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

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E. V. Zhilina¹, N. A. Miropolskaya¹, I. A. Bass¹, K. L. Brodolin², and A. V. Kulbachinskiy^1*

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

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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 aquaticus (σ^A) is also able to induce transcription pausing by T. aquaticus RNAP. However, hybrid RNAP containing the σ^A 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 σ^A 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.

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KEY WORDS: RNA polymerase, σ-dependent pausing, transcription regulation

DOI: 10.1134/S0006297911100038

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