Genome-scale analysis reveals a role for NdgR in the XXXX oxidative stress response in @entity25068 .

@entity3534 @entity13131 @entity462 @entity368 @entity1432 @entity25068 @entity599 @entity3689
BACKGROUND: NdgR is an IclR-type transcription factor that regulates @entity368 biosynthesis and other metabolic pathways in @entity25068 . Recent study revealed that NdgR is one of the regulatory targets of SigR, an oxidative stress response sigma factor, suggesting that the NdgR plays an important physiological role in response to environmental stresses. Although the regulatory functions of NdgR were partly characterized, determination of its regulon is required for better understanding of the transcriptional regulatory network related with the oxidative stress response. RESULTS: We determined genome-wide binding loci of NdgR by using chromatin immunoprecipitation coupled with sequencing (ChIP-seq) and explored its physiological roles. The ChIP-seq profiles revealed 19 direct binding loci with a 15-bp imperfect palindromic motif, including 34 genes in their transcription units. Most genes in branched-chain @entity3689 and @entity462 biosynthesis pathways were involved in the NdgR regulon. We proved that ndgR is induced by SigR under the @entity1432 oxidation, and that an ndgR mutant strain is sensitive to the @entity1432 oxidizing agent, @entity13131 . Through the expression test of NdgR and the target genes for NdgR under @entity13131 treatment, regulatory motifs were suggested. Interestingly, NdgR constitutes two regulatory motifs, coherent and incoherent feed-forward loops (FFL), in order to control its regulon under the @entity13131 treatment. Using the regulatory motifs, NdgR regulates @entity462 biosynthesis in response to @entity1432 oxidative stress, enabling cells to maintain @entity599 assimilation with homeostasis under stress conditions. CONCLUSIONS: Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain @entity3534 biosynthesis and sulphur assimilation. The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing @entity3689 biosynthesis in the context of stress responses in @entity25068 .
