Figure 6.

Cartoon representation of protein-protein interactions at class I and class II SoxS-dependent promoters. The N-terminal and C-terminal domains of the two α subunits, which are connected by a flexible linker, and the β, β' and σ⁷⁰ subunits of holo-RNAP are labeled and colored as are the −10 and −35 promoter hexamers; the relative position of the start site of transcription is numbered and identified by an arrow. Region 4 and the C-terminal tail of the σ⁷⁰ subunit are denoted by a pink circle lying within the σ⁷⁰ subunit and labeled “R4”. SoxS is colored red and the yellow and green circles lying on it represent the class I/II and class II positive control surfaces, respectively⁵³. The soxbox is colored bronze. The backward orientation of SoxS bound to the soxbox and the soxbox itself at canonical class I promoters is denoted by writing “SoxS” from right to left. The protein-protein interactions between the class I/II surface of SoxS and the DNA-binding (265) determinant of the α-CTD⁵⁵ are denoted by the intersection of the yellow and dark blue circles, respectively. The location of the second α-CTD is unknown and thus is denoted by a question mark. The ability of σ⁷⁰ R4 to bind to the −35 promoter element of class I promoters and the absence of effects of tri-alanine substitutions on SoxS-dependent transcription activation at these promoters (Table 1) is denoted by the intersection of σ⁷⁰ R4 (a pink circle) and the promoter hexamer (a colorless rectangle). At canonical class II promoters, the binding of SoxS to the soxbox prevents amino acid residues within σ⁷⁰ R4 from binding to the −35 region (Table 1). However, amino acid residues within the distal end of R4 and the C-terminal end of σ⁷⁰ make specific contacts with amino acids within the class I/II surface of SoxS⁵⁶. For clarity, the interaction between the class II surface of SoxS (colored green) and the amino acids σ⁷⁰ R4 with which it interacts are not positioned accurately.