title: The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models.
abstract: 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.
authors.affiliation: Departamento de Ecologia, Instituto de Biociências, 05508-090, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Mathias M
authors.initials: MM
authors.lastname: Pires
authors.affiliation: Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada.
authors.forename: Maurício
authors.initials: M
authors.lastname: Cantor
authors.affiliation: Departamento de Ecologia, Instituto de Biociências, 05508-090, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Paulo R
authors.initials: PR
authors.lastname: Guimarães
authors.affiliation: Departamento de Física da Matéria Condensada, Instituto de Física 'Gleb Wataghin', 13083-859, Universidade Estadual de Campinas, Campinas, Brazil.
authors.forename: Marcus A M
authors.initials: MA
authors.lastname: de Aguiar
authors.affiliation: Departamento de Biologia Animal, Instituto de Biologia, 13083-970, Universidade Estadual de Campinas, Campinas, Brazil.
authors.forename: Sérgio F
authors.initials: SF
authors.lastname: Dos Reis
authors.affiliation: Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, 05508-000, Universidade de São Paulo, São Paulo, Brazil.
authors.forename: Patricia P
authors.initials: PP
authors.lastname: Coltri
mesh_terms: D020387:Food Chain; D006801:Humans; D008954:Models, Biological; D008962:Models, Theoretical; D060066:Protein Interaction Maps; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D017381:Spliceosomes / Q000235:genetics / Q000378:metabolism*
chemical_list: D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins