FIG. 6.

Repeat sequences in putative promoter regions of the Rtp genome. (A) Alignment of upstream regions of Rtp genes containing the repeat sequence TAGCA-(N)₅-TGCTA with one mismatch allowed. This 15-nt repeat sequence presents an inverted repeat with a 5-nt spacer. The inverted repeat (matching bases in uppercase letters) is followed downstream by a 22-nt spacer region and a hexamer that conforms to the −10 consensus sequence of E. coli σ⁷⁰-dependent promoters (consensus-matching bases in uppercase letters). Additional sequences flanking these elements are also shown. The bases that occupy the positions of a canonical −35 hexamer 17 nt upstream of the aligned −10 regions are underlined. These bases do not resemble −35 sequences of σ⁷⁰ promoters, even if a shift of 1 nt to the right or left is considered (16- or 18-nt promoter spacer). The consensus sequence of E. coli σ⁷⁰-dependent promoters is shown below the alignment, highly conserved bases are in uppercase, and less conserved bases are in lowercase (35a, 44, 50a); asterisks below the sequence alignment mark further conserved nucleotide positions that are not discussed. (B) Positions of the putative transcriptional regulatory regions. The listed coordinates on the Rtp genome start at the left end of the hyphenated TAGCA inverted repeats and end with the last nucleotide of the predicted −10 elements shown in panel A. The upstream region of gene rtp75 contains two copies of the motif; both are located much farther away from the start codon than in the other genes.