Characterization of signal and transit peptides based on motif composition and taxon-specific patterns

<p>These files contain data, sequences and supplementary information for the article entitled &#39;<em>Characterization of signal and transit peptides based on motif composition and taxon-specific patterns</em>&#39;.</p> <p><strong>Contents</strong></p> <ol> <li><strong>Raw_data.zip</strong> - contains raw data and sequences downloaded from UniProt and other databases. These files were used to create datasets used for described analyses.</li> <li><strong>Datasets.zip</strong> - presequence and peptide datasets obtained from raw data and used for all subsequent analyses.</li> <li><strong>Motif_analysis_reports_presequences_AMP.zip</strong> - HTML reports with detailed analyses of motif composition of presequences and AMPs</li> <li><strong>Motif_analysis_reports_presequences_encoded.zip</strong> - HTML reports with detailed analyses of motif composition of presequences using reduced alphabets</li> <li><strong>Motif_analysis_reports_presequences_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of presequences for different taxons</li> <li><strong>Motif_analysis_reports_SP_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of signal peptides on different taxonomic levels</li> <li><strong>Motif_analysis_reports_presequences_counts.zip </strong> - HTML reports with detailed analyses of motifs occuring more than once in presequences and AMPs</li> </ol> <p>&nbsp;</p> <p><strong>Abstract</strong></p> <p>Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum (ER), and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed a comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.</p>