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NdgR, an IclR-like regulator involved in amino-acid-dependent growth, quorum sensing, and antibiotic production in Streptomyces coelicolor

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Abstract

NdgR (regulator for nitrogen source-dependent growth and antibiotic production), an IclR-like regulator, has been initially identified as a binding protein to the promoters of doxorubicin biosynthetic genes in Streptomcyes peucetius by DNA affinity capture assay method. NdgR is well conserved throughout the Streptomcyes species and many other bacteria such as Mycobacteria and Corynebacteria. In Streptomcyes coelicolor, ndgR deletion mutant showed slow cell growth and defects in differentiation and enhances the production of actinorhodin (ACT) in minimal media containing certain amino acids where wild-type strain could not produce ACT. Although deletion mutant of ndgR showed different antibiotic production in minimal media containing Leu or Gln, it only showed reduced mRNA expression levels of the genes involved in leucine metabolism. Neither NdgR-dependent expression of glnA nor direct binding of NdgR protein to glnA, glnII, and glnR promoters was observed. However, ScbR, which is governed by NdgR shown by gel mobility shift assay, binds to promoter of glnR, suggesting indirect regulation of glutamine metabolism by NdgR. NdgR protein binds to intergenic region of ndgR–leuC, and scbR–scbA involved in γ-butyrolactone. Two-dimensional gel analysis has shown a global effect of ndgR deletion in protein expression, including up-regulated proteins involved in ACT synthesis and down-regulation of chaperones such as GroEL, GroES, and DnaK. These results suggest a global regulatory role for NdgR in amino acid metabolisms, quorum sensing, morphological changes, antibiotic production, and expression of chaperonines in S. coelicolor.

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Acknowledgments

The authors thank John Innes Center for providing the cosmid library and wish to acknowledge the Engineering Research Institute, Seoul National University. This work was partially supported by a grant funded by the Korea government (MOST; No. R0A-2007-000-10007-0) and a grant (Code # KRF-2005-005-J16002) from Korea Research Foundation, Republic of Korea.

Author information

Correspondence to Byung-Gee Kim.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supple. Fig. 1

Multiple alignment of NdgR homologues in various species (DOC 286 kb)

Supplementary Table 1

Strains, plasmids, and primers (DOC 105 kb)

Supplementary Table 2

The results of DNA affinity capture assay with various promoters from S. peucetius (DOC 31 kb)

Supplementary Table 3

NdgR regulators in various species (DOC 41 kb)

Supplementary Table 4

Sequences of newly shown NdgR homologues (DOC 27 kb)

Supplementary Table 5

Identified proteins by 2-D gel analysis (DOC 106 kb)

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Yang, Y., Song, E., Kim, E. et al. NdgR, an IclR-like regulator involved in amino-acid-dependent growth, quorum sensing, and antibiotic production in Streptomyces coelicolor . Appl Microbiol Biotechnol 82, 501–511 (2009). https://doi.org/10.1007/s00253-008-1802-x

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Keywords

  • Streptomyces coelicolor
  • Streptomyces peucetius
  • IclR-like regulator
  • DNA affinity capture assay
  • scbR