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Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor.

Kim JN, Jeong Y, Yoo JS, Roe JH, Cho BK, Kim BG - BMC Genomics (2015)

Bottom Line: Using the regulatory motifs, NdgR regulates cysteine biosynthesis in response to thiol oxidative stress, enabling cells to maintain sulfur assimilation with homeostasis under stress conditions.Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain amino acids biosynthesis and sulphur assimilation.The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing amino acid biosynthesis in the context of stress responses in S. coelicolor.

View Article: PubMed Central - PubMed

Affiliation: School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Korea. realkjw1@snu.ac.kr.

ABSTRACT

Background: NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. 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 amino acid and cysteine biosynthesis pathways were involved in the NdgR regulon. We proved that ndgR is induced by SigR under the thiol oxidation, and that an ndgR mutant strain is sensitive to the thiol oxidizing agent, diamide. Through the expression test of NdgR and the target genes for NdgR under diamide 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 diamide treatment. Using the regulatory motifs, NdgR regulates cysteine biosynthesis in response to thiol oxidative stress, enabling cells to maintain sulfur assimilation with homeostasis under stress conditions.

Conclusions: Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain amino acids biosynthesis and sulphur assimilation. The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing amino acid biosynthesis in the context of stress responses in S. coelicolor.

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Metabolic pathways directly regulated by NdgR. The proteins identified by ChIP-seq are depicted by red characters. (A) NdgR directly regulates genes in most steps of the BCAA biosynthesis pathways. Though LeuA was not annotated as a member of NdgR regulon, the putative motif from genome-wide prediction using FIMO and low binding signal in ChIP-seq data was observed in its upstream region. (B) The sulfur assimilation into the cysteine biosynthesis pathways.
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Fig3: Metabolic pathways directly regulated by NdgR. The proteins identified by ChIP-seq are depicted by red characters. (A) NdgR directly regulates genes in most steps of the BCAA biosynthesis pathways. Though LeuA was not annotated as a member of NdgR regulon, the putative motif from genome-wide prediction using FIMO and low binding signal in ChIP-seq data was observed in its upstream region. (B) The sulfur assimilation into the cysteine biosynthesis pathways.

Mentions: NdgR directly regulates eight genes in the biosynthetic pathways of branched chain amino acids (BCAAs) (Figure 3A). For instance, the first step in BCAA biosynthesis is catalyzed by acetohydroxy acid synthase/acetolactate synthase encoded by ilvBN. This enzyme catalyzes the condensation of two pyruvate molecules to acetolactate and 2-acetohydroxybutyrate from pyruvate and 2-ketobutyrate. The following reaction is catalyzed by ketol-acid reductoisomerase and dihydroxy-acid dehydratase encoded by ilvC and ilvD, respectively. The final transamination step, as well as the first step in the degradation pathways, is catalyzed by BCAA aminotransferases encoded by ilvE. Leucine is synthesized from α-ketoisovalerate, an intermediate in the valine pathway, through three enzymatic steps. The relevant enzymes are α-isopropylmalate synthase (LeuA), β-isopropylmalate dehydratase (LeuC, LeuD), and β-isopropylmalate dehydrogenase (LeuB). Despite the scattered locations of those genes along the chromosome, NdgR directly bound their upstream regions. Interestingly, the NdgR mutant (BG11) exhibited methionine auxotrophy, but not leucine auxotrophy [16]. Notwithstanding its direct binding at the promoters of genes in the BCAA biosynthetic pathway, NdgR was not essential for BCAA biosynthesis under the growth conditions used here. Thus, it is expected that NdgR plays a role in the fine-tuning of BCAA biosynthesis with the assistance of feedback regulation and translational attenuation common in amino acid biosynthetic pathways in bacteria [25-27].Figure 3


Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor.

Kim JN, Jeong Y, Yoo JS, Roe JH, Cho BK, Kim BG - BMC Genomics (2015)

Metabolic pathways directly regulated by NdgR. The proteins identified by ChIP-seq are depicted by red characters. (A) NdgR directly regulates genes in most steps of the BCAA biosynthesis pathways. Though LeuA was not annotated as a member of NdgR regulon, the putative motif from genome-wide prediction using FIMO and low binding signal in ChIP-seq data was observed in its upstream region. (B) The sulfur assimilation into the cysteine biosynthesis pathways.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340878&req=5

Fig3: Metabolic pathways directly regulated by NdgR. The proteins identified by ChIP-seq are depicted by red characters. (A) NdgR directly regulates genes in most steps of the BCAA biosynthesis pathways. Though LeuA was not annotated as a member of NdgR regulon, the putative motif from genome-wide prediction using FIMO and low binding signal in ChIP-seq data was observed in its upstream region. (B) The sulfur assimilation into the cysteine biosynthesis pathways.
Mentions: NdgR directly regulates eight genes in the biosynthetic pathways of branched chain amino acids (BCAAs) (Figure 3A). For instance, the first step in BCAA biosynthesis is catalyzed by acetohydroxy acid synthase/acetolactate synthase encoded by ilvBN. This enzyme catalyzes the condensation of two pyruvate molecules to acetolactate and 2-acetohydroxybutyrate from pyruvate and 2-ketobutyrate. The following reaction is catalyzed by ketol-acid reductoisomerase and dihydroxy-acid dehydratase encoded by ilvC and ilvD, respectively. The final transamination step, as well as the first step in the degradation pathways, is catalyzed by BCAA aminotransferases encoded by ilvE. Leucine is synthesized from α-ketoisovalerate, an intermediate in the valine pathway, through three enzymatic steps. The relevant enzymes are α-isopropylmalate synthase (LeuA), β-isopropylmalate dehydratase (LeuC, LeuD), and β-isopropylmalate dehydrogenase (LeuB). Despite the scattered locations of those genes along the chromosome, NdgR directly bound their upstream regions. Interestingly, the NdgR mutant (BG11) exhibited methionine auxotrophy, but not leucine auxotrophy [16]. Notwithstanding its direct binding at the promoters of genes in the BCAA biosynthetic pathway, NdgR was not essential for BCAA biosynthesis under the growth conditions used here. Thus, it is expected that NdgR plays a role in the fine-tuning of BCAA biosynthesis with the assistance of feedback regulation and translational attenuation common in amino acid biosynthetic pathways in bacteria [25-27].Figure 3

Bottom Line: Using the regulatory motifs, NdgR regulates cysteine biosynthesis in response to thiol oxidative stress, enabling cells to maintain sulfur assimilation with homeostasis under stress conditions.Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain amino acids biosynthesis and sulphur assimilation.The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing amino acid biosynthesis in the context of stress responses in S. coelicolor.

View Article: PubMed Central - PubMed

Affiliation: School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Korea. realkjw1@snu.ac.kr.

ABSTRACT

Background: NdgR is an IclR-type transcription factor that regulates leucine biosynthesis and other metabolic pathways in Streptomyces coelicolor. 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 amino acid and cysteine biosynthesis pathways were involved in the NdgR regulon. We proved that ndgR is induced by SigR under the thiol oxidation, and that an ndgR mutant strain is sensitive to the thiol oxidizing agent, diamide. Through the expression test of NdgR and the target genes for NdgR under diamide 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 diamide treatment. Using the regulatory motifs, NdgR regulates cysteine biosynthesis in response to thiol oxidative stress, enabling cells to maintain sulfur assimilation with homeostasis under stress conditions.

Conclusions: Our analysis revealed that NdgR is a global transcriptional regulator involved in the regulation of branched-chain amino acids biosynthesis and sulphur assimilation. The identification of the NdgR regulon broadens our knowledge regarding complex regulatory networks governing amino acid biosynthesis in the context of stress responses in S. coelicolor.

Show MeSH
Related in: MedlinePlus