Work

Computational prediction shines light on type III secretion origins

Year: 2016

Type: article

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.

Source: Scientific Reports

DOI: 10.1038/srep34516

Authors: Tatyana Goldberg, Burkhard Rost, Yana Bromberg

Institutions: Technical University of Munich, Columbia University, Rutgers, The State University of New Jersey

Language: English

Topic: Escherichia coli research studies

Subfield: Endocrinology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,690