A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments
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{"title"=>"A tale of two oxidation states: Bacterial colonization of arsenic-rich environments", "type"=>"journal", "authors"=>[{"first_name"=>"Daniel", "last_name"=>"Muller", "scopus_author_id"=>"7403362137"}, {"first_name"=>"Claudine", "last_name"=>"Médigue", "scopus_author_id"=>"55944409500"}, {"first_name"=>"Sandrine", "last_name"=>"Koechler", "scopus_author_id"=>"14043587000"}, {"first_name"=>"Valérie", "last_name"=>"Barbe", "scopus_author_id"=>"6603517774"}, {"first_name"=>"Mohamed", "last_name"=>"Barakat", "scopus_author_id"=>"7101803619"}, {"first_name"=>"Emmanuel", "last_name"=>"Talla", "scopus_author_id"=>"6602495281"}, {"first_name"=>"Violaine", "last_name"=>"Bonnefoy", "scopus_author_id"=>"7004218045"}, {"first_name"=>"Evelyne", "last_name"=>"Krin", "scopus_author_id"=>"6603839880"}, {"first_name"=>"Florence", "last_name"=>"Arsène-Ploetze", "scopus_author_id"=>"6507073441"}, {"first_name"=>"Christine", "last_name"=>"Carapito", "scopus_author_id"=>"10340276000"}, {"first_name"=>"Michael", "last_name"=>"Chandler", "scopus_author_id"=>"57189040361"}, {"first_name"=>"Benoît", "last_name"=>"Cournoyer", "scopus_author_id"=>"7003664155"}, {"first_name"=>"Stéphane", "last_name"=>"Cruveiller", "scopus_author_id"=>"6602351966"}, {"first_name"=>"Caroline", "last_name"=>"Dossat", "scopus_author_id"=>"24170861000"}, {"first_name"=>"Simon", "last_name"=>"Duval", "scopus_author_id"=>"24536969700"}, {"first_name"=>"Michael", "last_name"=>"Heymann", "scopus_author_id"=>"57197079080"}, {"first_name"=>"Emmanuelle", "last_name"=>"Leize", "scopus_author_id"=>"7003371238"}, {"first_name"=>"Aurélie", "last_name"=>"Lieutaud", "scopus_author_id"=>"57189297433"}, {"first_name"=>"Didier", "last_name"=>"Lièvremont", "scopus_author_id"=>"6603103401"}, {"first_name"=>"Yuko", "last_name"=>"Makita", "scopus_author_id"=>"7101638634"}, {"first_name"=>"Sophie", "last_name"=>"Mangenot", "scopus_author_id"=>"6603116479"}, {"first_name"=>"Wolfgang", "last_name"=>"Nitschke", "scopus_author_id"=>"7005804256"}, {"first_name"=>"Philippe", "last_name"=>"Ortet", "scopus_author_id"=>"8931003000"}, {"first_name"=>"Nicolas", "last_name"=>"Perdrial", "scopus_author_id"=>"16245486500"}, {"first_name"=>"Barbara", "last_name"=>"Schoepp", "scopus_author_id"=>"6603347972"}, {"first_name"=>"Patricia", "last_name"=>"Siguier", "scopus_author_id"=>"6504081154"}, {"first_name"=>"Diliana D.", "last_name"=>"Simeonova", "scopus_author_id"=>"6506776156"}, {"first_name"=>"Zoé", "last_name"=>"Rouy", "scopus_author_id"=>"8859541500"}, {"first_name"=>"Béatrice", "last_name"=>"Segurens", "scopus_author_id"=>"6508380416"}, {"first_name"=>"Evelyne", "last_name"=>"Turlin", "scopus_author_id"=>"6602100518"}, {"first_name"=>"David", "last_name"=>"Vallenet", "scopus_author_id"=>"6508213959"}, {"first_name"=>"Alain", "last_name"=>"Van Dorsselaer", "scopus_author_id"=>"7007142561"}, {"first_name"=>"Stéphanie", "last_name"=>"Weiss", "scopus_author_id"=>"57199678985"}, {"first_name"=>"Jean", "last_name"=>"Weissenbach", "scopus_author_id"=>"55634467800"}, {"first_name"=>"Marie Claire", "last_name"=>"Lett", "scopus_author_id"=>"6603732591"}, {"first_name"=>"Antoine", "last_name"=>"Danchin", "scopus_author_id"=>"7103235597"}, {"first_name"=>"Philippe N.", "last_name"=>"Bertin", "scopus_author_id"=>"56487202300"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-34247589893", "sgr"=>"34247589893", "pui"=>"46683468", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"17432936", "doi"=>"10.1371/journal.pgen.0030053"}, "id"=>"1e054256-5c5d-339b-b537-f0f781af4b99", "abstract"=>"<title>Author Summary</title><sec id=\"st1\"><title/><p>Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in <italic>Herminiimonas arsenicoxydans,</italic> a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.</p></sec>", "link"=>"http://www.mendeley.com/research/tale-two-oxidation-states-bacterial-colonization-arsenicrich-environments", "reader_count"=>131, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>12, "Student > Doctoral Student"=>7, "Researcher"=>42, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>2, "Student > Master"=>14, "Other"=>4, "Student > Bachelor"=>11, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>12, "Student > Doctoral Student"=>7, "Researcher"=>42, "Student > Ph. D. 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  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"14"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/951185"], "description"=>"<p>The <i>aoxAB</i> operon is close to arsenic-resistance genes in H. arsenicoxydans, <i>A. faecalis, X. autotrophicus, N. hamburgensis,</i> and <i>C. phaeobacteroides.</i> In the first three bacteria, these genes are associated with an <i>aoxRS</i> two-component regulatory system. In <i>H. arsenicoxydans,</i> the CDS number of <i>aoxABCD, aoxRS,</i> and <i>arsRCBCH</i> are <i>hear</i>0479–0476, <i>hear</i>0483–0482, and <i>hear</i>0499–0503, respectively. Sequence information of other genes was obtained from GenBank database and their localization on the chromosome or the plasmid is given by nucleotide numbering. The following bacterial genomes were used: <i>Alcaligenes faecalis</i>, Agrobacterium tumefaciens, Rhodoferax ferrireducens, Burkholderia multivorans, Xanthobacter autotrophicus, <i>Roseovarius</i> sp217, Nitrobacter hamburgensis, Chlorobium phaerobacteroides, Chloroflexus aurentiacus, Thermus thermophilus HB8, Aeropyrum pernix, Sulfolobus tokodai, Environmental sample 1, and Environmental sample 2.</p>", "links"=>[], "tags"=>["arsenic-metabolizing"], "article_id"=>621453, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Organization_of_the_aox_Gene_Cluster_in_H_arsenicoxydans_and_Various_Arsenic_Metabolizing_Microorganisms_/621453", "title"=>"Organization of the <i>aox</i> Gene Cluster in H. arsenicoxydans and Various Arsenic-Metabolizing Microorganisms", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:24:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/951521"], "description"=>"<p>The proteins of loci 1 (HEAR3302), 2 (HEAR0500), and 4 (HEAR3207) in cluster with reductases present in <i>acr3</i>-type transporter operons. In <i>H. arsenicoxydans,</i> two of them are, however, associated with an ArsB-type transporter<i>.</i> Protein sequences involved in arsenate reduction were retrieved from the National Center for Biotechnology Information GenBank database (<a href=\"http://www.ncbi.nlm.nih.gov/entrez\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/entrez</a>) and phylogenetic trees were reconstructed from multiple sequence alignments using the neighbor-joining algorithm implemented in ClustalX. The following sequences were used as references: <i>Roseovarius nubinhibens, Xanthobacter autotrophicus, Rhodospirillum rubrum, Bradyrhizobium japonicum, Rhodopseudomonas palustris, Nitrobacter winogradskyi, Nitrobacter hamburgensis, Xanthobacter autotrophicus, Acidovorax sp., Comamonas sp., Rubrivivax gelatinosus, Delftia acidovorans, Azotobacter vinelandii, Rubrivivax gelatinosus, Burkholderia multivorans, Ralstonia metallidurans, Shigella flexneri, Shigella flexneri, Polaromonas naphthalenivorans, Comamonas testosteroni, Burkholderia vietnamiensis, Burkholderia pseudomallei, Burkholderia mallei, Azoarcus sp., Methylobacillus flagellatus, Alcaligenes faecalis, Rhodoferax ferrireducens, Pseudomonas syringae, Pseudomonas putida, Pseudomonas aeruginosa, Shewanella oneidensis, Wolinella succinogenes, Corynebacterium efficiens, Corynebacterium efficiens, Alkalilimnicola ehrlichei,</i> and Chlorobium phaeobacteroides.</p>", "links"=>[], "tags"=>["arsca", "arsenate", "reductases", "arsenic-resistant"], "article_id"=>621786, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g005", "stats"=>{"downloads"=>4, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Tree_of_ArsCa_Arsenate_Reductases_in_Various_Arsenic_Resistant_Microorganisms_/621786", "title"=>"Phylogenetic Tree of ArsCa Arsenate Reductases in Various Arsenic-Resistant Microorganisms", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:29:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/951774"], "description"=>"<p>Motility assays were performed in the presence of an increasing concentration of As[III], Co[II], or Fe[III]. The level of motility of ULPAs wild-type strain and of its <i>aoxAB</i> knockout derivative was evaluated as the diameter of the swimming ring expressed in millimeters. The results are the mean value of three independent experiments.</p>", "links"=>[], "tags"=>["metalloid"], "article_id"=>622036, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_Metal_and_Metalloid_Concentration_on_Swimming_Properties_in_H_arsenicoxydans_/622036", "title"=>"Effect of Metal and Metalloid Concentration on Swimming Properties in H. arsenicoxydans", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/951337"], "description"=>"<p>The three operons identified by complementation of an <i>E. coli ars</i>-deficient strain code for an ArsR regulator, one or two ArsC arsenate reductases, an As[III] extrusion pump, and an ArsH putative flavoprotein. The fourth operon present in the genome lacks the As[III] pump-encoding gene.</p>", "links"=>[], "tags"=>["arsenate-resistance", "operons"], "article_id"=>621616, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g004", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Organization_of_Arsenate_Resistance_Operons_ars_in_H_arsenicoxydans_/621616", "title"=>"Organization of Arsenate-Resistance Operons <i>(ars)</i> in <i>H. arsenicoxydans</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:26:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/469754", "https://ndownloader.figshare.com/files/469792", "https://ndownloader.figshare.com/files/469802", "https://ndownloader.figshare.com/files/469818", "https://ndownloader.figshare.com/files/469832", "https://ndownloader.figshare.com/files/469849", "https://ndownloader.figshare.com/files/469859", "https://ndownloader.figshare.com/files/469868", "https://ndownloader.figshare.com/files/469878", "https://ndownloader.figshare.com/files/469883", "https://ndownloader.figshare.com/files/469891"], "description"=>"<div><p>Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.</p></div>", "links"=>[], "tags"=>["oxidation", "bacterial", "colonization", "arsenic-rich", "environments"], "article_id"=>152590, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0030053.sg001", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg002", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg003", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg004", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg005", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg006", "https://dx.doi.org/10.1371/journal.pgen.0030053.sg007", "https://dx.doi.org/10.1371/journal.pgen.0030053.st001", "https://dx.doi.org/10.1371/journal.pgen.0030053.st002", "https://dx.doi.org/10.1371/journal.pgen.0030053.st003", "https://dx.doi.org/10.1371/journal.pgen.0030053.st004"], "stats"=>{"downloads"=>46, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Tale_of_Two_Oxidation_States_Bacterial_Colonization_of_Arsenic_Rich_Environments/152590", "title"=>"A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-04-13 00:43:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/950740"], "description"=>"<p>Circles display (from the outside inward): (rings 1 and 2) predicted CDSs transcribed in a clockwise/counterclockwise direction, (ring 3) tRNA (green) and rRNA (violetblue), (ring 4) ISs (yellow) and prophagic regions (violetbrown), (ring 5) clusters of genes involved in arsenic (red; numbered as shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030053#pgen-0030053-g004\" target=\"_blank\">Figure 4</a>)/metal resistance (dark blue), (ring 6) GC deviation (GC<sub>window</sub> − average GC of genome, using a 1kb window); (7) GC skew (using a 1kb window). The high GC-rich island described in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030053#pgen-0030053-g002\" target=\"_blank\">Figure 2</a> is shown in red.</p>", "links"=>[], "tags"=>["Computational biology", "ecology", "genetics and genomics", "microbiology"], "article_id"=>621011, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_Representation_of_H_arsenicoxydans_Genome_/621011", "title"=>"Circular Representation of H. arsenicoxydans Genome", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:16:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/951006"], "description"=>"<p>The chromosomal segment extends between positions 1.97 and 2.07 Mb on the H. arsenicoxydans chromosome. Frames display (from top to bottom): (1) %GC along this island; (2) annotated CDSs on the direct (D) and reverse (R) strand: <i>ars</i>III gene cluster (six genes in red arrows), part of the <i>clc</i> element of plasmid (or phage) origin, initially described in Pseudomonas sp. strain B13 [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030053#pgen-0030053-b022\" target=\"_blank\">22</a>] (64 genes in light blue arrows), and phage-related function (DNA repair, integrase) associated with metabolic capabilities, such as formaldelyde oxidation (17 genes in light green arrows), small genes are represented by a line; (3) synteny maps, calculated on a set of selected genomes (RALME, Ralstonia metallidurans CH34; BURXE, Burkholderia xenovorans LB400; AZOSE, Azoarcus sp. EbN1; PSEF5, Pseudomonas fluorescens Pf-5; and XANAC, Xanthomonas campestris 85–10). A line contains the similarity results between H. arsenicoxydans and one given genome. A rectangle represents a putative ortholog between one CDS of the compared genome and the CDS of the H. arsenicoxydans genome opposite. When, for several CDSs colocalized on the H. arsenicoxydans genome, several colocalized orthologs have been identified in the compared genome, the rectangles will be of the same color. Otherwise, the rectangle is white. A group of rectangles of the same color therefore indicates the existence of a synteny between H. arsenicoxydans and the compared genome, using a gap parameters of five genes maximum [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030053#pgen-0030053-b063\" target=\"_blank\">63</a>]. Details on correspondences between genes in the synteny (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030053#pgen-0030053-st002\" target=\"_blank\">Table S2</a>) show that the light blue section of this island in H. arsenicoxydans is also found at the same chromosomal location in the compared genomes.</p>", "links"=>[], "tags"=>["gc-rich"], "article_id"=>621281, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_View_of_a_GC_Rich_Island_/621281", "title"=>"Detailed View of a GC-Rich Island", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/951948"], "description"=>"<div><p>(A) Chemoattraction to As[III]. Left: low melting agar with chemotaxis buffer, right: low melting agar with chemotaxis buffer supplemented with 2 mM As[III]. Bright ring of cells around agarose plugs is indicative of chemotaxis.</p><p>(B) Transmission electron microscopy (TEM) picture of H. arsenicoxydans grown in As-enriched medium. Circles represent the X-ray spot of analysis, while I and II are the energy dispersive X-Ray spectroscopy corresponding values. Cl and K peaks show organic constituents and Cu labels represent peaks due to supporting grid. Arsenic content is 16.5 % weight as As<sub>2</sub>O<sub>3</sub> in I. and 0.0% weight in II; both including microgrid C-coating quantification.</p></div>", "links"=>[], "tags"=>["eps", "synthesis"], "article_id"=>622207, "categories"=>["Biological Sciences", "Ecology", "Genetics", "Microbiology"], "users"=>["Daniel Müller", "Claudine Médigue", "Sandrine Koechler", "Valérie Barbe", "Mohamed Barakat", "Emmanuel Talla", "Violaine Bonnefoy", "Evelyne Krin", "Florence Arsène-Ploetze", "Christine Carapito", "Michaël Chandler", "Benoit Cournoyer", "Stéphane Cruveiller", "Caroline Dossat", "Simon Duval", "Michael Heymann", "Emmanuelle Leize", "Aurélie Lieutaud", "Didier Lièvremont", "Yuko Makita", "Sophie Mangenot", "Wolfgang Nitschke", "Philippe Ortet", "Nicolas Perdrial", "Barbara Schoepp", "Patricia Siguier", "Diliana D Simeonova", "Zoé Rouy", "Beatrice Segurens", "Evelyne Turlin", "David Vallenet", "Alain Van Dorsselaer", "Stéphanie Weiss", "Jean Weissenbach", "Marie-Claire Lett", "Antoine Danchin", "Philippe N Bertin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030053.g007", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chemotaxis_and_EPS_Synthesis_in_H_arsenicoxydans_in_Response_to_Arsenic_/622207", "title"=>"Chemotaxis and EPS Synthesis in H. arsenicoxydans in Response to Arsenic", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-13 00:36:47"}

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  • {"unique-ip"=>"29", "full-text"=>"31", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"4"}
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  • {"unique-ip"=>"25", "full-text"=>"13", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"30", "full-text"=>"25", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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  • {"unique-ip"=>"15", "full-text"=>"13", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"28", "full-text"=>"29", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"2", "cited-by"=>"1", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"18", "full-text"=>"27", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"7", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"19", "full-text"=>"22", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"13", "full-text"=>"10", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"28", "full-text"=>"35", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"8", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"16", "full-text"=>"17", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
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  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
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  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"10", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"10", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"1"}
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Relative Metric

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