Abstract
BackgroundProtein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa.ResultsTo better understand the interactions of proteins in Oryza sativa, we have developed PRIN, a Predicted Rice Interactome Network. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where large-scale protein-protein interaction experiments have been applied: yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), human (Homo sapiens), Escherichia coli K12 and Arabidopsis thaliana. With certain quality controls, altogether we obtained 76,585 non-redundant rice protein interaction pairs among 5,049 rice proteins. Further analysis showed that the topology properties of predicted rice protein interaction network are more similar to yeast than to the other 5 organisms. This may not be surprising as the interologs based on yeast contribute nearly 74% of total interactions. In addition, GO annotation, subcellular localization information and gene expression data are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization.ConclusionsPRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology.PRIN is available online at http://bis.zju.edu.cn/prin/.
Highlights
Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms
Six model organisms are selected as the reference species for our prediction: Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens and Escherichia coli K12, whose experimental interactomes are the most complete and reliable
Among these 6 model organisms, Arabidopsis thaliana, a plant species, logically shares the highest evolutionary conservation with rice, while Saccharomyces cerevisiae has the best coverage of its genome
Summary
Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. High-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa. Our work presents a computational approach to predict protein-protein interactions in Oryza sativa Proteins seldom perform their biological function independently. Protein-protein interactions play fundamental roles in almost all biological processes such as signal transduction, internal equilibrium maintenance and organs formation [1]. Combined with literature extraction of existing protein interactions [12], genomic information, protein structure and annotation information, bioinformatics play an important role in method study of protein-protein interaction prediction, high-quality protein-protein interaction databases establishment, software and webserver development for visualizing protein-protein interaction networks and genome-scale analysis of protein interaction networks [13,14,15,16,17,18]
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