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Hoque RA, Yadav M, Yadava U, Rai N, Negi S, Yadav HS. Active site determination of novel plant versatile peroxidase extracted from Citrus sinensis and bioconversion of β-naphthol. 3 Biotech 2023; 13:345. [PMID: 37719748 PMCID: PMC10501043 DOI: 10.1007/s13205-023-03758-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/20/2023] [Indexed: 09/19/2023] Open
Abstract
A ligninolytic peroxidase called versatile peroxidase, VP, (EC 1.11.1.16) is an iron-containing metalloenzyme. The most distinctive feature of this enzyme is its composite molecular framework, which combines lignin peroxidase's capacity to oxidize compounds with high-redox potential with manganese peroxidase's capacity to oxidize Mn2+ to Mn3+. In this study, we have extracted amino acid sequences from the Citrus sinensis source and subjected them to various computation tools to visualize the insight secondary and 3D structure, physicochemical properties, and validation of the structure which have not been studied so far to further investigate the catalytic efficiency and effectiveness of VP. The binding energies of HEME and HEME C (HEC) ligands with produced PDB (6rqf.1. A) have been also assessed, analyzed, and confirmed utilizing AutoDock. Binding energies were calculated using the AutoDock and validated by MD simulation using SCHRODINGER DESMOND. Most stable confirmation was achieved through a protein-ligand interaction study. Bio-technological use of VP in the biotransformation of β-naphthol has also been studied. The findings in the current study will have a substantial impact on proteomics, biochemistry, biotechnology, and possible uses of versatile peroxidase in the bio-remediation of different toxic organic compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03758-x.
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Affiliation(s)
- Rohida Amin Hoque
- Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Itanagar, AP 791109 India
| | - Meera Yadav
- Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Itanagar, AP 791109 India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009 India
| | - Nivedita Rai
- Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Itanagar, AP 791109 India
| | - Shivani Negi
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009 India
| | - Hardeo Singh Yadav
- Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Itanagar, AP 791109 India
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Mali T, Laine K, Hamberg L, Lundell T. Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101199] [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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3
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Carrillo-Díaz MI, Miranda-Romero LA, Chávez-Aguilar G, Zepeda-Batista JL, González-Reyes M, García-Casillas AC, Tirado-González DN, Tirado-Estrada G. Improvement of Ruminal Neutral Detergent Fiber Degradability by Obtaining and Using Exogenous Fibrolytic Enzymes from White-Rot Fungi. Animals (Basel) 2022; 12:843. [PMID: 35405833 PMCID: PMC8997131 DOI: 10.3390/ani12070843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
The present review examines the factors and variables that should be considered to obtain, design, and evaluate EFEs that might enhance ruminal NDF degradability. Different combinations of words were introduced in Google Scholar, then scientific articles were examined and included if the reported factors and variables addressed the objective of this review. One-hundred-and-sixteen articles were included. The fungal strains and culture media used to grow white-rot fungi induced the production of specific isoforms of cellulases and xylanases; therefore, EFE products for ruminant feed applications should be obtained in cultures that include the high-fibrous forages used in the diets of those animals. Additionally, the temperature, pH, osmolarity conditions, and EFE synergisms and interactions with ruminal microbiota and endogenous fibrolytic enzymes should be considered. More consistent results have been observed in studies that correlate the cellulase-to-xylanase ratio with ruminant productive behavior. EFE protection (immobilization) allows researchers to obtain enzymatic products that may act under ruminal pH and temperature conditions. It is possible to generate multi-enzyme cocktails that act at different times, re-associate enzymes, and simulate natural protective structures such as cellulosomes. Some EFEs could consistently improve ruminal NDF degradability if we consider fungal cultures and ruminal environmental conditions variables, and include biotechnological tools that might be useful to design novel enzymatic products.
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Affiliation(s)
- María Isabel Carrillo-Díaz
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Colima, Tecomán 8930, Colima, Mexico; (M.I.C.-D.); (J.L.Z.-B.); (A.C.G.-C.)
| | - Luis Alberto Miranda-Romero
- Posgrado en Producción Animal, Departamento de Zootecnia, Universidad Autónoma Chapingo, Texcoco 56230, Edo. México, Mexico;
| | - Griselda Chávez-Aguilar
- Centro Nacional de Investigación Disciplinaria Agricultura Familiar (CENID AF), Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Ojuelos de Jalisco 47540, Jalisco, Mexico;
| | - José Luis Zepeda-Batista
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Colima, Tecomán 8930, Colima, Mexico; (M.I.C.-D.); (J.L.Z.-B.); (A.C.G.-C.)
| | - Mónica González-Reyes
- División de Estudios de Posgrado (DEPI), Tecnológico Nacional de México Aguascalientes (TecNM)/Instituto Tecnológico El Llano Aguascalientes (ITEL), El Llano 20330, Aguascalientes, Mexico;
| | - Arturo César García-Casillas
- Facultad de Medicina Veterinaria y Zootecnia, Universidad de Colima, Tecomán 8930, Colima, Mexico; (M.I.C.-D.); (J.L.Z.-B.); (A.C.G.-C.)
| | - Deli Nazmín Tirado-González
- Departamento de Ingenierías, Tecnológico Nacional de México Aguascalientes (TecNM)/Instituto Tecnológico El Llano Aguascalientes (ITEL), El Llano 20330, Aguascalientes, Mexico
| | - Gustavo Tirado-Estrada
- División de Estudios de Posgrado (DEPI), Tecnológico Nacional de México Aguascalientes (TecNM)/Instituto Tecnológico El Llano Aguascalientes (ITEL), El Llano 20330, Aguascalientes, Mexico;
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4
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Trejo-López M, Ayala-Martínez M, Zepeda-Bastida A, Franco-Fernández M, Soto-Simental S. Using spent Pleurotus ostreatus substrate to supplemented goats to increase fresh cheese yields. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2020.106297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mäkinen MA, Risulainen N, Mattila H, Lundell TK. Transcription of lignocellulose-decomposition associated genes, enzyme activities and production of ethanol upon bioconversion of waste substrate by Phlebia radiata. Appl Microbiol Biotechnol 2018; 102:5657-5672. [PMID: 29728725 DOI: 10.1007/s00253-018-9045-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/17/2018] [Accepted: 04/21/2018] [Indexed: 12/30/2022]
Abstract
Previously identified twelve plant cell wall degradation-associated genes of the white rot fungus Phlebia radiata were studied by RT-qPCR in semi-aerobic solid-state cultures on lignocellulose waste material, and on glucose-containing reference medium. Wood-decay-involved enzyme activities and ethanol production were followed to elucidate both the degradative and fermentative processes. On the waste lignocellulose substrate, P. radiata carbohydrate-active enzyme (CAZy) genes encoding cellulolytic and hemicellulolytic activities were significantly upregulated whereas genes involved in lignin modification displayed a more complex response. Two lignin peroxidase genes were differentially expressed on waste lignocellulose compared to glucose medium, whereas three manganese peroxidase-encoding genes were less affected. On the contrary, highly significant difference was noticed for three cellulolytic genes (cbhI_1, eg1, bgl1) with higher expression levels on the lignocellulose substrate than on glucose. This indicates expression of the wood-attacking degradative enzyme system by the fungus also on the recycled, waste core board material. During the second week of cultivation, ethanol production increased on the core board to 0.24 g/L, and extracellular activities against cellulose, xylan, and lignin were detected. Sugar release from the solid lignocellulose resulted with concomitant accumulation of ethanol as fermentation product. Our findings confirm that the fungus activates its white rot decay system also on industrially processed lignocellulose adopted as growth substrate, and under semi-aerobic cultivation conditions. Thus, P. radiata is a good candidate for lignocellulose-based renewable biotechnology to make biofuels and biocompounds from materials with less value for recycling or manufacturing.
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Affiliation(s)
- Mari A Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland.
| | - Netta Risulainen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Hans Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina K Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
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Production of cellulases and xylanases by white-rot fungi cultured in corn stover media for ruminant feed applications. Anim Feed Sci Technol 2016. [DOI: 10.1016/j.anifeedsci.2016.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nakazawa T, Tsuzuki M, Irie T, Sakamoto M, Honda Y. Marker recycling via 5-fluoroorotic acid and 5-fluorocytosine counter-selection in the white-rot agaricomycete Pleurotus ostreatus. Fungal Biol 2016; 120:1146-55. [PMID: 27567720 DOI: 10.1016/j.funbio.2016.06.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 01/06/2023]
Abstract
Of all of the natural polymers, lignin, an aromatic heteropolymer in plant secondary cell walls, is the most resistant to biological degradation. White-rot fungi are the only known organisms that can depolymerize or modify wood lignin. Investigating the mechanisms underlying lignin biodegradation by white-rot fungi would contribute to the ecofriendly utilization of woody biomass as renewable resources in the future. Efficient gene disruption, which is generally very challenging in the white-rot fungi, was established in Pleurotus ostreatus (the oyster mushroom). Some of the genes encoding manganese peroxidases, enzymes that are considered to be involved in lignin biodegradation, were disrupted separately, and the phenotype of each single-gene disruptant was analysed. However, it remains difficult to generate multi-gene disruptants in this fungus. Here we developed a new genetic transformation marker in P. ostreatus and demonstrated two marker recycling methods that use counter-selection to generate a multigene disruptant. This study will enable future genetic studies of white-rot fungi, and it will increase our understanding of the complicated mechanisms, which involve various enzymes, including lignin-degrading enzymes, underlying lignin biodegradation by these fungi.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masami Tsuzuki
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toshikazu Irie
- Environmental Science Graduate School, The University of Shiga Prefecture, Hikone, Shiga, 522-8533, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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Limits of Versatility of Versatile Peroxidase. Appl Environ Microbiol 2016; 82:4070-4080. [PMID: 27129968 DOI: 10.1128/aem.00743-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/22/2016] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Although Mn(2+) is the most abundant substrate of versatile peroxidases (VPs), repression of Pleurotus ostreatus vp1 expression occurred in Mn(2+)-sufficient medium. This seems to be a biological contradiction. The aim of this study was to explore the mechanism of direct oxidation by VP1 under Mn(2+)-deficient conditions, as it was found to be the predominant enzyme during fungal growth in the presence of synthetic and natural substrates. The native VP1 was purified and characterized using three substrates, Mn(2+), Orange II (OII), and Reactive Black 5 (RB5), each oxidized by a different active site in the enzyme. While the pH optimum for Mn(2+) oxidation is 5, the optimum pH for direct oxidation of both dyes was found to be 3. Indeed, effective in vivo decolorization occurred in media without addition of Mn(2+) only under acidic conditions. We have determined that Mn(2+) inhibits in vitro the direct oxidation of both OII and RB5 while RB5 stabilizes both Mn(2+) and OII oxidation. Furthermore, OII was found to inhibit the oxidation of both Mn(2+) and RB5. In addition, we could demonstrate that VP1 can cleave OII in two different modes. Under Mn(2+)-mediated oxidation conditions, VP1 was able to cleave the azo bond only in asymmetric mode, while under the optimum conditions for direct oxidation (absence of Mn(2+) at pH 3) both symmetric and asymmetric cleavages occurred. We concluded that the oxidation mechanism of aromatic compounds by VP1 is controlled by Mn(2+) and pH levels both in the growth medium and in the reaction mixture. IMPORTANCE VP1 is a member of the ligninolytic heme peroxidase gene family of the white rot fungus Pleurotus ostreatus and plays a fundamental role in biodegradation. This enzyme exhibits a versatile nature, as it can oxidize different substrates under altered environmental conditions. VPs are highly interesting enzymes due to the fact that they contain unique active sites that are responsible for direct oxidation of various aromatic compounds, including lignin, in addition to the well-known Mn(2+) binding active site. This study demonstrates the limits of versatility of P. ostreatus VP1, which harbors multiple active sites, exhibiting a broad range of enzymatic activities, but they perform differently under distinct conditions. The versatility of P. ostreatus and its enzymes is an advantageous factor in the fungal ability to adapt to changing environments. This trait expands the possibilities for the potential utilization of P. ostreatus and other white rot fungi.
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Knop D, Yarden O, Hadar Y. The ligninolytic peroxidases in the genus Pleurotus: divergence in activities, expression, and potential applications. Appl Microbiol Biotechnol 2014; 99:1025-38. [PMID: 25503316 DOI: 10.1007/s00253-014-6256-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/29/2022]
Abstract
Mushrooms of the genus Pleurotus are comprised of cultivated edible ligninolytic fungi with medicinal properties and a wide array of biotechnological and environmental applications. Like other white-rot fungi (WRF), they are able to grow on a variety of lignocellulosic biomass substrates and degrade both natural and anthropogenic aromatic compounds. This is due to the presence of the non-specific oxidative enzymatic systems, which are mainly consisted of lacasses, versatile peroxidases (VPs), and short manganese peroxidases (short-MnPs). Additional, less studied, peroxidase are dye-decolorizing peroxidases (DyPs) and heme-thiolate peroxidases (HTPs). During the past two decades, substantial information has accumulated concerning the biochemistry, structure and function of the Pleurotus ligninolytic peroxidases, which are considered to play a key role in many biodegradation processes. The production of these enzymes is dependent on growth media composition, pH, and temperature as well as the growth phase of the fungus. Mn(2+) concentration differentially affects the expression of the different genes. It also severs as a preferred substrate for these preoxidases. Recently, sequencing of the Pleurotus ostreatus genome was completed, and a comprehensive picture of the ligninolytic peroxidase gene family, consisting of three VPs and six short-MnPs, has been established. Similar enzymes were also discovered and studied in other Pleurotus species. In addition, progress has been made in the development of molecular tools for targeted gene replacement, RNAi-based gene silencing and overexpression of genes of interest. These advances increase the fundamental understanding of the ligninolytic system and provide the opportunity for harnessing the unique attributes of these WRF for applied purposes.
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Affiliation(s)
- Doriv Knop
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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10
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Salame TM, Knop D, Levinson D, Mabjeesh SJ, Yarden O, Hadar Y. Inactivation of a Pleurotus ostreatus versatile peroxidase-encoding gene (mnp2) results in reduced lignin degradation. Environ Microbiol 2013; 16:265-77. [PMID: 24119015 DOI: 10.1111/1462-2920.12279] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/29/2013] [Accepted: 09/01/2013] [Indexed: 11/27/2022]
Abstract
Lignin biodegradation by white-rot fungi is pivotal to the earth's carbon cycle. Manganese peroxidases (MnPs), the most common extracellular ligninolytic peroxidases produced by white-rot fungi, are considered key in ligninolysis. Pleurotus ostreatus, the oyster mushroom, is a preferential lignin degrader occupying niches rich in lignocellulose such as decaying trees. Here, we provide direct, genetically based proof for the functional significance of MnP to P. ostreatus ligninolytic capacity under conditions mimicking its natural habitat. When grown on a natural lignocellulosic substrate of cotton stalks under solid-state culture conditions, gene and isoenzyme expression profiles of its short MnP and versatile peroxidase (VP)-encoding gene family revealed that mnp2 was predominately expressed. mnp2, encoding the versatile short MnP isoenzyme 2 was disrupted. Inactivation of mnp2 resulted in three interrelated phenotypes, relative to the wild-type strain: (i) reduction of 14% and 36% in lignin mineralization of stalks non-amended and amended with Mn(2+), respectively; (ii) marked reduction of the bioconverted lignocellulose sensitivity to subsequent bacterial hydrolyses; and (iii) decrease in fungal respiration rate. These results may serve as the basis to clarify the roles of the various types of fungal MnPs and VPs in their contribution to white-rot decay of wood and lignocellulose in various ecosystems.
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Affiliation(s)
- Tomer M Salame
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel
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Abstract
Manganese peroxidases (MnPs) are key players in the ligninolytic system of white rot fungi. In Pleurotus ostreatus (the oyster mushroom) these enzymes are encoded by a gene family comprising nine members, mnp1 to -9 (mnp genes). Mn(2+) amendment to P. ostreatus cultures results in enhanced degradation of recalcitrant compounds (such as the azo dye orange II) and lignin. In Mn(2+)-amended glucose-peptone medium, mnp3, mnp4, and mnp9 were the most highly expressed mnp genes. After 7 days of incubation, the time point at which the greatest capacity for orange II decolorization was observed, mnp3 expression and the presence of MnP3 in the extracellular culture fluids were predominant. To determine the significance of MnP3 for ligninolytic functionality in Mn(2+)-sufficient cultures, mnp3 was inactivated via the Δku80 strain-based P. ostreatus gene-targeting system. In Mn(2+)-sufficient medium, inactivation of mnp3 did not significantly affect expression of nontargeted MnPs or their genes, nor did it considerably diminish the fungal Mn(2+)-mediated orange II decolorization capacity, despite the significant reduction in total MnP activity. Similarly, inactivation of either mnp4 or mnp9 did not affect orange II decolorization ability. These results indicate functional redundancy within the P. ostreatus MnP gene family, enabling compensation upon deficiency of one of its members.
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Salame TM, Knop D, Levinson D, Mabjeesh SJ, Yarden O, Hadar Y. Release of Pleurotus ostreatus versatile-peroxidase from Mn2+ repression enhances anthropogenic and natural substrate degradation. PLoS One 2012; 7:e52446. [PMID: 23285046 PMCID: PMC3528650 DOI: 10.1371/journal.pone.0052446] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/13/2012] [Indexed: 11/18/2022] Open
Abstract
The versatile-peroxidase (VP) encoded by mnp4 is one of the nine members of the manganese-peroxidase (MnP) gene family that constitutes part of the ligninolytic system of the white-rot basidiomycete Pleurotus ostreatus (oyster mushroom). VP enzymes exhibit dual activity on a wide range of substrates. As Mn(2+) supplement to P. ostreatus cultures results in enhanced degradation of recalcitrant compounds and lignin, we examined the effect of Mn(2+) on the expression profile of the MnP gene family. In P. ostreatus (monokaryon PC9), mnp4 was found to be the predominantly expressed mnp in Mn(2+)-deficient media, whereas strongly repressed (to approximately 1%) in Mn(2+)-supplemented media. Accordingly, in-vitro Mn(2+)-independent activity was found to be negligible. We tested whether release of mnp4 from Mn(2+) repression alters the activity of the ligninolytic system. A transformant over-expressing mnp4 (designated OEmnp4) under the control of the β-tubulin promoter was produced. Now, despite the presence of Mn(2+) in the medium, OEmnp4 produced mnp4 transcript as well as VP activity as early as 4 days after inoculation. The level of expression was constant throughout 10 days of incubation (about 0.4-fold relative to β-tubulin) and the activity was comparable to the typical activity of PC9 in Mn(2+)-deficient media. In-vivo decolorization of the azo dyes Orange II, Reactive Black 5, and Amaranth by OEmnp4 preceded that of PC9. OEmnp4 and PC9 were grown for 2 weeks under solid-state fermentation conditions on cotton stalks as a lignocellulosic substrate. [(14)C]-lignin mineralization, in-vitro dry matter digestibility, and neutral detergent fiber digestibility were found to be significantly higher (about 25%) in OEmnp4-fermented substrate, relative to PC9. We conclude that releasing Mn(2+) suppression of VP4 by over-expression of the mnp4 gene in P. ostreatus improved its ligninolytic functionality.
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Affiliation(s)
- Tomer M. Salame
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doriv Knop
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Levinson
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sameer J. Mabjeesh
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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14
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Fungal pretreatment of lignocellulosic biomass. Biotechnol Adv 2012; 30:1447-57. [DOI: 10.1016/j.biotechadv.2012.03.003] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/25/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
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15
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Mancilla RA, Canessa P, Manubens A, Vicuña R. Effect of manganese on the secretion of manganese-peroxidase by the basidiomycete Ceriporiopsis subvermispora. Fungal Genet Biol 2010; 47:656-61. [PMID: 20434578 DOI: 10.1016/j.fgb.2010.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/26/2010] [Accepted: 04/18/2010] [Indexed: 11/17/2022]
Abstract
The ligninolytic machinery of the widely used model fungus Ceriporiopsis subvermispora includes the enzymes manganese-peroxidase (MnP) and laccase (Lcs). In this work the effect of Mn(II) on the secretion of MnP was studied. Cultures grown in the absence of Mn(II) showed high levels of mnp transcripts. However, almost no MnP enzyme was detected in the extracellular medium, either by enzymatic activity assays or Western blot hybridizations. In the corresponding mycelia, immuno-electron microscopy experiments showed high levels of MnP enzyme within intracellular compartments. These results suggest that in addition to its well-known effect on transcription regulation of mnp genes, manganese influences secretion of MnP to the extracellular medium. Experiments carried out in the presence of cycloheximide confirmed that the metal is required to secrete MnP already synthesized and retained within the cell.
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Affiliation(s)
- Rodrigo A Mancilla
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Instituto Milenio de Biología Fundamental y Aplicada, Santiago, Chile
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Analysis of wide-domain transcriptional regulation in solid-state cultures of Aspergillus oryzae. J Ind Microbiol Biotechnol 2010; 37:455-69. [DOI: 10.1007/s10295-010-0691-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 01/18/2010] [Indexed: 10/19/2022]
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WIDIASTUTI HAPPY, SUHARYANTO, WULANINGTYAS AGUSTINA, SUTAMIHARDJA. Activity of Ligninolytic Enzymes during Growth and Fruiting Body Development of White Rot Fungi Omphalina sp. and Pleurotus ostreatus. HAYATI JOURNAL OF BIOSCIENCES 2008. [DOI: 10.4308/hjb.15.4.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Assi J, King A. Manganese Amendment and Pleurotus ostreatus Treatment to Convert Tomato Pomace for Inclusion in Poultry Feed. Poult Sci 2008; 87:1889-96. [DOI: 10.3382/ps.2007-00376] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mechanism for oxidation of high-molecular-weight substrates by a fungal versatile peroxidase, MnP2. Appl Environ Microbiol 2008; 74:2873-81. [PMID: 18326680 DOI: 10.1128/aem.02080-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unlike general peroxidases, Pleurotus ostreatus MnP2 was reported to have a unique property of direct oxidization of high-molecular-weight compounds, such as Poly R-478 and RNase A. To elucidate the mechanism for oxidation of polymeric substrates by MnP2, a series of mutant enzymes were produced by using a homologous gene expression system, and their reactivities were characterized. A mutant enzyme with an Ala substituting for an exposing Trp (W170A) drastically lost oxidation activity for veratryl alcohol (VA), Poly R-478, and RNase A, whereas the kinetic properties for Mn(2+) and H(2)O(2) were substantially unchanged. These results demonstrated that, in addition to VA, the high-molecular-weight substrates are directly oxidized by MnP2 at W170. Moreover, in the mutants Q266F and V166/168L, amino acid substitution(s) around W170 resulted in a decreased activity only for the high-molecular-weight substrates. These results, along with the three-dimensional modeling of the mutants, suggested that the mutations caused a steric hindrance to access of the polymeric substrates to W170. Another mutant, R263N, contained a newly generated N glycosylation site and showed a higher molecular mass in sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Interestingly, the R263N mutant exhibited an increased reactivity with VA and high-molecular-weight substrates. The existence of an additional carbohydrate modification and the catalytic properties in this mutant are discussed. This is the first study of a direct mechanism for oxidation of high-molecular-weight substrates by a fungal peroxidase using a homologous gene expression system.
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Manubens A, Canessa P, Folch C, Avila M, Salas L, Vicuña R. Manganese affects the production of laccase in the basidiomycete Ceriporiopsis subvermispora. FEMS Microbiol Lett 2007; 275:139-45. [PMID: 17711455 DOI: 10.1111/j.1574-6968.2007.00874.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The authors have previously identified and characterized lcs, a gene encoding laccase in the white-rot basidiomycete Ceriporiopsis subvermispora. In this work, the effect of Mn2+ in the production of extracellular laccase in liquid cultures of this fungus has been assessed. It was observed that at low (0-10 microM) concentrations of Mn2+, high titers of lcs-mRNA were obtained, whereas at high (160-194 microM) concentrations of this metal ion, transcripts levels decreased markedly. This phenomenon was observed at different days of growth. On the other hand, Cu2+ or Ag+, but not Zn2+ or Cd2+, led to an accumulation of lcs transcripts only in cultures grown in the absence of Mn2+. A dramatic increase in lcs transcript levels was also obtained with syringic acid, a lignin-related aromatic compound. This effect was more pronounced in cultures lacking Mn2+. In the course of these studies it was observed that Mn2+ stimulates mycelium growth. Thus, although extracellular laccase activity appeared higher in cultures containing 160 or 194 microM Mn2+, i.e. when lcs transcripts were lower, a correlation between lcs-mRNA levels and enzymatic activity was observed when values of the latter were corrected by the amount of mycelium present in the cultures.
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Affiliation(s)
- Augusto Manubens
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Rodriguez Estrada AE, Royse DJ. Yield, size and bacterial blotch resistance of Pleurotus eryngii grown on cottonseed hulls/oak sawdust supplemented with manganese, copper and whole ground soybean. BIORESOURCE TECHNOLOGY 2007; 98:1898-906. [PMID: 16973354 DOI: 10.1016/j.biortech.2006.07.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 07/10/2006] [Accepted: 07/11/2006] [Indexed: 05/11/2023]
Abstract
Experiments were performed to determine effects of supplementation of cottonseed hull/sawdust substrate with Mn, Cu, and ground soybean on yield, mushroom size, and bacterial blotch resistance of two commercial strains of Pleurotus eryngii. A basal formulation (d.w.) of cottonseed hulls (62%), aged red oak sawdust (27%), whole ground soybean (6%), corn distiller's waste (4%) and calcium sulfate (1%) was supplemented to 50, 150 or 250 microg/g Mn or Cu and to 4%, 8% and 12% whole ground soybean. The cottonseed hulls content in the basal substrate was adjusted to compensate for the addition of ground soybean. Formulated substrates were mixed, placed in 1050ml bottles, and sterilized at 121 degrees C for 90min. Mushroom yields were significantly higher from substrates containing Mn at 50 microg/g and soybean at 8% and 12% supplementation compared to the basal substrate. As the level of soybean addition to substrate increased, yield also increased. The addition of Mn at levels of 150 and 250 microg/g significantly enhanced yield as well, although less than did the 50 microg/g treatment. To assess the influence of mushroom strain and substrate composition on blotch disease severity, pilei of P. eryngii were inoculated with Pseudomonas tolaasii. Strain WC888 was more resistant to disease than WC846. Disease severity was greater when substrates were amended with Cu to 150 or 250 microg/g. There was a significant difference in inherent levels of Cu in the basidiomata of different strains, but P. eryngii did not accumulate Cu and disease severity was not correlated with Cu content of the basidiomata.
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Affiliation(s)
- A E Rodriguez Estrada
- Department of Plant Pathology, 316 Buckhout Laboratory, The Pennsylvania State University, University Park, PA 16802-4507, USA
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Minami M, Kureha O, Mori M, Kamitsuji H, Suzuki K, Irie T. Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2007; 75:609-18. [PMID: 17308906 DOI: 10.1007/s00253-007-0850-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 01/18/2007] [Accepted: 01/21/2007] [Indexed: 11/29/2022]
Abstract
To analyze the transcriptome profile during the initiation of manganese peroxidase (MnP) and lignin peroxidase (LiP) production in Phanerochaete chrysosporium, we constructed long serial analysis of gene expression (LongSAGE) libraries. A total of 13,666 tags (the number of cumulative counted tags) that included 6,945 unique tags (the number of distinct tags) were isolated from the day-3 culture, which just started the enzymes production and was 24 h after veratryl alcohol addition and oxygen-purge into the culture (day-2 culture). A total of 12,402 tags that included 6,396 unique tags were isolated from the day-2 culture, in which the activity of enzymes is not detected. The comparison of the two libraries suggested that 38 genes showed significant (p < or = 0.01) fourfold or greater upregulation; this included the MnP gene (mnp2, mnp3) and LiP H8 gene. On the other hand, 43 genes showed significant (p < or = 0.01) fourfold or greater downregulation. This LongSAGE analysis found many new candidate genes regulating the enzymes production.
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Affiliation(s)
- Masahiko Minami
- Department of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
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Qi X, Zhang Y, Chai T. Characterization of a novel plant promoter specifically induced by heavy metal and identification of the promoter regions conferring heavy metal responsiveness. PLANT PHYSIOLOGY 2007; 143:50-9. [PMID: 16861574 PMCID: PMC1761991 DOI: 10.1104/pp.106.080283] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Accepted: 07/10/2006] [Indexed: 05/11/2023]
Abstract
The bean (Phaseolus vulgaris) stress-related gene number 2 (PvSR2) gene responds to heavy metals but not to other forms of environmental stresses. To elucidate its heavy metal-regulatory mechanism at the transcriptional level, we isolated and characterized the promoter region (-1623/+48) of PvSR2. Deletions from the 5' end revealed that a sequence between -222 and -147 relative to the transcriptional start site was sufficient for heavy metal-specific induction of the promoter region of PvSR2. Detailed analysis of this 76-bp fragment indicated that heavy metal-responsive elements were localized in two regions (-222/-188 and -187/-147), each of which could separately confer heavy metal-responsive expression on the beta-glucuronidase gene in the context of a minimal cauliflower mosaic virus 35S promoter. Region I (-222/-188) contains a motif (metal-regulatory element-like sequence) similar to the consensus metal-regulatory element of the animal metallothionein gene, and mutation of this motif eliminated the heavy metal-inducible function of region I. Region II (-187/-147) had no similarity to previously identified cis-acting elements involved in heavy metal induction, suggesting the presence of a novel heavy metal-responsive element. Transformed tobacco (Nicotiana tabacum) seedlings expressing beta-glucuronidase under control of the PvSR2 promoter region (-687/+48) showed heavy metal-specific responsive activity that depended on the type and concentration of the heavy metal and the type of organ. These findings further our understanding of the regulation of PvSR2 expression and provide a new heavy-metal-inducible promoter system in transgenic plants.
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Affiliation(s)
- Xiaoting Qi
- Department of Biology, Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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24
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Hildén K, Martinez AT, Hatakka A, Lundell T. The two manganese peroxidases Pr-MnP2 and Pr-MnP3 of Phlebia radiata, a lignin-degrading basidiomycete, are phylogenetically and structurally divergent. Fungal Genet Biol 2005; 42:403-19. [PMID: 15809005 DOI: 10.1016/j.fgb.2005.01.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 12/22/2004] [Accepted: 01/13/2005] [Indexed: 11/18/2022]
Abstract
Two new, at primary sequence and protein structure levels different, manganese peroxidase encoding genes from the white rot basidiomycete Phlebia radiata are described. Both genes are expressed in liquid cultures of P. radiata containing milled alder wood or glucose as carbon source, and high Mn(2+) concentration. The gene Pr-mnp2 contains 7 introns and codes for a 390 amino-acid polypeptide, whereas Pr-mnp3 presents 11 introns and codes for a 362 amino-acid protein. The 3-D molecular models confirm this diversity; the predicted Pr-MnP2 with a long C-terminal extension has the highest structural similarity with the crystal structure of Phanerochaete chrysosporium MnP1, whereas the shorter Pr-MnP3 protein is structurally more related to lignin peroxidases (P. chrysosporium LiPH8/H2). In Pr-MnP3, however, an alanine replaces the exposed tryptophan present in LiP and versatile peroxidases, and both Pr-MnPs include the conserved Mn(2+)-binding amino-acid ligands. This is the first occasion when two enzymes of similar function and origin fall into phylogenetically distinct subfamilies within the expanding dendrogram of the class II fungal secretory heme peroxidases.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Conserved Sequence
- DNA, Complementary/chemistry
- DNA, Complementary/isolation & purification
- DNA, Fungal/chemistry
- DNA, Fungal/isolation & purification
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Introns
- Models, Molecular
- Molecular Sequence Data
- Peroxidases/chemistry
- Peroxidases/genetics
- Phanerochaete/enzymology
- Phylogeny
- Polyporales/enzymology
- RNA, Fungal/analysis
- RNA, Messenger/analysis
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology
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Affiliation(s)
- Kristiina Hildén
- Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, Viikinkaari 9, University of Helsinki, FIN-00014 Helsinki, Finland
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Kamitsuji H, Honda Y, Watanabe T, Kuwahara M. Mn2+ is dispensable for the production of active MnP2 by Pleurotus ostreatus. Biochem Biophys Res Commun 2005; 327:871-6. [PMID: 15649426 DOI: 10.1016/j.bbrc.2004.12.084] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Indexed: 11/29/2022]
Abstract
The regulation mechanism for expression of versatile peroxidase MnP2 by the basidiomycete fungus Pleurotus ostreatus was examined using chemically defined synthetic media. Expression of MnP2 was down-regulated at the transcription level by nutrient nitrogen, e.g., NH(4)(+), arginine or urea. As is often the case with other fungal manganese peroxidases, active MnP2 was not detected when Mn(2+) was omitted from the culture, while mnp2 transcription was barely affected by Mn(2+). However, Mn(2+) can be substituted by an MnP2 substrate, Poly R-478, since active MnP2 was detected extracellularly when the compound was added to the culture without Mn(2+). Enzyme stability assays with the purified MnP2 indicated an indispensable requirement for a substrate that can be used to complete the catalytic cycle, and avoid inactivation resulting from an excess H(2)O(2). This report is the first of the Mn(2+)-independent production of an active versatile peroxidase by P. ostreatus.
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Affiliation(s)
- Hisatoshi Kamitsuji
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
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Manubens A, Avila M, Canessa P, Vicuña R. Differential regulation of genes encoding manganese peroxidase (MnP) in the basidiomycete Ceriporiopsis subvermispora. Curr Genet 2003; 43:433-8. [PMID: 12802504 DOI: 10.1007/s00294-003-0410-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2003] [Revised: 05/07/2003] [Accepted: 05/12/2003] [Indexed: 11/26/2022]
Abstract
We previously identified and characterized three mnp genes coding for manganese peroxidase (MnP) in the white rot fungus Ceriporiopsis subvermispora. In this work, we assessed transcript levels of mnp genes in liquid cultures of this fungus grown under various conditions. In the absence of Mn(2+), mnp1 and mnp2 mRNA were detected by Northern hybridization, irrespective of the lack of extracellular MnP activity. Addition of Mn(2+) to the cultures led to a marked increase in both transcripts, the highest titers being observed at 10 micro M Mn(2+). mnp1 mRNA was not detected at Mn(2+ )concentrations above 80 micro M, whereas mnp2 mRNA was still observed at 320 micro M Mn(2+). Differential regulation of these genes was confirmed by the addition of Cu(2+), Zn(2+), Ag(+) and Cd(2+). These metal ions dramatically elevated both transcripts and also allowed the detection of the mnp3 transcript. In most cases, the increase in mRNA levels was partially abolished by the simultaneous presence of Mn(2+), although the latter was strictly required to detect extracellular MnP activity. However, the lignin-related compound syringic acid specifically increased the mnp1 transcript, although only in the absence of Mn(2+). These results indicate that there is no clear correlation between mnp mRNA levels and MnP activity. In addition, they strongly suggest that Mn(2+) plays a post-transcriptional role which is essential for the presence of active MnP in the extracellular fluid.
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Affiliation(s)
- Augusto Manubens
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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