Molecular gymnastics: distortion of an RNA polymerase σ factor

Genetic evidence for a novel interaction between transcriptional activator SoxS and region 4 of the σ(70) subunit of RNA polymerase at class II SoxS-dependent promoters in Escherichia coli

Escherichia coli SoxS activates transcription of the genes of the soxRS regulon, which provide the cell's defense against oxidative stress. In response to this stress, SoxS is synthesized de novo. Because the DNA binding site of SoxS is highly degenerate, SoxS efficiently activates transcription by the mechanism of prerecruitment. In prerecruitment, newly synthesized SoxS first forms binary complexes with RNA polymerase. These complexes then scan the chromosome for class I and II SoxS-dependent promoters, using the specific DNA-recognition properties of SoxS and σ(70) to distinguish SoxS-dependent promoters from the vast excess of sequence-equivalent soxboxes that do not reside in promoters. Previously, we determined that SoxS interacts with RNA polymerase in two ways: by making protein-protein interactions with the DNA-binding determinant of the α subunit and by interacting with σ(70) region 4 (σ(70) R4) both "on-DNA" and "off-DNA." Here, we address the question of how SoxS and σ(70) R4 coexist at class II promoters, where the binding site for SoxS either partially or completely overlaps the -35 region of the promoter, which is usually bound by σ(70) R4. To do so, we created a tri-alanine scanning library that covers all of σ(70) R4. We determined that interactions between σ(70) R4 and the DNA in the promoter's -35 region are required for activation of class I promoters, where the binding site lies upstream of the -35 hexamer, but they are not required at class II promoters. In contrast, specific three-amino-acid stretches are required for activation of class I (lac) and class II (galP1) cyclic AMP receptor protein-dependent promoters. We conclude from these data that SoxS and σ(70) R4 interact with each other in a novel way at class II SoxS-dependent promoters such that the two proteins do not accommodate one another in the -35 region but instead SoxS binding there occludes the binding of σ(70) R4.

Direct activator/co-activator interaction is essential for bacteriophage T4 middle gene expression

The bacteriophage T4 AsiA protein is a bifunctional regulator that inhibits transcription from the major class of bacterial promoters and also serves as an essential co-activator of transcription from T4 middle promoters. AsiA binds the primary s factor in Escherichia coli, sigma(70), and modifies the promoter recognition properties of the sigma(70)-containing RNA polymerase(RNAP) holoenzyme. In its role as co-activator, AsiA directs RNAP to T4 middle promoters in the presence of the T4-encoded activator MotA. According to the current model for T4 middle promoter activation, AsiA plays an indirect role in stabilizing the activation complex by facilitating interaction between DNA-bound MotA and sigma(70). Here we show that AsiA also plays a direct role in T4 middle promoter activation by contacting the MotA activation domain. Furthermore,we show that interaction between AsiA and the beta-flap domain of RNAP is important for co-activation. Based on our findings, we propose a revised model for T4 middle promoter activation, with AsiA organizing the activation complex via three distinct protein-protein interactions.

Middle promoters constitute the most abundant and diverse class of promoters in bacteriophage T4

The temporally regulated transcription program of bacteriophage T4 relies upon the sequential utilization of three classes of promoters: early, middle and late. Here we show that middle promoters constitute perhaps the largest and the most diverse class of T4 promoters. In addition to 45 T4 middle promoters known to date, we mapped 13 new promoters, 10 of which deviate from the consensus MotA box, with some of them having no obvious match to it. So, 30 promoters of 58 identified now deviate from the consensus sequence deduced previously. In spite of the differences in their sequences, the in vivo activities of these T4 middle promoters were demonstrated to be dependent on both activators, MotA and AsiA. Traditionally, the MotA box was restricted to a 9 bp sequence with the highly conserved motif TGCTT. New logo based on the sequences of currently known middle promoters supports the conclusion that the consensus MotA box is comprised of 10 bp with the highly conserved central motif GCT. However, some apparently good matches to the consensus of middle promoters do not produce transcripts either in vivo or in vitro, indicating that the consensus sequence alone does not fully define a middle promoter.