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- Publisher Website: 10.1371/journal.pone.0012781
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- PMID: 20877647
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Article: Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group.
Title | Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. |
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Authors | |
Issue Date | 2010 |
Publisher | Public 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? |
Abstract | 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. 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 Identifier | http://hdl.handle.net/10722/181261 |
ISSN | 2023 Impact Factor: 2.9 2023 SCImago Journal Rankings: 0.839 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | OlivaresHernández, R | en_US |
dc.contributor.author | Sunner, H | en_US |
dc.contributor.author | Frisvad, JC | en_US |
dc.contributor.author | Olsson, L | en_US |
dc.contributor.author | Nielsen, J | en_US |
dc.contributor.author | Panagiotou, G | en_US |
dc.date.accessioned | 2013-02-21T02:03:34Z | - |
dc.date.available | 2013-02-21T02:03:34Z | - |
dc.date.issued | 2010 | en_US |
dc.identifier.citation | Plos One, 2010, v. 5 n. 9, p. e12781 | en_US |
dc.identifier.issn | 1932-6203 | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/181261 | - |
dc.description.abstract | 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. 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.language | eng | en_US |
dc.publisher | Public Library of Science. The Journal's web site is located at http://www.plosone.org/home.action | en_US |
dc.relation.ispartof | PLoS ONE | en_US |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject.mesh | Ascomycota - Chemistry - Classification - Enzymology - Genetics | en_US |
dc.subject.mesh | Carboxylic Ester Hydrolases - Chemistry - Genetics - Metabolism | en_US |
dc.subject.mesh | Fungal Proteins - Chemistry - Genetics - Metabolism | en_US |
dc.subject.mesh | Hydrolysis | en_US |
dc.subject.mesh | Kinetics | en_US |
dc.subject.mesh | Molecular Sequence Data | en_US |
dc.subject.mesh | Phylogeny | en_US |
dc.subject.mesh | Substrate Specificity | en_US |
dc.title | Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group. | en_US |
dc.type | Article | en_US |
dc.identifier.email | Panagiotou, G: gipa@hku.hk | en_US |
dc.identifier.authority | Panagiotou, G=rp01725 | en_US |
dc.description.nature | published_or_final_version | en_US |
dc.identifier.doi | 10.1371/journal.pone.0012781 | - |
dc.identifier.pmid | 20877647 | en_US |
dc.identifier.scopus | eid_2-s2.0-77958510380 | en_US |
dc.identifier.volume | 5 | en_US |
dc.identifier.issue | 9 | en_US |
dc.identifier.spage | e12781 | en_US |
dc.identifier.isi | WOS:000282053100008 | - |
dc.publisher.place | United States | en_US |
dc.identifier.scopusauthorid | OlivaresHernández, R=36158611900 | en_US |
dc.identifier.scopusauthorid | Sunner, H=36599295900 | en_US |
dc.identifier.scopusauthorid | Frisvad, JC=7006810606 | en_US |
dc.identifier.scopusauthorid | Olsson, L=7203077540 | en_US |
dc.identifier.scopusauthorid | Nielsen, J=7404066338 | en_US |
dc.identifier.scopusauthorid | Panagiotou, G=8566179700 | en_US |
dc.identifier.issnl | 1932-6203 | - |