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Characteristics of σ-Dependent Pausing by RNA Polymerases from Escherichia coli and Thermus aquaticus

E. V. Zhilina1, N. A. Miropolskaya1, I. A. Bass1, K. L. Brodolin2, and A. V. Kulbachinskiy1*

1Institute of Molecular Genetics, Russian Academy of Sciences, pl. Kurchatova 2, 123182 Moscow, Russia; fax: (499) 196-0221; E-mail: akulb@img.ras.ru

2Université Montpellier 1, Université Montpellier 2, CNRS UMR 5236, Centre d’études d’agents Pathogènes et Biotechnologies pour la Santé, Montpellier 34293, France

* To whom correspondence should be addressed.

Received May 27, 2011
The σ70 subunit of RNA polymerase (RNAP) is the major transcription initiation factor in Escherichia coli. During transcription initiation, conserved region 2 of the σ70 subunit interacts with the –10 promoter element and plays a key role in DNA melting around the starting point of transcription. During transcription elongation, the σ70 subunit can induce pauses in RNA synthesis owing to interactions of region 2 with DNA regions similar to the –10 promoter element. We demonstrated that the major σ subunit from Thermus aquaticusA) is also able to induce transcription pausing by T. aquaticus RNAP. However, hybrid RNAP containing the σA subunit and E. coli core RNAP is unable to form pauses during elongation, while being able to recognize promoters and initiate transcription. Inability of the σA subunit to induce pausing by E. coli RNAP is explained by the substitutions of non-conserved amino acids in region 2, in the subregions interacting with the RNAP core enzyme. Thus, changes in the structure of region 2 of the σ70 subunit have stronger effects on transcription pausing than on promoter recognition, likely by weakening the interactions of the σ subunit with the core RNAP during transcription elongation.
KEY WORDS: RNA polymerase, σ-dependent pausing, transcription regulation

DOI: 10.1134/S0006297911100038