Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission
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Mendeley | Further Information

{"title"=>"Structural insights into viral determinants of nematode mediated grapevine fanleaf virus transmission", "type"=>"journal", "authors"=>[{"first_name"=>"Pascale", "last_name"=>"Schellenberger", "scopus_author_id"=>"36025940000"}, {"first_name"=>"Claude", "last_name"=>"Sauter", "scopus_author_id"=>"7005129398"}, {"first_name"=>"Bernard", "last_name"=>"Lorber", "scopus_author_id"=>"7006283821"}, {"first_name"=>"Patrick", "last_name"=>"Bron", "scopus_author_id"=>"6701497874"}, {"first_name"=>"Stefano", "last_name"=>"Trapani", "scopus_author_id"=>"36020833100"}, {"first_name"=>"Marc", "last_name"=>"Bergdoll", "scopus_author_id"=>"7005286606"}, {"first_name"=>"Aurélie", "last_name"=>"Marmonier", "scopus_author_id"=>"24503488300"}, {"first_name"=>"Corinne", "last_name"=>"Schmitt-Keichinger", "scopus_author_id"=>"6507059827"}, {"first_name"=>"Olivier", "last_name"=>"Lemaire", "scopus_author_id"=>"6603914868"}, {"first_name"=>"Gérard", "last_name"=>"Demangeat", "scopus_author_id"=>"6603299760"}, {"first_name"=>"Christophe", "last_name"=>"Ritzenthaler", "scopus_author_id"=>"6602159102"}], "year"=>2011, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537374", "scopus"=>"2-s2.0-79958068763", "sgr"=>"79958068763", "pui"=>"361895929", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "pmid"=>"21625570", "doi"=>"10.1371/journal.ppat.1002034"}, "id"=>"f1a4a292-79b1-3d55-8b1c-937118c48ef7", "abstract"=>"Many animal and plant viruses rely on vectors for their transmission from host to host. Grapevine fanleaf virus (GFLV), a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode Xiphinema index. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP), carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD) poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp) in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by X. index. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode's feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.", "link"=>"http://www.mendeley.com/research/structural-insights-viral-determinants-nematode-mediated-grapevine-fanleaf-virus-transmission", "reader_count"=>39, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>32, "Medicine and Dentistry"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>32}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Morocco"=>1, "France"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/774590"], "description"=>"<p>(<b>A</b>) Representation of the GFLV-F13 capsid with red, blue and\n white regions showing negative, positive and neutral electrostatic\n surface potentials, respectively. The black line highlights a single CP\n subunit and arrows denote the 5-, 3-, and 2-fold axes. (<b>A1</b>)\n Residue 297 is indicated by an open black circle on the left side of the\n positively charged pocket. (<b>A2</b>) Detailed view of the\n positively charged pocket. The electrostatic potential was calculated\n with APBS and visualized from -3 to 3 k/e<sup>-</sup> with\n <i>Chimera</i> using a probe of 3 Å to display a\n smoother surface. (<b>B</b>) Top views of the putative\n ligand-binding pocket at the surface of the GFLV-F13 capsid.\n (<b>B1</b>) View of GFLV-F13 outer-surface residues at the\n same magnification and orientation than in A2. Residues of the putative\n ligand-binding pocket are colored using the following color code: GH\n loop (purple), BC loop (yellow), C′C″ loop (blue) and base\n of the pocket (red). A green line delineates the Gly<sup>297</sup> and\n region R2. (<b>B2</b>) Ribbon view of the putative ligand-binding\n pocket using the same color code as in B1.</p>", "links"=>[], "tags"=>["ligand-binding"], "article_id"=>444955, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_ligand_binding_pocket_/444955", "title"=>"Putative ligand-binding pocket.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:22:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/774444"], "description"=>"<p>(<b>A</b>) The mutants differed in their CP B domain, some of them\n containing modifications in the R2 region (residues 188 to 198) and/or\n at position 297. The nature of residue 297 is indicated and the R2\n region consisted of GFLV (open rectangle with orange border) or ArMV\n (grey rectangle with orange border) sequences. The sequence differences\n are highlighted in grey in the enlargement of ArMV CP R2 region.\n (<b>B</b>) Transmission rate is expressed as the percentage of\n infected plants over the plants tested.</p>", "links"=>[], "tags"=>["gflv", "cp"], "article_id"=>444809, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g005", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nematode_transmission_of_GFLV_CP_mutants_/444809", "title"=>"Nematode transmission of GFLV CP mutants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:20:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/773940"], "description"=>"<p><b>(A)</b> Genomic organization of GFLV. The 5′ and 3′\n untranslated regions are denoted by single lines and the VPg is\n represented by a black circle. Polyproteins encoded by RNA1 and RNA2 are\n cleaved in five (1A–1E) and three (2A–2C) final maturation\n products (open boxes), respectively. 1B, helicase (Hel); 1C, viral\n protein genome-linked (VPg); 1D, protease (Pro); 1E, RNA-dependent RNA\n polymerase (Pol); 2A, homing protein (HP); 2B, movement protein (MP) and\n 2C, coat protein (CP). As indicated, the CP is composed of three domains\n called C, B, and A. In the variant GFLV-TD, the CP residue Gly at\n position 297 is replaced by Asp. <b>(B)</b> Transmission of wild\n type GFLV-F13, GFLV-TD and GFLV-G<sub>297</sub>D (the two latter with a\n Gly<sup>297</sup> to Asp<sup>297</sup> substitution) and wild type\n ArMV by <i>X. index</i> and <i>X.\n diversicaudatum</i>. Transmission rates are expressed as the\n percentage of ELISA-positive plants. <b>(C)</b> Virus detection in\n <i>X. index</i> at the end of the AAP and the IAP showed\n that the mutated viruses and ArMV were ingested but not retained by\n nematodes. Thirty nematode specimens exposed to source plants infected\n with GFLV-F13 (lane 1), GFLV-TD (lane 2), GFLV-G<sub>297</sub>D (lane\n 3), ArMV (lane 5), or mock inoculated plants (lanes 4 and 6) were\n randomly collected and tested by RT-PCR with GFLV (lanes 1–4) or\n ArMV (lanes 5 and 6) specific primers. DNA products were analyzed by\n electrophoresis on 1.5% agarose gels.</p>", "links"=>[], "tags"=>["capsid", "residue", "297", "nematode"], "article_id"=>444295, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Involvement_of_capsid_protein_residue_297_in_nematode____transmission_/444295", "title"=>"Involvement of capsid protein residue 297 in nematode\n transmission.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:11:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/774067"], "description"=>"<p>(<b>A</b>) The structures of GFLV-F13 and of GFLV-TD are very\n similar as illustrated by the extremely low r.m.s.d. values (see\n <b><a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002034#ppat.1002034.s008\" target=\"_blank\">Table S1</a></b>). For this reason\n only the highest resolution model (GFLV-TD) is represented in this\n figure. The ribbon diagram of the virus capsid is viewed down an\n icosahedral 2-fold axis normal to the plane of the paper. Sixty copies\n of the CP are arranged in an icosahedral pseudo\n <i>T</i> = 3 symmetry. The black line\n delineates one CP position. The grey pentagon, triangle and oval\n symbolize the icosahedral 5-fold, 3-fold and 2-fold symmetry axes,\n respectively. (<b>B</b>) Each CP comprises three jellyroll β\n sandwiches termed C, B and A domains from the N- to the C-terminus and\n are depicted in green, red and blue, respectively. A star indicates the\n position of residue 297. (<b>C</b>) The central section of the\n <i>2Fo-Fc</i> electron density map (2 σ contour level)\n of a GFLV-F13 particle is viewed down a viral 2-fold axis. The outer\n radial dimensions along the icosahedral symmetry axes are indicated.\n (<b>D</b>) A thin slice of 2<i>Fo-Fc</i> electron\n density map (contoured at 1σ) reveals a strong density peak (about 3\n σ in the 2<i>Fo-Fc</i> and 17 σ in the\n <i>Fo-Fc</i> map) on the 5-fold axis of GFLV-TD. The arrow\n symbolizing the axis points towards the outer surface of the particle as\n well as neighbouring charged residues (Lys<sup>414</sup> and\n Glu<sup>411</sup>) whereas Phe<sup>412</sup> side chains are\n directed towards the viral cavity. The right panel shows a slightly\n shifted top view illustrating the organisation of the residues around\n the 5-fold axis. Five water molecules bridge Gly<sup>413</sup> carbonyl\n groups and Asp<sup>411</sup> side chains to the large central ion,\n possibly a phosphate coming from the crystallization medium.</p>", "links"=>[], "tags"=>["structures", "gflv-f13"], "article_id"=>444422, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g002", "stats"=>{"downloads"=>2, "page_views"=>76, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystal_structures_of_GFLV_F13_and_GFLV_TD_/444422", "title"=>"Crystal structures of GFLV-F13 and GFLV-TD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:13:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/388351", "https://ndownloader.figshare.com/files/388373", "https://ndownloader.figshare.com/files/388411", "https://ndownloader.figshare.com/files/388450", "https://ndownloader.figshare.com/files/388494", "https://ndownloader.figshare.com/files/388554", "https://ndownloader.figshare.com/files/388585", "https://ndownloader.figshare.com/files/388639", "https://ndownloader.figshare.com/files/388685"], "description"=>"<div><p>Many animal and plant viruses rely on vectors for their transmission from host to host. <em>Grapevine fanleaf virus</em> (GFLV), a picorna-like virus from plants, is transmitted specifically by the ectoparasitic nematode <em>Xiphinema index</em>. The icosahedral capsid of GFLV, which consists of 60 identical coat protein subunits (CP), carries the determinants of this specificity. Here, we provide novel insight into GFLV transmission by nematodes through a comparative structural and functional analysis of two GFLV variants. We isolated a mutant GFLV strain (GFLV-TD) poorly transmissible by nematodes, and showed that the transmission defect is due to a glycine to aspartate mutation at position 297 (Gly297Asp) in the CP. We next determined the crystal structures of the wild-type GFLV strain F13 at 3.0 Å and of GFLV-TD at 2.7 Å resolution. The Gly297Asp mutation mapped to an exposed loop at the outer surface of the capsid and did not affect the conformation of the assembled capsid, nor of individual CP molecules. The loop is part of a positively charged pocket that includes a previously identified determinant of transmission. We propose that this pocket is a ligand-binding site with essential function in GFLV transmission by <em>X. index</em>. Our data suggest that perturbation of the electrostatic landscape of this pocket affects the interaction of the virion with specific receptors of the nematode's feeding apparatus, and thereby severely diminishes its transmission efficiency. These data provide a first structural insight into the interactions between a plant virus and a nematode vector.</p> </div>", "links"=>[], "tags"=>["insights", "viral", "determinants", "nematode", "mediated", "fanleaf"], "article_id"=>136687, "categories"=>["Cancer", "Cell Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1002034.s001", "https://dx.doi.org/10.1371/journal.ppat.1002034.s002", "https://dx.doi.org/10.1371/journal.ppat.1002034.s003", "https://dx.doi.org/10.1371/journal.ppat.1002034.s004", "https://dx.doi.org/10.1371/journal.ppat.1002034.s005", "https://dx.doi.org/10.1371/journal.ppat.1002034.s006", "https://dx.doi.org/10.1371/journal.ppat.1002034.s007", "https://dx.doi.org/10.1371/journal.ppat.1002034.s008", "https://dx.doi.org/10.1371/journal.ppat.1002034.s009"], "stats"=>{"downloads"=>9, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structural_Insights_into_Viral_Determinants_of_Nematode_Mediated____Grapevine_fanleaf_virus_Transmission/136687", "title"=>"Structural Insights into Viral Determinants of Nematode Mediated\n <em>Grapevine fanleaf virus</em> Transmission", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-19 01:51:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/774344"], "description"=>"<p>The conformation of the GH loop in GFLV-F13 (<b>A</b>) and GFLV-TD\n (<b>B</b>) are identical. The only difference is restricted to\n the presence of additional electron density corresponding to the\n Asp<sup>297</sup> side chain in GFLV-TD in (<b>B</b>, star).\n <i>2Fo-Fc</i> electron density maps are contoured at 1.2\n σ.</p>", "links"=>[], "tags"=>["protruding", "gh", "cp", "of", "gflv-f13"], "article_id"=>444700, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g004", "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Close_up_view_of_the_protruding_GH_loop_within_the_CP_B_domain_of____GFLV_F13_and_GFLV_TD_/444700", "title"=>"Close-up view of the protruding GH loop within the CP B domain of\n GFLV-F13 and GFLV-TD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:18:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/774212"], "description"=>"<p>Secondary structures observed in GFLV and TRSV crystal structures are\n indicated by arrows (β strands) and grey blocks (α helices). The\n sequence alignment was created with Clustal X. The same color code as in\n <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002034#ppat-1002034-g002\" target=\"_blank\"><b>Figure\n 2</b></a> is used for strands to indicate the three CP\n domains: green, red and blue for the C, B, and A domains, respectively.\n Residues located at the outer surface of the GFLV capsid are underlined.\n Residues present at position 297 in GFLV-TD, GFLV-F13, ArMV and TRSV are\n boxed in red. Regions R2, R3 and R5 (see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002034#ppat.1002034-Schellenberger1\" target=\"_blank\">[32]</a> are\n indicated below the alignments. Stars indicate residues at the bottom of\n the putative ligand-binding pocket.</p>", "links"=>[], "tags"=>["cp", "amino", "sequences", "armv", "and"], "article_id"=>444568, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_the_CP_amino_acid_sequences_of_GFLV_ArMV_and____TRSV_/444568", "title"=>"Alignment of the CP amino acid sequences of GFLV, ArMV and\n TRSV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 01:16:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/774718"], "description"=>"£<p>Statistics are given for reflections with\n I> = 0 and values in parentheses are for the\n highest resolution shell.</p><p>†R<sub>merge</sub> = \n σ<i><sub>hkl</sub></i>\n σ<i><sub>i</sub></i>\n |<i>I<sub>i</sub>(hkl)</i> -\n <<i>I(hkl)</i>>|/σ<i><sub>hkl</sub></i>\n σ<i><sub>i</sub> I<sub>i</sub>(hkl)</i>.</p>#<p>The high R-factor can be explained, among other reasons, by the model\n used (a low resolution EM reconstruction, without filtering) and the\n absence of a bulk solvent correction.</p><p>*The cross-validation (R-free) was calculated with 5% of\n the data.</p><p>**ADPs: Atomic displacement parameters.</p>", "links"=>[], "tags"=>["gflv"], "article_id"=>445084, "categories"=>["Virology", "Plant Biology"], "users"=>["Pascale Schellenberger", "Claude Sauter", "Bernard Lorber", "Patrick Bron", "Stefano Trapani", "Marc Bergdoll", "Aurélie Marmonier", "Corinne Schmitt-Keichinger", "Olivier Lemaire", "Gérard Demangeat", "Christophe Ritzenthaler"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1002034.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystallographic_analysis_of_GFLV_particles_/445084", "title"=>"Crystallographic analysis of GFLV particles.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:24:44"}

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