However, not all three of these promoter elements need to be present for promoter function. It is known that residues in region 2 recognize a −10 element (TATAAT) ( 37), residues in region 3 recognize an extended TGn −10 motif (positions −15 to −13) ( 1), and residues in region 4 recognize a −35 element (TTGACA) ( 4). Primary σ factors have four regions of similarity. ![]() coli, σ 70, is used during exponential growth and belongs to a large family of prokaryotic primary σ factors related to each other by sequence, structure, and function ( 15, 39). The presence of specific σ factors allows bacteria to coordinate the expression of gene sets and is one of the major ways bacteria regulate expression in response to changing growth conditions. Each σ factor interacts with different DNA sequences, and thus the recognition and usage of a given promoter is dependent upon the σ present in the holoenzyme. coli encodes several σ factors that can be part of the holoenzyme, which are used under various conditions of growth and stress ( 39). In Escherichia coli, these elements are recognized by a σ factor when σ is present in RNA polymerase holoenzyme, (σ plus core ) ( 15, 36). Recognition and binding of DNA promoter elements by RNA polymerase set the start site for transcription initiation. P minor represents one of the few −35/TGn promoters that have been characterized and serves as a model for investigating functional differences between these promoters and the better-characterized −10/−35 and extended −10 promoters used by E. We also demonstrate that transcription from P minor incorporates nontemplated ribonucleoside triphosphates at the 5′ end of the P minor transcript, which results in an anomalous assignment for the start site when primer extension analysis is used. Potassium permanganate footprinting on the nontemplate and template strands indicates that when polymerase is in a stable (open) complex with P minor, the DNA is single stranded from positions −11 to +4. ![]() Mutation of the TGn motif can be compensated for by mutations that make the −10 element more canonical, thus converting the −35/TGn promoter to a −35/−10 promoter. We demonstrate that P minor is active both in vivo and in vitro and that mutations in either the −35 or the TGn motif eliminate its activity. However, P minor contains an extremely poor σ 70 −10 element. We report here an investigation of a promoter, P minor, that has a nearly perfect match to the −35 sequence and has the TGn motif. Escherichia coli σ 70-dependent promoters have typically been characterized as either −10/−35 promoters, which have good matches to both the canonical −10 and the −35 sequences or as extended −10 promoters (TGn/−10 promoters), which have the TGn motif and an excellent match to the −10 consensus sequence.
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