The cyanobacterial principal σ factor region 1.1 is involved in DNA-binding in the free form and in transcription activity as holoenzyme

Cyanobacterial principal σ factor, σA, includes a specifically conserved cluster of basic amino acids in the amino-terminal extension called region 1.1. We found that the σA in a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 binds DNA in the absence of the core RNA polymerase and that σA lacking region 1.1 is not able to bind DNA. This indicates that, in the cyanobacterium, region 1.1 participates in DNA-binding, rather than inhibiting the interaction between free σ and DNA, as found in other principal σ factors of eubacteria. The results of in vitro transcription assays with the reconstituted RNA polymerase showed that region 1.1 reduces transcription activity from the cpc promoter.