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Nucleic Acids Research Advance Access published online on July 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm509
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon

Irina Saraiva Franco1, Luís Jaime Mota1, Cláudio Manuel Soares2 and Isabel de Sá-Nogueira1,3,*

1Laboratory of Microbial Genetics and 2Laboratory of Protein Modeling, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Apt. 127, 2781-901 Oeiras and 3Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal

*To whom correspondence should be addressed. Tel: +351 21 4469524; Fax: +351 21 4411277; Email: sanoguei{at}itqb.unl.pt

Received May 11, 2007. Revised June 7, 2007. Accepted June 12, 2007.

In the absence of arabinose, the AraR transcription factor represses the expression of genes involved in the utilization of arabinose, xylose and galactose in Bacillus subtilis. AraR exhibits a chimeric organization: the N-terminal DNA-binding region belongs to the GntR family and the C-terminal effector-binding domain is homologous to the GalR/LacI family. Here, the AraR–DNA-binding interactions were characterized in vivo and in vitro. The effect of residue substitutions in the AraR N-terminal domain and of base-pair exchanges into an AraR–DNA-binding operator site were examined by assaying for AraR-mediated regulatory activity in vivo and DNA-binding activity in vitro. The results showed that residues K4, R45 and Q61, located in or near the winged-helix DNA-binding motif, were the most critical amino acids required for AraR function. In addition, the analysis of the various mutations in an AraR palindromic operator sequence indicated that bases G9, A11 and T16 are crucial for AraR binding. Moreover, an AraR mutant M34T was isolated that partially suppressed the effect of mutations in the regulatory cis-elements. Together, these findings extend the knowledge on the nature of AraR nucleoprotein complexes and provide insight into the mechanism that underlies the mode of action of AraR and its orthologues.

Present address: Luís Jaime Mota. Imperial College London, Center for Molecular Microbiology and Infection, Armstrong Road, Flowers Building – 2nd floor, London SW7 2AZ, UK


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