Structural determinants of the ligand-binding site of the human retinoic acid receptor alpha

Anti-HBV activity of retinoid drugs in vitro versus in vivo

We describe here the anti-HBV activity of natural and synthetic retinoids in primary human hepatocytes (PHHs). The most potent compounds inhibited HBsAg, HBeAg, viral RNA and DNA production by HBV infected cells with EC₅₀ values ranging from 0.4 to 2.6 μM. The activity was independent of PHH donor and HBV genotype used in testing. 13-cis retinoic acid (Accutane) was selected for further evaluation in the PXB chimeric mouse model of HBV infection at doses allowing to achieve Accutane peak serum concentrations near its antiviral EC₉₀ and exposures ∼5-fold higher than a typical clinical dose. While these supraclinical exposures of 100 mg/kg/day were well-tolerated by regular Balb/c mice, PXB mice were more sensitive and even a lower those of 60 mg/kg/day led to significant weight loss. Despite dosing at this maximal tolerated dose for 28 days, Accutane failed to show any anti-HBV activity. RAR target engagement was verified using transcriptome analysis of liver samples from treated versus vehicle groups. However, gene expression changes in PXB liver samples were vastly muted when compared to the in vitro PHH system. When comparing transcriptional changes associated with the conditioning of fresh hepatocytes toward enabling HBV infection, we also observed a large number of changes. Noticeably, a significant number of genes that were up- or down-regulated by the conditioning process were down- or up-regulated by HBV infected PHH treatment with Accutane, respectively. While the lack of efficacy in the PXB model may have many explanations, the observed, opposing transcriptional changes upon conditioning PHH and treating these cultured, HBV-infected PHH with Accutane allow for the possibility that the PHH system may yield artificial anti-HBV hits.

The proliferating cell nuclear antigen regulates retinoic acid receptor transcriptional activity through direct protein-protein interaction

Retinoic acid receptors (RARs) interact, in a ligand-dependent fashion, with many coregulators that participate in a wide spectrum of biological responses, ranging from embryonic development to cellular growth control. The transactivating function of these ligand-inducible transcription factors reside mainly, but not exclusively, in their ligand-binding domain (AF2), which recruits or dismiss coregulators in a ligand-dependent fashion. However, little is known about AF2-independent function(s) of RARs. We have isolated the proliferating cell nuclear antigen (PCNA) as a repressor of RAR transcriptional activity, able to interact with an AF2-crippled RAR. The N-terminus of PCNA interacts directly with the DNA-binding domain of RAR, and PCNA is recruited to a retinoid-regulated promoter in intact cells. This interaction affects the transcriptional response to retinoic acid in a promoter-specific manner, conferring an unanticipated role to PCNA in transcriptional regulation. Our findings also suggest a role for RAR as a factor coordinating DNA transcription and repair.

Transcriptional activities of retinoic acid receptors

Vitamin A derivatives plays a crucial role in embryonic development, as demonstrated by the teratogenic effect of either an excess or a deficiency in vitamin A. Retinoid effects extend however beyond embryonic development, and tissue homeostasis, lipid metabolism, cellular differentiation and proliferation are in part controlled through the retinoid signaling pathway. Retinoids are also therapeutically effective in the treatment of skin diseases (acne, psoriasis and photoaging) and of some cancers. Most of these effects are the consequences of retinoic acid receptors activation, which triggers transcriptional events leading either to transcriptional activation or repression of retinoid-controlled genes. Synthetic molecules are able to mimic part of the biological effects of the natural retinoic acid receptors, all-trans retinoic acid. Therefore, retinoic acid receptors are considered as highly valuable therapeutic targets and limiting unwanted secondary effects due to retinoid treatment requires a molecular knowledge of retinoic acid receptors biology. In this review, we will examine experimental evidence which provide a molecular basis for the pleiotropic effects of retinoids, and emphasize the crucial roles of coregulators of retinoic acid receptors, providing a conceptual framework to identify novel therapeutic targets.

Intestinal antiinflammatory effect of 5-aminosalicylic acid is dependent on peroxisome proliferator-activated receptor-gamma

5-aminosalicylic acid (5-ASA) is an antiinflammatory drug widely used in the treatment of inflammatory bowel diseases. It is known to inhibit the production of cytokines and inflammatory mediators, but the mechanism underlying the intestinal effects of 5-ASA remains unknown. Based on the common activities of peroxisome proliferator–activated receptor-γ (PPAR-γ) ligands and 5-ASA, we hypothesized that this nuclear receptor mediates 5-ASA therapeutic action. To test this possibility, colitis was induced in heterozygous PPAR-γ^+/− mice and their wild-type littermates, which were then treated with 5-ASA. 5-ASA treatment had a beneficial effect on colitis only in wild-type and not in heterozygous mice. In epithelial cells, 5-ASA increased PPAR-γ expression, promoted its translocation from the cytoplasm to the nucleus, and induced a modification of its conformation permitting the recruitment of coactivators and the activation of a peroxisome-proliferator response element–driven gene. Validation of these results was obtained with organ cultures of human colonic biopsies. These data identify PPAR-γ as a target of 5-ASA underlying antiinflammatory effects in the colon.

Retinoic acid receptor-alpha is stabilized in a repressive state by its C-terminal, isotype-specific F domain

Retinoic acid receptors (RARs) are hormone-regulated transcription factors that play multiple roles in vertebrate development and differentiation. Three isotypes of RARs, alpha, beta, and gamma, are encoded by distinct genetic loci and possess distinct transcriptional properties. Typically, RARalpha represses target gene transcription in the absence of hormone, whereas RARbeta and gamma fail to repress under these conditions. This inability of RARbeta and RARgamma to repress transcription is due to intramolecular interactions between helix 3 and helix 12 of the hormone binding domains of these isotypes that inhibit corepressor binding while favoring coactivator binding. We report here that the converse ability of RARalpha to repress requires the integrity of the receptor F domain, a domain that maps C-terminal to helix 12, varies in sequence among different nuclear receptors, and is of poorly understood function. The F domain appears to help stabilize helix 12 of RARalpha in a more open position that enhances corepressor binding and inhibits coactivator binding in the absence of hormone. Intriguingly, the RARalpha F domain is isotype autonomous in its function. We speculate that the RARalpha F domain may dock elsewhere on the receptor surface, and this intramolecular interaction may maintain RARalpha helix 12 in an open, repression-competent conformation.

Retinoid X receptor alpha (RXRalpha) helix 12 plays an inhibitory role in the recruitment of the p160 co-activators by unliganded RXRalpha/retinoic acid receptor alpha heterodimers

Retinoid X receptor (RXR)/retinoic acid receptor (RAR) heterodimers control gene expression through recruitment of co-repressors or co-activators, depending on their hormone binding status. We show that the helix 12 of RXRalpha and RARalpha is critical for recruitment of the co-regulators and transcriptional regulation by RXRalpha, RARalpha, and RXRalpha/RARalpha. LG268, an RXR-specific agonist, was able to promote co-activator association with the heterodimers, but was unable to dissociate co-repressors. Reconstitution experiments in yeast demonstrated that LG268 was capable of activating transcription by RXRalpha/RARalpha through recruitment of the co-activator. We hypothesize that the inability to release co-repressors from RXRalpha/RARalpha is responsible for the inability of LG268 to activate RXRalpha/RARalpha heterodimers in mammalian cells. Deletion of RARalpha helix 12 (RXRalpha/RARalpha Delta403) abolished both hormone-dependent dissociation from co-repressors and hormone-dependent association with co-activators. Deletion of RXRalpha helix 12 (RXRalpha Delta443/RARalpha) resulted in a higher binding affinity for co-repressors. Unexpectedly, RXRalpha Delta443/RARalpha also gained hormone-independent co-activator binding activity. Moreover, LG268 became an antagonist to RXRalpha Delta443/RARalpha heterodimers. These data suggest that the helix 12 of RXRalpha plays an inhibitory role in the recruitment of co-activators by unliganded RXRalpha/RARalpha.

Retinoic acid receptors inhibit AP1 activation by regulating extracellular signal-regulated kinase and CBP recruitment to an AP1-responsive promoter

Retinoids exhibit antineoplastic activities that may be linked to retinoid receptor-mediated transrepression of activating protein 1 (AP1), a heterodimeric transcription factor composed of fos- and jun-related proteins. Here we show that transcriptional activation of an AP1-regulated gene through the mitogen-activated protein kinase (MAPK)-extracellular signal-regulated kinase (ERK) pathway (MAPK(ERK)) is characterized, in intact cells, by a switch from a fra2-junD dimer to a junD-fosB dimer loading on its promoter and by simultaneous recruitment of ERKs, CREB-binding protein (CBP), and RNA polymerase II. All-trans-retinoic acid (atRA) receptor (RAR) was tethered constitutively to the AP1 promoter. AP1 transrepression by retinoic acid was concomitant to glycogen synthase kinase 3 activation, negative regulation of junD hyperphosphorylation, and to decreased RNA polymerase II recruitment. Under these conditions, fra1 loading to the AP1 response element was strongly increased. Importantly, CBP and ERKs were excluded from the promoter in the presence of atRA. AP1 transrepression by retinoids was RAR and ligand dependent, but none of the functions required for RAR-mediated transactivation was necessary for AP1 transrepression. These results indicate that transrepressive effects of retinoids are mediated through a mechanism unrelated to transcriptional activation, involving the RAR-dependent control of transcription factors and cofactor assembly on AP1-regulated promoters.

Selective alteration of gene expression in response to natural and synthetic retinoids

BACKGROUND

Retinoids are very potent inducers of cellular differentiation and apoptosis, and are efficient anti-tumoral agents. Synthetic retinoids are designed to restrict their toxicity and side effects, mostly by increasing their selectivity toward each isotype of retinoic acids receptors (RARalpha,beta, gamma and RXRalpha, beta, gamma). We however previously showed that retinoids displayed very different abilities to activate retinoid-inducible reporter genes, and that these differential properties were correlated to the ability of a given ligand to promote SRC-1 recruitment by DNA-bound RXR:RAR heterodimers. This suggested that gene-selective modulation could be achieved by structurally distinct retinoids.

RESULTS

Using the differential display mRNA technique, we identified several genes on the basis of their differential induction by natural or synthetic retinoids in human cervix adenocarcinoma cells. Furthermore, this differential ability to regulate promoter activities was also observed in murine P19 cells for the RARbeta2 and CRABPII gene, showing conclusively that retinoid structure has a dramatic impact on the regulation of endogenous genes.

CONCLUSIONS

Our findings therefore show that some degree of selective induction or repression of gene expression may be achieved when using appropriately designed ligands for retinoic acid receptors, extending the concept of selective modulators from estrogen and peroxisome proliferator activated receptors to the class of retinoid receptors.

Chromosomal integration of retinoic acid response elements prevents cooperative transcriptional activation by retinoic acid receptor and retinoid X receptor

All-trans-retinoic acid receptors (RAR) and 9-cis-retinoic acid receptors (RXR) are nuclear receptors known to cooperatively activate transcription from retinoid-regulated promoters. By comparing the transactivating properties of RAR and RXR in P19 cells using either plasmid or chromosomal reporter genes containing the mRAR beta 2 gene promoter, we found contrasting patterns of transcriptional regulation in each setting. Cooperativity between RXR and RAR occurred at all times with transiently introduced promoters, but was restricted to a very early stage (<3 h) for chromosomal promoters. This time-dependent loss of cooperativity was specific for chromosomal templates containing two copies of a retinoid-responsive element (RARE) and was not influenced by the spacing between the two RAREs. This loss of cooperativity suggested a delayed acquisition of RAR full transcriptional competence because (i) cooperativity was maintained at RAR ligand subsaturating concentrations, (ii) overexpression of SRC-1 led to loss of cooperativity and even to strong repression of chromosomal templates activity, and (iii) loss of cooperativity was observed when additional cis-acting response elements were activated. Surprisingly, histone deacetylase inhibitors counteracted this loss of cooperativity by repressing partially RAR-mediated activation of chromosomal promoters. Loss of cooperativity was not correlated to local histone hyperacetylation or to alteration of constitutive RNA polymerase II (RNAP) loading at the promoter region. Unexpectedly, RNAP binding to transcribed regions was correlated to the RAR activation state as well as to acetylation levels of histones H3 and H4, suggesting that RAR acts at the mRAR beta promoter by triggering the switch from an RNA elongation-incompetent RNAP form towards an RNA elongation-competent RNAP.

Control of retinoic acid receptor heterodimerization by ligand-induced structural transitions. A novel mechanism of action for retinoid antagonists

Heterodimerization of retinoic acid receptors (RARs) with 9-cis-retinoic receptors (RXRs) is a prerequisite for binding of RXR.RAR dimers to DNA and for retinoic acid-induced gene regulation. Whether retinoids control RXR/RAR solution interaction remains a debated question, and we have used in vitro and in vivo protein interaction assays to investigate the role of ligand in modulating RXR/RAR interaction in the absence of DNA. Two-hybrid assay in mammalian cells demonstrated that only RAR agonists were able to increase significantly RAR interaction with RXR, whereas RAR antagonists inhibited RXR binding to RAR. Quantitative glutathione S-transferase pull-down assays established that there was a strict correlation between agonist binding affinity for the RAR monomer and the affinity of RXR for liganded RAR, but RAR antagonists were inactive in inducing RXR recruitment to RAR in vitro. Alteration of coactivator- or corepressor-binding interfaces of RXR or RAR did not alter ligand-enhanced dimerization. In contrast, preventing the formation of a stable holoreceptor structure upon agonist binding strongly altered RXR.RAR dimerization. Finally, we observed that RAR interaction with RXR silenced RXR ligand-dependent activation function. We propose that ligand-controlled dimerization of RAR with RXR is an important step in the RXR.RAR activation process. This interaction is dependent upon adequate remodeling of the AF-2 structure and amenable to pharmacological inhibition by structurally modified retinoids.

Role of Ser(289) in RARgamma and its homologous amino acid residue of RARalpha and RARbeta in the binding of retinoic acid

The biological actions of retinoic acid (RA) are mediated by retinoic acid receptors (RARalpha, -beta, and -gamma) and retinoid X receptors (RXRalpha, -beta, and -gamma). Although the ligand-binding domains of RARs and RXRs have been suggested to share the same novel folding pattern, the ligand-binding pockets of each of the retinoid receptors must have unique structural features since it has been possible to develop RAR subtype-selective and RXR-selective retinoids. We have previously demonstrated the importance for RA binding and RA-dependent transactivation of Arg(276) in RARalpha and Arg(278) in RARgamma; however, in RARbeta Arg(269) functions in conjunction with Lys(220). Here we have examined the role of the hydroxyl group of RARgamma Ser(289) and its homologous amino acid residues in RARalpha (Ser(287)) and RARbeta (Ser(280)) alone and in conjunction with their respective RARgamma Arg(278) homologs for RA binding and RA-dependent transactivation activity. The hydroxyl group of this Ser in all three RARs was found by itself not to be important for RA binding and RA-dependent transactivation activity. However, in RARalpha and RARgamma this Ser appears to play a small role in conjunction with Arg(276) and Arg(278), respectively, for these activities. Alternatively, strong synergism was observed in RARbeta between Ser(280) and Arg(269) for RA-binding and RA-dependent transactivation activity. This provides further evidence that the mechanism of interaction between the carboxylate group of retinoids and the amino acid residues in the ligand binding pocket of RARbeta is different from that of RARalpha and RARgamma.

Allosteric regulation of the discriminative responsiveness of retinoic acid receptor to natural and synthetic ligands by retinoid X receptor and DNA

Transcriptional activation by retinoids is mediated through two families of nuclear receptors, all-trans-retinoic acid (RARs) and 9-cis retinoic acid receptors (RXRs). Conformationally restricted retinoids are used to achieve selective activation of RAR isotype alpha, beta or gamma, which reduces side effects in therapeutical applications. Synthetic retinoids mimic some of all-trans retinoic acid biological effects in vivo but interact differently with the ligand binding domain of RARalpha and induce distinct structural transitions of the receptor. In this report, we demonstrate that RAR-selective ligands have distinct quantitative activation properties which are reflected by their abilities to promote interaction of DNA-bound human RXRalpha (hRXRalpha)-hRARalpha heterodimers with the nuclear receptor coactivator (NCoA) SRC-1 in vitro. The hormone response element core motifs spacing defined the relative affinity of liganded heterodimers for two NCoAs, SRC-1 and RIP140. hRXRalpha activating function 2 was critical to confer hRARalpha full responsiveness but not differential sensitivity of hRARalpha to natural or synthetic retinoids. We also provide evidence showing that lysines located in helices 3 and 4, which define part of hRARalpha NCoA binding surface, contribute differently to (i) the transcriptional activity and (ii) the interaction of RXR-RAR heterodimers with SRC-1, when challenged by either natural or RAR-selective retinoids. Thus, ligand structure, DNA, and RXR exert allosteric regulations on hRARalpha conformation organized as a DNA-bound heterodimer. We suggest that the use of physically distinct NCoA binding interfaces may be important in controlling specific genes by conformationally restricted ligands.

A unique carboxy-terminus truncation mutant of the retinoic acid receptor alpha gene associated with a variant marker chromosome in a retinoic acid resistant HL-60 subline

In order to contribute to the study of the molecular basis of leukemic cellular resistance to the induction of differentiation by all-trans retinoic acid (RA) we have generated and analyzed a mutant, RA-resistant HL-60 cell line. Molecular analysis of the retinoic acid receptor alpha (RARalpha) cDNA disclosed, in one of the two alleles, a novel mutation consisting of a 7-base deletion in the ligand binding domain that includes part of a FokI restriction endonuclease site previously described. As a consequence of this deletion and translational frame-shift, a stop signal is created that truncates the protein at codon 421, disrupting an essential functional component of the receptor. Transducing an epitope tagged RARalpha into the mutant is sufficient to inhibit clonal growth in the presence of RA. Standard cytogenetic analysis, fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH) analysis revealed the presence of two RARalpha loci, and showed a composite karyotype with additional abnormalities with respect to the parental line, including a chromosome 8 insertion in a chromosome previously known as marker three.

H11-H12 loop retinoic acid receptor mutants exhibit distinct trans-activating and trans-repressing activities in the presence of natural or synthetic retinoids

Retinoids, such as the naturally occurring all-trans-retinoic acid (atRA) and synthetic ligand CD367 modulate ligand-dependent transcription through retinoic acid receptors (RARs). Retinoid binding to RAR is believed to trigger structural transitions in the ligand-binding domain (LBD), leading to helix H1 and helix H12 repositioning and coactivator recruitment and corepressor release. Here, we carried out a detailed mutagenesis analysis of the H11-H12 loop (designated the L box) to study its contribution to hRARalpha activation process. Point mutations that reduced transactivation by atRA also reduced atRA-induced transrepression of AP1 transcription, correlating ligand-induced activation and repression. However, a correlation was not observed with these mutations when tested with another ligand CD367, a synthetic agonist with binding properties identical to those of atRA. Transcription was strongly inhibited in the presence of CD367 for some mutants, thus leading to an inverse agonist activity of this ligand. None of these mutations significantly altered binding affinity for either ligand, indicating that altered transcription was not caused by altered ligand binding by these mutations. Although simple correlations with transcriptional activities were not found, these mutations were also characterized by altered ligand-induced structural transitions, which were distinct for the atRA-hRARalpha or CD367-hRARalpha complexes. These results indicate that amino acids in the L box are involved in specifying trans-repressive and trans-activating properties of the hRARalpha, and support the notion that different agonists induce distinct conformations in the LBD of the receptor.

Distinct modes of interaction of the retinoic acid receptor alpha with natural and synthetic retinoids

Retinoids regulate key cellular processes through their binding to their cognate nuclear receptors, RARs and RXRs. Synthetic ligands mimic most of their biological effects and alteration of their chemical structure confers selectivity for RAR isotypes alpha, beta or gamma. In this study, we have examined the contribution of a domain (L box) of hRARalpha located at the C-terminus of the ligand binding domain (LBD), between helices H11 and H12, to the ligand binding activity of this receptor. By site-directed mutagenesis, we demonstrate that, in the absence of the ligand-dependent activation domain 2 (AF2-AD), the receptor discriminates between classes of structurally distinct retinoids. This property was lost in the presence of the AF2-AD domain, evidencing major structural transitions in this part of the receptor. We propose that ligand binding occurs in two steps: first, the ligand interacts with the LBD in its opened, holo-receptor conformation in which the L box plays a crucial role in defining the ligand binding repertoire of hRARalpha; secondly, the LBD adopts its closed conformation in which the ligand interacts with the receptor mostly through its carboxylic moiety.

Evidence for the Involvement of Both Retinoic Acid Receptor- and Retinoic X Receptor-Dependent Signaling Pathways in the Induction of Tissue Transglutaminase and Apoptosis in the Human Myeloma Cell Line RPMI 8226

In this study, we show that both all-trans-retinoic acid (atRA) and 9-cis-retinoic acid (9-cis-RA) are potent inducers of tissue transglutaminase (TGase II), an enzyme involved in apoptosis, at the level of both enzyme activity and mRNA in the human myeloma cell line RPMI 8226. RPMI 8226 cells were shown to express mRNAs for all the retinoid receptors subtypes, ie, RARα, RARβ, RARγ, RXRα, RXRβ, and RXRγ. To identify which of these receptors are involved in regulating TGase II expression, several receptor-selective synthetic retinoids were used. Neither CD367, a very potent retinoid that selectively binds and activates receptors of the RAR family, nor CD2425, an RXR-selective agonist, induced TGase II when used alone. However, combination of CD367 and CD2425 resulted in nearly full induction of the enzyme. Moreover, when used in combination with atRA, CD367 partially inhibited the atRA-dependent induction of TGase II, whereas CD2425 enhanced it. The effects of Am 580, CD417, and CD437, three synthetic retinoids selective for the RARs subtypes RARα, RARβ, and RARγ, respectively, were also investigated. None of these compounds was able to induce TGase II when used alone; however, the combination of each of them with CD2425 resulted in strong induction of the enzyme activity, reaching 30% to 50% of the values obtained in the presence of retinoic acid and suggesting functional redundancy between the RAR subtypes. Finally, treatment with atRA or the combination of CD367 and CD2425, but not with CD367 or CD2425 alone, was also shown to trigger apoptosis in RPMI 8226 cells, with prominent accumulation of TGase II immunoreactivity in apoptotic cells. Taken together these data suggest that the induction of TGase II expression and apoptosis in the RPMI 8226 myeloma cell line required ligand-dependent activation of both the RAR and RXR receptors.

Evidence for the Involvement of Both Retinoic Acid Receptor- and Retinoic X Receptor-Dependent Signaling Pathways in the Induction of Tissue Transglutaminase and Apoptosis in the Human Myeloma Cell Line RPMI 8226

In this study, we show that both all-trans-retinoic acid (atRA) and 9-cis-retinoic acid (9-cis-RA) are potent inducers of tissue transglutaminase (TGase II), an enzyme involved in apoptosis, at the level of both enzyme activity and mRNA in the human myeloma cell line RPMI 8226. RPMI 8226 cells were shown to express mRNAs for all the retinoid receptors subtypes, ie, RARα, RARβ, RARγ, RXRα, RXRβ, and RXRγ. To identify which of these receptors are involved in regulating TGase II expression, several receptor-selective synthetic retinoids were used. Neither CD367, a very potent retinoid that selectively binds and activates receptors of the RAR family, nor CD2425, an RXR-selective agonist, induced TGase II when used alone. However, combination of CD367 and CD2425 resulted in nearly full induction of the enzyme. Moreover, when used in combination with atRA, CD367 partially inhibited the atRA-dependent induction of TGase II, whereas CD2425 enhanced it. The effects of Am 580, CD417, and CD437, three synthetic retinoids selective for the RARs subtypes RARα, RARβ, and RARγ, respectively, were also investigated. None of these compounds was able to induce TGase II when used alone; however, the combination of each of them with CD2425 resulted in strong induction of the enzyme activity, reaching 30% to 50% of the values obtained in the presence of retinoic acid and suggesting functional redundancy between the RAR subtypes. Finally, treatment with atRA or the combination of CD367 and CD2425, but not with CD367 or CD2425 alone, was also shown to trigger apoptosis in RPMI 8226 cells, with prominent accumulation of TGase II immunoreactivity in apoptotic cells. Taken together these data suggest that the induction of TGase II expression and apoptosis in the RPMI 8226 myeloma cell line required ligand-dependent activation of both the RAR and RXR receptors.

Mutational analysis reveals that all-trans-retinoic acid, 9-cis-retinoic acid, and antagonist interact with distinct binding determinants of RARalpha

Retinoids exert their pleiotropic effects on cell differentiation and proliferation through specific nuclear receptors, the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). Two biologically highly active natural retinoids have been identified, all-trans-retinoic acid (t-RA) and 9-cis-retinoic acid (9-cis-RA). The RXRs exclusively bind 9-cis-RA, whereas the RARs bind both isomers of RA with comparable affinity. Recently published results suggest that RARs have the same binding site for t-RA and 9-cis-RA but with different determinants (1-3). Antagonist binding on RARalpha has been suggested to induce distinct conformational changes in comparison with agonist binding. To elucidate the region minimally required for efficient binding of agonist (t-RA and 9-cis-RA) and antagonist Ro 41-5253 to the RARalpha, we generated N- and C-terminally truncated mutants of the receptor. Characterization of these deletion mutant proteins using protease mapping and ligand binding experiments revealed that different parts of the ligand-binding domain are necessary for t-RA, 9-cis-RA, and antagonist binding. Three distinct regions of the ligand-binding domain of the human retinoic acid receptor-alpha are required for binding of t-RA (RARalpha187-402), 9-cis-RA (RARalpha188-409), and the antagonist Ro 41-5253 (RARalpha226-414).

Solving inconsistencies in the analysis of receptor-ligand interactions

According to the occupation model, the observed sigmoidicity in receptor-binding studies frequently yields non-integer values for the number of molecules that bind per receptor, which may suggest inconsistencies of the model. Here, Bertil Tuk and Michael van Oostenbruggen re-examine the derivation of the model and pinpoint the origin of the observed inconsistencies, thereby demonstrating that these inconsistencies may lead to substantial error in estimates of receptor affinity, number of molecules that bind per receptor and cooperativity. A reformulated model allows more information to be derived from receptor-binding experiments, yielding integer estimates of the number of molecules that bind per receptor and quantitatively estimating the degree of cooperativity.

Analysis of the ligand-binding domain of human retinoic acid receptor alpha by site-directed mutagenesis

Three subtypes of retinoic acid receptors (RAR), termed RAR alpha, RAR beta, and RAR gamma, have been described. They are composed of different structural domains, including distinct domains for DNA and ligand binding. RARs specifically bind all-trans-retinoic acid (RA), 9-cis-RA, and retinoid analogs. In this study, we examined the functional role of cysteine and arginine residues in the ligand-binding domain of hRAR alpha (hRAR alpha-LBD, amino acids 154 to 462). All conserved cysteine and arginine residues in this domain were mutated by site-directed mutagenesis, and the mutant proteins were characterized by blocking reactions, ligand-binding experiments, transactivation assays, and protease mapping. Changes of any cysteine residue of the hRAR alpha-LBD had no significant influence on the binding of all-trans RA or 9-cis RA. Interestingly, residue C-235 is specifically important in antagonist binding. With respect to arginine residues, only the two single mutations of R-276 and R-394 to alanine showed a dramatic decrease of agonist and antagonist binding whereas the R272A mutation showed only a slight effect. For all other arginine mutations, no differences in affinity were detectable. The two mutations R217A and R294A caused an increased binding efficiency for antagonists but no change in agonist binding. From these results, we can conclude that electrostatic interactions of retinoids with the RAR alpha-LBD play a significant role in ligand binding. In addition, antagonists show distinctly different requirements for efficient binding, which may contribute to their interference in the ligand-inducible transactivation function of RAR alpha.

Modular structure of glucocorticoid receptor domains is not equivalent to functional independence. Stability and activity of the steroid binding domain are controlled by sequences in separate domains

A long-standing conundrum of glucocorticoid receptors has been why the steroid binding domain is active in hybrid proteins but not in isolation. For this reason, the precise boundaries of the steroid binding domain have not been defined. These questions have now been systematically examined with a variety of receptor deletion constructs. Plasmids encoding amino acids 537-673 and 537-795 of the rat receptor did not yield stable proteins, while the fusion of receptor or non-receptor sequences upstream of 537-673 afforded stable proteins that did not bind steroid. Wild type steroid binding affinity could be obtained, however, when proteins such as beta-galactosidase or dihydrofolate reductase were fused upstream of receptor amino acids 537-795. Studies of a series of dhfr/receptor constructs with deletions at the amino- and carboxyl-terminal ends of the receptor sequence localized the boundaries of the steroid binding domain to 550-795. The absence of steroid binding upon deletion of sequences in the carboxyl-terminal half of this domain was consistent with improperly folded receptor sequences. This conclusion was supported by analyses of the proteolysis and thermal stability of the mutant receptors. Thus, three independent regions appear to be required for the generation of the steroid binding form of receptors: 1) a protein sequence upstream of the steroid binding domain, which conveys stability to the steroid binding domain, 2) sequences of the carboxyl-terminal amino acids (674-795), which are required for the correct folding of the steroid binding domain, and 3) amino-terminal sequences (550-673), which may be sufficient for steroid binding after the entire steroid binding domain is properly folded. These results establish that the steroid binding domain of glucocorticoid receptors is not independently functional and illustrate the importance of both protein stability and protein folding when constructing mutant proteins.

Identification of amino acids critical for the DNA binding and dimerization properties of the human retinoic acid receptor alpha. Importance of lysine 360, lysine 365, and valine 361

Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) activate target genes by binding to retinoic acid response elements (RAREs) as heterodimeric, asymmetrical complexes, and display a high degree of cooperativity in binding to RAREs. We have examined here the effect of lysine, cysteine, arginine, histidine, and tyrosine side chain chemical modification on the DNA binding, homo- and heterodimerization properties of the full-length human retinoic acid receptor alpha (hRARalpha). Lysines are the only residues to be engaged in the dimerization with human retinoid X receptor alpha (hRXRalpha) in the absence of DNA, whereas histidines are selectively involved in the homodimerization of hRARalpha in the presence of a RARE. Arginine modification affected the DNA binding activity of each type of dimer, whereas cysteines and tyrosines were primarily involved in the homo- or heterodimerization process in the presence of the same RARE. Modified lysines, interfering with the dimerization with hRXRalpha, were identified by receptor labeling and peptide mapping. They are located in the hormone binding domain eighth heptad repeat, at positions 360 and 365. In keeping with these results, mutation of Lys360, Val361, and Lys365 diminished strongly the DNA binding activity of hRARalpha as a homodimer or a heterodimer. Our results thus provide direct evidence for the differential involvement of basic, polar, or aromatic amino acids in the DNA binding, homodimerization, and heterodimerization properties of hRARalpha. Furthermore, they demonstrate the use of distinct dimerization interfaces and identify the type of amino acids involved in these protein-protein interactions.