DNA binding properties of peroxisome proliferator-activated receptor subtypes on various natural peroxisome proliferator response elements - Importance of the 5'-flanking region

The three subtypes of the peroxisome proliferator-activated receptors (PPAR alpha, beta/delta, and gamma) form heterodimers with the 9-cis-retinoic acid receptor (RXR) and bind to a common consensus response element, which consists of a direct repeat of two hexanucleotides spaced by one nucleotide (DR1), As a first step toward understanding the molecular mechanisms determining PPAR subtype specificity, we evaluated by electrophoretic mobility shift assays the binding properties of the three PPAR subtypes, in association with either RXR alpha or RXR gamma, on 16 natural PPAR response elements (PPREs). The main results are as follows, (i) PPAR gamma in combination with either RXR alpha or RXR gamma binds more strongly than PPAR alpha or PPAR beta to all natural PPREs tested. (ii) The binding of PPAR to sarong elements is reinforced if the heterodimerization partner is RXR gamma. In contrast, weak elements favor RXR alpha as heterodimerization partner, (iii) The ordering of the 16 natural PPREs from strong to weak elements does not depend on the core DR1 sequence, which has a relatively uniform degree of conservation, but correlates with the number of identities of the 5'-flanking nucleotides with respect to a consensus element, This 5'-flanking sequence is essential for PPAR alpha binding and thus contributes to subtype specificity, As a demonstration of this, the PPAR gamma-specific element ARE6 PPRE is able to bind PPAR alpha only if its 5'-flanking region is exchanged with that of the more promiscuous HMG PPRE.