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Volume 272, Number 46, Issue of November 14, 1997 pp. 29243-29254
©1997 by The American Society for Biochemistry and Molecular Biology, Inc.

The Fundamental Ribosomal RNA Transcription Initiation Factor-IB (TIF-IB, SL1, Factor D) Binds to the rRNA Core Promoter Primarily by Minor Groove Contacts

(Received for publication, May 27, 1997, and in revised form, August 12, 1997)

From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870

Acanthamoeba castellanii transcription initiation factor-IB (TIF-IB) is the TATA-binding protein-containing transcription factor that binds the rRNA promoter to form the committed complex. Minor groove-specific drugs inhibit TIF-IB binding, with higher concentrations needed to disrupt preformed complexes because of drug exclusion by bound TIF-IB. TIF-IB/DNA interactions were mapped by hydroxyl radical and uranyl nitrate footprinting. TIF-IB contacts four minor grooves in its binding site. TIF-IB and DNA wrap around each other in a right-handed superhelix of high pitch, so the upstream and downstream contacts are on opposite faces of the helix. Dimethyl sulfate protection assays revealed limited contact with a few guanines in the major groove. This detailed analysis suggests significant DNA conformation dependence of the interaction.

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