Abstract
BackgroundOur understanding of how fungi evolved to develop a variety of ecological niches, is limited but of fundamental biological importance. Specifically, the evolution of enzymes affects how well species can adapt to new environmental conditions. Feruloyl esterases (FAEs) are enzymes able to hydrolyze the ester bonds linking ferulic acid to plant cell wall polysaccharides. The diversity of substrate specificities found in the FAE family shows that this family is old enough to have experienced the emergence and loss of many activities.Methodology/Principal FindingsIn this study we evaluate the relative activity of FAEs against a variety of model substrates as a novel predictive tool for Ascomycota taxonomic classification. Our approach consists of two analytical steps; (1) an initial unsupervised analysis to cluster the FAEs substrate specificity data which were generated by cultivation of 34 Ascomycota strains and then an analysis of the produced enzyme cocktail against 10 substituted cinnamate and phenylalkanoate methyl esters, (2) a second, supervised analysis for training a predictor built on these substrate activities. By applying both linear and non-linear models we were able to correctly predict the taxonomic Class (∼86% correct classification), Order (∼88% correct classification) and Family (∼88% correct classification) that the 34 Ascomycota belong to, using the activity profiles of the FAEs.Conclusion/SignificanceThe good correlation with the FAEs substrate specificities that we have defined via our phylogenetic analysis not only suggests that FAEs are phylogenetically informative proteins but it is also a considerable step towards improved FAEs functional prediction.
Highlights
Microorganisms are estimated to make up more than one-third of Earth’s biomass [1]
In this study we evaluate the relative activity of feruloyl esterases (FAEs, E.C. 3.1.1.73) against a variety of model substrates as a novel predictive tool of the Ascomycota taxonomic classification
We examined the relationships between Ascomycota and Feruloyl esterases (FAEs) and to what extent the substrate specificity of FAEs is a biomarker of the known taxonomy
Summary
Microorganisms are estimated to make up more than one-third of Earth’s biomass [1]. They play essential roles in the cycling of nutrients, interact intimately with animals and plants, and directly influence Earth’s climate. A large selection of genes and/or proteins are concatenated and used for inferring phylogenetic relationships, thereby increasing the phylogenetic signal considerably [12,13,14,15] This approach does not take into consideration the evolutionary history of each individual gene and it depends on the availability of complete genome data. Several fungal FAEs, responsible for cleaving the ester-link between the polysaccharides main chain of xylans and monomeric or dimeric ferulic acid, have been purified and partially characterized [16] These enzymes exhibit different hydrolysis profiles against a wide range of model substrates, depending on: (a) changes in the type and the number of substitutions on the benzene ring, (b) changes in the distance between the ester bond and the benzene ring, and (c) change of the aliphatic region from saturated to unsaturated [17]. In this study we demonstrate for the first time, with the use of advanced machine learning tools, that the substrate specificity of just one enzyme class, the FAEs, accurately reflects organismal relationships
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