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

These files contain data, sequences and supplementary information for the article entitled '<em>Characterization of signal and transit peptides based on motif composition and taxon-specific patterns</em>'. <strong>Contents</strong> <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. <strong>Datasets.zip</strong> - presequence and peptide datasets obtained from raw data and used for all subsequent analyses. <strong>Motif_analysis_reports_presequences_AMP.zip</strong> - HTML reports with detailed analyses of motif composition of presequences and AMPs <strong>Motif_analysis_reports_presequences_encoded.zip</strong> - HTML reports with detailed analyses of motif composition of presequences using reduced alphabets <strong>Motif_analysis_reports_presequences_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of presequences for different taxons <strong>Motif_analysis_reports_SP_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of signal peptides on different taxonomic levels <strong>Motif_analysis_reports_presequences_counts.zip </strong> - HTML reports with detailed analyses of motifs occuring more than once in presequences and AMPs <strong>Abstract</strong> 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.本套件包含题为《基于基序（motif）组成与类群特异性模式的信号肽与转运肽特征解析》的学术论文配套的数据、序列及补充信息。 <strong>内容</strong> <strong>Raw_data.zip</strong>：包含从UniProt及其他数据库下载的原始数据与序列，本研究所用数据集即由这些文件生成，用于文中所述的各项分析。 <strong>Datasets.zip</strong>：包含从原始数据中提取的前序列（presequence）与肽数据集，用于所有后续分析工作。 <strong>Motif_analysis_reports_presequences_AMP.zip</strong>：包含前序列与抗菌肽（antimicrobial peptides, AMPs）基序组成的详细分析HTML报告。 <strong>Motif_analysis_reports_presequences_encoded.zip</strong>：包含使用简化字母表对前序列基序组成进行详细分析的HTML报告。 <strong>Motif_analysis_reports_presequences_taxonomy.zip</strong>：包含不同类群前序列基序组成的详细分析HTML报告。 <strong>Motif_analysis_reports_SP_taxonomy.zip</strong>：包含不同分类层级下信号肽（signal peptides, SP）基序组成的详细分析HTML报告。 <strong>Motif_analysis_reports_presequences_counts.zip</strong>：包含前序列与抗菌肽中出现频次大于1的基序的详细分析HTML报告。 <strong>摘要</strong> 靶向肽或称前序列（presequence）是蛋白质的N端延伸片段，可编码蛋白质的细胞定位信息。这类肽段包括将蛋白质靶向至内质网（endoplasmic reticulum, ER）的信号肽，以及将蛋白质引导至内共生起源细胞器——叶绿体与线粒体——的转运肽（transit peptides, TP）。已有假说提出，转运肽起源于抗菌肽（AMPs），而抗菌肽负责宿主对细菌、真菌、病毒等微生物的防御。 本研究基于一套经专家筛选验证的实验蛋白质集，对靶向肽与抗菌肽的氨基酸基序开展了全面的生物信息学分析。我们鉴定出了在各类前序列中高频出现的基序，这些基序呈现出与其氨基酸组成相关的特异性模式，并对其在前序列内的位置进行了探究。此外，我们还对比了不同类群间的基序模式，鉴定出类群特异性特征，为演化研究提供了新的视角。鉴于靶向肽与抗菌肽的功能重要性及诸多实际应用场景，我们认为本研究的分析结果将有助于这类肽段的设计，并加深人们对蛋白质导入机制与前序列演化的理解。