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A more recent version of this article appeared on August 17, 2001
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M105027200v1
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Papers In Press, published online ahead of print July 6, 2001
J. Biol. Chem, 10.1074/jbc.M105027200
Submitted on June 1, 2001
Revised on July 6, 2001
Accepted on July 5, 2001

Different roles for basic and aromatic amino acids in conserved region 2 of E. coli sigma {70} in the nucleation and maintenance of the single stranded DNA bubble in open RNA polymerase-promoter complexes

Mark Tomsic, Laura Tsujikawa, Gianina Panaghie, Yang Wang, Joseph Azok, and Pieter L deHaseth

Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106-4935

Corresponding Author: pld2{at}po.cwru.edu

Amino acid residues in region 2 of sigma {70} have been shown to play an important role in the strand separation step which is necessary for formation of the functional or open RNA polymerase- promoter complex. Here we present a comparison of the roles of basic and aromatic amino acids in the accomplishment of this process, using RNA polymerase bearing alanine substitutions for both types of amino acids in region 2. We determined the effects of the substitutions on the kinetics of open complex formation, as well as on the ability of the RNA polymerase to form complexes with single stranded DNA, and with forked DNA duplexes carrying a single stranded overhang consisting of bases in the -10 region. We conclude that two basic amino acids (K414 and K418) are important for promoter binding and demonstrate distinct roles, at a subsequent step, for two aromatic amino acids (Y430 and W433). It is likely that these 4 amino acids, which are close to each other in the structure of sigma {70}, together are involved in the nucleation of the strand separation process.


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