A conformational switch in nuclear hormone receptors is involved in coupling hormone binding to corepressor release

A novel role for helix 12 of retinoid X receptor in regulating repression

Nutrients, drugs, and hormones influence transcription during differentiation and metabolism by binding to high-affinity nuclear receptors. In the absence of ligand, some but not all nuclear receptors repress transcription as a heterodimer with retinoid X receptor (RXR). Here we define a novel role for helix 12 (H12) in sterically masking the corepressor (CoR) binding site in apo-RXR. Removing H12 converts RXR to a potent transcriptional repressor. The length but not the specific sequence of H12 is critical for masking RXR's intrinsic repression function. This contrasts with the amphipathic character required for mediating ligand-dependent activation and coactivator recruitment. Physiologically, we show that heterodimerization of RXR with apo-thyroid hormone receptor (TR) unmasks the CoR binding site in RXR and allows the TR-RXR heterodimer to repress. A molecular mechanism that involves sequence-specific interaction between RXR H12 and the coactivator-binding surface of the nuclear receptor is proposed for this heterodimerization-mediated unmasking. Peroxisome proliferator-activated receptor gamma does not interact as well with RXR H12, thus explaining its inability to repress transcription as an RXR heterodimer. The requirement to unmask RXR's latent repression function explains why only certain RXR partners repress transcription.

Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes

The binding/escape mechanism of all- trans retinoic acid with respect to the ligand-binding domain of the nuclear receptor RARgamma has been studied by molecular dynamic simulations. The entry/exit channel was shown to be on the side of the activation helix by the use of multiple copy dynamics. Three independent minimum energy paths from the liganded structure to a model for the unliganded structure were calculated with the conjugate peak refinement method. Ligand escape takes place in the early steps of the transition during rearrangement of the binding pocket; the latter involves inward motion of the beta-sheet and outward motions of the Omega-loop and helix H6. The correlated rearrangements involved in the escape phase are similar and occur in the same order for the different paths. After the escape phase, the conformational changes affect primarily the C-terminal helices H11-H12 and the Omega-loop. The three paths are significantly different for this reorganization phase and reveal a multiplicity of possibilities, in agreement with the idea that the apo state is structurally less constrained. The present calculations extend the crystallographic results, confirming the "mouse trap" mechanism and stressing the importance of the helix H3 conformation and of the contacts between the Omega-loop and helices H11 and H6. They are in good agreement with known mutants and point to other functionally important residues, especially in helices H3 and H11, suggesting mutations that may affect the ligand-binding function and the associated conformational changes.

SMRTER, a Drosophila nuclear receptor coregulator, reveals that EcR-mediated repression is critical for development

The Drosophila ecdysone receptor (EcR)/ultraspiracle (USP) heterodimer is a key regulator in molting and metamorphoric processes, activating and repressing transcription in a sequence-specific manner. Here, we report the isolation of an EcR-interacting protein, SMRTER, which is structurally divergent but functionally similar to the vertebrate nuclear corepressors SMRT and N-CoR. SMRTER mediates repression by interacting with Sin3A, a repressor known to form a complex with the histone deacetylase Rpd3/HDAC. Importantly, we identify an EcR mutant allele that fails to bind SMRTER and is characterized by developmental defects and lethality. Together, these results reveal a novel nuclear receptor cofactor that exhibits evolutionary conservation in the mechanism to achieve repression and demonstrate the essential role of repression in hormone signaling.

Alien, a highly conserved protein with characteristics of a corepressor for members of the nuclear hormone receptor superfamily

Some members of nuclear hormone receptors, such as the thyroid hormone receptor (TR), silence gene expression in the absence of the hormone. Corepressors, which bind to the receptor's silencing domain, are involved in this repression. Hormone binding leads to dissociation of corepressors and binding of coactivators, which in turn mediate gene activation. Here, we describe the characteristics of Alien, a novel corepressor. Alien interacts with TR only in the absence of hormone. Addition of thyroid hormone leads to dissociation of Alien from the receptor, as shown by the yeast two-hybrid system, glutathione S-transferase pull-down, and coimmunoprecipitation experiments. Reporter assays indicate that Alien increases receptor-mediated silencing and that it harbors an autonomous silencing function. Immune staining shows that Alien is localized in the cell nucleus. Alien is a highly conserved protein showing 90% identity between human and Drosophila. Drosophila Alien shows similar activities in that it interacts in a hormone-sensitive manner with TR and harbors an autonomous silencing function. Specific interaction of Alien is seen with Drosophila nuclear hormone receptors, such as the ecdysone receptor and Seven-up, the Drosophila homologue of COUP-TF1, but not with retinoic acid receptor, RXR/USP, DHR 3, DHR 38, DHR 78, or DHR 96. These properties, taken together, show that Alien has the characteristics of a corepressor. Thus, Alien represents a member of a novel class of corepressors specific for selected members of the nuclear hormone receptor superfamily.

Retinoid-mediated signaling pathways in CD38 antigen expression in myeloid leukemia cells

The lymphocyte cell surface antigen CD38, which was originally described as a differentiation marker, has emerged as an important multifunctional protein. Its most intriguing and well characterized function is its ability to catalyze the synthesis of cyclic ADP-ribose (cADPR) from NAD. cADPR serves as an important second messenger in controlling the release of intracellular calcium from ryanodine-sensitive intracellular pools. By virtue of its ability to synthesize cADPR as well as to act as an adhesion and signal transduction molecule, CD38 may play a role in such diverse physiological processes as cell growth, apoptosis, differentiation, and inflammation. Equally interesting is the pattern of CD38 expression in hematopoietic cells. In the bone marrow, early precursor cells predominantly express CD38 antigen, whereas mature circulating blood cells lack or express very low levels. The expression is also high on malignant hematopoietic cells and thus may be of prognostic relevance in certain leukemias. Presently, there is little information available on the factors that regulate the expression of CD38 antigen in hematopoietic cells. In this review, we summarize recent findings on the regulation of CD38 antigen by retinoids (vitamin A and related compounds). At least in the myeloid cell lineage, retinoids appear to be exquisitely potent and specific inducers of CD38 antigen expression, and retinoid-induced expression of CD38 is mediated via activation of the retinoic acid-alpha (RAR alpha) nuclear receptor.

Retinoid isomers differ in the ability to induce release of SMRT corepressor from retinoic acid receptor-alpha

Nuclear hormone receptors are ligand-regulated transcription factors that modulate the expression of specific target genes in response to the binding of small, hydrophobic hormone ligands. Many nuclear hormone receptors, such as the retinoic acid receptors, can both repress and activate target gene expression; these bimodal transcription properties are mediated by the ability of these receptors to tether auxiliary factors, denoted corepressors and coactivators. Corepressors are typically bound by receptors in the absence of cognate hormone, whereas binding of an appropriate hormone agonist induces an allosteric alteration in the receptor resulting in release of the corepressor and recruitment of coactivator. Structural analysis indicates that there is a close induced fit between the hormone ligand and the receptor polypeptide chain. This observation suggests that different ligands, once bound, may confer distinct conformations on the receptor that may invoke, in turn, distinct functional consequences. We report here that different retinoids do differ in the ability to release corepressor once bound to retinoic acid receptor and suggest that these differences in corepressor release may manifest as differences in transcriptional regulation.

A novel natural mutation in the thyroid hormone receptor defines a dual functional domain that exchanges nuclear receptor corepressors and coactivators

In a patient with severe resistance to thyroid hormone (RTH), we found a novel mutation (leucine to serine in codon 454, L454S) of the thyroid hormone receptor beta. This mutation is in the ligand-dependent transactivation domain that has been shown to interact with transcriptional coactivators (CoAs). The mutant protein binds T3, but its ability to activate transcription of a positively regulated gene (TRE-tk-Luc), and to repress a negatively regulated gene (TSHalpha-Luc), is markedly impaired. As anticipated from its location, the L454S mutant interacts weakly with CoAs, such as SRC1 and glucocorticoid receptor interacting protein 1 (GRIP1) in gel mobility shift assays and in mammalian two-hybrid assays, even in the presence of the maximal dose of T3. In contrast, in the absence of T3, the L454S mutant interacts much more strongly with nuclear receptor corepressor (NCoR) than does the wild-type receptor, and the T3-dependent release of NCoR is markedly impaired. By comparison, the NCoR interaction and T3-dependent dissociation of an adjacent AF-2 domain mutant (E457A) are normal. These findings reveal that the Leu 454 is involved directly, or indirectly, in the release of corepressors (CoRs) as well as in the recruitment of CoAs. The strong interaction with NCoR at a physiological concentration of T3 results in constitutive activation of the TSH genes as well as constitutive silencing of positively regulated genes. When the dominant negative effect was examined among various mutants, it correlated surprisingly well with the potency of NCoR binding but not with the degree of impairment in CoA binding. These findings suggest that the defective release of NCoRs, along with retained dimerization and DNA binding, are critical features for the inhibitory action of mutant thyroid hormone receptors. These studies also suggest that helix 12 of the thyroid hormone receptor acts as a dual functional domain. After the binding of T3, its conformation changes, causing the disruption of CoR binding and the recruitment of CoAs.

Components of the SMRT corepressor complex exhibit distinctive interactions with the POZ domain oncoproteins PLZF, PLZF-RARalpha, and BCL-6

Many transcription factors function by repressing gene transcription. For a variety of these transcription factors the ability to physically recruit auxiliary proteins, denoted corepressors, is crucial for the ability to silence gene expression. We and others have previously implicated the SMRT corepressor in the actions of the PLZF transcription factor and in the function of its oncogenic derivative, PLZF-retinoic acid receptor (RARalpha), in promyelocytic leukemia. We report here that PLZF, and a structurally similar transcriptional repressor, BCL-6, can interact with a variety of corepressor proteins in addition to SMRT, including the mSin3A protein and (for PLZF) histone deacetylase-1. Unexpectedly, these additional interactions with corepressor components are nonequivalent for these otherwise similar oncoproteins, suggesting that transcriptional repression by BCL-6 and by PLZF may differ in mechanism. Furthermore, we demonstrate that the oncogenic PLZF-RARalpha chimera lacks several important corepressor interaction sites that are present in the native PLZF protein. Thus the t(11;17) translocation that creates the PLZF-RARalpha chimera generates an oncoprotein with potentially novel regulatory properties distinct from those of either parental protein. Our results demonstrate that otherwise similar transcription factors can differ notably in their interactions with the corepressor machinery.

Transcriptional silencing is defined by isoform- and heterodimer-specific interactions between nuclear hormone receptors and corepressors

Nuclear hormone receptors are ligand-regulated transcription factors that play critical roles in metazoan homeostasis, development, and reproduction. Many nuclear hormone receptors exhibit bimodal transcriptional properties and can either repress or activate the expression of a given target gene. Repression appears to require a physical interaction between a receptor and a corepressor complex containing the SMRT/TRAC or N-CoR/RIP13 polypeptides. We wished to better elucidate the rules governing the association of receptors with corepressors. We report here that different receptors interact with different domains in the SMRT and N-CoR corepressors and that these divergent interactions may therefore contribute to distinct repression phenotypes. Intriguingly, different isoforms of a single nuclear hormone receptor class also differ markedly in their interactions with corepressors, indicative of their nonidentical actions in cellular regulation. Finally, we present evidence that combinatorial interactions between different receptors can, through the formation of heterodimeric receptors, result in novel receptor-corepressor interactions not observed for homomeric receptors.

Signaling by tyrosine kinases negatively regulates the interaction between transcription factors and SMRT (silencing mediator of retinoic acid and thyroid hormone receptor) corepressor

Nuclear hormone receptors are hormone-regulated transcription factors that bind to specific sites on DNA and modulate the expression of adjacent target genes. Many nuclear hormone receptors display bimodal transcriptional properties; thyroid hormone receptors, for example, typically repress target gene expression in the absence of hormone, but activate target gene expression in the presence of hormone. The ability to repress is closely linked to the ability of the apo-receptor to physically bind to auxiliary corepressor proteins denoted SMRT (silencing mediator of retinoic acid and thyroid hormone receptor) and N-CoR (nuclear receptor corepressor), which, in turn, help mediate the actual molecular events involved in transcriptional silencing. We report here that repression by thyroid hormone receptors can be regulated not only by cognate hormone, but also by certain tyrosine kinase signal transduction pathways, such as that represented by the epidermal growth factor-receptor. Activation of tyrosine kinase signaling leads to inhibition of T3R-mediated repression with relatively little effect on activation. These effects appear to be mediated by a kinase-initiated disruption of the ability of T3R to interact with SMRT corepressor. Intriguingly, tyrosine kinase signaling similarly disrupted the interactions of SMRT with v-Erb A, with retinoic acid receptors, and with PLZF, a nonreceptor transcriptional repressor. We conclude that tyrosine kinase signaling exerts potentially important regulatory effects on transcriptional silencing mediated by a variety of transcription factors that operate through the SMRT corepressor complex.

Mechanisms of the mouse orphan nuclear receptor TR2-11-mediated gene suppression

The mouse orphan nuclear receptor TR2-11 functions as a repressor for reporter genes containing a direct repeat-5 or direct repeat-4 hormone response element. The functional domains responsible for its suppressive activity are defined, including the DNA-binding domain and the ligand-binding domain. The C-terminal 30 amino acid residues can be deleted without compromising its suppressive activity, whereas a deletion for 40 amino acids completely abolishes the suppressive activity and receptor dimerization, and reduces the DNA-binding affinity. Point mutation at three conserved leucine residues located on the predicted dimer interface abolishes the suppressive activity, receptor dimerization and its DNA binding property. However, mutation at two consecutive glutamate residues located within the hinge between the last two helices of the ligand-binding domain (helix 10 and helix 11 according to the human retinoid receptor X alpha structure) drastically reduces its DNA-binding affinity and abrogates the suppressive activity without compromising its ability to dimerize, indicating that receptor dimerization property can be functionally uncoupled from its suppressive activity. A transferable, active silencing activity is encoded within the DEF segment of the receptor molecule, as evidenced by the suppression of a GAL4 reporter by a chimeric protein containing the DNA-binding domain of GAL4 and the DEF segment of TR2-11. Moreover, the C-terminal 49 amino acid sequence is required for this trans-suppressive activity. It is suggested that TR2-11 functions as a repressor, mediated by mechanisms requiring high affinity DNA binding, receptor dimerization, and active silencing.

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.