Abstract
BackgroundTranscription initiation is in bacteria exhibited by different σ factors, most of which fall within σ70 family. This family is diverse, ranging from the housekeeping Group I (RpoDs), to Group IV (ECF) σ factors, that transcribe smaller regulons under more stringent conditions. RpoDs employ a kinetic mix-and-match mechanism, where promoter elements complement each other binding strengths in achieving sufficient transcription activity. On the other hand, it is assumed that ECF σs, which are the most distant from the housekeeping σ factors, cannot exhibit mix-and-matching. However, mix-and-matching for ECF σ factors was not quantitatively checked before, and recent results show a much larger flexibility in the promoter recognition by the members of this group.ResultsTo this end, we quantitatively investigate mix-and-matching in two canonical ECF σ family members (σE and σW), for which we use a biophysics based model of transcription initiation. For σE, we perform a separate analysis for in-vitro active and in-vitro inactive promoters, which allows us investigating how mix-and-matching depends on the external factors that may control transcription activity in the in-vitro inactive set. We show that the promoter elements of canonical ECF σs significantly complement each other strengths, where such mix-and-matching is in the in-vitro active set even stronger compared to the correlations observed for the housekeeping σs. This complementation however significantly decreases for the in-vitro inactive set, which we propose is due to mix-and-matching with regulatory sequences outside of the canonical promoter elements. In line with this proposition, we show that a conserved spacer element, which appears in the in-vitro inactive promoter set, significantly increases the promoter element complementation. While RpoD promoter elements mix-and-match to achieve sufficient total transcription activity, for σE they complement each other to achieve sufficiently strong total binding affinity, which we relate to differences in physiological responses between the two groups of σ factors.ConclusionDespite a common notion that smaller σ factor specificity leads to a larger mix-and-matching, we here obtain a larger promoter element complementation for σE compared to RpoDs. Finally, to explain this finding, we propose a simple model which relates the size of σ factor regulon with the extent of mix-and-matching, based on an assumption of a selection pressure on promoters that are near the non-specific binding boundary to remain functional.
Highlights
Transcription initiation is in bacteria exhibited by different σ factors, most of which fall within σ70 family
Despite a common notion that smaller σ factor specificity leads to a larger mix-and-matching, we here obtain a larger promoter element complementation for σE compared to RpoDs
Adding strengths of the promoter elements that interact with σ factor in ssDNA form – that is, including both ssDNA and dsDNA-interacting promoter elements – gives an estimate of the log total promoter strength, which corresponds to the promoter transcription activity under the unsaturated approximation
Summary
Transcription initiation is in bacteria exhibited by different σ factors, most of which fall within σ70 family. This family is diverse, ranging from the housekeeping Group I (RpoDs), to Group IV (ECF) σ factors, that transcribe smaller regulons under more stringent conditions. RpoDs employ a kinetic mix-and-match mechanism, where promoter elements complement each other binding strengths in achieving sufficient transcription activity. The core RNA polymerase catalyzes the reaction of phosphodiester bond formation in a growing RNA chain, which is preceded by transcription initiation exhibited through σ factor interactions with DNA promoter elements [1]. RNAP binds to double-stranded (dsDNA) promoter elements, and subsequently triggers the formation of a transcription bubble within −10 element. As a consequence, −35 and the upstream segment of −10 element (often called the extended −10 element, or −15 element), accomplish their σ factor-interactions in a doublestranded (dsDNA) form, while the downstream segment of −10 element (short −10 element) accomplishes its σ factor-interactions in a single-stranded (ssDNA) form (Fig. 1) [1]
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