Fig. S2.

E. coli σ^S factor. (A) A sequence alignment of the E. coli σ^S factor (RPOS_ECOLI, GenBank accession no. gi:1710676) with the Thermus thermophilus σ^A factor (SIGA_THET2, gi:81699349) and the E. coli σ⁷⁰ factor (RPOD_ECOLI, gi:1710680). Sequences are presented with the one-letter amino acid code; numbers at the beginning and end of each line indicate amino acid positions relative to the start of each protein sequence. Secondary structures (α helices) of the E. coli σ^S factor are indicated above the sequences, and evolutionarily conserved regions are labeled below the sequences. NCR marks the nonconserved region of the primary σ factors. (B) A comparison of the interactions of the σ2 domains of different σ factors with the RNAP core enzyme. Structures of the E. coli σ^S-TIC (Left), E. coli σ⁷⁰-RNAP holoenzyme (Ec σ⁷⁰-Holo, PDB ID code 4JKR) (Center), and the RNAP holoenzyme in the T. thermophilus initiation complex (Tth σ^A-Holo, PDB ID code 4G7H) (Right) are superimposed using the clamp helices (E. coli β′ residues 263–308; T. thermophilus β′ residues 538–583) and are shown separately in the same orientation. The σ factors are shown in surface representation; clamp helices are shown in ribbons; and the rest of the core enzymes are shown as Cα traces and are colored as in Fig. 1B. The σ^S residues D87, D135, P136, and E137 that interact with Crl are marked in red. The σ⁷⁰ factor acidic patch (residues 188–209) is modeled and shown in red. A fragment of the upstream DNA in the σ^S-TIC (NT strand, blue; T strand, orange) that interacts with the σ2 and σ3 domains is shown for reference. (C) Stereoview of the upstream fork region of the σ^S-TIC. The promoter DNA is shown as ladders (NT strand, blue; T strand, green); the NT-strand residues −11A and −7T are shown as magenta sticks.