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PubMed2000

CXR, a chicken xenobiotic-sensing orphan nuclear receptor, is related to both mammalian pregnane X receptor (PXR) and constitutive androstane receptor (CAR).

Nuclear receptors constitute a large family of ligand-modulated transcription factors that mediate cellular responses to small lipophilic molecules, including steroids, retinoids, fatty acids, and exogenous ligands. Orphan nuclear receptors with no known endogenous ligands have been discovered to regulate drug-mediated induction of cytochromes P450 (CYP), the major drug-metabolizing enzymes. Here, we report the cloning of an orphan nuclear receptor from chicken, termed chicken xenobiotic receptor (CXR), that is closely related to two mammalian xenobiotic-activated receptors, the pregnane X receptor (PXR) and the constitutive androstane receptor (CAR). Expression of CXR is restricted to tissues where drug induction of CYPs predominantly occurs, namely liver, kidney, small intestine, and colon. Furthermore, CXR binds to a previously identified phenobarbital-responsive enhancer unit (PBRU) in the 5'-flanking region of the chicken CYP2H1 gene. A variety of drugs, steroids, and chemicals activate CXR in CV-1 monkey cell transactivation assays. The same agents induce PBRU-dependent reporter gene expression and CYP2H1 transcription in a chicken hepatoma cell line. These results provide convincing evidence for a major role of CXR in the regulation of CYP2H1 and add a member to the family of xenobiotic-activated orphan nuclear receptors.

Amino Acid Sequence↗
PubMed1999

Hormone-independent transcriptional activation and coactivator binding by novel orphan nuclear receptor ERR3.

Orphan nuclear receptors share sequence homology with members of the nuclear receptor superfamily, but ligands are unknown or unnecessary. A novel orphan receptor, estrogen receptor-related protein 3 (ERR3), was identified by yeast two-hybrid screening, using the transcriptional coactivator glucocorticoid receptor interacting protein 1 (GRIP1) as bait. The putative full-length mouse ERR3 contains 458 amino acids and is closely related to two known orphan receptors ERR1 and ERR2. All the ERR family members share an almost identical DNA-binding domain, which has 68% amino acid identity with that of estrogen receptor. ERR3 bound specifically to an estrogen response element and activated reporter genes controlled by estrogen response elements, both in yeast and in mammalian cells, in the absence of any added ligand. A conserved AF-2 activation domain located in the hormone-binding domain of ERR3 was primarily responsible for transcriptional activation. The ERR3 AF-2 domain bound GRIP1 in a ligand-independent manner both in vitro and in vivo, through the LXXLL motifs of GRIP1, and GRIP1 functioned as a transcriptional coactivator for ERR3 in both yeast and mammalian cells. Expression of ERR3 in adult mouse was restricted; highest expression was observed in heart, kidney, and brain. In the mouse embryo no expression was observed at day 7, and highest expression occurred around the 11-15 day stages. Although ERR3 is much more closely related to ERR2 than to ERR1, the expression pattern for ERR3 was similar to that of ERR1 and distinct from that for ERR2, suggesting a unique role for ERR3 in development.

Amino Acid Sequence↗
PubMed2001

Orphan G protein-coupled receptor, GPR41, induces apoptosis via a p53/Bax pathway during ischemic hypoxia and reoxygenation.

Orphan receptors that couple to G protein without known ligands are considered to relate directly to drug discovery. Here, we examine the expression of various orphan receptors in H9c2 cells during ischemic hypoxia and reoxygenation. Among orphan receptors examined, the level of G protein-coupled receptor 41 (GPR41) mRNA increases significantly, with a peak at 2 h after reoxygenation, and recovers to the control level by 3 h after reoxygenation. The level of glyceraldehyde-3-phosphate dehydrogenase mRNA used as an internal control remains almost constant. The levels of c-fos and c-jun mRNA increase significantly with ischemic hypoxia and reoxygenation. The transfection of GPR41 into H9c2 cells results in a significant decrease in cell number, with DNA fragmentation observed by in vitro and in situ assay. The amount of p53 protein increases significantly in the nuclei of cells expressing GPR41, accompanying an increase in the transcriptional activity of p53. Consistent with the activation of p53, the level of bax mRNA is significantly increased, which leads to an increase in Bax protein. Furthermore, the expression of a deletion mutant of a GPR41, which lacks the G protein binding site and shows an attenuation of intracellular phosphorylation signals to H9c2 cells, inhibits cell death and the increase in p53 protein within 24 h after reoxygenation. These observations demonstrate that GPR41 is a novel receptor that activates p53 leading to apoptosis during reoxygenation after ischemic hypoxia in H9c2 cells. We have designated GPR41 as the hypoxia-induced apoptosis receptor, HIA-R.

Animals↗
PubMed2002

Orphan nuclear hormone receptor Rev-erbalpha regulates the human apolipoprotein CIII promoter.

Apolipoprotein CIII (apoCIII) plays an important role in plasma triglyceride and remnant lipoprotein metabolism. Because hypertriglyceridemia is an independent risk factor in coronary artery disease and the presence in plasma of triglyceride-rich remnant lipoproteins is correlated with atherosclerosis, considerable research efforts have been focused on the identification of factors regulating apoCIII gene expression to decrease its production. Here we report that the orphan nuclear hormone receptor Rev-erbalpha regulates the human apoCIII gene promoter. In apoCIII expressing human hepatic HepG2 cells, transfection of Rev-erbalpha specifically repressed apoCIII gene promoter activity. We determined by deletion and site-directed mutagenesis experiments that Rev-erbalpha dependent repression is mainly due to an element present in the proximal promoter of the apoCIII gene. In contrast, we found no functional Rev-erbalpha response elements in the convergently transcribed human apoAI gene or the common regulatory enhancer. The identified Rev-erbalpha response element coincides with a RORalpha1 element, and in the present study we provide evidence that functional cross-talk between these orphan receptors modulates the apoCIII promoter. In vitro binding analysis showed that monomers of Rev-erbalpha bound this element but not another upstream RORalpha1 response element. In addition, we showed that the closely related nuclear orphan receptor RVR also specifically repressed the human apoCIII gene. These studies underscore a novel physiological role for members of the Rev-erb family of nuclear receptors in the regulation of genes involved in triglyceride metabolism and the pathogenesis of atherosclerosis.

Apolipoprotein C-III↗
PubMed2004

Comparison of household-survey estimates with projections of mortality and orphan numbers in sub-Saharan Africa in the era of HIV/AIDS.

The United Nations publishes estimates of HIV prevalence, AIDS mortality, and orphan numbers for all countries of the world. It is important to assess the validity of these model-based estimates since they underpin much policy concerned with care and prevention. Household surveys that ask questions about the survival of children's parents (orphanhood) offer an independent source of data with which these estimates can be compared. Survey estimates of maternal and paternal orphans are significantly lower than model estimates for 40 surveys in 36 countries of sub-Saharan Africa (p < 0.001, p = 0.002). This is probably because adult mortality from causes other than AIDS is lower than assumed in the models, although under-reporting of orphanhood in surveys may also play a role. Reducing adult mortality from causes other than AIDS brings the model estimates into close agreement with the surveys. This suggests that the fraction of orphans attributable to AIDS is greater than estimated previously.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Regulation of xenobiotic metabolism by orphan nuclear receptors.

Nuclear receptors control gene transcription by binding to specific promoter regions of DNA in the presence of ligand. Orphan nuclear receptors are nuclear receptors for which the endogenous ligand(s) has yet to be identified. Systematic evaluation of orphan nuclear receptors can elucidate species differences in xenobiotic metabolism in addition to aiding in identification of endogenous ligands. The receptor-binding affinity and specificity of various chemicals, with subsequent determination of the genes controlled by nuclear receptors, are goals of investigations into orphan nuclear receptor structure/function and can provide valuable tools in predicting drug interactions and toxicity.

Animals↗
PubMed1999

Orphans of the AIDS epidemic in the United States: transition-related characteristics and psychosocial adjustment at 6 months after mother's death.

This study has two purposes: (1) to describe the characteristics related to the transition to orphanhood for children whose mothers die from AIDS and (2) to examine the psychosocial adjustment of these children at six months following maternal death. Twenty orphans and a control sample of 40 children from the same neighbourhoods, as well as their mothers or care-givers, served as participants. Two assessments occurred: (1) prior to the death of the mother in the orphan group and (2) six months after her death. The results indicated that relatives, particularly maternal grandparents, became the new care-giver of the orphans, no more than one residential move had occurred following the mother's death, and the new care-givers were providing a stable home environment. Child psychosocial adjustment did not change following maternal death.

Acquired Immunodeficiency Syndrome↗
PubMed1997

Modulation of retinoic acid sensitivity in lung cancer cells through dynamic balance of orphan receptors nur77 and COUP-TF and their heterodimerization.

The diverse function of retinoic acid (RA) is mediated by its nuclear receptors, the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). However, the RA response is often lost in cancer cells that express the receptors. Previously, it was demonstrated that the RA response is regulated by the COUP-TF orphan receptors. Here, we present evidence that nur77, another orphan receptor whose expression is highly induced by phorbol esters and growth factors, is involved in modulation of the RA response. Expression of nur77 enhances ligand-independent transactivation of RA response elements (RAREs) and desensitizes their RA responsiveness. Conversely, expression of COUP-TF sensitizes RA responsiveness of RAREs by repressing their basal transactivation activity. Unlike the effect of COUP-TFs, the function of nur77 does not require direct binding of nur77 to the RAREs, but is through interaction between nur77 and COUP-TFs. The interaction occurs in solution and results in inhibition of COUP-TF RARE binding and transcriptional activity. Unlike other nuclear receptors, a large portion of the carboxy-terminal end of nur77 is not required for its interaction with COUP-TF. In human lung cancer cell lines, COUP-TF is highly expressed in RA-sensitive cell lines while nur77 expression is associated with RA resistance. Stable expression of COUP-TF in nur77-positive, RA-resistant lung cancer cells enhances the inducibility of RARbeta gene expression and growth inhibition by RA. These observations demonstrate that a dynamic equilibrium between orphan receptors nur77 and COUP-TF, through their heterodimerization that regulates COUP-TF RARE binding, is critical for RA responsiveness of human lung cancer cells.

Animals↗
PubMed2001

The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes.

In genome projects of eukaryotic model organisms, a large number of novel genes of unknown function and evolutionary history ("orphans") are being identified. Since many orphans have no known homologs in distant species, it is unclear whether they are restricted to certain taxa or evolve rapidly, either because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving genes from a single sequence of Drosophila melanogaster. Thirteen candidate genes were chosen from the Adh region on the second chromosome and 1 from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of these in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insertions/deletions. A population survey of this gene suggests that its rapid evolution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed "normal" levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame within exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.

Animals↗
PubMed1998

The orphan nuclear receptor, COUP-TF II, inhibits myogenesis by post-transcriptional regulation of MyoD function: COUP-TF II directly interacts with p300 and myoD.

COUP-TF II is an orphan nuclear receptor that has no known ligand in the 'classical sense'. COUP-TF interacts with the corepressors N-CoR, SMRT and RIP13, and silences transcription by active repression and trans-repression. Forced expression of the orphan nuclear receptor COUP-TF II in mouse C2 myogenic cells has been demonstrated to inhibit morphological differentiation, and to repress the expression of: (i) the myoD gene family which encodes myogenic basic helix-loop-helix (bHLH) proteins; and (ii) the cell cycle regulator, p21(Waf-1/Cip-1). In the present study, we show that COUP-TF II efficiently inhibits the myoD -mediated myogenic conversion of pluripotential C3H10T1/2 cells by post-transcriptional mechanisms. Furthermore, repression of MyoD-dependent transcription by COUP-TF II occurs in the absence of the nuclear receptor cognate binding motif. The inhibition of MyoD-mediated trans-activation involves the direct binding of the DNA binding domain/C-region and hinge/D-regions [i.e. amino acid (aa) residues 78-213] of COUP-TF II to the N-terminal activation domain of MyoD. Over-expression of the cofactor p300, which functions as a coactivator of myoD-mediated transcription, alleviated repression by COUP-TF II. Further binding analysis demonstrated that COUP-TF II interacted with the N-terminal 149 aa residues of p300 which encoded the receptor interaction domain of the coactivator. Finally we observed that COUP-TF II, MyoD and p300 interact in a competitive manner, and that increasing amounts of COUP-TF II have the ability to reduce the interaction between myoD and p300 invitro. The experiments presented herein suggest thatCOUP-TF II post-transcriptionally regulates myoD activity/function, and that crosstalk between orphan nuclear receptors and the myogenic bHLH proteins has functional consequences for differentiation.

3T3 Cells↗
PubMed2001

Differential transcription of the orphan receptor RORbeta in nuclear extracts derived from Neuro2A and HeLa cells.

An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been identified. Very little is known about how these 'orphan' receptors regulate transcription. In this study we have analysed the biochemical and transcriptional properties of the neuronally expressed orphan nuclear receptor RORbeta (NR1F2) and compared them with the retinoic acid receptor heterodimer RXRalpha-RARalpha (NR2B1-NR1B1) and Gal-VP16 in vitro. Although RORbeta binds to its DNA-binding sites with comparatively low affinity, it efficiently directs transcription in nuclear extracts derived from a neuronal cell line, Neuro2A, but not in nuclear extracts from non-neuronal HeLa cells. In contrast, RXRalpha-RARalpha and the acidic transcription factor Gal-VP16 support transcription in Neuro2A and HeLa nuclear extracts equally efficiently. These observations point to a different (co)factor requirement for transactivation by members of the NR1 subfamily of nuclear receptors.

Base Sequence↗
PubMed2006

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

Algorithms↗
PubMed2003

Using nondenaturing mass spectrometry to detect fortuitous ligands in orphan nuclear receptors.

Nondenaturing electrospray mass spectrometry (ESI-MS) has been used to reveal the presence of potential ligands in the ligand-binding domain (LBD) of orphan nuclear receptors. This new approach, based on supramolecular mass spectrometry, allowed the detection and identification of fortuitous ligands for the retinoic acid-related orphan receptor beta (RORbeta) and the ultraspiracle protein (USP). These fortuitous ligands were specifically captured from the host cell with the proper stoichiometry. After organic extraction, these molecules have been characterized by classic analytical methods and identified as stearic acid for RORbeta and a phosphatidylethanolamine (PE) for USP, as confirmed by crystallography. These molecules act as "fillers" and may not be the physiological ligands, but they prove to be essential to stabilize the active conformation of the LBD, enabling its crystallization. The resulting crystal structures provide a detailed picture of the ligand-binding pocket, allowing the design of highly specific synthetic ligands that can be used to characterize the function of orphan nuclear receptors. An additional advantage of this new method is that it is not based on a functional test and that it can detect low-affinity ligands.

Animals↗
PubMed2005

A 2-year follow-up of orphans' competence, socioemotional problems and post-traumatic stress symptoms in traditional foster care and orphanages in Iraqi Kurdistan.

BACKGROUND: This paper aims to compare orphans' development in two different care systems. METHODS: Based on age, sex, psychological trauma scores, competence and psychological problem scores, two comparable samples were found representing orphans in the traditional foster care (n = 94) and the orphanages (n = 48) in a middle-large city in Iraqi Kurdistan. At an index interview, Child Behaviour Checklist (CBCL), Harvard-Uppsala Trauma Questionnaire for Children and Post-traumatic Stress Symptoms for Children (PTSS-C) were administered to the caregivers. After 1 year the CBCL, and after 2 years both the CBCL and the PTSS-C, were-re-administered, consecutively. RESULTS: Although both samples revealed significant decrease in the means of total competence and problem scores over time, the improvement in activity scale, externalizing problem scores and post-traumatic stress disorder-related symptoms proved to be more significant in the foster care than in the orphanages. While the activity scale improved in the foster care, the school competence deteriorated in both samples, particularly among the girls in the orphanages. The improvement of boys' activity scores in the foster care, and deterioration of girls' school competence in the orphanages were the most significant gender differences between samples over time. CONCLUSIONS: Even if the two orphan care systems showed more similarities than differences, the foster care revealed better outcomes over time. The results are discussed in relation to gender, age, socio-economic situation, cultural values and the characteristics of each care system.

Adolescent↗
PubMed2004

Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator.

RitR (formerly RR489) is an orphan two-component signal transduction response regulator in Streptococcus pneumoniae that has been shown to be required for lung pathogenicity. In the present study, by using the rough strain R800, inactivation of the orphan response regulator gene ritR by allele replacement reduced pathogenicity in a cyclophosphamide-treated mouse lung model but not in a thigh model, suggesting a role for RitR in regulation of tissue-specific virulence factors. Analysis of changes in genome-wide transcript mRNA levels associated with the inactivation of ritR compared to wild-type cells was performed by the use of high-density DNA microarrays. Genes with a change in transcript abundance associated with inactivation of ritR included piuB, encoding an Fe permease subunit, and piuA, encoding an Fe carrier-binding protein. In addition, a dpr ortholog, encoding an H(2)O(2) resistance protein that has been shown to reduce synthesis of reactive oxygen intermediates, was activated in the wild-type (ritR(+)) strain. Microarray experiments suggested that RitR represses Fe uptake in vitro by negatively regulating the Piu hemin-iron transport system. Footprinting experiments confirmed site-specific DNA-binding activity for RitR and identified three binding sites that partly overlap the +1 site for transcription initiation upstream of piuB. Transcripts belonging to other gene categories found to be differentially expressed in our array studies include those associated with (i) H(2)O(2) resistance, (ii) repair of DNA damage, (iii) sugar transport and capsule biosynthesis, and (iv) two-component signal transduction elements. These observations suggest that RitR is an important response regulator whose primary role is to maintain iron homeostasis in S. pneumoniae. The name ritR (repressor of iron transport) for the orphan response regulator gene, rr489, is proposed.

Animals↗
PubMed1992

COUP orphan receptors are negative regulators of retinoic acid response pathways.

The vitamin hormone retinoic acid (RA) regulates many complex biological programs. The hormonal signals are mediated at the level of transcription by multiple nuclear receptors. These receptors belong to the steroid/thyroid hormone receptor superfamily that also includes a large number of orphan receptors whose biological roles have not yet been determined. Although much has been learned in recent years about RA receptor (RAR) functions, little is known about how specific RA response programs are restricted to certain tissues and cell types during development and in the adult. It has been recently shown that RAR activities are regulated by retinoid X receptors (RXR) through heterodimer formation. In an effort to isolate and further characterize nuclear receptors that modulate RAR and/or RXR activities, we have screened cDNA libraries by using a RXR alpha cDNA probe. Two clones, COUP alpha and COUP beta, identical and closely related to the orphan receptor COUP-TF, were obtained. We show that COUP proteins dramatically inhibit retinoid receptor activities on certain response elements that are activated by RAR/RXR heterodimers or RXR homodimers. COUP alpha and -beta bind strongly to these response elements, including a palindromic thyroid hormone response element and a direct repeat RA response element as well as an RXR-specific response element. In addition, we found that the previously identified COUP-TF binding site in the ovalbumin gene functions in vitro as an RA response element that is repressed in the presence of COUP. Our data suggest that the COUP receptors are a novel class of RAR and RXR regulators that can restrict RA signaling to certain elements. The COUP orphan receptors may thus play an important role in cell- or tissue-specific repression of subsets of RA-sensitive programs during development and in the adult.

Base Sequence↗
PubMed1995

Determinants of target gene specificity for ROR alpha 1: monomeric DNA binding by an orphan nuclear receptor.

The ROR alpha isoforms are orphan members of the steroid/thyroid/retinoid receptor superfamily. Previous DNA-binding studies indicated that ROR alpha isoforms bind to response elements consisting of a single copy of the core recognition sequence AGGTCA preceded by a 6-bp A/T-rich sequence and that the distinct amino-terminal domains of each isoform influence DNA-binding specificity. In this report, we have investigated in detail the protein determinants of target gene specificity for the ROR alpha 1 isoform and have now identified the minimal sequence both in its amino- and carboxy-terminal domains required for high-affinity DNA binding. High-resolution methylation and ethylation interference analyses and mixing of truncated proteins in a DNA-binding assay show that ROR alpha 1 presumably binds along one face of the DNA helix as a monomer. By analogy to previous studies of the orphan receptors NGFI-B and FTZ-F1, extensive mutational analysis of the ROR alpha 1 protein shows that a domain extending from the carboxy-terminal end of the second conserved zinc-binding motif is required for specific DNA recognition. However, point mutations and domain swap experiments between ROR alpha 1 and NGFI-B demonstrated that sequence-specific recognition dictated by the carboxy-terminal extension is determined by distinct subdomains in the two receptors. These results demonstrate that monomeric nuclear receptors utilize diverse mechanisms to achieve high-affinity and specific DNA binding and that ROR alpha 1 represents the prototype for a distinct subfamily of monomeric orphan nuclear receptors.

Amino Acid Sequence↗
PubMed2004

The identification of ligands at orphan G-protein coupled receptors.

The completion of the human genome sequencing project has identified approximately 720 genes that belong to the G-protein coupled receptor (GPCR) superfamily. Approximately half of these genes are thought to encode sensory receptors. Of the remaining 360 receptors, the natural ligand has been identified for approximately 210 receptors, leaving 150 so-called orphan GPCRs with no known ligand or function. The identification of ligands active at orphan GPCRs has been achieved through the development of a number of experimental approaches, including the screening of putative small molecule and peptide ligands, reverse pharmacology, and the use of bioinformatics to predict candidate ligands. In this review, we discuss the methodologies developed for the identification of ligands at orphan GPCRs and include examples of their successful application.

Humans↗