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J. Biol. Chem., Vol. 278, Issue 32, 29728-29743, August 8, 2003
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54-RNA Polymerase Interactions at the 24 Consensus Promoter Element*


From the
Department of Biological Sciences, Sir Alexander Fleming Building,
Imperial College London, South Kensington Campus, London SW7 2AZ, United
Kingdom,
Waksman Institute and Department of
Genetics, Rutgers, The State University, Piscataway, New Jersey 08904, and
Nippon Institute for Biological Science,
Shin-machi 9-2221, Ome, Tokyo 198-0024, Japan
The
54 promoter specificity factor is distinct from
70-type factors. The
54-RNA polymerase
binds to promoters with conserved sequence elements at 24 and 12
and utilizes specialized enhancer-binding activators to convert, through an
ATP-dependent process, closed promoter complexes to open promoter complexes.
The interface between
54-RNA polymerase and promoter DNA is
poorly characterized, contrasting with
70. Here,
54 was modified with strategically positioned cleavage
reagents to provide physical evidence that the highly conserved RpoN box motif
of
54 is close to and may therefore interact with the
consensus 24 promoter element. We show that the spatial relationship
between the
54-RNA polymerase and the 24 promoter
element remains unchanged during closed to open complex conversion and
transcription initiation but changes during the early elongation phase. In
contrast, the spatial relationship between
54-RNA polymerase
and the consensus 12 promoter element changes upon conversion of the
closed promoter complex to an open one. We provide evidence that some
12 promoter region-
54 interactions are dependent upon
either the core RNA polymerase or a fork junction DNA structure at the
12-position, indicating that DNA fork junctions can substitute for core
RNAP. We also show the
-subunit flap domain contributes to different
sets of
-promoter DNA interactions at
54- and
70-dependent promoters.
Received for publication, April 7, 2003 , and in revised form, May 12, 2003.
* This work was supported by a Biotechnology and Biological Sciences Research Council project grant (to M. B.) and National Institutes of Health Grant RO1 GM64530 (to K. S.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
¶ To whom correspondence may be addressed. Tel.: 44-207-594-5366; Fax: 44-207-594-5419; E-mail: m.buck{at}imperial.ac.uk.
|| To whom correspondence may be addressed. Tel.: 44-207-594-5366; Fax: 44-207-594-5419; E-mail: s.r.wig{at}imperial.ac.uk.
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