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A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data

Publication Date: October 27, 2008
Journal: PLOS ONE
Authors: Konrad U. Foerstner, Tobias Doerks, Christopher J. Creevey, Anja Doerks, et al
Volume: 3
Issue: 10
Pages: e3515
DOI: https://dx.plos.org/10.1371/journal.pone.0003515
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0003515
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/18953415
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2568958
Europe PMC: http://europepmc.org/abstract/MED/18953415
Web of Science: 000265130500001
Scopus: 55849150893
Mendeley: http://www.mendeley.com/research/computational-screen-type-i-polyketide-synthases-metagenomics-shotgun-data

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{"title"=>"A computational screen for type I polyketide synthases in metagenomics shotgun data", "type"=>"journal", "authors"=>[{"first_name"=>"Konrad U.", "last_name"=>"Foerstner", "scopus_author_id"=>"9740594200"}, {"first_name"=>"Tobias", "last_name"=>"Doerks", "scopus_author_id"=>"6701481468"}, {"first_name"=>"Christopher J.", "last_name"=>"Creevey", "scopus_author_id"=>"6507448487"}, {"first_name"=>"Anja", "last_name"=>"Doerks", "scopus_author_id"=>"7801315624"}, {"first_name"=>"Peer", "last_name"=>"Bork", "scopus_author_id"=>"7103061421"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18953415", "isbn"=>"1932-6203 (Electronic)", "doi"=>"10.1371/journal.pone.0003515", "issn"=>"19326203", "scopus"=>"2-s2.0-55849150893", "pui"=>"352646685", "sgr"=>"55849150893"}, "id"=>"ea681ef4-cfef-3ba7-93fe-c3e856745371", "abstract"=>"BACKGROUND: Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS). METHODOLOGY/PRINCIPAL FINDINGS: We have estimated frequencies of type I PKS (PKS I) - a PKS subgroup - in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer. CONCLUSIONS/SIGNIFICANCE: The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.", "link"=>"http://www.mendeley.com/research/computational-screen-type-i-polyketide-synthases-metagenomics-shotgun-data", "reader_count"=>95, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>5, "Researcher"=>25, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>8, "Student > Master"=>14, "Other"=>7, "Student > Bachelor"=>3, "Lecturer"=>3, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>5, "Researcher"=>25, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>8, "Student > Master"=>14, "Other"=>7, "Student > Bachelor"=>3, "Lecturer"=>3, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>73, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>73}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Sweden"=>2, "United States"=>3, "Philippines"=>1, "Brazil"=>4, "Denmark"=>2, "United Kingdom"=>3, "Malaysia"=>1, "France"=>1, "Portugal"=>3, "Germany"=>2, "French Polynesia"=>1}, "group_count"=>5}

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Figshare 6602 Apr 20:03 UTC

Figshare

{"files"=>["https://ndownloader.figshare.com/files/917871"], "description"=>"<p>B – PKS I classified sequences normalized proteins-wise (all domains of one protein are counted together as one entity) by total number of screened proteins.</p>", "links"=>[], "tags"=>["pks", "classified", "sequences", "normalized", "screened"], "article_id"=>588327, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Foerstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003515.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_8211_PKS_I_classified_sequences_normalized_by_total_number_of_screened_proteins_/588327", "title"=>"A – PKS I classified sequences normalized by total number of screened proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-27 02:18:47"}
{"files"=>["https://ndownloader.figshare.com/files/918036"], "description"=>"<p>The soil sample has the highest density of type I PKS per genome.</p>", "links"=>[], "tags"=>["pks", "members", "genome", "minnesota", "sargasso", "drainage", "raes", "et"], "article_id"=>588483, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Foerstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003515.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Type_I_PKS_members_per_genome_equivalent_for_the_Minnesota_farm_soil_whale_falls_Sargasso_Sea_and_acid_mine_drainage_sample_estimated_by_Raes_et_al_31_/588483", "title"=>"Type I PKS members per genome equivalent for the Minnesota farm soil, whale falls, Sargasso Sea and acid mine drainage sample estimated by Raes et al. [31].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-27 02:21:23"}
{"files"=>["https://ndownloader.figshare.com/files/917728"], "description"=>"<p>Box plots of the bit score distribution of HMM search result sequences for the AT domain classified as PKS I or as non-PKS I using the tree.</p>", "links"=>[], "tags"=>["plots", "hmm", "sequences", "classified", "pks", "non-pks"], "article_id"=>588180, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Foerstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003515.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plots_of_the_bit_score_distribution_of_HMM_search_result_sequences_for_the_AT_domain_classified_as_PKS_I_or_as_non_PKS_I_using_the_tree_/588180", "title"=>"Box plots of the bit score distribution of HMM search result sequences for the AT domain classified as PKS I or as non-PKS I using the tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-27 02:16:20"}
{"files"=>["https://ndownloader.figshare.com/files/917791"], "description"=>"<p>The intensity of the color is equivalent to the relative number of sequences inside a data set. The KS domain has in the larger data sets the highest number of hits and the ratio of the AT, KS and PP domain is mostly similar.</p>", "links"=>[], "tags"=>["sequences", "sets", "annotated", "pks", "domains", "maximum-likelihood"], "article_id"=>588241, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Foerstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003515.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_sequences_in_the_data_sets_that_are_annotated_as_type_I_PKS_domains_based_on_the_maximum_likelihood_tree_/588241", "title"=>"Number of sequences in the data sets that are annotated as type I PKS domains based on the maximum-likelihood tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-27 02:17:21"}
{"files"=>["https://ndownloader.figshare.com/files/454138", "https://ndownloader.figshare.com/files/454176", "https://ndownloader.figshare.com/files/454206", "https://ndownloader.figshare.com/files/454233", "https://ndownloader.figshare.com/files/454362", "https://ndownloader.figshare.com/files/454396", "https://ndownloader.figshare.com/files/454418", "https://ndownloader.figshare.com/files/454457", "https://ndownloader.figshare.com/files/454528", "https://ndownloader.figshare.com/files/454589", "https://ndownloader.figshare.com/files/454667", "https://ndownloader.figshare.com/files/454740", "https://ndownloader.figshare.com/files/454805", "https://ndownloader.figshare.com/files/454878", "https://ndownloader.figshare.com/files/454947"], "description"=>"<div><h3>Background</h3><p>Polyketides are a diverse group of biotechnologically important secondary metabolites that are produced by multi domain enzymes called polyketide synthases (PKS).</p><h3>Methodology/Principal Findings</h3><p>We have estimated frequencies of type I PKS (PKS I) – a PKS subgroup – in natural environments by using Hidden-Markov-Models of eight domains to screen predicted proteins from six metagenomic shotgun data sets. As the complex PKS I have similarities to other multi-domain enzymes (like those for the fatty acid biosynthesis) we increased the reliability and resolution of the dataset by maximum-likelihood trees. The combined information of these trees was then used to discriminate true PKS I domains from evolutionary related but functionally different ones. We were able to identify numerous novel PKS I proteins, the highest density of which was found in Minnesota farm soil with 136 proteins out of 183,536 predicted genes. We also applied the protocol to UniRef database to improve the annotation of proteins with so far unknown function and identified some new instances of horizontal gene transfer.</p><h3>Conclusions/Significance</h3><p>The screening approach proved powerful in identifying PKS I sequences in large sequence data sets and is applicable to many other protein families.</p></div>", "links"=>[], "tags"=>["computational", "polyketide", "synthases", "metagenomics", "shotgun"], "article_id"=>149471, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Förstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003515.s001", "https://dx.doi.org/10.1371/journal.pone.0003515.s002", "https://dx.doi.org/10.1371/journal.pone.0003515.s003", "https://dx.doi.org/10.1371/journal.pone.0003515.s004", "https://dx.doi.org/10.1371/journal.pone.0003515.s005", "https://dx.doi.org/10.1371/journal.pone.0003515.s006", "https://dx.doi.org/10.1371/journal.pone.0003515.s007", "https://dx.doi.org/10.1371/journal.pone.0003515.s008", "https://dx.doi.org/10.1371/journal.pone.0003515.s009", "https://dx.doi.org/10.1371/journal.pone.0003515.s010", "https://dx.doi.org/10.1371/journal.pone.0003515.s011", "https://dx.doi.org/10.1371/journal.pone.0003515.s012", "https://dx.doi.org/10.1371/journal.pone.0003515.s013", "https://dx.doi.org/10.1371/journal.pone.0003515.s014", "https://dx.doi.org/10.1371/journal.pone.0003515.s015"], "stats"=>{"downloads"=>0, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Computational_Screen_for_Type_I_Polyketide_Synthases_in_Metagenomics_Shotgun_Data/149471", "title"=>"A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-10-27 02:37:51"}
{"files"=>["https://ndownloader.figshare.com/files/917570"], "description"=>"<p>Maximum likelihood-tree of the AT domain.</p>", "links"=>[], "tags"=>["likelihood-tree"], "article_id"=>588031, "categories"=>["Medicine", "Biological Sciences", "Pharmacology"], "users"=>["Konrad U. Foerstner", "Tobias Doerks", "Christopher J. Creevey", "Anja Doerks", "Peer Bork"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003515.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_tree_of_the_AT_domain_/588031", "title"=>"Maximum likelihood-tree of the AT domain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-27 02:13:51"}

PMC Usage Stats 175117 Oct 13:30 UTC

PMC Usage Stats | Further Information

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Relative Metric 144891805 Apr 17:34 UTC

Relative Metric

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F1000Prime23 Oct 10:38 UTC

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