Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters

Abstract

Bacterial RNA polymerase is composed of a core of subunits (β, β′, α1, α2, ω), which have RNA synthesizing activity, and a specificity factor (σ), which identifies the start of transcription by recognizing and binding to sequence elements within promoter DNA. Four core promoter consensus sequences, the −10 element, the extended −10 (TGn) element, the −35 element, and the UP elements, have been known for many years; the importance of a nontemplate G at position −5 has been recognized more recently. However, the functions of these elements are not the same. The AT-rich UP elements, the −35 elements (−35TTGACA−30), and the extended −10 (−15TGn−13) are recognized as double-stranded binding elements, whereas the −5 nontemplate G is recognized in the context of single-stranded DNA at the transcription bubble. Furthermore, the −10 element (−12TATAAT−7) is recognized as both double-stranded DNA for the T:A bp at position −12 and as nontemplate, single-stranded DNA from positions −11 to −7. The single-stranded sequences at positions −11 to −7 as well as the −5 contribute to later steps in transcription initiation that involve isomerization of polymerase and separation of the promoter DNA around the transcription start site. Recent work has demonstrated that the double-stranded elements may be used in various combinations to yield an effective promoter. Thus, while some minimal number of contacts is required for promoter function, polymerase allows the elements to be mixed and matched. Interestingly, which particular elements are used does not appear to fundamentally alter the transcription bubble generated in the stable complex. In this review, we discuss the multiple steps involved in forming a transcriptionally competent polymerase/promoter complex, and we examine what is known about polymerase recognition of core promoter elements. We suggest that considering promoter elements according to their involvement in early (polymerase binding) or later (polymerase isomerization) steps in transcription initiation rather than simply from their match to conventional promoter consensus sequences is a more instructive form of promoter classification.

The promoter spacer influences transcription initiation via σ 70 region 1.1 of Escherichia coli RNA polymerase

“…1C). Our previous work demonstrated that P minor and P min belong to a newly identified promoter class, Ϫ 35/TGn, that is characterized by a requirement for both an excellent Ϫ35 element and an extended Ϫ10 TGn sequence to compensate for a poor Ϫ10 element (1,37,38). To investigate whether the effect of region 1.1 with P minor reflects a general characteristic of Ϫ35/TGn promoters, we compared the formation of active transcription complexes at P min with that at P min16 , a derivative with perfect Ϫ35 and Ϫ10 elements, and at P min7 , a derivative with a good Ϫ35 and a perfect TGn and Ϫ10 element (Fig.…”

“…1). In addition, structures of , core polymerase, and holoenzyme from thermophilic bacteria (4,(24)(25)(26)(27)(28)(29) or portions of E. coli 70 (30,31) have provided 3D scaffolds on which to model these steps.…”

“…[1][2][3][4]. This process must be flexible enough to initiate transcription at a variety of promoter sequences yet rigid enough to provide specificity.…”

The Bordetella pertussis model of exquisite gene control by the global transcription factor BvgA

“…Transcription initiation proceeds through multiple steps (Kontur et al, 2008;Saecker et al, 2002; reviewed by Hook- Barnard & Hinton, 2007), from an initial closed complex (RP C ), in which the DNA is fully double-stranded, to an open complex (RP O ), in which polymerase has isomerized and the DNA has bent, opened and descended into the active site (Gries et al, 2010). Consequently, there are multiple points at which an activator might function.…”

“…In primary s factors, which are responsible for most transcription during exponential growth, four conserved regions (regions 1-4) mediate interactions between s and the core and/or promoter specificity (reviewed by Hook- Barnard & Hinton, 2007). Regions 2, 3 and 4 bind to specific recognition sites in the promoter DNA: the 210 element ( -12 TATAAT -7 ), an extended -10 element ( -15 TG -14 ) and the 235 element ( -35 TTGACA -30 ), respectively.…”