PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

Abstract

Background: Protein-protein interactions (PPIs) play very important roles in diverse biological processes. Experimentally validated or predicted PPI data have become increasingly available in diverse plant species. To further explore the biological functions of PPIs, understanding the interaction details of plant PPIs (e.g., the 3D structural contexts of interaction sites) is necessary. By integrating bioinformatics algorithms, interaction details can be annotated at different levels and then compiled into user-friendly databases. In our previous study, we developed AraPPISite, which aimed to provide interaction site information for PPIs in the model plant Arabidopsis thaliana. Considering that the application of AraPPISite is limited to one species, it is very natural that AraPPISite should be evolved into a new database that can provide interaction details of PPIs in multiple plants. Description: PlaPPISite (http://zzdlab.com/plappisite/index.php) is a comprehensive, high-coverage and interaction details-oriented database for 13 plant interactomes. In addition to collecting 121 experimentally verified structures of protein complexes, the complex structures of experimental/predicted PPIs in the 13 plants were also constructed, and the corresponding interaction sites were annotated. For the PPIs whose 3D structures could not be modelled, the associated domain-domain interactions (DDIs) and domain-motif interactions (DMIs) were inferred. To facilitate the reliability assessment of predicted PPIs, the source species of interolog templates, GO annotations, subcellular localizations and gene expression similarities are also provided. JavaScript packages were employed to visualize structures of protein complexes, protein interaction sites and protein interaction networks. We also developed an online tool for homology modelling and protein interaction site annotation of protein complexes. All data contained in PlaPPISite are also freely available on the Download page. Conclusion: PlaPPISite provides the plant research community with an easy-to-use and comprehensive data resource for the search and analysis of protein interaction details from the 13 important plant species.

Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis

“…niloticus protein interactions were first searched in the PDB database [65] by BLASTP. Five criteria were considered [66][67][68][69]: (1) the alignment between each interacting protein and the template had ≥30% sequence identity and covered ≥40% of the interacting protein length; (2) the templates of two interacting proteins came from different chains of a protein complex structure in the PDB database and further constituted the template complex; (3) the template complex with resolution below 5 Å was prioritized; (4) X-ray structure as template complex was preferred over NMR structure; (5) average sequence identity of two interacting proteins with the template complex was given priority over average coverage, except when several template complexes had similar sequence identity, in which case the template complex with a higher coverage was preferred. Further, five models for each protein were generated using Modeller [70] based on the template.…”

Expanding Interactome Analyses beyond Model Eukaryotes

“…The plant Arabidopsis thaliana, thale cress, was chosen as the first 'model' plant due to its small genome since and diploid nature that made genetic manipulation relatively simple [219]. A. thaliana has most well-characterised interactome of the plants with several experimental [220][221][222][223][224][225][226][227] and computational datasets [13,149,187,188,198,[228][229][230][231][232][233][234][235][236][237][238], many of which form the basis of interactome studies in other plants [238][239][240][241][242][243]. Cross-species interactomes have also investigated infection in this species [215,244].…”

“…RicePPINet used structural and functional information as machine learning inputs to predict the rice interactome and the resulting network was used to identify genes involved in disease resistance and drought tolerance [249]. PlaPPISite comprises 36,420 interologs predicted using several computational methods [238], while the predicted Rice Interactome Network, PRIN, contains 76,585 interologs [250,251]. RiceNet is a PFIN for rice produced using data from several model organisms [252]; an updated RiceNet network has 1,775,000 interactions between 25,765 genes [253].…”

“…BarleyNet is a PFIN for barley, Hordeum vulgare, based on orthology to Arabidopsis and rice [254]. Five computationally-predicted interactomes were produced for Zea mays, maize [13,231,238,239,255]. In horse gram, Macrotyloma uniflorum, an interolog network of over 6,000 interactions has been produced [256].…”

OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT

“…To accommodate the exponentially increased datasets of PPIs, a plethora of comprehensive and specific databases (e.g., BioGRID [36], APID [37], IntAct [38], HuRI [39], HIPPIE [40], HRPD [41], STRING [42], PlaPPISite [43]) have been constructed. These public repertories categorize hundreds and thousands of PPIs from many species.…”