Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

Abstract

In bacteria, multiple σs direct RNA polymerase to distinct sets of promoters. Housekeeping σs direct transcription from thousands of promoters, whereas most alternative σs are more selective, recognizing more highly conserved promoter motifs. For σ32 and σ28, two Escherichia coli Group 3 σs, altering a few residues in Region 2.3, the portion of σ implicated in promoter melting, to those universally conserved in housekeeping σs relaxed their stringent promoter requirements and significantly enhanced melting of suboptimal promoters. All Group 3 σs and the more divergent Group 4 σs have nonconserved amino acids at these positions and rarely transcribe >100 promoters. We suggest that the balance of "melting" and "recognition" functions of σs is critical to setting the stringency of promoter recognition. Divergent σs may generally use a nonoptimal Region 2.3 to increase promoter stringency, enabling them to mount a focused response to altered conditions. © 2009 by Cold Spring Harbor Laboratory Press.