AUF1 binding affinity to A+U-rich elements correlates with rapid mRNA degradation

Identification and characterization of proteins binding A + U-rich elements

A + U-Rich elements (AREs) have been extensively investigated as cis-acting determinants of rapid mRNA turnover. Recently, a number of RNA-binding proteins interacting with AREs have been described. This article presents strategies and techniques used by our laboratory to identify and characterize a family of ARE-binding proteins collectively termed AUF1. However, these techniques may be applied to the study of any protein displaying sequence-specific RNA binding activity. The techniques described here include the purification of native AUF1 from cultured cells as well as the preparation of recombinant AUF1 proteins using a bacterial expression system. Analyses of RNA-protein interactions are also described, including the use of gel mobility shift assays with synthetic RNA probes to monitor specific RNA binding activity in cell extracts or with recombinant proteins. Variations of this technique are also described to evaluate the RNA binding affinity of recombinant proteins and the use of specific RNA competitors to assess RNA determinants of protein binding specificity. Other techniques presented include the identification of specific proteins in RNA:protein complexes using antibody supershifts and the estimation of molecular weights of RNA-binding proteins by UV crosslinking. Results of individual experiments are presented as examples of some techniques. Throughout the article, suggestions are included to avoid commonly encountered problems and to assist in the optimization of these techniques for the study of other RNA-binding proteins.

Agonist-mediated destabilization of human beta1-adrenergic receptor mRNA: role of the 3' untranslated translated region

For proto-oncogenes and cytokines, regulation of gene expression at the level of mRNA stability is well established. In contrast, there is comparatively limited knowledge regarding this mechanism of regulation for G-protein-coupled receptors. To explore this process further, the human beta1-adrenergic receptor (AR) was stably expressed in tsAF8 cells. Treatment with beta-agonist decreased the half-life of beta1-AR mRNA by approximately 50%. Removal of the 3'UTR from the beta1-AR (coding region only) dramatically stabilized mRNA. Additionally, in a chimeric mRNA, the beta1-AR 3'UTR was able to target the normally highly stable beta-globin mRNA for accelerated decay. However, the chimera did not undergo agonist-mediated destabilization indicating that the 3'UTR may be "necessary but not sufficient" for agonist-mediated mRNA destabilization. Inhibition of translation significantly stabilized beta1-AR mRNA (approximately 2-fold); however, pretreatment of cells with beta-agonist prior to translational arrest produced the same degree of mRNA destabilization indicating that agonist-mediated destabilization may be independent of the translation process. Conversely, translational inhibition simultaneous with beta-agonist exposure abrogated agonist-mediated destabilization indicating a dependence on de novo protein synthesis.

Regulation of interleukin-1beta-induced interleukin-6 gene expression in human fibroblast-like synoviocytes by p38 mitogen-activated protein kinase

Involvement of p38 mitogen-activated protein (MAP) kinase in interleukin (IL)-6 gene expression of human fibroblast-like synoviocytes (FLSs) was assessed. p38 MAP kinase was constitutively expressed in human FLSs and activated in response to IL-1beta. A pyridinylimidazole compound, SB203580, inhibited p38 MAP kinase activity in vivo, since the activity of MAPKAP kinase-2 (a substrate of p38 MAP kinase) in IL-1beta-stimulated FLSs was totally suppressed by it. SB203580 concentration-dependently inhibited protein production and gene expression of IL-6 by human FLSs. The effect of SB203580 was dependent on de novo protein synthesis. SB203580 significantly reduced the stability of IL-6 mRNA without affecting the rate of IL-6 gene transcription. Here, we provide evidence that p38 MAP kinase is activated in response to IL-1beta in human FLSs and is involved in IL-6 synthesis by stabilizing IL-6 mRNA.

Microtubule involvement in translational regulation of fibronectin expression by light chain 3 of microtubule-associated protein 1 in vascular smooth muscle cells

Our previous studies suggested that enhanced fibronectin mRNA translation in ductus arteriosus compared with aortic smooth muscle cells is related to increased expression of light chain 3 (LC3) of microtubule-associated protein 1, which binds an AU-rich element in the 3' untranslated region of fibronectin mRNA. We therefore hypothesized that microtubules are involved in LC3-mediated fibronectin mRNA translational regulation. In this study we show that disruption of microtubules by colchicine inhibits fibronectin mRNA translation in cultured ductus arteriosus smooth muscle cells. We proposed that the mechanism might be related to decreased docking of fibronectin mRNA on the translational machinery, ie, membrane-bound polysomes on rough endoplasmic reticulum, and confirmed this by Northern blot analysis. To investigate the mechanism further, we carried out polysome analysis using sucrose gradient centrifugation and fractionation and studied the polysomal distribution of fibronectin mRNA and LC3 protein in the sucrose gradient by using RNase protection assay and Western immunoblotting, respectively. Colchicine treatment shifts fibronectin mRNA from the fractions containing membrane-bound polysomes to the fractions carrying free polysomes and concomitantly decreases the amount of LC3 protein in the fractions containing membrane-bound polysomes. Furthermore, an EDTA-release experiment demonstrates that LC3 protein associates with the 60S ribosomal subunit. Our data support the concept that microtubules may function with LC3 to facilitate sorting of fibronectin mRNA onto rough endoplasmic reticulum and translation.

In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein

The function(s) and RNA binding properties of vigilin, a ubiquitous protein with 14 KH domains, remain largely obscure. We recently showed that vigilin is the estrogen-inducible protein in polysome extracts which binds specifically to a segment of the 3' untranslated region (UTR) of estrogen-stabilized vitellogenin mRNA. In order to identify consensus mRNA sequences and structures important in binding of vigilin to RNA, before vigilin was purified, we developed a modified in vitro genetic selection protocol. We subsequently validated our selection procedure, which employed crude polysome extracts, by testing natural and in vitro-selected RNAs with purified recombinant vigilin. Most of the selected up-binding mutants exhibited hypermutation of G residues leading to a largely unstructured, single-stranded region containing multiple conserved (A)nCU and UC(A)n motifs. All eight of the selected down-binding mutants contained a mutation in the sequence (A)nCU. Deletion analysis indicated that approximately 75 nucleotides are required for maximal binding. Using this information, we predicted and subsequently identified a strong vigilin binding site near the 3' end of human dystrophin mRNA. RNA sequences from the 3' UTRs of transferrin receptor and estrogen receptor, which lack strong homology to the selected sequences, did not bind vigilin. These studies describe an aproach to identifying long RNA binding sites and describe sequence and structural requirements for interaction of vigilin with RNAs.

Structure and genomic organization of the human AUF1 gene: alternative pre-mRNA splicing generates four protein isoforms

The steady-state levels of many mRNAs are determined in part by their turnover rates. Turnover rates, in turn, are usually controlled by proteins that bind cis-acting sequence elements in mRNAs. One class of cis-acting instability determinants is composed of A + U-rich elements present in the 3'-UTRs of many labile mRNAs. Many A + U-rich elements are bound by the AUF1 family of RNA-binding proteins, which may target these mRNAs for rapid decay. cDNA cloning and immunoblot analyses suggest that the AUF1 family consists of at least four isoforms. Previous genomic cloning combined with FISH and Southern analyses of a panel of monochromosomal mouse/human or hamster/human somatic cell hybrids localized two AUF1 loci to human 4q21.1-q21.2 and Xq12 (B. Wagner et al., 1996, Genomics 34: 219-222). In the present study AUF1 gene organization was examined. The results suggest that the four known AUF1 isoforms are generated by alternative pre-mRNA splicing of a transcript encoded by the chromosome 4 locus. Functionally, this creates isoforms with different RNA-binding affinities and specificities. Thus, alternative pre-mRNA splicing may serve to create functional versatility within the AUF1 family of proteins.

Agonist regulation of human beta2-adrenergic receptor mRNA stability occurs via a specific AU-rich element

Prolonged agonist stimulation of beta2-adrenergic receptors results in receptor down-regulation, which is closely associated with a reduction of the corresponding mRNA, an effect mediated in part by changes in mRNA stability. Transfection experiments with human beta2-adrenergic receptor cDNAs bearing or lacking the untranslated regions suggested that the essential agonist sensitivity of the mRNA resides within the 3'-untranslated region. The importance of this region was further confirmed in gel shift experiments; cytosolic preparations from agonist-stimulated DDT1-MF2 smooth muscle cells caused a shift of beta2-adrenergic receptor mRNAs containing the 3'-untranslated region. Progressive 3'-terminal truncations of the receptor cDNA led to the identification of an AU-rich element at positions 329-337 of the 3'-untranslated region as the responsible cis-acting element. Substitution of this motif by cytosine residues almost completely abolished mRNA down-regulation and inhibited the formation of the RNA-protein complex. Even though the beta2-adrenergic receptor AU-rich element showed two U --> A transitions compared with the recently proposed AU-rich element consensus sequence, it revealed an almost identical destabilizing potency. Fusion of the beta2-adrenergic receptor 3'-untranslated region to the beta-globin coding sequence dramatically reduced the half-life of the chimeric transcript in an agonist- and cAMP-dependent manner. This suggests that the agonist-induced beta2-adrenergic receptor mRNA destabilization is regulated by cAMP-dependent RNA-binding protein(s) via a specific AU-rich element.

Structural determinants in AUF1 required for high affinity binding to A + U-rich elements

AUF1 is an RNA-binding protein that contains two nonidentical RNA recognition motifs (RRMs). AUF1 binds to A + U-rich elements (AREs) with high affinity. The binding of AUF1 to AREs is believed to serve as a signal to an mRNA-processing pathway that degrades mRNAs encoding many cytokines, oncoproteins, and G protein-coupled receptors. Because the ARE binding activity of AUF1 appears central to the regulation of many important genes, we analyzed the domains of the protein that are important for this activity. Examination of the RNA binding affinity of various AUF1 mutants suggests that both RRMs may be required for binding to the human c-fos ARE. However, the two RRMs together are not sufficient. Highest affinity binding of AUF1 to an ARE requires an alanine-rich region of the N terminus and a short glutamine-rich region in the C terminus. In addition, the N terminus is required for dimerization of AUF1. However, AUF1 binds an ARE as a hexameric protein. Thus, protein-protein interactions are important for high affinity ARE binding activity of AUF1.

Kidney extracts from spontaneously hypertensive rats (SHR) have greater dopamine 1A receptor RNA-binding activity than extracts from normotensive Wistar-Kyoto (WKY) rats

Rat kidney extracts contain a 52 kDa protein that binds to the 3' untranslated region of the dopamine 1A (D1A) receptor mRNA at a 243 base-long cis element starting at the stop codon and ending approximately 220 bases upstream of an AUUUA-rich region. The D1A receptor RNA-binding protein (D1A-BP) is redox-sensitive; free sulfhydryl groups on the protein are required for binding. Kidney extracts from SHR have significantly more D1A-BP activity than extracts from WKY rats. When kidney extracts were tested for binding to an 80-base RNA containing four AUUUA repeats, there was also greater binding activity in extracts from SHR. These increases are at least partly specific because there was no difference in catalase RNA-binding protein activity between the two rat strains. These data suggest D1A-BP and AUUUA-binding protein may play a role in posttranscriptional regulation of the D1A receptor in the hypertensive rat.

A cytidine deaminase expressed in the post-infective L3 stage of the filarial nematode, Brugia pahangi, has a novel RNA-binding activity

A number of genes have been identified that are highly expressed in the post-infective L3 stage of the filarial parasite, Brugia pahangi. Amongst these was a cDNA with homology to the cytidine deaminase (CDD) gene family. Phylogenetic analysis of the various cytosine nucleoside deaminases suggest that Brugia pahangi CDD evolved with significant divergence from the RNA editing family. In order to characterize its function, we have expressed Brugia pahangi CDD in bacteria as a chimera with maltose-binding protein (MBP). Biochemical analysis demonstrates the MBP-CDD fusion protein functions as an authentic cytidine deaminase with an obligate requirement for zinc. In addition to cytidine deaminase activity, however, the fusion protein demonstrates RNA binding activity with specificity for AU-rich sequences and was found to bind an RNA template spanning the edited site of mammalian apolipoprotein B (apoB) mRNA. This RNA binding activity was not found in two different recombinant bacterial CDD proteins. In vitro RNA editing assays revealed that MBP-CDD failed to mediate cytidine deamination of a mammalian apoB RNA template. Furthermore, binding of MBP-CDD to the apoB RNA did not inhibit in vitro editing of this template by apobec-1. The data suggest that the cytosine nucleoside deaminases and RNA editing deaminases have acquired different mechanisms of binding to an AU-rich RNA template, presumably with different functional implications.

Identification of AUF1 (heterogeneous nuclear ribonucleoprotein D) as a component of the alpha-globin mRNA stability complex

mRNA turnover is an important regulatory component of gene expression and is significantly influenced by ribonucleoprotein (RNP) complexes which form on the mRNA. Studies of human alpha-globin mRNA stability have identified a specific RNP complex (alpha-complex) which forms on the 3' untranslated region (3'UTR) of the mRNA and appears to regulate the erythrocyte-specific accumulation of alpha-globin mRNA. One of the protein activities in this multiprotein complex is a poly(C)-binding activity which consists of two proteins, alphaCP1 and alphaCP2. Neither of these proteins, individually or as a pair, can bind the alpha-globin 3'UTR unless they are complexed with the remaining non-poly(C) binding proteins of the alpha-complex. With the yeast two-hybrid screen, a second alpha-complex protein was identified. This protein is a member of the previously identified A+U-rich (ARE) binding/degradation factor (AUF1) family of proteins, which are also known as the heterogeneous nuclear RNP (hnRNP) D proteins. We refer to these proteins as AUF1/hnRNP-D. Thus, a protein implicated in ARE-mediated mRNA decay is also an integral component of the mRNA stabilizing alpha-complex. The interaction of AUF1/hnRNP-D is more efficient with alphaCP1 relative to alphaCP2 both in vitro and in vivo, suggesting that the alpha-complex might be dynamic rather than a fixed complex. AUF1/hnRNP-D could, therefore, be a general mRNA turnover factor involved in both stabilization and decay of mRNA.

Adhesion-dependent regulation of an A+U-rich element-binding activity associated with AUF1

Monocyte adherence results in the rapid transcriptional activation and mRNA stabilization of numerous mediators of inflammation and tissue repair. While the enhancer and promoter elements associated with transcriptional activation have been studied, mechanisms linking adhesion, mRNA stabilization, and translation are unknown. GROalpha and interleukin-1beta (IL-1beta) mRNAs are highly labile in nonadhered monocytes but stabilize rapidly after adherence. GROalpha and IL-1beta transcripts both contain A+U-rich elements (AREs) in the 3' untranslated region (UTR) which have been directly associated with rapid mRNA turnover. To determine if the GROalpha ARE region was recognized by factors associated with mRNA degradation, we carried out mobility gel shift analyses using a series of RNA probes encompassing the entire GROalpha transcript. Stable complexes were formed only with the proximal 3' UTR which contained the ARE region. The two slower-moving complexes were rapidly depleted following monocyte adherence but not direct integrin engagement. Deadherence reactivated the two largest ARE-binding complexes and destabilized IL-1beta transcripts. Antibody supershift studies demonstrated that both of these ARE RNA-binding complexes contained AUF1. The formation of these complexes and the accelerated mRNA turnover are phosphorylation-dependent events, as both are induced in adherent monocytes by the tyrosine kinase inhibitor genistein and the p38 MAP kinase inhibitor of IL-1beta translation, SK&F 86002. These results demonstrate that cell adhesion and deadhesion rapidly and reversibly modify both cytokine mRNA stability and the RNA-binding complexes associated with AUF1.

Mouse vitamin D-24-hydroxylase: molecular cloning, tissue distribution, and transcriptional regulation by 1alpha,25-dihydroxyvitamin D3

Vitamin D-24-hydroxylase (24-OHase) is a cytochrome P-450 enzyme that catalyzes the conversion of 25-hydroxyvitamin D3 (25OHD3) and 1alpha,25-dihydroxyvitamin D3 [1,25-(OH)2D3] to 24,25-dihydroxyvitamin D3 and 1,24,25-trihydroxyvitamin D3, respectively. A full-length complementary DNA for mouse 24-OHase has now been characterized. The complementary DNA consists of 3309 bp and encodes a protein of 514 amino acids that shows 82% and 95% sequence identity with the human and rat enzymes, respectively. Northern blot analysis of tissues from mice injected with 1,25-(OH)2D3 (24 pmol/g) revealed that the 3.4-kb 24-OHase messenger RNA (mRNA) is most abundant in kidney and intestine, with smaller amounts present in skin, thymus, and bone. RT-PCR and Southern blot analysis detected 24-OHase mRNA in several other tissues including lung, testis, spleen, pancreas, and heart. Intraperitoneal injection of 1,25-(OH)2D3 induced dose- and time-dependent increases in both 24-OHase mRNA abundance and enzyme activity in mouse kidney. Similarly, 1,25-(OH)2D3-induced increases in both 24-OHase mRNA and activity were apparent in the duodenum. Although 1,25-(OH)2D3 increased the amount of 24-OHase mRNA in skin, enzyme activity was not detected in this tissue. Pretreatment of mice with cycloheximide (400 microg/g), an inhibitor of protein synthesis, potentiated the increase in 24-OHase mRNA abundance, but blocked the increase in 24-OHase activity, induced by 1,25-(OH)2D3 in kidney and duodenum, suggesting that 24-OHase gene expression may be regulated not only by the vitamin D receptor but also by a short-lived repressor protein.

Molecular characterization of coding and untranslated regions of rat cortex lithium-sensitive myo-inositol monophosphatase cDNA

Lithium sensitive myo-inositol monophosphatase (IMPase) is a pivotal enzyme which controls the levels of brain inositol within the inositol-based signaling system. Its capacity to release free myo-inositol from inositol monophosphates generated from receptor-linked and de novo pathways is crucial to the maintenance of appropriate amounts of intracellular myo-inositol, which is essential for both inositol-based cell signaling and cell volume control. We present here the full length cDNA encompassing the coding and untranslated regions (5'- and 3'-UTRs) of rat brain IMPase. This cDNA was derived from rat cortex mRNA by the RT-PCR technique. Analysis of this cDNA revealed several interesting features which include a short 5'-untranslated region (5'-UTR) of 68 nucleotides followed by coding region of approximately 0.8 kb and a long 3'-untranslated region (3'-UTR) of 1.2 kb. Both 5'-rapid amplification of cDNA ends (5'-RACE) and 3'-RACE techniques were carried out to isolate both UTRs and double stranded sequencing was carried out to its entirety (approximately 2.1 kb) by 'gene walking' using several oligonucleotide primers. All nucleotides were sequenced unambiguously using the sense and antisense strands of DNA. PCR analysis for the coding region and the deduced amino acid sequence demonstrated a DNA fragment of 831 bp and 277 amino acids, respectively, which are strikingly similar to human hippocampal IMPase. The 5'-UTR demonstrated distinct CpG doublets, characteristic of 'housekeeping' genes. The sequence around the initiator methionine, AAGATGG, conforms well to the Kozak consensus sequence for mammalian protein biosynthesis and the 3'-UTR demonstrated three canonical (AATAAT, AATTAA, AATACA) and one unusual polyadenylation signals (ATTAAA) followed by a 31 base poly(A) tail. The presence of a CCTGTG in the 3'-UTR (putative carbohydrate response element) links IMPase mRNA to brain carbohydrate metabolic pathways. Computer analyses demonstrated several unique features of this mRNA, including the potential formation of hairpin loops which might be important in its intracellular regulation and turn-over. In summary, this lithium-sensitive brain IMPase mRNA has the following characteristics: a 5'-CpG-rich short untranslated segment, a highly conserved coding region, and a long 3'-untranslated region with several polyadenylation signals.

A 20-nucleotide (A + U)-rich element of beta2-adrenergic receptor (beta2AR) mRNA mediates binding to beta2AR-binding protein and is obligate for agonist-induced destabilization of receptor mRNA

The Mr 35,000 beta-adrenergic receptor mRNA-binding protein, termed betaARB protein, is induced by beta-adrenergic agonists and binds to beta2-receptor mRNAs that display agonist-induced destabilization. A cognate sequence in the mRNA was identified previously that provides for betaARB protein binding in vitro. In the present work, the sequence established in vitro for binding of betaARB protein to hamster beta2-adrenergic receptor mRNA was probed in vivo by site-directed mutagenesis of the 3'-untranslated region and expression in Chinese hamster ovary cells. A 20-nucleotide, (A + U)-rich region in the 3'-untranslated region consisting of an AUUUUA hexamer flanked by defined U-rich regions constitutes the binding domain for betaARB protein. U to G substitution in the hexamer region attenuates the binding of betaARB protein, whereas U to G substitution of hexamer and flanking U-rich domains abolishes binding of betaARB protein and stabilizes beta2-adrenergic receptor mRNA levels in transfectant clones challenged with either isoproterenol or cyclic AMP. These results demonstrate that binding of betaARB protein to the 20-nucleotide, (A + U)-rich domain mediates the agonist and cyclic AMP-induced mRNA decay of G protein-linked receptors, such as the beta2-adrenergic receptor.