Characteristics of [sigma]-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus

The σ^sup 70^ subunit of RNA polymerase (RNAP) is the major transcription initiation factor in Escherichia coli. During transcription initiation, conserved region 2 of the σ^sup 70^ 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 σ^sup 70^ 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^sup A^) is also able to induce transcription pausing by T. aquaticus RNAP. However, hybrid RNAP containing the σ^sup 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^sup 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 σ^sup 70^ 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.[PUBLICATION ABSTRACT]