title: An A-tract at the AtzR binding site assists DNA binding, inducer-dependent repositioning and transcriptional activation of the PatzDEF promoter.
abstract: The LysR-type regulator AtzR activates the Pseudomonas sp. ADP atzDEF operon in response to nitrogen limitation and cyanuric acid. Activation involves repositioning of the AtzR tetramer on the PatzDEF promoter and relaxation of an AtzR-induced DNA bend. Here we examine the in vivo and in vitro contribution of an A5 -tract present at the PatzDEF promoter region to AtzR binding and transcriptional activation. Substitution of the A-tract for the sequence ACTCA prevented PatzDEF activation and high-affinity AtzR binding, impaired AtzR contacts with the activator binding site and shifted the position of the AtzR-induced DNA bend. Analysis of a collection of mutants bearing different alterations in the A-tract sequence showed that the extent of AtzR-dependent activation does not correlate with the magnitude or orientation of the spontaneous DNA bend generated at this site. Our results support the notion that indirect readout of the A-tract-associated narrow minor groove is essential for the AtzR-DNA complex to achieve a conformation competent for activation of the PatzDEF promoter. Conservation of this motif in several binding sites of LysR-type regulators suggests that this mechanism may be shared by other proteins in this family.
authors.affiliation: Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain; Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain.
authors.forename: Odil
authors.initials: O
authors.lastname: Porrúa
authors.forename: Aroa
authors.initials: A
authors.lastname: López-Sánchez
authors.forename: Ana I
authors.initials: AI
authors.lastname: Platero
authors.forename: Eduardo
authors.initials: E
authors.lastname: Santero
authors.forename: Victoria
authors.initials: V
authors.lastname: Shingler
authors.forename: Fernando
authors.initials: F
authors.lastname: Govantes
mesh_terms: D004252:DNA Mutational Analysis; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011549:Pseudomonas / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D015533:Transcriptional Activation
chemical_list: D004269:DNA, Bacterial; D014157:Transcription Factors