ArticleBMC bioinformatics2017
Bacterial protein meta-interactomes predict cross-species interactions and protein function.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Functional flexibility in bacterial hub proteins is driven by proteome expansion.Scientific reports · 2026Article
- Synergistic Inhibitory Effect and Mechanism of Action of Cinnamaldehyde-Carvacrol Nanoemulsion on the Staphylococcus aureus and Escherichia coli Mixed Biofilms Formation.MicrobiologyOpen · 2026Article
- Targeting of interaction between BB0323-BB0238 informs new paradigms in Lyme disease therapeutics.PLoS pathogens · 2026Article
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- Bacterial Protein Interaction Networks: Connectivity is Ruled by Gene Conservation, Essentiality and Function.Current genomics · 2021Article
- Prediction of Human-Bioinformatics and biology insights · 2021Article
- Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions.Medical microbiology and immunology · 2020Review
- Heterogeneous Network Model to Identify Potential Associations BetweenInternational journal of molecular sciences · 2020Article
- Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action.International journal of molecular sciences · 2019Article
- Hot spot prediction in protein-protein interactions by an ensemble system.BMC systems biology · 2018Article
- INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.Nucleic acids research · 2018Article
- Proteome Data Improves Protein Function Prediction in the Interactome ofMolecular & cellular proteomics : MCP · 2018Article
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Authors and funding
5 authors.
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Abstract
backgroundProtein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens. The availability of interactome data has brought challenges, as these large data sets are difficult to compare across species, limiting their usefulness for broad studies of microbial genetics and evolution.
resultsIn this study, we use more than 52,000 unique protein-protein interactions (PPIs) across 349 different bacterial species and strains to determine their conservation across data sets and taxonomic groups. When proteins are collapsed into orthologous groups (OGs) the resulting meta-interactome still includes more than 43,000 interactions, about 14,000 of which involve proteins of unknown function. While conserved interactions provide support for protein function in their respective species data, we found only 429 PPIs (~1% of the available data) conserved in two or more species, rendering any cross-species interactome comparison immediately useful. The meta-interactome serves as a model for predicting interactions, protein functions, and even full interactome sizes for species with limited to no experimentally observed PPI, including Bacillus subtilis and Salmonella enterica which are predicted to have up to 18,000 and 31,000 PPIs, respectively.
conclusionsIn the course of this work, we have assembled cross-species interactome comparisons that will allow interactomics researchers to anticipate the structures of yet-unexplored microbial interactomes and to focus on well-conserved yet uncharacterized interactors for further study. Such conserved interactions should provide evidence for important but yet-uncharacterized aspects of bacterial physiology and may provide targets for anti-microbial therapies.
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