Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation
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{"title"=>"Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation", "type"=>"journal", "authors"=>[{"first_name"=>"Natalia", "last_name"=>"Pietrosemoli", "scopus_author_id"=>"22235317900"}, {"first_name"=>"Juan A.", "last_name"=>"García-Martín", "scopus_author_id"=>"55002266500"}, {"first_name"=>"Roberto", "last_name"=>"Solano", "scopus_author_id"=>"35482666000"}, {"first_name"=>"Florencio", "last_name"=>"Pazos", "scopus_author_id"=>"7004152530"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84873590183", "pui"=>"368311241", "doi"=>"10.1371/journal.pone.0055524", "sgr"=>"84873590183", "pmid"=>"23408995"}, "id"=>"dcf1d16f-915e-33ad-9981-0dedcb9e3200", "abstract"=>"Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.", "link"=>"http://www.mendeley.com/research/genomewide-analysis-protein-disorder-arabidopsis-thaliana-implications-plant-environmental-adaptatio-1", "reader_count"=>43, "reader_count_by_academic_status"=>{"Researcher"=>6, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>3, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Researcher"=>6, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>3, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>30, "Medicine and Dentistry"=>1, "Computer Science"=>4, "Unspecified"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/492451"], "description"=>"<p>Green nodes correspond to those GO:BP terms significantly enriched in disorder in Arabidopsis. Blue nodes correspond to those GO terms enriched in disorder in Arabidopsis compared to human. The red node represents the only common term between these two sets.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "Computational biology"], "article_id"=>162973, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subgraph_of_biological_process_8220_Response_of_stimulus_8221_GO_0050896_/162973", "title"=>"Subgraph of biological process “Response of stimulus” (GO:0050896).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:49:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/483614", "https://ndownloader.figshare.com/files/483635", "https://ndownloader.figshare.com/files/483637", "https://ndownloader.figshare.com/files/483638"], "description"=>"<div><p>Intrinsically Disordered Proteins/Regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in <em>Arabidopsis thaliana</em>, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.</p> </div>", "links"=>[], "tags"=>["genome-wide", "implications", "adaptation"], "article_id"=>156167, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0055524.s001", "https://dx.doi.org/10.1371/journal.pone.0055524.s002", "https://dx.doi.org/10.1371/journal.pone.0055524.s003", "https://dx.doi.org/10.1371/journal.pone.0055524.s004"], "stats"=>{"downloads"=>7, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Analysis_of_Protein_Disorder_in_Arabidopsis_thaliana_Implications_for_Plant_Environmental_Adaptation__/156167", "title"=>"Genome-Wide Analysis of Protein Disorder in <em>Arabidopsis thaliana</em>: Implications for Plant Environmental Adaptation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-07 01:42:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/492529"], "description"=>"<p>For each organism (Arabidopsis (green) and human (blue)) protein sequences and their corresponding Gene Ontology annotations are retrieved from Uniprot. For each protein, disordered regions (pink) are calculated using 3 different methods (Iupred, VSL2 and Disopred), and disordered-binding regions (DBRs) are predicted using ANCHOR. Proteins are assigned to GO:BP functional classes. For each GO functional class, a comparative analysis of the disorder levels of the proteins of each organism is performed, using different criteria for quantifying disorder in that given GO class. For those disorder criteria that assign a “yes/no” label to a given protein, contingency tables are constructed with the counts of disordered and not-disordered proteins in both organisms and a Chi-squared test is applied to them. For those criteria that quantify the disorder of a given protein, the tables contain the average values of that figure for both organisms, and a Wilcoxon rank sum test is applied.</p>", "links"=>[], "tags"=>["methodology", "comparative"], "article_id"=>163057, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_methodology_used_for_the_comparative_study_of_protein_disorder_in_A_thaliana_and_H_sapiens_/163057", "title"=>"Schematic representation of the methodology used for the comparative study of protein disorder in <i>A. thaliana</i> and <i>H. sapiens</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:50:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/492040"], "description"=>"<p>Left: percentages of disordered proteins (disordered proteins criterion: those proteins containing at least 50% disordered residues based on Disopred predictions). Right: average percentages of disordered residues involved in binding (DBRs), as predicted by ANCHOR. The stars denote significant differences evaluated with the same Chi-square tests described in the Methods section and illustrated in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone-0055524-g001\" target=\"_blank\">Figure 1</a> but using all proteins (i.e. not restricted to a particular GO functional class).</p>", "links"=>[], "tags"=>["disordered", "binding", "regions"], "article_id"=>162557, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overall_predicted_global_disorder_and_disordered_binding_regions_in_A_thaliana_and_H_sapiens_proteins_/162557", "title"=>"Overall predicted global disorder and disordered binding regions in <i>A. thaliana</i> and <i>H. sapiens</i> proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:42:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/492100"], "description"=>"<p>While the left panel of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone-0055524-g001\" target=\"_blank\">Figure 1</a> shows the content of highly disordered proteins (>50%), this is intended to evaluate this for different degrees of disorder. A) Protein disorder (as the percentage of disordered residues with respect to the sequence length) is binned into different ranges. Data based on Disopred predictions. B) The same for disordered residues involved in binding, as predicted by ANCHOR. The significance of the differences is evaluated as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone-0055524-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["proteins", "degrees", "disordered", "binding", "regions"], "article_id"=>162617, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g002", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fraction_of_proteins_with_different_degrees_of_predicted_disorder_and_disordered_binding_regions_in_A_thaliana_and_H_sapiens_/162617", "title"=>"Fraction of proteins with different degrees of predicted disorder and disordered binding regions in <i>A. thaliana</i> and <i>H. sapiens</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:43:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/492332"], "description"=>"<p>Disordered proteins here are again those with 1 or more LDWs based on Disopred predictions. Same REVIGO representation adaptation as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone-0055524-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["comparatively", "enriched", "disordered", "proteins"], "article_id"=>162853, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_the_GO_Biological_Processes_comparatively_enriched_in_disordered_proteins_in_A_thaliana_respect_to_H_sapiens_/162853", "title"=>"Representation of the GO “Biological Processes” comparatively enriched in disordered proteins in <i>A. thaliana</i> respect to <i>H. sapiens.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/492602"], "description"=>"<p>Results shown for Disopred (disorder prediction) and ANCHOR (Disorder binding regions, DBRs). For results with other predictors see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone.0055524.s001\" target=\"_blank\">Additional Data File S1</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055524#pone-0055524-t001\" target=\"_blank\">Table 1S</a>.</p>", "links"=>[], "tags"=>["intrinsic", "metrics", "thaliana"], "article_id"=>163123, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_intrinsic_disorder_metrics_for_A_thaliana_and_H_sapiens_/163123", "title"=>"Summary of intrinsic disorder metrics for <i>A. thaliana and H. sapiens</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-07 00:52:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/492171"], "description"=>"<p>Disordered proteins here correspond to those with one or more “long disordered windows” (LDW) based on Disopred predictions. Figure adapted from REVIGO, a system for summarizing and visualizing lists of GO terms. Each rectangle represents a cluster of related terms labeled according to a representative term. Rectangles are grouped in “superclusters” (identified with the same color) based on SimRel semantic similarity measure.</p>", "links"=>[], "tags"=>["enriched", "disordered", "proteins"], "article_id"=>162692, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Natalia Pietrosemoli", "Juan A. García-Martín", "Roberto Solano", "Florencio Pazos"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0055524.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_the_GO_Biological_Processes_significantly_enriched_in_disordered_proteins_in_A_thaliana_/162692", "title"=>"Representation of the GO “Biological Processes” significantly enriched in disordered proteins in <i>A. thaliana</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-07 00:44:52"}

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Relative Metric

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