AtlasT4SS: a curated database for type IV secretion systems

Abstract

Background: 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.

Description: 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.

Conclusions: 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.

Figure 1

Entity–relationship diagram of T4SS database. Entities are represented by boxes and relationships by lines joining the boxes. The general information of the genes found in the ORF entity. Each entity ORF is related to information from biological database (InterPro, Swiss-Prot, Kegg, etc.) and tools (Psort, Phobius, etc.). Gene annotations and annotator entities are described in Annotation and User, respectively. The identified clusters are described by the entity Clusters_Names.

Figure 2

Overview of annotation page of T4SS database. The image provides an example of the main data page for a T4SS entry. Primary identification and annotation data appear at the top of the page with a link to the amino acid sequence as well as the corresponding T4SS cluster. This is followed by functional annotation data, which provide information by Kegg and COG, including the blast results against Kegg database. Below this are the sections containing details about the InterProScan, Gene Ontology (GO) as well as the blastp results against UniProt/Swiss-Prot database. Finally, the page shows details about the amino acid sequence topology and protein subcellular location prediction.

Figure 3

Distribution of family sizes in the Atlas T4SS. The graphic shows the distribution of the 119 protein families annotated in the 2^nd category of the Atlas T4SS according to the number of entries per family. The colors within each bar indicate the percentage of entries annotated with a known or unknown function.

Figure 4

Clustering search tool of T4SS database. The image provides an example of the clustering search tool results with the keyword “virD4” in Agrobacterium tumefasciens C58 Cereon.

Figure 5

Blastp tool of T4SS database. The image provides an example of the blastp results with an unknown amino acid sequence query against the complete genome sequence of Agrobacterium tumefasciens C58 Cereon.

Figure 6

Blastx tool of T4SS database. The image provides an example of the blastx results with an unknown nucleotide sequence query against all biological sources of Atlas T4SS.