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

BMC Bioinformatics

Table 2 Predicted bacterial interactome sizes

	Predicted interactome^b size from …
Species and Strain Name	Meta-interactome (this study)	Published interactome^a	Meta-interactome, in PPIs^a	Meta-interactome (experimental PPI only), in PPIs^a	Proteins in proteome (vs. proteins in meta-interactome)
Bacillus subtilis str. 168	17146	N/A	117229	67921	4175 (1597)
Caulobacter crescentus CB15	25792	N/A	177318	1580788	3885 (1482)
Escherichia coli K-12	43702	25736	62770	30087	4306 (3593)
Helicobacter pylori 26695	10576	13275	14271	5455	1553 (1337)
Mesorhizobium loti MAFF303099	57905	50735	256414	50838	7272 (3456)
Mycoplasma genitalium G37	718	N/A	7331	N/A	475 (149)
Pseudomonas aeruginosa PAO1	47815	N/A	88143	7073281	5892 (2488)
Salmonella enterica subsp. enterica serovar Typhi	30788	N/A	268219	554147	4607 (2723)
Staphylococcus aureus NCTC 8325	9339	N/A	59233	650299	2767 (1099)
Synechocystis sp. PCC 6803	27816	11221	66575	11811	3575 (2311)
Treponema pallidum str. Nichols	6722	7433	10350	7762	1036 (835)

^aMethod of Stumpf et al. [7]
^bPublished interactomes are those specified in Table 1
The interactome size prediction methods in this study are the results of predicting that two different orthologous group members will interact as long as members of the two groups have been observed interacting in any bacterial species. The resulting totals are shown in the second column (Predicted interactome size from meta-interactome (this study)). Results from the interactome size prediction method used by Stumpf et al. [7] are shown here for comparison: where possible, these are used with interaction and interactor totals from published interactomes (third column). Two hybrid approaches are also presented, with the input for the Stumpf method provided by the total counts of interactors and interactions predicted by the interactome (fourth column) or by the experimentally-observed interactions in the meta-interactome only (fifth column). The final column provides the count of proteins in each respective proteome along with the fraction of those proteins present in the meta-interactome, including all proteins involved in functional predictions

ISSN: 1471-2105