Open complex DNA scrunching: A key to transcription start site selection and promoter escape

Abstract

Bacterial RNA polymerase-promoter open complexes can exist in a range of states in which the leading edge of the enzyme moves but the trailing edge does not, a phenomenon we refer to as "open complex scrunching." Here we describe how open complex scrunching can determine the position of the transcription start site for some promoters, modulate the level of expression, and potentially could be targeted by factors to regulate transcription. We suggest that open complex scrunching at the extraordinarily active ribosomal RNA promoters might have evolved to initiate transcription at an unusual position relative to the core promoter elements in order to maximize the rate of promoter escape.

Keywords: RNA polymerase; promoter; promoter escape; scrunching; transcription initiation; transcription start site selection.

Figure 1

Promoter elements and RNA polymerase regions responsible for recognition of each promoter element. A: Regions of core (αCTD and β) and σ⁷⁰ that make sequence-specific interactions with promoter DNA are indicated above the DNA elements with which they interact. The transcription start site (TSS) is shown as a bent arrow. αCTD (carboxyl-terminal domain of α subunit; -35 (-35 hexamer), Ext (extended -10 element), -10 (-10 hexamer), Dis (discriminator element), CRE (core recognition element). B: rrnB P1 and consensus sequence for σ⁷⁰-dependent promoters. rrnB P1 bases identical to the consensus sequence are indicated. Promoter elements are colored as in (A). W=A or T, n= any base. Spacing between -35 and extended -10 and between discriminator element and TSS are indicated by brackets. The number of bp separating elements is indicated.

Figure 2

Scrunching during transcription start site selection and initial transcription. RNAP is gray. Promoter DNA nucleotides (nt) are drawn as circles. The numbering is from wild-type rrnB P1. +1 is 9 bp downstream from the -10 hexamer. The -10 hexamer is shown as filled orange circles. Positions of two alternative transcription start sites are indicated as filled circles on the template strand, blue for the TSS 6 bp downstream from the end of the -10 element and red for the wild-type TSS 9 bp from the -10 element. The active site Mg²⁺ is shown as a filled purple circle. A: Scrunching during TSS selection. Two different forms of the open complex are shown. Top, non-scrunched complex results in a TSS 6 bp downstream from the -10 hexamer [1, 21]. Bottom, 3 nt of DNA are pulled into RNAP past the active site, resulting in a scrunched open complex and a TSS 9 bp downstream from the -10 hexamer. B: Scrunching during initial transcription. The proposed change in the DNA path during the transition from RP_O (top) at an rrnB P1 promoter variant with a TSS of +6 with respect to the end of the -10 hexamer [21], to an initial transcribing complex with a 5 nt RNA (RP_ITC5, bottom). RNA nt are shown as filled green circles. Similar structural changes occur during initial transcription and during TSS selection. In each case, interconversion between the scrunched and unscrunched forms is likely to occur.