Journal of Fungi Article New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lene Lange 1, Kristian Barrett 2 and Anne S. Meyer 2,* 1 BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark;
[email protected] 2 Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
[email protected] * Correspondence:
[email protected]; Tel.: +45-4525-2600 Abstract: Fungal genome sequencing data represent an enormous pool of information for enzyme dis- covery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate- active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked accord- ing to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several pro- tein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme Citation: Lange, L.; Barrett, K.; hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host Meyer, A.S.