Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy

• Published in: Applied microbiology and biotechnology 2018-02, Vol.102 (4), p.1629-1637
• Main Authors: Nguyen, Stanley T. C., Freund, Hannah L., Kasanjian, Joshua, Berlemont, Renaud
• Format: Article
• Language: English
• Subjects: Annotations; Biomedical and Life Sciences; Biotechnology; Carbohydrates; Cellulases - genetics; Cellulases - metabolism; Cellulose; Cellulose - metabolism; Chitin; Chitin - metabolism; Chitinases - genetics; Chitinases - metabolism; Databases, Genetic; Deconstruction; Enzymes; Gene sequencing; Genomes; Glycoside hydrolase; Hydrolysis; Life Sciences; Metadata; Microbial Genetics and Genomics; Microbiology; Mini-Review; Molecular Sequence Annotation; Observations; Physiological aspects; Polysaccharides; Protein families; Protein-protein interactions; Proteins; Saccharides; Xylan; Xylans; Xylans - metabolism; Xylosidases - genetics; Xylosidases - metabolism
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-018-8778-y

The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.