A 3RD RECOGNITION ELEMENT IN BACTERIAL PROMOTERS - DNA-BINDING BY THEALPHA-SUBUNIT OF RNA-POLYMERASE

A DNA sequence rich in (A + T), located upstream of the -10, -35 regio n of the Escherichia coli ribosomal RNA promoter rrnB P1 and called th e UP element, stimulates transcription by a factor of 30 in vivo, as w ell as in vitro in the absence of protein factors other than RNA polym erase (RNAP). When fused to other promoters, such as lacUV5, the UP el ement also stimulates transcription, indicating that it is a separable promoter module. Mutations in the carboxyl-terminal region of the alp ha subunit of RNAP prevent stimulation of these promoters by the UP el ement although the mutant enzymes are effective in transcribing the '' core'' promoters (those lacking the UP element). Protection of UP elem ent DNA by the mutant RNAPs is severely reduced in footprinting experi ments, suggesting that the selective decrease in transcription might r esult from defective interactions between alpha and the UP element. Pu rified alpha binds specifically to the UP element, confirming that alp ha acts directly in promoter recognition. Transcription of three other promoters was also reduced by the COOH-terminal alpha mutations. Thes e results suggest that UP elements comprise a third promoter recogniti on region (in addition to the -10, -35 recognition hexamers, which int eract with the sigma subunit) and may account for the presence of (A T)-rich DNA upstream of many prokaryotic promoters. Since the same al pha mutations also block activation by some transcription factors, mec hanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related.