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Wang J, Liu Y, Yin R, Wang N, Xiao T, Hirai H. RNA-Seq analysis of Phanerochaete sordida YK-624 degrades neonicotinoid pesticide acetamiprid. ENVIRONMENTAL TECHNOLOGY 2023; 44:2280-2287. [PMID: 34986752 DOI: 10.1080/09593330.2022.2026488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/22/2021] [Indexed: 06/04/2023]
Abstract
Acetamiprid (ACE) belongs to the group of neonicotinoid pesticides, which have become the most widely utilised pesticides around the world in the last two decades. The ability of Phanerochaete sordida YK-624 to degrade ACE under ligninolytic conditions has been demonstrated; however, the functional genes involved in ACE degradation have not been fully elucidated. In the present study, the differentially expressed genes of P. sordida YK-624 under ACE-degrading conditions and in the absence of ACE were elucidated by RNA sequencing (RNA-Seq). Based on the gene ontology enrichment results, the cell wall and cell membrane were significantly affected under ACE-degrading conditions. This result suggested that intracellular degradation of ACE might be mediated by this fungus. In addition, genes in metabolic pathways were the most enriched upregulated differentially expressed genes according to the KEGG pathway analysis. Eleven differentially expressed genes characterised as cytochrome P450s were upregulated, and these genes were determined to be particularly important for ACE degradation by P. sordida YK-624 under ligninolytic conditions.
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Affiliation(s)
- Jianqiao Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, People's Republic of China
| | - Yilin Liu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, People's Republic of China
| | - Ru Yin
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, People's Republic of China
| | - Nana Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, People's Republic of China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, People's Republic of China
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
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2
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Biotransformation of bisphenol F by white-rot fungus Phanerochaete sordida YK-624 under non-ligninolytic condition. Appl Microbiol Biotechnol 2022; 106:6277-6287. [DOI: 10.1007/s00253-022-12133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/02/2022]
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Lin S, Wei J, Yang B, Zhang M, Zhuo R. Bioremediation of organic pollutants by white rot fungal cytochrome P450: The role and mechanism of CYP450 in biodegradation. CHEMOSPHERE 2022; 301:134776. [PMID: 35500631 DOI: 10.1016/j.chemosphere.2022.134776] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Cytochrome P450 (CYP450) is a well-known protein family that is widely distributed in many organisms. Members of this family have been implicated in a broad range of reactions involved in the metabolism of various organic compounds. Recently, an increasing number of studies have shown that the CYP450 enzyme also participates in the elimination and degradation of organic pollutants, by white rot fungi (WRF), a famous group of natural degraders. This paper reviews previous investigations of white rot fungal CYP450 involved in the biodegradation of organic pollutants, with a special focus on inhibitory experiments, and the direct and indirect evidence of the role of white rot fungal CYP450 in bioremediation. The catalytic mechanisms of white rot fungal CYP450, its application potential, and future prospect for its use in bioremediation are then discussed.
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Affiliation(s)
- Shuqi Lin
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Jinchao Wei
- Zhongye Changtian International Engineering Co., Ltd., Changsha, 410205, PR China
| | - Bentao Yang
- Zhongye Changtian International Engineering Co., Ltd., Changsha, 410205, PR China
| | - Meng Zhang
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China
| | - Rui Zhuo
- Institute of Plant and Microbiology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410082, PR China.
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Cytochrome P450 Complement May Contribute to Niche Adaptation in Serpula Wood-Decay Fungi. J Fungi (Basel) 2022; 8:jof8030283. [PMID: 35330285 PMCID: PMC8949155 DOI: 10.3390/jof8030283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Serpula wood-decay fungi occupy a diverse range of natural and man-made ecological niches. Serpula himantioides is a forest-floor generalist with global coverage and strong antagonistic ability, while closely related species Serpula lacrymans contains specialist sister strains with widely differing ecologies. Serpula lacrymans var. shastensis is a forest-floor specialist in terms of resource preference and geographic coverage, while Serpula lacrymans var. lacrymans has successfully invaded the built environment and occupies a building-timber niche. To increase understanding of the cellular machinery required for niche adaptation, a detailed study of the P450 complement of these three strains was undertaken. Cytochrome P450 monooxygenases are present in all fungi and typically seen in high numbers in wood decay species, with putative roles in breakdown of plant extractives and lignocellulose metabolism. Investigating the genomes of these related yet ecologically diverse fungi revealed a high level of concordance in P450 complement, but with key differences in P450 family representation and expression during growth on wood, suggesting P450 proteins may play a role in niche adaptation. Gene expansion of certain key P450 families was noted, further supporting an important role for these proteins during wood decay. The generalist species S. himantioides was found to have the most P450 genes with the greatest family diversity and the highest number of P450 protein families expressed during wood decay.
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Latent potentials of the white-rot basidiomycete Phanerochaete chrysosporium responsible for sesquiterpene metabolism: CYP5158A1 and CYP5144C8 decorate (E)-α-bisabolene. Enzyme Microb Technol 2022; 158:110037. [DOI: 10.1016/j.enzmictec.2022.110037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/15/2022]
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Fessner ND, Grimm C, Kroutil W, Glieder A. Late-Stage Functionalisation of Polycyclic ( N-Hetero-) Aromatic Hydrocarbons by Detoxifying CYP5035S7 Monooxygenase of the White-Rot Fungus Polyporus arcularius. Biomolecules 2021; 11:1708. [PMID: 34827706 PMCID: PMC8615681 DOI: 10.3390/biom11111708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/04/2022] Open
Abstract
Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation of PAH compounds. In this paper, the recently discovered activity of the monooxygenase CYP5035S7 towards (N)PAHs was investigated in detail, and products formed from the substrates azulene, acenaphthene, fluorene, anthracene, and phenanthrene by whole-cell biocatalysis were isolated and characterised. The observed regioselectivity of CYP5035S7 could be explained by a combination of the substrate's electron density and steric factors influencing the substrate orientation giving insight into the active-site geometry of the enzyme.
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Affiliation(s)
- Nico D. Fessner
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria;
| | - Christopher Grimm
- Institute of Chemistry, University of Graz, NAWI Graz, 8010 Graz, Austria; (C.G.); (W.K.)
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, 8010 Graz, Austria; (C.G.); (W.K.)
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria;
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Fessner ND, Nelson DR, Glieder A. Evolution and enrichment of CYP5035 in Polyporales: functionality of an understudied P450 family. Appl Microbiol Biotechnol 2021; 105:6779-6792. [PMID: 34459954 PMCID: PMC8426240 DOI: 10.1007/s00253-021-11444-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/29/2021] [Accepted: 07/03/2021] [Indexed: 11/29/2022]
Abstract
Abstract Bioprospecting for innovative basidiomycete cytochrome P450 enzymes (P450s) is highly desirable due to the fungi’s enormous enzymatic repertoire and outstanding ability to degrade lignin and detoxify various xenobiotics. While fungal metagenomics is progressing rapidly, the biocatalytic potential of the majority of these annotated P450 sequences usually remains concealed, although functional profiling identified several P450 families with versatile substrate scopes towards various natural products. Functional knowledge about the CYP5035 family, for example, is largely insufficient. In this study, the families of the putative P450 sequences of the four white-rot fungi Polyporus arcularius, Polyporus brumalis, Polyporus squamosus and Lentinus tigrinus were assigned, and the CYPomes revealed an unusual enrichment of CYP5035, CYP5136 and CYP5150. By computational analysis of the phylogeny of the former two P450 families, the evolution of their enrichment could be traced back to the Ganoderma macrofungus, indicating their evolutionary benefit. In order to address the knowledge gap on CYP5035 functionality, a representative subgroup of this P450 family of P. arcularius was expressed and screened against a test set of substrates. Thereby, the multifunctional enzyme CYP5035S7 converting several plant natural product classes was discovered. Aligning CYP5035S7 to 102,000 putative P450 sequences of 36 fungal species from Joint Genome Institute-provided genomes located hundreds of further CYP5035 family members, which subfamilies were classified if possible. Exemplified by these specific enzyme analyses, this study gives valuable hints for future bioprospecting of such xenobiotic-detoxifying P450s and for the identification of their biocatalytic potential. Graphical abstract ![]()
Key points • The P450 families CYP5035 and CYP5136 are unusually enriched in P. arcularius. • Functional screening shows CYP5035 assisting in the fungal detoxification mechanism. • Some Polyporales encompass an unusually large repertoire of detoxification P450s. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11444-2.
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Affiliation(s)
- Nico D Fessner
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
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Iwata M, Gutiérrez A, Marques G, Sabat G, Kersten PJ, Cullen D, Bhatnagar JM, Yadav J, Lipzen A, Yoshinaga Y, Sharma A, Adam C, Daum C, Ng V, Grigoriev IV, Hori C. Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives. Sci Rep 2021; 11:12528. [PMID: 34131180 PMCID: PMC8206109 DOI: 10.1038/s41598-021-91756-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efficiently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defined media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was significantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi.
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Affiliation(s)
- Mana Iwata
- grid.39158.360000 0001 2173 7691Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 080-682 Japan
| | - Ana Gutiérrez
- grid.466818.50000 0001 2158 9975CSIC, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Reina Mercedes 10, 41012 Seville, Spain
| | - Gisela Marques
- grid.466818.50000 0001 2158 9975CSIC, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Reina Mercedes 10, 41012 Seville, Spain
| | - Grzegorz Sabat
- grid.28803.310000 0001 0701 8607University of Wisconsin Genetics Biotechnology Center, Madison, WI 53706 USA
| | - Philip J. Kersten
- grid.417548.b0000 0004 0478 6311Forest Products Laboratory, USDA, Madison, WI 53726 USA
| | - Daniel Cullen
- grid.417548.b0000 0004 0478 6311Forest Products Laboratory, USDA, Madison, WI 53726 USA
| | - Jennifer M. Bhatnagar
- grid.189504.10000 0004 1936 7558Department of Biology, Boston University, Boston, MA 02215 USA
| | - Jagjit Yadav
- grid.24827.3b0000 0001 2179 9593University of Cincinnati, Cincinnati, OH 45267 USA
| | - Anna Lipzen
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Yuko Yoshinaga
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Aditi Sharma
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Catherine Adam
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Christopher Daum
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Vivian Ng
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA
| | - Igor V. Grigoriev
- grid.451309.a0000 0004 0449 479XLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720 USA
| | - Chiaki Hori
- grid.39158.360000 0001 2173 7691Division of Applied Chemistry, Department of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628 Japan
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Dhillon B, Hamelin RC, Rollins JA. Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response. BMC Genomics 2021; 22:326. [PMID: 33952202 PMCID: PMC8097845 DOI: 10.1186/s12864-021-07644-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been found associated with live palm hosts. During the host plant colonization process, a massive transcriptional reorganization helps the fungus evade the host immune response and utilize plant cell wall polysaccharides. RESULTS A publicly available transcriptome of G. boninense - oil palm interaction was surveyed to profile transcripts that were differentially expressed in planta. Ten percent of the G. boninense transcript loci had altered expression as it colonized oil palm plants one-month post inoculation. Carbohydrate active enzymes (CAZymes), particularly those with a role in lignin degradation, and auxiliary enzymes that facilitate lignin modification, like cytochrome P450s and haloacid dehalogenases, were up-regulated in planta. Several lineage specific proteins and secreted proteins that lack known functional domains were also up-regulated in planta, but their role in the interaction could not be established. A slowdown in G. boninense respiration during the interaction can be inferred from the down-regulation of proteins involved in electron transport chain and mitochondrial biogenesis. Additionally, pathogenicity related genes and chitin degradation machinery were down-regulated during the interaction indicating G. boninense may be evading detection by the host immune system. CONCLUSIONS This analysis offers an overview of the dynamic processes at play in G. boninense - oil palm interaction and provides a framework to investigate biology of Ganoderma fungi across plantations and landscape.
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Affiliation(s)
- Braham Dhillon
- Department of Plant Pathology, University of Florida, Fort Lauderdale Research and Education Center, Davie, FL, 33314, USA.
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey A Rollins
- Department of Plant Pathology, University of Florida, 1453 Fifield Hall, Gainesville, FL, 32611-0680, USA
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Zhou Q, Wang J, Jiang H, Wang G, Wang Y. Deep sequencing of the Sanghuangporus vaninii transcriptome reveals dynamic landscapes of candidate genes involved in the biosynthesis of active compounds. Arch Microbiol 2021; 203:2315-2324. [PMID: 33646337 DOI: 10.1007/s00203-021-02225-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 01/14/2021] [Accepted: 02/11/2021] [Indexed: 11/25/2022]
Abstract
The medicinal fungus Sanghuang produces diverse bioactive compounds and is widely used in Asian countries. However, little is known about the genes and pathways involved in the biosynthesis of these active compounds. Based on our previous study providing Sanghuangporus vaninii genomic information, the transcriptomes of MY (mycelium), OY (1-year-old fruiting bodies), and TY (3-year-old fruiting bodies) were determined in this study. A significant number of genes (4774) were up- or downregulated between mycelium and fruiting bodies, but only 1422 differentially expressed genes were detected between OY and TY. 138 genes encoding P450s were identified in the fungal genome and grouped into 25 P450 families; more than 64% (88) of the genes were significantly differentially expressed between the mycelium and fruiting body, suggesting that these P450s are involved in fungal sexual development. Importantly, the expression of genes involved in bioactive compound (triterpenoids, polysaccharides, and flavonoids) biosynthesis in asexual (cultured with solid and liquid media) and sexual stages was explored and combined with transcriptome and quantitative PCR analyses. More genes involved in the biosynthesis of bioactive compounds were expressed more highly in mycelium than in fruiting bodies under liquid medium culture compared with solid medium culture, which was consistent with the yields of different bioactive compounds, suggesting that liquid fermentation of S. vaninii Kangneng can be used to obtain these bioactive compounds. A comprehensive understanding of the genomic information of S. vaninii will facilitate its potential use in pharmacological and industrial applications.
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Affiliation(s)
- Qiumei Zhou
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Jiuxiang Wang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Gaofei Wang
- Clinical Laboratory, The Central Hospital of Bianqiao Town, Bianqiao, 273305, China
| | - Yulong Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.
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Mori T, Ohno H, Ichinose H, Kawagishi H, Hirai H. White-rot fungus Phanerochaete chrysosporium metabolizes chloropyridinyl-type neonicotinoid insecticides by an N-dealkylation reaction catalyzed by two cytochrome P450s. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123831. [PMID: 33254812 DOI: 10.1016/j.jhazmat.2020.123831] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/28/2020] [Accepted: 08/21/2020] [Indexed: 06/12/2023]
Abstract
We previously identified a cytochrome P450 (CYP) derived from the white-rot fungus Phanerochaete chrysosporium as involved in degradation of acetamiprid, a neonicotinoid (NEO) insecticide. In the present study, we investigated biodegradation of other NEOs by P. chrysosporium, and attempted to identify the CYP enzyme responsible for NEO degradation. P. chrysosporium was able to degrade some NEOs (acetamiprid, clothianidin, imidacloprid, and thiacloprid) in nutrient-rich medium. Two CYPs in P. chrysosporium (PcCYPs), CYP5037B3 and CYP5147A3, were identified as major isozymes involved in metabolism of three neonicotinoids that have in common a chloropyridinyl moiety (acetamiprid, imidacloprid, and thiacloprid) by screening yeast that heterologously express PcCYPs. Both PcCYPs catalyzed cleavage of the chloropyridinyl moiety and side chain of the three NEOs by N-dealkylation, resulting in 6-chloro-3-pyridinemethanol and respective side chain fragments. In a culture of P. chrysosporium, 97 % and 74 % of imidacloprid and thiacloprid were modified to form degradation products, and one of these, 6-chloro-3-pyridinemethanol, was further degraded. These two PcCYPs catalyzed almost the same reaction but their substrate specificity and expression pattern are slightly different. Altogether, we found that P. chrysosporium degrades NEOs via the activity of at least two different CYP isozymes.
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Affiliation(s)
- Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Haruka Ohno
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirofumi Ichinose
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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12
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Zhang X, Guo J, Cheng F, Li S. Cytochrome P450 enzymes in fungal natural product biosynthesis. Nat Prod Rep 2021; 38:1072-1099. [PMID: 33710221 DOI: 10.1039/d1np00004g] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covering: 2015 to the end of 2020 Fungal-derived polyketides, non-ribosomal peptides, terpenoids and their hybrids contribute significantly to the chemical space of total natural products. Cytochrome P450 enzymes play essential roles in fungal natural product biosynthesis with their broad substrate scope, great catalytic versatility and high frequency of involvement. Due to the membrane-bound nature, the functional and mechanistic understandings for fungal P450s have been limited for quite a long time. However, recent technical advances, such as the efficient and precise genome editing techniques and the development of several filamentous fungal strains as heterologous P450 expression hosts, have led to remarkable achievements in fungal P450 studies. Here, we provide a comprehensive review to cover the most recent progresses from 2015 to 2020 on catalytic functions and mechanisms, research methodologies and remaining challenges in the fast-growing field of fungal natural product biosynthetic P450s.
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Affiliation(s)
- Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China. and Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Jiawei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fangyuan Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China. and Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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Dual Purpose of ligninolytic- basidiomycetes: mycoremediation of bioethanol distillation vinasse coupled to sustainable bio-based compounds production. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens. J Biotechnol 2020; 308:35-39. [PMID: 31778732 DOI: 10.1016/j.jbiotec.2019.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/23/2019] [Indexed: 11/23/2022]
Abstract
Heterologous production of fungal ligninolytic cocktails is challenging due to the low yields of catalytically active lignin modifying peroxidases. Production using a natural system, such as a wood-rotting fungus, is a promising alternative if specific or preferential induction of the ligninolytic activities could be achieved. Using transcriptomics, gene expression of the white-rot Dichomitus squalens during growth on mixtures of aromatic compounds, with ring structures representing the two major lignin sub-units, was compared to a wood substrate. Most of the genes encoding lignin modifying enzymes (laccases and peroxidases) categorised as highly or moderately expressed on wood were expressed similarly on aromatic compounds. Higher expression levels of a subset of manganese and versatile peroxidases was observed on di- compared to mono-methoxylated aromatics. The expression of polysaccharide degrading enzymes was lower on aromatic compounds compared to wood, demonstrating that the induction of lignin modifying enzymes became more specific. This study suggests potential for aromatic waste streams, e.g. from lignocellulose pretreatment, to produce a lignin-specific enzyme cocktail from D. squalens or other white-rot fungi.
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Wang J, Ohno H, Ide Y, Ichinose H, Mori T, Kawagishi H, Hirai H. Identification of the cytochrome P450 involved in the degradation of neonicotinoid insecticide acetamiprid in Phanerochaete chrysosporium. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:494-498. [PMID: 30875576 DOI: 10.1016/j.jhazmat.2019.03.042] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 02/20/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
We previously reported that cytochrome P450 s play critical roles in neonicotinoid insecticide biodegradation by white-rot fungi. Here, we investigated the biodegradation of acetamiprid (ACET) by Phanerochaete chrysosporium to identify the cytochrome P450 involved in this degradation process. During a 20-day incubation period, P. chrysosporium degraded 21% and 51% of ACET in ligninolytic and nonligninolytic media, respectively. The degradation rate of ACET was markedly decreased by the addition of cytochrome P450 inhibitors. Recombinant cytochrome P450s in P. chrysosporium (PcCYP) were heterologously expressed in Saccharomyces cerevisiae strain AH22, and the PcCYP involved in ACET degradation was identified. The results showed that CYP5147A3 can degrade ACET, and two ACET metabolites, N'-cyano-N-methyl acetamidine and 6-chloro-3-pyridinemethanol, were identified. To the best of our knowledge, this study provides the first characterization of the fungal cytochrome P450 that is responsible for the degradation and detoxification of ACET.
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Affiliation(s)
- Jianqiao Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Haruka Ohno
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuuri Ide
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirofumi Ichinose
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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16
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Yang C, Li W, Li C, Zhou Z, Xiao Y, Yan X. Metabolism of ganoderic acids by a Ganoderma lucidum cytochrome P450 and the 3-keto sterol reductase ERG27 from yeast. PHYTOCHEMISTRY 2018; 155:83-92. [PMID: 30077898 DOI: 10.1016/j.phytochem.2018.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Ganoderic acids, a group of oxygenated lanostane-type triterpenoids, are the major bioactive compounds produced by the well-known medicinal macro fungus Ganoderma lucidum. More than 150 ganoderic acids have been identified, and the genome of G. lucidum has been sequenced recently. However, the biosynthetic pathways of ganoderic acids have not yet been elucidated. Here, we report the functional characterization of a cytochrome P450 gene CYP512U6 from G. lucidum, which is involved in the ganoderic acid biosynthesis. CYP512U6 hydroxylates the ganoderic acids DM and TR at the C-23 position to produce hainanic acid A and ganoderic acid Jc, respectively. In addition, CYP512U6 can also hydroxylate a modified ganoderic acid DM in which the C-3 ketone has been reduced to hydroxyl by the sterol reductase ERG27 from Saccharomyces cerevisiae. An NADPH-dependent cytochrome P450 reductase from G. lucidum was also isolated and characterized. These results will help elucidate the biosynthetic pathways of ganoderic acids.
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Affiliation(s)
- Chengshuai Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weichao Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Chen Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Youli Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China.
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Fernández-González AJ, Valette N, Kohler A, Dumarçay S, Sormani R, Gelhaye E, Morel-Rouhier M. Oak extractive-induced stress reveals the involvement of new enzymes in the early detoxification response of Phanerochaete chrysosporium. Environ Microbiol 2018; 20:3890-3901. [DOI: 10.1111/1462-2920.14409] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 09/05/2018] [Accepted: 09/08/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio José Fernández-González
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
| | - Nicolas Valette
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
| | - Annegret Kohler
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
| | - Stéphane Dumarçay
- Université de Lorraine; EA4370 USC INRA 1445 Laboratoire d'Etudes et de Recherches sur le Matériau Bois; Faculté des Sciences et Technologies, Vandoeuvre-lès-Nancy Cedex France
| | - Rodnay Sormani
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
| | - Eric Gelhaye
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
| | - Mélanie Morel-Rouhier
- Université de Lorraine, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy Cedex France
- INRA, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes"; Faculté des Sciences et Technologies BP; Vandoeuvre-lès-Nancy Cedex France
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Ichinose H, Kitaoka T. Insight into metabolic diversity of the brown-rot basidiomycete Postia placenta responsible for sesquiterpene biosynthesis: semi-comprehensive screening of cytochrome P450 monooxygenase involved in protoilludene metabolism. Microb Biotechnol 2018; 11:952-965. [PMID: 30105900 PMCID: PMC6116744 DOI: 10.1111/1751-7915.13304] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022] Open
Abstract
A wide variety of sesquiterpenoids have been isolated from basidiomycetes, and their bioactive properties have attracted significant attention in an effort to understand biosynthetic machineries. As both sesquiterpene synthases and cytochrome P450 monooxygenases play key roles in the diversification of sesquiterpenoids, it is important to widely and mutually understand their biochemical properties. In this study, we performed genome‐wide annotation and functional characterization of sesquiterpene synthases from the brown‐rot basidiomycete Postia placenta. Using RT‐PCR, we isolated 16 sesquiterpene synthases genes as full‐length cDNAs. Heterologous expression revealed that the sesquiterpene synthases could produce a series of sesquiterpene scaffolds with distinct metabolic profiles. Based on metabolic studies, we identified 25 sesquiterpene scaffolds including Δ6‐protoilludene produced by the sesquiterpene synthases. In particular, a protoilludene synthase from the brown‐rot basidiomycete was characterized for the first time. Furthermore, we conducted a semi‐comprehensive functional screening of cytochrome P450 monooxygenases from P. placenta to elucidate biosynthetic machineries involved in metabolisms of Δ6‐protoilludene. Coexpression of protoilludene synthase and 184 isoforms of cytochrome P450 monooxygenases enabled the identification of CYP5344B1, CYP5348E1 and CYP5348J3, which catalysed the hydroxylation reaction of Δ6‐protoilludene to produce Δ6‐protoilludene‐8‐ol and Δ6‐protoilludene‐5‐ol. Furthermore, structural isomers of Δ7‐protoilludene‐6‐ol were obtained from incubation of Δ6‐protoilludene‐8‐ol in acidic culture medium.
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Affiliation(s)
- Hirofumi Ichinose
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
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19
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Liu J, Shamoun SF, Leal I, Kowbel R, Sumampong G, Zamany A. Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations. Microb Biotechnol 2018; 11:537-550. [PMID: 29611344 PMCID: PMC5954486 DOI: 10.1111/1751-7915.13259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
Characterization of genes involved in differentiation of pathogen species and isolates with variations of virulence traits provides valuable information to control tree diseases for meeting the challenges of sustainable forest health and phytosanitary trade issues. Lack of genetic knowledge and genomic resources hinders novel gene discovery, molecular mechanism studies and development of diagnostic tools in the management of forest pathogens. Here, we report on transcriptome profiling of Heterobasidion occidentale isolates with contrasting virulence levels. Comparative transcriptomic analysis identified orthologous groups exclusive to H. occidentale and its isolates, revealing biological processes involved in the differentiation of isolates. Further bioinformatics analyses identified an H. occidentale secretome, CYPome and other candidate effectors, from which genes with species- and isolate-specific expression were characterized. A large proportion of differentially expressed genes were revealed to have putative activities as cell wall modification enzymes and transcription factors, suggesting their potential roles in virulence and fungal pathogenesis. Next, large numbers of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected, including more than 14 000 interisolate non-synonymous SNPs. These polymorphic loci and species/isolate-specific genes may contribute to virulence variations and provide ideal DNA markers for development of diagnostic tools and investigation of genetic diversity.
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Affiliation(s)
- Jun‐Jun Liu
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Simon Francis Shamoun
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Isabel Leal
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Robert Kowbel
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Grace Sumampong
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
| | - Arezoo Zamany
- Natural Resources CanadaCanadian Forest ServicePacific Forestry Centre506 West Burnside RoadVictoriaBCV8Z 1M5Canada
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20
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Gomes TG, Hadi SIIA, Costa Alves GS, Mendonça S, De Siqueira FG, Miller RNG. Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2510-2522. [PMID: 29498277 DOI: 10.1021/acs.jafc.7b05691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.
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Affiliation(s)
- Taisa G Gomes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Sámed I I A Hadi
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas - ICB , Av. Pres. Antônio Carlos, 6627 , 31270-010 , Belo Horizonte , MG , Brazil
| | - Gabriel S Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Simone Mendonça
- Embrapa Agroenergia, STN-70297-400 , 70297-400 , Brasília , DF , Brazil
| | | | - Robert N G Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
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21
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Shin J, Kim JE, Lee YW, Son H. Fungal Cytochrome P450s and the P450 Complement (CYPome) of Fusarium graminearum. Toxins (Basel) 2018; 10:E112. [PMID: 29518888 PMCID: PMC5869400 DOI: 10.3390/toxins10030112] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/02/2018] [Accepted: 03/03/2018] [Indexed: 12/19/2022] Open
Abstract
Cytochrome P450s (CYPs), heme-containing monooxygenases, play important roles in a wide variety of metabolic processes important for development as well as biotic/trophic interactions in most living organisms. Functions of some CYP enzymes are similar across organisms, but some are organism-specific; they are involved in the biosynthesis of structural components, signaling networks, secondary metabolisms, and xenobiotic/drug detoxification. Fungi possess more diverse CYP families than plants, animals, or bacteria. Various fungal CYPs are involved in not only ergosterol synthesis and virulence but also in the production of a wide array of secondary metabolites, which exert toxic effects on humans and other animals. Although few studies have investigated the functions of fungal CYPs, a recent systematic functional analysis of CYP genes in the plant pathogen Fusarium graminearum identified several novel CYPs specifically involved in virulence, asexual and sexual development, and degradation of xenobiotics. This review provides fundamental information on fungal CYPs and a new platform for further metabolomic and biochemical studies of CYPs in toxigenic fungi.
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Affiliation(s)
| | | | | | - Hokyoung Son
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (J.S.); (J.-E.K.); (Y.-W.L.)
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22
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Valette N, Perrot T, Sormani R, Gelhaye E, Morel-Rouhier M. Antifungal activities of wood extractives. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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23
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Mgbeahuruike AC, Kovalchuk A, Ubhayasekera W, Nelson DR, Yadav JS. CYPome of the conifer pathogen Heterobasidion irregulare: Inventory, phylogeny, and transcriptional analysis of the response to biocontrol. Fungal Biol 2016; 121:158-171. [PMID: 28089047 DOI: 10.1016/j.funbio.2016.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/25/2016] [Accepted: 11/26/2016] [Indexed: 01/16/2023]
Abstract
The molecular mechanisms underlying the interaction of the pathogen, Heterobasidion annosum s.l., the conifer tree and the biocontrol fungus, Phlebiopsis gigantea have not been fully elucidated. Members of the cytochrome P450 (CYP) protein family may contribute to the detoxification of components of chemical defence of conifer trees by H. annosum during infection. Additionally, they may also be involved in the interaction between H. annosum and P. gigantea. A genome-wide analysis of CYPs in Heterobasidion irregulare was carried out alongside gene expression studies. According to the Standardized CYP Nomenclature criteria, the H. irregulare genome has 121 CYP genes and 17 CYP pseudogenes classified into 11 clans, 35 families, and 64 subfamilies. Tandem CYP arrays originating from gene duplications and belonging to the same family and subfamily were found. Phylogenetic analysis showed that all the families of H. irregulare CYPs were monophyletic groups except for the family CYP5144. Microarray analysis revealed the transcriptional pattern for 130 transcripts of CYP-encoding genes during growth on culture filtrate produced by P. gigantea. The high level of P450 gene diversity identified in this study could result from extensive gene duplications presumably caused by the high metabolic demands of H. irregulare in its ecological niches.
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Affiliation(s)
- Anthony C Mgbeahuruike
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria; Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria.
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Wimal Ubhayasekera
- Structure and Molecular Biology Program, Department of Cell and Molecular Biology, Uppsala University, Box 596, Biomedical Center, SE-751 24, Uppsala, Sweden
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee, Memphis, TN 38163, USA
| | - Jagjit S Yadav
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
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Degradation and polymerization of monolignols by Abortiporus biennis, and induction of its degradation with a reducing agent. J Microbiol 2016; 54:675-85. [DOI: 10.1007/s12275-016-6158-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/22/2016] [Accepted: 08/25/2016] [Indexed: 01/22/2023]
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25
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Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. Sci Rep 2016; 6:33099. [PMID: 27616185 PMCID: PMC5018878 DOI: 10.1038/srep33099] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/19/2016] [Indexed: 12/27/2022] Open
Abstract
Since the initial identification of cytochrome P450 monooxygenases (CYPs/P450s), great progress has been made in understanding their structure-function relationship, diversity and application in producing compounds beneficial to humans. However, the molecular evolution of P450s in terms of their dynamics both at protein and DNA levels and functional conservation across kingdoms still needs investigation. In this study, we analyzed 17 598 P450s belonging to 113 P450 families (bacteria -42; fungi -19; plant -28; animal -22; plant and animal -1 and common P450 family -1) and found highly conserved and rapidly evolving P450 families. Results suggested that bacterial P450s, particularly P450s belonging to mycobacteria, are highly conserved both at protein and DNA levels. Mycobacteria possess the highest P450 diversity percentage compared to other microbes and have a high coverage of P450s (≥1%) in their genomes, as found in fungi and plants. Phylogenetic and functional analyses revealed the functional conservation of P450s despite belonging to different biological kingdoms, suggesting the adherence of P450s to their innate function such as their involvement in either generation or oxidation of steroids and structurally related molecules, fatty acids and terpenoids. This study's results offer new understanding of the dynamic structural nature of P450s.
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Musilova L, Ridl J, Polivkova M, Macek T, Uhlik O. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments. Int J Mol Sci 2016; 17:E1205. [PMID: 27483244 PMCID: PMC5000603 DOI: 10.3390/ijms17081205] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 12/19/2022] Open
Abstract
Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.
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Affiliation(s)
- Lucie Musilova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
| | - Marketa Polivkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
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Durairaj P, Hur JS, Yun H. Versatile biocatalysis of fungal cytochrome P450 monooxygenases. Microb Cell Fact 2016; 15:125. [PMID: 27431996 PMCID: PMC4950769 DOI: 10.1186/s12934-016-0523-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/10/2016] [Indexed: 11/19/2022] Open
Abstract
Cytochrome P450 (CYP) monooxygenases, the nature’s most versatile biological catalysts have unique ability to catalyse regio-, chemo-, and stereospecific oxidation of a wide range of substrates under mild reaction conditions, thereby addressing a significant challenge in chemocatalysis. Though CYP enzymes are ubiquitous in all biological kingdoms, the divergence of CYPs in fungal kingdom is manifold. The CYP enzymes play pivotal roles in various fungal metabolisms starting from housekeeping biochemical reactions, detoxification of chemicals, and adaptation to hostile surroundings. Considering the versatile catalytic potentials, fungal CYPs has gained wide range of attraction among researchers and various remarkable strategies have been accomplished to enhance their biocatalytic properties. Numerous fungal CYPs with multispecialty features have been identified and the number of characterized fungal CYPs is constantly increasing. Literature reveals ample reviews on mammalian, plant and bacterial CYPs, however, modest reports on fungal CYPs urges a comprehensive review highlighting their novel catalytic potentials and functional significances. In this review, we focus on the diversification and functional diversity of fungal CYPs and recapitulate their unique and versatile biocatalytic properties. As such, this review emphasizes the crucial issues of fungal CYP systems, and the factors influencing efficient biocatalysis.
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Affiliation(s)
- Pradeepraj Durairaj
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
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Hatakeyama M, Kitaoka T, Ichinose H. Heterologous expression of fungal cytochromes P450 (CYP5136A1 and CYP5136A3) from the white-rot basidiomycete Phanerochaete chrysosporium: Functionalization with cytochrome b5 in Escherichia coli. Enzyme Microb Technol 2016; 89:7-14. [PMID: 27233123 DOI: 10.1016/j.enzmictec.2016.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/14/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
Cytochromes P450 from the white-rot basidiomycete Phanerochaete chrysosporium, CYP5136A1 and CYP5136A3, are capable of catalyzing oxygenation reactions of a wide variety of exogenous compounds, implying their significant roles in the metabolism of xenobiotics by the fungus. It is therefore interesting to explore their biochemistry to better understand fungal biology and to enable the use of fungal enzymes in the biotechnology sector. In the present study, we developed heterologous expression systems for CYP5136A1 and CYP5136A3 using the T7 RNA polymerase/promoter system in Escherichia coli. Expression levels of recombinant P450s were dramatically improved by modifications and optimization of their N-terminal amino acid sequences. A CYP5136A1 reaction system was reconstructed in E. coli whole cells by coexpression of CYP5136A1 and a redox partner, NADPH-dependent P450 reductase (CPR). The catalytic activity of CYP5136A1 was significantly increased when cytochrome b5 (Cyt-b5) was further coexpressed with CPR, indicating that Cyt-b5 supports electron transfer reactions from NAD(P)H to CYP5136A1. Notably, P450 reaction occurred in E. coli cells that harbored CYP5136A1 and Cyt-b5 but not CPR, implying that the reducing equivalents required for the P450 catalytic cycle were transferred via a CPR-independent pathway. Such an "alternative" electron transfer system in CYP5136A1 reaction was also demonstrated using purified enzymes in vitro. The fungal P450 reaction system may be associated with sophisticated electron transfer pathways.
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Affiliation(s)
- Mayumi Hatakeyama
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Hirofumi Ichinose
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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Schmidt-Dannert C. Biocatalytic portfolio of Basidiomycota. Curr Opin Chem Biol 2016; 31:40-9. [PMID: 26812494 DOI: 10.1016/j.cbpa.2016.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/04/2016] [Accepted: 01/08/2016] [Indexed: 11/16/2022]
Abstract
Basidiomycota fungi have received little attention for applications in biocatalysis and biotechnology and remain greatly understudied despite their importance for carbon recycling, ecosystem functioning and medicinal properties. The steady influx of genome data has facilitated detailed studies aimed at understanding the evolution and function of fungal lignocellulose degradation. These studies and recent explorations into the secondary metabolomes have uncovered large portfolios of enzymes useful for biocatalysis and biosynthesis. This review will provide an overview of the biocatalytic repertoires of Basidiomycota characterized to date with the hope of motivation more research into the chemical toolkits of this diverse group of fungi.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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Qhanya LB, Matowane G, Chen W, Sun Y, Letsimo EM, Parvez M, Yu JH, Mashele SS, Syed K. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens. PLoS One 2015; 10:e0142100. [PMID: 26536121 PMCID: PMC4633277 DOI: 10.1371/journal.pone.0142100] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens.
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Affiliation(s)
- Lehlohonolo Benedict Qhanya
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Godfrey Matowane
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yuxin Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Elizabeth Mpholoseng Letsimo
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Mohammad Parvez
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI, 53706, United States of America
| | - Samson Sitheni Mashele
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Khajamohiddin Syed
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
- * E-mail:
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31
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Ichinose H, Hatakeyama M, Yamauchi Y. Sequence modifications and heterologous expression of eukaryotic cytochromes P450 in Escherichia coli. J Biosci Bioeng 2015; 120:268-74. [DOI: 10.1016/j.jbiosc.2015.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/04/2023]
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Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes. Sci Rep 2015; 5:11572. [PMID: 26129850 PMCID: PMC4486971 DOI: 10.1038/srep11572] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/27/2015] [Indexed: 12/03/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins whose role as drug targets against pathogens, as well as in valuable chemical production and bioremediation, has been explored. In this study we performed comprehensive comparative analysis of P450s in 13 newly explored oomycete pathogens. Three hundred and fifty-six P450s were found in oomycetes. These P450s were grouped into 15 P450 families and 84 P450 subfamilies. Among these, nine P450 families and 31 P450 subfamilies were newly found in oomycetes. Research revealed that oomycetes belonging to different orders contain distinct P450 families and subfamilies in their genomes. Evolutionary analysis and sequence homology data revealed P450 family blooms in oomycetes. Tandem arrangement of a large number of P450s belonging to the same family indicated that P450 family blooming is possibly due to its members’ duplications. A unique combination of amino acid patterns was observed at EXXR and CXG motifs for the P450 families CYP5014, CYP5015 and CYP5017. A novel P450 fusion protein (CYP5619 family) with an N-terminal P450 domain fused to a heme peroxidase/dioxygenase domain was discovered in Saprolegnia declina. Oomycete P450 patterns suggested host influence in shaping their P450 content. This manuscript serves as reference for future P450 annotations in newly explored oomycetes.
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Kües U, Nelson DR, Liu C, Yu GJ, Zhang J, Li J, Wang XC, Sun H. Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles. PHYTOCHEMISTRY 2015; 114:18-37. [PMID: 25682509 DOI: 10.1016/j.phytochem.2014.11.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 06/04/2023]
Abstract
Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of Ganoderma species. The current review carries out a detailed comparison of the nuclear genomes, mitochondrial genomes and transcriptomes from several Ganoderma species. Genes involved in biosynthetic pathways such as CYP450 genes and in cellular development such as matA and matB genes are characterized and compared in detail, as examples to demonstrate the usefulness of comparative genomic analyses for the identification of critical genes. Resources needed for future data integration and exploitation are also discussed.
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Affiliation(s)
- Ursula Kües
- University of Göttingen, Büsgen-Institute, Department for Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, D-37077 Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Ave., Memphis, TN 38163, USA
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China.
| | - Guo-Jun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Jianhui Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jianqin Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xin-Cun Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
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Transcriptomic responses of Phanerochaete chrysosporium to oak acetonic extracts: focus on a new glutathione transferase. Appl Environ Microbiol 2014; 80:6316-27. [PMID: 25107961 DOI: 10.1128/aem.02103-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The first steps of wood degradation by fungi lead to the release of toxic compounds known as extractives. To better understand how lignolytic fungi cope with the toxicity of these molecules, a transcriptomic analysis of Phanerochaete chrysosporium genes was performed in the presence of oak acetonic extracts. It reveals that in complement to the extracellular machinery of degradation, intracellular antioxidant and detoxification systems contribute to the lignolytic capabilities of fungi, presumably by preventing cellular damages and maintaining fungal health. Focusing on these systems, a glutathione transferase (P. chrysosporium GTT2.1 [PcGTT2.1]) has been selected for functional characterization. This enzyme, not characterized so far in basidiomycetes, has been classified first as a GTT2 compared to the Saccharomyces cerevisiae isoform. However, a deeper analysis shows that the GTT2.1 isoform has evolved functionally to reduce lipid peroxidation by recognizing high-molecular-weight peroxides as substrates. Moreover, the GTT2.1 gene has been lost in some non-wood-decay fungi. This example suggests that the intracellular detoxification system evolved concomitantly with the extracellular ligninolytic machinery in relation to the capacity of fungi to degrade wood.
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Cajthaml T. Biodegradation of endocrine-disrupting compounds by ligninolytic fungi: mechanisms involved in the degradation. Environ Microbiol 2014; 17:4822-34. [DOI: 10.1111/1462-2920.12460] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/16/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Tomáš Cajthaml
- Institute of Microbiology; Academy of Sciences of the Czech Republic; Prague Czech Republic
- Institute for Environmental Studies; Faculty of Science; Charles University in Prague; Prague Czech Republic
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Comparative analysis of P450 signature motifs EXXR and CXG in the large and diverse kingdom of fungi: identification of evolutionarily conserved amino acid patterns characteristic of P450 family. PLoS One 2014; 9:e95616. [PMID: 24743800 PMCID: PMC3990721 DOI: 10.1371/journal.pone.0095616] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/28/2014] [Indexed: 11/25/2022] Open
Abstract
Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research.
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Syed K, Shale K, Pagadala NS, Tuszynski J. Systematic identification and evolutionary analysis of catalytically versatile cytochrome p450 monooxygenase families enriched in model basidiomycete fungi. PLoS One 2014; 9:e86683. [PMID: 24466198 PMCID: PMC3899305 DOI: 10.1371/journal.pone.0086683] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023] Open
Abstract
Genome sequencing of basidiomycetes, a group of fungi capable of degrading/mineralizing plant material, revealed the presence of numerous cytochrome P450 monooxygenases (P450s) in their genomes, with some exceptions. Considering the large repertoire of P450s found in fungi, it is difficult to identify P450s that play an important role in fungal metabolism and the adaptation of fungi to diverse ecological niches. In this study, we followed Sir Charles Darwin's theory of natural selection to identify such P450s in model basidiomycete fungi showing a preference for different types of plant components degradation. Any P450 family comprising a large number of member P450s compared to other P450 families indicates its natural selection over other P450 families by its important role in fungal physiology. Genome-wide comparative P450 analysis in the basidiomycete species, Phanerochaete chrysosporium, Phanerochaete carnosa, Agaricus bisporus, Postia placenta, Ganoderma sp. and Serpula lacrymans, revealed enrichment of 11 P450 families (out of 68 P450 families), CYP63, CYP512, CYP5035, CYP5037, CYP5136, CYP5141, CYP5144, CYP5146, CYP5150, CYP5348 and CYP5359. Phylogenetic analysis of the P450 family showed species-specific alignment of P450s across the P450 families with the exception of P450s of Phanerochaete chrysosporium and Phanerochaete carnosa, suggesting paralogous evolution of P450s in model basidiomycetes. P450 gene-structure analysis revealed high conservation in the size of exons and the location of introns. P450s with the same gene structure were found tandemly arranged in the genomes of selected fungi. This clearly suggests that extensive gene duplications, particularly tandem gene duplications, led to the enrichment of selective P450 families in basidiomycetes. Functional analysis and gene expression profiling data suggest that members of the P450 families are catalytically versatile and possibly involved in fungal colonization of plant material. To our knowledge, this is the first report on the identification and comparative-evolutionary analysis of P450 families enriched in model basidiomycetes.
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Affiliation(s)
- Khajamohiddin Syed
- Department of Life Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
- * E-mail:
| | - Karabo Shale
- Department of Life Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein, Free State, South Africa
| | | | - Jack Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
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Mathieu Y, Prosper P, Favier F, Harvengt L, Didierjean C, Jacquot JP, Morel-Rouhier M, Gelhaye E. Diversification of fungal specific class a glutathione transferases in saprotrophic fungi. PLoS One 2013; 8:e80298. [PMID: 24278272 PMCID: PMC3835915 DOI: 10.1371/journal.pone.0080298] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/01/2013] [Indexed: 11/17/2022] Open
Abstract
Glutathione transferases (GSTs) form a superfamily of multifunctional proteins with essential roles in cellular detoxification processes and endogenous metabolism. The distribution of fungal-specific class A GSTs was investigated in saprotrophic fungi revealing a recent diversification within this class. Biochemical characterization of eight GSTFuA isoforms from Phanerochaete chrysosporium and Coprinus cinereus demonstrated functional diversity in saprotrophic fungi. The three-dimensional structures of three P. chrysosporium isoforms feature structural differences explaining the functional diversity of these enzymes. Competition experiments between fluorescent probes, and various molecules, showed that these GSTs function as ligandins with various small aromatic compounds, derived from lignin degradation or not, at a L-site overlapping the glutathione binding pocket. By combining genomic data with structural and biochemical determinations, we propose that this class of GST has evolved in response to environmental constraints induced by wood chemistry.
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Affiliation(s)
- Yann Mathieu
- Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-les-Nancy, France ; INRA, IAM, UMR 1136, Champenoux, France ; Laboratoire de biotechnologie, Pôle Biotechnologie et Sylviculture Avancée, FCBA, Campus Forêt-Bois de Pierroton, Cestas, France
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Ichinose H, Wariishi H. High-level heterologous expression of fungal cytochrome P450s in Escherichia coli. Biochem Biophys Res Commun 2013; 438:289-94. [DOI: 10.1016/j.bbrc.2013.07.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 07/16/2013] [Indexed: 12/21/2022]
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40
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Wang M, Gu B, Huang J, Jiang S, Chen Y, Yin Y, Pan Y, Yu G, Li Y, Wong BHC, Liang Y, Sun H. Transcriptome and proteome exploration to provide a resource for the study of Agrocybe aegerita. PLoS One 2013; 8:e56686. [PMID: 23418592 PMCID: PMC3572045 DOI: 10.1371/journal.pone.0056686] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/14/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species. METHODOLOGY/PRINCIPAL FINDINGS To facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database. CONCLUSIONS/SIGNIFICANCE This is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry.
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Affiliation(s)
- Man Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Bianli Gu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Molecular Diagnosis Center, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, People's Republic of China
| | - Jie Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Shuai Jiang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yijie Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yalin Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yongfu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Guojun Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yamu Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Barry Hon Cheung Wong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yi Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Department of Clinical Immunology, Guangdong Medical College, Dongguan, People's Republic of China
| | - Hui Sun
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, People's Republic of China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, People's Republic of China
- * E-mail:
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Sakaki T, Yamamoto K, Ikushiro S. Possibility of application of cytochrome P450 to bioremediation of dioxins. Biotechnol Appl Biochem 2013; 60:65-70. [PMID: 23586993 DOI: 10.1002/bab.1067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/20/2012] [Indexed: 11/07/2022]
Abstract
Dioxins, including polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans, and coplanar polychlorinated biphenyls, are known to be metabolized by enzymes such as cytochrome (CYP) P450, angular dioxygenase, lignin peroxidase, and dehalogenase. It is noted that all of these enzymes have metal ions in their active centers, and the enzyme systems except for peroxidase each have a distinct electron transport chain. Among these enzyme systems, we have focused on cytochrome P450-dependent metabolism of dioxins from the viewpoint of practical use for bioremediation. Mammalian and fungal cytochromes P450 showed remarkable activity toward low-chlorinated PCDDs. In particular, mammalian cytochromes P450 belonging to the CYP1 family showed high activity. Rat CYP1A1 showed high activity toward 2,3,7-trichloro-dibenzo-p-dioxin but no detectable activity for 2,3,7,8-tetrachloro-dibenzo-p-dioxin (2,3,7,8-TCDD). On the basis of these results, we assumed that enlarging the space of the substrate-binding pocket of rat CYP1A1 might generate TCDD-metabolizing enzyme. Large-sized amino acids located at putative substrate-recognition sites and F-G loop were substituted for alanine by site-directed mutagenesis. Finally, we successfully generated 2,3,7,8-TCDD-metabolizing enzyme by site-directed mutagenesis of rat CYP1A1. We hope that recombinant microorganisms harboring genetically engineered cytochrome P450 will be used for bioremediation of soil contaminated with PCDDs, polychlorinated dibenzofurans, and coplanar polychlorinated biphenyls in the future.
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Affiliation(s)
- Toshiyuki Sakaki
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan.
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Ichinose H. Cytochrome P450 of wood-rotting basidiomycetes and biotechnological applications. Biotechnol Appl Biochem 2013; 60:71-81. [PMID: 23586994 DOI: 10.1002/bab.1061] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 11/09/2012] [Indexed: 12/23/2022]
Abstract
Wood-rotting basidiomycetes possess superior metabolic functions to degrade woody biomass, and these activities are indispensable for the carbon cycle of the biosphere. As well as basic studies of the biochemistry of basidiomycetes, many researchers have been focusing on utilizing basidiomycetes and/or their enzymes in the biotechnology sector; therefore, the unique activities of their extracellular and intracellular enzymes have been widely demonstrated. A rich history of applied study has established that basidiomycetes are capable of metabolizing a series of endogeneous and exogeneous compounds using cytochrome P450s (P450s). Recently, whole genome sequence analyses have revealed large-scale divergences in basidiomycetous P450s. The tremendous variation in P450s implies that basidiomycetes have vigorously diversified monooxygenase functions to acquire metabolic adaptations such as lignin degradation, secondary metabolite production, and xenobiotics detoxification. However, fungal P450s discovered from genome projects are often categorized into novel families and subfamilies, making it difficult to predict catalytic functions by sequence comparison. Experimental screening therefore remains essential to elucidate the catalytic potential of individual P450s, even in this postgenomic era. This paper archives the known metabolic capabilities of basidiomycetes, focusing on their P450s, outlines the molecular diversity of basidiomycetous P450s, and introduces new functions revealed by functionomic studies using a recently developed, rapid, functional screening system.
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Morel M, Meux E, Mathieu Y, Thuillier A, Chibani K, Harvengt L, Jacquot JP, Gelhaye E. Xenomic networks variability and adaptation traits in wood decaying fungi. Microb Biotechnol 2013; 6:248-63. [PMID: 23279857 PMCID: PMC3815920 DOI: 10.1111/1751-7915.12015] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/05/2012] [Accepted: 11/08/2012] [Indexed: 01/08/2023] Open
Abstract
Fungal degradation of wood is mainly restricted to basidiomycetes, these organisms having developed complex oxidative and hydrolytic enzymatic systems. Besides these systems, wood-decaying fungi possess intracellular networks allowing them to deal with the myriad of potential toxic compounds resulting at least in part from wood degradation but also more generally from recalcitrant organic matter degradation. The members of the detoxification pathways constitute the xenome. Generally, they belong to multigenic families such as the cytochrome P450 monooxygenases and the glutathione transferases. Taking advantage of the recent release of numerous genomes of basidiomycetes, we show here that these multigenic families are extended and functionally related in wood-decaying fungi. Furthermore, we postulate that these rapidly evolving multigenic families could reflect the adaptation of these fungi to the diversity of their substrate and provide keys to understand their ecology. This is of particular importance for white biotechnology, this xenome being a putative target for improving degradation properties of these fungi in biomass valorization purposes.
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Affiliation(s)
- Mélanie Morel
- Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-lès-Nancy, F-54506, France.
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Křesinová Z, Moeder M, Ezechiáš M, Svobodová K, Cajthaml T. Mechanistic study of 17α-ethinylestradiol biodegradation by Pleurotus ostreatus: tracking of extracelullar and intracelullar degradation mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:13377-13385. [PMID: 23150991 DOI: 10.1021/es3029507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The white rot fungus Pleurotus ostreatus is able to completely remove the synthetic hormone 17α-ethinylestradiol (EE2, 200 μg in 20 mL) from a liquid complex or mineral medium in 3 or 14 days, respectively. Its efficiency has also been documented in the removal of estrogenic activity that correlated with the EE2 degradation. A set of in vitro experiments using various cellular and enzyme fractions has been performed and the results showed that EE2 was degraded by isolated laccase (about 90% within 24 h). The degradation was also tested with concentrated extracellular liquid where degradation reached 50% mainly due to the laccase activity; however, after a supplementation with H₂O₂ and Mn²⁺, residual manganese-dependent peroxidase activities (40 times lower than Lac) raised the degradation to 100%. Moreover, the intracellular fraction and also laccase-like activity associated with fungal mycelium were found to be efficient in the degradation too. Isolated microsomal proteins appeared to also be involved in the process. The degradation was completely suppressed in the presence of cytochrome P-450 inhibitors, piperonylbutoxide and carbon monoxide, indicating a role of this monooxygenase in the degradation process. Attention was also paid to monitoring of changes in the estrogenic activity during these particular in vitro experiments when mainly degradations related to ligninolytic enzymes were found to decrease the estrogenic activity with EE2 removal proportionally. Several novel metabolites of EE2 were detected using different chromatographic method with mass spectrometric techniques (LC-MS, GC-MS) including also [¹³C]-labeled substrates. The results document the involvement of various different simultaneous mechanisms in the EE2 degradation by P. ostreatus by both the ligninolytic system and the eukaryotic machinery of cytochromes P-450.
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Affiliation(s)
- Zdena Křesinová
- Institute of Microbiology, Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic
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Ning D, Wang H. Involvement of cytochrome P450 in pentachlorophenol transformation in a white rot fungus Phanerochaete chrysosporium. PLoS One 2012; 7:e45887. [PMID: 23029295 PMCID: PMC3447798 DOI: 10.1371/journal.pone.0045887] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/27/2012] [Indexed: 12/22/2022] Open
Abstract
The occurrence of cytochrome P450 and P450-mediated pentachlorophenol oxidation in a white rot fungus Phanerochaete chrysosporium was demonstrated in this study. The carbon monoxide difference spectra indicated induction of P450 (103±13 pmol P450 per mg protein in the microsomal fraction) by pentachlorophenol. The pentachlorophenol oxidation by the microsomal P450 was NADPH-dependent at a rate of 19.0±1.2 pmol min−1 (mg protein)−1, which led to formation of tetrachlorohydroquinone and was significantly inhibited by piperonyl butoxide (a P450 inhibitor). Tetrachlorohydroquinone was also found in the cultures, while the extracellular ligninases which were reported to be involved in tetrachlorohydroquinone formation were undetectable. The formation of tetrachlorohydroquinone was not detectable in the cultures added with either piperonyl butoxide or cycloheximide (an inhibitor of de novo protein synthesis). These results revealed the pentachlorophenol oxidation by induced P450 in the fungus, and it should be the first time that P450-mediated pentachlorophenol oxidation was demonstrated in a microorganism. Furthermore, the addition of the P450 inhibitor to the cultures led to obvious increase of pentachlorophenol, suggesting that the relationship between P450 and pentachlorophenol methylation is worthy of further research.
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Affiliation(s)
- Daliang Ning
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, People's Republic of China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, People's Republic of China
- * E-mail:
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Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun 2012; 3:913. [PMID: 22735441 PMCID: PMC3621433 DOI: 10.1038/ncomms1923] [Citation(s) in RCA: 368] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/07/2023] Open
Abstract
Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi. Ganoderma lucidum is a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome of G. lucidum is sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.
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Ichinose H, Wariishi H. Heterologous expression and mechanistic investigation of a fungal cytochrome P450 (CYP5150A2): involvement of alternative redox partners. Arch Biochem Biophys 2011; 518:8-15. [PMID: 22206618 DOI: 10.1016/j.abb.2011.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/13/2011] [Accepted: 12/13/2011] [Indexed: 12/20/2022]
Abstract
A fungal cytochrome P450 monooxygenase (CYP5150A2) from the white-rot basidiomycete Phanerochaete chrysosporium was heterologously expressed in Escherichia coli and purified as an active form. The purified CYP5150A2 was capable of hydroxylating 4-propylbenzoic acid (PBA) with NADPH-dependent cytochrome P450 oxidoreductase (CPR) as the single redox partner; the reaction efficiency was improved by the addition of electron transfer protein cytochrome b5 (Cyt-b5). Furthermore, CYP5150A2 exhibited substantial activity with redox partners Cyt-b5 and NADH-dependent Cyt-b5 reductase (CB5R) even in the absence of CPR. These results indicated that a combination of CB5R and Cyt-b5 may be capable of donating both the first and the second electrons required for the monooxygenation reaction. Under reaction conditions in which the redox system was associated with the CB5R-dependent Cyt-b5 reduction system, the exogenous addition of CPR and NADPH had no effect on the PBA hydroxylation rate or on coupling efficiency, indicating that the transfer of the second electron from Cyt-b5 was the rate-limiting step in the monooxygenase system. In addition, the rate of PBA hydroxylation was significantly dependent on Cyt-b5 concentration, exhibiting Michaelis-Menten kinetics. This study provides indubitable evidence that the combination of CB5R and Cyt-b5 is an alternative redox partner facilitating the monooxygenase reaction catalyzed by CYP5150A2.
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Molecular identification and functional characterization of cytochrome P450 monooxygenases from the brown-rot basidiomycete Postia placenta. Arch Microbiol 2011; 194:243-53. [DOI: 10.1007/s00203-011-0753-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/19/2011] [Accepted: 09/02/2011] [Indexed: 12/21/2022]
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