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J Biol Chem, Vol. 273, Issue 21, 13307-13312, May 22, 1998

Ada Protein-RNA Polymerase  Subunit Interaction and  Subunit-Promoter DNA Interaction Are Necessary at Different Steps in Transcription Initiation at the Escherichia coli ada and aidB Promoters

Paolo Landini, Jonathan A. Bown, Michael R. Volkert^¶, and Stephen J. W. Busby

From the  School of Biochemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom, and the ^¶ Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts 01655

The methylated form of the Ada protein (^meAda) binds the ada and aidB promoters between 60 and 40 base pairs upstream from the transcription start and activates transcription of the Escherichia coli ada and aidB genes. This region is also a binding site for the  subunit of RNA polymerase and resembles the rrnB P1 UP element in A/T content and location relative to the core promoter. In this report, we show that deletion of the C-terminal domain of the  subunit severely decreases ^meAda-independent binding of RNA polymerase to ada and aidB, affecting transcription initiation at these promoters. We provide evidence that ^meAda activates transcription by direct interaction with the C-terminal domain of RNA polymerase ⁷⁰ subunit (amino acids 574-613). Several negatively charged residues in the ⁷⁰ C-terminal domain are important for transcription activation by ^meAda; in particular, a glutamic acid to valine substitution at position 575 has a dramatic effect on ^meAda-dependent transcription. Based on these observations, we propose that the role of the  subunit at ada and aidB is to allow initial binding of RNA polymerase to the promoters. However, transcription initiation is dependent on ^meAda-⁷⁰ interaction.

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