title: Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus.
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.
authors: Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan, iwan_naok@yahoo.co.jp.
authors: Naoki
authors: N
authors: Iwanaga
authors: Kaori
authors: K
authors: Ide
authors: Takeshi
authors: T
authors: Nagashima
authors: Takeo
authors: T
authors: Tomita
authors: Yoshihiro
authors: Y
authors: Agari
authors: Akeo
authors: A
authors: Shinkai
authors: Seiki
authors: S
authors: Kuramitsu
authors: Mariko
authors: M
authors: Okada-Hatakeyema
authors: Tomohisa
authors: T
authors: Kuzuyama
authors: Makoto
authors: M
authors: Nishiyama
mesh_terms: D001120:Arginine / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008239:Lysine / Q000096:biosynthesis; D008969:Molecular Sequence Data; D009876:Operon; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D016963:Thermus thermophilus / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: C087018:ArgR protein, Bacteria; D001426:Bacterial Proteins; D012097:Repressor Proteins; D001120:Arginine; D008239:Lysine