Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group

Roberto Olivares Hernandez, Hampus Sunner, Jens Christian Frisvad, Lisbeth Olsson, Jens Nielsen, Gianni Panagiotou

    Research output: Contribution to journalJournal articleResearchpeer-review

    227 Downloads (Pure)

    Abstract

    Background Our 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 Findings In 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/Significance The 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.
    Original languageEnglish
    JournalP L o S One
    Volume5
    Issue number9
    ISSN1932-6203
    DOIs
    Publication statusPublished - 2010

    Bibliographical note

    This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

    Fingerprint

    Dive into the research topics of 'Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group'. Together they form a unique fingerprint.

    Cite this