AtlasT4SS: A curated database for type IV secretion systems

Abstract

BackgroundThe type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system.DescriptionThe AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins.ConclusionsIn our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br.

Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus

“…The products of these genes form part of a F-T4SS [97], however unlike the VirB/D4 genes associated with the P-T4SS, F-T4SS are most likely concerned with bacterial conjugation and DNA exchange [91].…”

The expanding bacterial type IV secretion lexicon

“…To curate the available information and for high-throughput prospecting for new T4SSs, various web-based algorithms have been described. We list some here for the interested reader: i) Named entity recognition for bacterial T4SSs (http://www.nactem.ac.uk/T4SS_NER/top.py, http://patricbrc.vbi.vt.edu/portal/partic/NACTEM) (Ananiadou et al, 2011), ii) AtlasT4SS (htt://www.t4ss.lncc.br), a curated database for T4SSs (Souza et al, 2012), iii) MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER), for identification of bacterial genomic islands (Ou et al, 2007), iv) A T4SS identification program (http://t4ss.bioinfoicdc.org/), (Zhang et al, 2012) v) (http://www.tau.ac.il/~tlap/LegionellaMachineLearning), a machine learning approach for genome-scale identification of L. pneumophila effectors (Burstein et al, 2009), and vi) identification of Anaplasma marginale T4SS effectors (Lockwood et al, 2011). …”

Nuevos genes relacionados con el sistema secretor tipo 4 de Edwardsiella tarda

“…was developed to help the assignment of given coding sequence (Souza et al, 2012). The identified genes in E. tarda ETSJ54 indicate that this bacterium possess a T4SS that maybe involved in protein-ss DNA complex transfer but functions in adhesion and invasion of fish tissues cannot be excluded.…”