Promoter selectivity of Escherichia coli RNA polymerase E sigma(70) and E sigma(38) holoenzymes - Effect of DNA supercoiling

The functional specificity was compared between two sigma factors, sigma(70) (the major sigma at exponentially growing phase) and sigma(38) (the essential sigma at stationary growth phase), of Escherichia coli RNA polymerase. The core enzyme binding affinity of sigma(38) was less than half the level of sigma(70) as measured by gel filtration column chromatography or by titrating the concentration of sigma required for the maximum transcription in the presence of a fixed amount of core enzyme. In addition, the holoenzyme concentration required for the maximum transcription of a fixed amount of templates was higher for E sigma(38) than E sigma(70). The transcription by E sigma(38) was, however, enhanced with the use of templates with low superhelical density, in good agreement with the decrease in DNA superhelicity in the stationary growth phase. We thus propose that the selective transcription of stationary-specific genes by E sigma(38) holoenzyme requires either a specific reaction condition(s) or a specific factor(s) such as template DNA with low superhelical density.