RNA-POLYMERASE BINDING USING A STRONGLY ACIDIC HYDROPHOBIC-REPEAT REGION OF SIGMA(54)

sigma(54) is a rare bacterial protein that substitutes for sigma(70) i n the case of Escherichia coli genes transcribed by certain activators with enhancer protein-like properties. It contains a strongly acidic region of previously unknown function. Gel mobility-shift assays using sigma(54) deletion mutants show that this region is essential for sig ma(54) to bind the core RNA polymerase and recruit it to the promoter. Multiple-point mutational analysis shows that the acidic amino acids and overlapping periodic hydrophobic amino acids are necessary for thi s binding. Related sequences are not found within the core binding det erminant of sigma(70), which binds the same core RNA polymerase. This comparison suggests that the core RNA polymerase interacts differently with the two a factors, likely contributing to the critical differenc es in transcription mechanism in the two cases.