FIG. 2.
Comparison of fimS transcriptional start sites (TS) from 33277 and W83 by 5′ RLM-RACE. (A) Alignments of 33277 (327) and W83 fimS sequences around the FimS N-terminal coding regions. Originally predicted amino acid-coding sequences are shown in uppercase letters, and sequences from the inserted fragment in W83 are shown in italics. Arrows indicate three gene-specific reverse primers used for 5′ RACE (Table 1). (B) Results of nested PCR of 5′ RACE. Reaction mixtures were separated on a 3.5% agarose gel. The PCR products shown in lanes 1, 2, and 3 in both panels were amplified by using reverse primers GSP1, GSP2, and GSP3, respectively. The fragments indicated by arrowheads are TS-containing PCR products with the 29-bp 5′ adapter sequence. The products by GSP3 primer from both strains (lane 3) also were extracted and sequenced to determine TSs, which are boxed in Fig. 2A (A−18 for 33277 and G35 for W83).