Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

Table 1 Evolution of gene regulation by duplication or by convergent evolution

Type of shared regulation	Interactions (n)	Percentage
All three types of shared regulation, combined	425	14.2%
Evolved by duplication	145	4.8%
Unclear	94	3.1%
Convergent evolution	186	6.2%
Interactions that are not shared with paralogs	2,570	85.8%
All of RegulonDB (with autoregulation removed)	2,995	100.0%
Type 1: paralogous TFs regulate the same genes	212	7.1%
Evolved by duplication	84	2.8%
Unclear	64	2.1%
Relative ages are unclear, and TFs bind the same site	62	2.1%
Duplication of TFs is recent, but TFs bind different sites	2	0.1%
Convergent evolution	64	2.1%
Duplication of TFs is old, and TFs bind different sites	26	0.9%
Duplication of TFs is old, but TFs bind the same site	28	0.9%
Duplication of TFs is old, and sites are not known	10	0.3%
Type 2: paralogous genes are regulated by the same TF	290	9.7%
Evolved by duplication	76	2.5%
Unclear	26	0.9%
Convergent evolution	188	6.3%
Differences in operon structure	166	5.5%
Operons are consistent, but acquired after duplication	22	0.7%
Type 3: paralogous TFs regulate paralogous genes	54	1.8%
Evolved by duplication (similar ages)	8	0.3%
Convergent evolution	46	1.5%
Complex HGT of regulated genes after TF duplication	16	0.5%
TF duplication precedes that of regulated genes	30	1.0%

For each case of shared regulation between paralogs, we examined the evolutionary histories of the duplicated genes to determine whether the regulation was likely to be conserved from the common ancestor. If so, then the regulatory similarity probably evolved by duplication; if not, then the similarity results from convergent evolution. For cases where two paralogous transcription factors (TFs) regulate the same operon, we also considered whether the TFs bind to the same site. For cases where two paralogous genes are regulated by the same TF, we also considered whether the first genes in the operons were homologous, as would be expected for evolution by duplication. The results are tabulated here (see Additional data file 5 for individual interactions). Because some regulatory interactions are shared with paralogs in more than one way, the totals are smaller than the sums over the types.

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