Limits...
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.

Show MeSH

Related in: MedlinePlus

Functional classification of genes in the NdgR regulon. Hierarchical functional class is defined by The Sanger Institute database. Genes in this chart are described in Table 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Functional classification of genes in the NdgR regulon. Hierarchical functional class is defined by The Sanger Institute database. Genes in this chart are described in Table 2.

Mentions: Genes in the NdgR regulon were further classified into functional categories according to gene classifications defined by The Sanger Institute database (ftp://ftp.sanger.ac.uk/pub/S_coelicolor/classwise.txt) (Figure 2). The metabolism of small molecule category is highly dominant (62%, 21/34 genes). Among the genes in this category, 43% and 33% were assigned to amino acid biosynthesis (9/21 genes) and central intermediary metabolism (7/21 genes), respectively, and 14% (3/21 genes) were included in biosynthesis of cofactors and carriers.Figure 2


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)

Functional classification of genes in the NdgR regulon. Hierarchical functional class is defined by The Sanger Institute database. Genes in this chart are described in Table 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Functional classification of genes in the NdgR regulon. Hierarchical functional class is defined by The Sanger Institute database. Genes in this chart are described in Table 2.
Mentions: Genes in the NdgR regulon were further classified into functional categories according to gene classifications defined by The Sanger Institute database (ftp://ftp.sanger.ac.uk/pub/S_coelicolor/classwise.txt) (Figure 2). The metabolism of small molecule category is highly dominant (62%, 21/34 genes). Among the genes in this category, 43% and 33% were assigned to amino acid biosynthesis (9/21 genes) and central intermediary metabolism (7/21 genes), respectively, and 14% (3/21 genes) were included in biosynthesis of cofactors and carriers.Figure 2

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