Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays...

Area of Science:

• Molecular Biology
• Systems Biology
• Bioinformatics

Background:

• Large-scale protein-protein interaction (PPI) studies using affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have generated extensive interaction networks.
• However, the accuracy and biological relevance of these large PPI networks are frequently debated, with many identified interactions occurring between functionally unrelated proteins.

Purpose of the Study:

• To critically reanalyze existing bacterial PPI datasets and present a high-confidence PPI network for Desulfovibrio vulgaris.
• To establish more stringent benchmarks for the properties of reliable protein interactomes.

Main Methods:

• Performed an AP-MS survey on Desulfovibrio vulgaris.
• Critically reanalyzed nine published bacterial yeast two-hybrid and AP-MS screens.
• Identified high-confidence PPIs based on stringent criteria.

Main Results:

• Generated a high-confidence PPI network for D. vulgaris with 459 interactions and for Escherichia coli with 391 interactions.
• The newly generated interactomes are smaller, less connected, and have significantly lower false discovery rates compared to previously published networks.
• Identified PPIs are significantly enriched for protein pairs encoded in the same operon, possessing similar functions, and validated in independent assays.

Conclusions:

• The study establishes more rigorous benchmarks for assessing the quality of protein interactomes.
• Bona fide PPIs are more frequently associated with proteins of similar functions or those validated through independent assays than previously suggested by large-scale screening studies.