Abstract
Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence, and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration.
Highlights
The increasing number of complete genome sequences has revealed the entire structure and composition of proteins, based mainly on theoretical predictions utilizing their corresponding DNA sequences
Protein-protein interactions (PPIs), which play central roles in signal transduction and metabolic pathways, were predicted based on the assumption that evolutionarily conserved proteins would be likely to exhibit conserved interactions. This process is known as interaction ortholog mapping and served as an established method for predicting interactomes[38]
It has been successfully applied in human[30], yeast[31], Arabidopsis[23,24], rice[26] and Brassica rapa[27]
Summary
The increasing number of complete genome sequences has revealed the entire structure and composition of proteins, based mainly on theoretical predictions utilizing their corresponding DNA sequences. In several model organisms, including Arabidopsis thaliana[4,5], Caenorhabditis elegans[6,7], Drosophila melanogaster[8,9], Homo sapiens[10,11,12], and Saccharomyces cerevisiae[13,14], genome-wide yeast two-hybrid (Y2H) systems and large-scale affinity purification/mass spectrometry (MS) studies have been conducted to map the interactomes Certain databases, such as IntAct[15], BioGRID16 and DIP17, have been established as repositories to collect and organize the reported protein interactions of nonspecific species. This resource and the related documents are freely accessible at http://bdg.hfut.edu.cn/ptir/index.html
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