Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens
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{"title"=>"Genomic characterization of methanomicrobiales reveals three classes of methanogens", "type"=>"journal", "authors"=>[{"first_name"=>"Iain", "last_name"=>"Anderson", "scopus_author_id"=>"7201352574"}, {"first_name"=>"Luke E.", "last_name"=>"Ulrich", "scopus_author_id"=>"9939811300"}, {"first_name"=>"Boguslaw", "last_name"=>"Lupa", "scopus_author_id"=>"8550693500"}, {"first_name"=>"Dwi", "last_name"=>"Susanti", "scopus_author_id"=>"24067761300"}, {"first_name"=>"Iris", "last_name"=>"Porat", "scopus_author_id"=>"7004497195"}, {"first_name"=>"Sean D.", "last_name"=>"Hooper", "scopus_author_id"=>"9941819700"}, {"first_name"=>"Athanasios", "last_name"=>"Lykidis", "scopus_author_id"=>"6602741895"}, {"first_name"=>"Magdalena", "last_name"=>"Sieprawska-Lupa", "scopus_author_id"=>"14045881300"}, {"first_name"=>"Lakshmi", "last_name"=>"Dharmarajan", "scopus_author_id"=>"25823087500"}, {"first_name"=>"Eugene", "last_name"=>"Goltsman", "scopus_author_id"=>"6602377914"}, {"first_name"=>"Alla", "last_name"=>"Lapidus", "scopus_author_id"=>"35248496000"}, {"first_name"=>"Elizabeth", "last_name"=>"Saunders", "scopus_author_id"=>"7102174440"}, {"first_name"=>"Cliff", "last_name"=>"Han", "scopus_author_id"=>"7403379551"}, {"first_name"=>"Miriam", "last_name"=>"Land", "scopus_author_id"=>"35277054300"}, {"first_name"=>"Susan", "last_name"=>"Lucas", "scopus_author_id"=>"35353275800"}, {"first_name"=>"Biswarup", "last_name"=>"Mukhopadhyay", "scopus_author_id"=>"7101857372"}, {"first_name"=>"William B.", "last_name"=>"Whitman", "scopus_author_id"=>"7006592064"}, {"first_name"=>"Carl", "last_name"=>"Woese", "scopus_author_id"=>"7005491275"}, {"first_name"=>"James", "last_name"=>"Bristow", "scopus_author_id"=>"7102284465"}, {"first_name"=>"Nikos", "last_name"=>"Kyrpides", "scopus_author_id"=>"34570925900"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-67149096055", "sgr"=>"67149096055", "pui"=>"354729035", "isbn"=>"8143852393", "pmid"=>"19495416", "doi"=>"10.1371/journal.pone.0005797"}, "id"=>"39b38b0e-4c65-3248-b99c-5b8c14dff254", "abstract"=>"BACKGROUND Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. METHODOLOGY/PRINCIPAL FINDINGS In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. CONCLUSIONS/SIGNIFICANCE Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).", "link"=>"http://www.mendeley.com/research/genomic-characterization-methanomicrobiales-reveals-three-classes-methanogens", "reader_count"=>131, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>5, "Researcher"=>31, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>4, "Other"=>6, "Student > Master"=>20, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>5, "Researcher"=>31, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>4, "Other"=>6, "Student > Master"=>20, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>16, "Engineering"=>3, "Environmental Science"=>21, "Biochemistry, Genetics and Molecular Biology"=>17, "Agricultural and Biological Sciences"=>63, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>2, "Computer Science"=>2, "Immunology and Microbiology"=>3, "Earth and Planetary Sciences"=>1, "Energy"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Energy"=>{"Energy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>63}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}, "Unspecified"=>{"Unspecified"=>16}, "Environmental Science"=>{"Environmental Science"=>21}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Puerto Rico"=>1, "Sweden"=>1, "United States"=>6, "Brazil"=>1, "Mexico"=>3, "Italy"=>1, "United Kingdom"=>1, "Chile"=>1, "Germany"=>3}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/443464"], "description"=>"<div><h3>Background</h3><p>Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.</p><h3>Methodology/Principal Findings</h3><p>In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, <em>Methanocorpusculum labreanum</em> Z and <em>Methanoculleus marisnigri</em> JR1, and compared them with the genome of a third, <em>Methanospirillum hungatei</em> JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, <em>M. labreanum</em> and <em>M. hungatei</em> contain hydrogenases similar to the <em>Pyrococcus furiosus</em> Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales.</p><h3>Conclusions/Significance</h3><p>Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).</p></div>", "links"=>[], "tags"=>["genomic", "characterization", "methanomicrobiales", "reveals", "classes", "methanogens"], "article_id"=>147403, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Characterization_of_Methanomicrobiales_Reveals_Three_Classes_of_Methanogens/147403", "title"=>"Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-04 02:03:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/895581"], "description"=>"<p>Methanomicrobiales are predicted to couple formylmethanofuran formation and CoM-CoB heterodisulfide reduction to ion gradients. Fd: ferredoxin; MF: methanofuran; H<sub>4</sub>MPT: tetrahydromethanopterin.</p>", "links"=>[], "tags"=>["pathway", "methanogenesis"], "article_id"=>566010, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proposed_pathway_for_methanogenesis_in_Methanomicrobiales_/566010", "title"=>"Proposed pathway for methanogenesis in Methanomicrobiales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-04 01:40:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/895666"], "description"=>"<p>Class I methanogens and Methanomicrobiales use a partial reductive citric acid cycle while Methanosarcinales use a partial oxidative citric acid cycle.</p>", "links"=>[], "tags"=>["pathways", "synthesis", "2-oxoglutarate"], "article_id"=>566101, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alternate_pathways_for_synthesis_of_2_oxoglutarate_from_oxaloacetate_/566101", "title"=>"Alternate pathways for synthesis of 2-oxoglutarate from oxaloacetate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-04 01:41:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/895759"], "description"=>"<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005797#s4\" target=\"_blank\">Materials and Methods</a> for a list of the proteins and organisms included. Protein sequences were concatenated and aligned with Clustal W. The tree was generated with MrBayes 3.1.2 and viewed with TreeView.</p>", "links"=>[], "tags"=>["methanogens", "enzymes", "methanogenesis", "cofactor"], "article_id"=>566195, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_methanogens_based_on_seven_core_enzymes_of_methanogenesis_and_cofactor_biosynthesis_/566195", "title"=>"Phylogenetic tree of methanogens based on seven core enzymes of methanogenesis and cofactor biosynthesis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-04 01:43:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/895874"], "description"=>"<p>The clusters were generated using a spectral clustering procedure (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005797#s4\" target=\"_blank\">Materials and Methods</a> section for details). Signature protein clusters were identified as clusters for which a member protein was present in every analyzed species from one or more classes of methanogens. The number of exclusive, shared, and common signature clusters associated with each methanogen class are shown. The functions of characterized proteins belonging to exclusive signature clusters and to clusters shared between the Methanomicrobiales and the Methanosarcinales are also noted.</p>", "links"=>[], "tags"=>["diagram"], "article_id"=>566316, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_of_signature_clusters_/566316", "title"=>"Venn diagram of signature clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-04 01:45:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/895989"], "description"=>"<p>General genome statistics.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>566426, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_genome_statistics_/566426", "title"=>"General genome statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-04 01:47:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/896048"], "description"=>"<p>Frh: F<sub>420</sub>-reducing hydrogenase; Mvh: F<sub>420</sub>-non-reducing hydrogenase; Eha: energy-converting hydrogenase A; Ehb: energy-converting hydrogenase B; Ech: energy-converting hydrogenase; Mbh: membrane-bound hydrogenase; Msp: <i>Methanosphaera stadtmanae</i>; Mka: <i>Methanopyrus kandleri</i>; Mac: <i>Methanosarcina acetivorans</i>; Mba: <i>Methanosarcina barkeri</i>; Mmz: <i>Methanosarcina mazei</i>; Mmar: <i>Methanoculleus marisnigri</i>; Mlab: <i>Methanocorpusculum labreanum</i>; Mhun: <i>Methanospirillum hungatei</i>.</p>", "links"=>[], "tags"=>["methanogen"], "article_id"=>566483, "categories"=>["Microbiology", "Genetics", "Cell Biology"], "users"=>["Iain Anderson", "Luke E. Ulrich", "Boguslaw Lupa", "Dwi Susanti", "Iris Porat", "Sean D. Hooper", "Athanasios Lykidis", "Magdalena Sieprawska-Lupa", "Lakshmi Dharmarajan", "Eugene Goltsman", "Alla Lapidus", "Elizabeth Saunders", "Cliff Han", "Miriam Land", "Susan Lucas", "Biswarup Mukhopadhyay", "William B. Whitman", "Carl Woese", "James Bristow", "Nikos Kyrpides"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005797.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrogenases_in_methanogen_genomes_/566483", "title"=>"Hydrogenases in methanogen genomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-04 01:48:03"}

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  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"11", "full-text"=>"8", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2009-01-01T00:00:00Z", "end_date"=>"2009-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[349, 614, 744, 851, 955, 1059, 1167, 1262, 1352, 1431, 1516, 1593, 1668, 1746, 1817, 1883, 1950, 2017, 2075, 2141, 2198, 2254, 2313, 2368, 2424, 2474, 2534, 2591, 2651, 2710, 2776, 2837, 2892, 2953, 3014, 3072, 3130, 3186, 3251, 3307, 3366, 3427, 3500, 3561, 3627, 3688, 3759, 3821, 3888, 3950, 4010, 4070, 4131, 4189, 4242, 4307, 4370, 4431, 4491, 4549, 4608]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[335, 600, 731, 835, 935, 1034, 1138, 1230, 1320, 1399, 1485, 1570, 1643, 1714, 1791, 1859, 1928, 1987, 2040, 2104, 2157, 2210, 2261, 2320, 2373, 2432, 2486, 2543, 2603, 2655, 2720, 2787, 2844, 2901, 2952, 3005, 3065, 3119, 3176, 3236, 3305, 3373, 3432, 3492, 3558, 3614, 3676, 3736, 3801, 3869, 3930, 3973, 4031, 4096, 4176, 4234, 4283, 4338, 4405, 4464, 4512]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[366, 637, 775, 896, 999, 1118, 1230, 1322, 1416, 1516, 1602, 1685, 1767, 1849, 1914, 1982, 2049, 2120, 2185, 2246, 2303, 2363, 2409, 2473, 2535, 2599, 2655, 2717, 2777, 2842, 2906, 2977, 3021, 3088, 3144, 3199, 3253, 3317, 3379, 3456, 3508, 3567, 3634, 3716, 3781, 3853, 3911, 3974, 4040, 4118, 4170, 4218, 4285, 4341, 4404, 4467, 4527, 4584, 4631, 4689, 4725]}]}
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