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The [sigma]-like factor Yvrl and coregulator YvrHa activate transcription from a small set of conserved promoters in Bacillus subtilis. We report here that these two proteins independently contribute [sigma]-region 2 and [sigma]-region 4 functions to a holoenzyme-promoter DNA complex. Yvrl binds RNA polymerase (RNAP) through a region 4 interaction with the [beta]-subunit flap domain and mediates specific promoter recognition but cannot initiate DNA melting at the -10 promoter element. Conversely, YvrHa possesses sequence similarity to a conserved core-binding motif in [sigma]-region 2 and binds to the N-terminal coiled-coil element in the RNAP [beta]-subunit previously implicated in interaction with region 2 of [sigma]-factors. YvrHa plays an essential role in stabilizing the open complex and interacts specifically with the N-terminus of Yvrl. Based on these results, we propose that YvrHa is situated in the transcription complex proximal to the -10 element of the promoter, whereas Yvrl is responsible for -35 region recognition. This system presents an unusual example of a two-subunit bacterial [sigma]-factor. RNA polymerase | initiation | promoter | open complex doi/ 10.1073/pnas.0910006106

The σ-like factor Yvrl and coregulator YvrHa activate transcription from a small set of conserved promoters in Bacillus subtilis. We report here that these two proteins independently contribute σ-region 2 and σ-region 4 functions to a holoenzyme-promoter DNA complex. Yvrl binds RNA polymerase (RNAP) through a region 4 interaction with the β-subunit flap domain and mediates specific promoter recognition but cannot initiate DNA melting at the -10 promoter element. Conversely, YvrHa possesses sequence similarity to a conserved core-binding motif in σ-region 2 and binds to the N-terminal coiled-coil element in the RNAP β-subunit previously implicated in interaction with region 2 of σ-factors. YvrHa plays an essential role in stabilizing the open complex and interacts specifically with the N-terminus of Yvrl. Based on these results, we propose that YvrHa is situated in the transcription complex proximal to the -10 element of the promoter, whereas Yvrl is responsible for -35 region recognition. This system presents an unusual example of a two-subunit bacterial σ-factor. [ABSTRACT FROM AUTHOR]