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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, 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 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., (© 2023. Springer Nature Limited.)

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https://biogenies.info/PlastoGram and as an R package at https://github.com/BioGenies/PlastoGram . The code used for described analyses is available at https://github.com/BioGenies/PlastoGram-analysis ., (© 2023. The Author(s).)