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Wu JM, Zhang YZ. Gene Expression in Secondary Metabolism and Metabolic Switching Phase of Phanerochaete chrysosporium. Appl Biochem Biotechnol 2010; 162:1961-77. [DOI: 10.1007/s12010-010-8973-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 04/18/2010] [Indexed: 12/12/2022]
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Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl Environ Microbiol 2010; 76:3599-610. [PMID: 20400566 DOI: 10.1128/aem.00058-10] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.
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53
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Lundell TK, Mäkelä MR, Hildén K. Lignin-modifying enzymes in filamentous basidiomycetes--ecological, functional and phylogenetic review. J Basic Microbiol 2010; 50:5-20. [PMID: 20175122 DOI: 10.1002/jobm.200900338] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Filamentous fungi owe powerful abilities for decomposition of the extensive plant material, lignocellulose, and thereby are indispensable for the Earth's carbon cycle, generation of soil humic matter and formation of soil fine structure. The filamentous wood-decaying fungi belong to the phyla Basidiomycota and Ascomycota, and are unique organisms specified to degradation of the xylem cell wall components (cellulose, hemicelluloses, lignins and extractives). The basidiomycetous wood-decaying fungi form brackets, caps or resupinaceous (corticioid) fruiting bodies when growing on wood for dissemination of their sexual basidiospores. In particular, the ability to decompose the aromatic lignin polymers in wood is mostly restricted to the white rot basidiomycetes. The white-rot decay of wood is possible due to secretion of organic acids, secondary metabolites, and oxidoreductive metalloenzymes, heme peroxidases and laccases, encoded by divergent gene families in these fungi. The brown rot basidiomycetes obviously depend more on a non-enzymatic strategy for decomposition of wood cellulose and modification of lignin. This review gives a current ecological, genomic, and protein functional and phylogenetic perspective of the wood and lignocellulose-decaying basidiomycetous fungi.
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Affiliation(s)
- Taina K Lundell
- Fungal Biotechnology Group, Department of Applied Chemistry and Microbiology, Division of Microbiology, Viikki Biocenter, University of Helsinki, Finland.
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Mahajan S, Master ER. Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose. Appl Microbiol Biotechnol 2010; 86:1903-14. [PMID: 20306191 DOI: 10.1007/s00253-010-2516-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/19/2010] [Accepted: 02/20/2010] [Indexed: 11/29/2022]
Abstract
Proteins secreted by the white-rot, softwood-degrading fungus Phanerochaete carnosa during growth on cellulose and spruce were analyzed using tandem mass spectrometry and de novo sequencing. Homology-driven proteomics was applied to compare P. carnosa peptide sequences to proteins in Phanerochaete chrysosporium using MS BLAST and non-gapped alignment. In this way, 665 and 365 peptides from cellulose and spruce cultivations, respectively, were annotated. Predicted activities included endoglucanases from glycoside hydrolase (GH) families 5, 16, and 61, cellobiohydrolases from GH6 and GH7, GH3 beta-glucosidases, xylanases from GH10 and GH11, GH2 beta-mannosidases, and debranching hemicellulases from GH43 and CE15. Peptides corresponding to glyoxal oxidases, peroxidases, and glycopeptides that could participate in lignin degradation were also detected. Overall, predicted activities detected in extracellular filtrates of cellulose and spruce cultures were similar, suggesting that the adaptation of P. carnosa to growth on lignocellulose might result from fine tuning the expression of similar enzyme families.
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Affiliation(s)
- Sonam Mahajan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
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Kim DW, Kim A, Kim RN, Nam SH, Kang A, Chung WT, Choi SH, Park HS. Comparative analysis of expressed sequence tags from the white-rot fungi (Phanerochaete chrysosporium). Mol Cells 2010; 29:131-44. [PMID: 20069385 DOI: 10.1007/s10059-010-0018-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/22/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022] Open
Abstract
Comprehensive analysis of the transcriptome of the P. chrysosporium is a useful approach to improve our understanding of its special and unique enzyme system and fungal evolution in molecular and industrial aspects. In order to unveil the functional diversity of this white-rot fungus in gene level and the expression patterns of its genes, in this study we carried out sequencing and annotation of 4,917 P. chrysosporium expressed sequence tags (ESTs). Through our bioinformatic ESTs analysis, we elucidated that 1,751 genes were derived from the present dataset of 4,917 ESTs, based on clustering and comparative genomic analyses of the ESTs. Of the 1,751 unique ESTs, 1,006 (57.5%) had homologues and orthologues in similarity searches. Our P. chrysosporium ESTs showed many genes for encoding 23 secreted proteins, many proteins for the degradation of cellulose and hemicelluloses, and heat shock proteins for stress resistance, which explain the reason why P. chrysosporium is very important and unique white-rot fungus in dealing with contaminated resources and in degrading lignin and in applying this organism to several industrial aspects.In addition, comparative analysis has shed the fresh light on the mystery about how its unique enzyme system and stress resistance have been evolved differently from its closest relatives.
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Affiliation(s)
- Dae-Won Kim
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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56
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Choi J, Park J, Kim D, Jung K, Kang S, Lee YH. Fungal secretome database: integrated platform for annotation of fungal secretomes. BMC Genomics 2010; 11:105. [PMID: 20146824 PMCID: PMC2836287 DOI: 10.1186/1471-2164-11-105] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Accepted: 02/11/2010] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD). DESCRIPTION A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository. CONCLUSIONS The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at http://fsd.snu.ac.kr/.
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Affiliation(s)
- Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Jongsun Park
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
| | - Donghan Kim
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Kyongyong Jung
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
| | - Seogchan Kang
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul 151-921, Korea
- Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea
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Vincent D, Balesdent MH, Gibon J, Claverol S, Lapaillerie D, Lomenech AM, Blaise F, Rouxel T, Martin F, Bonneu M, Amselem J, Dominguez V, Howlett BJ, Wincker P, Joets J, Lebrun MH, Plomion C. Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 2010; 30:4118-36. [PMID: 19960477 DOI: 10.1002/elps.200900415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
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58
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Sato S, Feltus FA, Iyer P, Tien M. The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak. Curr Genet 2009; 55:273-86. [DOI: 10.1007/s00294-009-0243-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 03/14/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
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Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. Appl Environ Microbiol 2009; 75:4058-68. [PMID: 19376920 DOI: 10.1128/aem.00314-09] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wood decay basidiomycete Phanerochaete chrysosporium was grown under standard ligninolytic or cellulolytic conditions and subjected to whole-genome expression microarray analysis and liquid chromatography-tandem mass spectrometry of extracellular proteins. A total of 545 genes were flagged on the basis of significant changes in transcript accumulation and/or peptide sequences of the secreted proteins. Under nitrogen or carbon limitation, lignin and manganese peroxidase expression increased relative to nutrient replete medium. Various extracellular oxidases were also secreted in these media, supporting a physiological connection based on peroxide generation. Numerous genes presumed to be involved in mobilizing and recycling nitrogen were expressed under nitrogen limitation, and among these were several secreted glutamic acid proteases not previously observed. In medium containing microcrystalline cellulose as the sole carbon source, numerous genes encoding carbohydrate-active enzymes were upregulated. Among these were six members of the glycoside hydrolase family 61, as well as several polysaccharide lyases and carbohydrate esterases. Presenting a daunting challenge for future research, more than 190 upregulated genes are predicted to encode proteins of unknown function. Of these hypothetical proteins, approximately one-third featured predicted secretion signals, and 54 encoded proteins detected in extracellular filtrates. Our results affirm the importance of certain oxidative enzymes and, underscoring the complexity of lignocellulose degradation, also support an important role for many new proteins of unknown function.
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60
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Shah P, Atwood JA, Orlando R, El Mubarek H, Podila GK, Davis MR. Comparative Proteomic Analysis of Botrytis cinerea Secretome. J Proteome Res 2009; 8:1123-30. [DOI: 10.1021/pr8003002] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Punit Shah
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - James A. Atwood
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Ron Orlando
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Hind El Mubarek
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Gopi K. Podila
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
| | - Maria R. Davis
- Complex Carbohydrate Research Center and the Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, Athens, Georgia 30602, and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, Alabama 35899
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Mondego JMC, Carazzolle MF, Costa GGL, Formighieri EF, Parizzi LP, Rincones J, Cotomacci C, Carraro DM, Cunha AF, Carrer H, Vidal RO, Estrela RC, García O, Thomazella DPT, de Oliveira BV, Pires AB, Rio MCS, Araújo MRR, de Moraes MH, Castro LAB, Gramacho KP, Gonçalves MS, Neto JPM, Neto AG, Barbosa LV, Guiltinan MJ, Bailey BA, Meinhardt LW, Cascardo JC, Pereira GAG. A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao. BMC Genomics 2008; 9:548. [PMID: 19019209 PMCID: PMC2644716 DOI: 10.1186/1471-2164-9-548] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 11/18/2008] [Indexed: 11/10/2022] Open
Abstract
Background The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches' Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. M. perniciosa, together with the related species M. roreri, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of M. perniciosa was analyzed to evaluate the overall gene content of this phytopathogen. Results Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that M. perniciosa has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that M. perniciosa have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in M. perniciosa genome survey. Conclusion This genome survey gives an overview of the M. perniciosa genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the M. perniciosa/cacao pathosystem.
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Affiliation(s)
- Jorge M C Mondego
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas, SP, Brazil.
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Differential expression in Phanerochaete chrysosporium of membrane-associated proteins relevant to lignin degradation. Appl Environ Microbiol 2008; 74:7252-7. [PMID: 18849459 DOI: 10.1128/aem.01997-08] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fungal lignin-degrading systems likely include membrane-associated proteins that participate in diverse processes such as uptake and oxidation of lignin fragments, production of ligninolytic secondary metabolites, and defense of the mycelium against ligninolytic oxidants. Little is known about the nature or regulation of these membrane-associated components. We grew the white rot basidiomycete Phanerochaete chrysosporium on cellulose or glucose as the carbon source and monitored the mineralization of a (14)C-labeled synthetic lignin by these cultures to assess their ligninolytic competence. The results showed that the cellulose-grown cultures were ligninolytic, whereas the glucose-grown ones were not. We isolated microsomal membrane fractions from both types of culture and analyzed tryptic digests of their proteins by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the results against the predicted P. chrysosporium proteome showed that a catalase (Joint Genome Institute P. chrysosporium protein identification number [I.D.] 124398), an alcohol oxidase (126879), two transporters (137220 and 132234), and two cytochrome P450s (5011 and 8912) were upregulated under ligninolytic conditions. Quantitative reverse transcription-PCR assays showed that RNA transcripts encoding all of these proteins were also more abundant in ligninolytic cultures. Catalase 124398, alcohol oxidase 126879, and transporter 137220 were found in a proteomic analysis of partially purified plasma membranes from ligninolytic P. chrysosporium and are therefore most likely associated with the outer envelope of the fungus.
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63
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Dhawan S, Kaur J. Microbial Mannanases: An Overview of Production and Applications. Crit Rev Biotechnol 2008; 27:197-216. [DOI: 10.1080/07388550701775919] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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64
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Ravalason H, Jan G, Mollé D, Pasco M, Coutinho PM, Lapierre C, Pollet B, Bertaud F, Petit-Conil M, Grisel S, Sigoillot JC, Asther M, Herpoël-Gimbert I. Secretome analysis of Phanerochaete chrysosporium strain CIRM-BRFM41 grown on softwood. Appl Microbiol Biotechnol 2008; 80:719-33. [DOI: 10.1007/s00253-008-1596-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 11/28/2022]
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65
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Fungal secretomes—nature’s toolbox for white biotechnology. Appl Microbiol Biotechnol 2008; 80:381-8. [DOI: 10.1007/s00253-008-1572-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 06/09/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
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66
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Guais O, Borderies G, Pichereaux C, Maestracci M, Neugnot V, Rossignol M, François JM. Proteomics analysis of "Rovabiot Excel", a secreted protein cocktail from the filamentous fungus Penicillium funiculosum grown under industrial process fermentation. J Ind Microbiol Biotechnol 2008; 35:1659-68. [PMID: 18696134 DOI: 10.1007/s10295-008-0430-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/30/2008] [Indexed: 11/25/2022]
Abstract
MS/MS techniques are well customized now for proteomic analysis, even for non-sequenced organisms, since peptide sequences obtained by these methods can be matched with those found in databases from closely related sequenced organisms. We used this approach to characterize the protein content of the "Rovabio Excel", an enzymatic cocktail produced by Penicillium funiculosum that is used as feed additive in animal nutrition. Protein separation by bi-dimensional electrophoresis yielded more than 100 spots, from which 37 proteins were unambiguously assigned from peptide sequences. By one-dimensional SDS-gel electrophoresis, 34 proteins were identified among which 8 were not found in the 2-DE analysis. A third method, termed 'peptidic shotgun', which consists in a direct treatment of the cocktail by trypsin followed by separation of the peptides on two-dimensional liquid chromatography, resulted in the identification of two additional proteins not found by the two other methods. Altogether, more than 50 proteins, among which several glycosylhydrolytic, hemicellulolytic and proteolytic enzymes, were identified by combining three separation methods in this enzymatic cocktail. This work confirmed the power of proteome analysis to explore the genome expression of a non-sequenced fungus by taking advantage of sequences from phylogenetically related filamentous fungi and pave the way for further functional analysis of P. funiculosum.
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Characterization of an endoglucanase belonging to a new subfamily of glycoside hydrolase family 45 of the basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2008; 74:5628-34. [PMID: 18676702 DOI: 10.1128/aem.00812-08] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wood decay fungus Phanerochaete chrysosporium has served as a model system for the study of lignocellulose conversions, but aspects of its cellulolytic system remain uncertain. Here, we report identifying the gene that encodes the glycoside hydrolase (GH) family 45 endoglucanase (EG) from the fungus, cloning the cDNA, determining its heterologous expression in the methylotrophic yeast Pichia pastoris, and characterizing the recombinant protein. The cDNA consisted of 718 bp, including an open reading frame encoding a 19-amino-acid signal peptide, a 7-amino-acid presequence at the N-terminal region, and a 180-amino-acid mature protein, which has no cellulose binding domain. Analysis of the amino acid sequence revealed that the protein has a low similarity (<22%) to known fungal EGs belonging to the GH family 45 (EGVs). No conserved domain of this family was found by a BLAST search, suggesting that the protein should be classified into a new subdivision of this GH family. The recombinant protein has hydrolytic activity toward amorphous cellulose, carboxylmethyl cellulose, lichenan, barley beta-glucan, and glucomannan but not xylan. Moreover, a synergistic effect was observed with the recombinant GH family 6 cellobiohydrolase from the same fungus toward amorphous cellulose as a substrate, indicating that the enzyme may act in concert with other cellulolytic enzymes to hydrolyze cellulosic biomass in nature.
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69
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Sato S, Liu F, Koc H, Tien M. Expression analysis of extracellular proteins from Phanerochaete chrysosporium grown on different liquid and solid substrates. MICROBIOLOGY-SGM 2007; 153:3023-3033. [PMID: 17768245 PMCID: PMC2885613 DOI: 10.1099/mic.0.2006/000513-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
White-rot fungi secret a large number of hydrolytic and oxidative enzymes for degradation of lignocellulosic material. The sequencing of the genome of the white-rot fungus Phanerochaete chrysosporium has facilitated the characterization of its complete extracellular proteome. P. chrysosporium was grown on liquid medium, containing glucose, cellulose or wood chips as the carbon source, and also in solid substrate fermentation bags. For liquid-grown cultures, the extracellular protein fraction was separated by 2D gel electrophoresis. Protein spots were analysed by in-gel digestion and liquid chromatography (LC)/MS/MS. A total of 18 additional protein spots from the 2D gels yielded hits from blast searches. From solid substrate cultures in which the fungus was grown in bags, the proteins were resolved by SDS-PAGE, subjected to in-gel digestion and then identified by LC/MS/MS. An additional 16 proteins yielded hits on blast searches. Enzymes involved in cellulose, hemicellulose, lignin and protein degradation were identified. Expression patterns were very similar between cellulose-grown cultures and wood-grown cultures. In addition to enzymes which act on lignocellulosic material, proteases were also found, indicating the need of fungi to scavenge for nitrogen in wood.
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Affiliation(s)
- Shin Sato
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Feng Liu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hasan Koc
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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Ishida T, Yaoi K, Hiyoshi A, Igarashi K, Samejima M. Substrate recognition by glycoside hydrolase family 74 xyloglucanase from the basidiomycetePhanerochaete chrysosporium. FEBS J 2007; 274:5727-36. [DOI: 10.1111/j.1742-4658.2007.06092.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kim Y, Nandakumar MP, Marten MR. Proteomics of filamentous fungi. Trends Biotechnol 2007; 25:395-400. [PMID: 17681627 DOI: 10.1016/j.tibtech.2007.07.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 05/24/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
Proteomic analysis, defined here as the global assessment of cellular proteins expressed in a particular biological state, is a powerful tool that can provide a systematic understanding of events at the molecular level. Proteomic studies of filamentous fungi have only recently begun to appear in the literature, despite the prevalence of these organisms in the biotechnology industry, and their importance as both human and plant pathogens. Here, we review recent publications that have used a proteomic approach to develop a better understanding of filamentous fungi, highlighting sample preparation methods and whole-cell cytoplasmic proteomics, as well as subproteomics of cell envelope, mitochondrial and secreted proteins.
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Affiliation(s)
- Yonghyun Kim
- Department of Chemical and Biochemical Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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72
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Ohnishi Y, Nagase M, Ichiyanagi T, Kitamoto Y, Aimi T. Transcriptional regulation of two endoglucanase-encoding genes (cel3A and cel4) from the wood-degrading basidiomycete Polyporus arcularius. FEMS Microbiol Lett 2007; 274:218-25. [PMID: 17608693 DOI: 10.1111/j.1574-6968.2007.00831.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In the current study, the genomic and cDNA clones encoding the endoglucanase (cel4) of Polyporus arcularius were sequenced and characterized. The amino acid sequence of Cel4 indicated that it is a glycosyl hydrolase family 5 protein. The expressions of the previously cloned endoglucanase cel3A and cel4 were induced by Avicel (microcrystalline cellulose) and cellopentaose but repressed by glucose, cellobiose, cellotriose, and cellotetraose. There was a low level of transcription of both genes regardless of the carbon source. These results suggest that P. arcularius cells constitutively express a very low level of cellulase that can degrade insoluble crystalline cellulose and that the transcription of cel3A and cel4 in the cells is induced by products produced by these endoglucanases such as cellooligosaccharides.
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Affiliation(s)
- Yuka Ohnishi
- Faculty of Agriculture, Tottori University, Tottori-shi, Tottori, Japan
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73
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Kersten P, Cullen D. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 2007; 44:77-87. [PMID: 16971147 DOI: 10.1016/j.fgb.2006.07.007] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 07/20/2006] [Indexed: 11/17/2022]
Abstract
The US Department of Energy has assembled a high quality draft genome of Phanerochaete chrysosporium, a white rot Basidiomycete capable of completely degrading all major components of plant cell walls including cellulose, hemicellulose and lignin. Hundreds of sequences are predicted to encode extracellular enzymes including an impressive number of oxidative enzymes potentially involved in lignocellulose degradation. Herein, we summarize the number, organization, and expression of genes encoding peroxidases, copper radical oxidases, FAD-dependent oxidases, and multicopper oxidases. Possibly relevant to extracellular oxidative systems are genes involved in posttranslational processes and a large number of hypothetical proteins.
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Affiliation(s)
- Phil Kersten
- Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA
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74
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Larrondo LF, Canessa P, Vicuña R, Stewart P, Vanden Wymelenberg A, Cullen D. Structure and transcriptional impact of divergent repetitive elements inserted within Phanerochaete chrysosporium strain RP-78 genes. Mol Genet Genomics 2006; 277:43-55. [PMID: 17033809 DOI: 10.1007/s00438-006-0167-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 09/06/2006] [Indexed: 12/01/2022]
Abstract
We describe the structure, organization, and transcriptional impact of repetitive elements within the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Searches of the P. chrysosporium genome revealed five copies of pce1, a ~1,750-nt non-autonomous, class II element. Alleles encoding a putative glucosyltransferase and a cytochrome P450 harbor pce insertions and produce incomplete transcripts. Class I elements included pcret1, an intact 8.14-kb gypsy-like retrotransposon inserted within a member of the multicopper oxidase gene family. Additionally, we describe a complex insertion of nested transposons within another putative cytochrome P450 gene. The disrupted allele lies within a cluster of >14 genes, all of which encode family 64 cytochrome P450s. Components of the insertion include a disjoint copia-like element, pcret3, the pol domain of a second retroelement, pcret2, and a duplication of an extended ORF of unknown function. As in the case of the pce elements, pcret1 and pcret2/3 insertions are confined to single alleles, transcripts of which are truncated. The corresponding wild-type alleles are apparently unaffected. In aggregate, P. chrysosporium harbors a complex array of repetitive elements, at least five of which directly influence expression of genes within families of structurally related sequences.
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Affiliation(s)
- Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile and Instituto Milenio de Biología Fundamental y Aplicada, Santiago, Chile
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75
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Vanden Wymelenberg A, Sabat G, Mozuch M, Kersten PJ, Cullen D, Blanchette RA. Structure, organization, and transcriptional regulation of a family of copper radical oxidase genes in the lignin-degrading basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2006; 72:4871-7. [PMID: 16820482 PMCID: PMC1489383 DOI: 10.1128/aem.00375-06] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The white rot basidiomycete Phanerochaete chrysosporium produces an array of nonspecific extracellular enzymes thought to be involved in lignin degradation, including lignin peroxidases, manganese peroxidases, and the H2O2-generating copper radical oxidase, glyoxal oxidase (GLX). Preliminary analysis of the P. chrysosporium draft genome had identified six sequences with significant similarity to GLX and designated cro1 through cro6. The predicted mature protein sequences diverge substantially from one another, but the residues coordinating copper and constituting the radical redox site are conserved. Transcript profiles, microscopic examination, and lignin analysis of inoculated thin wood sections are consistent with differential regulation as decay advances. The cro2-encoded protein was detected by liquid chromatography-tandem mass spectrometry in defined medium. The cro2 cDNA was successfully expressed in Aspergillus nidulans under the control of the A. niger glucoamylase promoter and secretion signal. The recombinant CRO2 protein had a substantially different substrate preference than GLX. The role of structurally and functionally diverse cro genes in lignocellulose degradation remains to be established.
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Affiliation(s)
- Amber Vanden Wymelenberg
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Grzegorz Sabat
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael Mozuch
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Philip J. Kersten
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Dan Cullen
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
- Corresponding author. Mailing address: Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726. Phone: (608) 231-9468. Fax: (608) 231-9262. E-mail:
| | - Robert A. Blanchette
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726, Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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Vanden Wymelenberg A, Minges P, Sabat G, Martinez D, Aerts A, Salamov A, Grigoriev I, Shapiro H, Putnam N, Belinky P, Dosoretz C, Gaskell J, Kersten P, Cullen D. Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Fungal Genet Biol 2006; 43:343-56. [PMID: 16524749 DOI: 10.1016/j.fgb.2006.01.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 12/30/2005] [Accepted: 01/11/2006] [Indexed: 11/28/2022]
Abstract
The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.
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77
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Kawai R, Igarashi K, Samejima M. Gene Cloning and Heterologous Expression of Glycoside Hydrolase Family 55 β-1,3-Glucanase from the Basidiomycete Phanerochaete Chrysosporium. Biotechnol Lett 2006; 28:365-71. [PMID: 16614901 DOI: 10.1007/s10529-005-6179-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 12/12/2005] [Indexed: 10/24/2022]
Abstract
The basidiomycete Phanerochaete chrysosporium produces several beta-1,3-glucanases when grown on laminarin, a beta-1,3/1,6-glucan, as the sole carbon source. To characterize one of the major unknown beta-1, 3-glucanases with a molecular mass of 83 kDa, identification, cloning, and heterologous over-expression were carried out using the total genomic information of P. chrysosporium. The cDNA encoding this enzyme included an ORF of 2337 bp and the deduced amino acid sequence contains a predicted signal peptide of 26 amino acids and the mature protein of 752 amino acids. The amino acid sequence showed a significant similarity with glycoside hydrolase family 55 enzymes from filamentous fungi and was named Lam55A. Since the recombinant Lam55A expressed in the methylotrophic yeast Pichia pastoris degraded branched beta-1,3/1,6-glucan as well as linear beta-1,3-glucan, the kinetic features of the enzyme were compared with those of other beta-1,3-glucanases.
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Affiliation(s)
- Rie Kawai
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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79
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:128-39. [PMID: 16402416 DOI: 10.1002/jms.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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80
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O'Toole N, Min XJ, Butler G, Storms R, Tsang A. Sequence-Based Analysis of Fungal Secretomes. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1874-5334(06)80015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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81
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Kawai R, Igarashi K, Yoshida M, Kitaoka M, Samejima M. Hydrolysis of beta-1,3/1,6-glucan by glycoside hydrolase family 16 endo-1,3(4)-beta-glucanase from the basidiomycete Phanerochaete chrysosporium. Appl Microbiol Biotechnol 2005; 71:898-906. [PMID: 16374635 DOI: 10.1007/s00253-005-0214-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 10/07/2005] [Accepted: 10/10/2005] [Indexed: 10/25/2022]
Abstract
When Phanerochaete chrysosporium was grown with laminarin (a beta-1,3/1,6-glucan) as the sole carbon source, a beta-1,3-glucanase with a molecular mass of 36 kDa was produced as a major extracellular protein. The cDNA encoding this enzyme was cloned, and the deduced amino acid sequence revealed that this enzyme belongs to glycoside hydrolase family 16; it was named Lam16A. Recombinant Lam16A, expressed in the methylotrophic yeast Pichia pastoris, randomly hydrolyzes linear beta-1,3-glucan, branched beta-1,3/1,6-glucan, and beta-1,3-1,4-glucan, suggesting that the enzyme is a typical endo-1,3(4)-beta-glucanase (EC 3.2.1.6) with broad substrate specificity for beta-1,3-glucans. When laminarin and lichenan were used as substrates, Lam16A produced 6-O-glucosyl-laminaritriose (beta-D-Glcp-(1->6)-beta-D-Glcp-(1->3)-beta-D-Glcp-(1->3)-D-Glc) and 4-O-glucosyl-laminaribiose (beta-D-Glcp-(1->4)-beta-D-Glcp-(1->3)-D-Glc), respectively, as one of the major products. These results suggested that the enzyme strictly recognizes beta-D-Glcp-(1->3)-D-Glcp at subsites -2 and -1, whereas it permits 6-O-glucosyl substitution at subsite +1 and a beta-1,4-glucosidic linkage at the catalytic site. Consequently, Lam16A generates non-branched oligosaccharide from branched beta-1,3/1,6-glucan and, thus, may contribute to the effective degradation of such molecules in combination with other extracellular beta-1,3-glucanases.
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Affiliation(s)
- Rie Kawai
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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