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Vijay K, Shibasini M, Sivasakthivelan P, Kavitha T. Microbial siderophores as molecular shuttles for metal cations: sources, sinks and application perspectives. Arch Microbiol 2023; 205:322. [PMID: 37644212 DOI: 10.1007/s00203-023-03644-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023]
Abstract
Iron is one of the highly abundant elements on the earth's crust, an essential micronutrient for a majority of life forms, and exists in two frequent oxidation states such as ferrous (Fe2+) and ferric (Fe3+). These two oxidation states are interconvertible by redox reactions and form complexes with a wide range of siderophores. At neutral pH in soil, Fe2+ is highly soluble upto 100 mM but have less biological value, whereas Fe3+ is less soluble upto 10-9 M. This reduced bioavailability of Fe3+ induces competition among microorganisms. As many microorganisms need at least 10-6 M of Fe3+ form of iron for their growth, siderophores from these microbes readily withdraw Fe3+ iron from a variety of habitats for their survival. In this review, we bring into light the several recent investigations related to diverse chemistry of microbial siderophores, mechanisms of siderophore uptake, biosynthetic gene clusters in microbial genomes, various sources of heavy metal cations in soil, siderophore-binding protein receptors and commercialisation perspectives of siderophores. Besides, this review unearths the recent advancements in the characterisation of novel siderophores and its heavy metal complexes alongside the interaction kinetics with receptors.
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Affiliation(s)
- Karuppiah Vijay
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630 003, India
| | - Murugan Shibasini
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630 003, India
| | - Panneerselvam Sivasakthivelan
- Department of Agricultural Microbiology, Faculty of Agriculture, Annamalai University, Annamalai Nagar, Chidambaram, Tamil Nadu, 608 002, India
| | - Thangavel Kavitha
- Department of Microbiology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, 630 003, India.
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Li G, Wang Y, Yu D, Zhu P, Zhao G, Liu C, Zhao H. Ligninolytic characteristics of Pleurotus ostreatus cultivated in cotton stalk media. Front Microbiol 2022; 13:1035040. [PMID: 36504763 PMCID: PMC9726710 DOI: 10.3389/fmicb.2022.1035040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Abstract
Biodelignification is widely regarded as a low-efficiency process because it is usually slow and difficult to control. To improve its efficiency and understand its mechanism, the present study analyzed the delignification characteristics of Pleurotus ostreatus grown on a cotton stalk medium. The results demonstrated that all strains of P. ostreatus can selectively degrade the cotton stalk lignin. When cultured in a cotton stalk medium for 60 days, P. ostreatus degraded lignin primarily during its mycelium growth with up to 54.04% lignin degradation and produced laccase and manganese dependent peroxidase with high activity levels at the peaks of 70.17 U/ml and 62.39 U/ml, respectively, but no detectable lignin peroxidase. The results of nuclear magnetic resonance spectroscopy and Fourier transform infrared spectroscopy analyses of significant changes in lignin structure revealed that syringyl (S) lignin units were more degraded than guaiacyl (G) lignin units, with a significantly elevated G/S ratio. The Gas Chromatography-Mass Spectrometer analysis of low-molecular-weight compounds revealed that the delignification resulted in the formation of alcohols, organic acids, benzodiazepines, and alkanes. Identified benzodiazepines implied the degradation of G and S units of lignin. These findings will help to improve the efficiency of biodelignification and expand our understanding of its mechanism.
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Affiliation(s)
- Guoqing Li
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China,College of Life Science, Anhui Agricultural University, Hefei, China,Provincial Resource Database of Wood Rot Edible Mushrooms in Anhui Province, Hefei, China
| | - Yahui Wang
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Deshui Yu
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Peilei Zhu
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Guiyun Zhao
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Caiyu Liu
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Hongyuan Zhao
- State Key Laboratory of Horticultural Crop Germplasm Resources Creation and Utilization of Ministry of Agriculture and Rural Affairs, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, China,*Correspondence: Hongyuan Zhao,
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Functional Characterization of Laccase Isozyme (PoLcc1) from the Edible Mushroom Pleurotus ostreatus Involved in Lignin Degradation in Cotton Straw. Int J Mol Sci 2022; 23:ijms232113545. [PMID: 36362331 PMCID: PMC9658089 DOI: 10.3390/ijms232113545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Fungal laccases play important roles in the degradation of lignocellulose. In this study, the laccase producing cotton straw medium for Pleurotus ostreatus was optimized by single-factor and orthogonal experiments, and to investigate the role of Lacc1 gene, one of the laccase-encoding genes, in the degradation of cotton straw lignin, an overexpression strain of Lacc1 gene was constructed, which was analyzed for the characteristics of lignin degradation. The results demonstrated that the culture conditions with the highest lignin degradation efficiency of the P. ostreatus were the cotton straw particle size of 0.75 mm, a solid–liquid ratio of 1:3 and containing 0.25 g/L of Tween in the medium, as well as an incubation temperature of 26 °C. Two overexpression strains (OE L1-1 and OE L1-4) of Lacc1 gene were obtained, and the gene expression increased 12.08- and 33.04-fold, respectively. The results of 1H-NMR and FTIR analyses of significant changes in lignin structure revealed that Lacc1 gene accelerated the degradation of lignin G-units and involved in the cleavage of β-O-4 linkages and the demethylation of lignin units. These findings will help to improve the efficiency of biodelignification and expand our understanding of its mechanism.
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Fungal Siderophores: Prospects and Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-53077-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chaput G, Billings AF, DeDiego L, Orellana R, Adkins JN, Nicora CD, Kim YM, Chu R, Simmons B, DeAngelis KM. Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1. PLoS One 2020; 15:e0233823. [PMID: 32941430 PMCID: PMC7497984 DOI: 10.1371/journal.pone.0233823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/26/2020] [Indexed: 11/19/2022] Open
Abstract
Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of de-lignification, with a growing interest in the use of microbes. Here we investigate the physiology and molecular response of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, to lignin under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 accumulates higher biomass and has a shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in late logarithmic phase. Ferrozine assays of the supernatant confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.
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Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, MA, United States of America
| | - Andrew F. Billings
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, MA, United States of America
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, MA, United States of America
| | - Roberto Orellana
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Playa Ancha, Valparaíso, Chile
| | - Joshua N. Adkins
- Biological Sciences Department, Pacific Northwest National Laboratory, Richland, Washington, DC, United States of America
| | - Carrie D. Nicora
- Biological Sciences Department, Pacific Northwest National Laboratory, Richland, Washington, DC, United States of America
| | - Young-Mo Kim
- Biological Sciences Department, Pacific Northwest National Laboratory, Richland, Washington, DC, United States of America
| | - Rosalie Chu
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, DC, United States of America
| | - Blake Simmons
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, MA, United States of America
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Multiple Factors Influencing the Strategy of Lignin Mycodegradation. Fungal Biol 2019. [DOI: 10.1007/978-3-030-23834-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kido R, Takeeda M, Manabe M, Miyagawa Y, Itakura S, Tanaka H. Presence of extracellular NAD(+) and NADH in cultures of wood-degrading fungi. Biocontrol Sci 2016; 20:105-13. [PMID: 26133508 DOI: 10.4265/bio.20.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Our previous studies indicated that extracellular glycoproteins produced by some white-rot and brown-rot basidiomycetous fungi reduce Fe(III) to Fe(II) and O2 to H2O2 and produce hydroxyl radicals. The continuous generation of hydroxyl radicals requires a constant supply of O2 and an electron donor for the reduction of oxidized forms of the glycoproteins to the reduced forms. However, electron donors for this reaction, such as NADH, have not been identified. In this study, the amounts of the extracellular pyridine coenzymes, NAD(+) and NADH, were measured in agar cultures of four white-rot fungi, one brown-rot fungus, and three soft-rot fungi. The sums of NAD(+) and NADH detected in wood-containing cultures of all five basidiomycetes were greater than those in glucose cultures. The amounts of NAD(+) were higher than those of NADH in all wood-containing cultures except that of Irpex lacteus, and NAD(+) was greater than NADH in all glucose cultures except that of Fomitopsis palustris. Significant amounts of pyridine coenzymes were present in glucose and wood-containing cultures of the three soft-rot fungi. The non-wood-degrading fungus, Penicillium funiculosum, did not produce NAD(+) or NADH in either glucose or wood-containing cultures. The extracellular pyridine coenzyme levels were relatively high compared to the rates of extracellular hydroxyl radical generation in wood-degrading fungal cultures. Thus, white-, brown-, and soft-rot fungi produce pyridine coenzymes that could serve as electron donors for the production of hydroxyl radicals during wood degradation.
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Affiliation(s)
- Ryuta Kido
- Department of Applied Biological Chemistry, Graduate School of Agriculture Kinki University
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E. AA, D. MC. Oyster mushrooms (Pleurotus) are useful for utilizing lignocellulosic biomass. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajb2014.14249] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Ahmed E, Holmström SJM. Siderophores in environmental research: roles and applications. Microb Biotechnol 2014; 7:196-208. [PMID: 24576157 PMCID: PMC3992016 DOI: 10.1111/1751-7915.12117] [Citation(s) in RCA: 427] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/13/2014] [Accepted: 01/21/2014] [Indexed: 12/17/2022] Open
Abstract
Siderophores are organic compounds with low molecular masses that are produced by microorganisms and plants growing under low iron conditions. The primary function of these compounds is to chelate the ferric iron [Fe(III)] from different terrestrial and aquatic habitats and thereby make it available for microbial and plant cells. Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. Their significance in these applications is because siderophores have the ability to bind a variety of metals in addition to iron, and they have a wide range of chemical structures and specific properties. For instance, siderophores function as biocontrols, biosensors, and bioremediation and chelation agents, in addition to their important role in weathering soil minerals and enhancing plant growth. The aim of this literature review is to outline and discuss the important roles and functions of siderophores in different environmental habitats and emphasize the significant roles that these small organic molecules could play in applied environmental processes.
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Affiliation(s)
- E Ahmed
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
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Paliwal R, Rawat AP, Rawat M, Rai JPN. Bioligninolysis: recent updates for biotechnological solution. Appl Biochem Biotechnol 2012; 167:1865-89. [PMID: 22639362 DOI: 10.1007/s12010-012-9735-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 05/10/2012] [Indexed: 10/28/2022]
Abstract
Bioligninolysis involves living organisms and/or their products in degradation of lignin, which is highly resistant, plant-originated polymer having three-dimensional network of dimethoxylated (syringyl), monomethoxylated (guaiacyl), and non-methoxylated (p-hydroxyphenyl) phenylpropanoid and acetylated units. As a major repository of aromatic chemical structures on earth, lignin bears paramount significance for its removal owing to potential application of bioligninolytic systems in industrial production. Early reports illustrating the discovery and cloning of ligninolytic biocatalysts in fungi was truly a landmark in the field of enzymatic delignification. However, the enzymology for bacterial delignification is hitherto poorly understood. Moreover, the lignin-degrading bacterial genes are still unknown and need further exploration. This review deals with the current knowledge about ligninolytic enzyme families produced by fungi and bacteria, their mechanisms of action, and genetic regulation and reservations, which render them attractive candidates in biotechnological applications.
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Affiliation(s)
- Rashmi Paliwal
- Ecotechnology Laboratory, Department of Environmental Science, G.B.Pant. University of Agriculture and Technology, Pantnagar 263145, India
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Grinhut T, Salame TM, Chen Y, Hadar Y. Involvement of ligninolytic enzymes and Fenton-like reaction in humic acid degradation by Trametes sp. Appl Microbiol Biotechnol 2011; 91:1131-40. [PMID: 21541787 DOI: 10.1007/s00253-011-3300-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/29/2011] [Accepted: 03/31/2011] [Indexed: 10/18/2022]
Abstract
Trametes sp. M23, isolated from biosolids compost was found to decompose humic acids (HA). A low N (LN) medium (C/N, 53) provided suitable conditions for HA degradation, whereas in a high N (HN) medium (C/N, 10), HA was not degraded. In the absence of Mn(2+), HA degradation was similar to that in Mn(2+)-containing medium. In contrast, MnP activity was significantly affected by Mn(2+). Laccase activity exhibited a negative correlation to HA degradation, while LiP activity was not detected. Thus, ligninolytic enzymes activity could provide only a partial explanation for the HA-degradation mechanism. The decolorization of two dyes, Orange II and Brilliant Blue R250, was also determined. Similar to HA degradation, under LN conditions, decolorization occurred independently of the presence of Mn(2+). We investigated the possible involvement of a Fenton-like reaction in HA degradation. The addition of DMSO, an OH-radical scavenger, to LN media resulted in a significant decrease in HA bleaching. The rate of extracellular Fe(3+) reduction was much higher in the LN vs. HN medium. In addition, the rate of reduction was even higher in the presence of HA in the medium. In vitro HA bleaching in non-inoculated media was observed with H(2)O(2) amendment to a final concentration of 200 mM (obtained by 50 mM amendments for 4 days) and Fe(2+) (36 mM). After 4 days of incubation, HA decolorization was similar to the biological treatment. These results support our hypothesis that a Fenton-like reaction is involved in HA degradation by Trametes sp. M23.
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Affiliation(s)
- Tzafrir Grinhut
- Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel
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Dashtban M, Schraft H, Qin W. Fungal bioconversion of lignocellulosic residues; opportunities & perspectives. Int J Biol Sci 2009; 5:578-95. [PMID: 19774110 PMCID: PMC2748470 DOI: 10.7150/ijbs.5.578] [Citation(s) in RCA: 324] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/02/2009] [Indexed: 11/28/2022] Open
Abstract
The development of alternative energy technology is critically important because of the rising prices of crude oil, security issues regarding the oil supply, and environmental issues such as global warming and air pollution. Bioconversion of biomass has significant advantages over other alternative energy strategies because biomass is the most abundant and also the most renewable biomaterial on our planet. Bioconversion of lignocellulosic residues is initiated primarily by microorganisms such as fungi and bacteria which are capable of degrading lignocellulolytic materials. Fungi such as Trichoderma reesei and Aspergillus niger produce large amounts of extracellular cellulolytic enzymes, whereas bacterial and a few anaerobic fungal strains mostly produce cellulolytic enzymes in a complex called cellulosome, which is associated with the cell wall. In filamentous fungi, cellulolytic enzymes including endoglucanases, cellobiohydrolases (exoglucanases) and beta-glucosidases work efficiently on cellulolytic residues in a synergistic manner. In addition to cellulolytic/hemicellulolytic activities, higher fungi such as basidiomycetes (e.g. Phanerochaete chrysosporium) have unique oxidative systems which together with ligninolytic enzymes are responsible for lignocellulose degradation. This review gives an overview of different fungal lignocellulolytic enzymatic systems including extracellular and cellulosome-associated in aerobic and anaerobic fungi, respectively. In addition, oxidative lignocellulose-degradation mechanisms of higher fungi are discussed. Moreover, this paper reviews the current status of the technology for bioconversion of biomass by fungi, with focus on mutagenesis, co-culturing and heterologous gene expression attempts to improve fungal lignocellulolytic activities to create robust fungal strains.
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Affiliation(s)
- Mehdi Dashtban
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Heidi Schraft
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Wensheng Qin
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
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Haibo Z, Yinglong Z, Feng H, Peiji G, Jiachuan C. Purification and characterization of a thermostable laccase with unique oxidative characteristics from Trametes hirsuta. Biotechnol Lett 2009; 31:837-43. [DOI: 10.1007/s10529-009-9945-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 01/12/2009] [Accepted: 01/13/2009] [Indexed: 11/29/2022]
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