Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes - PubMed (original) (raw)

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur et al. Biotechnol Biofuels. 2013.

Abstract

Background: Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category.

Results: Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot).

Conclusions: The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.

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Figures

Figure 1

Figure 1

Examples of modular AA proteins. The additional modules represented include: carbohydrate-binding modules (CBMs; green), conserved modules of unknown function (X; red) and other domains (labelled grey boxes). Signal peptides (purple), proline/serine-rich linkers (cyan) and unassigned connecting regions (unlabelled grey boxes) are also shown.

Figure 2

Figure 2

Number of AA proteins in the 41 selected fungal genomes. Basidiomycetes are depicted in blue and ascomycetes are depicted in grey.

Figure 3

Figure 3

Distribution of AA proteins in the 41 selected fungal genomes.

Figure 4

Figure 4

Comparison of the ligninolytic AA repertoires identified in the selected fungal genomes using double hierarchical clustering. Top tree: family number according to the AA classification. Left tree: Fungal genomes analyzed. A and B correspond to the Ascomycotina and Basidiomycotina divisions, respectively. The abundance of the different AA proteins within a family is represented by a colour scale from 0 (dark blue) to ≥ 10 occurrences (red) per species. Note that only ligninolytic AA families were selected (AA1 to AA8).

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