title: Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group.
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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Roberto
authors.initials: R
authors.lastname: Olivares-Hernández
authors.forename: Hampus
authors.initials: H
authors.lastname: Sunner
authors.forename: Jens C
authors.initials: JC
authors.lastname: Frisvad
authors.forename: Lisbeth
authors.initials: L
authors.lastname: Olsson
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
authors.forename: Gianni
authors.initials: G
authors.lastname: Panagiotou
mesh_terms: D001203:Ascomycota / Q000737:chemistry / Q000145:classification* / Q000201:enzymology* / Q000235:genetics; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006868:Hydrolysis; D007700:Kinetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D013379:Substrate Specificity
chemical_list: D005656:Fungal Proteins; D002265:Carboxylic Ester Hydrolases; C070196:feruloyl esterase