BMC Genomics 2006, 7:21 http://www.biomedcentral.com/1471-2164/7/21 gFRliaugtiauomr/ieinctu2emnsIiBty21(m03/aw)ipthlothdaetdoufctehdefwroilmd-tDypNeAstmraicinroCa.rgrlauytahmyibcruimdizAatTioCnCs c1o3m03p2aring the transcriptome of the dtxR mutant C. Ratio/intensity (m/a) plot deduced from DNA microarray hybridizations comparing the transcriptome of the dtxR mutant C. glutamicum IB2103 with that of the wild-type strain C. glutamicum ATCC 13032. The analyzed strains were cultivated in low- iron CGXII medium to mid-exponential growth phase. Then, 10 mg/l FeSO4 was added to the medium, and the cultures were incubated for further 15 min. Subsequently, total RNA was isolated from two biological replicates and used for DNA microar- ray hybridizations including label swapping. Genes showing enhanced expression in the dtxR mutant C. glutamicum IB2103 are marked by black diamonds; genes with decreased expression are indicated by black triangles; genes without differential expres- sion pattern are shown by gray spots. Differentially expressed genes later on assigned to the DtxR regulon of C. glutamicum are named by their identifiers. Genes were regarded as being differentially expressed with a-values equal or greater than 7.0 and m-values equal or greater than 1 (up-regulation) or equal or smaller than -1 (down-regulation). is supplied with the synthetic culture medium. This dis- tinct phenotype of C. glutamicum IB2103 was suited to perform comparative transcriptomic studies with the wild-type strain to identify genes that belong to the tran- scriptional regulatory network of DtxR. Genome-wide transcriptional profiling of the dtxR mutant C. glutamicum IB2103 in comparison to the wild-type strain ATCC 13032 by DNA microarray hybridization To identify genes that are differentially expressed in the transcriptome of C. glutamicum IB2103, the global gene expression pattern of the dtxR mutant was compared with that of the wild-type strain by DNA microarray hybridiza- tion. Since C. glutamicum IB2103 was unable to grow in CGXII minimal medium (Figure 1), both strains were cul- tivated in shaking flasks to mid-exponential growth phase by using low-iron CGXII medium. The cultures revealed a very similar growth behavior that was characterized by almost identical doubling times of the dtxR mutant (4.8 ± 0.41 h) and the wild-type (4.4 ± 0.18 h), indicating that differences in growth of both strains were apparently min- imized under the selected cultivation conditions. At the time when the C. glutamicum strains were grown to an optical density of four (OD600 nm), 10 mg/l FeSO4 was added to the growth medium, and the cultures were culti- vated for further 15 min before harvesting cells and pre- paring total RNA. Addition of iron to the wild-type culture should result in a "switch-off" of expression of those genes that are part of the DtxR regulon, whereas the respective genes should be further on expressed in the dtxR mutant Page 4 of 19 (page number not for citation purposes)