Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways
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{"title"=>"Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways", "type"=>"journal", "authors"=>[{"first_name"=>"R. Cameron", "last_name"=>"Coates", "scopus_author_id"=>"24075240800"}, {"first_name"=>"Sheila", "last_name"=>"Podell", "scopus_author_id"=>"6601930561"}, {"first_name"=>"Anton", "last_name"=>"Korobeynikov", "scopus_author_id"=>"24076450500"}, {"first_name"=>"Alla", "last_name"=>"Lapidus", "scopus_author_id"=>"35248496000"}, {"first_name"=>"Pavel", "last_name"=>"Pevzner", "scopus_author_id"=>"7006158805"}, {"first_name"=>"David H.", "last_name"=>"Sherman", "scopus_author_id"=>"7401446334"}, {"first_name"=>"Eric E.", "last_name"=>"Allen", "scopus_author_id"=>"7202717583"}, {"first_name"=>"Lena", "last_name"=>"Gerwick", "scopus_author_id"=>"6506616376"}, {"first_name"=>"William H.", "last_name"=>"Gerwick", "scopus_author_id"=>"7005717721"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84899714134", "sgr"=>"84899714134", "issn"=>"19326203", "arxiv"=>"1500", "doi"=>"10.1371/journal.pone.0085140", "pmid"=>"24475038", "isbn"=>"0166-8595", "pui"=>"373007998"}, "id"=>"3d6798c9-e74e-39d6-9d88-1779f99a205c", "abstract"=>"Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.", "link"=>"http://www.mendeley.com/research/characterization-cyanobacterial-hydrocarbon-composition-distribution-biosynthetic-pathways", "reader_count"=>106, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>22, "Student > Doctoral Student"=>10, "Student > Ph. D. Student"=>28, "Student > Master"=>20, "Other"=>5, "Student > Bachelor"=>9, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>22, "Student > Doctoral Student"=>10, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1361206", "https://ndownloader.figshare.com/files/1361207", "https://ndownloader.figshare.com/files/1361208", "https://ndownloader.figshare.com/files/1361209", "https://ndownloader.figshare.com/files/1361210", "https://ndownloader.figshare.com/files/1361211", "https://ndownloader.figshare.com/files/1361212", "https://ndownloader.figshare.com/files/1361213", "https://ndownloader.figshare.com/files/1361214"], "description"=>"<div><p>Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three <i>Moorea</i> strains and <i>Leptolyngbya sp.</i> PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.</p></div>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds", "cyanobacterial", "hydrocarbon", "biosynthetic"], "article_id"=>913754, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085140.s001", "https://dx.doi.org/10.1371/journal.pone.0085140.s002", "https://dx.doi.org/10.1371/journal.pone.0085140.s003", "https://dx.doi.org/10.1371/journal.pone.0085140.s004", "https://dx.doi.org/10.1371/journal.pone.0085140.s005", "https://dx.doi.org/10.1371/journal.pone.0085140.s006", "https://dx.doi.org/10.1371/journal.pone.0085140.s007", "https://dx.doi.org/10.1371/journal.pone.0085140.s008", "https://dx.doi.org/10.1371/journal.pone.0085140.s009"], "stats"=>{"downloads"=>14, "page_views"=>43, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characterization_of_Cyanobacterial_Hydrocarbon_Composition_and_Distribution_of_Biosynthetic_Pathways_/913754", "title"=>"Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-27 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1361200"], "description"=>"<p>Percentages are displayed as mean percentage between three replicates except for those indicated with an asterisk for strains that were characterized using a single sample. Blue strain names indicate strains possessing the FAAR/ADO pathway and red indicates those with the OLS pathway. Purple strain names indicate a strain that does not have a genome sequence and therefore the pathway type is unknown. To the left of the figure, a 16S rRNA phylogenetic tree (Maximum Likelihood, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085140#pone.0085140.s002\" target=\"_blank\">Figure S2</a> for complete tree) is presented for all 32 displayed strains. Branch tips are aligned to the corresponding strain names. Branches corresponding to <i>W. intricata</i> HT-29-1, <i>cf. Phormidium sp.</i> ISB 3/Nov/94-8 and <i>Pleurocapsa sp.</i> PCC 7320 are not shown because 16s rRNA sequences are not available for these strains. Vertical connection lengths were modified to accommodate the location of these three strains in the table.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds", "hydrocarbons", "32", "strains", "cyanobacteria", "displayed", "phylogenetic", "pathway"], "article_id"=>913749, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085140.g004", "stats"=>{"downloads"=>3, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrocarbon_composition_expressed_as_a_percentage_of_total_hydrocarbons_for_32_strains_of_cyanobacteria_displayed_by_phylogenetic_relationship_and_pathway_distribution_/913749", "title"=>"Hydrocarbon composition expressed as a percentage of total hydrocarbons for 32 strains of cyanobacteria displayed by phylogenetic relationship and pathway distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-27 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1361196"], "description"=>"<p>The 16S rRNA phylogeny of publicly available genome sequenced cyanobacteria (128) and additional strains investigated in this study (14) including <i>G. violaceus</i> PCC 7421 as the outgroup. Blue strain names indicate strains possessing the FAAR/ADO pathway and red indicates those with the OLS pathway. Purple strain names indicate a strain that does not have a genome sequence and therefore pathway presence cannot yet be verified. Cyanobacterial subdivisions are labeled using colored branches following the key in the upper left: (1) Subdivision 1. Uniceullular (Formerly Chroococcales), Subdivision II. Baeocystous (Formerly Pleurocapsales), Subdivision III. Filamentous (Formerly Oscillatoriales), Subdivision IV. Heterocystous (Formerly Nostocales), Subdivision V. Ramified or True Branching (Formerly Stigonematales). The clade indicated as “A” represents the main clade of cyanobacteria with the OLS pathway while clade “B” indicates the <i>Moorea</i> strains and clade “C” indicates the clade containing <i>Leptolyngbya sp.</i> PCC 6404. Baysian posterior probabilities are displayed at nodes (o = posterior support<0.5).</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds", "16s", "rrna", "phylogeny", "hydrocarbon", "pathway"], "article_id"=>913745, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085140.g002", "stats"=>{"downloads"=>2, "page_views"=>56, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cyanobacterial_16S_rRNA_phylogeny_and_hydrocarbon_pathway_distribution_/913745", "title"=>"Cyanobacterial 16S rRNA phylogeny and hydrocarbon pathway distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-27 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1361188"], "description"=>"<p>A) The Fatty Acyl-ACP Reductase (FAAR)/Aldehyde Deformylating Oxygenase (ADO) involves first a reduction of a fatty acyl substrate to a fatty aldehyde followed by an oxidative conversion to an alkane with the release of formate <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085140#pone.0085140-Li1\" target=\"_blank\">[17]</a>. The OLS (olefin producing) pathway involves a polyketide synthase that first elongates a fatty acyl-CoA by two carbons from malonyl-CoA via ketosynthase (KS) and acyl transferase (AT) domains followed by reduction to the β-hydroxyacid by a ketoreductase (KR). The ST activates the β-hydroxy group via sulfonation, and then the thioesterase (TE) acts on this substrate to catalyze decarboxylation and loss of sulfate to form the terminal alkene.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds", "biosynthetic", "pathways"], "article_id"=>913738, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085140.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrocarbon_biosynthetic_pathways_in_cyanobacteria_/913738", "title"=>"Hydrocarbon biosynthetic pathways in cyanobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-27 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1361201"], "description"=>"<p>Fatty acid analysis from single samples of A<i>nabaena (Nostoc) sp.</i> PCC 7120, <i>M. producens</i> 3L, and <i>Synechococcus sp.</i> PCC 7002. All three strains exhibit similar proportions of hexadecanoic acid and 9-hexadecenoic acid; however, A<i>nabaena (Nostoc) sp.</i> PCC 7120 exhibits a higher proportion of 9-octadecenoic acid and 11-octadecenoic acid and tetradecanoic acid is absent. <i>M. producens</i> 3L contains 11-hexadecenoic acid and no octadecanoic acid. <i>Synechococcus sp.</i> PCC 7002 exhibited a similar composition to A<i>nabaena (Nostoc) sp.</i> PCC 7120 yet has a higher proportion of hexadecanoic acid.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds"], "article_id"=>913750, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085140.g005", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fatty_acid_analysis_of_three_cyanobacteria_/913750", "title"=>"Fatty acid analysis of three cyanobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-27 02:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1361198"], "description"=>"<p>Specific hydrocarbons for each strain are color coded and stacked to depict the overall quantitative yield. Standard error bars are given for each hydrocarbon and each strain. Quantitative hydrocarbon yields ranged from 0.024%±0.01% in <i>Cyanothece sp.</i> PCC 7425 to 0.262%±0.01% in <i>Pleurocapsa sp.</i> PCC 7516. Blue strain names indicate strains possessing the FAAR/ADO pathway and red indicates those with the OLS pathway. Purple strain names indicate a strain that does not have a genome sequence and therefore the pathway type is unknown. To the left of the figure, a 16S rRNA phylogenetic tree (Maximum Likelihood, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085140#pone.0085140.s001\" target=\"_blank\">Figure S1</a> for complete tree) is presented for all 20 displayed strains. Branch tips are aligned to corresponding strain names except for <i>Westiella intricata</i> HT-29-1 for which no 16S rRNA sequence is available. Vertical connection lengths were modified to accommodate the location of <i>W. intricata</i> HT-29-1 in the table.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "biocatalysis", "biomaterials", "Small molecules", "Evolutionary biology", "Evolutionary systematics", "Phyletic patterns", "Organismal evolution", "Microbial evolution", "Marine biology", "Marine technology", "microbiology", "Industrial microbiology", "Microbial metabolism", "Analytical chemistry", "Chemical analysis", "chemical biology", "organic chemistry", "Organic compounds", "yields", "hydrocarbons", "percent", "biomass", "20", "cyanobacteria", "displayed", "phylogenetic", "pathway"], "article_id"=>913747, "categories"=>["Biological Sciences", "Chemistry"], "users"=>["R. Cameron Coates", "Sheila Podell", "Anton Korobeynikov", "Alla Lapidus", "Pavel Pevzner", "David H. Sherman", "Eric E. Allen", "Lena Gerwick", "William H. Gerwick"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085140.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_yields_of_hydrocarbons_as_percent_dry_weight_of_biomass_from_20_cyanobacteria_displayed_by_phylogenetic_relationship_and_pathway_distribution_/913747", "title"=>"Quantitative yields of hydrocarbons as percent dry weight of biomass from 20 cyanobacteria displayed by phylogenetic relationship and pathway distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-27 02:58:11"}

PMC Usage Stats | Further Information

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