Bacterial protein meta-interactomes predict cross-species interactions and protein function

Area of Science:

• Microbiology
• Systems Biology
• Bioinformatics

Background:

• Protein-protein interactions (PPIs) are crucial for understanding protein function within cellular systems.
• Bacterial interactome studies are abundant but present challenges in cross-species data comparison, hindering broader evolutionary and genetic analyses.
• Existing interactome data is difficult to compare across species, limiting its utility for large-scale microbial research.

Purpose of the Study:

• To analyze the conservation of protein-protein interactions (PPIs) across diverse bacterial species and taxonomic groups.
• To develop a comprehensive meta-interactome from existing bacterial PPI data.
• To establish a framework for predicting protein functions and interactome sizes in bacteria with limited experimental data.

Main Methods:

• Compiled over 52,000 unique PPIs from 349 bacterial species and strains.
• Grouped proteins into orthologous groups (OGs) to create a meta-interactome.
• Quantified the conservation of PPIs across different species and taxonomic levels.

Main Results:

• The meta-interactome contains over 43,000 interactions, with approximately 14,000 involving proteins of unknown function.
• Only 429 PPIs (about 1% of the data) were found to be conserved in two or more species.
• Developed predictive models for interactome size and protein function, estimating up to 18,000 PPIs for Bacillus subtilis and 31,000 for Salmonella enterica.

Conclusions:

• Cross-species interactome comparisons are limited but valuable for identifying conserved interactions.
• The meta-interactome aids in anticipating microbial interactome structures and prioritizing uncharacterized conserved proteins for study.
• Conserved interactions can illuminate bacterial physiology and identify potential antimicrobial targets.