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Nucleic Acids Research, 2003, Vol. 31, No. 22 6598-6609
© 2003 Oxford University Press

Article

Molecular determinants of the hpa regulatory system of Escherichia coli: the HpaR repressor

Beatriz Galán, Annie Kolb1, Jesús M. Sanz2, José Luis García and María A. Prieto*

Department of Molecular Microbiology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, 1 Laboratoire des Régulations Transcriptionnelles, Institut Pasteur, Paris, France and 2 Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain

*To whom correspondence should be addressed. Tel: +34 91 8373112; Fax: +34 91 5360432; Email: auxi{at}cib.csic.es

The HpaR-mediated regulation of the hpa-meta operon (Pg promoter) of the 4-hydroxyphenylacetic acid catabolic pathway of Escherichia coli has been studied. The HpaR regulator was purified to homogeneity showing that it is able to bind selectively to 4-hydroxyphenylacetic, 3-hydroxyphenylacetic and 3,4-dihydroxyphenylacetic acids, which act as inducers of the system. The role of HpaR as a repressor and the requirement for cAMP receptor protein for maximal activity have been confirmed by in vitro transcription analyses. Two DNA operators, OPR1 and OPR2, have been identified in the intergenic region located between the hpa-meta operon and the hpaR gene. The OPR1 operator contains a perfect palindromic sequence overlapping the transcriptional +1 start site of the Pg promoter. The OPR2 operator shows a similar but imperfect palindromic sequence and is located far downstream of the +1 start site of the Pr promoter. The binding of HpaR to OPR2 displays a clear cooperativity with OPR1 binding. Based on the above observations and the results of permanganate footprinting experiments, a repression mechanism for HpaR is postulated. A 3-dimensional model of HpaR, generated by comparison with the crystal structures of the homologous regulators, MarR and MexR, suggests that HpaR is a dimer that contains a typical winged-helix DNA binding motif in each subunit.


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