PT  - JOURNAL ARTICLE
AU  - Tatyana Goldberg
AU  - Burkhard Rost
AU  - Yana Bromberg
TI  - Computational prediction shines light on type III secretion origins
AID  - 10.1101/036251
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 036251
4099  - http://biorxiv.org/content/early/2016/10/04/036251.short
4100  - http://biorxiv.org/content/early/2016/10/04/036251.full
AB  - 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.