Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group
Journal article, 2010

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 (similar to 86% correct classification), Order (similar to 88% correct classification) and Family (similar to 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.

methyl phenylalkanoates






Roberto Olivares Hernandez

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Hampus Sunner

Chalmers, Chemical and Biological Engineering, Life Sciences, Food and Nutrition Science

J. C. Frisvad

Technical University of Denmark (DTU)

Lisbeth Olsson

Chalmers, Chemical and Biological Engineering, Industrial biotechnology

Jens B Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

G. Panagiotou

Technical University of Denmark (DTU)


1932-6203 (ISSN)

Vol. 5 9 Article Number: e12781- e12781

Subject Categories

Industrial Biotechnology

Areas of Advance

Life Science Engineering (2010-2018)



More information

Latest update