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

By A. Levasseur, Elodie Drula, Vincent Lombard, Pedro M. Coutinho, Bernard Henrissat. 2013

1,166 citations recorded by the source corpus.

BackgroundSince 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.ResultsBecause 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).ConclusionsThe 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.

Subfields: Biomedical Engineering, Molecular Biology, Plant Science

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “Orthologous Groups were functionally annotated using updated versions of Gene Ontology (36), KEGG pathways (37), SMART / PFAM domains (38) and expanded to CAZy (39) and KEGG modules.”
The carbohydrate-active enzymes database (CAZy) in 2013 (2013, positive): “Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with polysaccharide lytic monooxygenases (LPMO), families of lignin degradation enzymes and of LPMOs have been used to define a new CAZy class that we hav”
Enzymatic breakdown of lignocellulosic biomass: the role of glycosyl hydrolases and lytic polysaccharide monooxygenases (2017, background): “LPMO auxiliary activity families Four families of LPMOs that fall under auxiliary activity families in the CAZy database have been identified, so far [117].”
Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry (2015, methodology): “…were selected based on current understanding of catalytic mechanism and known activities of each gene family or superfamily in the CAZy database (Levasseur et al., 2013; Lombard et al., 2014), as well as searching the fluorogenic and colorimetric substrates used in assays of each enzyme…”
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, methodology): “However, it is also accepted that other enzymes, such as laccases, cellobiose dehydrogenases, and potentially many others, can contribute to white rot (62, 73, 74); accordingly, a database of functional annotations has been dedicated to cataloging lignin-degrading enzymes (49) (Figs.”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, background): “A new protein class, ‘lignin-degradation enzymes,’ was defined by including the protein families from AA1 to AA8 as suggested by [31].”