A Carboxyl-terminal Extension of the Zinc Finger Domain Contributes to the Specificity and Polarity of Peroxisome Proliferator-activated Receptor DNA Binding

Mei-Hui Hsu,Colin N.A Palmer,Wu Song,Keith J Griffin,Eric F Johnson

doi:10.1074/jbc.273.43.27988

Mei-Hui Hsu, Colin N.A Palmer + Show 3 more

Open Access

https://doi.org/10.1074/jbc.273.43.27988

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Abstract

Heterodimers of the peroxisome proliferator-activated receptors (PPAR) and the retinoid X receptors (RXR) recognize response elements (PPREs) that exhibit the consensus sequence 5'-A(A/T)CT(A/G)GGNCAAAG(G/T)TCA-3'. The consensus PPRE includes both a 5'-extension and a direct repeat (DR1) comprised of two canonical core recognition sequences (underlined) for nuclear receptor zinc fingers separated by a single nucleotide spacer. The extended binding site recognized by PPARs is very similar to sites that bind monomers of the nuclear receptors Rev-ErbA and ROR suggesting that the latter could bind to PPREs and affect gene transcription. However, Rev-ErbA and ROR bind weakly to naturally occurring PPREs relative to the consensus binding site, and significant effects on PPARalpha transactivation of a CYP4A6-Z reporter were not observed. In contrast, PPAR/RXR heterodimers bind to a DR2 element containing the conserved 5'-extended sequence that is recognized by dimers of RORalpha or Rev-ErbA. PPARalpha/RXRalpha positively regulate transcription from this element, and co-expression of Rev-ErbA blocks this effect. The nuclear receptors NGFI-B and ROR utilize a carboxyl-terminal extension (CTE) of the zinc finger DNA binding domain in their interactions with the 5'-extension of a single zinc finger-binding site. DNA binding domains (DBD) of PPARs alpha, delta, and gamma that contain the zinc finger motif and a CTE display binding to core recognition sequences that is dependent on the 5'-extended sequence found in PPREs. Unlike DBDs of other nuclear receptors that form heterodimers with RXR, the PPAR-DBDs did not exhibit cooperative binding with the DBD of RXR and exhibit the opposite polarity for binding to the direct repeat motif. In contrast to the corresponding DBD of RXR, the PPAR-DBDs bind as monomers to a single extended binding site as well as to the consensus PPRE. A chimera linking the zinc finger domain of RXRalpha to the CTE from PPARalpha bound to a single extended binding site indicating a functional role for the CTE of PPARs in extended binding site recognition.

Highlights

The peroxisome proliferator activated receptor ␣ (PPAR␣)1 mediates the transcriptional regulation of several genes encoding enzymes involved in lipid metabolism in response to peroxisome proliferators and fatty acids
The striking similarity between the 5Ј-extended site recognized by peroxisome proliferator-activated receptors (PPAR) and the binding sites for monomers of the orphan nuclear receptors Rev-ErbA and ROR (Table I) suggested that receptors such as ROR␣ and Rev-ErbA might bind to natural PPAR␣ binds to response elements (PPREs) leading to cross-talk and/or competitive inhibition of signal transduction
The PPAR-DNA binding domain (DBD) binds as a monomer to the 5Ј core recognition site of the PPRE, and this binding is dependent on a conserved upstream sequence

Summary

EXPERIMENTAL PROCEDURES

Expression of Receptor DNA Binding Domains in Escherichia coli— PCR was utilized to generate truncated receptor cDNAs. The segment encoding amino acids 88 –210 of PPAR (PPAR-DBD-L) was amplified using primers PPARDBDU, cgtggatcccat atg Gct AGC ACG GAC GAG TCC CCC, and PPARDBDL, gggggatcc tca GAT TCT CTT GCC CAG AGA TTT GAG. The segment encoding amino acids 88 –195, PPAR-DBD, was generated as described above using a different lower primer, PPARDBDL3, gggggatcc tca CAG GTC GTG TTC ACA GGT AAG. The segment encoding the RXR-DBD (amino acids 127–235) was generated using RXRDBDU, cgtggatcccat ATG GCT TCC TTC ACC AAG CAC; and RXRDBDL, gggggatcc tca CTT GGG CTC CAC GGC CAG CTC. Lysates of cultures of E. coli XL-1 Blue cells (Stratagene, La Jolla, CA) expressing the individual DNA binding domains were prepared as described previously [12]. The luciferase activity obtained for individual cultures was expressed relative to the ␤-galactosidase activity obtained for the same preparation of lysate

TATCA AGGTCA

RESULTS

DISCUSSION