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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (BETHESDA, MD.) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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Serbent MP, Magario I, Saux C. Immobilizing white-rot fungi laccase: Toward bio-derived supports as a circular economy approach in organochlorine removal. Biotechnol Bioeng 2024; 121:434-455. [PMID: 37990982 DOI: 10.1002/bit.28591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/23/2023] [Accepted: 10/28/2023] [Indexed: 11/23/2023]
Abstract
Despite their high persistence in the environment, organochlorines (OC) are widely used in the pharmaceutical industry, in plastics, and in the manufacture of pesticides, among other applications. These compounds and the byproducts of their decomposition deserve attention and efficient proposals for their treatment. Among sustainable alternatives, the use of ligninolytic enzymes (LEs) from fungi stands out, as these molecules can catalyze the transformation of a wide range of pollutants. Among LEs, laccases (Lac) are known for their efficiency as biocatalysts in the conversion of organic pollutants. Their application in biotechnological processes is possible, but the enzymes are often unstable and difficult to recover after use, driving up costs. Immobilization of enzymes on a matrix (support or solid carrier) allows recovery and stabilization of this catalytic capacity. Agricultural residual biomass is a passive environmental asset. Although underestimated and still treated as an undesirable component, residual biomass can be used as a low-cost adsorbent and as a support for the immobilization of enzymes. In this review, the adsorption capacity and immobilization of fungal Lac on supports made from residual biomass, including compounds such as biochar, for the removal of OC compounds are analyzed and compared with the use of synthetic supports. A qualitative and quantitative comparison of the reported results was made. In this context, the use of peanut shells is highlighted in view of the increasing peanut production worldwide. The linkage of methods with circular economy approaches that can be applied in practice is discussed.
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Affiliation(s)
- Maria Pilar Serbent
- Centro de Investigación y Tecnología Química (CITeQ), Facultad Regional Córdoba, Universidad Tecnológica Nacional (CONICET), Córdoba, Argentina
- Programa de Pós-Graduação em Ciências Ambientais (PPGCAMB), Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brasil
| | - Ivana Magario
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada (IPQA), Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (CONICET), Córdoba, Argentina
| | - Clara Saux
- Centro de Investigación y Tecnología Química (CITeQ), Facultad Regional Córdoba, Universidad Tecnológica Nacional (CONICET), Córdoba, Argentina
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Umar A, Ahmed S. Optimization, purification and characterization of laccase from Ganoderma leucocontextum along with its phylogenetic relationship. Sci Rep 2022; 12:2416. [PMID: 35165332 PMCID: PMC8844424 DOI: 10.1038/s41598-022-06111-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
The aim of this work to study an efficient laccase producing fungus Ganoderma leucocontextum, which was identified by ITS regions of DNA and phylogenetic tree was constructed. This study showed the laccase first-time from G. leucocontextum by using medium containing guaiacol. The growth cultural (pH, temperature, incubation days, rpm) and nutritional (carbon and nitrogen sources) conditions were optimized, which enhanced the enzyme production up to 4.5-folds. Laccase production increased 855 U/L at 40 °C. The pH 5.0 was suitable for laccase secretion (2517 U/L) on the 7th day of incubation at 100 rpm (698.3 U/L). Glucose and sucrose were good carbon source to enhance the laccase synthesis. The 10 g/L beef (4671 U/L) and yeast extract (5776 U/L) were the best nitrogen source for laccase secretion from G. leucocontextum. The laccase was purified from the 80% ammonium sulphate precipitations of protein identified by nucleotides sequence. The molecular weight (65.0 kDa) of purified laccase was identified through SDS and native PAGE entitled as Glacc110. The Glacc110 was characterized under different parameters. It retained > 90% of its activity for 16 min incubation at 60 °C in acidic medium (pH 4.0). This enzyme exerted its optimal activity at pH 3.0 and temperature 70 °C with guaiacol substrate. The catalytic parameters Km and Vmax was 1.658 (mM) and 2.452 (mM/min), respectively. The thermo stability of the laccase produced by submerged fermentation of G. leucocontextum has potential for industrial and biotechnology applications. The results remarked the G. leucocontextum is a good source for laccase production.
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Bleha R, Třešnáková L, Sushytskyi L, Capek P, Čopíková J, Klouček P, Jablonský I, Synytsya A. Polysaccharides from Basidiocarps of the Polypore Fungus Ganoderma resinaceum: Isolation and Structure. Polymers (Basel) 2022; 14:255. [PMID: 35054662 PMCID: PMC8778809 DOI: 10.3390/polym14020255] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
In this study, we focused on the isolation and structural characterization of polysaccharides from a basidiocarp of polypore fungus Ganoderma resinaceum. Polysaccharide fractions were obtained by successive extractions with cold water at room temperature (20 °C), hot water under reflux (100 °C), and a solution of 1 mol L-1 sodium hydroxide. The purity of all fractions was controlled mainly by Fourier transform infrared (FTIR) spectroscopy, and their composition and structure were characterized by organic elemental analysis; neutral sugar and methylation analyses by gas chromatography equipped with flame ionization detector (GC/FID) and mass spectrometry detector (GC/MS), respectively; and by correlation nuclear magnetic resonance (NMR) spectroscopy. The aqueous extracts contained two main polysaccharides identified as a branched O-2-β-d-mannosyl-(1→6)-α-d-galactan and a highly branched (1→3)(1→4)(1→6)-β-d-glucan. Mannogalactan predominated in the cold water extract, and β-d-glucan was the main product of the hot water extract. The hot water soluble fraction was further separated by preparative anion exchange chromatography into three sub-fractions; two of them were identified as branched β-d-glucans with a structure similar to the corresponding polysaccharide of the original fraction. The alkaline extract contained a linear (1→3)-α-d-glucan and a weakly branched (1→3)-β-d-glucan having terminal β-d-glucosyl residues attached to O-6 of the backbone. The insoluble part after all extractions was identified as a polysaccharide complex containing chitin and β-d-glucans.
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Affiliation(s)
- Roman Bleha
- Department of Carbohydrates and Cereals, UCT Prague, 166 28 Prague, Czech Republic; (L.T.); (L.S.); (J.Č.)
| | - Lucie Třešnáková
- Department of Carbohydrates and Cereals, UCT Prague, 166 28 Prague, Czech Republic; (L.T.); (L.S.); (J.Č.)
| | - Leonid Sushytskyi
- Department of Carbohydrates and Cereals, UCT Prague, 166 28 Prague, Czech Republic; (L.T.); (L.S.); (J.Č.)
| | - Peter Capek
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 842 38 Bratislava, Slovakia;
| | - Jana Čopíková
- Department of Carbohydrates and Cereals, UCT Prague, 166 28 Prague, Czech Republic; (L.T.); (L.S.); (J.Č.)
| | - Pavel Klouček
- Department of Gardening, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Ivan Jablonský
- Department of Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Andriy Synytsya
- Department of Carbohydrates and Cereals, UCT Prague, 166 28 Prague, Czech Republic; (L.T.); (L.S.); (J.Č.)
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Improvement of laccase activity by silencing PacC in Ganoderma lucidum. World J Microbiol Biotechnol 2022; 38:32. [PMID: 34989903 DOI: 10.1007/s11274-021-03216-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 12/18/2021] [Indexed: 10/19/2022]
Abstract
Ganoderma lucidum is a representative white-rot fungus that has great potential to degrade lignocellulose biomass. Laccase is recognized as a class of the most important lignin-degrading enzymes in G. lucidum. However, the comprehensive regulatory mechanisms of laccase are still lacking. Based on the genome sequence of G. lucidum, 15 laccase genes were identified and their encoding proteins were analyzed in this study. All of the laccase proteins are predicted to be multicopper oxidases with conserved copper-binding domains. Most laccase proteins were secreted enzymes in addition to Lac14 in which the signal peptide could not be predicted. The activity of all laccases showed the highest level at pH 3.0 or pH 7.0, with total laccase activity of approximately 200 U/mg protein. Silencing PacC resulted in a 5.2 fold increase in laccase activity compared with WT. Five laccase genes (lac1, lac6, lac9, lac10 and lac14) showed an increased transcription levels (approximately 1.5-5.6 fold) in the PacC-silenced strains versus that in WT, while other laccase genes were downregulated or unchanged. The extracellular pH value was about 3.1, which was more acidic in the PacC-silenced strains than in the WT (pH 3.5). Moreover, maintaining the fermentation pH resulted in a downregulation of laccase activity which is induced by silencing PacC. Our findings indicate that in addition to its function in acidification of environmental pH, PacC plays an important role in regulating laccase activity in fungi.
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Wu Q, Zhang R, Jin M, Jiang Y, Wang Y, Zhou X. Screening of engineered Pichia pastoris mutant with enhanced production of a functional rFIP-glu protein and investigating its potential bioactivities. Lett Appl Microbiol 2021; 73:770-778. [PMID: 34597432 DOI: 10.1111/lam.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 12/01/2022]
Abstract
An engineered Pichia pastoris GS115 with a FIP-glu gene was mutated using ultraviolet (UV) radiation, and a high-throughput screening method was established for screening of high-yield strains. Meanwhile, a preliminary study was conducted to determine the bioactivity of the rFIP-glu. Based on OD600 value and the mortality of engineered P. pastoris GS115, the best UV irradiation time was determined. Bradford method and SDS-PAGE method were employed to analyze the concentration and yield of rFIP-glu. Melanoma B16 cells were employed to evaluate the biological activities of rFIP-glu in vitro. Results showed that the protein yield of the best mutant #4-336 screened from 3680 mutant strains increased from 242 to 469 μg ml-1 . In vitro assays of biological activity indicated that rFIP-glu had significant toxicity and possessed the ability to affect melanin content and enhance tyrosinase activity in B16 cells. In conclusion, an effective high-throughput screening approach was established for screening mutant strains. The screened mutant possesses a good ability to enhance the production of rFIP-glu, and recombinant proteins display a better biological activity on melanoma B16 cells. The engineered P. pastoris mutant seems promising as a potential source for industrial production of rFIP-glu and should be a candidate industrial strain for further study.
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Affiliation(s)
- Q Wu
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - R Zhang
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - M Jin
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Y Jiang
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Y Wang
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - X Zhou
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Biocatalytic potential of basidiomycetes: Relevance, challenges and research interventions in industrial processes. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Gryzenhout M, Ghosh S, Tchotet Tchoumi JM, Vermeulen M, Kinge TR. Ganoderma: Diversity, Ecological Significances, and Potential Applications in Industry and Allied Sectors. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fryssouli V, Zervakis GI, Polemis E, Typas MA. A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa. MycoKeys 2020; 75:71-143. [PMID: 33304123 PMCID: PMC7723883 DOI: 10.3897/mycokeys.75.59872] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/16/2023] Open
Abstract
Ganoderma P. Karst. is a cosmopolitan genus of white-rot fungi which comprises species with highly-prized pharmaceutical properties, valuable biotechnological applications and of significant phytopathological interest. However, the status of the taxonomy within the genus is still highly controversial and ambiguous despite the progress made through molecular approaches. A metadata analysis of 3908 nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences obtained from GenBank/ENA/DDBJ and UNITE was performed by targeting sequences annotated as Ganoderma, but also sequences from environmental samples and from material examined for the first time. Ganoderma taxa segregated into five main lineages (Clades A to E). Clade A corresponds to the core of laccate species and includes G. shanxiense and three major well-supported clusters: Cluster A.1 ('G. lucidum sensu lato') consists of taxa from Eurasia and North America, Cluster A.2 of material with worldwide occurrence including G. resinaceum and Cluster A.3 is composed of species originating from all continents except Europe and comprises G. lingzhi. Clade B includes G. applanatum and allied species with a Holarctic distribution. Clade C comprises taxa from Asia and Africa only. Clade D consists of laccate taxa with tropical/subtropical occurrence, while clade E harbours the highest number of non-laccate species with a cosmopolitan distribution. The 92 Ganoderma-associated names, initially used for sequences labelling, correspond to at least 80 taxa. Amongst them, 21 constitute putatively new phylospecies after our application of criteria relevant to the robustness/support of the terminal clades, intra- and interspecific genetic divergence and available biogeographic data. Moreover, several other groups or individual sequences seem to represent distinct taxonomic entities and merit further investigation. A particularly large number of the public sequences was revealed to be insufficiently and/or incorrectly identified, for example, 87% and 78% of entries labelled as G. australe and G. lucidum, respectively. In general, ITS demonstrated high efficacy in resolving relationships amongst most of the Ganoderma taxa; however, it was not equally useful at elucidating species barriers across the entire genus and such cases are outlined. Furthermore, we draw conclusions on biogeography by evaluating species occurrence on a global scale in conjunction with phylogenetic structure/patterns. The sequence variability assessed in ITS spacers could be further exploited for diagnostic purposes.
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Affiliation(s)
- Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Georgios I. Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Milton A. Typas
- National and Kapodistrian University of Athens, Department of Genetics and Biotechnology, Faculty of Biology, Panepistemiopolis, Athens 15701, Greece
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Yuliana T, Putri NZ, Komara DZ, Mardawati E, Lanti I, Rahimah S. Study of <i>Ganoderma lucidum </i>in Laccase Production using Corncob and Paddies Straw Substrates on Submerged Fermentation System. Pak J Biol Sci 2020; 23:1060-1065. [PMID: 32700857 DOI: 10.3923/pjbs.2020.1060.1065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Ganoderma lucidum a white rot fungi, produce laccase which capable to degrade lignin due to its activity as ligninolytic enzymes. The production of laccase by G. lucidum using various agroindustrial wastes, including corncob and paddies straw, as substrates have been studied. The purpose of this study was to determine substrate that able to produce the highest activity of the laccase from the G. lucidum. MATERIALS AND METHODS The method used an experimental design followed by descriptive analysis using 4 treatments with duplication including treatment G. lucidum growth into A (control, Potato Dextrose Broth (PDB)), B (PDB+corncob), C (PDB+rice straw) and D (PDB+corncob+rice straw). This study includes; (1) Qualitative assay determination of laccase, (2) Extraction and laccase activity, (3) Cell concentration of G. lucidum measurement and (4) pH measurement. RESULTS Laccase qualitative assay showed brownish red ring on PDA media that indicated a positive of the laccase enzyme secreted by G. lucidum. Enzyme activity under submerged fermentation condition was achieved by the treatment of adding corncobs with the highest activity accounting 68.75 U mL-1. The fermentation process causes a decrease in pH during the incubation time to pH 4.83. The results of pH measurements showed that the laccase enzyme from G. lucidum worked optimally at pH 4-5 achieved after 5 day of incubation. CONCLUSION Our results suggest that G. lucidum has potential to produce laccase enzyme by using substrate comprising corncob and rice straw on submerged fermentation.
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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Osorio-González CS, Chaali M, Hegde K, Brar SK, Kermanshahipour A, Avalos-Ramírez A. Production and Processing of the Enzymes from Lignocellulosic Biomass. VALORIZATION OF BIOMASS TO VALUE-ADDED COMMODITIES 2020. [DOI: 10.1007/978-3-030-38032-8_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA. Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 2019; 7:e8065. [PMID: 31879570 PMCID: PMC6927665 DOI: 10.7717/peerj.8065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis. Discussion This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
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Affiliation(s)
- Ahmad Bazli Ramzi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Muhammad Lutfi Che Me
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Ummul Syafiqah Ruslan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Palazzolo MA, Postemsky PD, Kurina-Sanz M. From agro-waste to tool: biotechnological characterization and application of Ganoderma lucidum E47 laccase in dye decolorization. 3 Biotech 2019; 9:213. [PMID: 31114737 DOI: 10.1007/s13205-019-1744-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/08/2019] [Indexed: 10/26/2022] Open
Abstract
The culture of fungal species from agro-waste allows for the sustainable preparation of valuable biotechnological products and contributes to establish the Circular Economy concept. The Ganoderma lucidum species is well known as producer of laccases (EC 1.10.3.2), which serves as a tool to oxidize chemicals. When producing G. lucidum E47 basidiomes with edible purposes out of rice crop residues, its laccase remains as by-product. In this work, we report the biotechnological characterization and application of the laccase recovered from spent cultures of the G. lucidum E47 strain. We detected at least one polypeptide (ca. 59 kDa) which displays attractive activity and stability values when used in the range of 18-45 °C in mildly acidic environment (pH 4.8-5.8). These parameters can be enhanced in the presence of organic cosolvents such as butyl acetate and methyl iso-butyl ketone, but the opposite effect is observed with solvents of lower log P. The best activity-stability performance is reached when the biocatalyst is used in pH 4.8 buffer with 5% (v/v) butyl acetate at 37 °C. The laccase was capable of decolorizing xanthene, azo and triarylmethane dyes, exhibiting excellent selectivity on bromocresol green and bromocresol purple. Furthermore, the biocatalyst displayed an attractive activity when assessed for the decolorization of bromocresol green in a proof-of-concept effluent biotreatment.
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BolaÑOs AC, Bononi VLÚCR, Londoño JM, Castillo A, Vitali VM, Gugliotta ADM, Muñoz JE. Detecting Manganese Peroxidase (MnP) Gene in GanodermaSpecies. CRYPTOGAMIE MYCOL 2018. [DOI: 10.7872/crym/v39.iss3.2018.325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ana Cristina BolaÑOs
- Universidad del Valle, Facultad de Ciencias, Departamento de Biología, calle 13 No. 100 - 00, Cali – Colombia
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Vera LÚCia Ramos Bononi
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Jorge Mario Londoño
- Universidad Nacional de Colombia, Sede Palmira, Colombia, Carrera 32 No 12 - 00 Chapinero, Vía Candelaria, Palmira Valle del Cauca – Colombia
| | - Andrés Castillo
- Universidad del Valle, Facultad de Ciencias, Departamento de Biología, calle 13 No. 100 - 00, Cali – Colombia
| | - Vera MarÍA Vitali
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Adriana De Mello Gugliotta
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Jaime Eduardo Muñoz
- Universidad Nacional de Colombia, Sede Palmira, Colombia, Carrera 32 No 12 - 00 Chapinero, Vía Candelaria, Palmira Valle del Cauca – Colombia
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Zhou S, Zhang J, Ma F, Tang C, Tang Q, Zhang X. Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses. PLoS One 2018; 13:e0198404. [PMID: 29852018 PMCID: PMC5979026 DOI: 10.1371/journal.pone.0198404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/20/2018] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a medicinal mushroom that is well known for its ability to enhance human health, and products made from this fungus have been highly profitable. The substrate-degrading ability of G. lucidum could be related to its growth. CAZy proteins were more abundant in its genome than in the other white rot fungi models. Among these CAZy proteins, changes in lignocellulolytic enzymes during growth have not been well studied. Using genomic, transcriptomic and secretomic analyses, this study focuses on the lignocellulolytic enzymes of G. lucidum strain G0119 to determine which of these degradative enzymes contribute to its growth. From the genome sequencing data, genes belonging to CAZy protein families, especially genes involved in lignocellulose degradation, were investigated. The gene expression, protein abundance and enzymatic activity of lignocellulolytic enzymes in mycelia over a growth cycle were analysed. The overall expression cellulase was higher than that of hemicellulase and lignin-modifying enzymes, particularly during the development of fruiting bodies. The cellulase and hemicellulase abundances and activities increased after the fruiting bodies matured, when basidiospores were produced in massive quantities till the end of the growth cycle. Additionally, the protein abundances of the lignin-modifying enzymes and the expression of their corresponding genes, including laccases and lignin-degrading heme peroxidases, were highest when the mycelia fully spread in the compost bag. Type I cellobiohydrolase was observed to be the most abundant extracellular lignocellulolytic enzyme produced by the G. lucidum strain G0119. The AA2 family haem peroxidases were the dominant lignin-modifying enzyme expressed during the mycelial growth phase, and several laccases might play roles during the formation of the primordium. This study provides insight into the changes in the lignocellulose degradation ability of G. lucidum during its growth and will facilitate the discovery of new approaches to accelerate the growth of G. lucidum in culture.
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Affiliation(s)
- Shuai Zhou
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.,National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Jingsong Zhang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Fuying Ma
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Chuanhong Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Qingjiu Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China
| | - Xiaoyu Zhang
- Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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17
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Zhang W, Liu W, Hou R, Zhang L, Schmitz-Esser S, Sun H, Xie J, Zhang Y, Wang C, Li L, Yue B, Huang H, Wang H, Shen F, Zhang Z. Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. ISME JOURNAL 2018; 12:1319-1328. [PMID: 29391488 PMCID: PMC5931968 DOI: 10.1038/s41396-018-0051-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/30/2017] [Accepted: 01/10/2018] [Indexed: 01/06/2023]
Abstract
The giant panda feeds almost exclusively on bamboo, a diet highly enriched in lignin and cellulose, but is characterized by a digestive tract similar to carnivores. It is still large unknown if and how the giant panda gut microbiota contributes to lignin and cellulose degradation. Here we show the giant pandas’ gut microbiota does not significantly contribute to cellulose and lignin degradation. We found that no operational taxonomic unit had a nearest neighbor identified as a cellulolytic species or strain with a significant higher abundance in juvenile than cubs, a very low abundance of putative lignin and cellulose genes existed in part of analyzing samples but a significant higher abundance of genes involved in starch and hemicellulose degradation in juveniles than cubs. Moreover, a significant lower abundance of putative cellulolytic genes and a significant higher abundance of putative α-amylase and hemicellulase gene families were present in giant pandas than in omnivores or herbivores.
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Affiliation(s)
- Wenping Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China.
| | - Wenbin Liu
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | | | - Huaibo Sun
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Yunfei Zhang
- Biogas Institute of Ministry of Agriculture, Chengdu, 610064, Sichuan, China
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Lifeng Li
- Novogene Bioinformatics Institute, Beijing, 100083, PR China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China
| | - Zhihe Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 611081, Sichuan, China.
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18
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Shao J, Chen H, Yang D, Jiang M, Zhang H, Wu B, Li J, Yuan L, Liu C. Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum. Sci Rep 2017; 7:5711. [PMID: 28720793 PMCID: PMC5515960 DOI: 10.1038/s41598-017-04303-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/12/2017] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
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Affiliation(s)
- Junjie Shao
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Dan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Hui Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Bin Wu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Jianqin Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Lichai Yuan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China.
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19
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Bilal M, Asgher M, Iqbal HMN, Hu H, Zhang X. Biotransformation of lignocellulosic materials into value-added products-A review. Int J Biol Macromol 2017; 98:447-458. [PMID: 28163129 DOI: 10.1016/j.ijbiomac.2017.01.133] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/25/2017] [Accepted: 01/31/2017] [Indexed: 02/08/2023]
Abstract
In the past decade, with the key biotechnological advancements, lignocellulosic materials have gained a particular importance. In serious consideration of global economic, environmental and energy issues, research scientists have been re-directing their interests in (re)-valorizing naturally occurring lignocellulosic-based materials. In this context, lignin-modifying enzymes (LMEs) have gained considerable attention in numerous industrial and biotechnological processes. However, their lower catalytic efficiencies and operational stabilities limit their practical and multipurpose applications in various sectors. Therefore, to expand the range of natural industrial biocatalysts e.g. LMEs, significant progress related to the enzyme biotechnology has appeared. Owing to the abundant lignocellulose availability along with LMEs in combination with the scientific advances in the biotechnological era, solid-phase biocatalysts can be economically tailored on a large scale. This review article outlines first briefly on the lignocellulose materials as a potential source for biotransformation into value-added products including composites, fine chemicals, nutraceutical, delignification, and enzymes. Comprehensive information is also given on the purification and characterization of LMEs to present their potential for the industrial and biotechnological sector.
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Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Muhammad Asgher
- Industrial Biotechnology Laboratory, Department of Biochemistry, University of Agriculture Faisalabad, Pakistan
| | - Hafiz M N Iqbal
- School of Engineering and Science, Tecnologico de Monterrey, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., CP 64849, Mexico.
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Xu H, Guo MY, Gao YH, Bai XH, Zhou XW. Expression and characteristics of manganese peroxidase from Ganoderma lucidum in Pichia pastoris and its application in the degradation of four dyes and phenol. BMC Biotechnol 2017; 17:19. [PMID: 28231778 PMCID: PMC5324234 DOI: 10.1186/s12896-017-0338-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 02/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Manganese peroxidase (MnP) of white rot basidiomycetes, an extracellular heme enzyme, is part of a peroxidase superfamily that is capable of degrading the different phenolic compounds. Ganoderma, a white rot basidiomycete widely distributed worldwide, could secrete lignin-modifying enzymes (LME), including laccase (Lac), lignin peroxidases (LiP) and MnP. Results After the selection of a G. lucidum strain from five Ganoderma strains, the 1092 bp full-length cDNA of the MnP gene, designated as G. lucidum MnP (GluMnP1), was cloned from the selected strain. We subsequently constructed an eukaryotic expression vector, pAO815:: GlMnP, and transferred it into Pichia pastoris SMD116. Recombinant GluMnP1 (rGluMnP1) was with a yield of 126 mg/L and a molecular weight of approximately 37.72 kDa and a specific enzyme activity of 524.61 U/L. The rGluMnP1 could be capable of the decolorization of four types of dyes and the degradation of phenol. Phenol and its principal degradation products including hydroquinone, pyrocatechol, resorcinol, benzoquinone, were detected successfully in the experiments. Conclusions The rGluMnP1 could be effectively expressed in Pichia pastoris and with a higher oxidation activity. We infer that, in the initial stages of the reaction, the catechol-mediated cycle should be the principal route of enzymatic degradation of phenol and its oxidation products. This study highlights the potential industrial applications associated with the production of MnP by genetic engineering methods, and the application of industrial wastewater treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0338-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Xu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Meng-Yuan Guo
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yan-Hua Gao
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiao-Hui Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Xuan-Wei Zhou
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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21
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Gelatin-Immobilized Manganese Peroxidase with Novel Catalytic Characteristics and Its Industrial Exploitation for Fruit Juice Clarification Purposes. Catal Letters 2016. [DOI: 10.1007/s10562-016-1848-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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22
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Manavalan T, Manavalan V, Thangavelu KP, Kutzner A, Heese K. Characterization of a Solvent-Tolerant Manganese Peroxidase (MnP) from G
anoderma Lucidum
and Its Application in Fruit Juice Clarification. J Food Biochem 2015. [DOI: 10.1111/jfbc.12188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tamilvendan Manavalan
- Centre for Advanced Studies in Botany; University of Madras; Chennai Tamil Nadu 600025 India
| | - Vetriselvan Manavalan
- Department of Pharmacology and Toxicology; University of Arkansas for Medical Sciences; Little Rock AR
| | - Kalaichelvan P. Thangavelu
- Centre for Advanced Studies in Botany; University of Madras; Chennai Tamil Nadu 600025 India
- Alka-Research Foundation; Coimbatore Tamil Nadu 641046 India
| | - Arne Kutzner
- Department of Information Systems; College of Engineering; Hanyang University; 222 Wangsimni-ro Seoul Seongdong-gu 133-791 Rep. of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering; Hanyang University; 222 Wangsimni-ro Seoul Seongdong-gu 133-791 Rep. of Korea
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23
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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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Manavalan T, Manavalan A, Thangavelu KP, Heese K. Characterization of a novel endoglucanase from Ganoderma lucidum. J Basic Microbiol 2015; 55:761-71. [PMID: 25895101 DOI: 10.1002/jobm.201400808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/01/2015] [Indexed: 12/28/2022]
Abstract
We evaluated the production and characterization of endoglucanase from Ganoderma lucidum using different lignocellulose biomasses. We purified a novel carboxymethyl cellulose (CMC) hydrolyzing endoglucanase from the white-rot fungus G. lucidum when the medium was supplemented with 1% (w/v) wheat bran. Endoglucanase was purified 12.5-fold via ammonium sulfate fractionation, Sephadex G-100, and Q-Sepharose column chromatography with a final yield of 15%. SDS-PAGE analysis revealed that the endoglucanase had a molecular mass of 64.0 kDa. The optimal activity of purified endoglucanase was at pH 5.0 and 35 °C, though it was stable between pH 4.0-7.0 and temperatures of 30-60 °C. The purified enzyme was specific to CMC as a suitable substrate. The metal ions Hg(2+), Fe(2+), and Cr(2+) inhibited enzyme activity, while Ca(2+), Mg(2+), and Mn(2+) enhanced enzyme activity. The endoglucanase showed high activity and stability in the presence of different surfactants and non-polar hydrophobic organic solvents. This endoglucanase is tolerant to high temperature, metal ions, surfactants, and solvents, suggesting that it is appropriate for use in biomass conversion for biofuel production under harsh environmental conditions.
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Affiliation(s)
- Tamilvendan Manavalan
- Centre for Advanced Studies in Botany, University of Madras, Chennai, Tamil Nadu, India
| | - Arulmani Manavalan
- School of Biological Sciences, Nanyang Technological University, Singapore.,Institute of Advanced Studies, Nanyang Technological University, Singapore
| | | | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Republic of Korea
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25
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Fang Z, Liu X, Chen L, Shen Y, Zhang X, Fang W, Wang X, Bao X, Xiao Y. Identification of a laccase Glac15 from Ganoderma lucidum 77002 and its application in bioethanol production. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:54. [PMID: 25883681 PMCID: PMC4399389 DOI: 10.1186/s13068-015-0235-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/09/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND Laccases have potential applications in detoxification of lignocellulosic biomass after thermochemical pretreatment and production of value-added products or biofuels from renewable biomass. However, their application in large-scale industrial and environmental processes has been severely thwarted by the high cost of commercial laccases. Therefore, it is necessary to identify new laccases with lower cost but higher activity to detoxify lignocellulosic hydrolysates and better efficiency to produce biofuels such as bioethanol. Laccases from Ganoderma lucidum represent proper candidates in processing of lignocellulosic biomass. RESULTS G. lucidum 77002 produces three laccase isoenzymes with a total laccase activity of 141.1 U/mL within 6 days when using wheat bran and peanut powder as energy sources in liquid culture medium. A new isoenzyme named Glac15 was identified, purified, and characterized. Glac15 possesses an optimum pH of 4.5 to 5.0 and a temperature range of 45°C to 55°C for the substrates tested. It was stable at pH values ranging from 5.0 to 7.0 and temperatures lower than 55°C, with more than 80% activity retained after incubation for 2 h. When used in bioethanol production process, 0.05 U/mL Glac15 removed 84% of the phenolic compounds in prehydrolysate, and the yeast biomass reached 11.81 (optimal density at 600 nm (OD600)), compared to no growth in the untreated one. Addition of Glac15 before cellulase hydrolysis had no significant effect on glucose recovery. However, ethanol yield were improved in samples treated with laccases compared to that in control samples. The final ethanol concentration of 9.74, 10.05, 10.11, and 10.81 g/L were obtained from samples containing only solid content, solid content treated with Glac15, solid content containing 50% prehydrolysate, and solid content containing 50% prehydrolysate treated with Glac15, respectively. CONCLUSIONS The G. lucidum laccase Glac15 has potentials in bioethanol production industry.
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Affiliation(s)
- Zemin Fang
- />School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601 China
- />Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, Anhui 230601 China
| | - Xiaoman Liu
- />School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601 China
- />Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, Anhui 230601 China
| | - Liyuan Chen
- />The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100 China
| | - Yu Shen
- />The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100 China
| | - Xuecheng Zhang
- />School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601 China
- />Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, Anhui 230601 China
| | - Wei Fang
- />School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601 China
- />Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, Anhui 230601 China
| | - Xiaotang Wang
- />Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199 USA
| | - Xiaoming Bao
- />The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100 China
| | - Yazhong Xiao
- />School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601 China
- />Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, 111 Jiulong Road, Hefei, Anhui 230601 China
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26
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Akpinar M, Urek RO. Extracellular ligninolytic enzymes production by Pleurotus eryngii on agroindustrial wastes. Prep Biochem Biotechnol 2015; 44:772-81. [PMID: 24279903 DOI: 10.1080/10826068.2013.867870] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Pleurotus eryngii (DC.) Gillet (MCC58) was investigated for its ligninolytic ability to produce laccase (Lac), manganese peroxidase (MnP), aryl alcohol oxidase (AAO), and lignin peroxidase (LiP) enzymes through solid-state fermentation using apricot and pomegranate agroindustrial wastes. The reducing sugar, protein, lignin, and cellulose levels in these were studied. Also, the production of these ligninolytic enzymes was researched over the growth of the microorganism throughout 20 days, and the reducing sugar, protein, and nitrogen levels were recorded during the stationary cultivation at 28 ± 0.5°C. The highest Lac activity was obtained as 1618.5 ± 25 U/L on day 12 of cultivation using apricot. The highest MnP activity was attained as 570.82 ± 15 U/L on day 17 in pomegranate culture and about the same as apricot culture. There were low LiP activities in both cultures. The maximum LiP value detected was 16.13 ± 0.8 U/L in apricot cultures. In addition, AAO activities in both cultures showed similar trends up to day 17 of cultivation, with the highest AAO activity determined as 105.99 ± 6.3 U/L on day 10 in apricot cultures. Decolorization of the azo dye methyl orange was also achieved with produced ligninolytic enzymes by P. eryngii using apricot and pomegranate wastes.
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Affiliation(s)
- Merve Akpinar
- a Graduate School of Natural and Applied Sciences, Chemistry Department , Dokuz Eylül University , Buca-Izmir , Turkey
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27
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Characterization of Lignocellulolytic Enzymes from White-Rot Fungi. Curr Microbiol 2014; 70:485-98. [DOI: 10.1007/s00284-014-0743-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/27/2014] [Indexed: 12/26/2022]
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