title: Computational prediction shines light on type III secretion origins.
abstract: Type III secretion system is a key bacterial symbiosis and pathogenicity mechanism responsible for a variety of infectious diseases, ranging from food-borne illnesses to the bubonic plague. In many Gram-negative bacteria, the type III secretion system transports effector proteins into host cells, converting resources to bacterial advantage. Here we introduce a computational method that identifies type III effectors by combining homology-based inference with de novo predictions, reaching up to 3-fold higher performance than existing tools. Our work reveals that signals for recognition and transport of effectors are distributed over the entire protein sequence instead of being confined to the N-terminus, as was previously thought. Our scan of hundreds of prokaryotic genomes identified previously unknown effectors, suggesting that type III secretion may have evolved prior to the archaea/bacteria split. Crucially, our method performs well for short sequence fragments, facilitating evaluation of microbial communities and rapid identification of bacterial pathogenicity - no genome assembly required. pEffect and its data sets are available at http://services.bromberglab.org/peffect.
authors.affiliation: Department of Informatics, Bioinformatics &Computational Biology - I12, TUM, Garching, Germany.|Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM, Garching, Germany.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Goldberg
authors.affiliation: Department of Informatics, Bioinformatics &Computational Biology - I12, TUM, Garching, Germany.|Institute for Advanced Study (TUM-IAS), Garching, Germany.|Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
authors.affiliation: Institute for Advanced Study (TUM-IAS), Garching, Germany.|Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Yana
authors.initials: Y
authors.lastname: Bromberg
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial; D040901:Proteomics; D000069296:Type III Secretion Systems / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D000069296:Type III Secretion Systems