| Summary: | <p>Abstract</p> <p>Background</p> <p>The knowledge about complete bacterial genome sequences opens the way to reconstruct the qualitative topology and global connectivity of transcriptional regulatory networks. Since iron is essential for a variety of cellular processes but also poses problems in biological systems due to its high toxicity, bacteria have evolved complex transcriptional regulatory networks to achieve an effective iron homeostasis. Here, we apply a combination of transcriptomics, bioinformatics, <it>in vitro </it>assays, and comparative genomics to decipher the regulatory network of the iron-dependent transcriptional regulator DtxR of <it>Corynebacterium glutamicum</it>.</p> <p>Results</p> <p>A deletion of the <it>dtxR </it>gene of <it>C. glutamicum </it>ATCC 13032 led to the mutant strain <it>C. glutamicum </it>IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of <it>C. glutamicum </it>were detected in the <it>dtxR </it>mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in <it>C. glutamicum </it>IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated <it>in vitro </it>by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of <it>C. efficiens</it>, <it>C. diphtheriae </it>and <it>C. jeikeium </it>identified evolutionary conserved elements of the DtxR network.</p> <p>Conclusion</p> <p>This work adds considerably to our currrent understanding of the transcriptional regulatory network of <it>C. glutamicum </it>genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of <it>C. glutamicum </it>genes.</p>
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