AtlasT4SS: a curated database for type IV secretion systems

• Published in: BMC microbiology 2012-08, Vol.12 (1), p.172-172, Article 172
• Main Authors: Souza, Rangel C, del Rosario Quispe Saji, Guadalupe, Costa, Maiana O C, Netto, Diogo S, Lima, Nicholas C B, Klein, Cecília C, Vasconcelos, Ana Tereza R, Nicolás, Marisa F
• Format: Article
• Language: English
• Subjects: Agrobacterium tumefaciens; Analysis; Archaea; Archaea - genetics; Bacteria; Bacteria - genetics; Bacterial genetics; Bacterial Secretion Systems; Bacteriology; Catalysts; Conjugation; Data processing; Databases, Genetic; DNA; Evolution; Genetic aspects; Genomes; Genomics; Gram-positive bacteria; Homology; Host plants; Language; Macromolecules; Membrane Transport Proteins - genetics; Microbiology; Nucleoproteins; Physiological aspects; Plasmids; protein families; Protein transport; Proteins; Secretion; T-DNA
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/1471-2180-12-172

The 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. The 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. In 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.