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J. Biol. Chem., Vol. 277, Issue 15, 12507-12515, April 12, 2002
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From the Centre d'Ingénierie des Protéines,
Université de Liège, Institut de Chimie B6,
Sart-Tilman, B-4000, Liège, Belgium
Haydon and Guest (Haydon, D. J, and Guest,
J. R. (1991) FEMS Microbiol. Lett. 63, 291-295) first described the helix-turn-helix GntR family of
bacterial regulators. They presented them as transcription factors
sharing a similar N-terminal DNA-binding (D-b) domain, but
they observed near-maximal divergence in the C-terminal
effector-binding and oligomerization (E-b/O) domain. To elucidate this
C-terminal heterogeneity, structural, phylogenetic, and functional
analyses were performed on a family that now comprises about 270 members. Our comparative study first focused on the C-terminal E-b/O
domains and next on DNA-binding domains and palindromic operator
sequences, has classified the GntR members into four subfamilies
that we called FadR, HutC, MocR, and YtrA. Among these subfamilies a
degree of similarity of about 55% was observed throughout the entire sequence. Structure/function associations were highlighted although they were not absolutely stringent. The consensus sequences deduced for
the DNA-binding domain were slightly different for each subfamily, suggesting that fusion between the D-b and E-b/O domains have occurred
separately, with each subfamily having its own D-b domain ancestor.
Moreover, the compilation of the known or predicted palindromic
cis-acting elements has highlighted different operator sequences according to our subfamily subdivision. The observed C-terminal E-b/O domain heterogeneity was therefore reflected on the
DNA-binding domain and on the cis-acting elements,
suggesting the existence of a tight link between the three regions
involved in the regulating process.
Subdivision of the Helix-Turn-Helix GntR Family of Bacterial
Regulators in the FadR, HutC, MocR, and YtrA Subfamilies*
,
*
This work was supported by the "Fonds pour la Formation
à la Recherche dans l'Industrie et dans l'Agriculture" (FRIA,
Brussels, Belgium).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed. Tel.: +32-4-366-33-77;
Fax: +32-4-366-33-64; E-mail: srigali@student.ulg.ac.be.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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