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Zhang X, Huang Z, Wang D, Zhang Y, Eser BE, Gu Z, Dai R, Gao R, Guo Z. A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126860. [PMID: 34399224 DOI: 10.1016/j.jhazmat.2021.126860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/22/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Extradiol dioxygenases (EDOs) catalyze the meta cleavage of catechol into 2-hydroxymuconaldehyde, a critical step in the degradation of aromatic compounds in the environment. In the present work, a novel thermophilic extradiol dioxygenase from Thermomonospora curvata DSM43183 was cloned, expressed, and characterized by phylogenetic and biochemical analyses. This enzyme exhibited excellent thermo-tolerance, displaying optimal activity at 50 °C, remaining >40% activity at 70 °C. Structural modeling and molecular docking demonstrated that both active center and pocket-construction loops locate at the C-terminal domain. Site-specific mutants D285A, H205V, F301V based on a rational design were obtained to widen the entrance of substrates; resulting in significantly improved catalytic performance for all the 3 mutants. Compared to the wild-type, the mutant D285A showed remarkably improved activities with respect to the 3,4-dihydroxyphenylacetic acid, catechol, and 3-chlorocatechol, by 17.7, 6.9, and 3.7-fold, respectively. The results thus verified the effectiveness of modeling guided design; and confirmed that the C-terminal loop structure indeed plays a decisive role in determining catalytic ring-opening efficiency and substrate specificity of the enzyme. This study provided a novel thermostable dioxygenase with a broad substrate promiscuity for detoxifying environmental pollutants and provided a new thinking for further enzyme engineering of EDOs.
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Affiliation(s)
- Xiaowen Zhang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China; Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Dan Wang
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Yan Zhang
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China
| | - Rongrong Dai
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of life Science, Jilin University, Changchun 130021, China.
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
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2
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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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Vignali E, Pollegioni L, Di Nardo G, Valetti F, Gazzola S, Gilardi G, Rosini E. Multi‐Enzymatic Cascade Reactions for the Synthesis of
cis,cis
‐Muconic Acid. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Elisa Vignali
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Silvia Gazzola
- Department of Science and High Technology University of Insubria Via Valleggio 9 22100 Como Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology University of Turin Via Accademia Albertina 13 10123 Torino Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences University of Insubria Via J. H. Dunant 3 21100 Varese Italy
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4
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Li J, Li Z, Cao M, Liu J. Expression and characterization of catechol 1,2-dioxygenase from Oceanimonas marisflavi 102-Na3. Protein Expr Purif 2021; 188:105964. [PMID: 34454050 DOI: 10.1016/j.pep.2021.105964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/11/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
The gene of catechol 1, 2-dioxygenase was identified and cloned from the genome of Oceanimonas marisflavi 102-Na3. The protein was expressed in Escherichia coli BL21 (DE3) and purified to homogeneity of a dimer with molecular mass of 69.2 kDa. The enzyme was highly stable in pH 6.0-9.5 and below 45 °C and exhibited the maximum activity at pH 8.0 and 30 °C. Being the first characterized intradiol dioxygenase from marine bacteria Oceanimonas sp., the enzyme showed catalytic activity for catechol, 3-methylcatechol, 4-methylcatechol, 3-chlorocatechol, 4-chlorocatechol and pyrogallol. For catechol, Km and Vmax were 11.2 μM and 13.4 U/mg of protein, respectively. The enzyme also showed resistance to most of the metal ions, surfactants and organic solvents, being a promising biocatalyst for biodegradation of aromatic compounds in complex environments.
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Affiliation(s)
- Jing Li
- Centre for Bioengineering & Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Ziyi Li
- Centre for Bioengineering & Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Meiwen Cao
- Centre for Bioengineering & Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China.
| | - Jianguo Liu
- Centre for Bioengineering & Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, PR China.
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5
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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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6
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Schlachter CR, Daneshian L, Amaya J, Klapper V, Wybouw N, Borowski T, Van Leeuwen T, Grbic V, Grbic M, Makris TM, Chruszcz M. Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 107:19-30. [PMID: 30529144 PMCID: PMC6768081 DOI: 10.1016/j.ibmb.2018.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/20/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Genome analyses of the polyphagous spider mite herbivore Tetranychus urticae (two-spotted spider mite) revealed the presence of a set of 17 genes that code for secreted proteins belonging to the "intradiol dioxygenase-like" subgroup. Phylogenetic analyses indicate that this novel enzyme family has been acquired by horizontal gene transfer. In order to better understand the role of these proteins in T. urticae, we have structurally and functionally characterized one paralog (tetur07g02040). It was demonstrated that this protein is indeed an intradiol ring-cleavage dioxygenase, as the enzyme is able to cleave catechol between two hydroxyl-groups using atmospheric dioxygen. The enzyme was characterized functionally and structurally. The active site of the T. urticae enzyme contains an Fe3+ cofactor that is coordinated by two histidine and two tyrosine residues, an arrangement that is similar to those observed in bacterial homologs. However, the active site is significantly more solvent exposed than in bacterial proteins. Moreover, the mite enzyme is monomeric, while almost all structurally characterized bacterial homologs form oligomeric assemblies. Tetur07g02040 is not only the first spider mite dioxygenase that has been characterized at the molecular level, but is also the first structurally characterized intradiol ring-cleavage dioxygenase originating from a eukaryote.
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Affiliation(s)
- Caleb R Schlachter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Jose Amaya
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Vincent Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Nicky Wybouw
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands; Department of Plants and Crops, Ghent University, Ghent, B-9000, Belgium
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Krakow, Poland
| | - Thomas Van Leeuwen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands; Department of Plants and Crops, Ghent University, Ghent, B-9000, Belgium
| | - Vojislava Grbic
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada; University of La Rioja, Logrono, Spain
| | - Miodrag Grbic
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada; University of La Rioja, Logrono, Spain
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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7
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Kim JY, Yoo HW, Lee PG, Lee SG, Seo JH, Kim BG. In vivo Protein Evolution, Next Generation Protein Engineering Strategy: from Random Approach to Target-specific Approach. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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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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9
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Barry KP, Cohn EF, Ngu A, Taylor EA. Improving alternate lignin catabolite utilization of LigAB from Sphingobium sp. strain SYK-6 through site directed mutagenesis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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10
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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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11
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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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12
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Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
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13
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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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14
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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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15
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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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Dror A, Fishman A. Engineering non-heme mono- and dioxygenases for biocatalysis. Comput Struct Biotechnol J 2012; 2:e201209011. [PMID: 24688652 PMCID: PMC3962191 DOI: 10.5936/csbj.201209011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022] Open
Abstract
Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.
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Affiliation(s)
- Adi Dror
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 78:8421-30. [PMID: 23001678 DOI: 10.1128/aem.01983-12] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adipic acid is a high-value compound used primarily as a precursor for the synthesis of nylon, coatings, and plastics. Today it is produced mainly in chemical processes from petrochemicals like benzene. Because of the strong environmental impact of the production processes and the dependence on fossil resources, biotechnological production processes would provide an interesting alternative. Here we describe the first engineered Saccharomyces cerevisiae strain expressing a heterologous biosynthetic pathway converting the intermediate 3-dehydroshikimate of the aromatic amino acid biosynthesis pathway via protocatechuic acid and catechol into cis,cis-muconic acid, which can be chemically dehydrogenated to adipic acid. The pathway consists of three heterologous microbial enzymes, 3-dehydroshikimate dehydratase, protocatechuic acid decarboxylase composed of three different subunits, and catechol 1,2-dioxygenase. For each heterologous reaction step, we analyzed several potential candidates for their expression and activity in yeast to compose a functional cis,cis-muconic acid synthesis pathway. Carbon flow into the heterologous pathway was optimized by increasing the flux through selected steps of the common aromatic amino acid biosynthesis pathway and by blocking the conversion of 3-dehydroshikimate into shikimate. The recombinant yeast cells finally produced about 1.56 mg/liter cis,cis-muconic acid.
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Siloto RM, Weselake RJ. Site saturation mutagenesis: Methods and applications in protein engineering. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Park ES, Shin JS. Free energy analysis of ω-transaminase reactions to dissect how the enzyme controls the substrate selectivity. Enzyme Microb Technol 2011; 49:380-7. [DOI: 10.1016/j.enzmictec.2011.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 05/18/2011] [Accepted: 06/23/2011] [Indexed: 11/25/2022]
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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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Jochens H, Bornscheuer UT. Natural Diversity to Guide Focused Directed Evolution. Chembiochem 2010; 11:1861-6. [DOI: 10.1002/cbic.201000284] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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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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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