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Li S, He L, Shi N, Chen Y, Saeed M, Ni Z, Chen H. Preparing the pure lignin peroxidase and exploring the effects of chemicals on the activity. Prep Biochem Biotechnol 2024; 54:660-667. [PMID: 37843104 DOI: 10.1080/10826068.2023.2268181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Heterogous expression of lignin peroxidase (LiP) from Phanerochaete chrysosporium was performed in by E. coli prokaryotic expression system, and pure LiP was prepared by washing, refolding, and purification. The enzyme activity was measured by the resveratrol oxidation method. The effects of different chemicals on LiP activity were explored by adding different kinds of metal ions, acids/phenols, and surfactants. The optimal pH and temperature are 4.2 and 40 °C. The single-factor screening experiment showed that adding 1 mM Mn2+, 0.1 mM DL-lactic acid, and 2% PEG-4000 had the best promotion effect on the enzyme activity of recombinant LiP, which was 160.61%, 188.46%, and 247.83%, respectively. Further, the synergistic addition of Mn2+ and PEG-4000 achieved the best enzyme activity promotion effect of 277.51%. In addition, the addition of DL-lactic acid alone could promote LiP activity. However, the co-addition of lactic acid with Mn2+ and PEG-4000 contributed only 247.87%, which indicated that the addition of DL-lactic acid had an inhibitory effect when applied synergistically. For the first time, it was found that PEG-4000 increased LiP enzyme activity obviously and had a synergistic effect with Mn2+, serving as a reference for LiP in studies and applications pertaining to lignin breakdown.
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Affiliation(s)
- Shouzhi Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lu He
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Na Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yanzhen Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Muhammad Saeed
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Huayou Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Lim SH, Jang H, Kim MJ, Wee KR, Lim DH, Kim YI, Cho DW. Visible-Light-Induced Selective C–C Bond Cleavage Reactions of Dimeric β-O-4 and β-1 Lignin Model Substrates Utilizing Amine-Functionalized Fullerene. J Org Chem 2022; 87:2289-2300. [DOI: 10.1021/acs.joc.1c01991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suk Hyun Lim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Hannara Jang
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Min-Ji Kim
- Department of Chemistry and Institute of Natural Science, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Kyung-Ryang Wee
- Department of Chemistry and Institute of Natural Science, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Dong Hyun Lim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Young-Il Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Dae Won Cho
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
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Calderaro F, Bevers LE, van den Berg MA. Oxidative Power: Tools for Assessing LPMO Activity on Cellulose. Biomolecules 2021; 11:biom11081098. [PMID: 34439765 PMCID: PMC8391687 DOI: 10.3390/biom11081098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cellulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have been elucidated, the need for fast and reliable methods to assess its activity have become clear. Several aspects such as its co-substrates, electron donors, inhibiting factors, and the inhomogeneity of lignocellulose had to be considered during experimental design and data interpretation, as they can impact and often hamper outcomes. This review provides an overview of the currently available methods to measure LPMO activity, including their potential and limitations, and it is illustrated with practical examples.
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Affiliation(s)
- Federica Calderaro
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
- Molecular Enzymolog y Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Correspondence: ; Tel.: +31-6-36028569
| | - Loes E. Bevers
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
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Singh AK, Bilal M, Iqbal HMN, Raj A. Lignin peroxidase in focus for catalytic elimination of contaminants - A critical review on recent progress and perspectives. Int J Biol Macromol 2021; 177:58-82. [PMID: 33577817 DOI: 10.1016/j.ijbiomac.2021.02.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/05/2023]
Abstract
Lignin peroxidase (LiP) seems to be a catalyst for cleaving high-redox potential non-phenolic compounds with an oxidative cleavage of CC and COC bonds. LiP has been picked to seek a practical and cost-effective alternative to the sustainable mitigation of diverse environmental contaminants. LiP has been an outstanding tool for catalytic cleaning and efficient mitigation of environmental pollutants, including lignin, lignin derivatives, dyes, endocrine-disrupting compounds (EDCs), and persistent organic pollutants (POPs) for the past couple of decades. The extended deployment of LiP has proved to be a promising method for catalyzing these environmentally related hazardous pollutants of supreme interest. The advantageous potential and capabilities to act at different pH and thermostability offer its working tendencies in extended environmental engineering applications. Such advantages led to the emerging demand for LiP and increasing requirements in industrial and biotechnological sectors. The multitude of the ability attributed to LiP is triggered by its stability in xenobiotic and non-phenolic compound degradation. However, over the decades, the catalytic activity of LiP has been continuing in focus enormously towards catalytic functionalities over the available physiochemical, conventional, catalyst mediated technology for catalyzing such molecules. To cover this literature gap, this became much more evident to consider the catalytic attributes of LiP. In this review, the existing capabilities of LiP and other competencies have been described with recent updates. Furthermore, numerous recently emerged applications, such as textile effluent treatment, dye decolorization, catalytic elimination of pharmaceutical and EDCs compounds, have been discussed with suitable examples.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Functional Redundancy in the Hydroxycinnamate Catabolism Pathways of the Salt Marsh Bacterium Sagittula stellata E-37. Appl Environ Microbiol 2018; 84:AEM.02027-18. [PMID: 30242006 DOI: 10.1128/aem.02027-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/18/2018] [Indexed: 11/20/2022] Open
Abstract
The hydroxycinnamates (HCAs) ferulate and p-coumarate are among the most abundant constituents of lignin, and their degradation by bacteria is an essential step in the remineralization of vascular plant material. Here, we investigate the catabolism of these two HCAs by the marine bacterium Sagittula stellata E-37, a member of the roseobacter lineage with lignolytic potential. Bacterial degradation of HCAs is often initiated by the activity of a hydroxycinnamoyl-coenzyme A (hydroxycinnamoyl-CoA) synthase. Genome analysis of S. stellata revealed the presence of two feruloyl-CoA (fcs) synthase homologs, an unusual occurrence among characterized HCA degraders. In order to elucidate the role of these homologs in HCA catabolism, fcs-1 and fcs-2 were disrupted using insertional mutagenesis, yielding both single and double fcs mutants. Growth on p-coumarate was abolished in the fcs double mutant, whereas maximum cell yield on ferulate was only 2% of that of the wild type. Interestingly, the single mutants demonstrated opposing phenotypes, where the fcs-1 mutant showed impaired growth (extended lag and ∼60% of wild-type rate) on p-coumarate, and the fcs-2 mutant showed impaired growth (extended lag and ∼20% of wild-type rate) on ferulate, pointing to distinct but overlapping roles of the encoded fcs homologs, with fcs-1 primarily dedicated to p-coumarate utilization and fcs-2 playing a dominant role in ferulate utilization. Finally, a tripartite ATP-independent periplasmic (TRAP) family transporter was found to be required for growth on both HCAs. These findings provide evidence for functional redundancy in the degradation of HCAs in S. stellata E-37 and offer important insight into the genetic complexity of aromatic compound degradation in bacteria.IMPORTANCE Hydroxycinnamates (HCAs) are essential components of lignin and are involved in various plant functions, including defense. In nature, microbial degradation of HCAs is influential to global carbon cycling. HCA degradation pathways are also of industrial relevance, as microbial transformation of the HCA, ferulate, can generate vanillin, a valuable flavoring compound. Yet, surprisingly little is known of the genetics underlying bacterial HCA degradation. Here, we make comparisons to previously characterized bacterial HCA degraders and use a genetic approach to characterize genes involved in catabolism and uptake of HCAs in the environmentally relevant marine bacterium Sagittula stellata We provide evidence of overlapping substrate specificity between HCA degradation pathways and uptake proteins. We conclude that S. stellata is uniquely poised to utilize HCAs found in the complex mixtures of plant-derived compounds in nature. This strategy may be common among marine bacteria residing in lignin-rich coastal waters and has potential relevance to biotechnology sectors.
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Abstract
Fungi are among the microorganisms able to generate electricity as a result of their metabolic processes. Throughout the last several years, a large number of papers on various microorganisms for current production in microbial fuel cells (MFCs) have been published; however, fungi still lack sufficient evaluation in this regard. In this review, we focus on fungi, paying special attention to their potential applicability to MFCs. Fungi used as anodic or cathodic catalysts, in different reactor configurations, with or without the addition of an exogenous mediator, are described. Contrary to bacteria, in which the mechanism of electron transfer is pretty well known, the mechanism of electron transfer in fungi-based MFCs has not been studied intensively. Thus, here we describe the main findings, which can be used as the starting point for future investigations. We show that fungi have the potential to act as electrogens or cathode catalysts, but MFCs based on bacteria–fungus interactions are especially interesting. The review presents the current state-of-the-art in the field of MFC systems exploiting fungi.
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Houtman CJ, Maligaspe E, Hunt CG, Fernández-Fueyo E, Martínez AT, Hammel KE. Fungal lignin peroxidase does not produce the veratryl alcohol cation radical as a diffusible ligninolytic oxidant. J Biol Chem 2018; 293:4702-4712. [PMID: 29462790 DOI: 10.1074/jbc.ra117.001153] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Indexed: 11/06/2022] Open
Abstract
Peroxidases are considered essential agents of lignin degradation by white-rot basidiomycetes. However, low-molecular-weight oxidants likely have a primary role in lignin breakdown because many of these fungi delignify wood before its porosity has sufficiently increased for enzymes to infiltrate. It has been proposed that lignin peroxidases (LPs, EC 1.11.1.14) fulfill this role by oxidizing the secreted fungal metabolite veratryl alcohol (VA) to its aryl cation radical (VA+•), releasing it to act as a one-electron lignin oxidant within woody plant cell walls. Here, we attached the fluorescent oxidant sensor BODIPY 581/591 throughout beads with a nominal porosity of 6 kDa and assessed whether peroxidase-generated aryl cation radical systems could oxidize the beads. As positive control, we used the 1,2,4,5-tetramethoxybenzene (TMB) cation radical, generated from TMB by horseradish peroxidase. This control oxidized the beads to depths that increased with the amount of oxidant supplied, ultimately resulting in completely oxidized beads. A reaction-diffusion computer model yielded oxidation profiles that were within the 95% confidence intervals for the data. By contrast, bead oxidation caused by VA and the LPA isozyme of Phanerochaete chrysosporium was confined to a shallow shell of LP-accessible volume at the bead surface, regardless of how much oxidant was supplied. This finding contrasted with the modeling results, which showed that if the LP/VA system were to release VA+•, it would oxidize the bead interiors. We conclude that LPA releases insignificant quantities of VA+• and that a different mechanism produces small ligninolytic oxidants during white rot.
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Affiliation(s)
- Carl J Houtman
- United States Forest Products Laboratory, Madison, Wisconsin 53726
| | - Eranda Maligaspe
- United States Forest Products Laboratory, Madison, Wisconsin 53726
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Kenneth E Hammel
- United States Forest Products Laboratory, Madison, Wisconsin 53726; Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706.
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Abstract
The global push toward an efficient and economical biobased economy has driven research to develop more cost-effective applications for the entirety of plant biomass, including lignocellulosic crops. As discussed elsewhere (Karlsson M, Atanasova L, Funck Jensen D, Zeilinger S, in Heitman J et al. [ed], Tuberculosis and the Tubercle Bacillus, 2nd ed, in press), significant progress has been made in the use of polysaccharide fractions from lignocellulose, cellulose, and various hemicellulose types. However, developing processes for use of the lignin fraction has been more challenging. In this chapter, we discuss characteristics of lignolytic enzymes and the fungi that produce them as well as potential and current uses of lignin-derived products.
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Khatoon N, Jamal A, Ali MI. Polymeric pollutant biodegradation through microbial oxidoreductase: A better strategy to safe environment. Int J Biol Macromol 2017. [PMID: 28648638 DOI: 10.1016/j.ijbiomac.2017.06.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The detoxification of xenobiotic organic compounds by various microorganisms through oxidative coupling is facilitated with oxidoreductases. With the help of energy yielding biochemical reactions, these microbes extract energy for their metabolic pathway. They promote the transfer of electrons from a reduced organic substrate to another chemical compound. During such oxidation-reduction reactions, the toxic polymeric substance is finally oxidized into harmless compounds. Enzymatic bioremediation of toxic organic pollutant is a very effective strategy in complex environmental conditions. Oxidoreductases enzymes have a significant potential for the bioremediation of the xenobiotic compounds. Various electron donor complex polymeric substrates containing Phenol and aromatic amines are oxidized by peroxidase in the presence of H2O2 while O2 in the case of dioxygenase. This review attempts to present relevant information on the peroxidases and dioxygenase from various microbial isolates involved in the biodegradation of a wide range of pollutants.
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Affiliation(s)
- Nazia Khatoon
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Asif Jamal
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ishtiaq Ali
- Environmental Microbiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Castro L, Crawford LE, Mutengwa A, Götze JP, Bühl M. Insights into structure and redox potential of lignin peroxidase from QM/MM calculations. Org Biomol Chem 2016; 14:2385-2389. [PMID: 26815633 DOI: 10.1039/c6ob00037a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Redox potentials are computed for the active form (compound I) of lignin peroxidase (LiP) using a suitable QM/MM methodology (B3LYP/SDD/6-311G**//BP86/SVP:CHARMM). Allowing for dynamic conformational averaging, a potential of 0.67(33) V relative to ferrocenium/ferrocene is obtained for the active form with its oxoiron(iv) core. The computed redox potential is very sensitive to the charge distribution around the active site: protonation of titratable residues close to the metal center increases the redox potential, thereby rationalising the known pH dependence of LiP activity. A simple MM-charge deletion scheme is used to identify residues that are critical for the redox potential. Two mutant proteins are studied through homology modelling, E40Q and D183N, which are predicted to have an increased redox potential by 140 mV and 190 mV, respectively, relative to the wild type. These mutant proteins are thus promising targets for synthesis and further exploration toward a rational design of biocatalytic systems for oxidative degradation of lignin.
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Affiliation(s)
- Ludovic Castro
- EastChem School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | - L Ellis Crawford
- EastChem School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | - Archford Mutengwa
- EastChem School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | - Jan P Götze
- EastChem School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | - Michael Bühl
- EastChem School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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dos Santos TC, de Brito AR, Bonomo RCF, Pires AJV, Aguiar-Oliveira E, Silva TP, Franco M. Statistical Optimization of Culture Conditions and Characterization for Ligninolytic Enzymes Produced fromRhizopusSp. Using Prickly Palm Cactus Husk. CHEM ENG COMMUN 2016. [DOI: 10.1080/00986445.2016.1230851] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Tay T, Köse E, Keçili R, Say R. Design and Preparation of Nano-Lignin Peroxidase (NanoLiP) by Protein Block Copolymerization Approach. Polymers (Basel) 2016; 8:polym8060223. [PMID: 30979315 PMCID: PMC6432496 DOI: 10.3390/polym8060223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/09/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022] Open
Abstract
This study describes the preparation of nanoprotein particles having lignin peroxidase (LiP) using a photosensitive microemulsion polymerization technique. The protein-based nano block polymer was synthesized by cross-linking of ligninase enzyme with ruthenium-based aminoacid monomers. This type polymerization process brought stability in different reaction conditions, reusability and functionality to the protein-based nano block polymer system when compared the traditional methods. After characterization of the prepared LiP copolymer nanoparticles, enzymatic activity studies of the nanoenzymes were carried out using tetramethylbenzidine (TMB) as the substrate. The parameters such as pH, temperature and initial enzyme concentration that affect the activity, were investigated by using prepared nanoLip particles and compared to free LiP. The reusability of the nano-LiP particles was also investigated and the obtained results showed that the nano-LiP particles exhibited admirable potential as a reusable catalyst.
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Affiliation(s)
- Turgay Tay
- Department of Chemistry, Anadolu University, 26470 Eskisehir, Turkey.
| | - Ender Köse
- Karen Biotechnol Ltd., Anadolu University, Technol Pk, 26470 Eskisehir, Turkey.
| | - Rüstem Keçili
- Yunus Emre Vocational School, Department of Medical Services and Techniques, Anadolu University, 26470 Eskisehir, Turkey.
| | - Rıdvan Say
- Department of Chemistry, Anadolu University, 26470 Eskisehir, Turkey.
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Characterization of lignin-degrading enzymes (LDEs) from a dimorphic novel fungus and identification of products of enzymatic breakdown of lignin. 3 Biotech 2016; 6:56. [PMID: 28330126 PMCID: PMC4752945 DOI: 10.1007/s13205-016-0384-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/20/2015] [Indexed: 11/07/2022] Open
Abstract
Lignin is a major component of all plants, the degradation of which remains a major challenge to date owing to its recalcitrant nature. Several classes of fungi have been studied to carry out this process to some extent, but overall the process remains inefficient. We have isolated a novel alkalophilic dimorphic lignin-degrading Deuteromycete from soil, identified as “uncultured” and coded as MVI.2011. Supernatant from 12-h culture of MVI.2011 in optimized mineral medium containing lignin pH 9.0 was analysed for Lignin Peroxidase, Manganese Peroxidase and Laccase. Enzyme purification was carried out by standard protocols using ammonium sulphate precipitation followed by further purification by Gel Permeation Chromatography. Analysis of total protein, specific enzyme activity and molecular weight of the GPC-purified LiP, MnP and Laccase showed 93.83 μg/ml, 5.27 U/mg, 42 kDa; 78.13 μg/ml, 13.18 U/mg, 45 kDa and 85.81 μg/ml, 4.77 U/mg, 62 kDa, respectively. The purified enzymes possessed high activity over a wide range of pH (4–11), and temperature (30–55 °C). The optimum substrate concentration was 20 μg/ml of lignin for all the three enzymes. CD spectra suggested that the predominant secondary structure was helix in LiP, and, turns in MnP and Laccase. The breakdown products of lignin degradation by MVI.2011 and the three purified enzymes were detected and identified by FTIR and GC–MS. They were oxalic acid, hentriacontane, derivatives of octadecane, nonane, etc. These vital compounds are certain to find application as biofuels, an alternate energy source in various industries.
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Abdel-Hamid AM, Solbiati JO, Cann IKO. Insights into lignin degradation and its potential industrial applications. ADVANCES IN APPLIED MICROBIOLOGY 2016; 82:1-28. [PMID: 23415151 DOI: 10.1016/b978-0-12-407679-2.00001-6] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lignocellulose is an abundant biomass that provides an alternative source for the production of renewable fuels and chemicals. The depolymerization of the carbohydrate polymers in lignocellulosic biomass is hindered by lignin, which is recalcitrant to chemical and biological degradation due to its complex chemical structure and linkage heterogeneity. The role of fungi in delignification due to the production of extracellular oxidative enzymes has been studied more extensively than that of bacteria. The two major groups of enzymes that are involved in lignin degradation are heme peroxidases and laccases. Lignin-degrading peroxidases include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). LiP, MnP, and VP are class II extracellular fungal peroxidases that belong to the plant and microbial peroxidases superfamily. LiPs are strong oxidants with high-redox potential that oxidize the major non-phenolic structures of lignin. MnP is an Mn-dependent enzyme that catalyzes the oxidation of various phenolic substrates but is not capable of oxidizing the more recalcitrant non-phenolic lignin. VP enzymes combine the catalytic activities of both MnP and LiP and are able to oxidize Mn(2+) like MnP, and non-phenolic compounds like LiP. DyPs occur in both fungi and bacteria and are members of a new superfamily of heme peroxidases called DyPs. DyP enzymes oxidize high-redox potential anthraquinone dyes and were recently reported to oxidize lignin model compounds. The second major group of lignin-degrading enzymes, laccases, are found in plants, fungi, and bacteria and belong to the multicopper oxidase superfamily. They catalyze a one-electron oxidation with the concomitant four-electron reduction of molecular oxygen to water. Fungal laccases can oxidize phenolic lignin model compounds and have higher redox potential than bacterial laccases. In the presence of redox mediators, fungal laccases can oxidize non-phenolic lignin model compounds. In addition to the peroxidases and laccases, fungi produce other accessory oxidases such as aryl-alcohol oxidase and the glyoxal oxidase that generate the hydrogen peroxide required by the peroxidases. Lignin-degrading enzymes have attracted the attention for their valuable biotechnological applications especially in the pretreatment of recalcitrant lignocellulosic biomass for biofuel production. The use of lignin-degrading enzymes has been studied in various applications such as paper industry, textile industry, wastewater treatment and the degradation of herbicides.
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Affiliation(s)
- Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois, IL, USA; Institute for Genomic Biology, University of Illinois, IL, USA
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Lim SH, Lee WS, Kim YI, Sohn Y, Cho DW, Kim C, Kim E, Latham JA, Dunaway-Mariano D, Mariano PS. Photochemical and enzymatic SET promoted C–C bond cleavage reactions of lignin β-1 model compounds containing varying number of methoxy substituents on their arene rings. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Pollegioni L, Tonin F, Rosini E. Lignin-degrading enzymes. FEBS J 2015; 282:1190-213. [DOI: 10.1111/febs.13224] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/29/2014] [Accepted: 01/30/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli Studi dell'Insubria; Italy
| | - Fabio Tonin
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli Studi dell'Insubria; Italy
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Linde D, Ruiz-Dueñas FJ, Fernández-Fueyo E, Guallar V, Hammel KE, Pogni R, Martínez AT. Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance. Arch Biochem Biophys 2015; 574:66-74. [PMID: 25637654 DOI: 10.1016/j.abb.2015.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
Abstract
The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Kenneth E Hammel
- US Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Rebecca Pogni
- Dept. Biotechnologies, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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Ligninolytic Enzymes for Water Depollution, Coal Breakdown, and Paper Industry. ENVIRONMENTAL CHEMISTRY FOR A SUSTAINABLE WORLD 2015. [DOI: 10.1007/978-3-319-11906-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Bacterial Enzymes and Their Role in Decolorization of Azo Dyes. MICROBIAL DEGRADATION OF SYNTHETIC DYES IN WASTEWATERS 2015. [DOI: 10.1007/978-3-319-10942-8_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Zucca P, Rescigno A, Rinaldi AC, Sanjust E. Biomimetic metalloporphines and metalloporphyrins as potential tools for delignification: Molecular mechanisms and application perspectives. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcata.2013.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Behnood M, Nasernejad B, Nikazar M. Biodegradation of crude oil from saline waste water using white rot fungus Phanerochaete chrysosporium. J IND ENG CHEM 2014. [DOI: 10.1016/j.jiec.2013.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Lim SH, Nahm K, Ra CS, Cho DW, Yoon UC, Latham JA, Dunaway-Mariano D, Mariano PS. Effects of alkoxy groups on arene rings of lignin β-O-4 model compounds on the efficiencies of single electron transfer-promoted photochemical and enzymatic C-C Bond Cleavage Reactions. J Org Chem 2013; 78:9431-43. [PMID: 23992466 DOI: 10.1021/jo401680z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To gain information about how alkoxy substitution in arene rings of β-O-4 structural units within lignin governs the efficiencies/rates of radical cation C1-C2 bond cleavage reactions, single electron transfer (SET) photochemical and lignin peroxidase-catalyzed oxidation reactions of dimeric/tetrameric model compounds have been explored. The results show that the radical cations derived from less alkoxy-substituted dimeric β-O-4 models undergo more rapid C1-C2 bond cleavage than those of more alkoxy-substituted analogues. These findings gained support from the results of DFT calculations, which demonstrate that C1-C2 bond dissociation energies of β-O-4 radical cations decrease as the degree of alkoxy substitution decreases. In SET reactions of tetrameric compounds consisting of two β-O-4 units, containing different degrees of alkoxy substitution, regioselective radical cation C-C bond cleavage was observed to occur in one case at the C1-C2 bond in the less alkoxy-substituted β-O-4 moiety. However, regioselective C1-C2 cleavage in the more alkoxy-substituted β-O-4 moiety was observed in another case, suggesting that other factors might participate in controlling this process. These observations show that lignins containing greater proportions of less rather than more alkoxylated rings as part of β-O-4 units would be more efficiently cleaved by SET mechanisms.
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Affiliation(s)
- Suk Hyun Lim
- Department of Chemistry, Yeungnam University , Gyeongsan, Gyeongbuk 712-749, Korea
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23
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Poraj-Kobielska M, Kinne M, Ullrich R, Scheibner K, Hofrichter M. A spectrophotometric assay for the detection of fungal peroxygenases. Anal Biochem 2012; 421:327-9. [DOI: 10.1016/j.ab.2011.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/19/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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Abstract
Over the past three decades, the activities of four kinds of enzyme have been purported to furnish the mechanistic foundations for macromolecular lignin depolymerization in decaying plant cell walls. The pertinent fungal enzymes comprise lignin peroxidase (with a relatively high redox potential), manganese peroxidase, an alkyl aryl etherase, and laccase. The peroxidases and laccase, but not the etherase, are expressed extracellularly by white-rot fungi. A number of these microorganisms exhibit a marked preference toward lignin in their degradation of lignocellulose. Interestingly, some white-rot fungi secrete both kinds of peroxidase but no laccase, while others that are equally effective express extracellular laccase activity but no peroxidases. Actually, none of these enzymes has been reported to possess significant depolymerase activity toward macromolecular lignin substrates that are derived with little chemical modification from the native biopolymer. Here, the assays commonly employed for monitoring the traditional fungal peroxidases, alkyl aryl etherase, and laccase are described in their respective contexts. A soluble native polymeric substrate that can be isolated directly from a conventional milled-wood lignin preparation is characterized in relation to its utility in next-generation lignin-depolymerase assays.
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Affiliation(s)
- Yi-ru Chen
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, USA
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25
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Bugg TDH, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep 2011; 28:1883-96. [PMID: 21918777 DOI: 10.1039/c1np00042j] [Citation(s) in RCA: 457] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignin is a heterogeneous aromatic polymer found as 10-35% of lignocellulose, found in plant cell walls. The bio-conversion of plant lignocellulose to glucose is an important part of second generation biofuel production, but the resistance of lignin to breakdown is a major obstacle in this process, hence there is considerable interest in the microbial breakdown of lignin. White-rot fungi are known to break down lignin with the aid of extracellular peroxidase and laccase enzymes. There are also reports of bacteria that can degrade lignin, and recent work indicates that bacterial lignin breakdown may be more significant than previously thought. The review will discuss the enzymes for lignin breakdown in fungi and bacteria, and the catabolic pathways for breakdown of the β-aryl ether, biphenyl and other components of lignin in bacteria and fungi. The review will also discuss small molecule phenolic breakdown products from lignin that have been identified from lignin-degrading microbes, and includes a bioinformatic analysis of the occurrence of known lignin-degradation pathways in Gram-positive and Gram-negative bacteria.
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Yadav M, Singh SK, Sharma JK, Yadav KDS. Oxidation of polyaromatic hydrocarbons in systems containing water miscible organic solvents by the lignin peroxidase of Gleophyllum striatum MTCC-1117. ENVIRONMENTAL TECHNOLOGY 2011; 32:1287-1294. [PMID: 21970171 DOI: 10.1080/09593330.2010.535177] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lignin peroxidase has been purified to homogeneity using a process of concentration by ultrafiltration and anion exchange chromatography on diethylaminoethyl (DEAE) cellulose from the liquid culture filtrate of the brown rot fungi Gleophyllum striatum MTCC-1117. The molecular mass of the purified enzyme is 43 kDa as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. The K(m) values for the enzyme using veratryl alcohol, hydrogen peroxide and n-propanol were 66 microM, 82 microM and 476 microM, respectively. The pH and temperature optima of the enzyme were 2.8 and 25 degrees C, respectively. The enzyme is completely inhibited by 20% of the water miscible organic solvents acetone dioxane, diethylether, acetonitrile and dimethylformamide. The lignin peroxidase oxidizes polycyclic aromatic hydrocarbons pyrene, acenaphthene, anthracene, dibenothiophene and 9-methyl anthracene.
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Affiliation(s)
- M Yadav
- Department of Chemistry, DDU Gorakhpur University, Gorakhpur 273009, India.
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Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MCY. Discovery and characterization of heme enzymes from unsequenced bacteria: application to microbial lignin degradation. J Am Chem Soc 2011; 133:18006-9. [PMID: 21671563 DOI: 10.1021/ja203972q] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria and other living organisms offer a potentially unlimited resource for the discovery of new chemical catalysts, but many interesting reaction phenotypes observed at the whole organism level remain difficult to elucidate down to the molecular level. A key challenge in the discovery process is the identification of discrete molecular players involved in complex biological transformations because multiple cryptic genetic components often work in concert to elicit an overall chemical phenotype. We now report a rapid pipeline for the discovery of new enzymes of interest from unsequenced bacterial hosts based on laboratory-scale methods for the de novo assembly of bacterial genome sequences using short reads. We have applied this approach to the biomass-degrading soil bacterium Amycolatopsis sp. 75iv2 ATCC 39116 (formerly Streptomyces setonii and S. griseus 75vi2) to discover and biochemically characterize two new heme proteins comprising the most abundant members of the extracellular oxidative system under lignin-reactive growth conditions.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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28
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Cho DW, Latham JA, Park HJ, Yoon UC, Langan P, Dunaway-Mariano D, Mariano PS. Regioselectivity of Enzymatic and Photochemical Single Electron Transfer Promoted Carbon−Carbon Bond Fragmentation Reactions of Tetrameric Lignin Model Compounds. J Org Chem 2011; 76:2840-52. [DOI: 10.1021/jo200253v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dae Won Cho
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - John A. Latham
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Hea Jung Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Ung Chan Yoon
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Paul Langan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Patrick S. Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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29
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Eisenstadt MA, Bogolitsyn KG. Peroxidase oxidation of lignin and its model compounds. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010. [DOI: 10.1134/s1068162010070034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Cho DW, Parthasarathi R, Pimentel AS, Maestas GD, Park HJ, Yoon UC, Dunaway-Mariano D, Gnanakaran S, Langan P, Mariano PS. Nature and Kinetic Analysis of Carbon−Carbon Bond Fragmentation Reactions of Cation Radicals Derived from SET-Oxidation of Lignin Model Compounds. J Org Chem 2010; 75:6549-62. [DOI: 10.1021/jo1012509] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dae Won Cho
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico
87131
| | | | - Adam S. Pimentel
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico
87131
| | - Gabriel D. Maestas
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico
87131
| | - Hea Jung Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Ung Chan Yoon
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Debra Dunaway-Mariano
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico
87131
| | - S. Gnanakaran
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Paul Langan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Patrick S. Mariano
- Department of Chemistry and
Chemical Biology, University of New Mexico, Albuquerque, New Mexico
87131
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32
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Hofrichter M, Ullrich R, Pecyna MJ, Liers C, Lundell T. New and classic families of secreted fungal heme peroxidases. Appl Microbiol Biotechnol 2010; 87:871-97. [PMID: 20495915 DOI: 10.1007/s00253-010-2633-0] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/14/2010] [Accepted: 04/14/2010] [Indexed: 01/15/2023]
Abstract
Heme-containing peroxidases secreted by fungi are a fascinating group of biocatalysts with various ecological and biotechnological implications. For example, they are involved in the biodegradation of lignocelluloses and lignins and participate in the bioconversion of other diverse recalcitrant compounds as well as in the natural turnover of humic substances and organohalogens. The current review focuses on the most recently discovered and novel types of heme-dependent peroxidases, aromatic peroxygenases (APOs), and dye-decolorizing peroxidases (DyPs), which catalyze remarkable reactions such as peroxide-driven oxygen transfer and cleavage of anthraquinone derivatives, respectively, and represent own separate peroxidase superfamilies. Furthermore, several aspects of the "classic" fungal heme-containing peroxidases, i.e., lignin, manganese, and versatile peroxidases (LiP, MnP, and VP), phenol-oxidizing peroxidases as well as chloroperoxidase (CPO), are discussed against the background of recent scientific developments.
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Affiliation(s)
- Martin Hofrichter
- Department of Environmental Biotechnology, International Graduate School of Zittau, Markt 23, 02763, Zittau, Germany.
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33
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Bogolitsyn KG, Aizenshtadt MA, Pryakhin AN, Lunin VV, Pokryshkin SA. Kinetics of the catalytic oxidation of model compounds of lignin with hydrogen peroxide in the presence of peroxidase from horse-radish. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410090116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Aitken MD, Irvine RL. Stability testing of ligninase and Mn-peroxidase from Phanerochaete chrysosporium. Biotechnol Bioeng 2009; 34:1251-60. [PMID: 18588065 DOI: 10.1002/bit.260341003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The white-rot fungus Phanerochaete chrysosporium produces extracellular peroxidases (ligninase and Mn-peroxidase) believed to be involved in lignin degradation. These extracellular enzymes have also been implicated in the degradation of recalcitrant pollutants by the organism. Commercial application of ligninase has been proposed both for biomechanical pulping of wood and for wastewater treatment. In vitro stability of lignin degrading enzymes will be an important factor in determining both the economic and technical feasibility of application for industrial uses, and also will be critical in optimizing commercial production of the enzymes. The effects of a number of variables on in vitro stability of ligninase and Mn-peroxidase are presented in this paper. Thermal stability of ligninase was found to improve by increasing pH and by increasing enzyme concentration. For a fixed pH and enzyme concentration, ligninase stability was greatly enhanced in the presence of its substrate veratryl alcohol (3,4-dimethoxybenzyl alcohol). Ligninase also was found to be inactivated by hydrogen peroxide in a second-order process that is proposed to involve the formation of the unreactive peroxidase intermediate Compound III. Mn-peroxidase was less susceptible to inactivation by peroxide, which corresponds to observations by others that Compound III of Mn-peroxidase forms less readily than Compound III of ligninase.
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Affiliation(s)
- M D Aitken
- Center for Bioengineering and Pollution Control and Department of Civil Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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35
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Hugo M, Turell L, Manta B, Botti H, Monteiro G, Netto LES, Alvarez B, Radi R, Trujillo M. Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics. Biochemistry 2009; 48:9416-26. [PMID: 19737009 DOI: 10.1021/bi901221s] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug resistance and virulence of Mycobacterium tuberculosis are partially related to the pathogen's antioxidant systems. Peroxide detoxification in this bacterium is achieved by the heme-containing catalase peroxidase and different two-cysteine peroxiredoxins. M. tuberculosis genome also codifies for a putative one-cysteine peroxiredoxin, alkyl hydroperoxide reductase E (MtAhpE). Its expression was previously demonstrated at a transcriptional level, and the crystallographic structure of the recombinant protein was resolved under reduced and oxidized states. Herein, we report that the conformation of MtAhpE changed depending on its single cysteine redox state, as reflected by different tryptophan fluorescence properties and changes in quaternary structure. Dynamics of fluorescence changes, complemented by competition kinetic assays, were used to perform protein functional studies. MtAhpE reduced peroxynitrite 2 orders of magnitude faster than hydrogen peroxide (1.9 x 10(7) M(-1) s(-1) vs 8.2 x 10(4) M(-1) s(-1) at pH 7.4 and 25 degrees C, respectively). The latter also caused cysteine overoxidation to sulfinic acid, but at much slower rate constant (40 M(-1) s(-1)). The pK(a) of the thiol in the reduced enzyme was 5.2, more than one unit lower than that of the sulfenic acid in the oxidized enzyme. The pH profile of hydrogen peroxide-mediated thiol and sulfenic acid oxidations indicated thiolate and sulfenate as the reacting species. The formation of sulfenic acid as well as the catalytic peroxidase activity of MtAhpE was demonstrated using the artificial reducing substrate thionitrobenzoate. Taken together, our results indicate that MtAhpE is a relevant component in the antioxidant repertoire of M. tuberculosis probably involved in peroxide and specially peroxynitrite detoxification.
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Affiliation(s)
- Martín Hugo
- Departamento de Bioqumica, Facultad de Medicina, Center for Free Radical and Biomedical Research, Universidad de la República, Montevideo, Uruguay
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Kinne M, Poraj-Kobielska M, Ralph SA, Ullrich R, Hofrichter M, Hammel KE. Oxidative cleavage of diverse ethers by an extracellular fungal peroxygenase. J Biol Chem 2009; 284:29343-9. [PMID: 19713216 DOI: 10.1074/jbc.m109.040857] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many litter-decay fungi secrete heme-thiolate peroxygenases that oxidize various organic chemicals, but little is known about the role or mechanism of these enzymes. We found that the extracellular peroxygenase of Agrocybe aegerita catalyzed the H2O2-dependent cleavage of environmentally significant ethers, including methyl t-butyl ether, tetrahydrofuran, and 1,4-dioxane. Experiments with tetrahydrofuran showed the reaction was a two-electron oxidation that generated one aldehyde group and one alcohol group, yielding the ring-opened product 4-hydroxybutanal. Investigations with several model substrates provided information about the route for ether cleavage: (a) steady-state kinetics results with methyl 3,4-dimethoxybenzyl ether, which was oxidized to 3,4-dimethoxybenzaldehyde, gave parallel double reciprocal plots suggestive of a ping-pong mechanism (K(m)((peroxide)), 1.99 +/- 0.25 mM; K(m)((ether)), 1.43 +/- 0.23 mM; k(cat), 720 +/- 87 s(-1)), (b) the cleavage of methyl 4-nitrobenzyl ether in the presence of H2(18)O2 resulted in incorporation of 18O into the carbonyl group of the resulting 4-nitrobenzaldehyde, and (c) the demethylation of 1-methoxy-4-trideuteromethoxybenzene showed an observed intramolecular deuterium isotope effect [(k(H)/k(D))(obs)] of 11.9 +/- 0.4. These results suggest a hydrogen abstraction and oxygen rebound mechanism that oxidizes ethers to hemiacetals, which subsequently hydrolyze. The peroxygenase appeared to lack activity on macromolecular ethers, but otherwise exhibited a broad substrate range. It may accordingly have a role in the biodegradation of natural and anthropogenic low molecular weight ethers in soils and plant litter.
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Affiliation(s)
- Matthias Kinne
- From the Unit of Environmental Biotechnology, International Graduate School of Zittau, 02763 Zittau, Germany
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37
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Peroxidase from Bacillus sp. VUS and its role in the decolorization of textile dyes. BIOTECHNOL BIOPROC E 2009. [DOI: 10.1007/s12257-008-0242-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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38
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Jarosz-Wilkołazka A, Luterek J, Olszewska A. Catalytic activity of versatile peroxidase fromBjerkandera fumosaat different pH. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701830082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Aranda E, Kinne M, Kluge M, Ullrich R, Hofrichter M. Conversion of dibenzothiophene by the mushrooms Agrocybe aegerita and Coprinellus radians and their extracellular peroxygenases. Appl Microbiol Biotechnol 2009; 82:1057-66. [DOI: 10.1007/s00253-008-1778-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 11/24/2022]
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40
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Dhanve RS, Kalyani DC, Phugare SS, Jadhav JP. Coordinate action of exiguobacterial oxidoreductive enzymes in biodegradation of reactive yellow 84A dye. Biodegradation 2008; 20:245-55. [DOI: 10.1007/s10532-008-9217-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
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41
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Zhou GP, Zhang Y, Huang XR, Shi CH, Liu WF, Li YZ, Qu YB, Gao PJ. Catalytic activities of fungal oxidases in hydrophobic ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate-based microemulsion. Colloids Surf B Biointerfaces 2008; 66:146-9. [PMID: 18602799 DOI: 10.1016/j.colsurfb.2008.05.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/17/2022]
Abstract
For hydrophobic ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]), an H(2)O-in-[BMIM][PF(6)] microemulsion could be formed in the presence of nonionic surfactant Triton X-100 (TX-100). In such a medium, both lignin peroxidase (LiP) and laccase could express their catalytic activity with the optimum molar ratio of H(2)O to TX-100 at 8.0 for LiP and >20 for laccase, and the optimum pH values at 3.2 for LiP and 4.2 for laccase, respectively. As compared with pure or water saturated [BMIM][PF(6)], in which the two oxidases had negligible catalytic activity due to the strong inactivating effect of [BMIM][PF(6)] on both enzymes, the use of the [BMIM][PF(6)]-based microemulsion had some advantages. Not only the catalytic activities of both fungal oxidases greatly enhanced, but also the apparent viscosity of the medium decreased.
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Affiliation(s)
- Gui-Ping Zhou
- Key Laboratory of Colloid & Interface Chemistry of the Education Ministry of China, Shandong University, Jinan 250100, People's Republic of China
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Structure and action mechanism of ligninolytic enzymes. Appl Biochem Biotechnol 2008; 157:174-209. [PMID: 18581264 DOI: 10.1007/s12010-008-8279-z] [Citation(s) in RCA: 392] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 05/05/2008] [Indexed: 10/21/2022]
Abstract
Lignin is the most abundant renewable source of aromatic polymer in nature, and its decomposition is indispensable for carbon recycling. It is chemically recalcitrant to breakdown by most organisms because of the complex, heterogeneous structure. The white-rot fungi produce an array of extracellular oxidative enzymes that synergistically and efficiently degrade lignin. The major groups of ligninolytic enzymes include lignin peroxidases, manganese peroxidases, versatile peroxidases, and laccases. The peroxidases are heme-containing enzymes with catalytic cycles that involve the activation by H2O2 and substrate reduction of compound I and compound II intermediates. Lignin peroxidases have the unique ability to catalyze oxidative cleavage of C-C bonds and ether (C-O-C) bonds in non-phenolic aromatic substrates of high redox potential. Manganese peroxidases oxidize Mn(II) to Mn(III), which facilitates the degradation of phenolic compounds or, in turn, oxidizes a second mediator for the breakdown of non-phenolic compounds. Versatile peroxidases are hybrids of lignin peroxidase and manganese peroxidase with a bifunctional characteristic. Laccases are multi-copper-containing proteins that catalyze the oxidation of phenolic substrates with concomitant reduction of molecular oxygen to water. This review covers the chemical nature of lignin substrates and focuses on the biochemical properties, molecular structures, reaction mechanisms, and related structures/functions of these enzymes.
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Degradation of sulfonated azo dyes by the purified lignin peroxidase from Brevibacillus laterosporus MTCC 2298. BIOTECHNOL BIOPROC E 2008. [DOI: 10.1007/s12257-008-0008-5] [Citation(s) in RCA: 17] [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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Expression in yeast of secreted lignin peroxidase with improved 2,4-dichlorophenol degradability by DNA shuffling. J Biotechnol 2008; 135:241-6. [PMID: 18514942 DOI: 10.1016/j.jbiotec.2008.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 04/02/2008] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
Abstract
Lignin peroxidase (LiP) from Phanerochaete chrysosporium was shown to mineralize a variety of recalcitrant aromatic compounds and oxidize a number of polycyclic aromatic and phenolic compounds. The major problem of the wild type LiP is that it can be inactivated by excess H(2)O(2) and high concentrations of aromatic compounds. We applied a directed evolution technique coupled with a rapid colorimetric screening method to obtain mutant genes with improved H(2)O(2) stability and polychlorinated phenol degradability, and they were successfully expressed as the secretive LiPs in recombinant Saccharomyces cerevisiae. The resulting variants showed approximately 1.6-fold improved 2,4-dichlorophenol (2,4-DCP) degradation activity and stability against H(2)O(2) compared with the parent strain. The kinetic properties of the variants toward 2,4-DCP and H(2)O(2) were also increased compared with the wild type for all three mutants studied. Amino acid sequence analysis indicated that the greatest number of amino acid substitutions was located near the surface or Ca(2+) binding sites of the enzyme.
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LIU JT, HUANG XR, GAO PJ. Kinetic Studies on the Lignin Peroxidase Catalyzed Oxidation of Veratryl Alcohol by H2O2 in AOT/Isooctane/Toluene/Water Reverse Micelles. CHINESE J CHEM 2007. [DOI: 10.1002/cjoc.200790301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Functionality improvement of fungal lignin peroxidase by DNA shuffling for 2,4-dichlorophenol degradability and H2O2 stability. J Biotechnol 2007; 133:110-5. [PMID: 17961781 DOI: 10.1016/j.jbiotec.2007.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 08/27/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
Abstract
One of the major problems of wild-type lignin peroxidase (LiP) is its inactivity at the presence of excess H(2)O(2) and high concentration of aromatic compounds. Little is known about the substrate-binding site of LiP, and functionality improvement of LiP was not actively tried by genetic engineering and directed evolution. In order to improve LiPs functionality, we performed directed evolution with a colorimetric screening method. Finally, three types of LiP mutants were screened. The catalytic efficiency of the variants toward 2,4-dichlorophenol (DCP) degradation activity and the stability against H(2)O(2) was increased over the wild type. The K(m) value of the variants toward H(2)O(2) was increased, but K(m) value toward 2,4-DCP degradation was reduced. Overall, The K(cat)/K(m) values of the mutants toward 2,4-DCP was increased ca. 4-fold, and that toward H(2)O(2) was increased ca. 89-fold. Amino acid sequence analysis indicated that the most of the mutations were located on the enzyme surface. We expect that these results coupled with recombining mutation can be successfully applied to the molecular evolution cycles for screening of LiPs and other oxidative enzymes with improved functionality and stability.
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Gavril M, Hodson PV, McLellan J. Decoloration of Amaranth by the white-rot fungusTrametes versicolor. Part I. Statistical analysis. Can J Microbiol 2007; 53:313-26. [PMID: 17496981 DOI: 10.1139/w06-123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The white-rot fungus Trametes versicolor decolorized the mono-azo-substituted naphthalenic dye Amaranth. The relationship between the amount of enzymes present in the system and the efficiency of the decoloration process was investigated. The two responses used to quantify the process of decoloration (i.e., initial decoloration rate, v0, and the percent concentration of dye decolorized in 1 h, %c) were correlated with the amount of three enzymes considered for the study (lignin peroxidase, manganese peroxidase, and laccase) and analyzed through stepwise regression analysis (forward, backward, and mixed). The results of the correlation analysis and those of the regression analysis indicated that lignin peroxidase is the enzyme having the greatest influence on the two responses.
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Affiliation(s)
- Mihaela Gavril
- Department of Environmental and Water Research Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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Lan J, Huang X, Hu M, Li Y, Qu Y, Gao P, Wu D. High efficient degradation of dyes with lignin peroxidase coupled with glucose oxidase. J Biotechnol 2006; 123:483-90. [PMID: 16698106 DOI: 10.1016/j.jbiotec.2005.12.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2005] [Revised: 11/14/2005] [Accepted: 12/15/2005] [Indexed: 11/21/2022]
Abstract
The H(2)O(2) supply strategy was one of crucial factors for high efficient degradation of pollutants with lignin peroxidase (LiP). In this paper, an attempt was made to couple a H(2)O(2) producing enzymatic reaction to the LiP catalyzed oxidation of dyes. H(2)O(2) needed was generated by glucose oxidase (GOD) and its substrate glucose. The generation rate of H(2)O(2) could be easily controlled by adjusting the pH of the degradation system and the amount of GOD added. Due to the controlled release of H(2)O(2), a sustainable constant activity of LiP was observed. The inhibition of LiP by high level H(2)O(2) supplied externally by a single addition at the beginning of the experiments could be avoided. Degradation of three dyes (xylene cyanol, fuchsine and rhodamine B) with LiP coupled with GOD indicated that the present H(2)O(2) supply strategy was very effective for improvement of the efficiency of the decolourization of dyes.
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Affiliation(s)
- Jing Lan
- Key Laboratory of Colloid & Interface Chemistry of the Education Ministry of China, Shandong University, Jinan 250100, PR China
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Zhang W, Huang X, Li Y, Qu Y, Gao P. Catalytic activity of lignin peroxidase and partition of veratryl alcohol in AOT/isooctane/toluene/water reverse micelles. Appl Microbiol Biotechnol 2006; 70:315-20. [PMID: 16080008 DOI: 10.1007/s00253-005-0048-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2004] [Revised: 05/12/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
The activity of lignin peroxidase (LiP) and the partition of its optimum substrate veratryl alcohol (VA) in sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/isooctane/toluene/water reverse micelles were studied in this paper to understand the microheterogeneous effect of the medium on the catalytic properties of LiP hosted in the reverse micelle. Results showed that LiP from Phanerochaete chrysosporium could express its activity in the reverse micelles, but its activity depended, to a great extent, on the composition of the reverse micelles. Optimum activity occurred at a molar ratio of water to AOT (omega0) of 11, a pH value of 3.6, and a volume ratio of isooctane to toluene of 7-9. Under optimum conditions, the half-life of LiP was circa 12 h. The dependence of LiP activity on the volume fraction of water in the medium (theta), at a constant omega0 value of 11, indicated that VA was mainly solubilized in the pseudophase of the reverse micelle. Based on the pseudobiphasic model and the corresponding kinetic method, a linear line can be obtained in a plot of apparent Michaelis constant of VA vs theta, and the partition coefficient of VA between the pseudophase and the organic solvent phase was determined to be 35.8, which was higher than that (22.3) between bulk water and the corresponding mixed organic solvent. H2O2 inhibited LiP at concentrations higher than 80 microM; this concentration value seems to be different from that in aqueous solution (about 3 mM). The differences mentioned above should be ascribed to the microheterogeneity and the interface of the AOT reverse micelle.
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Affiliation(s)
- Wenjuan Zhang
- Key Lab for Colloid and Interface Chemistry of the Education Ministry of China, Shandong University, Jinan, 250100, People's Republic of China
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Verdín J, Pogni R, Baeza A, Baratto MC, Basosi R, Vázquez-Duhalt R. Mechanism of versatile peroxidase inactivation by Ca(2+) depletion. Biophys Chem 2006; 121:163-70. [PMID: 16488071 DOI: 10.1016/j.bpc.2006.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/13/2006] [Accepted: 01/16/2006] [Indexed: 10/25/2022]
Abstract
Versatile peroxidase (VP) from Bjerkandera adusta, as other class II peroxidases, is inactivated by Ca(2+) depletion. In this work, the spectroscopic characterizations of Ca(2+)-depleted VP at pH 4.5 (optimum for activity) and pH 7.5 are presented. Previous works on other ligninolytic peroxidases, such as lignin peroxidase and manganese peroxidase, have been performed at pH 7.5; nevertheless, at this pH these enzymes are inactive independently of their Ca(2+) content. At pH 7.5, UV-Vis spectra indicate a heme-Fe(3+) transition from 5-coordinated high-spin configuration in native peroxidase to 6-coordinated low-spin state in the inactive Ca(2+)-depleted form. This Fe(3+) hexa-coordination has been proposed as the origin of inactivation. However, our results at pH 4.5 show that Ca(2+)-depleted enzyme has a high spin Fe(3+). EPR measurements on VP confirm the differences in the Fe(3+) spin states at pH 4.5 and at 7.5 for both, native and Ca(2+)-depleted enzymes. In addition, EPR spectra recorded after the addition of H(2)O(2) to Ca(2+)-depleted VP show the formation of compound I with the radical species delocalized on the porphyrin ring. The lack of radical delocalization on an amino acid residue exposed to solvent, W170, as determined in native enzyme at pH 4.5, explains the inability of Ca(2+)-depleted VP to oxidize veratryl alcohol. These observations, in addition to a notorious redox potential decrease, suggest that Ca(2+)-depleted versatile peroxidase is able to form the active intermediate compound I but its long range electron transfer has been disrupted.
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Affiliation(s)
- Jorge Verdín
- Institute of Biotechnology, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62250, Mexico
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