Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers
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Mendeley | Further Information

{"title"=>"Phylogenomics of unusual histone H2A variants in bdelloid rotifers", "type"=>"journal", "authors"=>[{"first_name"=>"Karine", "last_name"=>"Van Doninck", "scopus_author_id"=>"6603008034"}, {"first_name"=>"Morgan L.", "last_name"=>"Mandigo", "scopus_author_id"=>"25960909100"}, {"first_name"=>"Jae H.", "last_name"=>"Hur", "scopus_author_id"=>"25960881000"}, {"first_name"=>"Peter", "last_name"=>"Wang", "scopus_author_id"=>"55494825900"}, {"first_name"=>"Julien", "last_name"=>"Guglielmini", "scopus_author_id"=>"24461638900"}, {"first_name"=>"Michel", "last_name"=>"C.Milinkovitch", "scopus_author_id"=>"55666978100"}, {"first_name"=>"William S.", "last_name"=>"Lane", "scopus_author_id"=>"7102391928"}, {"first_name"=>"Matthew", "last_name"=>"Meselson", "scopus_author_id"=>"7003379433"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-62149116543", "doi"=>"10.1371/journal.pgen.1000401", "sgr"=>"62149116543", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"19266019", "issn"=>"15537390", "pui"=>"354404884"}, "id"=>"4cbb916e-81e4-3888-b535-7e6695427ddc", "abstract"=>"Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in Adineta vaga and Philodina roseola, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers.", "link"=>"http://www.mendeley.com/research/phylogenomics-unusual-histone-h2a-variants-bdelloid-rotifers", "reader_count"=>52, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>15, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>41, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>41}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>2, "United Kingdom"=>3, "Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/906766"], "description"=>"<p>The histone proteins extracted from the nuclei of <i>Adineta vaga</i> (<i>Av</i>), <i>Philodina roseola</i> (<i>Pr</i>), <i>Brachionus plicatilis</i> (<i>Bp</i>) and human HeLa cells (Hu) are represented on SDS-PAGE gels. All the bands visible on the gel up to ∼25 kD for both bdelloid species and till ∼20 kD for <i>B. plicatilis</i> were identified by mass spectrometry: only histone bands are labelled here. The numbered bands in lane M (marker) represent the protein size ladder in kD.</p>", "links"=>[], "tags"=>["gels", "bdelloid", "histone"], "article_id"=>577218, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g002", "stats"=>{"downloads"=>2, "page_views"=>85, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SDS_PAGE_gels_of_bdelloid_histone_proteins_/577218", "title"=>"SDS-PAGE gels of bdelloid histone proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 02:00:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/907059"], "description"=>"<p>(A) Ka/Ks ratios of the bdelloid rotifer histone genes: inter-species, intra co-linear pair comparisons between <i>Adineta vaga</i> (Av) and <i>Philodina roseola</i> (Pr). The line present in the 3 graphs of the first column represents the start of the C-terminus tail beyond the LLPKK motif in H2A genes. (B) Maximum Likelihood phylogram of bdelloid H2A gene variants inferred with RaxML. Bootstrap supports >50% are shown for each node. The arrow indicates the branch with bootstrap <50%.</p>", "links"=>[], "tags"=>["bdelloid-specific", "h2a"], "article_id"=>577509, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g004", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_evolution_of_bdelloid_specific_H2A_variants_/577509", "title"=>"Molecular evolution of bdelloid-specific H2A variants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 02:05:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/906631"], "description"=>"<p>(A) All three bdelloid H2A variants (<i>H2Abd</i>, <i>H2Abd1</i> and <i>H2Abd2</i>), with their respective name code for each copy, are given. Each copy of the histone gene cluster is also represented, being organized as co-linear pairs A and B. Presented in light grey boxes are genes likely present in the nucleosomes; dark grey boxes represent expressed variants found in the bdelloid proteome (see below); white boxes represent unknown expression status. (B) Multiple alignment using MAFFT v6 of the histone H2A genes of the bdelloid species Av and Pr and the monogonont rotifer <i>Brachionus plicatilis</i> (Bp) with canonical H2A, H2AX and H2AZ variants of few other model eukaryotes. Red, blue and yellow boxes indicate the bdelloid <i>H2Abd</i>, <i>H2Abd1</i> and <i>H2Abd2</i> genes, respectively. The red arrow indicates the start of the C-terminal tail beyond the conserved LLPKK motif. Protein interaction domains (“loop1” and “docking”) are indicated and taken from <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000401#pgen.1000401-Redon1\" target=\"_blank\">[37]</a>. The regions of primer design are in a dashed box and the light grey boxes represent the regions where H2AZ differs substantially from canonical H2A.</p>", "links"=>[], "tags"=>["histone", "h2a", "variants", "bdelloid"], "article_id"=>577079, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unusual_histone_H2A_variants_of_the_bdelloid_species_Adineta_vaga_Av_and_Philodina_roseola_Pr_/577079", "title"=>"Unusual histone H2A variants of the bdelloid species <i>Adineta vaga</i> (Av) and <i>Philodina roseola</i> (Pr).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 01:57:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/907429"], "description"=>"<p>Maximum likelihood bootstrap consensus cladogram, inferred using the program Bootstrap RaxML, of canonical H2A and H2AX of fungi, insects, plants and vertebrates. Bootstrap values >50% are shown. Eukaryotic groups are colour-coded; H2AX is in red and canonical H2As in black.</p>", "links"=>[], "tags"=>["canonical", "h2a", "h2ax"], "article_id"=>577882, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g006", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_canonical_H2A_and_H2AX_proteins_/577882", "title"=>"Phylogeny of canonical H2A and H2AX proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 02:11:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/906925"], "description"=>"<p>(A) Alignment of the <i>H2Abd</i> C-terminus tails of <i>Adineta vaga</i> (Av) and <i>Philodina roseola</i> (Pr); conserved amino acids are framed. (B) Alignment in Logos format of the <i>H2Abd1</i> C-terminal tails of Av and Pr; a putative SPKK class of motif is represented in a box. (C) Alignment of the <i>H2Abd2</i> C-terminus tails of Av and Pr; conserved amino acids are framed. (D) Sequence Logo representation of the conserved 3′ UTR stem-loop and downstream sequence (45 bp) of all histone genes in Av and Pr (except <i>H2Abd2</i> that does not exhibit a stem-loop). UTR, untranslated region.</p>", "links"=>[], "tags"=>["bdelloid-specific", "h2a", "carboxy-terminal", "tails", "nucleotide", "stem-loop"], "article_id"=>577372, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g003", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignments_of_the_bdelloid_specific_H2A_carboxy_terminal_tails_and_nucleotide_stem_loop_sequences_/577372", "title"=>"Alignments of the bdelloid-specific H2A carboxy-terminal tails and nucleotide stem-loop sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 02:02:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/907266"], "description"=>"<p>Maximum likelihood bootstrap consensus cladogram, inferred using the program Bootstrap RaxML, of canonical H2A and variants. Bootstrap values >50% are shown. Variants are colour-coded and all canonical H2As are in blue and H2AX in red. All H2A bdelloid rotifer genes form, with canonical H2As of <i>Brachionus plicatlis</i>, a distinct lineage (orange) nested within the eukaryotic canonical H2As.</p>", "links"=>[], "tags"=>["h2a"], "article_id"=>577725, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000401.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_H2A_proteins_/577725", "title"=>"Phylogeny of H2A proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-06 02:08:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/448242", "https://ndownloader.figshare.com/files/448252", "https://ndownloader.figshare.com/files/448262"], "description"=>"<div><p>Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in <em>Adineta vaga</em> and <em>Philodina roseola</em>, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers.</p></div>", "links"=>[], "tags"=>["phylogenomics", "histone", "h2a", "variants", "bdelloid", "rotifers"], "article_id"=>148319, "categories"=>["Evolutionary Biology", "Molecular Biology"], "users"=>["Karine Van Doninck", "Morgan L. Mandigo", "Jae H. Hur", "Peter Wang", "Julien Guglielmini", "Michel C. Milinkovitch", "William S. Lane", "Matthew Meselson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000401.s001", "https://dx.doi.org/10.1371/journal.pgen.1000401.s002", "https://dx.doi.org/10.1371/journal.pgen.1000401.s003"], "stats"=>{"downloads"=>10, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenomics_of_Unusual_Histone_H2A_Variants_in_Bdelloid_Rotifers/148319", "title"=>"Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-03-06 02:18:39"}

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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
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Relative Metric

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