DNA-binding Domain Of Vitamin D Receptor Research Articles

Relationship of structure and function of DNA-binding domain in vitamin D receptor.

While the structure of the DNA-binding domain (DBD) of the vitamin D receptor (VDR) has been determined in great detail, the roles of its domains and how to bind the motif of its target genes are still under debate. The VDR DBD consists of two zinc finger modules and a C-terminal extension (CTE), at the end of the C-terminal of each structure presenting α-helix. For the first zinc finger structure, N37 and S-box take part in forming a dimer with 9-cis retinoid X receptor (RXR), while V26, R50, P-box and S-box participate in binding with VDR response elements (VDRE). For the second zinc finger structure, P61, F62 and H75 are essential in the structure of the VDR homodimer with the residues N37, E92 and F93 of the downstream of partner VDR, which form the inter-DBD interface. T-box of the CTE, especially the F93 and I94, plays a critical role in heterodimerization and heterodimers–VDRE binding. Six essential residues (R102, K103, M106, I107, K109, and R110) of the CTE α-helix of VDR construct one interaction face, which packs against the DBD core of the adjacent symmetry mate. In 1,25(OH)2D3-activated signaling, the VDR-RXR heterodimer may bind to DR3-type VDRE and ER9-type VDREs of its target gene directly resulting in transactivation and also bind to DR3-liked nVDRE of its target gene directly resulting in transrepression. Except for this, 1α,25(OH)2D3 ligand VDR-RXR may bind to 1αnVDRE indirectly through VDIR, resulting in transrepression of the target gene. Upon binding of 1α,25(OH)2D3, VDR can transactivate and transrepress its target genes depending on the DNA motif that DBD binds.

Hereditary 1,25-dihydroxyvitamin D-resistant rickets with alopecia resulting from a novel missense mutation in the DNA-binding domain of the vitamin D receptor

The rare genetic recessive disease, hereditary vitamin D resistant rickets (HVDRR), is caused by mutations in the vitamin D receptor (VDR) that result in resistance to the active hormone 1,25-dihydroxyvitamin D(3) (1,25(OH)(2)D(3) or calcitriol). In this study, we examined the VDR from a young boy with clinical features of HVDRR including severe rickets, hypocalcemia, hypophosphatemia and partial alopecia. The pattern of alopecia was very unusual with areas of total baldness, adjacent to normal hair and regions of scant hair. The child failed to improve on oral calcium and vitamin D therapy but his abnormal chemistries and his bone X-rays normalized with intravenous calcium therapy. We found that the child was homozygous for a unique missense mutation in the VDR gene that converted valine to methionine at amino acid 26 (V26M) in the VDR DNA-binding domain (DBD). The mutant VDR was studied in the patient's cultured skin fibroblasts and found to exhibit normal [(3)H]1,25(OH)(2)D(3) binding and protein expression. However, the fibroblasts were unresponsive to treatment with high concentrations of 1,25(OH)(2)D(3) as demonstrated by their failure to induce CYP24A1 gene expression, a marker of 1,25(OH)(2)D(3) responsiveness. We recreated the V26M mutation in the WT VDR and showed that in transfected COS-7 cells the mutation abolished 1,25(OH)(2)D(3)-mediated transactivation. The mutant VDR exhibited normal ligand-induced binding to RXRalpha and to the coactivator DRIP205. However, the V26M mutation inhibited VDR binding to a consensus vitamin D response element (VDRE). In summary, we have identified a novel V26M mutation in the VDR DBD as the molecular defect in a patient with HVDRR and an unusual pattern of alopecia.

Oncogenic nucleoporin CAN/Nup214 interacts with vitamin D receptor and modulates its function

Vitamin D receptor (VDR) is a ligand-dependent transcription factor and should be located in nucleus to transactivate target genes. To explore the molecules that interact with VDR and facilitate its nuclear localization, we screened a human kidney cDNA library using the yeast two-hybrid approach, and found that VDR binds to the carboxy-terminal region of an oncogenic nucleoporin, CAN/Nup214. CAN/Nup214 was originally identified through its involvement in a certain type of acute myeloid leukemia, and is a component of nuclear pore complex (NPC). Co-immunoprecipitation experiments confirmed the interaction between VDR and the carboxy-terminus of CAN/Nup214 containing a cluster of the phenylalanine-glycine (FG) repeat in mammalian cells. The exogenously expressed full-length CAN/Nup214 was localized predominantly at the nuclear envelope, suggesting its integration in the NPCs. We then examined the effects of exogenous expression of full-length CAN/Nup214 and its carboxy-terminal fragment on the VDR-mediated transactivation. The overexpression of full-length CAN/Nup214 facilitated the VDR-mediated transactivation, while the expression of the carboxy-terminal fragment suppressed it. The DNA-binding domain of VDR was required for the facilitation of the VDR-dependent transactivation by CAN/Nup214. Although the subcellular distribution of VDR was not obviously altered by the overexpression of full-length CAN/Nup214 or the carboxy-terminal fragment, the expression of the carboxy-terminal fragment inhibited the interaction between full-length CAN/Nup214 and VDR. These results indicate that CAN/Nup214 interacts with VDR and modulates its function as a transcription factor.

Evidence for 1,25-Dihydroxyvitamin D3-independent Transactivation by the Vitamin D Receptor: UNCOUPLING THE RECEPTOR AND LIGAND IN KERATINOCYTES

The vitamin D endocrine system plays critical although poorly understood roles in skin. Vitamin D receptor (VDR) knock-out (VDRKO) mice have defects in hair follicle cycling and keratinocyte proliferation leading to epidermal thickening, dermal cyst formation, and alopecia. Surprisingly, skin defects are not apparent in mice lacking 25-hydroxyvitamin D 1alpha-hydroxylase, the enzyme required for 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) hormone biosynthesis. These disparate phenotypes indicate that VDR effects in skin are independent of the 1,25(OH)2D3 ligand. However, cellular or molecular data supporting this hypothesis are lacking. Here, we show transcriptional activation of the vitamin D-responsive 24-hydroxylase promoter by VDR in primary keratinocytes that is independent of the 1,25(OH)2D3 ligand. This activity required functional vitamin D-responsive promoter elements as well as an intact VDR DNA binding domain and thus could not be distinguished from 1,25(OH)2D3-dependent VDR transactivation. The 1,25(OH)2D3-independent activation of VDR was also observed in keratinocytes from 1alpha-hydroxylase knock-out mice, indicating that it is not due to endogenous 1,25(OH)2D3 production. Mammalian two-hybrid studies showed strong, 1,25(OH)2D3-independent interaction between VDR and retinoid X receptors in primary keratinocytes, indicating that enhanced heterodimerization of these receptors was involved. Indeed, this 1,25(OH)2D3-independent VDR-RXR heterodimerization was sufficient to drive transactivation by VDR(L233S), an inactive ligand binding mutant of VDR that was previously shown to rescue the skin phenotype of VDR null mice. Cumulatively, these studies support the concept that transactivation by VDR in keratinocytes may be uncoupled from the 1,25(OH)2D3 ligand.

Vitamin D Receptor–DNA Interactions

The vitamin D receptor (VDR) is a member of the steroid and nuclear hormone receptor superfamily of eukaryotic transcription factors and binds target DNA, or response elements, as a homodimer or heterodimer with the 9-cis retinoid X receptor (RXR). In this chapter, we survey the current understanding of VDR-DNA interactions, emphasizing recent structural insights. We highlight the stereochemical interactions that dictate DNA binding and hexameric half-site sequence affinity as well as the protein-protein interactions that account for preferential binding to a direct repeat of half-sites with three base pairs of spacer DNA (DR3). In addition, we review alternative response element arrangements other than those with DR3. Finally, the chapter discusses the VDR DNA binding domain (DBD) and suggests that it violates classical canons because it does not heterodimerize with the RXR DBD. This unique behavior of VDR is considered in light of recent results demonstrating the formation of VDR DBD-DNA and DR3 DBD-DNA complexes with RXR using a mutant VDR protomer.

Targeted ablation of the vitamin D receptor: an animal model of vitamin D-dependent rickets type II with alopecia.

Vitamin D, the major steroid hormone that controls mineral ion homeostasis, exerts its actions through the vitamin D receptor (VDR). The VDR is expressed in many tissues, including several tissues not thought to play a role in mineral metabolism. Studies in kindreds with VDR mutations (vitamin D-dependent rickets type II, VDDR II) have demonstrated hypocalcemia, hyperparathyroidism, rickets, and osteomalacia. Alopecia, which is not a feature of vitamin D deficiency, is seen in some kindreds. We have generated a mouse model of VDDR II by targeted ablation of the second zinc finger of the VDR DNA-binding domain. Despite known expression of the VDR in fetal life, homozygous mice are phenotypically normal at birth and demonstrate normal survival at least until 6 months. They become hypocalcemic at 21 days of age, at which time their parathyroid hormone (PTH) levels begin to rise. Hyperparathyroidism is accompanied by an increase in the size of the parathyroid gland as well as an increase in PTH mRNA levels. Rickets and osteomalacia are seen by day 35; however, as early as day 15, there is an expansion in the zone of hypertrophic chondrocytes in the growth plate. In contrast to animals made vitamin D deficient by dietary means, and like some patients with VDDR II, these mice develop progressive alopecia from the age of 4 weeks.

Zinc binding properties of the DNA binding domain of the 1,25-dihydroxyvitamin D3 receptor.

To assess the zinc binding stoichiometry and the structural changes induced upon the binding of zinc to the human vitamin D receptor (VDR), we expressed the DNA binding domain (DBD) of the human VDR in bacteria as a soluble glutathione-S-transferase fusion protein at 20 degrees C, and examined the apo-protein and metal-liganded protein by mass spectrometry, and circular dichroism and nuclear magnetic resonance spectroscopy. Following final preparation with a zinc-free buffer, the VDR DBD bound 2 mol of zinc/mol of protein as measured by inductively coupled plasma-mass spectrometry and electrospray ionization-mass spectrometry. When protein preparation was carried out in a zinc containing buffer and zinc content of the protein was assesed by the same methods, VDR DBD bound 4 mol of zinc/mol of protein. Analysis of the protein using circular dichroism spectroscopy demonstrated that the EDTA-treated protein increased in alpha-helical content from 16 to 27% on the addition of zinc. Equilibrium ultracentrifugal analyses of the VDR DBD indicated that the protein was present in solution as a monomer. Gel mobility shift analyses of the VDR DBD with several vitamin D response elements (VDREs) in the absence of accessory proteins such as retinoic acid receptor, showed that VDR DBD was able to form a protein/VDRE DNA structural complex. In the presence of zinc, proton NMR NOESY spectra showed that the protein possessed elements of secondary structure. The addition of VDRE DNA, but not random DNA, caused changes in the proton NMR spectra of VDRE DNA indicating specific interaction between protein and DNA groups. We conclude that the DBD of the VDR binds zinc and DNA and undergoes conformational changes on binding to the metal and DNA.

Distinct conformations of vitamin D receptor/retinoid X receptor-alpha heterodimers are specified by dinucleotide differences in the vitamin D-responsive elements of the osteocalcin and osteopontin genes.

The 1 alpha,25-dihydroxyvitamin D3 (VD3)-dependent stimulation of osteocalcin (OC) and osteopontin (OP) gene transcription in bone tissue is mediated by interactions of trans-activating factors with distinct VD3-responsive elements (VDREs). Sequence variation between the OC- and OP-VDRE steroid hormone half-elements provides the potential for recognition by distinct hormone receptor homo- and heterodimers. However, the exact composition of endogenous VD3- induced complexes recognizing the OC- and OP-VDREs in osteoblasts has not been definitively established. To determine the identity of these complexes, we performed gel shift immunoassays with nuclear proteins from ROS 17/ 2.8 osteoblastic cells using a panel of monoclonal antibodies. We show that VD3- inducible complexes interacting with the OC- and OP-VDREs represent two distinct heterodimeric complexes, each composed of the vitamin D receptor (VDR) and the retinoid X receptor-alpha (RXR). The OC- and OP-VDR/RXR alpha heterodimers are immunoreactive with RXR antibodies and several antibodies directed against the ligand-binding domain of the VDR. However, while the OC-VDRE complex is also efficiently recognized by specific monoclonal antibodies contacting epitopes in or near the VDR DNA-binding domain (DBD) (between amino acids 57-164), the OP-VDRE complex is not efficiently recognized by these antibodies. By systematically introducing a series of point-mutations in the OC-VDRE, we find that two internal nucleotides of the proximal OC-VDRE half-site (nucleotide -449 and -448; 5'-AGGACA) determine differences in VDR immunoreactivity. These results are consistent with the well established polarity of RXR heterodimer binding to bipartite hormone response elements, with the VDR recognizing the 3'-half-element. Furthermore, our data suggest that the DBD of the VDR adopts different protein conformations when contacting distinct VDREs. Distinctions between the OC- and OP-VDR/RXR alpha complexes may reflect specialized requirements for VD3 regulation of OC and OP gene expression in response to physiological cues mediating osteoblast differentiation.

Calreticulin inhibits vitamin D3 signal transduction.

Calreticulin is a calcium binding protein present primarily in the lumen of the endoplasmic reticulum. However, it can also localize to the cytoplasm adjacent to the cell membrane where it binds integrins, and to the nucleus. Recent studies showed that calreticulin inhibits DNA binding and transcriptional activity of glucocorticoid, androgen and retinoic acid receptors. The DNA binding domains of nuclear receptors share a common motif based upon the amino acid sequence KVFFKR which has been implicated in the binding of calreticulin. The vitamin D receptor (VDR) DNA binding domain contains the related motif KgFFrR. Here we show that calreticulin blocks specific DNA binding by the isolated VDR DNA binding domain in DNA mobility shift assays. Importantly, calreticulin blocks specific DNA binding by the full length VDR-RXR heterodimers. By contrast, calreticulin had no effect on specific DNA binding by the transcription factor ATF-a delta which lacks a KVFFKR-like motif in its DNA binding domain. We further showed that overexpression of calreticulin in the rat osteoblast-like cell line (ROS 17/2.8) inhibited the 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] responsive transcriptional activation of a vitamin D-sensitive reporter gene, whereas the response to forskolin stimulation of a control promoter-reporter construct containing a cAMP response element (CRE), but no vitamin D response element (VDRE), was not affected by overexpression of calreticulin. Thus, calreticulin inhibits transcriptional activation by the VDR in vivo. Given the ubiquitous expression of calreticulin and the widespread expression of the VDR the studies described here may point to an important new mechanism whereby VDR mediated gene transcription can be modulated.

Vitamin D receptor interaction with specific DNA. Association as a 1,25-dihydroxyvitamin D3-modulated heterodimer.

The vitamin D receptor (VDR) is a member of the steroid receptor gene family. In this report, we examine the nature of specific VDR DNA binding utilizing the vitamin D-responsive element derived from the human osteocalcin promoter. Association of the VDR with the human osteocalcin 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) responsive element (VDRE) in vitro was characterized on VDRE affinity columns by both weak and strong interactions. Weak interaction was a property of the VDR itself, monomeric in nature, and determined exclusively by the VDR's DNA-binding domain. Strong interaction, in contrast, was dependent upon an intact receptor molecule as well as a heterologous mammalian cell nuclear accessory factor (NAF). Heteromeric interaction between VDR and NAF was independent of the VDR DNA-binding domain, suggesting the presence of a functional dimerization domain separate from that for DNA binding. Direct association of NAF with immobilized VDR revealed that the interaction does not require the presence of DNA. Most importantly, while occupancy of the VDR by 1,25(OH)2D3 was not required for VDR interactions with either DNA or NAF, the presence of hormone increased the apparent relative affinity of the VDR for NAF approximately 10-fold. These studies suggest that high affinity association of the VDR with DNA requires both the DNA-binding domain as well as an additional independent structure located within the steroid-binding region. This protein subdomain interacts with NAF and is regulated by 1,25(OH)2D3.