IDENTIFICATION OF AN UP ELEMENT CONSENSUS SEQUENCE FOR BACTERIAL PROMOTERS

The UP element, a component of bacterial promoters located upstream of the -35 hexamer, increases transcription by interacting with the RNA polymerase alpha-subunit. By using a modification of the SELEX procedu re for identification of protein-binding sites, we selected in vitro a nd subsequently screened in vivo for sequences that greatly increased promoter activity when situated upstream of the Escherichia coil rrnB P1 core promoter. A set of 31 of these upstream sequences increased tr anscription from 136- to 326-fold in vivo, considerably more than the natural rrnB P1 UP element, and was used to derive a consensus sequenc e: -59 nnAAA(A/T) (A/T)T(A/T)TTTTnnAAAAnnn -38. The most active select ed sequence contained the derived consensus, displayed all of the prop erties of an UP element, and the interaction of this sequence with the alpha C-terminal domain was similar to that of previously characteriz ed UP elements. The identification of the UP element consensus should facilitate a detailed understanding of the alpha-DNA interaction. Base d on the evolutionary conservation of the residues in alpha responsibl e for interaction with UP elements, we suggest that the UP element con sensus sequence should be applicable throughout eubacteria, should gen erally facilitate promoter prediction, and may be of use for biotechno logical applications.