Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium

Kristian Barrett,Jens C Frisvad,Kristian Jensen,Lene Lange,Anne S Meyer

doi:10.1038/s41598-020-61907-1

Kristian Barrett, Jens C Frisvad + Show 3 more

Open Access

https://doi.org/10.1038/s41598-020-61907-1

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Abstract

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of “EC-Function;CAZy-Family” observations. These “Function;Family”-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of “Function;Family” enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme “Function;Family” profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by “shared presence“ and “shared absence” of CAZyme “Function;Family” observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.

Highlights

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitatrelated substrate utilization
We report a remarkable agreement between the “Function;Family”-annotated enzyme profile relatedness (EPR)-based dendrogram and the organismal taxonomy and phylogeny of the genera Aspergillus and Penicillium
The Conserved Unique Peptide Patterns (CUPP) method was used to annotate each protein with CAZyme family and corresponding function (EC number), and subsequently create the “Function;Family” CAZyme profile of all the secreted carbohydrate-active enzymes for each species

Summary

Introduction

Fungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitatrelated substrate utilization. We calculated CAZyme “Function;Family” profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Since different types of carbohydrate structures, down to differences in linkage configuration, each requires specific types of unique, highly specific CAZymes for their enzymatic modification[1] such a functional subdivision can ease the derivation of an association between fungal enzyme proteins and the specific carbohydrate carbon sources of the fungus It is an inherent characteristic of the heterotrophic fungal lifestyle (except for e.g. the very specialized biotrophs on animal-derived substrates) to have a broad arsenal of carbohydrate-active enzymes with functions for efficiently degrading the available biomass in their habitat. Such experimental limitations might be overcome through genome-based prediction of the secretome

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