Cell wall degrading enzymes in a new class of their own

Carbohydrate active enzymes are typically found in fungi including white rot, brown rot and plant pathogenic fungi. These micro-organisms degrade the complex matrix of the plant cell wall containing lignin, hemicelluloses, cellulose, polysacchariades and pectin. Since 1998, the CAZy database has carefully curated data on five families of carbohydrate active enzymes: glycoside hydrolases (GH), glycosyltransferases (GT),  polysaccharide lyases (PL), carbohydrate esterases (CE), and carbohydrate-binding modules (CBM).

The recent discovery that some members of the CBM and GH enzyme families share a mode of action, as lytic polysaccharide monooxygenases (LPMO), has led the curators of CAZy to make a major update to the database.  In their publication in Biotechnology for Biofuels, Levasseur and colleagues also note that enzymes need to act in synergy, in order to break down the interlinked components of the plant cell wall. With this in mind, they have created a new category of enzymes with auxiliary activities (AAs) to encompass the LPMOs, together with families of redox lignin degradation enzymes that are thought to act in concert.

The auxiliary enzymes are classified into 10 families, based on protein sequence similarity and having the function of “helper enzymes” that improve the access of the other classes of enzymes to degrade plant cell wall components. Biochemical and 3D structural information for enzyme families is inferred from the literature, with each family having at least one biochemically-characterized founding member.

A comparative genomic analysis of enzyme repertoires was also made, from 1576 AA enzymes that could be identified across 41 fungal genomes. Notably, a low number of AAs are found in Trichoderma reesi, the fungus that is widely used in industry to produce enzymes for carbohydrate conversion.  Bacterial degradation enzymes are less well explored than those of fungi and the authors propose that the lignin degrading bacteria found in the gut flora of ruminants and in soil will be an avenue for future research.

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