Berkeley Lab

Benchmark properties for highly accurate bacterial protein interactions

D. vulgaris protein interaction network comprised of 459 high confidence PPIs. Grey background highlights complexes associated with specific functional categories i.e. energy conservation (a1-a3), cofactor biosynthesis (b1-b3), RNA synthesis and degradation (c1-c3), motility (d1-d3), megaplasmid encoded complexes (e1-e5) and novel and uncharacterized complexes (f1-f2)


Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial Y2H and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli. Compared to the nine published interactomes, our two networks are smaller; are much less highly connected; have significantly lower false discovery rates; and are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.

Mapping the protein interactome of the model sulfate reducing obligate anaerobe Desulfovibrio vulgaris

  • Advance one of ENIGMA’s key missions, evidence based annotation of gene function, by determining the stable protein interactome of the model sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough.

New Science

  • Conducted high throughput affinity purifications – mass spectrometry study using D. vulgaris
  • Used logistic regression to predict a high confidence D. vulgaris interaction network composed of 459 protein-protein interactions (PPIs) at a low 17% false discovery rate
  • Established that our two networks are smaller, much less highly connected and have significantly lower false discovery rates than nine published bacterial protein interactomes
  • PPIs in our networks are highly enriched for those encoded by the same operon and/or those which share similar annotated functions


  • Established stringent benchmark properties for highly accurate bacterial protein interactomes

Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.  Mol Cell Proteomics. 2016 Feb 12. pii: mcp.M115.054692. PMID: 26873250.