Evolutionary Descent of Prion Genes from the ZIP Family of Metal Ion Transporters
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{"title"=>"Evolutionary descent of prion genes from the ZIP family of metal Ion transporters", "type"=>"journal", "authors"=>[{"first_name"=>"Gerold", "last_name"=>"Schmitt-Ulms", "scopus_author_id"=>"6508293809"}, {"first_name"=>"Sepehr", "last_name"=>"Ehsani", "scopus_author_id"=>"23099742400"}, {"first_name"=>"Joel C.", "last_name"=>"Watts", "scopus_author_id"=>"8789165800"}, {"first_name"=>"David", "last_name"=>"Westaway", "scopus_author_id"=>"7006295116"}, {"first_name"=>"Holger", "last_name"=>"Wille", "scopus_author_id"=>"7006251768"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-70349669073", "pui"=>"355371441", "doi"=>"10.1371/journal.pone.0007208", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"70349669073", "pmid"=>"19784368"}, "id"=>"bf23108e-1e1c-39c5-aa52-9e5f05439e88", "abstract"=>"In the more than twenty years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into a possible function of PrP may be obtained through the characterization of its molecular neighborhood in cells. Quantitative interactome data demonstrated the spatial proximity of two metal ion transporters of the ZIP family, ZIP6 and ZIP10, to mammalian prion proteins in vivo. A subsequent bioinformatic analysis revealed the unexpected presence of a PrP-like amino acid sequence within the N-terminal, extracellular domain of a distinct sub-branch of the ZIP protein family that includes ZIP5, ZIP6 and ZIP10. Additional structural threading and orthologous sequence alignment analyses argued that the prion gene family is phylogenetically derived from a ZIP-like ancestral molecule. The level of sequence homology and the presence of prion protein genes in most chordate species place the split from the ZIP-like ancestor gene at the base of the chordate lineage. This relationship explains structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The phylogenetic and spatial connection to ZIP proteins is expected to open new avenues of research to elucidate the biology of the prion protein in health and disease.", "link"=>"http://www.mendeley.com/research/evolutionary-descent-prion-genes-zip-family-metal-ion-transporters", "reader_count"=>78, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>11, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>11, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>15, "Agricultural and Biological Sciences"=>44, "Medicine and Dentistry"=>6, "Neuroscience"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Chemistry"=>2, "Computer Science"=>2, "Earth and Planetary Sciences"=>1, "Engineering"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>44}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Thailand"=>1, "France"=>1, "Spain"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/882254"], "description"=>"<p>Cartoon depicting the emergence of members of the prion gene family from ZIP ancestor gene(s): (i) hypothetical Sho ancestor gene, (ii) prion gene founder and (iii) evolutionary intermediate prion gene family ancestor. Alternative hypotheses for the origin of prion genes: (1) insertion of ZIP ancestor-derived PL domain into Sho ancestor molecule; or (2) duplication of N-terminal ZIP ancestor fragment followed by expansion of hydrophobic domain and differentiation of former transmembrane domain into signal peptide for attachment of GPI anchor. Based on the above models, Sho genes either (1) evolved independently or (2) were themselves derived from a ZIP ancestor. Please note that our current analyses favor model (2).</p>", "links"=>[], "tags"=>["depicting", "evolutionary", "topology", "members", "prion", "hypothetical", "zip", "zip10"], "article_id"=>552704, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Models_depicting_evolutionary_origin_and_topology_of_members_of_prion_protein_family_hypothetical_ZIP_ancestor_and_ZIP10_transporter_/552704", "title"=>"Models depicting evolutionary origin and topology of members of prion protein family, hypothetical ZIP ancestor and ZIP10 transporter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-28 00:45:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/882380"], "description"=>"a<p>In amino acids. Numbers for ZIP proteins are tentative because the exact N-terminal boundary of their transmembrane domain 1 is not known. N-terminal signal peptides included.</p>b<p>Not determined.</p>", "links"=>[], "tags"=>["prp", "paralogs", "zips"], "article_id"=>552840, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_mouse_PrP_gene_family_paralogs_with_ZIPs_5_6_10_/552840", "title"=>"Comparison of mouse PrP gene family paralogs with ZIPs 5/6/10.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-28 00:47:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/437539", "https://ndownloader.figshare.com/files/437715", "https://ndownloader.figshare.com/files/437829", "https://ndownloader.figshare.com/files/437885", "https://ndownloader.figshare.com/files/437906", "https://ndownloader.figshare.com/files/437963"], "description"=>"<div><p>In the more than twenty years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into a possible function of PrP may be obtained through the characterization of its molecular neighborhood in cells. Quantitative interactome data demonstrated the spatial proximity of two metal ion transporters of the ZIP family, ZIP6 and ZIP10, to mammalian prion proteins <em>in vivo</em>. A subsequent bioinformatic analysis revealed the unexpected presence of a PrP-like amino acid sequence within the N-terminal, extracellular domain of a distinct sub-branch of the ZIP protein family that includes ZIP5, ZIP6 and ZIP10. Additional structural threading and orthologous sequence alignment analyses argued that the prion gene family is phylogenetically derived from a ZIP-like ancestral molecule. The level of sequence homology and the presence of prion protein genes in most chordate species place the split from the ZIP-like ancestor gene at the base of the chordate lineage. This relationship explains structural and functional features found within mammalian prion proteins as elements of an ancient involvement in the transmembrane transport of divalent cations. The phylogenetic and spatial connection to ZIP proteins is expected to open new avenues of research to elucidate the biology of the prion protein in health and disease.</p></div>", "links"=>[], "tags"=>["evolutionary", "descent", "prion", "genes", "zip", "ion", "transporters"], "article_id"=>146251, "categories"=>["Cancer", "Evolutionary Biology", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007208.s001", "https://dx.doi.org/10.1371/journal.pone.0007208.s002", "https://dx.doi.org/10.1371/journal.pone.0007208.s003", "https://dx.doi.org/10.1371/journal.pone.0007208.s004", "https://dx.doi.org/10.1371/journal.pone.0007208.s005", "https://dx.doi.org/10.1371/journal.pone.0007208.s006"], "stats"=>{"downloads"=>24, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolutionary_Descent_of_Prion_Genes_from_the_ZIP_Family_of_Metal_Ion_Transporters/146251", "title"=>"Evolutionary Descent of Prion Genes from the ZIP Family of Metal Ion Transporters", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-09-28 01:44:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/882346"], "description"=>"a<p>Proteins were sorted into specific versus unspecific binder categories based on their iTRAQ distribution, i.e. proteins were considered unspecific interactors if their derived CID spectra revealed iTRAQ114 to 117 signature mass peak signal intensities which exceeded 10% of combined intensities for all samples including the unspecific control.</p>b<p>For the calculation of iTRAQ values the intensity of individual peptide associated iTRAQ signature peaks was normalized to combine to 100% per peptide and subsequently averaged. Standard deviations were determined and are listed in <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone.0007208.s004\" target=\"_blank\">Table S1</a></b>.</p>c<p>Length of precursor molecules prior to posttranslational processing.</p>d<p>Only CID spectra underlying different peptides were considered i.e. if the same peptide was identified with different charge states or modifications it counted as one hit.</p>e<p>Total number of unique CID spectra. Please note that the same peptide was only counted more than once if it was identified with different charge states or modifications.</p>f<p>Percent sequence coverage based on the presence of peptides for which no higher ranked assignment to other proteins could be made.</p>", "links"=>[], "tags"=>["prp", "sho", "interactomes", "identifies", "ion", "transporters", "zip", "spatial", "proximity", "members", "mammalian", "prion"], "article_id"=>552793, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.t001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_analysis_of_mouse_Dpl_PrP_and_Sho_interactomes_identifies_metal_ion_transporters_of_the_ZIP_protein_family_in_spatial_proximity_to_all_three_members_of_the_mammalian_prion_protein_family_/552793", "title"=>"Quantitative analysis of mouse Dpl, PrP and Sho interactomes identifies metal ion transporters of the ZIP protein family in spatial proximity to all three members of the mammalian prion protein family.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-28 00:46:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/882006"], "description"=>"<p>A, Schematic drawing depicting the molecular organization of ZIPs 5, 6, 10 (only consensus features shown) and PrP. B, Comparison of orientation and membrane topology of mammalian prion family proteins, and a consensus ZIP5/6/10 molecule. C, Tree diagram depicting the human ZIP family of zinc metal ion transporters. The ZIP protein family in humans (and mice) consists of fourteen paralogs which can be grouped into four subfamilies based on sequence similarities (indicated by different background shading) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone.0007208-Taylor1\" target=\"_blank\">[19]</a>. Green shading indicates the sub-branch of paralog ZIP sequences most similar to prion family gene sequences. The right side of the panel compares the molecular organization of N-terminal domains within human ZIPs. Please note the divergence in lengths and molecular organization of N-terminal sequences which is contrasted by the presence of a relatively well-conserved cysteine-flanked core (present in 8 out of 14 paralogs) and highly conserved transmembrane domains. D, Simplified phylogenetic tree (modeled after <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone.0007208-Dunn1\" target=\"_blank\">[65]</a>; arbitrary branch lengths) and table depicting the wide distribution of ZIP sequences in most organisms. Green shading indicates the phylogenetic branch of chordates with widespread existence of prion gene ortholog sequences in their genome. The paralog distribution was deduced from an ortholog alignment of 633 ZIP sequences published by the Sanger Institute (TreeFam release 7.0, <a href=\"http://www.treefam.org\" target=\"_blank\">http://www.treefam.org</a>) or was determined by aligning representative ZIP protein sequences to genomic sequences (proteobacteria, archaea, Cnidaria and fish). The number of ZIP subfamily IV (LIV-1) paralogs containing a cysteine-flanked core (CFC) domain (indicated in brackets) was determined by inspection of sequences for the presence of cysteines that (i) flank a PALLY-like signature motif, and (ii) adhere to CFC consensus distance constraints derived from the multiple alignment of confirmed CFC domains: the cysteine-to-cysteine distance and the cysteine-to-transmembrane attachment site distance. Please note that ZIP proteins harboring CFC sequences N-terminal to their transmembrane domains can be found in organisms with relatively primitive body plans such as hydra (<i>H. magnipapillata</i>) or protostomia such as the fruitfly (<i>D. melanogaster</i>).</p>", "links"=>[], "tags"=>["membrane", "attachment", "phylogenetic", "zip", "prion"], "article_id"=>552458, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.g002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_organization_mode_of_membrane_attachment_and_phylogenetic_relationship_of_ZIP_and_prion_gene_families_/552458", "title"=>"Molecular organization, mode of membrane attachment and phylogenetic relationship of ZIP and prion gene families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-28 00:40:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/881902"], "description"=>"<p>A, Structural threading of the PL domain within ZIP10 predicts striking resemblance to PrP and Dpl with regard to relative position and order of secondary structure motifs. The secondary structure for the PL domain of ZIP10 was ranked according to the frequency of the prediction in separate threadings (<i>H</i> 75–100% and <i>H</i> 50–75% for α-helices; the same scale applies to β-sheeted structures “<i>E</i><i>/E</i>”). Also shown is a matrix of amino acid identities and similarities between depicted sequences of ZIP10, PrP and Dpl. B, Comparison of high-resolution nuclear magnetic resonance structures of PrP (PDB entry: 1ag2) and Dpl (PDB entry:1I17) with a predicted structure for the ZIP10 PL domain. Dark green, grey and black highlights depict conserved, similar and identical residues, respectively. ‘S’ and ‘G’ labels indicate sites of disulfide linkages and glycosylation, respectively.</p>", "links"=>[], "tags"=>["prp"], "article_id"=>552357, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_similarity_between_mouse_ZIP10_PrP_and_Dpl_/552357", "title"=>"Structural similarity between mouse ZIP10, PrP and Dpl.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-28 00:39:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/882142"], "description"=>"<p>A, Multiple sequence alignment of PrP globular domain with ZIP10 PL of selected ortholog sequences. B, Multiple sequence alignment of N-terminal Sho and ZIP5 sequences from pufferfish, zebrafish and mouse. Please note the greater divergence of ZIP10 and PrP in human (Hs: <i>H. sapiens</i>) and murine (Mm: <i>M. musculus</i>) sequences relative to the respective sequence pairs in turtle (Ts: <i>T. scripta</i>) and pufferfish species (Tn: <i>T. nigroviridis</i> and Tr: <i>T. rubripes</i>). Highlight colors used in the alignments are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone-0007208-g001\" target=\"_blank\">Figure 1</a>. ‘N’, ‘S’, ‘G’ and ‘C’ labels indicate N-termini, disulfide linkages, glycosylation sites and C-termini, respectively. Colors used in the schematic drawing are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone-0007208-g002\" target=\"_blank\">Figure 2A</a>. For full-length multiple alignments of a subset of these and related sequences, please see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007208#pone.0007208.s002\" target=\"_blank\">Figure S2</a>.</p>", "links"=>[], "tags"=>["divergent", "members", "zip", "prion"], "article_id"=>552594, "categories"=>["Virology", "Evolutionary Biology", "Infectious Diseases", "Neuroscience", "Medicine"], "users"=>["Gerold Schmitt-Ulms", "Sepehr Ehsani", "Joel C. Watts", "David Westaway", "Holger Wille"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007208.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_evidence_for_common_origin_and_divergent_sequence_evolution_of_members_of_ZIP_and_prion_protein_families_/552594", "title"=>"Sequence evidence for common origin and divergent sequence evolution of members of ZIP and prion protein families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-28 00:43:14"}

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  • {"unique-ip"=>"17", "full-text"=>"47", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

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