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Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus

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Abstract

ArgR is known to serve as a repressor/activator of the metabolism of arginine. To elucidate the role of ArgR in the metabolism of Thermus thermophilus cells, comparative genome-wide comprehensive analysis was conducted for wild-type T. thermophilus and its mutant lacking the argR gene. Transcriptome analysis and chromatin affinity precipitation coupled with high-density tiling chip (ChAP-chip) analysis identified 34 genetic loci that are directly regulated by ArgR and indicated that ArgR decreases the expression of arginine biosynthesis and also regulates several other genes involved in amino acid metabolism, including lysine biosynthetic genes, as suggested by our previous study. Among genes whose expression was regulated by ArgR, the largest effect of argR knockout was observed in a putative operon, including genes TTHA0284, TTHA0283, and TTHA0282 involved in arginine biosynthesis. The promoter of this operon, argG, was repressed approximately 21-fold by ArgR. DNase I footprint analysis coupled with electrophoretic mobility shift assay suggested that high arginine-dependent repression was attributed to the fact that the promoter contains three operators for ArgR binding and ArgR is bound to the binding sites cooperatively, possibly forming a DNA loop, in the hexameric form stabilized by arginine binding.

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Acknowledgments

We thank Dr. N. Ogasawara and Dr. S. Ishikawa (Nara Institute of Science and Technology) for their useful advice on ChAP-chip analysis. This work was supported by a Grant-in-aid for scientific research from the Ministry of Education, Culture, Sports, Science and Technology Japan, from Nagase Science and Technology Foundation, from the Asahi Glass Foundation, from the Charitable Trust Araki Medical and Biochemistry Memorial Research Promotion Fund, and from Noda Institute for Scientific Research.

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Authors and Affiliations

  1. Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan

    Naoki Iwanaga, Takeo Tomita, Tomohisa Kuzuyama & Makoto Nishiyama

  2. RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Kaori Ide, Takeshi Nagashima & Mariko Okada-Hatakeyema

  3. RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan

    Yoshihiro Agari, Akeo Shinkai, Seiki Kuramitsu & Makoto Nishiyama

  4. Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan

    Seiki Kuramitsu

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  1. Naoki Iwanaga
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  2. Kaori Ide
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  3. Takeshi Nagashima
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  9. Tomohisa Kuzuyama
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  10. Makoto Nishiyama
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Correspondence to Naoki Iwanaga.

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Communicated by M. da Costa.

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Iwanaga, N., Ide, K., Nagashima, T. et al. Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus . Extremophiles 18, 995–1008 (2014). https://doi.org/10.1007/s00792-014-0669-2

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