title: The fundamental ribosomal RNA transcription initiation factor-IB (TIF-IB, SL1, factor D) binds to the rRNA core promoter primarily by minor groove contacts.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA.
authors.forename: G K
authors.initials: GK
authors.lastname: Geiss
authors.forename: C A
authors.initials: CA
authors.lastname: Radebaugh
authors.forename: M R
authors.initials: MR
authors.lastname: Paule
mesh_terms: D001483:Base Sequence; D004247:DNA; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000378:metabolism*; D003855:Deoxyribose / Q000378:metabolism; D004214:Distamycins / Q000378:metabolism; D008969:Molecular Sequence Data; D010710:Phosphates / Q000378:metabolism; D035463:Pol1 Transcription Initiation Complex Proteins; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012335:RNA, Ribosomal / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D004214:Distamycins; D010710:Phosphates; D035463:Pol1 Transcription Initiation Complex Proteins; D012335:RNA, Ribosomal; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C063660:transcription initiation factor TIF-IB; D003855:Deoxyribose; C030000:stallimycin; D004247:DNA