The value of genome sequences in the rapid identification of novel genes encoding specific plant cell wall degrading enzymes

The potential of a genome sequence for the rapid identification of genes encoding specific enzymes was evaluated using the Aspergillus nidulans genome and plant cell wall polysaccharide degrading enzymes as an example. These enzymes are used in many industrial applications and many genes encoding these enzymes have already been identified in Aspergillus. Detailed in silica analysis of the ORFs assigned to the relevant families of the Carbohydrate Active enzyme database (CAZY, http://afmb.cnrs-mrs.fr/CAZY/index.html), using the Blast and Clustal programs, resulted in a reliable assignment of enzymatic function for most ORFs. This analysis demonstrated that approximately two-third of the A. nidulans ORFs do not yet have a characterised Aspergillus orthologue and also identified some ORFs encoding enzyme functions that have not yet been cloned in Aspergillus. A comparison of the biochemical characteristics of previously purified enzymes from A. nidulans to the A. nidulans ORFs did not result in the identification of the ORF corresponding to the enzyme activity. However, using an elimination strategy the number of candidate ORFs could be reduced to between 2 and 5. The analysis also revealed that the A. nidulans genome contains at least 33 ORFs that encode putative intracellular oligosaccharides degrading enzymes as well as ORFs with homology to oligosaccharides transporters of other organisms. This suggests that oligosaccharides are not exclusively degraded extracellularly, but can also be imported and degraded inside the cell.