Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group
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{"title"=>"Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group", "type"=>"journal", "authors"=>[{"first_name"=>"Roberto", "last_name"=>"Olivares-Hernández", "scopus_author_id"=>"36158611900"}, {"first_name"=>"Hampus", "last_name"=>"Sunner", "scopus_author_id"=>"36599295900"}, {"first_name"=>"Jens C.", "last_name"=>"Frisvad", "scopus_author_id"=>"7006810606"}, {"first_name"=>"Lisbeth", "last_name"=>"Olsson", "scopus_author_id"=>"7203077540"}, {"first_name"=>"Jens", "last_name"=>"Nielsen", "scopus_author_id"=>"55572933700"}, {"first_name"=>"Gianni", "last_name"=>"Panagiotou", "scopus_author_id"=>"8566179700"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"20877647", "scopus"=>"2-s2.0-77958510380", "pui"=>"359826742", "doi"=>"10.1371/journal.pone.0012781", "sgr"=>"77958510380"}, "id"=>"74ce9f80-4ebc-374b-af36-058e70064f5c", "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.\\n\\nMETHODOLOGY/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.\\n\\nCONCLUSION/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.", "link"=>"http://www.mendeley.com/research/combining-substrate-specificity-analysis-support-vector-classifiers-reveals-feruloyl-esterase-phylog", "reader_count"=>28, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>1, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>2, "Japan"=>1, "Mexico"=>3}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/828985"], "description"=>"<p>149 unique putative proteins with a blast expect value ∼10<sup>−40</sup> to any of the queries were aligned and a maximum likelihood phylogeny constructed as the consensus cladogram having at least 70% support in 100 bootstrap replicates. Bootstrap support (%) is shown at internal nodes. For each sequence, the organism, accession number and taxonomic class are shown. For biochemically characterized FAEs, the type A–D, is also indicated. Sequences have been colored according to taxonomic class.</p>", "links"=>[], "tags"=>["putative", "fungal", "proteins", "ncbi", "institute", "10", "fae", "amino", "sequences", "query", "indicated"], "article_id"=>499336, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_putative_fungal_proteins_selected_by_BLAST_from_NCBI_and_the_Broad_Institute_using_10_known_FAE_amino_acid_sequences_as_the_BLAST_query_sequences_indicated_by_a_dagger_8224_/499336", "title"=>"Phylogeny of putative fungal proteins selected by BLAST from NCBI and the Broad Institute using 10 known FAE amino acid sequences as the BLAST query (sequences indicated by a dagger, †).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/829102"], "description"=>"<p>For the substrate at which each strain shows the highest activity an arbitrary value was set to 1 and the activity against all the other substrates were scaled based on this. The red font in the structure indicates that at least one of the examined strains showed activity against this substrate, whereas, the green font indicates that none of the strains has demonstrated activity. Substrate (1): methyl-2-hydroxy cinnamate, (2): methyl-4-hydroxy benzoate, (3): methyl-3,4,5-trimethoxycinnamate, (4): methyl-4-hydroxy-3,5-dimethoxy cinnamate, (5): methyl-4-hydroxy-3-methoxy benzoate, (6): methyl-4-hydroxy cinnamate, (7): methyl-3,4-dihydroxy cinnamate, (8): methyl-4-hydroxy phenyl acetate, (9): methyl-3-hydroxy cinnamate, (10) methyl-4-hydroxy-methoxy cinnamate.</p>", "links"=>[], "tags"=>["feruloyl", "esterase", "34", "ascomycota", "10"], "article_id"=>499465, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.g002", "stats"=>{"downloads"=>4, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_feruloyl_esterase_activity_of_the_34_Ascomycota_against_10_model_substrates_/499465", "title"=>"Relative feruloyl esterase activity of the 34 Ascomycota against 10 model substrates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:37:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/829457"], "description"=>"<p>Performance of the different classification methods across the taxonomical categories.</p>", "links"=>[], "tags"=>["classification", "methods", "taxonomical"], "article_id"=>499820, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_the_different_classification_methods_across_the_taxonomical_categories_/499820", "title"=>"Performance of the different classification methods across the taxonomical categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:43:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/829429"], "description"=>"<p>Optimal parameters for the Multilayer Perceptron for the different taxonomic categories.</p>", "links"=>[], "tags"=>["parameters", "multilayer", "perceptron", "taxonomic"], "article_id"=>499790, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.t003", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimal_parameters_for_the_Multilayer_Perceptron_for_the_different_taxonomic_categories_/499790", "title"=>"Optimal parameters for the Multilayer Perceptron for the different taxonomic categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:43:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/829298"], "description"=>"<p>In parenthesis next to the strain names, a three-letter code is given that corresponds to the Class-Order-Family the strain belongs to. The full names for Class, Order and Family are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012781#pone-0012781-t001\" target=\"_blank\">Table 1</a>. Different strengths of red correspond to the degree of activity on the respective substrate in relation to the activities on the rest of the substrates.</p>", "links"=>[], "tags"=>["34", "ascomycota", "strains", "produced", "enzyme", "cocktail", "10", "substituted", "cinnamate", "phenylalkanoate", "methyl", "esters", "s1", "s10", "correspond", "substrates"], "article_id"=>499634, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_34_Ascomycota_strains_in_rows_based_on_the_produced_enzyme_cocktail_against_10_substituted_cinnamate_and_phenylalkanoate_methyl_esters_in_columns_S1_to_S10_correspond_to_substrates_as_given_in_Table_2_/499634", "title"=>"Clustering of 34 Ascomycota strains (in rows) based on the produced enzyme cocktail against 10 substituted cinnamate and phenylalkanoate methyl esters (in columns, S1 to S10 correspond to substrates as given in <b>Table 2</b>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:40:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/829535"], "description"=>"<p>Optimized parameters for the Sequential Minimal Optimization (SMO) for the different taxonomic categories.</p>", "links"=>[], "tags"=>["parameters", "sequential", "optimization", "taxonomic"], "article_id"=>499892, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.t004", "stats"=>{"downloads"=>5, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimized_parameters_for_the_Sequential_Minimal_Optimization_SMO_for_the_different_taxonomic_categories_/499892", "title"=>"Optimized parameters for the Sequential Minimal Optimization (SMO) for the different taxonomic categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:44:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/412625", "https://ndownloader.figshare.com/files/412643"], "description"=>"<div><h3>Background</h3><p>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.</p><h3>Methodology/Principal Findings</h3><p>In this study we evaluate the relative activity of FAEs against a variety of model substrates as a novel predictive tool for <em>Ascomycota</em> 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 <em>Ascomycota</em> 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 <em>Ascomycota</em> belong to, using the activity profiles of the FAEs.</p><h3>Conclusion/Significance</h3><p>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.</p></div>", "links"=>[], "tags"=>["combining", "substrate", "specificity", "vector", "classifiers", "reveals", "feruloyl", "esterase", "phylogenetically", "informative"], "article_id"=>141518, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012781.s001", "https://dx.doi.org/10.1371/journal.pone.0012781.s002"], "stats"=>{"downloads"=>14, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combining_Substrate_Specificity_Analysis_with_Support_Vector_Classifiers_Reveals_Feruloyl_Esterase_as_a_Phylogenetically_Informative_Protein_Group/141518", "title"=>"Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-22 00:25:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/829497"], "description"=>"<p>Taxonomic classification of the 34 Ascomycota used in this study.</p>", "links"=>[], "tags"=>["classification", "34", "ascomycota"], "article_id"=>499864, "categories"=>["Evolutionary Biology"], "users"=>["Roberto Olivares-Hernández", "Hampus Sunner", "Jens C. Frisvad", "Lisbeth Olsson", "Jens Nielsen", "Gianni Panagiotou"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012781.t001", "stats"=>{"downloads"=>15, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomic_classification_of_the_34_Ascomycota_used_in_this_study_/499864", "title"=>"Taxonomic classification of the 34 Ascomycota used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:44:24"}

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