Widespread Occurrence of Expressed Fungal Secretory Peroxidases in Forest Soils
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{"title"=>"Widespread occurrence of expressed fungal secretory peroxidases in forest soils", "type"=>"journal", "authors"=>[{"first_name"=>"Harald", "last_name"=>"Kellner", "scopus_author_id"=>"10142828200"}, {"first_name"=>"Patricia", "last_name"=>"Luis", "scopus_author_id"=>"10141673000"}, {"first_name"=>"Marek J.", "last_name"=>"Pecyna", "scopus_author_id"=>"36854292000"}, {"first_name"=>"Florian", "last_name"=>"Barbi", "scopus_author_id"=>"56146157000"}, {"first_name"=>"Danuta", "last_name"=>"Kapturska", "scopus_author_id"=>"25627620400"}, {"first_name"=>"Dirk", "last_name"=>"Krug??er", "scopus_author_id"=>"10241433800"}, {"first_name"=>"Donald R.", "last_name"=>"Zak", "scopus_author_id"=>"7006751939"}, {"first_name"=>"Roland", "last_name"=>"Marmeisse", "scopus_author_id"=>"6701778759"}, {"first_name"=>"Micheline", "last_name"=>"Vandenbol", "scopus_author_id"=>"6701757005"}, {"first_name"=>"Martin", "last_name"=>"Hofrichter", "scopus_author_id"=>"55839719100"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24763280", "pui"=>"373008149", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0095557", "scopus"=>"2-s2.0-84899718348", "sgr"=>"84899718348"}, "id"=>"976ee980-0ddd-378d-8c01-3689252d72da", "abstract"=>"Fungal secretory peroxidases mediate fundamental ecological functions in the conversion and degradation of plant biomass. Many of these enzymes have strong oxidizing activities towards aromatic compounds and are involved in the degradation of plant cell wall (lignin) and humus. They comprise three major groups: class II peroxidases (including lignin peroxidase, manganese peroxidase, versatile peroxidase and generic peroxidase), dye-decolorizing peroxidases, and heme-thiolate peroxidases (e.g. unspecific/aromatic peroxygenase, chloroperoxidase). Here, we have repeatedly observed a widespread expression of all major peroxidase groups in leaf and needle litter across a range of forest ecosystems (e.g. Fagus, Picea, Acer, Quercus, and Populus spp.), which are widespread in Europe and North America. Manganese peroxidases and unspecific peroxygenases were found expressed in all nine investigated forest sites, and dye-decolorizing peroxidases were observed in five of the nine sites, thereby indicating biological significance of these enzymes for fungal physiology and ecosystem processes. Transcripts of selected secretory peroxidase genes were also analyzed in pure cultures of several litter-decomposing species and other fungi. Using this information, we were able to match, in environmental litter samples, two manganese peroxidase sequences to Mycena galopus and Mycena epipterygia and one unspecific peroxygenase transcript to Mycena galopus, suggesting an important role of this litter- and coarse woody debris-dwelling genus in the disintegration and transformation of litter aromatics and organic matter formation.", "link"=>"http://www.mendeley.com/research/widespread-occurrence-expressed-fungal-secretory-peroxidases-forest-soils", "reader_count"=>37, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>26, "Chemistry"=>1, "Computer Science"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>2, "Taiwan"=>1, "United Kingdom"=>1, "France"=>1, "Switzerland"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1474866"], "description"=>"<p>Colored arrows indicate specific reactions of particular peroxidases. Black arrows in the left panel relate to reactions catalyzed by all peroxidases as well as laccase (Lcc). Members of the class II peroxidases not found expressed in litter samples were excluded (LiP, VP).</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "catalyzed", "peroxidases", "litter-decomposing", "modified"], "article_id"=>1007532, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reactions_catalyzed_by_peroxidases_of_litter_decomposing_fungi_found_in_this_study_based_on_and_modified_according_48_51_/1007532", "title"=>"Reactions catalyzed by peroxidases of litter-decomposing fungi found in this study (based on and modified according [48]–[51]).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474867"], "description"=>"<p>Three acidic amino acid residues marked red in <i>P. chrysosporium</i> MnP1 (AAA33744) and <i>B. adusta</i> VP (AAO47909) are crucial for Mn<sup>2+</sup> oxidation, and the tryptophan residue marked green in <i>P. chrysosporium</i> LiPH8 (AAA53109) and <i>B. adusta</i> VP is responsible for oxidation of phenolic compounds. <i>Coprinopsis cinerea</i> GP (CAA50060) does not include these catalytic residues. Red and green arrows mark the catalytically important sites within the amplified sequences.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "ii", "peroxidase", "sequences", "clades", "calculated", "phylogenetic"], "article_id"=>1007533, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_class_II_peroxidase_full_length_reference_protein_sequences_red_and_a_selection_of_partial_protein_sequences_found_in_this_study_representing_different_clades_of_the_calculated_phylogenetic_tree_/1007533", "title"=>"Alignment of class II peroxidase full length reference protein sequences (red) and a selection of partial protein sequences found in this study, representing different clades of the calculated phylogenetic tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474868"], "description"=>"1<p>Michigan Gradient Study; <a href=\"http://www.webpages.uidaho.edu/nitrogen-gradient/default.htm\" target=\"_blank\">http://www.webpages.uidaho.edu/nitrogen-gradient/default.htm</a>.</p>2<p>FACTSII, Aspen-FACE; <a href=\"http://www.nrs.fs.fed.us/disturbance/climate_change/face/\" target=\"_blank\">http://www.nrs.fs.fed.us/disturbance/climate_change/face/</a>.</p>3<p>CarboEurope-IP field site; <a href=\"http://www.carboeurope.org/\" target=\"_blank\">http://www.carboeurope.org/</a>.</p>4<p>SOERE F-ORE-T experimental site; <a href=\"http://www.gip-ecofor.org/f-ore-t/breuil.php\" target=\"_blank\">http://www.gip-ecofor.org/f-ore-t/breuil.php</a>.</p>5<p>Biodiversity Exploratories; <a href=\"http://www.biodiversity-exploratories.de/\" target=\"_blank\">http://www.biodiversity-exploratories.de/</a>.</p>6<p>Puéchabon experimental site; <a href=\"http://www2.cnrs.fr/sites/communique/fichier/fluxletterlight_1.pdf\" target=\"_blank\">http://www2.cnrs.fr/sites/communique/fichier/fluxletterlight_1.pdf</a>.</p>7<p>measured using substrate and peroxide, phenol oxidase activity without peroxide was subtracted.</p><p>n.a. not available.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "sites", "sampling"], "article_id"=>1007534, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Research_sites_and_sampling_parameters_/1007534", "title"=>"Research sites and sampling parameters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474869"], "description"=>"<p>*sequences include Asp-175 (in <i>P. chrysosporium</i> MnP1).</p>#<p>not appearing in classic group A.1 LiP clade (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095557#pone.0095557.s001\" target=\"_blank\">Fig. S1</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "phylogenetically", "characterized", "peroxidase", "groups"], "article_id"=>1007535, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Richness_of_phylogenetically_characterized_peroxidase_super_families_and_groups_in_different_forest_ecosystems_/1007535", "title"=>"Richness of phylogenetically characterized peroxidase (super)families and groups in different forest ecosystems.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474870"], "description"=>"<p>Number of unique sequence types is shown for the pool of PCR products.</p>$<p>partially published in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095557#pone.0095557-Kellner1\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "replicates", "achieved", "pcr", "peroxidase"], "article_id"=>1007536, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_field_site_replicates_and_number_of_subsequent_achieved_PCR_products_is_given_for_each_peroxidase_type_/1007536", "title"=>"Number of field site replicates and number of subsequent achieved PCR products is given for each peroxidase type.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474871"], "description"=>"<p>Extracellular peroxidase activities in selected litter samples (n = 3).</p>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "peroxidase", "activities", "litter", "samples"], "article_id"=>1007537, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extracellular_peroxidase_activities_in_selected_litter_samples_n_8202_8202_3_/1007537", "title"=>"Extracellular peroxidase activities in selected litter samples (n = 3).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-24 04:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1474872", "https://ndownloader.figshare.com/files/1474873", "https://ndownloader.figshare.com/files/1474874", "https://ndownloader.figshare.com/files/1474875"], "description"=>"<div><p>Fungal secretory peroxidases mediate fundamental ecological functions in the conversion and degradation of plant biomass. Many of these enzymes have strong oxidizing activities towards aromatic compounds and are involved in the degradation of plant cell wall (lignin) and humus. They comprise three major groups: class II peroxidases (including lignin peroxidase, manganese peroxidase, versatile peroxidase and generic peroxidase), dye-decolorizing peroxidases, and heme-thiolate peroxidases (e.g. unspecific/aromatic peroxygenase, chloroperoxidase). Here, we have repeatedly observed a widespread expression of all major peroxidase groups in leaf and needle litter across a range of forest ecosystems (e.g. <i>Fagus</i>, <i>Picea</i>, <i>Acer</i>, <i>Quercus</i>, and <i>Populus</i> spp.), which are widespread in Europe and North America. Manganese peroxidases and unspecific peroxygenases were found expressed in all nine investigated forest sites, and dye-decolorizing peroxidases were observed in five of the nine sites, thereby indicating biological significance of these enzymes for fungal physiology and ecosystem processes. Transcripts of selected secretory peroxidase genes were also analyzed in pure cultures of several litter-decomposing species and other fungi. Using this information, we were able to match, in environmental litter samples, two manganese peroxidase sequences to <i>Mycena galopus</i> and <i>Mycena epipterygia</i> and one unspecific peroxygenase transcript to <i>Mycena galopus</i>, suggesting an important role of this litter- and coarse woody debris-dwelling genus in the disintegration and transformation of litter aromatics and organic matter formation.</p></div>", "links"=>[], "tags"=>["Biochemistry", "enzymology", "enzymes", "ecology", "ecosystems", "ecosystem functioning", "microbial ecology", "microbiology", "Microbial physiology", "Fungal physiology", "Mycology", "Fungal biochemistry", "organisms", "fungi", "Soil science", "Soil ecology", "occurrence", "fungal", "secretory", "peroxidases"], "article_id"=>1007538, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Harald Kellner", "Patricia Luis", "Marek J. Pecyna", "Florian Barbi", "Danuta Kapturska", "Dirk Krüger", "Donald R. Zak", "Roland Marmeisse", "Micheline Vandenbol", "Martin Hofrichter"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095557.s001", "https://dx.doi.org/10.1371/journal.pone.0095557.s002", "https://dx.doi.org/10.1371/journal.pone.0095557.s003", "https://dx.doi.org/10.1371/journal.pone.0095557.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Widespread_Occurrence_of_Expressed_Fungal_Secretory_Peroxidases_in_Forest_Soils_/1007538", "title"=>"Widespread Occurrence of Expressed Fungal Secretory Peroxidases in Forest Soils", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-24 04:26:53"}

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Relative Metric

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