FOLy: An integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds

Levasseur, Anthony; Piumi, François; Coutinho, Pedro M.; Rancurel, Corinne; Asther, Michèle; Delattre, Michel; Henrissat, Bernard; Pontarotti, Pierre; Asther, Marcel; Record, Éric

doi:10.1016/j.fgb.2008.01.004

Cited by 121 publications

(76 citation statements)

References 48 publications

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“…Only proteins identified in our metaproteomic analyses (at least one peptide matching with Ͻ10-ppm error; see below for details) were included in the final protein prediction data set. Eukaryotic Orthologous Group (KOG) (28) and Pfam (29) annotations were constructed using reverse PSI-BLAST (RPS-BLAST) (30) (E value, 1eϪ5), carbohydrate-active enzymes (CAZymes) (31) were identified using methods previously described (16), fungal oxidative lignin-degrading enzymes (FOLymes) (32) were identified by comparing all predictions to proteins on the FOLy database (downloaded 1 November 2012) using BLASTP (E value, 1eϪ10), and proteases were predicted using the MEROPS database (33). The annotations for all predicted CAZymes, FOLymes, and proteases were inspected manually.…”

Section: Methodsmentioning

confidence: 99%

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Aylward

Burnum-Johnson

Tringe

et al. 2013

Appl Environ Microbiol

100

106

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h Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.

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Section: Methodsmentioning

confidence: 99%

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Aylward

Burnum-Johnson

Tringe

et al. 2013

Appl Environ Microbiol

100

106

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“…The Fungal oxidative lignin enzymes database has classified lignin-degrading enzymes into two major classes: lignin-oxidising enzymes (LO) and lignin-degrading auxiliary enzymes (Levasseur et al 2008; Kameshwar and Qin 2016a). LO include laccase (LO1), lignin peroxidase (LO2), manganese peroxidase (LO2), versatile peroxidase (LO2) and cellobiose dehydrogenase (CDH; LO3).…”

Section: Distribution Of Cazymes Among White Rot Brown Rot and Soft mentioning

confidence: 99%

“…LO include laccase (LO1), lignin peroxidase (LO2), manganese peroxidase (LO2), versatile peroxidase (LO2) and cellobiose dehydrogenase (CDH; LO3). Similarly, lignin-degrading auxiliary enzymes majorly includes hydrogen peroxide-generating enzymes such as aryl alcohol oxidase (LDA1), vanillyl alcohol oxidase (LDA2), glyoxal oxidase (LDA3), pyranose oxidase (LDA4), galactose oxidase (LDA5), glucose oxidase (LDA6) and benzoquinone reductase (LDA7) (Levasseur et al 2008; Kameshwar and Qin 2016a). …”

Section: Distribution Of Cazymes Among White Rot Brown Rot and Soft mentioning

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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“…Based on the CAZy Auxiliary Activities (www.cazy.org/Auxiliary-Activities.html) database (Levasseur et al, 2008) and other publicly available information (Olson et al, 2012), we characterized and performed qRT-PCR expression profiling of the gene families coding for oxidative enzymes putatively involved in the conversion and degradation of lignin by H. irregulare on defined lignin and spruce cellulose media, and on natural lignocellulose substrates (heartwood and RZ defense wood).…”

Section: Introductionmentioning

confidence: 99%

Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation

Yakovlev¹,

Hietala²,

Courty

et al. 2013

Fungal Genetics and Biology

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FOLy: An integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds

Cited by 121 publications

References 48 publications

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

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

Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation

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