RNA-POLYMERASE ALPHA-SUBUNIT BINDING-SITE IN POSITIVELY CONTROLLED PROMOTERS - A NEW MODEL FOR RNA POLYMERASE-PROMOTER INTERACTION AND TRANSCRIPTIONAL ACTIVATION IN THE ESCHERICHIA-COLI ADA AND AIDB GENES

The ada and aidB genes are part of the adaptive response to DNA methyl ation damage in Escherichia coli. Transcription of the ada and the aid B genes is triggered by binding of the methylated Ada protein ((me)Ada ) to a specific sequence located 40-60 base pairs upstream of the tran scriptional start, which is internal to an A/T-rich region. In this re port we demonstrate that the Ada binding site is also a binding site f or RNA polymerase. RNA polymerase is able to bind the -40 to -60 regio n of the ada and the aidB promoters in the absence of (me)Ada, and its binding is mediated by the a subunit. This region resembles the UP el ement of the rrnB P1 promoter in location, sequence and mechanism of i nteraction with RNA polymerase. We discuss the function of UP-like ele ments in positively controlled promoters and provide evidence that Ada does not act by enhancing RNA polymerase binding affinity to the prom oter region. Instead, Ada stimulates transcription by modifying the na ture of the RNA polymerase-promoter interaction, allowing RNA polymera se to recognize the core promoter -35 and -10 elements in addition to the UP-like element.