Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context

Abstract

Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify putative T4Es from the complete genome of α- and γ-proteobacteria, we developed a Perl-based command line bioinformatics tool called S4TE (searching algorithm for type-IV secretion system effectors). The tool predicts and ranks T4E candidates by using a combination of 13 sequence characteristics, including homology to known effectors, homology to eukaryotic domains, presence of subcellular localization signals or secretion signals, etc. S4TE software is modular, and specific motif searches are run independently before ultimate combination of the outputs to generate a score and sort the strongest T4Es candidates. The user keeps the possibility to adjust various searching parameters such as the weight of each module, the selection threshold or the input databases. The algorithm also provides a GC% and local gene density analysis, which strengthen the selection of T4E candidates. S4TE is a unique predicting tool for T4Es, finding its utility upstream from experimental biology.

Comparative Genomics of the Zoonotic Pathogen Ehrlichia chaffeensis Reveals Candidate Type IV Effectors and Putative Host Cell Targets

“…The repertoires of T4Es were predicted using a S4TE algorithm with default parameters (Meyer et al, 2013). S4TE 1.4 predicts and ranks candidate T4Es by using a combination of 11 independent modules to explore 14 characteristics of type IV effectors.…”

“…S4TE 1.4 predicts and ranks candidate T4Es by using a combination of 11 independent modules to explore 14 characteristics of type IV effectors. One module searches for consensus motifs in promoter regions; three modules search for the five features of the type IV secretion signal (C-terminal basicity, C-terminal charges, C-terminal hydrophobicity, overall hydrophilicity, and E-blocks); six modules search for several domains (eukaryotic–like domains, the DUF domain, EPIYA motifs, the nuclear localization signal, the mitochondrial localization signal, the prenylation domain, coiled-coil domains); and one module searches for homology with known T4Es (Meyer et al, 2013)…”

“…Our laboratory developed a searching algorithm for type IV effector proteins (S4TE), which identifies candidate T4Es in genome sequences based on a combinatorial approach with 14 different parameters (Meyer et al, 2013). …”

HydroCalc Proteome: a tool to identify distinct characteristics of effector proteins

“…Furthermore, this tool was presented with execution errors in terms of access to the database during majority of the attempts made for the analysis. The S4TE tool, available for download at http://sate.cirad.fr/ (accessed April 20, 2015), is a tool for predicting type IV effector proteins (Meyer et al, 2013). However, this tool is not directly available on the web.…”

“…The positive charge at the C-terminus is an important feature for the identification of effector proteins (Vergunst et al, 2005). The effector proteins identified to date contain at least three basic polar amino acids at the C-terminus (Meyer et al, 2013).…”