The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models

Lade...
Vorschaubild
Dateien
Pires_2-3o8k2z3kh0s97.pdf
Pires_2-3o8k2z3kh0s97.pdfGröße: 942.63 KBDownloads: 154
Datum
2015
Autor:innen
Pires, Mathias M.
Guimarães, Paulo R.
de Aguiar, Marcus A. M.
Dos Reis, Sérgio F.
Coltri, Patricia P.
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
DOI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
Link zur Lizenz
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Open Access Gold
Sammlungen
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Zusammenfassung

The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690PIRES, Mathias M., Mauricio CANTOR, Paulo R. GUIMARÃES, Marcus A. M. DE AGUIAR, Sérgio F. DOS REIS, Patricia P. COLTRI, 2015. The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models. In: Scientific reports. Springer Nature. 2015, 5(1), 14865. eISSN 2045-2322. Available under: doi: 10.1038/srep14865
BibTex
@article{Pires2015-10-07netwo-50663,
  year={2015},
  doi={10.1038/srep14865},
  title={The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models},
  number={1},
  volume={5},
  journal={Scientific reports},
  author={Pires, Mathias M. and Cantor, Mauricio and Guimarães, Paulo R. and de Aguiar, Marcus A. M. and Dos Reis, Sérgio F. and Coltri, Patricia P.},
  note={Article Number: 14865}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/50663">
    <dc:contributor>Dos Reis, Sérgio F.</dc:contributor>
    <dc:contributor>Guimarães, Paulo R.</dc:contributor>
    <dc:creator>Coltri, Patricia P.</dc:creator>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
    <dc:creator>Dos Reis, Sérgio F.</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-02T10:10:26Z</dcterms:available>
    <dc:contributor>Pires, Mathias M.</dc:contributor>
    <dc:contributor>de Aguiar, Marcus A. M.</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/50663/3/Pires_2-3o8k2z3kh0s97.pdf"/>
    <dc:language>eng</dc:language>
    <dcterms:issued>2015-10-07</dcterms:issued>
    <dc:creator>Guimarães, Paulo R.</dc:creator>
    <dc:contributor>Coltri, Patricia P.</dc:contributor>
    <dc:creator>Pires, Mathias M.</dc:creator>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dcterms:abstract xml:lang="eng">The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation.</dcterms:abstract>
    <dc:creator>de Aguiar, Marcus A. M.</dc:creator>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/50663/3/Pires_2-3o8k2z3kh0s97.pdf"/>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/50663"/>
    <dcterms:title>The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models</dcterms:title>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-09-02T10:10:26Z</dc:date>
    <dc:contributor>Cantor, Mauricio</dc:contributor>
    <dc:creator>Cantor, Mauricio</dc:creator>
    <dc:rights>Attribution 4.0 International</dc:rights>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Begutachtet
Ja
Diese Publikation teilen