Glycosyl Hydrolase Genes and Enzymes of Neurospora crassa

Alan Radford

Faculty of Biological Sciences, The University of Leeds, Leeds LS2 9JT, U K;

Fungal Genetics Newsletter 53:12-14

An analysis of the genome of Neurospora crassa has identified genes encoding 84 putative glycosyl hydrolases, representing 24 different families in Henrissat's classification. Functionally, they include enzymes for the degradation of all major polysaccharides (including cellulase, hemicellulase, chitinase and pectinase).There is evidence of high levels of gene amplification, despite the presence of RIP, as there are eight representatives of family 3 (beta-glucosidases and xylosidases), five of family 7 (endo- and exo-glucanases), six of family 13 (amylases and maltase), nine of family 18 (chitinase), eight of family 47 (ER alpha-mannosidases), eleven of family 61 (endoglucanases) and seven of family 76 (alpha-mannanases).

In The Mycota III: Biochemistry and Molecular Biology, 2^nd edn. (ed. Brambl & Marzluf), p 243, I included a preliminary list of the glycosyl hydrolases of Neurospora crassa identified in assembly 3 of the Neurospora genome (Radford, 2004). This listed putative NCU identities by glycosyl hydrolase family (Henrissat and Romeu 1995), and the different enzyme activities found in each family; n.b. in some families, different members may have different enzyme activities. These data have been reassessed in genome assembly 7, and only those confirmed by current annotation, Pfam glycosyl hydrolase family predictions and close Blast hits to homologs with identified enzyme activities are included in the table below.

Glycosyl hydrolases are what might be termed “modular” enzymes. They are normally under carbon catabolite regulation, and typically have one or more copies of the C-regulation motif (consensus 5'-G/CPyGGGG-3') upstream of the ORF. The table includes the number of such motifs identified for each gene. Some glycosyl hydrolases also have a substrate-binding domain, located at either the N- or the C-terminus of the mature enzyme. Only the unique glucoamylase has an identifiable starch-binding domain (SBD: PF00686). Three chitinases have a chitin-recognition region. Some cellulases and xylanases have what is commonly called a fungal cellulose-binding domain (CBD: PF00734). Finally, most glycosyl hydrolases are targetted for secretion, to the cell wall, etc., and the presence of signal peptides has been identified by the SignalP v 3.0 web server (Bendtsen et al. 2004).

Because of the level of confidence in the identification of the glycosyl hydrolases, gene symbols have been assigned, as shown in the final column of Table 1. Some of these genes, cbh-1, gla-1, gla-2, inv and tre-2 have already been described and named (Perkins et al. 2001). I have chosen to base the nomenclature of the new genes on the glycosyl hydrolase family number rather than the specific enzyme activity, gh1 (glycosyl hydrolase family 1), gh2 (glycosyl hydrolase family 2), etc. as the symbols and names. Where there is more than one gene in a family, hyphenated numbering is used, e.g. gh3-1, gh3-2, gh3-3.

Table 1 The glycosyl hydrolases of Neurospora crassa