Human phosducin-like protein (hPhLP) messenger RNA stability is regulated by cis-acting instability elements present in the 3'-untranslated region

Cleavage and polyadenylation: Ending the message expands gene regulation

Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.

Alternative polyadenylation: less than meets the eye?

With the advances in deep-sequencing techniques over the last decade, the study of alternative cleavage and polyadenylation (APA) has shifted from individual gene to whole transcriptome analysis. Findings from such global studies have elevated APA to its currently accepted status as a major player in the regulation of eukaryotic gene expression. Although ~70% of human genes have been shown to contain multiple cleavage and polyadenylation sites, the extent of the consequences of APA and its role in regulating physiological processes are still largely unknown. The present review aims to summarize the experimental evidence that supports a physiological role of APA and highlights some of the shortcomings that need addressing to substantiate the widely proposed claim that APA is a key player in global gene regulation.

Human sphingomyelin synthase 1 gene (SMS1): organization, multiple mRNA splice variants and expression in adult tissues

We have previously characterized the structure of the human MOB gene (TMEM23), which encodes a hypothetical transmembrane protein (Vladychenskaya et al., 2002, 2004). The primary structure of the peptide that we predicted coincided completely with the amino acid sequence of the later identified sphingomyelin synthase 1 protein (SMS1), which catalyses the transfer of a phosphorylcholine moiety from phosphatidylcholine to ceramide, producing sphingomyelin and diacylglycerol (Huitema et al., 2004; Yamaoka et al., 2004). The gene we found was the SMS1 gene. The combination of in silico and RT-PCR data helped us identify and characterize numerous new transcripts of the human SMS1 gene. We identified mRNA isoforms that vary in the 5'-untranslated region (UTR) and encode the full-length protein, and transcripts resulting from alternative combinations of the exons in the coding region of the gene and the 3'-UTR. Comparison of the discovered transcripts' structures with the sequence of human chromosome 10 showed that the human SMS1 gene comprises at least 24 exons. RT-PCR and real-time PCR data showed that the expression patterns of the alternative SMS1 transcripts are tissue specific. Our results indicate that the regulation of SMS1 expression is complex and occurs at the transcriptional, post-transcriptional and translational levels.

In-channel atom-transfer radical polymerization of thermoset polyester microfluidic devices for bioanalytical applications

A new technique for polymer microchannel surface modification, called in-channel atom-transfer radical polymerization, has been developed and applied in the surface derivatization of thermoset polyester (TPE) microdevices with poly(ethylene glycol) (PEG). X-ray photoelectron spectroscopy, electroosmotic flow (EOF), and contact angle measurements indicate that PEG has been grafted on the TPE surface. Moreover, PEG-modified microchannels have much lower and more pH-stable EOF, more hydrophilic surfaces and reduced nonspecific protein adsorption. Capillary electrophoresis separation of amino acid and peptide mixtures in these PEG-modified TPE microchips had good reproducibility. Phosducin-like protein and phosphorylated phosducin-like protein were also separated to measure the phosphorylation efficiency. Our results indicate that PEG-grafted TPE microchips have broad potential application in biomolecular analysis.

Regulation of alpha-synuclein expression in alcohol-preferring and -non preferring rats

The alpha-synuclein (Snca) gene is expressed at higher levels in alcohol-naïve, inbred alcohol-preferring (iP) rats than in alcohol-non preferring (iNP) rats. Snca modulates dopamine transmission and the dopamineregic system, which play a role in mediating the rewarding properties of alcohol consumption. Thus, understanding regulation of Snca gene expression could provide insight into the relationship of Snca and alcohol consumption. To study regulation of rat Snca expression, 1,912 bp of the iP and iNP 5'-regions were cloned and sequenced. 5'-rapid amplification of cDNA ends (RACE), primer extension and RT-PCR mapped three transcription start site clusters (clusters TSS1, TSS2 and TSS3), suggesting that the Snca proximal promoter region has a complex architecture. This proximal promoter region has three TATA-less core promoters containing SP1 binding sites, initiator elements and downstream core promoter elements, which are often located in such promoters. Snca-luc constructs transiently transfected into SK-N-SH neuroblastoma cells showed that the region from - 1,912 to - 1,746 contained a strong core promoter, and that the entire approximately 2 kb region had significant promoter activity. Five polymorphisms identified between the iP and iNP in the proximal promoter region did not influence differential expression between the strains. In contrast, a single nucleotide polymorphism (SNP) at + 679 in the 3'-untranslated region (UTR) resulted in a 1.3-fold longer half-life of iP mRNA compared with iNP mRNA, which is consistent with the differential expression observed between the iP and iNP strains. These results suggest that regulation of rat Snca gene expression is complex and may contribute to alcohol preference in the iP rats.

Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection

Lipopolysaccharide (LPS) activation of murine RAW 264.7 macrophages influences the expression of multiple genes through transcriptional and post-transcriptional mechanisms. We observed a 5-fold increase in CstF-64 expression following LPS treatment of RAW macrophages. The increase in CstF-64 protein was specific in that several other factors involved in 3'-end processing were not affected by LPS stimulation. Activation of RAW macrophages with LPS caused an increase in proximal poly(A) site selection within a reporter mini-gene containing two linked poly(A) sites that occurred concomitant with the increase in CstF-64 expression. Furthermore, forced overexpression of the CstF-64 protein also induced alternative poly(A) site selection on the reporter minigene. Microarray analysis performed on CstF-64 overexpressing RAW macrophages revealed that elevated levels of CstF-64 altered the expression of 51 genes, 14 of which showed similar changes in gene expression with LPS stimulation. Sequence analysis of the 3'-untranslated regions of these 51 genes revealed that over 45% possess multiple putative poly(A) sites. Two of these 51 genes demonstrated alternative polyadenylation under both LPS-stimulating and CstF-64-overexpressing conditions. We concluded that the physiologically increased levels of CstF-64 observed in LPS-stimulated RAW macrophages contribute to the changes in expression and alternative polyadenylation of a number of genes, thus identifying another level of gene regulation that occurs in macrophages activated with LPS.

Regulation of angiotensin II-induced G protein signaling by phosducin-like protein

Phosducin-like protein (PhLP) is a broadly expressed member of the phosducin (Pd) family of G protein betagamma subunit (Gbetagamma)-binding proteins. Though PhLP has been shown to bind Gbetagamma in vitro, little is known about its physiological function. In the present study, the effect of PhLP on angiotensin II (Ang II) signaling was measured in Chinese hamster ovary cells expressing the type 1 Ang II receptor and various amounts of PhLP. Up to 3.6-fold overexpression of PhLP had no effect on Ang II-stimulated inositol trisphosphate (IP(3)) formation, whereas further increases caused an abrupt decrease in IP(3) production with half-maximal inhibition occurring at 6-fold PhLP overexpression. This threshold level for inhibition corresponds to the cellular concentration of cytosolic chaperonin complex, a recently described binding partner that preferentially binds PhLP over Gbetagamma. Results of pertussis toxin sensitivity, GTPgammaS binding, and immunoprecipitation experiments suggest that PhLP inhibits phospholipase Cbeta activation by dual mechanisms: (i) steric blockage of Gbetagamma activation of PLCbeta and (ii) interference with Gbetagamma-dependent cycling of G(q)alpha by the receptor. These results suggest that G protein signaling may be regulated through controlling the cellular concentration of free PhLP by inducing its expression or by regulating its binding to the chaperonin.

Regulatory interaction of phosducin-like protein with the cytosolic chaperonin complex

Phosducin and phosducin-like protein (PhLP) bind G protein betagamma subunits and regulate their activity. This report describes a previously uncharacterized binding partner unique to PhLP that was discovered by coimmunoprecipitation coupled with mass spectrometric identification. Chaperonin containing tailless complex polypeptide 1 (CCT), a cytosolic chaperone responsible for the folding of many cellular proteins, binds PhLP with a stoichiometry of one PhLP per CCT complex. Unlike protein-folding substrates of CCT, which interact only in their nonnative conformations, PhLP binds in its native state. Native PhLP competes directly for binding of protein substrates of CCT and thereby inhibits CCT activity. Overexpression of PhLP inhibited the ability of CCT to fold newly synthesized beta-actin by 80%. These results suggest that the interaction between PhLP and CCT may be a means to regulate CCT-dependent protein folding or alternatively, to control the availability of PhLP to modulate G protein signaling.

Polymorphisms in the 3'-untranslated region of human and monkey dopamine transporter genes affect reporter gene expression

Dopamine transporter (DAT) levels vary in normal subjects and deviate from the normal range in pathological states. We investigated mechanisms by which the DAT gene may influence DAT protein expression. As the 3'-untranslated region (3'-UTR) of the DAT gene varies with regard to length and single nucleotide polymorphisms (SNPs), we addressed whether the 3'-UTR of sequence-defined DAT alleles can differentially affect the level of reporter gene expression in vitro. We first established that within individual rhesus monkeys, two alleles of the DAT gene were expressed in the substantia nigra. We then transfected HEK-293 cells with HSV-TK- and SV40-driven luciferase expression vectors harboring downstream DAT 3'-UTR segments of alleles containing polymorphisms of length (human: 9 or 10 repeat units) or SNPs within alleles of fixed length (human: DraI-sensitive (DraI+) vs. DraI-insensitive (DraI-) 10-repeat alleles; rhesus monkey: Bst1107I-sensitive (Bst+) vs. Bst1107I-insensitive (Bst-) 12-repeat alleles). Vectors containing the 3'-UTR segment of a human DAT allele containing nine tandem repeat units resulted in significantly higher levels of luciferase production than analogous vectors containing 10 tandem repeat units. Depending on the promoter used, vectors containing the human or monkey 3'-UTR segments that differed on the basis of an SNP resulted in increases or decreases in luciferase gene expression. This report provides experimental evidence that variability in the length or the sequence of the 3'-UTR of the DAT gene may influence levels of DAT protein in the brain.

Evidence for in vivo modulation of chloroplast RNA stability by 3'-UTR homopolymeric tails in Chlamydomonas reinhardtii

Polyadenylation of synthetic RNAs stimulates rapid degradation in vitro by using either Chlamydomonas or spinach chloroplast extracts. Here, we used Chlamydomonas chloroplast transformation to test the effects of mRNA homopolymer tails in vivo, with either the endogenous atpB gene or a version of green fluorescent protein developed for chloroplast expression as reporters. Strains were created in which, after transcription of atpB or gfp, RNase P cleavage occurred upstream of an ectopic tRNA(Glu) moiety, thereby exposing A(28), U(25)A(3), [A+U](26), or A(3) tails. Analysis of these strains showed that, as expected, polyadenylated transcripts failed to accumulate, with RNA being undetectable either by filter hybridization or reverse transcriptase-PCR. In accordance, neither the ATPase beta-subunit nor green fluorescent protein could be detected. However, a U(25)A(3) tail also strongly reduced RNA accumulation relative to a control, whereas the [A+U] tail did not, which is suggestive of a degradation mechanism that does not specifically recognize poly(A), or that multiple mechanisms exist. With an A(3) tail, RNA levels decreased relative to a control with no added tail, but some RNA and protein accumulation was observed. We took advantage of the fact that the strain carrying a modified atpB gene producing an A(28) tail is an obligate heterotroph to obtain photoautotrophic revertants. Each revertant exhibited restored atpB mRNA accumulation and translation, and seemed to act by preventing poly(A) tail exposure. This suggests that the poly(A) tail is only recognized as an instability determinant when exposed at the 3' end of a message.

Mydj2 as a potent partner of hsc70 in mammalian cells

Dj2 is a member of the DnaJ family of proteins, which regulate the chaperoning function of the hsp70s. We isolated a monkey cDNA dj2 clone corresponding to the large mRNA species encoded by the gene. This mRNA differs from the small mRNA produced by the same gene in that it contains a long 3' untranslated region. Both messages were found to be equally stable and to produce the same protein, which is susceptible to farnesylation. Studies in mouse tissues and various cell lines revealed that these messages and their products are differentially expressed. Surprisingly, we found that only the nonfarnesylated form of dj2 is capable of translocating to the cell nucleus, especially after heat shock. Finally, based on protein interaction studies, our results indicate that dj2 is a specific partner for hsc70 and not for hsp70.

Nucleotide sequence of the mouse VEGF 3'UTR and quantitative analysis of sites of polyadenylation

Sequencing of rat and human vascular endothelial growth factor (VEGF) cDNA clones has previously identified a 3' untranslated region of approximately 1.9 kb, although the apparent site of polyadenylation differed in the two species, despite a high degree of sequence conservation in the region. Neither site is preceded by a canonical AAUAAA polyadenylation signal, a situation frequently found in genes that are subject to alternative polyadenylation. We have sequenced 2.25 kb of the 3' region of the mouse VEGF gene and mapped the usage of potential polyadenylation sites in fibroblasts cultured under both normoxic and hypoxic conditions. We find that two sites for polyadenylation are present in the mouse VEGF gene but the majority of transcripts contain the longer form of the 3'UTR and that their usage is not effected by environmental oxygen tension.

Characterization of a human gene encoding nucleosomal binding protein NSBP1

We characterize the cDNA and genomic structure of NSBP1, and demonstrate that it is a nuclear protein and the homologue of mouse Nsbp1, which is known to encode a nucleosomal binding and transcriptional activating protein related to the HMG-14/-17 chromosomal proteins. The encoded NSBP1 protein has 86% amino acid similarity to Nsbp1, including identity in nucleosomal binding domains of the HMG-14/-17 proteins. Our radiation hybrid data localize NSBP1 and Nsbp1 to homologous regions of chromosome X, with NSBP1 in Xq13.3 between DXS983 and DXS995 and Nsbp1 in the interval DXMit65 and DXMit39. Although Nsbp1 produces one mRNA transcript, NSBP1 produces three transcripts with alternate polyadenylated sites. The 3' untranslated region (UTR) of NSPB1 mRNA also contains several AU-rich elements (AREs), which are associated with rapid mRNA turnover. Northern analysis of NSBP1/Nsbp1 shows differences in transcript abundance among adult and fetal tissues, with predominant expression in liver, kidney, trabecular bone, and bone marrow stromal cells. However, a reverse transcriptase-PCR analysis shows nearly ubiquitous expression of the three NSBP1 transcripts in all tissues examined, although the abundance of each transcript was not quantified. NSBP1 is encoded by six exons and has exon-intron boundaries identical to the HMG-14/-17 genes. The last exon and the 3' UTR of NSBP1 contain retrotransposon sequences of HAL1, HERV-H, and L1MB7, suggesting that these retrotransposons were involved in the origin of NSPB1 from an ancestral-like HMG-14/-17 gene. The similarities among NSBP1, Nsbp1, and the HMG-14/-17 proteins suggest that NSBP1 may function as a nucleosomal binding and transcriptional activating element. Further, the AREs in the 3' UTR of NSPB1 suggest that alternate poly(A) site selection may mediate the mRNA stability of this gene.

The pharmacology of phosducin

The discovery of phosducin (Phd) in photoreceptor cells of the retina and the further identification of phosducin-like proteins (PhdLP) emphasizes the existence of a family of proteins characterized as cytosolic regulators of G protein functions. The individual members represent phosphoproteins with distinct tissue distributions whose highest concentrations were in the retina and the pineal gland, while lower levels were reported for tissues such as liver, spleen, striated muscle, and the brain. Several functions of Phd and PhdLP have been suggested, but their most important ability appears to be their high affinity sequestration with G betagamma subunits of heterotrimeric G proteins. This finding suggests that neutralization of G betagamma by Phd effectively impedes G protein-mediated signal transmission, since G alpha cannot reassemble with G betagamma to provide a functional G protein trimer (G alphabetagamma). Thus, it is the scavenger quality of Phd that is hypothesized to diminish intracellular communication simply by reducing the number of G proteins. An additional important function of Phd relates to the inhibition of G alpha subunits' inherent GTPase. The ability of Phd to directly bind G alpha subunits is probably of minor significance as the affinity between both proteins is low. In general, similar mechanisms have been reported for PhdLPs. In the majority of investigations concerning the interference of Phd with physiological mechanisms, the dark/light adaptation of retinal photoreceptor cells has been the most frequently studied aspect of Phd. More recently, Phd was associated with the adenylyl cyclase of olfactory cilia, as in the presence of the phosphoprotein an increased concentration of cAMP is observed. This finding is in line with the experimental outcome of permanent cell lines transfected to overexpress Phd, which exhibit sensitization to excitatory acting PGE(1), and isoproterenol, respectively. Furthermore, Phd was found to effectively slow down the mechanism of internalization of G protein-coupled opioid receptors. Pathophysiological processes associated with Phd were found for certain eye diseases. Experimental evidence suggests the development of retinal inflammation as a consequence of an autoimmunization process triggered by Phd or shorter fragments thereof. Thus, our present knowledge regarding the functions of members of the Phd family is limited currently to their control of G protein-mediated intracellular signal transmission, the process of endocytosis, and certain autoimmune diseases of the uvea and the pineal gland. However, recent information regarding the presence of certain members of the Phd family in the cell nucleus may bear new insights into the function of these compounds.

Size distribution of the urokinase mRNA decay intermediates in different tissues and cell lines

Many genes, particularly those encoding the products participating in the regulation of transcription, replication and tissue remodeling, produce short-lived mRNA. It has been commonly accepted that once mRNA is disintegrated, the degradation process is so rapid that the decay intermediates cannot be detected. In the present study we verified this postulate and focused our attention on the quantification of the decay products of the urokinase-type plasminogen activator (uPA) mRNA that belongs to short-lived mRNAs. Using a previously described modified quantitative RT-PCR method, we have shown that intact uPA mRNA coexists in normal human tissues, Jurkat and 5637 cells with a great abundance of its degradation products. The uPA mRNA decay products were not detected in T24P cells. The content of intact uPA mRNA in normal tissues was as low as 5% of the total amount of its poly(A)(+) fraction. The size distribution of the mRNA decay products suggests that the mRNA is digested by exonucleases or/and non-specific endonuclease with cut sites evenly distributed along the mRNA chain. Different decay degrees were demonstrated for subpopulation of the uPA mRNA molecules with intact 3' and 5' ends.

Regulation of exocytosis in chromaffin cells by phosducin-like protein, a protein interacting with G protein betagamma subunits

Phosducin and related proteins have been identified as ubiquitous regulators of signalling mediated by betagamma subunits of trimeric G proteins. To explore a role for phosducin in regulated exocytosis, we have examined the distribution and putative function of phosducin-like protein (PhLP) in adrenal medullary chromaffin cells. The full-length cDNA encoding the short splice variant of PhLP (PhLPs) was cloned from cultured chromaffin cells. Native PhLPs was found associated with plasma membranes and detected in the subplasmalemmal area of resting chromaffin cells by confocal immunofluorescence analysis. Stimulation with secretagogues triggered a massive redistribution of PhLPs into the cytoplasm. When microinjected into individual chromaffin cells, recombinant PhLPs inhibited catecholamine secretion evoked by a depolarizing concentration of K+ without affecting calcium mobilization. Thus, PhLPs may participate directly in the regulation of calcium-evoked exocytosis.

Molecular cloning and characterization of the human phosducin-like protein (hPhLP) promoter

Phosducin-like protein (PhLP) is an inducible Gbetagamma binding protein which is hypothesized to be a ubiquitous G protein regulator. To elucidate the mechanisms regulating the expression of the human PhLP (hPhLP) gene, we have cloned and characterized its 5'-flanking region. Primer extension analysis identified a major transcription initiation site 172 bp upstream of the ATG start codon. Analysis of the 5'-flanking region revealed that, although it lacked a TATA box element, the hPhLP promoter did contain several consensus binding motifs including AP4, CCAAT, CREB, NF-kappaB, SP1 and E2F. Transient transfection analyses using a series of 5'-flanking deletion/luciferase reporter gene constructs identified a 25 bp sequence (-80 to -55 bp) that is necessary for basal level transcription of the hPhLP gene in all the cell lines investigated. Interestingly, dependent upon the cell line, distinct transcription factors bind to this region suggesting that basal level hPhLP gene transcription may be regulated in a tissue-specific manner.