Several Genes Encoding Enzymes with the Same Activity Are Necessary for Aerobic Fungal Degradation of Cellulose in Nature
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{"title"=>"Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature", "type"=>"journal", "authors"=>[{"first_name"=>"Peter K.", "last_name"=>"Busk", "scopus_author_id"=>"6603973859"}, {"first_name"=>"Mette", "last_name"=>"Lange", "scopus_author_id"=>"56437275200"}, {"first_name"=>"Bo", "last_name"=>"Pilgaard", "scopus_author_id"=>"56437599700"}, {"first_name"=>"Lene", "last_name"=>"Lange", "scopus_author_id"=>"16487448600"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84914703871", "pui"=>"600627516", "doi"=>"10.1371/journal.pone.0114138", "isbn"=>"1932-6203", "sgr"=>"84914703871", "pmid"=>"25461894"}, "id"=>"778de8b6-739e-381a-a78c-6cf1ac145710", "abstract"=>"The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. The entanglement of glycoside hydrolase families and functions makes it difficult to predict the enzymatic activity of glycoside hydrolases based on their sequence. In the present study we further developed the method Peptide Pattern Recognition to an automatic approach not only to find all genes encoding glycoside hydrolases and lytic polysaccharide monooxygenases in fungal genomes but also to predict the function of the genes. The functional annotation is an important feature as it provides a direct route to predict function from primary sequence. Furthermore, we used Peptide Pattern Recognition to compare the cellulose-degrading enzyme activities encoded by 39 fungal genomes. The results indicated that cellobiohydrolases and AA9 lytic polysaccharide monooxygenases are hallmarks of cellulose-degrading fungi except brown rot fungi. Furthermore, a high number of AA9, endocellulase and β-glucosidase genes were identified, not in what are known to be the strongest, specialized lignocellulose degraders but in saprophytic fungi that can use a wide variety of substrates whereas only few of these genes were found in fungi that have a limited number of natural, lignocellulotic substrates. This correlation suggests that enzymes with different properties are necessary for degradation of cellulose in different complex substrates. Interestingly, clustering of the fungi based on their predicted enzymes indicated that Ascomycota and Basidiomycota use the same enzymatic activities to degrade plant cell walls.", "link"=>"http://www.mendeley.com/research/several-genes-encoding-enzymes-same-activity-necessary-aerobic-fungal-degradation-cellulose-nature", "reader_count"=>49, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>15, "Student > Ph. D. Student"=>21, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>15, "Student > Ph. D. Student"=>21, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>32, "Medicine and Dentistry"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>32}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Finland"=>1, "Switzerland"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1813891"], "description"=>"<p>Blue lines represent DNA sequences. Red arrows represent protein sequences. Short purple lines represent short peptides. See “<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114138#s2\" target=\"_blank\">Materials and Methods</a>” for details.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257440, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g001", "stats"=>{"downloads"=>2, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_scheme_for_the_Hotpep_analysis_/1257440", "title"=>"Flow scheme for the Hotpep analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813933"], "description"=>"<p>The average number of genes predicted to encode each of the activities endoglucanase (EC 3.2.1.4), β-glucosidase (EC 3.2.1.21) and cellobiohydrolases (EC 3.2.1.91, non-reducing end and EC 3.2.1.176, reducing end) and the LPMOs (AA9 and AA11) in the cellulose-degraders and non-cellulose degraders.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257481, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g004", "stats"=>{"downloads"=>4, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_number_of_genes_encoding_each_cellulose_degrading_enzyme_in_the_fungi_/1257481", "title"=>"Average number of genes encoding each cellulose-degrading enzyme in the fungi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813946"], "description"=>"a<p>Two CAZy hits to one PPR hit.</p><p>Comparison of GH43 genes found by PPR and annotated in CAZy.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257493, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.t002", "stats"=>{"downloads"=>4, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_GH43_genes_found_by_PPR_and_annotated_in_CAZy_/1257493", "title"=>"Comparison of GH43 genes found by PPR and annotated in CAZy.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813943"], "description"=>"<p>CAZymes in fungal genomes found by PPR and annotated in CAZy.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257492, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.t001", "stats"=>{"downloads"=>3, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CAZymes_in_fungal_genomes_found_by_PPR_and_annotated_in_CAZy_/1257492", "title"=>"CAZymes in fungal genomes found by PPR and annotated in CAZy.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813907"], "description"=>"<p>All GH and LPMOs (CAZy auxiliary activity families AA9, AA10 and AA11) were annotated in the genome sequences of the 39 fungi. Next, as many as possible of these genes were assigned an EC number as described in “<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114138#s2\" target=\"_blank\">Materials and Methods</a>”.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257457, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g002", "stats"=>{"downloads"=>2, "page_views"=>60, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_GH_and_LPMO_encoding_genes_and_functionally_predicted_genes_in_the_39_fungi_/1257457", "title"=>"Number of GH- and LPMO-encoding genes and functionally predicted genes in the 39 fungi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813938"], "description"=>"<p>A) Average number of endoglucanase-genes in each GH families per fungal genome. B) Average number of β-glucosidase-genes in GH families per fungal genome. The GH families of each functionally annotated endoglucanase (EC 3.2.1.4) and β-glucosidase (EC 3.2.1.21) was counted.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257486, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g005", "stats"=>{"downloads"=>0, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_endoglucanases_and_946_glucosidases_in_many_different_GH_families_/1257486", "title"=>"Distribution of endoglucanases and β-glucosidases in many different GH families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813948"], "description"=>"<p>List of fungi whose genomes were mined for GH- and LPMO-encoding genes.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257496, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.t003", "stats"=>{"downloads"=>14, "page_views"=>43, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_fungi_whose_genomes_were_mined_for_GH_and_LPMO_encoding_genes_/1257496", "title"=>"List of fungi whose genomes were mined for GH- and LPMO-encoding genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813929"], "description"=>"<p>A) Cluster analysis based on the number and types of GH-families and AA families 9–11. B) Cluster analysis based on EC numbers for the GH genes an on the AA families 9 and 11. Cluster analysis was performed as described in “<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114138#s2\" target=\"_blank\">Materials and Methods</a>”. Light blue is used as background color for non-cellulose-degraders, brown for brown rot and light red for other cellulose-degraders.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257477, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g003", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_analysis_based_on_GH_and_LPMO_encoding_genes_of_the_cellulose_degrading_and_non_cellulose_degrading_fungi_/1257477", "title"=>"Cluster analysis based on GH- and LPMO-encoding genes of the cellulose-degrading and non-cellulose-degrading fungi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813971", "https://ndownloader.figshare.com/files/1813972", "https://ndownloader.figshare.com/files/1813973", "https://ndownloader.figshare.com/files/1813974", "https://ndownloader.figshare.com/files/1813975", "https://ndownloader.figshare.com/files/1813976", "https://ndownloader.figshare.com/files/1813977", "https://ndownloader.figshare.com/files/1813978"], "description"=>"<div><p>The cellulose-degrading fungal enzymes are glycoside hydrolases of the GH families and lytic polysaccharide monooxygenases. The entanglement of glycoside hydrolase families and functions makes it difficult to predict the enzymatic activity of glycoside hydrolases based on their sequence. In the present study we further developed the method Peptide Pattern Recognition to an automatic approach not only to find all genes encoding glycoside hydrolases and lytic polysaccharide monooxygenases in fungal genomes but also to predict the function of the genes. The functional annotation is an important feature as it provides a direct route to predict function from primary sequence. Furthermore, we used Peptide Pattern Recognition to compare the cellulose-degrading enzyme activities encoded by 39 fungal genomes. The results indicated that cellobiohydrolases and AA9 lytic polysaccharide monooxygenases are hallmarks of cellulose-degrading fungi except brown rot fungi. Furthermore, a high number of AA9, endocellulase and β-glucosidase genes were identified, not in what are known to be the strongest, specialized lignocellulose degraders but in saprophytic fungi that can use a wide variety of substrates whereas only few of these genes were found in fungi that have a limited number of natural, lignocellulotic substrates. This correlation suggests that enzymes with different properties are necessary for degradation of cellulose in different complex substrates. Interestingly, clustering of the fungi based on their predicted enzymes indicated that <i>Ascomycota</i> and <i>Basidiomycota</i> use the same enzymatic activities to degrade plant cell walls.</p></div>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257518, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0114138.s001", "https://dx.doi.org/10.1371/journal.pone.0114138.s002", "https://dx.doi.org/10.1371/journal.pone.0114138.s003", "https://dx.doi.org/10.1371/journal.pone.0114138.s004", "https://dx.doi.org/10.1371/journal.pone.0114138.s005", "https://dx.doi.org/10.1371/journal.pone.0114138.s006", "https://dx.doi.org/10.1371/journal.pone.0114138.s007", "https://dx.doi.org/10.1371/journal.pone.0114138.s008"], "stats"=>{"downloads"=>29, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Several_Genes_Encoding_Enzymes_with_the_Same_Activity_Are_Necessary_for_Aerobic_Fungal_Degradation_of_Cellulose_in_Nature_/1257518", "title"=>"Several Genes Encoding Enzymes with the Same Activity Are Necessary for Aerobic Fungal Degradation of Cellulose in Nature", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-02 03:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1813942"], "description"=>"<p>The average number of genes predicted to encode cellulose-degrading activities (EC 3.2.1.4, 3.2.1.21, EC 3.2.1.91 and EC 3.2.1.176 and LPMOs), hemicellulose-degrading activities (EC 3.2.1.37, 3.2.1.151, 3.2.1.8, 3.2.1.55, 3.2.1.23, 3.2.1.59, 3.2.1.131, 3.2.1.177, 3.2.1.78, 3.2.1.67, 2.4.1.183, 3.2.1.25, 3.2.1.31, 3.2.1.15, 3.2.1.39, 3.2.1.58, 3.2.1.63, 3.2.1.22, 3.2.1.99, 3.2.1.75, 3.2.1.52, 3.2.1.6, 3.2.1.106, 3.2.1.51, 3.2.1.113, 2.4.1.18, 2.4.1.25, 3.2.1.28, 3.2.1.45, 3.2.1.18, 3.2.1.3, 3.2.1.26, 3.2.1.24, 2.4.1.20, 3.2.1.40 and 3.2.1.171) or other activities (EC 3.2.1.1, 3.2.1.20, 3.2.1.10, 3.2.1.165, 3.2.1.132, 3.2.1.14, 3.2.1.145, 3.2.1.89 and 3.2.1.164) in the cellulose-degraders and non-cellulose degraders. The division of enzyme activities (EC numbers) on cellulose-degradation, hemicellulose-degradation or other was described previously <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114138#pone.0114138-VandenBrink1\" target=\"_blank\">[2]</a>.</p>", "links"=>[], "tags"=>["glycoside hydrolase families", "Peptide Pattern Recognition", "enzyme", "substrate", "gh", "sequence", "lytic polysaccharide monooxygenases", "method Peptide Pattern Recognition", "genes encoding glycoside hydrolases", "AA 9 lytic polysaccharide monooxygenases", "Plant cell walls", "Glycoside hydrolases", "function", "Aerobic Fungal Degradation", "Several Genes Encoding Enzymes", "genome", "fungi"], "article_id"=>1257490, "categories"=>["Biological Sciences"], "users"=>["Peter K. Busk", "Mette Lange", "Bo Pilgaard", "Lene Lange"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114138.g006", "stats"=>{"downloads"=>4, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_number_of_genes_encoding_glycoside_hydrolase_and_LPMO_enzymes_in_the_39_fungi_/1257490", "title"=>"Average number of genes encoding glycoside hydrolase and LPMO enzymes in the 39 fungi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-02 03:34:53"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
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