BMC Genomics 2006, 7:21 http://www.biomedcentral.com/1471-2164/7/21 FDiegtuairled4genetic maps of upstream regions of selected genes belonging to the DtxR regulon of C. glutamicum Detailed genetic maps of upstream regions of selected genes belonging to the DtxR regulon of C. glutamicum. The nucleotide sequences shown indicate the DtxR binding sites (gray boxes) and the identified transcriptional start sites that were mapped with the RACE method (+1). Bold-faced nucleotides display deduced -35 and -10 hexamer sequences of corynebacterial pro- moter regions. Potential ribosome-binding sites (RBS) in front of the coding regions are underlined; the ATG start codon is double underlined. The cg0527, cg2782 and cg3327 genes are expressed by leaderless transcripts. Previously identified RipA binding sites in front of the cg0445 genes are marked [23]. orthologous genes that are most likely under transcrip- tional regulation by DtxR in three corynebacterial species includes the orthologs of the cg0466 gene cluster (Figure 5) that encode components of an iron ABC transport sys- tem in C. glutamicum, C. diphtheriae and C. jeikeium and the orthologs of the cg0926 gene cluster that are appar- ently involved in iron uptake in C. glutamicum, C. efficiens and C. jeikeium. Orthologs of the sdh gene cluster and the ftn gene, whose expression decreased in the dtxR mutant C. glutamicum IB2103, are apparently under direct tran- scriptional control by DtxR in C. efficiens and C. diphthe- riae, indicating that the DtxR regulator might be involved in the activation of gene expression also in these species. Regulatory genes orthologous with cg0527 of C. glutami- cum are present in the genomes of C. efficiens and C. diph- theriae [7] and all are presumably regulated by DtxR, suggesting similar hierarchical topologies of the respective DtxR regulons. However, most of the identified genes that are under transcriptional control by DtxR are species-spe- cific, although one has to keep in mind that some non- orthologous genes might share similar physiological func- tions. This comparative content analysis led to the conclu- sion that the DtxR regulons of corynebacteria are quite different in their genetic composition, although they rely on an orthologous regulatory protein and similar 19-bp motifs for regulator binding. Nevertheless, some interest- ing regulatory features deduced from the experimental characterization of the DtxR regulon of C. glutamicum are apparently realized also in the topology of DtxR regulons of other corynebacteria. Discussion In the present study, the genetic network of the transcrip- tional regulator DtxR was examined in C. glutamicum, and the topology of the DtxR regulon was deduced from DNA microarray hybridizations, bioinformatics approaches, in vivo studies of differential gene expression, and DNA band shift assays. For these purposes, a defined deletion was Page 10 of 19 (page number not for citation purposes)