Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages
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{"title"=>"Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages", "type"=>"journal", "authors"=>[{"first_name"=>"Christine N.", "last_name"=>"Shulse", "scopus_author_id"=>"37040832400"}, {"first_name"=>"Eric E.", "last_name"=>"Allen", "scopus_author_id"=>"7202717583"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361794900", "sgr"=>"79956266058", "issn"=>"19326203", "pmid"=>"21629834", "scopus"=>"2-s2.0-79956266058", "doi"=>"10.1371/journal.pone.0020146", "isbn"=>"1932-6203"}, "id"=>"5a5a100e-ddce-3268-ac3f-119c209dc9c4", "abstract"=>"Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as \"Pfa synthases\". In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of \"secondary lipids\" to describe these biosynthetic pathways and products, a proposition consistent with the \"secondary metabolite\" vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages.", "link"=>"http://www.mendeley.com/research/widespread-occurrence-secondary-lipid-biosynthesis-potential-microbial-lineages", "reader_count"=>78, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>4, "Researcher"=>24, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>3, "Student > Bachelor"=>7, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>5, "Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>45, "Medicine and Dentistry"=>3, "Chemistry"=>5, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>5}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>3, "United Kingdom"=>1, "Chile"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/774358"], "description"=>"1<p>Bowman JP, McCammon SA, Lewis T, Skerratt JH, Brown JL, et al.\n (1998) <i>Psychroflexus torquis</i> gen. nov., sp.\n nov., a psychrophilic species from Antarctic sea ice, and\n reclassification of <i>Flavobacterium gondwanense</i>\n (Dobson et al. 1993) as <i>Psychroflexus\n gondwanense</i> gen. nov., comb. nov.\n <i>Microbiol</i> 144: 1601–1609.</p>2<p>Pinhassi J, Zweifel UL, Hagstrom A (1997) Dominant marine\n bacterioplankton species found among colony-forming bacteria.\n <i>Appl Environ Microbiol</i> 63:\n 3359–3366.</p>3<p>Starkey RL, De PK (1939) A new species of\n <i>Azotobacter</i>. <i>Soil Sci</i>ence\n 47: 329–343.</p>", "links"=>[], "tags"=>["lipid", "synthase", "types", "with", "characterized"], "article_id"=>444736, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Membership_and_description_of_secondary_lipid_synthase_types_with_____characterized_products_/444736", "title"=>"Membership and description of secondary lipid synthase types with\n characterized products.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:18:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/388914", "https://ndownloader.figshare.com/files/388944", "https://ndownloader.figshare.com/files/388992", "https://ndownloader.figshare.com/files/389012", "https://ndownloader.figshare.com/files/389045", "https://ndownloader.figshare.com/files/389065"], "description"=>"<div><p>Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5<em>n</em>-3) and docosahexaenoic acid (DHA, 22:6<em>n</em>-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for <em>de novo</em> bacterial PUFA biosynthesis, designated <em>pfaEABCD</em>, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as “Pfa synthases”. In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of <em>“secondary lipids”</em> to describe these biosynthetic pathways and products, a proposition consistent with the “secondary metabolite” vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages.</p> </div>", "links"=>[], "tags"=>["occurrence", "lipid", "biosynthesis", "in", "microbial", "lineages"], "article_id"=>136787, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020146.s001", "https://dx.doi.org/10.1371/journal.pone.0020146.s002", "https://dx.doi.org/10.1371/journal.pone.0020146.s003", "https://dx.doi.org/10.1371/journal.pone.0020146.s004", "https://dx.doi.org/10.1371/journal.pone.0020146.s005", "https://dx.doi.org/10.1371/journal.pone.0020146.s006"], "stats"=>{"downloads"=>12, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Widespread_Occurrence_of_Secondary_Lipid_Biosynthesis_Potential_in___Microbial_Lineages/136787", "title"=>"Widespread Occurrence of Secondary Lipid Biosynthesis Potential in\n Microbial Lineages", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-19 01:53:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/774331"], "description"=>"1<p>So CM, Young LY (1999) Isolation and characterization of a\n sulfate-reducing bacterium that anaerobically degrades alkanes.\n Applied and Environmental Microbiology 65: 2969–2976.</p>2<p>Ophel K, Kerr A (1990) <i>Agrobacterium vitis</i> sp.\n nov. for Strains of <i>Agrobacterium</i> biovar 3 from\n Grapevines. International Journal of Systematic Bacteriology 40:\n 236–241.</p>3<p>Labeda DP (1987) Transfer of the Type Strain of\n <i>Streptomyces erythraeus</i> (Waksman 1923)\n Waksman and Henrici 1948 to the Genus\n <i>Saccharopolyspora</i> Lacy and Goodfellow 1975\n as <i>Saccharopolyspora erythraea</i> sp. nov., and\n Designation of a Neotype Strain for <i>Streptomyces\n erythraeus</i>. International Journal of Systematic\n Bacteriology 37: 19–22.</p>4<p>Aeckersberg F, Bak F, Widdel F (1991) Anaerobic oxidation of\n saturated hydrocarbons to CO2 by a new type of sulfate-reducing\n bacterium. Archives of Microbiology 156: 5–14.</p>5<p>Chi XY, Yang QL, Zhao FQ, Qin S, Yang Y, et al. (2008)\n Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial\n Genomes. Comparative and Functional Genomics.</p>6<p>KomukaiNakamura S, Sugiura K, YamauchiInomata Y, Toki H,\n Venkateswaran K, et al. (1996) Construction of bacterial\n consortia that degrade Arabian light crude oil. Journal of\n Fermentation and Bioengineering 82: 570–574.</p>7<p>Brysch K, Schneider C, Fuchs G, Widdel F (1987) Lithoautotrophic\n growth of sulfate-reducing bacteria, and description of\n <i>Desulfobacterium autotrophicum</i> gen. nov.,\n sp. nov. Archives of Microbiology 148: 264–274.</p>8<p>McBee R (1954) The characteristics of <i>Clostridium\n thermocellum</i>. Journal of Bacteriology 67:\n 505–506.</p>", "links"=>[], "tags"=>["lipid", "synthase", "types", "with", "uncharacterized"], "article_id"=>444707, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.t002", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Membership_and_description_of_secondary_lipid_synthase_types_with_____uncharacterized_products_/444707", "title"=>"Membership and description of secondary lipid synthase types with\n uncharacterized products.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:18:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/773951"], "description"=>"<p>Eighty-six microbial genomes with either the <i>pfa</i> gene\n cluster or a homolog were identified. Type designations are based on KS\n phylogeny, conserved domain structure and product information, if\n available.</p>", "links"=>[], "tags"=>["microbiology", "Biochemistry"], "article_id"=>444324, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_of_pfa_like_gene_clusters_/444324", "title"=>"Diversity of <i>pfa</i>-like gene clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:12:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/774264"], "description"=>"<p>Gray tracts indicate regions of homology between genomes. The\n <i>pfa</i> genes are labeled in the <i>Vibrio\n splendidus</i> 12B01 genome and are absent in the other\n <i>Vibrio</i> genomes.</p>", "links"=>[], "tags"=>["12b01", "corresponding", "genomic", "regions", "multiple"], "article_id"=>444638, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plot_of_Vibrio_splendidus_12B01_pfa____region_versus_corresponding_genomic_regions_of_multiple_____Vibrio_species_/444638", "title"=>"Plot of <i>Vibrio splendidus</i> 12B01 <i>pfa</i>\n region versus corresponding genomic regions of multiple\n <i>Vibrio</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:17:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/774178"], "description"=>"<p>Clades in red contain putative secondary lipid gene clusters. Tree\n modified from the Interactive Tree of Life.</p>", "links"=>[], "tags"=>["clusters", "and"], "article_id"=>444553, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_distribution_of_pfa_gene_clusters_and____homologues_/444553", "title"=>"Phylogenetic distribution of <i>pfa</i> gene clusters and\n homologues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:15:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/774072"], "description"=>"<p>Gene cluster Types are colored and given a letter label. Asterisks\n represent Types first clustered and described in this study. Bootstrap\n values ≥50% are indicated by dots. The <i>Escherichia\n coli</i> DH10B FabF protein was used as the outgroup.</p>", "links"=>[], "tags"=>["phylogenetic", "proximal", "keto-acyl", "synthase", "domains", "conserved", "amino"], "article_id"=>444436, "categories"=>["Biochemistry", "Microbiology"], "users"=>["Christine N. Shulse", "Eric E. Allen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020146.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_of_proximal_keto_acyl_synthase____protein_domains_364_conserved_amino_acids_/444436", "title"=>"Maximum likelihood phylogenetic tree of proximal keto-acyl synthase\n protein domains (364 conserved amino acids).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:13:56"}

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Relative Metric

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