coli K-12 substrain MG1655 (Fig. 1; Rhodius et al., 2006). This sequence is this website not present in strain BEN2908 due to the integration of a pathogenicity island at this site (Chouikha et al., 2006). A signal structure proposed by Laikova to be the XylR-binding site was also found between the putative ribosome-binding site and the σ70−10 promoter sequence, suggesting, as it was proposed, that the yicJI operon is a member of the xylose regulons (Fig. 2a; Laikova et al., 2001). This motif was not found in the yicI-ORF1frz intergenic region. Finally, a motif containing

a palindromic sequence was found in the identified promoter sequence of the yicJI operon and three nucleotides upstream of the σ70−35 promoter sequence of the frz operon (Fig. 2b). This motif is correctly spaced to be a binding site for a regulator involved in the transcription of the two operons. Works are in progress in our laboratory to determine whether it represents an FrzR-binding site. The identification of a common motif in the yicJI and frz intergenic regions prompted us to test whether the two operons are cotranscribed. We previously identified a hairpin structure containing a G+C-rich region in the yicI-ORF1frz intergenic region (294 nt)

selleck screening library of strain BEN2908. This RNA secondary structure begins 13 nucleotides after the stop codon of yicI and is followed by a polyU sequence. These features indicate the presence of a rho-independent transcription terminator. We also identified Tryptophan synthase σ70−10 and σ70−35 putative promoter sequences beginning 54 and 76 nucleotides upstream of ORF1frz, respectively (EMBL accession number FM253092). To determine whether the yicJI and the frz operons are cotranscribed, RT-PCR experiments were performed with a reverse primer localized at the 5′ end of ORF1frz and a forward primer localized at the 3′ end of the yicI gene. The functionality of the ORF1frz identified promoter was also tested by RT-PCR using a reverse primer localized at the 5′ end of ORF1frz and a forward primer localized between the identified σ70−10 ORF1frz promoter

sequence and the start codon of ORF1frz. As a control, transcription of the yicI gene was tested by RT-PCR with reverse and forward primers, both localized in the yicI gene. Figure 3 indicates that some transcripts of yicI pass through the transcriptional terminator identified in the yicI-ORF1frz intergenic region and form cotranscripts with frz genes (lanes 2 and 4). The stronger amplification of ORF1frz transcripts by RT-PCR with primers localized in ORF1frz and between its promoter and start codon than with primers localized in yicI and in ORF1frz suggests that the ORF1frz promoter identified is functional (Fig. 3, lanes 4 and 6). The identification of a similar DNA motif in the yicJI and frz promoter regions and of yicJI and frz cotranscripts suggests that these two operons could be involved in the same physiological pathway.