The logic of sharing

By implementing a systematic chromatin immunoprecipitation-microarray (ChIP-chip) analysis of the heat-shock σ-factor regulon (σ³²) of Escherchia coli , Wade et al. reveal the surprising finding that there is functional overlap between σ factors.

Sigma factors confer specificity on the bacterial RNA polymerase (RNAP), directing this enzyme to promoter sequences, positioning the RNAP at the promoter and effecting local unwinding of the DNA duplex near to the transcription start site. In addition to the main σ⁷⁰ factor that directs transcription of housekeeping genes, most bacteria synthesize alternative σ factors that enable recognition of different sets of promoters by the RNAP — a neat solution to the problem of how to rapidly modulate global transcription in response to changing conditions.

The availability of whole-genome microarrays has allowed researchers to attempt to exhaustively catalogue all the members of the σ³² regulon. ChIP-chip studies are an ideal tool for delineating regulons, since they do not rely on artificially overproducing proteins in cells, but instead can detect DNA sequences that are bound by physiological levels of regulatory proteins. Using this approach, the authors identified a minimum of 87 promoters — they estimate that the true number might be closer to 120–150 — that are bound by σ³²-RNAP (Eσ³²), a massive increase on the previous known size of this regulon.

Perhaps it is not surprising that the heat-shock regulon is large, given that heat shock is a drastic environmental shift, but close inspection of the promoters recognized by Eσ³² led the researchers to some surprising conclusions. First, 22 heat-shock promoters were located in coding or intergenic regions rather than promoter regions, with 3 promoters postulated to transcribe regulatory RNAs. Second, by comparing the regulon with the predicted σ⁷⁰ regulon (not yet published) the authors found significant overlap in targets that are bound by both σ³² and σ⁷⁰. Traditional biochemistry confirmed that Eσ⁷⁰ can indeed transcribe from five selected Eσ³² promoters. In addition, comparing the σ⁷⁰ and previously published σ²⁴ (σ^E) regulons also revealed an extensive overlap between target promoters.

The hypothesis arising from this research is that alternative σ factors primarily evolved to augment σ⁷⁰ transcription and generate complex regulatory patterns, and the authors argue that this is a key feature of transcriptional logic. The power of using a systems-wide approach to detect regulatory networks is clearly shown by these unexpected findings.