Alternative sigma factors direct transcription to a specific subset of regulons in response to environmental signals and exhibit stringent promoter specificity. A crucial step in transcription initiation is the melting of the double-stranded promoter DNA by the bound RNA polymerase holoenzyme. Conserved amino acids in primary sigma factors initiate strand separation within the –10 region in target promoters; however, alternative sigma factors do not contain these key residues. The authors of this study investigated the mechanism of promoter melting by the Escherichia coli alternative sigma factor σE and solved the structure of the complex that is formed between σE and its cognate –10 promoter. They identified specific intramolecular contacts and found that σE induced strand separation by flipping out a single nucleotide from the non-template strand. Sequence-specific recognition of this nucleotide was mediated by a variable loop, which might explain the increased promoter stringency.
References
Campagne, S. et al. Structural basis for –10 promoter element melting by environmentally induced sigma factors. Nature Struct. Mol. Biol. http://dx.doi.org/10.1038/nsmb.2777 (2014)
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Du Toit, A. Promoter melting by alternative sigma factors. Nat Rev Microbiol 12, 235 (2014). https://doi.org/10.1038/nrmicro3250
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DOI: https://doi.org/10.1038/nrmicro3250