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Originally published In Press as doi:10.1074/jbc.M110147200 on November 28, 2001

J. Biol. Chem., Vol. 277, Issue 10, 7776-7784, March 8, 2002
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Comparison of TATA-binding Protein Recognition of a Variant and Consensus DNA Promoters*

Robyn M. Powell, Kay M. Parkhurst, and Lawrence J. ParkhurstDagger

From the Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304

Assembly of transcription pre-initiation complexes proceeds from the initial complex formed between "TATA" bearing promoter DNA and the TATA-binding protein (TBP). Our laboratory has been investigating the relationships among TATA sequence, TBP·TATA solution structure, recognition mechanisms, and transcription efficiency. TBP·TATA interactions have been modeled by global analysis of detailed kinetic and thermodynamic data obtained using fluorimetric and fluorometric techniques in conjunction with fluorescence resonance energy transfer. We have reported recently that TBP recognition of two consensus promoters, adenovirus major late (AdMLP: TATAAAAG) and E4 (TATATATA), is well described by a linear two-intermediate mechanism with simultaneous DNA binding and bending. Similar DNA geometries and high transcription efficiencies characterize these TBP·TATA complexes. Here we show that, in contrast to the consensus sequences, TBP recognition of a variant sequence (C7: TATAAACG) is described by a three-step model with two branching pathways. One pathway proceeds through an intermediate having severely bent DNA, reminiscent of the consensus interactions, with the other branch yielding a unique conformer with shallowly bent DNA. The resulting TBP·C7 complex has a dramatically different solution conformation than for TBP·DNACONSENSUS and is correlated with diminished relative transcription activity. The temperature dependence of the TBP·C7 helical bend is postulated to derive from population shifts between the conformers with slightly and severely bent DNA.

* This work was supported by the Program in Mathematics and Molecular Biology at Florida State University, which is sponsored by National Science Foundation Grant DMS-9406348 (to R. M. P.), by Presidential and McDonald Fellowships (to R. M. P.) from the College of Graduate Studies, University of Nebraska-Lincoln, and by National Institutes of Health Grants GM59346 and CA76049 (to L. J. P.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Dagger To whom correspondence should be addressed: From the Dept. of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304. Tel.: 402-472-3316; Fax: 402-472-2044; E-mail: lparkhurst1@unl.edu.

Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.


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