Thermoirreversible and thermoreversible promoter opening by two Escherichia coli RNA polymerase holoenzymes

Abstract

Promoter opening, in which the complementary DNA strands separate around the transcriptional start site, is generally thermoreversible. An exceptional case of thermoirreversible opening of the T4 late promoter has been analyzed by KMnO4 footprinting and transcription. T4 late promoters, which consist of an 8-base pair (bp) TATA box "-10" element, are recognized by the small, phage-encoded, highly diverged σ-family initiation subunit gp55. The T4 late promoter only opens above 15-20 °C, but once it has been formed remains open and transcriptionally active for days at -0.5 °C. The low temperature-trapped open complex and its isothermally formed state are shown to be structurally distinctive. Two "extended -10" σ70 promoters, which, like the T4 late promoter, lack "-35" sites, have been subjected to a comparative analysis: the T4 middle promoter PrIIB2 opens and closes thermoreversibly under conditions of basal and MotA- and AsiA-activated transcription. The open galP1 promoter complex, whose transcription bubble is very AT-rich, also closes reversibly upon shift to -0.5 °C, but more slowly than does the rIIB2 promoter. Formation of a trapped-open low temperature state of the promoter complex appears to be a singular property of gp55-RNA polymerase holoenzyme.