Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in Rubrivivax gelatinosus
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{"title"=>"Genome annotation provides insight into carbon monoxide and hydrogen metabolism in Rubrivivax gelatinosus", "type"=>"journal", "authors"=>[{"first_name"=>"Karen", "last_name"=>"Wawrousek", "scopus_author_id"=>"47361536000"}, {"first_name"=>"Scott", "last_name"=>"Noble", "scopus_author_id"=>"56448205000"}, {"first_name"=>"Jonas", "last_name"=>"Korlach", "scopus_author_id"=>"6602617398"}, {"first_name"=>"Jin", "last_name"=>"Chen", "scopus_author_id"=>"55317118400"}, {"first_name"=>"Carrie", "last_name"=>"Eckert", "scopus_author_id"=>"28067800000"}, {"first_name"=>"Jianping", "last_name"=>"Yu", "scopus_author_id"=>"55682152600"}, {"first_name"=>"Pin Ching", "last_name"=>"Maness", "scopus_author_id"=>"7005755297"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84918505068", "pui"=>"600696764", "pmid"=>"25479613", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0114551", "sgr"=>"84918505068"}, "id"=>"59eee12d-45eb-313b-b45b-974e9871ba8e", "abstract"=>"We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium Rubrivivax gelatinosus CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO2 and H2 as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of Rx. gelatinosus CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H2 in support of cell growth, and a regulatory hydrogenase that senses H2 and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables Rx. gelatinosus CBS to thrive on CO or H2 in support of cell growth.", "link"=>"http://www.mendeley.com/research/genome-annotation-provides-insight-carbon-monoxide-hydrogen-metabolism-rubrivivax-gelatinosus", "reader_count"=>10, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1825972"], "description"=>"<p>Identity percentage of <i>Rubrivivax gelatinosus</i> CBS Hyp1, Hyp2 proteins and the Hyp proteins from <i>Ralstonia eutropha</i> H16, generated by NCBI P-BLAST search.</p>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262517, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114551.t003", "stats"=>{"downloads"=>5, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identity_percentage_of_Rubrivivax_gelatinosus_CBS_Hyp1_Hyp2_proteins_and_the_Hyp_proteins_from_Ralstonia_eutropha_H16_generated_by_NCBI_P_BLAST_search_/1262517", "title"=>"Identity percentage of <i>Rubrivivax gelatinosus</i> CBS Hyp1, Hyp2 proteins and the Hyp proteins from <i>Ralstonia eutropha</i> H16, generated by NCBI P-BLAST search.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:01:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1825971"], "description"=>"<p>HupUV is a sensor hydrogenase, with HupU being the small subunit and HupV being the large, catalytic subunit. HupAB comprises a membrane-bound uptake hydrogenase with a small HupA subunit and a large, catalytic HupB subunit. Analysis was done using a NCBI P-BLAST search.</p><p>Similarity, identity, and coverage of select hydrogenase proteins comparing the <i>Rubrivivax gelatinosus</i> CBS sensor and uptake hydrogenases to other bacterial species including <i>Ralstonia eutropha</i> H16.</p>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262516, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114551.t002", "stats"=>{"downloads"=>4, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_identity_and_coverage_of_select_hydrogenase_proteins_comparing_the_Rubrivivax_gelatinosus_CBS_sensor_and_uptake_hydrogenases_to_other_bacterial_species_including_Ralstonia_eutropha_H16_/1262516", "title"=>"Similarity, identity, and coverage of select hydrogenase proteins comparing the <i>Rubrivivax gelatinosus</i> CBS sensor and uptake hydrogenases to other bacterial species including <i>Ralstonia eutropha</i> H16.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-05 03:01:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1825968"], "description"=>"<p>(A) Gene structure of CO metabolism genes in <i>Rubrivivax gelatinosus</i> CBS. The <i>hyp</i> genes putatively responsible for <i>coo</i> hydrogenase maturation are clustered among the <i>coo</i> CODH and hydrogenase genes. The gene encoding RcoM, the putative transcription factor for the <i>coo</i> CODH and hydrogenase genes is located among the <i>hyp</i> genes within this cluster of CO metabolism genes. (B) Gene structure of CO metabolism genes in <i>Rhodospirillum rubrum</i>. The <i>cooA</i> gene, encoding the CooA CO-responsive transcription factor, directly follows the CODH genes. (C) Gene structure of CO metabolism genes in <i>Carboxydothermus hydrogenoformans</i>. <i>C. hydrogenoformans</i> has five CODH complexes, but the genes for only one CODH are co-located with the genes for an energy-conserving hydrogenase <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114551#pone.0114551-Wu1\" target=\"_blank\">[36]</a>. The <i>cooA</i> and <i>hypC</i> genes precede the <i>cooMKLXUH</i> hydrogenase genes, which are followed by <i>hypA</i> and the <i>cooFS</i> CODH genes.</p>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262513, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114551.g003", "stats"=>{"downloads"=>0, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Organization_of_genes_encoding_anaerobic_CO_metabolism_in_multiple_bacteria_/1262513", "title"=>"Organization of genes encoding anaerobic CO metabolism in multiple bacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:01:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1825987", "https://ndownloader.figshare.com/files/1825988", "https://ndownloader.figshare.com/files/1825989", "https://ndownloader.figshare.com/files/1825990", "https://ndownloader.figshare.com/files/1825991", "https://ndownloader.figshare.com/files/1825992"], "description"=>"<div><p>We report here the sequencing and analysis of the genome of the purple non-sulfur photosynthetic bacterium <i>Rubrivivax gelatinosus</i> CBS. This microbe is a model for studies of its carboxydotrophic life style under anaerobic condition, based on its ability to utilize carbon monoxide (CO) as the sole carbon substrate and water as the electron acceptor, yielding CO<sub>2</sub> and H<sub>2</sub> as the end products. The CO-oxidation reaction is known to be catalyzed by two enzyme complexes, the CO dehydrogenase and hydrogenase. As expected, analysis of the genome of <i>Rx. gelatinosus</i> CBS reveals the presence of genes encoding both enzyme complexes. The CO-oxidation reaction is CO-inducible, which is consistent with the presence of two putative CO-sensing transcription factors in its genome. Genome analysis also reveals the presence of two additional hydrogenases, an uptake hydrogenase that liberates the electrons in H<sub>2</sub> in support of cell growth, and a regulatory hydrogenase that senses H<sub>2</sub> and relays the signal to a two-component system that ultimately controls synthesis of the uptake hydrogenase. The genome also contains two sets of hydrogenase maturation genes which are known to assemble the catalytic metallocluster of the hydrogenase NiFe active site. Collectively, the genome sequence and analysis information reveals the blueprint of an intricate network of signal transduction pathways and its underlying regulation that enables <i>Rx. gelatinosus</i> CBS to thrive on CO or H<sub>2</sub> in support of cell growth.</p></div>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262530, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0114551.s001", "https://dx.doi.org/10.1371/journal.pone.0114551.s002", "https://dx.doi.org/10.1371/journal.pone.0114551.s003", "https://dx.doi.org/10.1371/journal.pone.0114551.s004", "https://dx.doi.org/10.1371/journal.pone.0114551.s005", "https://dx.doi.org/10.1371/journal.pone.0114551.s006"], "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Annotation_Provides_Insight_into_Carbon_Monoxide_and_Hydrogen_Metabolism_in_Rubrivivax_gelatinosus_/1262530", "title"=>"Genome Annotation Provides Insight into Carbon Monoxide and Hydrogen Metabolism in <i>Rubrivivax gelatinosus</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-05 03:01:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1825965"], "description"=>"<p>There are 643 subsystems, 4852 coding sequences, and 58 RNAs.</p>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262510, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114551.g002", "stats"=>{"downloads"=>0, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Organism_Overview_for_Rubrivivax_gelatinosus_CBS_/1262510", "title"=>"Organism Overview for <i>Rubrivivax gelatinosus</i> CBS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:01:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1825961"], "description"=>"<p>The common section of the small satellite and the chromosome are highlighted in red. Not drawn to scale.</p>", "links"=>[], "tags"=>["gelatinosus CBS", "carboxydotrophic life style", "H 2", "uptake hydrogenase", "presence", "genome Annotation Provides Insight", "senses H 2", "co", "enzyme complexes", "Cell growth", "signal transduction pathways", "analysis", "hydrogenase maturation genes"], "article_id"=>1262506, "categories"=>["Biological Sciences"], "users"=>["Karen Wawrousek", "Scott Noble", "Jonas Korlach", "Jin Chen", "Carrie Eckert", "Jianping Yu", "Pin-Ching Maness"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114551.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_novo_genome_assembly_results_for_Rubrivivax_gelatinosus_CBS_resulting_in_one_bacterial_chromosome_and_two_satellite_DNA_elements_/1262506", "title"=>"<i>De novo</i> genome assembly results for <i>Rubrivivax gelatinosus</i> CBS, resulting in one bacterial chromosome and two satellite DNA elements.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-05 03:01:10"}
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Relative Metric

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