Welcome to T3Enc
Type III Secretion System (T3SS) play an important role bacterial interaction with host eukaryotic cells. A wide range of pathogenic or symbiotic bacteria contain T3SSs. Many of the bacteria are important human pathogens such as
Salmonella spp., Shigella spp., Yersinia spp., EPEC, Bordetella spp., Chlamydia spp., etc; some are plant pathogenic bacteria, such as Erwinia spp., Pseudomonas syringae, Ralstonia solanacearum, etc; others are endosymbionts such as Rhizobium spp., Sodalis glossinidius, and so on.
Previously, we curated a database (T3DB: http://www.szu-bioinf.org/T3DB), in which we manually annotated 36 well-studied T3SSs from 26 bacterial genera. The composition genes of T3SSs were also organized as four main categories: Apparatus, Effector, Chaperone and Regulator. Apparatus genes were further classified into 10 functional components. For each apparatus component, effector, chaperone or regulator, we also annotated a ‘T3-Ortholog’group, according to the sequence similarity and structure or functional similarity annotated from literature. The database is still regularly updated, which makes deep annotation and knowledge mining for the few model T3SSs.
Recently, we built Hidden Markov Models on ten core T3SS apparatus-encoding proteins, and based on the models, bacterial genomes were screened for possible T3SSs. With a manual examination and comparative genomic analysis, 179 T3SSs with different evolutionary origin were identified from 113 different bacterial genera. The T3SSs were robustly classified into 13 major groups. All experimentally validated effectors were annotated manually. A homology-searching strategy was adopted to screen all homologs of known effectors from all the bacterial strains with T3SS(s). Besides, the key transcription regulators or regulatory circuits were also annotated. The current version of T3SS database, T3Enc 1.0, curates all the information on these T3SSs, their classification and sequences, effectors and regalators.
04 April, 2017, our paper systematically surveying the T3SSs, category, effectors and regulatory conduits is accepted by EMI.
30 June, 2016, T3Enc 1.0 is released.
Hu Y, Huang H, Cheng X, Shu X, White AP, Stavrinides J, Koster W, Zhu G, Zhao Z, Wang Y. A global survey of bacterial type III secretion systems and their effectors. Environ. Microbiol. 2017 Apr 12. doi: 10.1111/1462-2920.13755. Pubmed