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Science 1 February 2002:
Vol. 295. no. 5556, pp. 855 - 857
DOI: 10.1126/science.1066303
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Reports

A Role for Interaction of the RNA Polymerase Flap Domain with the &sfgr; Subunit in Promoter Recognition

Konstantin Kuznedelov,1*dagger Leonid Minakhin,1* Anita Niedziela-Majka,2ddagger Simon L. Dove,3 Dragana Rogulja,1 Bryce E. Nickels,3 Ann Hochschild,3 Tomasz Heyduk,2 Konstantin Severinov1§

In bacteria, promoter recognition depends on the RNA polymerase sigma  subunit, which combines with the catalytically proficient RNA polymerase core to form the holoenzyme. The major class of bacterial promoters is defined by two conserved elements (the -10 and -35 elements, which are 10 and 35 nucleotides upstream of the initiation point, respectively) that are contacted by sigma in the holoenzyme. We show that recognition of promoters of this class depends on the "flexible flap" domain of the RNA polymerase beta  subunit. The flap interacts with conserved region 4 of sigma  and triggers a conformational change that moves region 4 into the correct position for interaction with the -35 element. Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well.

1 Waksman Institute, Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA.
2 E. A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical School, St. Louis, MO 63104, USA.
3 Harvard Medical School, Department of Microbiology and Molecular Genetics, Boston, MA 02115, USA.
*   These authors contributed equally to this work.

dagger    On leave from Limnological Institute of the Russian Academy of Sciences, Irkutsk, Russia.

ddagger    On leave from Department of Organic Chemistry, Biochemistry and Biotechnology, Wroclaw University of Technology, Wroclaw, Poland.

§   To whom correspondence should be addressed. E-mail: severik{at}waksman.rutgers.edu

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