Curation of characterized glycoside hydrolases of Fungal origin

Murphy, Caitlin; Powlowski, Justin; Wu, Min; Butler, Gregory; Tsang, Adrian

doi:10.1093/database/bar020

Cited by 87 publications

(69 citation statements)

References 34 publications

(28 reference statements)

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“…For example, the thorough degradation of cellulose requires the collaboration of endoglucanase, cellobiohydrolase, and β-1, 4-glucosidase [29-31]. The GH class contributes the most catalytic enzymes to the degradation of lignocelluloses [3], such as cellulases in families GH1, GH3, GH5, GH45, and GH74 [1,4,31], xylanases in families GH3, GH10, GH11, and GH39 [1,32]. At least 29 GH families are known to be involved in the degradation of plant biomass [1,4,28,31] (Table 2).…”

Section: Resultsmentioning

confidence: 99%

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Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

et al. 2013

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BackgroundFungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported.ResultsIn this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family.ConclusionsOur study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

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Section: Resultsmentioning

confidence: 99%

“…Fungi can produce all kinds of CAZymes [1,3]. Among them, plant cell wall degrading enzymes received special attentions because of their importance in fungal pathogens for penetration and successful infection of their hosts.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

et al. 2013

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“…According to CAZy and mycoCLAP (202), to date, there are no GH5, GH16, or GH44 XEGs characterized from fungi. Thus, we considered only GH12 and GH74 XEGs from aspergilli, due to the lack of characterized gene models for the GH5, GH16, and GH44 families.…”

Section: Hemicellulasesmentioning

confidence: 99%

Genomics Review of Holocellulose Deconstruction by Aspergilli

Segato

Damásio

Lucas

et al. 2014

Microbiol Mol Biol Rev

113

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SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.

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“…Most of them encode enzymes for breaking down starch, cellulose, hemicelluloses, or pectin. The production and characterization of these enzymes have been curated (Murphy et al 2011 ) and are periodically updated in the mycoCLAP database ( https:// mycoclap.fungalgenomics.ca ). Production and secretion of heterologous proteins appear to be protein-dependent; some proteins, although driven by the same promoter and secretion signal, are secreted at much lower levels than others.…”

Section: Production Of Extracellular Proteinsmentioning

confidence: 99%