The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

Levasseur, Anthony; Lomascolo, Anne; Chabrol, Olivier; Ruíz-Dueñas, Francisco J.; Boukhris-Uzan, Eva; Piumi, François; Kües, Ursula; Ram, Arthur F. J.; Murat, Claude; Haon, Mireille; Benoit, Isabelle; Arfi, Yonathan; Chevret, Didier; Drula, Élodie; Kwon, Min Jin; Gouret, Philippe; Lesage‐Meessen, Laurence; Lombard, Vincent; Mariette, Jérôme; Noirot, Céline; Park, Joohae; Patyshakuliyeva, Aleksandrina; Sigoillot, Jean‐Claude; Wiebenga, Ad; Wösten, Han A. B.; Martin, Francis; Coutinho, Pedro M.; Vries, Ronald P. de; Martínez, Ángel T.; Klopp, Christophe; Pontarotti, Pierre; Henrissat, Bernard; Record, Éric

doi:10.1186/1471-2164-15-486

Cited by 97 publications

(89 citation statements)

References 118 publications

(142 reference statements)

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“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”

Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

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Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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“…In addition, nine sequences for which biochemical data are available were included: glucose oxidases from Aspergillus niger (GenBank accession numbers AAA32695.1 and CAC12802.1), Penicillium chrysogenum (GenBank AFA42947.1), and Penicillium amagasakiense (GenBank P81156); glucose dehydrogenases from Pycnoporus cinnabarinus (GenBank KJ934222) and Glomerella cingulata (JF731352); and aryl alcohol oxidases from Pleurotus eryngii (GenBank AAC72747.1), Bjerkandera adusta (JGI identification number |Bjead1_1|171002), and Pleurotus pulmonarius (GenBank AAF31169.1). Finally, the three new recombinant P. cinnabarinus AA3_2 enzymes (PcAAQO1, PcAAQO2, and PcAAQO3) identified in the secretomes (26) were also included. Sequence alignments on the resulting 485 sequences were done using ClustalW, and phylogenetic analyses were conducted using the MEGA6 (neighbor-joining) program (37).…”

Section: Methodsmentioning

confidence: 99%

“…Secretome studies in liquid cultures and solid-state fermentation obtained with several substrates highlighted three laccases present under all conditions, demonstrating that these enzymes are efficiently produced by the fungus. Also, four AA3_2 enzymes (scf184803.g17, scf185002.g8, scf184611.g7, and scf184746.g13) were detected in liquid cultures grown on both maltose and birchwood as substrates (26). The enzyme corresponding to scf184803.g17, closely related to glucose oxidase (GOX), was recently characterized and identified as a glucose dehydrogenase, based on its inability to use oxygen as an electron acceptor (31).…”

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Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass

Mathieu

Piumi

Valli

et al. 2016

Appl Environ Microbiol

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Auxiliary activities family 3 subfamily 2 (AA3_2) from the CAZy database comprises various functions related to ligninolytic enzymes, such as fungal aryl alcohol oxidases (AAO) and glucose oxidases, both of which are flavoenzymes. The recent study of the Pycnoporus cinnabarinus CIRM BRFM 137 genome combined with its secretome revealed that four AA3_2 enzymes are secreted during biomass degradation. One of these AA3_2 enzymes, scf184803.g17, has recently been produced heterologously in Aspergillus niger. Based on the enzyme's activity and specificity, it was assigned to the glucose dehydrogenases (P. cinnabarinus GDH [PcGDH]). Here, we analyze the distribution of the other three AA3_2 enzymes (scf185002.g8, scf184611.g7, and scf184746.g13) to assess their putative functions. These proteins showed the highest homology with aryl alcohol oxidase from Pleurotus eryngii. Biochemical characterization demonstrated that they were also flavoenzymes harboring flavin adenine dinucleotide (FAD) as a cofactor and able to oxidize a wide variety of phenolic and nonphenolic aryl alcohols and one aliphatic polyunsaturated primary alcohol. Though presenting homology with fungal AAOs, these enzymes exhibited greater efficiency in reducing electron acceptors (quinones and one artificial acceptor) than molecular oxygen and so were defined as aryl-alcohol: quinone oxidoreductases (AAQOs) with two enzymes possessing residual oxidase activity (PcAAQO2 and PcAAQO3). Structural comparison of PcAAQO homology models with P. eryngii AAO demonstrated a wider substrate access channel connecting the active-site cavity to the solvent, explaining the absence of activity with molecular oxygen. Finally, the ability of PcAAQOs to reduce radical intermediates generated by laccase from P. cinnabarinus was demonstrated, shedding light on the ligninolytic system of this fungus.A uxiliary activities (AA) are a widespread group of catalytic modules involved in plant cell wall degradation. They were first introduced in 2013 into the carbohydrate-active enzymes (CAZy [www.cazy.org]) database (1). This AA class encompasses and extends an earlier classification dedicated to fungal ligninolytic enzymes and comprises 10 families, some of which have subfamilies (2). The AA family group enzymes possess the potential ability to help the original carbohydrate-active enzymes gain access to the carbohydrates embedded in the plant cell wall. Lignin, the main noncarbohydrate structural component of plant cell walls, consists of an intricate network of aromatic compounds forming a strong, hydrophobic, insoluble barrier closing access to the carbohydrates. Microorganisms have therefore set up different strategies to either modify or degrade lignin as a first step to gain access to the carbohydrate moiety and convert it into an energy source (3).In this new AA classification, family AA3 belongs to the glucose-methanol-choline (GMC) oxidoreductase family first defined by Cavener (4). AA3 enzymes are flavoproteins containing a flavin adenine dinucleotide (FAD)-binding domai...

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“…Fr. which has been shown to secrete large amounts of laccase into culture media (Levasseur et al 2014).…”

Section: Introductionmentioning

confidence: 99%

The saprotrophic wood-degrading abilities of <i>Rigidoporus microporus</i>

Oghenekaro¹,

Daniel²,

Asiegbu³

2015

Silva Fenn.

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• Rigidoporus microporus isolates displayed varying saprotrophic capabilities on wood blocks of Rubber tree (Hevea brasiliensis).• Percentage mass loss of (Hevea brasiliensis) wood blocks caused by the pathogenic Rigidoporus microporus was significantly higher than that observed with the endophytic isolate.• The endophytic isolate has very poor saprotrophic ability on Hevea brasiliensis wood blocks. AbstractSaprotrophic wood-decaying abilities of Rigidoporus microporus (Polyporales, Basidiomycota) syn. Rigidoporus lignosus and the structural alterations induced in wood blocks of Hevea brasiliensis Muell. Arg were studied. Mass loss of wood blocks was analyzed after 3 and 6 months respectively and the patterns of decay by pathogenic and endophytic isolates of this fungus were investigated using light microscopy. Effects of temperature on growth of the isolates on malt extract agar were also investigated. The R. microporus isolated from a non-H. brasiliensis host caused the highest percentage mass loss (27.2% after 6 months), followed by isolates ED310 (21.1%) and M13 (15.7%), both collected from diseased H. brasiliensis plantations. The isolate initially identified as an endophyte showed very low saprotrophic wood decay capability (4.3% after 6 months). The optimal temperature for growth of the isolates was 30 °C; except for the endophytic isolate which showed highest growth at 25 °C. Wood samples degraded by the R. microporus isolates showed simultaneous attack of wood cell walls, typical of white rot fungi. Results of the study indicate variability in the wood degrading abilities of the isolates and the potential differences in their physiology are discussed. Our findings further support the need for a taxonomical revision of the Rigidoporus genus.

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The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

Cited by 97 publications

References 118 publications

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass

The saprotrophic wood-degrading abilities of <i>Rigidoporus microporus</i>

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