Fig. 6

Recognition by Mtb σ^L of σ^L-promoter -10 element: experimental data. a Systematic-substitution experiments defining σ^L-dependent promoter -10-element consensus sequence. Relative transcriptional activities of derivatives of σ^L-dependent promoter P-sigL having all possible single base-pair substitutions at each position of promoter -10 element, “-12” through “-7”. Inferred consensus nucleotides are shown at the bottom, and data for inferred consensus nucleotides are hatched. Error bars, SE (N = 3). b Sequence logo for σ^L-promoter -10-element consensus sequence [generated using transcription data from (a) and enoLOGOS⁷¹ (http://biodev.hgen.pitt.edu/enologos/); input setting “energy (2)” and weight-type setting “probabilities”]. c Alanine-scanning experiments⁴¹ demonstrating functional importance of observed amino acid-base interactions in recognition of σ^L-promoter -10 element. Effects on transcription of alanine substitutions of σ^L amino acids that contact σ^L-dependent promoter -10 element, positions “-12” through “-7” (identities of contacting amino acids from Figs. 3 and 5). d, e Loss-of-contact experiments^42,43,44,45 indicating that σ^L residues His54 and Asp60 determine specificity at position “-12” and “-11”, respectively. Left: transcriptional activity with wild-type σ^L for all possible single base-pair-substitutions at indicated position (strong specificity for consensus base pair). Right: transcriptional activity of σ^L derivatives having alanine substitutions (no specificity for consensus base pair). Error bars, SE (N = 3). See Supplementary Fig. 6. Source data are provided as a Source Data file