitting dioxygenase genes acquired by horizontal gene transfer. Strikingly, transcriptional profiles of tomato-adapted mites resembled those of multipesticide-resistant strains, and adaptation to tomato decreased the susceptibility to unrelated pesticide classes. Our findings suggest key roles for both an expanded environmental response gene repertoire and transcriptional regulation in the life history of generalist herbivores. They also support a model whereby selection for the ability to mount a broad response to the diverse defense chemistry of plants predisposes the evolution of pesticide resistance in generalists.
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Affiliation(s)
- Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Nicky Wybouw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, B-9000 Ghent, Belgium
| | - John Vontas
- Faculty of Applied Biology and Biotechnology, Department of Biology, University of Crete, 71409 Heraklion, Greece
| | - Miodrag Grbić
- Department of Biology, University of Western Ontario, London N6A 5B7 ON, Canada
- Instituto de Ciencias de la Vid y del Vino Consejo Superior de Investigaciones Cientificas, Universidad de la Rioja, 26006 Logroño, Spain
| | - Richard M. Clark
- Department of Biology, University of Utah, Salt Lake City, UT 84112
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112; and
| | - René Feyereisen
- Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique and Université de Nice Sophia Antipolis, 06903 Sophia Antipolis, France
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
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An EPR, thermostability and pH-dependence study of wild-type and mutant forms of catechol 1,2-dioxygenase from Acinetobacter radioresistens S13. Biometals 2012; 26:75-84. [PMID: 23224984 DOI: 10.1007/s10534-012-9595-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
Intradiol dioxygenase are iron-containing enzymes involved in the bacterial degradation of natural and xenobiotic aromatic compounds. The wild-type and mutants forms of catechol 1,2-dioxygenase Iso B from Acinetobacter radioresistens LMG S13 have been investigated in order to get an insight on the structure-function relationships within this system. 4K CW-EPR spectroscopy highlighted different oxygen binding properties of some mutants with respect to the wild-type enzyme, suggesting that a fine tuning of the substrate-binding determinants in the active site pocket may indirectly result in variations of the iron reactivity. A thermostability investigation by optical spectroscopy, that reports on the state of the metal center, showed that the structural stability is more influenced by the type rather than by the position of the mutation. Finally, the influence of pH and temperature on the catalytic activity was monitored and discussed in terms of perturbations induced on the tertiary contact network of the enzyme.
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Roopesh K, Abhilash J, Haridas M, Sabu A, Isabelle PG, Roussos S, Augur C. Dioxygenase from Aspergillus fumigatusMC8: molecular modelling and in silicostudies on enzyme–substrate interactions. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.608672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Visvaganesan K, Ramachitra S, Palaniandavar M. Functional models for enzyme–substrate adducts of catechol dioxygenase enzymes: The Lewis basicity of facially coordinating tridentate phenolate ligands tunes the rate of dioxygenation and product selectivity. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Oliaro-Bosso S, Caron G, Taramino S, Ermondi G, Viola F, Balliano G. Characterization of the channel constriction allowing the access of the substrate to the active site of yeast oxidosqualene cyclase. PLoS One 2011; 6:e22134. [PMID: 21811565 PMCID: PMC3141018 DOI: 10.1371/journal.pone.0022134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 06/16/2011] [Indexed: 12/03/2022] Open
Abstract
In oxidosqualene cyclases (OSCs), an enzyme which has been extensively studied as a target for hypocholesterolemic or antifungal drugs, a lipophilic channel connects the surface of the protein with the active site cavity. Active site and channel are separated by a narrow constriction operating as a mobile gate for the substrate passage. In Saccharomyces cerevisiae OSC, two aminoacidic residues of the channel/constriction apparatus, Ala525 and Glu526, were previously showed as critical for maintaining the enzyme functionality. In this work sixteen novel mutants, each bearing a substitution at or around the channel constrictions, were tested for their enzymatic activity. Modelling studies showed that the most functionality-lowering substitutions deeply alter the H-bond network involving the channel/constriction apparatus. A rotation of Tyr239 is proposed as part of the mechanism permitting the access of the substrate to the active site. The inhibition of OSC by squalene was used as a tool for understanding whether the residues under study are involved in a pre-catalytic selection and docking of the substrate oxidosqualene.
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Affiliation(s)
- Simonetta Oliaro-Bosso
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
| | - Giulia Caron
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
| | - Silvia Taramino
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
| | - Giuseppe Ermondi
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
| | - Franca Viola
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
| | - Gianni Balliano
- Dipartimento di Scienza e Tecnologia del Farmaco, Facoltà di Farmacia, Università degli Studi di Torino, Turin, Italy
- * E-mail:
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PALANIANDAVAR MALLAYAN, VISVAGANESAN KUSALENDIRAN. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of N-alkyl substitution on regioselectivity and reaction rate. J CHEM SCI 2011. [DOI: 10.1007/s12039-011-0110-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Wójcik A, Borowski T, Broclawik E. The mechanism of the reaction of intradiol dioxygenase with hydroperoxy probe. Catal Today 2011. [DOI: 10.1016/j.cattod.2010.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Moreno MDL, Sánchez-Porro C, Piubeli F, Frias L, García MT, Mellado E. Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans. PLoS One 2011; 6:e21049. [PMID: 21695219 PMCID: PMC3112211 DOI: 10.1371/journal.pone.0021049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/18/2011] [Indexed: 11/28/2022] Open
Abstract
Background Extensive use of phenolic compounds in industry has resulted in the generation of saline wastewaters that produce significant environmental contamination; however, little information is available on the degradation of phenolic compounds in saline conditions. Halomonas organivorans G-16.1 (CECT 5995T) is a moderately halophilic bacterium that we isolated in a previous work from saline environments of South Spain by enrichment for growth in different pollutants, including phenolic compounds. PCR amplification with degenerate primers revealed the presence of genes encoding ring-cleaving enzymes of the β-ketoadipate pathway for aromatic catabolism in H. organivorans. Findings The gene cluster catRBCA, involved in catechol degradation, was isolated from H. organivorans. The genes catA, catB, catC and the divergently transcribed catR code for catechol 1,2-dioxygenase (1,2-CTD), cis,cis-muconate cycloisomerase, muconolactone delta-isomerase and a LysR-type transcriptional regulator, respectively. The benzoate catabolic genes (benA and benB) are located flanking the cat genes. The expression of cat and ben genes by phenol and benzoic acid was shown by RT-PCR analysis. The induction of catA gene by phenol and benzoic acid was also probed by the measurement of 1,2-CTD activity in H. organivorans growth in presence of these inducers. 16S rRNA and catA gene-based phylogenies were established among different degrading bacteria showing no phylogenetic correlation between both genes. Conclusions/Significance In this work, we isolated and determined the sequence of a gene cluster from a moderately halophilic bacterium encoding ortho-pathway genes involved in the catabolic metabolism of phenol and analyzed the gene organization, constituting the first report characterizing catabolic genes involved in the degradation of phenol in moderate halophiles, providing an ideal model system to investigate the potential use of this group of extremophiles in the decontamination of saline environments.
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Affiliation(s)
| | | | - Francine Piubeli
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - Luciana Frias
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - María Teresa García
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
| | - Encarnación Mellado
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
- * E-mail:
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Rustiguel JK, Pinheiro MP, Araújo APU, Nonato MC. Crystallization and preliminary X-ray diffraction analysis of recombinant chlorocatechol 1,2-dioxygenase from Pseudomonas putida. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:507-9. [PMID: 21505253 PMCID: PMC3080162 DOI: 10.1107/s174430911100635x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 02/19/2011] [Indexed: 11/10/2022]
Abstract
Chlorocatechol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida (Pp 1,2-CCD) is considered to be an important biotechnological tool owing to its ability to process a broad spectrum of organic pollutants. In the current work, the crystallization, crystallographic characterization and phasing of the recombinant Pp 1,2-CCD enzyme are described. Reddish-brown crystals were obtained in the presence of polyethylene glycol and magnesium acetate by utilizing the vapour-diffusion technique in sitting drops. Crystal dehydration was the key step in obtaining data sets, which were collected on the D03B-MX2 beamline at the CNPEM/MCT - LNLS using a MAR CCD detector. Pp 1,2-CCD crystals belonged to space group P6(1)22 and the crystallographic structure of Pp 1,2-CCD has been solved by the MR-SAD technique using Fe atoms as scattering centres and the coordinates of 3-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus (PDB entry 2boy) as the search model. The initial model, which contains three molecules in the asymmetric unit, has been refined to 3.4 Å resolution.
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Affiliation(s)
- Joane Kathelen Rustiguel
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Matheus Pinto Pinheiro
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Ana Paula Ulian Araújo
- Grupo de Biofísica Molecular, Instituto de Física de São Carlos – USP, Avenida do Trabalhador Sãocarlense, São Carlos, 13560-970 São Paulo, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
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Anitha N, Palaniandavar M. Mononuclear iron(iii) complexes of 3N ligands in organized assemblies: spectral and redox properties and attainment of regioselective extradiol dioxygenase activity. Dalton Trans 2011; 40:1888-901. [DOI: 10.1039/c0dt01012j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Sundaravel K, Suresh E, Saminathan K, Palaniandavar M. Iron(III) complexes of N2O and N3O donor ligands as functional models for catechol dioxygenase enzymes: ether oxygen coordination tunes the regioselectivity and reactivity. Dalton Trans 2011; 40:8092-107. [DOI: 10.1039/c0dt01598a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Karuppasamy Sundaravel
- Centre for Bioinorganic Chemistry, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India
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Singh R, Banerjee A, Rajak KK. Iron(III) complexes using NNS reduced Schiff bases and NNOS coordinating tetradentate ligands: Synthesis, structure and catecholase activity. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.05.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Micalella C, Martignon S, Bruno S, Pioselli B, Caglio R, Valetti F, Pessione E, Giunta C, Rizzi M. X-ray crystallography, mass spectrometry and single crystal microspectrophotometry: a multidisciplinary characterization of catechol 1,2 dioxygenase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:817-23. [PMID: 20869471 DOI: 10.1016/j.bbapap.2010.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/06/2010] [Accepted: 09/09/2010] [Indexed: 10/19/2022]
Abstract
Intradiol-cleaving catechol 1,2 dioxygenases are Fe(III) dependent enzymes that act on catechol and substituted catechols, including chlorocatechols pollutants, by inserting molecular oxygen in the aromatic ring. Members of this class are the object of intense biochemical investigations aimed at the understanding of their catalytic mechanism, particularly for designing mutants with selected catalytic properties. We report here an in depth investigation of catechol 1,2 dioxygenase IsoB from Acinetobacter radioresistens LMG S13 and its A72G and L69A mutants. By applying a multidisciplinary approach that includes high resolution X-rays crystallography, mass spectrometry and single crystal microspectrophotometry, we characterised the phospholipid bound to the enzyme and provided a structural framework to understand the inversion of substrate specificity showed by the mutants. Our results might be of help for the rational design of enzyme mutants showing a biotechnologically relevant substrate specificity, particularly to be used in bioremediation. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Chiara Micalella
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP. Usberti 23/A, 43100 Parma, Italy
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Melo FA, Araújo AP, Costa-Filho AJ. Role of cis–cis muconic acid in the catalysis of Pseudomonas putida chlorocatechol 1,2-dioxygenase. Int J Biol Macromol 2010; 47:233-7. [DOI: 10.1016/j.ijbiomac.2010.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/22/2010] [Accepted: 04/23/2010] [Indexed: 11/15/2022]
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Experimental and theoretical affinity studies of substituted phenols to chlorocatechol 1,2-dioxygenases: A step toward the comprehension of inhibitor/substrate binding to intradiol dioxygenases. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Matera I, Ferraroni M, Kolomytseva M, Golovleva L, Scozzafava A, Briganti F. Catechol 1,2-dioxygenase from the Gram-positive Rhodococcus opacus 1CP: Quantitative structure/activity relationship and the crystal structures of native enzyme and catechols adducts. J Struct Biol 2010; 170:548-64. [DOI: 10.1016/j.jsb.2009.12.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 12/23/2009] [Indexed: 11/25/2022]
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El Azhari N, Devers-Lamrani M, Chatagnier G, Rouard N, Martin-Laurent F. Molecular analysis of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHs. JOURNAL OF HAZARDOUS MATERIALS 2010; 177:593-601. [PMID: 20096999 DOI: 10.1016/j.jhazmat.2009.12.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 12/15/2009] [Accepted: 12/17/2009] [Indexed: 05/28/2023]
Abstract
A PCR-based molecular tool was developed to estimate the diversity of the catechol-degrading bacterial community in a coal wasteland heavily contaminated with PAHS. A degenerate primer pair specific to catA sequences was designed by multiple alignment of known sequences coding a key intermediate of the beta-ketoadiapate pathway degrading catechol, namely catechol 1,2-dioxygenase. The specificity of this primer pair was assessed in 21 pure strains by PCR and sequencing. Comparison of the 16S rDNA and catA phylogenies revealed an absence of congruence between these two genes. The primer set was able to amplify catA sequences in DNA extracts from an industrial soil highly contaminated with heavy metals and polycyclic aromatic hydrocarbons (PAHs). RFLP screening of the catA library (95 clones) yielded 32 RFLP families. All of the 43 clone sequences obtained exhibited 86% identity on average to known CatA. Phylogenetic analysis revealed that these CatA sequences were related to Actinobacteria, alpha-, beta- and gamma-Proteobacteria phyla and confirmed the absence of congruence with 16S rDNA sequences, which implies horizontal gene transfer of the cat gene cluster between soil microbiota. Our results suggest that the diversity of the catA bacterial community is maintained in highly contaminated soil.
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Affiliation(s)
- Najoi El Azhari
- INRA/Université de Bourgogne, Soil and Environmental Microbiology, 17 rue sully, BP 86510, 21065 Dijon Cedex, France.
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