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

TitleCombining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group.
Authors
Issue Date2010
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
Plos One, 2010, v. 5 n. 9, p. e12781 How to Cite?
AbstractOur 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. 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. 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.
Persistent Identifierhttp://hdl.handle.net/10722/181261
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorOlivaresHernández, Ren_US
dc.contributor.authorSunner, Hen_US
dc.contributor.authorFrisvad, JCen_US
dc.contributor.authorOlsson, Len_US
dc.contributor.authorNielsen, Jen_US
dc.contributor.authorPanagiotou, Gen_US
dc.date.accessioned2013-02-21T02:03:34Z-
dc.date.available2013-02-21T02:03:34Z-
dc.date.issued2010en_US
dc.identifier.citationPlos One, 2010, v. 5 n. 9, p. e12781en_US
dc.identifier.issn1932-6203en_US
dc.identifier.urihttp://hdl.handle.net/10722/181261-
dc.description.abstractOur 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. 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. 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.en_US
dc.languageengen_US
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.actionen_US
dc.relation.ispartofPloS oneen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshAscomycota - Chemistry - Classification - Enzymology - Geneticsen_US
dc.subject.meshCarboxylic Ester Hydrolases - Chemistry - Genetics - Metabolismen_US
dc.subject.meshFungal Proteins - Chemistry - Genetics - Metabolismen_US
dc.subject.meshHydrolysisen_US
dc.subject.meshKineticsen_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshPhylogenyen_US
dc.subject.meshSubstrate Specificityen_US
dc.titleCombining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group.en_US
dc.typeArticleen_US
dc.identifier.emailPanagiotou, G: gipa@hku.hken_US
dc.identifier.authorityPanagiotou, G=rp01725en_US
dc.description.naturepublished_or_final_versionen_US
dc.identifier.doi10.1371/journal.pone.0012781-
dc.identifier.pmid20877647en_US
dc.identifier.scopuseid_2-s2.0-77958510380en_US
dc.identifier.volume5en_US
dc.identifier.issue9en_US
dc.identifier.spagee12781en_US
dc.identifier.isiWOS:000282053100008-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridOlivaresHernández, R=36158611900en_US
dc.identifier.scopusauthoridSunner, H=36599295900en_US
dc.identifier.scopusauthoridFrisvad, JC=7006810606en_US
dc.identifier.scopusauthoridOlsson, L=7203077540en_US
dc.identifier.scopusauthoridNielsen, J=7404066338en_US
dc.identifier.scopusauthoridPanagiotou, G=8566179700en_US

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