A four-amino-acid insertion in the ligand-binding domain inactivates hRXRbeta and renders dominant negative activity

Splice variants of metabolic nuclear receptors: Relevance for metabolic disease and therapeutic targeting

Metabolic nuclear receptors are ligand-activated transcription factors which control a wide range of metabolic processes and signaling pathways in response to nutrients and xenobiotics. Targeting these NRs is at the forefront of our endeavours to generate novel treatment options for diabetes, metabolic syndrome and fatty liver disease. Numerous splice variants have been described for these metabolic receptors. Structural changes, as a result of alternative splicing, lead to functional differences among NR isoforms, resulting in the regulation of different metabolic pathways by these NR splice variants. In this review, we describe known splice variants of FXR, LXRs, PXR, RXR, LRH-1, CAR and PPARs. We discuss their structure and functions, and elaborate on the regulation of splice variant abundance by nutritional signals. We conclude that NR splice variants pose an intriguing new layer of complexity in metabolic signaling, which needs to be taken into account in the development of treatment strategies for metabolic diseases.

Function of alternative splicing

Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from the surprisingly low number of human genes. Unlike promoter activity, which primarily regulates the amount of transcripts, alternative splicing changes the structure of transcripts and their encoded proteins. Together with nonsense-mediated decay (NMD), at least 25% of all alternative exons are predicted to regulate transcript abundance. Molecular analyses during the last decade demonstrate that alternative splicing determines the binding properties, intracellular localization, enzymatic activity, protein stability and posttranslational modifications of a large number of proteins. The magnitude of the effects range from a complete loss of function or acquisition of a new function to very subtle modulations, which are observed in the majority of cases reported. Alternative splicing factors regulate multiple pre-mRNAs and recent identification of physiological targets shows that a specific splicing factor regulates pre-mRNAs with coherent biological functions. Therefore, evidence is now accumulating that alternative splicing coordinates physiologically meaningful changes in protein isoform expression and is a key mechanism to generate the complex proteome of multicellular organisms.

Molecular cloning and characterization of two novel human RXR alpha splice variants

Two novel cDNAs encoding RXR alpha splice variants (RXR alpha 2 and RXR alpha 3) were identified among human full-length cDNA libraries. RXR alpha 2 and RXR alpha 3 cDNAs possess open reading frames, leading to production of proteins lacking the N-terminal 27 and 97 amino acid residues of the RXR alpha 1 product, respectively. RXR alpha 2 and RXR alpha 3 genes have respective 5'-terminal exons. RXR alpha 3 is expressed in brain, spleen and prostate whereas the expression of RXR alpha 2 was below the detectable level. Both RXR alpha 2 and RXR alpha 3 showed a level of transcriptional activity and a dose response curve against the agonist LG100268 similar to RXR alpha 1 in reporter assay for the RXR alpha homodimer or that for the heterodimer with PPAR gamma 2. However, clear differences were observed among the splice variants when dose response curves were compared by the assay in the presence of coactivators such as SRC-1 and PGC-1. These results suggest specific physiological roles of two novel human RXR alpha splice variants.

Alternatively spliced isoforms of the human constitutive androstane receptor

The nuclear receptor CAR (NR1I3) regulates transcription of genes encoding xenobiotic- and steroid-metabolizing enzymes. Regulatory processes that are mediated by CAR are modulated by a structurally diverse array of chemicals including common pharmaceutical and environmental agents. Here we describe four in-frame splice variants of the human CAR receptor gene. The variant mRNA splice transcripts were expressed in all human livers evaluated. Molecular modeling of the splice variant proteins predicts that the structural effects are localized within the receptor's ligand-binding domain. Assays to assess function indicate that the variant proteins, when compared with the reference protein isoform, exhibit compromised activities with respect to DNA binding, transcriptional activation and coactivator recruitment.

Vitamin D receptor and retinoid X receptor interactions in motion

Vitamin D receptor (VDR) and retinoid X receptor (RXR) are members of the nuclear receptor superfamily and they bind target DNA sequences as heterodimers to regulate transcription. This article surveys the latest findings regarding the roles of dimerizing RXR in VDR function and emphasizes potential areas for future developments. We first highlight the importance of dimerization with RXR for both the ligand-independent (hair growth) and ligand-dependent functions of VDR (calcium homeostasis, bone development and mineralization, control of cell growth and differentiation). Emerging information regarding the regulatory control of dimerization based on biochemical, structural, and genetic studies is then presented. Finally, the main focus of this article is a new dynamic perspective of dimerization functions, based on recent research with fluorescent protein chimeras in living cells by microscopy. These studies revealed that both VDR and RXR constantly shuttle between the cytoplasm and the nucleus and between subnuclear compartments, and showed the transient nature of receptor--DNA and receptor--coregulator interactions. Because RXR dimerizes with most of the nuclear receptors, regulation of receptor dynamics by RXR has a broad significance.

RXR beta isoforms in neuroblastoma cells and evidence for a novel 3'-end transcript

RXR beta is predominantly involved in retinoid responses in neuroblastoma cells, in particular the N-type SH SY 5Y cells and the S-type SH S EP cells, both derivatives of a mixed phenotype neuroblastoma cell line. The aim of this study was to identify RXR beta isoforms expressed in neuroblastoma cells and to characterise a putative novel RXR beta transcript. RXR beta 1 and RXR beta 2 were expressed in these neuroblastoma cells. An isoform with an insertion into the ligand binding domain, RXR beta(SLSR) (referred to in previous studies as RXR beta 3), was expressed at a similar level to RXR beta. A novel RXR beta transcript was identified by RNase protection assays and was at least as abundant as the expected RXR beta transcript and expressed in other cell types. Evidence suggests that this novel transcript was transcribed from an internal promoter between exons 5 and 6, contained a retained intron (intron 6) and was alternatively spliced with and without the SLSR insertion. These data show that the pattern of RXR beta expression is complex. The relative abundance of the novel RXR beta transcript suggests that it may be an important aspect of RXR beta function or regulation in a range of cell types.

Differential regulation of ligand-dependent and ligand-independent functions of the mouse retinoid X receptor beta by alternative splicing

RXR is involved in two distinct signal transduction pathways. RXR activates transcription ligand-dependently on RXRE and behaves as a positive heterodimer partner with permissive receptors; while it behaves as a ligand-independent silent partner with nonpermissive receptors. We studied the functions of a unique isoform of mouse RXRbeta2 (mRXRbeta2E) which has an in-frame four-amino-acid insertion in the ligand binding domain. mRXRbeta2E did not bind 9-cis RA with high affinity and did not activate transcription on RXRE. However, mRXRbeta2E formed heterodimers with TR, VDR, RAR, and LXR, and enhanced transcriptional activity of the nonpermissive VDR to the same extent as mRXRbeta2. With the permissive LXR, mRXRbeta2E did not show 9-cis RA-dependent transactivation and inhibited mRXRbeta2 activity. Thus, although mRXRbeta2E can perform ligand-independent functions of RXR, it cannot mediate the ligand-dependent functions of RXR, indicating that alternative splicing plays an important role in the differential regulation of these two important functions of RXR.

Identification and characterization of baxepsilon, a novel bax variant missing the BH2 and the transmembrane domains

The Bax gene is a member of the Bcl2 family that functions to regulate the programmed cell death process. A number of Bax isoforms have been previously identified: alpha, beta, gamma, delta, and omega. Here we report the identification and characterization of an additional Bax variant, termed Baxepsilon. The newly identified Bax variant contains a 97-base insertion generated by alternative splicing which includes a previously unidentified exon between exons 4 and 5. The insertion causes the production of a truncated Bax protein, termed Baxepsilon, which encodes a protein of 164 residues with a calculated molecular weight of 18 kDa. The last 69 amino acids of Baxalpha that encompass the BH2 and the TM domains are missing in Baxepsilon. The Baxepsilon protein, when expressed as a GST fusion protein, associated efficiently with Baxalpha, Baxepsilon, Bcl2, and Bcl-xL. In addition, Baxepsilon was active in inducing apoptosis when tested in a transient transfection assay. Furthermore, the presence of antiapoptotic genes including Bcl2, Bcl-xL, and baculovirus p35 abrogated Baxepsilon and Baxalpha function. Although the newly identified Bax variant was detectable by RT-PCR in several normal mouse tissues, the role of this variant in controlling programmed cell death is currently unknown.