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Nakazawa T, Yamaguchi I, Zhang Y, Saka C, Wu H, Kayama K, Kawauchi M, Sakamoto M, Honda Y. Experimental evidence that lignin-modifying enzymes are essential for degrading plant cell wall lignin by Pleurotus ostreatus using CRISPR/Cas9. Environ Microbiol 2023; 25:1909-1924. [PMID: 37218079 DOI: 10.1111/1462-2920.16427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Lignin-modifying enzymes (LMEs), which include laccases (Lacs), manganese peroxidases (MnPs), versatile peroxidases (VPs), and lignin peroxidases (LiPs), have been considered key factors in lignin degradation by white-rot fungi because they oxidize lignin model compounds and depolymerize synthetic lignin in vitro. However, it remains unclear whether these enzymes are essential/important in the actual degradation of natural lignin in plant cell walls. To address this long-standing issue, we examined the lignin-degrading abilities of multiple mnp/vp/lac mutants of Pleurotus ostreatus. One vp2/vp3/mnp3/mnp6 quadruple-gene mutant was generated from a monokaryotic wild-type strain PC9 using plasmid-based CRISPR/Cas9. Also, two vp2/vp3/mnp2/mnp3/mnp6, two vp2/vp3/mnp3/mnp6/lac2 quintuple-gene mutants, and two vp2/vp3/mnp2/mnp3/mnp6/lac2 sextuple-gene mutants were generated. The lignin-degrading abilities of the sextuple and vp2/vp3/mnp2/mnp3/mnp6 quintuple-gene mutants on the Beech wood sawdust medium reduced drastically, but not so much for those of the vp2/vp3/mnp3/mnp6/lac2 mutants and the quadruple mutant strain. The sextuple-gene mutants also barely degraded lignin in Japanese Cedar wood sawdust and milled rice straw. Thus, this study presented evidence that the LMEs, especially MnPs and VPs, play a crucial role in the degradation of natural lignin by P. ostreatus for the first time.
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Affiliation(s)
| | - Iori Yamaguchi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yufan Zhang
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Chinami Saka
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hongli Wu
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Keita Kayama
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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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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Xu H, Nakazawa T, Zhang Y, Oh M, Bao D, Kawauchi M, Sakamoto M, Honda Y. Introducing multiple-gene mutations in Pleurotus ostreatus using a polycistronic tRNA and CRISPR guide RNA strategy. FEMS Microbiol Lett 2022; 369:6776014. [PMID: 36302144 DOI: 10.1093/femsle/fnac102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/26/2022] [Accepted: 10/25/2022] [Indexed: 12/13/2022] Open
Abstract
The white-rot fungus Pleurotus ostreatus is an agaricomycete that is frequently used in molecular genetics studies as many useful tools are applicable to the fungus. In particular, efficient gene targeting using homologous recombination and CRISPR/Cas9 enables the introduction of a mutation in the gene of interest for functional analysis. Multiple genes encoding various lignocellulose-degrading enzymes are predicted to be present in the genome; therefore, analyses of multiple-gene mutants are required to elucidate the mechanisms underlying lignocellulose degradation by P. ostreatus. Conventional tools for generating multiple-gene mutations in P. ostreatus are laborious and time-consuming. Therefore, more efficient and practical methods are needed. In this study, we introduced CRISPR/Cas9-assisted multiple-gene mutations using a polycistronic tRNA and CRISPR guide RNA approach. The frequency (triple-gene mutation in fcy1, vp2, and 62347) was only 3.3% when a tetracistronic tRNA-sgRNA containing four different sgRNAs targeting fcy1, vp2, vp3, or 62347 was expressed. It increased to 20% (triple-gene mutation in vp1, vp2, and vp3) after a tricistronic tRNA-sgRNA was expressed with replaced/modulated promoter and tRNA sequences. This study demonstrated, for the first time, the applicability of a strategy to induce multiple-gene mutations in P. ostreatus in a transformation experiment.
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Affiliation(s)
- Haibo Xu
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yufan Zhang
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Minji Oh
- Mushroom division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Bisan-ro, Eumseong-gun, Chungcheongbuk-do 22709, Republic of Korea
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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4
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Wu H, Nakazawa T, Morimoto R, Sakamoto M, Honda Y. Targeted disruption of hir1 alters the transcriptional expression pattern of putative lignocellulolytic genes in the white-rot fungus Pleurotus ostreatus. Fungal Genet Biol 2021; 147:103507. [PMID: 33383191 DOI: 10.1016/j.fgb.2020.103507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/28/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
Abstract
Pleurotus ostreatus is frequently used in molecular genetics and genomic studies on white-rot fungi because various molecular genetic tools and relatively well-annotated genome databases are available. To explore the molecular mechanisms underlying wood lignin degradation by P. ostreatus, we performed mutational analysis of a newly isolated mutant UVRM28 that exhibits decreased lignin-degrading ability on the beech wood sawdust medium. We identified that a mutation in the hir1 gene encoding a putative histone chaperone, which probably plays an important role in DNA replication-independent nucleosome assembly, is responsible for the mutant phenotype. The expression pattern of ligninolytic genes was altered in hir1 disruptants. The most highly expressed gene vp2 was significantly inactivated, whereas the expression of vp1 was remarkably upregulated (300-400 fold) at the transcription level. Conversely, many cellulolytic and xylanolytic genes were upregulated in hir1 disruptants. Chromatin immunoprecipitation analysis suggested that the histone modification status was altered in the 5'-upstream regions of some of the up- and down-regulated lignocellulolytic genes in hir1 disruptants compared with that in the 20b strain. Hence, our data provide new insights into the regulatory mechanisms of lignocellulolytic genes in P. ostreatus.
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Affiliation(s)
- Hongli Wu
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Ryota Morimoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, 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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5
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Nguyen DX, Nakazawa T, Myo G, Inoue C, Kawauchi M, Sakamoto M, Honda Y. A promoter assay system using gene targeting in agaricomycetes Pleurotus ostreatus and Coprinopsis cinerea. J Microbiol Methods 2020; 179:106053. [PMID: 32918936 DOI: 10.1016/j.mimet.2020.106053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022]
Abstract
A novel promoter assay was developed for Agaricomycetes, using a gene-targeting approach, with or without the CRISPR/Cas9 technique. It enables precise evaluation of promoter activity at the original site of the chromosome without random and multiple integrations in conventional transformation experiments.
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Affiliation(s)
- Dong Xuan Nguyen
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Viet Nam.
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Genki Myo
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Chikako Inoue
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, 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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Feldman D, Yarden O, Hadar Y. Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles. Front Microbiol 2020; 11:455. [PMID: 32265881 PMCID: PMC7105643 DOI: 10.3389/fmicb.2020.00455] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small secreted proteins (SSPs) comprise 40–60% of the total fungal secretome and are present in fungi of all phylogenetic groups, representing the entire spectrum of lifestyles. They are characteristically shorter than 300 amino acids in length and have a signal peptide. The majority of SSPs are coded by orphan genes, which lack known domains or similarities to known protein sequences. Effectors are a group of SSPs that have been investigated extensively in fungi that interact with living hosts, either pathogens or mutualistic systems. They are involved in suppressing the host defense response and altering its physiology. Here, we aim to delineate some of the potential roles of SSPs in saprotrophic fungi, that have been bioinformatically predicted as effectors, and termed in this mini-review as “effector-like” proteins. The effector-like Ssp1 from the white-rot fungus Pleurotus ostreatus is presented as a case study, and its potential role in regulating the ligninolytic system, secondary metabolism, development, and fruiting body initiation are discussed. We propose that deciphering the nature of effector-like SSPs will contribute to our understanding of development and communication in saprophytic fungi, as well as help, to elucidate the origin, regulation, and mechanisms of fungal-host, fungal-fungal, and fungal-bacterial interactions.
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Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
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Manipulating the Expression of Small Secreted Protein 1 (Ssp1) Alters Patterns of Development and Metabolism in the White-Rot Fungus Pleurotus ostreatus. Appl Environ Microbiol 2019; 85:AEM.00761-19. [PMID: 31101610 DOI: 10.1128/aem.00761-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/09/2019] [Indexed: 01/30/2023] Open
Abstract
The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of SSPs at the onset of secondary metabolism, during colony development, and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in the regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analysis was performed during the trophophase and the idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns: OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, the OEssp1 strain exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild type into idiophase. The pigment was produced earlier and in a larger amount in the OEssp1 strain and was absent from the KDssp1 strain. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in the initiation of fruiting body formation as well as earlier aging. We propose that Ssp1 might function as a part of the fungal communication network and regulate the pattern of fungal development and metabolism in P. ostreatus IMPORTANCE Small secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred to as "effectors." We propose that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging, and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.
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Nakazawa T, Morimoto R, Wu H, Kodera R, Sakamoto M, Honda Y. Dominant effects of gat1 mutations on the ligninolytic activity of the white-rot fungus Pleurotus ostreatus. Fungal Biol 2018; 123:209-217. [PMID: 30798876 DOI: 10.1016/j.funbio.2018.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
In nature, white-rot fungi efficiently degrade lignin present in wood biomass. Elucidation of molecular mechanisms underlying wood lignin biodegradation by white-rot fungi would contribute to the development of efficient and ecofriendly methods of producing valuable chemical products from wood biomass. Here, using forward genetics approach, we demonstrate that the mutant of a putative transcription factor gene, gat1-1, significantly decreases the ligninolytic activity of the white-rot fungus Pleurotus ostreatus, when grown on beech wood sawdust medium. We also show that this phenotype is dominant. In Schizophyllum commune, Gat1 was previously shown to be involved in fruiting body development. In this study, we reveal that the mutations in gat1 gene cause defects in fruiting body development in P. ostreatus. Unlike the previously reported recessive gene mutations that decrease the ligninolytic activity of P. ostreatus, the gat1-1 mutation and Δgat1 are dominant and would thus be useful for future studies on the functional role of the orthologs in other white-rot fungi.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Ryota Morimoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hongli Wu
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Rina Kodera
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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9
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Enzymatic gene expression by Pleurotus tuoliensis (Bailinggu): differential regulation under low temperature induction conditions. World J Microbiol Biotechnol 2018; 34:160. [PMID: 30341455 DOI: 10.1007/s11274-018-2487-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
Pleurotus tuoliensis is a valuable, rare and edible mushroom that is been commercially cultivated and is rapidly developing in China markets. Low temperatures are required to induces primordia initiation for the successful production of fruiting bodies (basidiomes) during commercial cultivation. In this work, we investigated the enzymatic activities and performed transcription profiling analysis of enzymatic genes under different low temperature conditions. The results suggest that the enzymatic activities and transcription levels decrease or increase significantly at 4 and 13 °C. Lacc10 and mnp6 seems to play a dominant role during nutrition growth. Furthermore, the expression of laccase and peroxidase genes was highly correlated to the detected extracellular enzymatic activity. Cold stress genes expression profiles were upregulated under 4 °C/13 °C (3 days), while only the Hsp70 gene was downregulated (at the stage of fruiting bodies production) at 13 °C (12 days). Our results showed that the transcriptional regulation of laccase and ligninolytic peroxidase genes plays an important role in the fruiting bodies of Bailinggu under low temperature induction (4 °C). Induction at low temperatures was a highly important cultivation condition in Bailinggu.
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Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y. A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus. Sci Rep 2017; 7:14553. [PMID: 29109463 PMCID: PMC5674062 DOI: 10.1038/s41598-017-15112-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022] Open
Abstract
Small secreted proteins (SSPs), along with lignocellulose degrading enzymes, are integral components of the secretome of Pleurotus ostreatus, a white rot fungus. In this study, we identified 3 genes (ssp1, 2 and 3) encoding proteins that are annotated as SSPs and that exhibited of ~4,500- fold expression, 24 hr following exposure to the toxic compound 5-hydroxymethylfurfural (HMF). Homologues to genes encoding these SSPs are present in the genomes of other basidiomycete fungi, however the role of SSPs is not yet understood. SSPs, aryl-alcohol oxidases (AAO) and the intracellular aryl-alcohol dehydrogenases (AAD) were also produced after exposure to other aryl-alcohols, known substrates and inducers of AAOs, and during idiophase (after the onset of secondary metabolism). A knockdown strain of ssp1 exhibited reduced production of AAO-and AAD-encoding genes after HMF exposure. Conversely, a strain overexpressing ssp1 exhibited elevated expression of genes encoding AAOs and ADD, resulting in a 3-fold increase in enzymatic activity of AAOs, as well as increased expression and protein abundance of versatile peroxidase 1, which directly degrades lignin. We propose that in addition to symbionts and pathogens, SSPs also have roles in saprophytes and function in P. ostreatus as components of the ligninolytic system.
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Affiliation(s)
- Daria Feldman
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel
| | - David J Kowbel
- University of California at Berkeley UC Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California, 94720, USA
| | - N Louise Glass
- University of California at Berkeley UC Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California, 94720, USA
| | - Oded Yarden
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel
| | - Yitzhak Hadar
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel.
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Nakazawa T, Izuno A, Kodera R, Miyazaki Y, Sakamoto M, Isagi Y, Honda Y. Identification of two mutations that cause defects in the ligninolytic system through an efficient forward genetics in the white-rot agaricomycete Pleurotus ostreatus. Environ Microbiol 2017; 19:261-272. [PMID: 27871142 DOI: 10.1111/1462-2920.13595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/10/2016] [Indexed: 01/13/2023]
Abstract
White-rot fungi play an important role in the global carbon cycle because they are the species that almost exclusively biodegrade wood lignin in nature. Lignin peroxidases (LiPs), manganese peroxidases (MnPs) and versatile peroxidases (VPs) are considered key players in the ligninolytic system. Apart from LiPs, MnPs and VPs, however, only few other factors involved in the ligninolytic system have been investigated using molecular genetics, implying the existence of unidentified elements. By combining classical genetic techniques with next-generation sequencing technology, they successfully showed an efficient forward genetics approach to identify mutations causing defects in the ligninolytic system of the white-rot fungus Pleurotus ostreatus. In this study, they identified two genes - chd1 and wtr1 - mutations in which cause an almost complete loss of Mn2+ -dependent peroxidase activity. The chd1 gene encodes a putative chromatin modifier, and wtr1 encodes an agaricomycete-specific protein with a putative DNA-binding domain. The chd1-1 mutation and targeted disruption of wtr1 hamper the ability of P. ostreatus to biodegrade wood lignin. Examination of the effects of the aforementioned mutation and disruption on the expression of certain MnP/VP genes suggests that a complex mechanism underlies the ligninolytic system in P. ostreatus.
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Affiliation(s)
- Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ayako Izuno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Rina Kodera
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasumasa Miyazaki
- Department of Applied Microbiology, Forestry and Forest Product Research Institute, P O Box 16, Tsukuba-Norin, 305-8687, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuji Isagi
- 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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12
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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: 24] [Impact Index Per Article: 3.0] [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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13
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Armas-Tizapantzi A, Montiel-González AM. RNAi silencing: A tool for functional genomics research on fungi. FUNGAL BIOL REV 2016. [DOI: 10.1016/j.fbr.2016.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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: 3.6] [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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Sindhu R, Binod P, Pandey A. Biological pretreatment of lignocellulosic biomass--An overview. BIORESOURCE TECHNOLOGY 2016; 199:76-82. [PMID: 26320388 DOI: 10.1016/j.biortech.2015.08.030] [Citation(s) in RCA: 369] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 05/06/2023]
Abstract
Pretreatment is an important step involved in the production of bioethanol from lignocelluosic biomass. Though several pretreatment regimes are available, biological pretreatment seems to be promising being an eco-friendly process and there is no inhibitor generation during the process. In the current scenario there are few limitations in using this strategy for pilot scale process. The first and foremost one is the long incubation time for effective delignification. This can be minimized to an extent by using suitable microbial consortium. There is an urgent need for research and development activities and fine tuning of the process for the development of an economically viable process. This review presents an overview of various aspects of biological pretreatment, enzymes involved in the process, parameters affecting biological pretreatment as well as future perspectives.
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Affiliation(s)
- Raveendran Sindhu
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
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Hori C, Cullen D. Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Development of a transformation system for the edible mushroom Grifola frondosa: Demonstrating heterologous gene expression and RNAi-mediated gene silencing. MYCOSCIENCE 2015. [DOI: 10.1016/j.myc.2014.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pozdnyakova NN, Jarosz-Wilkolazka A, Polak J, Grąz M, Turkovskaya OV. Decolourisation of anthraquinone-and anthracene-type dyes by versatile peroxidases frombjerkandera fumosa and pleurotus ostreatusD1. BIOCATAL BIOTRANSFOR 2015. [DOI: 10.3109/10242422.2015.1060227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Pezzella C, Guarino L, Piscitelli A. How to enjoy laccases. Cell Mol Life Sci 2015; 72:923-40. [PMID: 25577278 PMCID: PMC11113763 DOI: 10.1007/s00018-014-1823-9] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 01/08/2023]
Abstract
An analysis of the scientific literature published in the last 10 years reveals a constant growth of laccase applicative research in several industrial fields followed by the publication of a great number of patents. The Green Chemistry journal devoted the cover of its September 2014 issue to a laccase as greener alternative for chemical oxidation. This indicates that laccase "never-ending story" has found a new promising trend within the constant search for efficient (bio)catalysts able to meet the 12 green chemistry principles. A survey of ancient and cutting-edge uses of laccase in different industrial sectors is offered in this review with the aim both to underline their potential and to provide inspiration for new ones. Applications in textile and food fields have been deeply described, as well as examples concerning polymer synthesis and laccase-catalysed grafting. Recent applications in pharmaceutical and cosmetic industry have also been reviewed.
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Affiliation(s)
- Cinzia Pezzella
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte S. Angelo, via Cintia 4, 80126, Naples, Italy,
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van Kuijk S, Sonnenberg A, Baars J, Hendriks W, Cone J. Fungal treated lignocellulosic biomass as ruminant feed ingredient: A review. Biotechnol Adv 2015; 33:191-202. [DOI: 10.1016/j.biotechadv.2014.10.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 09/23/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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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: 60] [Impact Index Per Article: 6.0] [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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Effects of calmodulin on expression of lignin-modifying enzymes in Pleurotus ostreatus. Curr Genet 2014; 61:127-40. [DOI: 10.1007/s00294-014-0460-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 10/26/2014] [Accepted: 10/29/2014] [Indexed: 01/28/2023]
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Koch L, Lodin A, Herold I, Ilan M, Carmeli S, Yarden O. Sensitivity of Neurospora crassa to a marine-derived Aspergillus tubingensis anhydride exhibiting antifungal activity that is mediated by the MAS1 protein. Mar Drugs 2014; 12:4713-31. [PMID: 25257783 PMCID: PMC4178490 DOI: 10.3390/md12094713] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 02/04/2023] Open
Abstract
The fungus Aspergillustubingensis (strain OY907) was isolated from the Mediterranean marine sponge Ircinia variabilis. Extracellular extracts produced by this strain were found to inhibit the growth of several fungi. Among the secreted extract components, a novel anhydride metabolite, tubingenoic anhydride A (1) as well as the known 2-carboxymethyl-3-hexylmaleic acid anhydride, asperic acid, and campyrone A and C were purified and their structure elucidated. Compound 1 and 2-carboxymethyl-3-hexylmaleic acid anhydride inhibited Neurospora crassa growth (MIC = 330 and 207 μM, respectively) and affected hyphal morphology. We produced a N. crassa mutant exhibiting tolerance to 1 and found that a yet-uncharacterized gene, designated mas-1, whose product is a cytosolic protein, confers sensitivity to this compound. The ∆mas-1 strain showed increased tolerance to sublethal concentrations of the chitin synthase inhibitor polyoxin D, when compared to the wild type. In addition, the expression of chitin synthase genes was highly elevated in the ∆mas-1 strain, suggesting the gene product is involved in cell wall biosynthesis and the novel anhydride interferes with its function.
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Affiliation(s)
- Liat Koch
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Anat Lodin
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv 69978, Israel.
| | - Inbal Herold
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Shmuel Carmeli
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv 69978, Israel.
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
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Mn²⁺-deficiency reveals a key role for the Pleurotus ostreatus versatile peroxidase (VP4) in oxidation of aromatic compounds. Appl Microbiol Biotechnol 2014; 98:6795-804. [PMID: 24737058 DOI: 10.1007/s00253-014-5689-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Abstract
The manganese peroxidase gene family (mnps) is a part of the ligninolytic system of Pleurotus ostreatus. This gene family is comprised of nine members, mnp1-9, encoding short manganese peroxidases (short-MnPs) or versatile peroxidases (VPs). We show that unlike in Mn(2+)-amended glucose-peptone (GP) medium, where redundancy among mnps was reported, in Mn(2+)-deficient GP medium mnp4 [encoding versatile peroxidase isoenzyme 4 (VP4)] has a key and nonredundant function. The abundance of mnps transcripts at time points corresponding to the tropophase (active growth), early idiophase, and idiophase indicates that mnp4 is the predominantly expressed mnp gene and that its relative predominance is dependent on the age of the culture. In this medium, azo dye, Orange II (OII) decolorization occurs only during the idiophase and a Δmnp4 strain showed a drastic reduction in this decolorization. Three degradation metabolites were identified by liquid chromatography-mass spectroscopy (LC-MS), indicating both asymmetric and symmetric enzymatic cleavage of the azo-bond. In addition, the culture filtrate of Δmnp4 showed negligible values of oxidation capability of four typical VP substrates: Mn(2+), 2,6-dimethoxyphenol, phenol red, and Reactive Black 5 (RB5), compared to the wild-type strain PC9. We concluded that under Mn(2+)-deficient GP culture, VP4 (encoded by mnp4) is the main active ligninolytic enzyme able to oxidize Mn(2+) as well as high and low redox potential aromatic substrate, including dyes. Furthermore, other VPs/MnPs do not compensate for the lack of VP4 activity.
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26
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Fernández-Fueyo E, Castanera R, Ruiz-Dueñas FJ, López-Lucendo MF, Ramírez L, Pisabarro AG, Martínez AT. Ligninolytic peroxidase gene expression by Pleurotus ostreatus: differential regulation in lignocellulose medium and effect of temperature and pH. Fungal Genet Biol 2014; 72:150-161. [PMID: 24560615 DOI: 10.1016/j.fgb.2014.02.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 02/03/2014] [Accepted: 02/09/2014] [Indexed: 11/16/2022]
Abstract
Pleurotus ostreatus is an important edible mushroom and a model lignin degrading organism, whose genome contains nine genes of ligninolytic peroxidases, characteristic of white-rot fungi. These genes encode six manganese peroxidase (MnP) and three versatile peroxidase (VP) isoenzymes. Using liquid chromatography coupled to tandem mass spectrometry, secretion of four of these peroxidase isoenzymes (VP1, VP2, MnP2 and MnP6) was confirmed when P. ostreatus grows in a lignocellulose medium at 25°C (three more isoenzymes were identified by only one unique peptide). Then, the effect of environmental parameters on the expression of the above nine genes was studied by reverse transcription-quantitative PCR by changing the incubation temperature and medium pH of P. ostreatus cultures pre-grown under the above conditions (using specific primers and two reference genes for result normalization). The cultures maintained at 25°C (without pH adjustment) provided the highest levels of peroxidase transcripts and the highest total activity on Mn(2+) (a substrate of both MnP and VP) and Reactive Black 5 (a VP specific substrate). The global analysis of the expression patterns divides peroxidase genes into three main groups according to the level of expression at optimal conditions (vp1/mnp3>vp2/vp3/mnp1/mnp2/mnp6>mnp4/mnp5). Decreasing or increasing the incubation temperature (to 10°C or 37°C) and adjusting the culture pH to acidic or alkaline conditions (pH 3 and 8) generally led to downregulation of most of the peroxidase genes (and decrease of the enzymatic activity), as shown when the transcription levels were referred to those found in the cultures maintained at the initial conditions. Temperature modification produced less dramatic effects than pH modification, with most genes being downregulated during the whole 10°C treatment, while many of them were alternatively upregulated (often 6h after the thermal shock) and downregulated (12h) at 37°C. Interestingly, mnp4 and mnp5 were the only peroxidase genes upregulated under alkaline pH conditions. The differences in the transcription levels of the peroxidase genes when the culture temperature and pH parameters were changed suggest an adaptive expression according to environmental conditions. Finally, the intracellular proteome was analyzed, under the same conditions used in the secretomic analysis, and the protein product of the highly-transcribed gene mnp3 was detected. Therefore, it was concluded that the absence of MnP3 from the secretome of the P. ostreatus lignocellulose cultures was related to impaired secretion.
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Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain
| | - Raul Castanera
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | | | - María F López-Lucendo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain
| | - Lucía Ramírez
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | - Antonio G Pisabarro
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.
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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: 3.1] [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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Sakamoto T, Honda Y, Kameshita I, Suzuki K, Irie T. Isolation and heterologous expression of the Phanerochaete chrysosporium calmodulin gene. MYCOSCIENCE 2013. [DOI: 10.1016/j.myc.2012.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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29
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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: 2.7] [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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Amore A, Honda Y, Faraco V. Copper induction of enhanced green fluorescent protein expression inPleurotus ostreatusdriven by laccasepoxa1bpromoter. FEMS Microbiol Lett 2012; 337:155-63. [DOI: 10.1111/1574-6968.12023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022] Open
Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences; University of Naples ‘Federico II’; Complesso Universitario Monte S. Angelo; Napoli; Italy
| | - Yoichi Honda
- Graduate School of Agriculture; Kyoto University; Kyoto; Japan
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Amore A, Honda Y, Faraco V. Enhanced Green Fluorescent Protein Expression in Pleurotus ostreatus for In Vivo Analysis of Fungal Laccase Promoters. Appl Biochem Biotechnol 2012; 168:761-9. [DOI: 10.1007/s12010-012-9816-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
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Predominance of a versatile-peroxidase-encoding gene, mnp4, as demonstrated by gene replacement via a gene targeting system for Pleurotus ostreatus. Appl Environ Microbiol 2012; 78:5341-52. [PMID: 22636004 DOI: 10.1128/aem.01234-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pleurotus ostreatus (the oyster mushroom) and other white rot filamentous basidiomycetes are key players in the global carbon cycle. P. ostreatus is also a commercially important edible fungus with medicinal properties and is important for biotechnological and environmental applications. Efficient gene targeting via homologous recombination (HR) is a fundamental tool for facilitating comprehensive gene function studies. Since the natural HR frequency in Pleurotus transformations is low (2.3%), transformed DNA is predominantly integrated ectopically. To overcome this limitation, a general gene targeting system was developed by producing a P. ostreatus PC9 homokaryon Δku80 strain, using carboxin resistance complemented by the development of a protocol for hygromycin B resistance protoplast-based DNA transformation and homokaryon isolation. The Δku80 strain exhibited exclusive (100%) HR in the integration of transforming DNA, providing a high efficiency of gene targeting. Furthermore, the Δku80 strains produced showed a phenotype similar to that of the wild-type PC9 strain, with similar growth fitness, ligninolytic functionality, and capability of mating with the incompatible strain PC15 to produce a dikaryon which retained its resistance to the corresponding selection and was capable of producing typical fruiting bodies. The applicability of this system is demonstrated by inactivation of the versatile peroxidase (VP) encoded by mnp4. This enzyme is part of the ligninolytic system of P. ostreatus, being one of the nine members of the manganese-peroxidase (MnP) gene family, and is the predominantly expressed VP in Mn(2+)-deficient media. mnp4 inactivation provided a direct proof that mnp4 encodes a key VP responsible for the Mn(2+)-dependent and Mn(2+)-independent peroxidase activity under Mn(2+)-deficient culture conditions.
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Transcriptional analysis of Pleurotus ostreatus laccase genes. Appl Microbiol Biotechnol 2012; 97:705-17. [DOI: 10.1007/s00253-012-3980-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
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Golan-Rozen N, Chefetz B, Ben-Ari J, Geva J, Hadar Y. Transformation of the recalcitrant pharmaceutical compound carbamazepine by Pleurotus ostreatus: role of cytochrome P450 monooxygenase and manganese peroxidase. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:6800-6805. [PMID: 21744850 DOI: 10.1021/es200298t] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Carbamazepine (CBZ) is an environmentally recalcitrant compound highly stable in soil and during wastewater treatment. In this study, we examined the mechanisms by which the white-rot fungus Pleurotus ostreatus metabolizes CBZ in liquid culture using a physiological approach. P. ostreatus PC9 was grown in media known to support different levels of a multiplicity of enzyme systems such as cytochrome P450 (CYP450) and manganese peroxidase (MnP). When both CYP450 and MnP systems were active, 99% of the added CBZ was eliminated from the solution and transformed to 10,11-epoxycarbamazepine. High removal of CBZ was also obtained when either MnP or CYP450 was active. When both CYP450 and MnP were inactivated, only 10 to 30% of the added CBZ was removed. In this latter system, removal of CBZ might be partially attributed to the activity of versatile peroxidase. P. ostreatus was able to eliminate CBZ in liquid culture even when CBZ was added at an environmentally relevant concentration (1 μg L(-1)). On the basis of our study, we suggest that two families of enzymes are involved in the oxidation of CBZ in liquid culture: MnP in a Mn(2+)-dependent or independent manner and CYP450. Our study also highlights the potential of using P. ostreatus for bioremediation systems.
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Affiliation(s)
- Naama Golan-Rozen
- 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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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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Michán C, Daniels C, Fernández M, Solano J, De La Campa AM, Ramos JL. Sugar (ribose), spice (peroxidase) and all things nice (laccase hair-dyes). Microb Biotechnol 2011; 3:131-3. [PMID: 21255315 PMCID: PMC3836576 DOI: 10.1111/j.1751-7915.2010.00167.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Department. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C-6, 2a Planta, 14071, Córdoba, Spain
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Salame TM, Ziv C, Hadar Y, Yarden O. RNAi as a potential tool for biotechnological applications in fungi. Appl Microbiol Biotechnol 2010; 89:501-12. [DOI: 10.1007/s00253-010-2928-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 09/29/2010] [Accepted: 09/29/2010] [Indexed: 12/28/2022]
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Differential gene expression of ligninolytic enzymes in Pleurotus ostreatus grown on olive oil mill wastewater. Appl Microbiol Biotechnol 2010; 88:541-51. [DOI: 10.1007/s00253-010-2750-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/17/2010] [Accepted: 06/20/2010] [Indexed: 10/19/2022]
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