Figure 2
σF-dependent genes and promoters. A. Genome organization of σF-dependent genes. For each open reading frame, the locus name and orientation on chromosome are indicated. Predicted σF-dependent promoters are shown by arrows. Organization of genes in operons was based on our transcriptome data and analyses of genomes presenting homologous of σF-dependent genes. B. Table showing the putative −35 and −10 promoter elements of genes directly regulated by σF. Promoter sequence motifs upstream from CC2907 and CC3254 were determined by 5´RACE experiments, while promoter elements of CC2748 were identified by a search for the σF-binding sequence (GTAACC-N16-CGAA) in the region encompassing nucleotides −600 to +100 relative to the predicted translation start site (+1), allowing for two substitutions. The “dna pattern” tool of RSA website (http://rsat.ulb.ac.be/rsat) was used in this search. The coordinate represents the position of the 3’end nucleotide of the putative σF-binding motif relative to the translation start site (+1). These sequences were compared to the promoter sequence located upstream of sigF, which was experimentally determined by primer extension [16]. Genes in parenthesis are proposed to be co-transcribed with the gene immediately downstream from the putative σF-binding motif.