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Regulation of arginine biosynthesis in the psychropiezophilic bacterium Moritella profunda: in vivo repressibility and in vitro repressor-operator contact probing
Xu, Y.; Sun, Y.; Huysveld, N.; Gigot, D.; Glansdorff, N.; Charlier, D. (2003). Regulation of arginine biosynthesis in the psychropiezophilic bacterium Moritella profunda: in vivo repressibility and in vitro repressor-operator contact probing. J. Mol. Biol. 326(2): 353-369. dx.doi.org/10.1016/S0022-2836(02)01375-X
In: Journal of Molecular Biology. Elsevier: London; New York. ISSN 0022-2836, more
Peer reviewed article  

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Keyword
    Marine
Author keywords
    Moritella profunda; psychrophiles; arginine metabolism; transcriptionregulation; protein-DNA contacts

Authors  Top 
  • Xu, Y.
  • Sun, Y.
  • Huysveld, N.
  • Gigot, D.
  • Glansdorff, N.
  • Charlier, D.

Abstract
    We report the cloning of the arginine repressor gene from the psychropiezophilic Gram-negative bacterium Moritella profunda, the purification of its product (ArgRMp), the identification of the operator in the bipolar argECBFGH(A) operon, in vivo repressibility studies, and an in vitro analysis of the repressor–operator interaction, including binding to mutant and heterologous arginine operators. The ArgRMp subunit shows about 70% amino acid sequence identity with Escherichia coli ArgR (ArgREc). Binding of purified hexameric ArgRMp to the control region of the divergent operon proved to be arginine-dependent, sequence-specific, and significantly more sensitive to heat than complex formation with ArgREc. ArgRMp binds E. coli arginine operators very efficiently, but hardly recognizes the operator from Bacillus stearothermophilus or Thermotoga maritima. ArgRMp binds to a single site overlapping the −35 element of argCP, but not argEP. Therefore, the arrangement of promoter and operator sites in the bipolar argECBFGH(A) operon of M. profunda is very different from the organization of control elements in the bipolar argECBH operon of E. coli, where both promoters overlap the common operator and are equally repressible. We demonstrate that M. profundaargCP is about 44-fold repressible, whereas argEP is fully constitutive. A high-resolution contact map of the ArgRMp–operator interaction was established by enzymatic and chemical footprinting, missing contact and base-specific premodification binding interference studies. The results indicate that the argC operator consists of two ARG box-like sequences (18 bp imperfect palindromes) separated by 3 bp. ArgRMp binds to one face of the DNA helix and establishes contacts with two major groove segments and the intervening minor groove of each ARG box, whereas the minor groove segment facing the repressor at the center of the operator remains largely uncontacted. This pattern is reminiscent of complex formation with the repressors of E. coli and B. stearothermophilus, and suggests that each ARG box is contacted by two ArgR subunits belonging to opposite trimers. Moreover, the premodification interference patterns and mutant studies clearly indicate that the inner, center proximal halves of each ARG box in the M. profundaargC operator are more important for complex formation and repression than the outermost halves. A close inspection of sequence conservation and of single base-pair Oc-type mutations indicate that the same conclusion can be generalized to E. coli operators.

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