Structural basis for -10 promoter element melting by environmentally-induced sigma factors

Orateur : Sébastien CAMPAGNE (ETH Honggerberg, Zurich Institute of Molecular biology and Biophysics)

Bacterial transcription is controlled by sigma factors, the bacterial initiation factors. While a single housekeeping sigma factor transcribes from thousands of promoter, environmentally-induced sigma factors redirect gene expression towards small regulons to carry out focused stress responses. This unequal division of tasks requires a primary sigma factor with broad promoter specificity, while alternative sigma factor need increased promoter stringency to ensure targeted transcriptional reprogramming that triggers adaptation and survival. Within alternative sigma factors, group IV (or ECF) sigma factors represent the minimal sigma factors (two domains s2 and s4) and are the most phylogenetically diverse class. Their high stringency of promoter recognition can be explained by several reasons : (i) the sequence of the -35 box is highly constrained because the initial step of promoter dsDNA recognition is exclusively realized by domain s4 ; (ii) the length of the linker between s2 and s4 constraints the optimal spacing between the -35 and -10 promoter elements ; (iii) and, finally, the domain s2 is highly degenerated compared to primary sigma factor and does not contain the ‘key promoter melting residues’ (W dyad and Q437). ECF sigma factors are probably using an alternative way to achieve the recognition of the -10 promoter element, the most important step of bacterial transcription initiation. Using structural, biochemical and physiological analysis, the molecular basis for -10 promoter element recognition by these minimal sigma factors were determined and reveal a new mechanism of promoter melting. Group IV sigma factors induce strand separation at the -10 promoter element by recognizing the non-template strand and by flipping out a single nucleotide from the ssDNA base stack. Unambiguous selection of this critical base is only driven by a dynamic loop that can be substitute to modify the specificity of promoter recognition. This alternative promoter melting mechanism explains the high diversity of promoter motifs associated with ECF sigma factors, their rapid evolution and their high stringency of promoter recognition needed to reprogram gene expression efficiently.

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