Abstract
The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. The entanglement of glycoside hydrolase families and functions makes it difficult to predict the enzymatic activity of glycoside hydrolases based on their sequence. In the present study we further developed the method Peptide Pattern Recognition to an automatic approach not only to find all genes encoding glycoside hydrolases and lytic polysaccharide monooxygenases in fungal genomes but also to predict the function of the genes. The functional annotation is an important feature as it provides a direct route to predict function from primary sequence. Furthermore, we used Peptide Pattern Recognition to compare the cellulose-degrading enzyme activities encoded by 39 fungal genomes. The results indicated that cellobiohydrolases and AA9 lytic polysaccharide monooxygenases are hallmarks of cellulose-degrading fungi except brown rot fungi. Furthermore, a high number of AA9, endocellulase and β-glucosidase genes were identified, not in what are known to be the strongest, specialized lignocellulose degraders but in saprophytic fungi that can use a wide variety of substrates whereas only few of these genes were found in fungi that have a limited number of natural, lignocellulotic substrates. This correlation suggests that enzymes with different properties are necessary for degradation of cellulose in different complex substrates. Interestingly, clustering of the fungi based on their predicted enzymes indicated that Ascomycota and Basidiomycota use the same enzymatic activities to degrade plant cell walls.
Highlights
Since fungi evolved enzymes for degradation of plant cell wall material they have been important contributors to the natural turnover of plant cell wall material [1]
By searching for homology to peptide patterns, it can be investigated whether a protein sequence contains a sufficient number of conserved peptides from a specific Peptide Pattern Recognition (PPR)-generated subfamily to be regarded as a member of this subfamily
The genomic analysis of glycoside hydrolase (GH)- and lytic polysaccharide monooxygenases (LPMO)-encoding genes in 39 fungi identified a set of cellulose-degrading enzyme activities found in almost all the fungi capable of decomposing the cellulose found in plant cell walls in nature [4, 5, 28, 40]
Summary
Since fungi evolved enzymes for degradation of plant cell wall material they have been important contributors to the natural turnover of plant cell wall material [1]. In its natural context the cellulose is protected from degradation by the complex structures of plant cell walls including both covalent links between cellulose and hemicellulose and entanglement of the cellulose with other macromolecules [8]. The presence of these structures turns enzymatic degradation of cellulose in nature into a complicated task that depends on degradation of the other components of the plant cell wall to facilitate the access of cellulose-degrading enzymes to their substrate [9]. Several reports show that the presence of hemicellulose-degrading enzymes can seriously enhance enzymatic hydrolysis of cellulose [10,11,12,13]
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