FIG. 1.
Promoters used in the present study. (A) Diagrammatic representation of loci used in the present study. (B) Mapping of the promoters under study. The two panels show primer extension of PexbB promoter (primer Ton-2, 5′-CTCCTTGTCTATGATAAAAC) and S1 mapping of the PnikR promoter. In both cases, the radioactively labeled primer or DNA probe was hybridized to 15 μg of total RNA extracted from logarithmically grown H. pylori G27 and either reverse transcribed (primer extension) or digested with S1 nuclease (S1 mapping), and the elongated products or RNA-protected bands are separated on an 8 M urea-polyacrylamide gel (lanes G27). For correct mapping of the elongated primer products, a sequencing reaction on the cloned promoter region, with the same primer as for the extension, was run in parallel on the gel (lanes G, A, T, and C). Instead, for correct mapping of the RNA-protected S1 products a G+A sequence reaction (19) on the radioactively labeled DNA probe was run in parallel on the gel (lane G+A). Bands representing the initiation of transcription of each promoter are highlighted with arrows and labeled accordingly. (C) Nucleotide sequences of the promoters mapped in the present study PexbB, and PnikR (Fig. 1B) and previous studies PureA (26) and Pfur (11). Alignment of the promoter sequences with respect to their transcriptional start sites (+1, in boldface) is shown. Putative −10 and −35 hexamers are highlighted in boldface, and the conservation with the E. coli σ70 consensus is underlined.