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PubMed1994

The human immunodeficiency virus type 1 Rev protein shuttles between the cytoplasm and nuclear compartments.

A retroviral regulatory protein, Rev (regulator of virion protein expression), is made in cells infected by human immunodeficiency virus (HIV). Rev is essential for the completion of the retroviral life cycle and interacts with the host cell at some posttranscriptional step in order to express the incompletely spliced HIV mRNAs from which HIV structural proteins are translated. Neither the host cell components nor the mechanisms responsible for this important regulation have been defined. We now report that Rev is a nucleocytoplasmic shuttle protein which is continuously transported between the cytoplasm, the nucleoli, and nucleoplasmic speckles enriched in RNA splicing and processing factors. The results show that Rev has the potential to interfere specifically with the splicing of the HIV pre-mRNA in the nucleoplasm and, next, guide such mRNAs to the cytoplasm for translation.

Amino Acid Sequence↗

PubMed2002

Inteins: structure, function, and evolution.

Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast to introns, inteins are transcribed and translated together with their host protein. Inteins appear most frequently in Archaea, but they are found in organisms belonging to all three domains of life and in viral and phage proteins. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonuclease that is important in the spread of inteins. This review focuses on the evolution and technical application of inteins and only briefly summarizes recent advances in the study of the catalytic activities and structures of inteins. In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins.

Amino Acid Motifs↗

PubMed1998

New splicing mutations in the human factor XIIIA gene, each producing multiple mutant transcripts of varying abundance.

Coagulation factor XIII, a transglutaminase which stabilises blood clots by covalently cross-linking fibrin, is essential for normal haemostasis. FXIII deficiency results in a life-long bleeding disorder with added complications in wound healing and tissue repair. Sequence changes in the human FXIIIA gene, largely missense mutations, are primarily responsible for inherited FXIII deficiency. We have carried out molecular analysis of the FXIIIA gene in two unrelated FXIII deficient individuals and identified three splice site mutations; a g-->a at the exon 6 acceptor splice site, a g-->a at the exon 7 donor splice site and a coding sequence T-->G at the exon 8 donor splice site. We have also examined the FXIIIA mRNA in these patients and find that each mutation gives rise to multiple transcripts which vary in their relative abundance. The precise molecular mechanisms which result in these variant transcripts, and their relative abundance in our FXIII deficient patients, are discussed.

Adolescent↗

PubMed2006

Regulation of DNA repair gene expression in human cancer cell lines.

Although most advanced cancers are incurable, the majority of testicular germ cell tumors can be cured using cisplatin-based combination chemotherapy. The nucleotide excision repair (NER) pathway removes most DNA adducts produced by cisplatin, and the low levels of NER in testis tumor cells may explain why these cancers are curable. Three NER proteins: ERCC1, XPF, and XPA, are present at low levels in testis tumor cell lines, and addition of these proteins to protein extracts of testis tumor cells increases their in vitro DNA repair capacity to normal levels. The aim of this study was to identify the mechanism responsible for the low levels of these DNA repair proteins. The levels of the mRNA transcripts for ERCC1, XPF, and XPA were measured in a panel of 14 different human cancer cell lines, using real-time PCR. Three ERCC1 splice variants were identified and quantitated. Three alternative transcription start points (TSPs) were identified for ERCC1 but none were testis-specific. The significantly lower levels of ERCC1, XPF, and XPA protein in testis tumor cell lines cannot be explained solely by differences in transcriptional efficiency or mRNA stability. For ERCC1, post-transcriptional control by alternative splicing does not account for the testis-specific low levels of protein expression. Pulse-chase experiments showed that the half-life of ERCC1 protein in a testis tumor cell line was not significantly different to that in a prostate cancer cell line. Taken together, these results suggest that constitutive levels of these DNA repair proteins are controlled at the level of translation.

3' Untranslated Regions↗

PubMed2001

Effects of activity on growth factor expression.

For some time, it has been appreciated that muscle mass is regulated locally as well as systemically. We have cloned the cDNA of two isoforms of IGF-1, which are derived from the IGF-1 gene by alternate splicing. The expression of one of these was only detectable after mechanical stimulation. For this reason, this has been called mechano growth factor (MGF). The MGF is not glycosylated, is smaller, and has a shorter half-life in the unbound state than the systemic liver type IGF-1. As the result of a reading frame shift the MGF peptide also has a different C terminal sequence and thus has different binding protein/receptor affinities. Another splice variant (muscle L.IGF-I) is expressed in muscle during rest but is also upregulated by exercise. The latter is similar to the systemic liver type IGF-1. The evidence suggests that MGF has a high potency for inducing local protein synthesis and preventing apoptosis and therefore has an important role in local tissue repair and remodeling. Our physiological experiments show that stretch and particularly stretch combined with electrical stimulation, rather than stimulation alone are important in inducing MGF expression. The mechanotransduction mechanism is believed to involve the muscle cytoskeleton. During aging, the production of growth hormone and IGF-1 by the liver declines markedly. The discovery of MGF and muscle IGF-1 provides a link between physical activity and gene expression. This underlines the need for the elderly to remain active as the locally produced growth factors supplement the circulating IGF-1 levels.

Adaptation, Physiological↗

PubMed1998

A novel splice site mutation in the tissue inhibitor of the metalloproteinases-3 gene in Sorsby's fundus dystrophy with unusual clinical features.

Sorsby's fundus dystrophy (SFD) is an autosomal dominant macular dystrophy which is developed usually in the third or fourth decade of life, and is characterized by central visual loss and nyctalopia due to fundus changes of exudative or atrophic macular lesions. Its functional prognosis is usually poor because of disciform macular scars and peripheral chorioretinal atrophies. To date, five different mutations in the tissue inhibitor of the metalloproteinases-3 (TIMP3) gene have been identified in families of a wide geographic origin, all of which are missense mutations that cause replacement by cysteine of conserved amino acids in the C-terminus of exon 5 of TIMP3. We have studied two Japanese families with SFD, the first report from the Eastern world, and identified a novel 3' splice site mutation in the TIMP3 gene, namely a single base insertion at the intron 4/exon 5 junction which converts the consensus sequence CAG to CAAG in the splice acceptor site. In addition, our patients displayed a distinctive clinical expression in that they developed macular dystrophies at an approximately 30-year later age of onset and preserved functional vision until later life with essentially uninvolved peripheral retina. The present findings may provide some insight into the genotype-phenotype relationship in SFD.

Aged↗

PubMed1999

In vivo analysis of HLA-DQ gene expression in heterozygous cell lines.

Regulation of HLA-DQ gene transcription is a complex phenomenon because the allelic polymorphism associated with these genes and their promoters is a putative source of differential allele expression. Both transcriptional and post-transcriptional regulation could account for the density of the molecules expressed at the cell surface and then for the specificity of the immune response. Different methods have been developed to evaluate the functional consequences of this polymorphism, but at present no universal method allows measurement of either the steady-state level or the half-life time of mRNA species of both DQA1 and DQB1 polymorphic genes in heterozygous cell lines. Here, we propose a potent method, based on relative quantification of reverse transcriptase-polymerase chain reaction products, which analyzes the differential expression of all DQA1 or DQB1 allele combinations. This method is used to analyze the differential expression of HLA-DQB1*020110402 alleles in the human heterozygous lymphoblastoid B-cell line. Nucleotidic sequences of the proximal upstream regulatory region of these alleles exhibit significant differences. We show that the DQB1*0402 promoter is able to mediate a transcription strength twice as efficiently as *0201. In addition, the *0402 mRNA steady-state level is also governed by a remarkable post-transcriptional regulation. Indeed, an important part (20%) of the *0402 primary transcript is derived by alternative splicing in a short mRNA translated into a nonfunctional protein. Despite their variable sequence and length, no difference in the half-life of DQB1*0201 and both DQB*0402 mRNAs was observed in B-lymphoblastoid cells. The implications of these findings are discussed.

Alleles↗

PubMed2001

Solid-state NMR data support a helix-loop-helix structural model for the N-terminal half of HIV-1 Rev in fibrillar form.

Rev is a 116 residue basic protein encoded by the genome of human immunodeficiency virus type 1 (HIV-1) that binds to multiple sites in the Rev response element (RRE) of viral mRNA transcripts in nuclei of host cells, leading to transport of incompletely spliced and unspliced viral mRNA to the cytoplasm of host cells in the latter phases of the HIV-1 life cycle. Rev is absolutely required for viral replication. Because Rev aggregates and fibrillizes in solution at concentrations required for crystal growth or liquid state NMR measurements, high-resolution structural characterization of full-length Rev has not been possible. Previously, circular dichroism studies have shown that approximately 50 % of the Rev sequence adopts helical secondary structure, predicted to correspond to a helix-loop-helix structural motif in the N-terminal half of the protein. We describe the application of solid-state NMR techniques to Rev fibrils as a means of obtaining site-specific, atomic-level structural constraints without requiring a high degree of solubility or crystallinity. Solid-state NMR measurements, using the double-quantum chemical shift anisotropy and constant-time double-quantum-filtered dipolar recoupling techniques, provide constraints on the phi and psi backbone dihedral angles at sites in which consecutive backbone carbonyl groups are labeled with (13)C. Quantitative analysis of the solid-state NMR data, by comparison with numerical simulations, indicates helical phi and psi angles at residues Leu13 and Val16 in the predicted helix 1 segment, and at residues Arg39, Arg 42, Arg43, and Arg44 in the predicted helix 2 segment. These data represent the first site-specific structural constraints from NMR spectroscopy on full-length Rev, and support the helix-loop-helix structural model for its N-terminal half.

Amino Acid Sequence↗

PubMed1996

The Rev Axis of HIV-1 and Its Associated Host Cofactors: A Viral Window onto the Workings of Eukaryotic Posttranscriptional RNA Processing.

The Rev axis of HIV is one of two key autoregulatory pathways required for viral replication and pathogenesis. The viral Rev protein interacts with its RNA target sequence, the RRE, to overcome the inhibitory effects of constitutive repressor sequences and promote nucleocytoplasmic transport and expression of viral RNAs. The Rev axis is the subject of intense scrutiny not only because it plays a central role in the viral life cycle, but also because it offers a window onto the workings of key mechanisms of posttranscriptional regulation, including splicing, polyadenylation, degradation, transport, and translation. Recent reports have conclusively demonstrated a central role for transport in the Rev mechanism and have identified cellular factors that are good candidates for mediating the transport phenomena. Other potentially involved cellular factors are being investigated. Much of the apparent heterogeneity in the observed effects of Rev may actually derive from heterogeneity in the constitutive repressor sequences rather than from heterogeneity in the mechanism of action of Rev per se. Copyright 1996 S. Karger AG, Basel

Journal Article↗

PubMed2004

Two functionally redundant isoforms of Drosophila melanogaster eukaryotic initiation factor 4B are involved in cap-dependent translation, cell survival, and proliferation.

Eukaryotic initiation factor (eIF) 4B is part of the protein complex involved in the recognition and binding of mRNA to the ribosome. DrosophilaeIF4B is a single-copy gene that encodes two isoforms, termed eIF4B-L (52.2 kDa) and eIF4B-S (44.2 kDa), generated as a result of the alternative recognition of two polyadeynlation signals during transcription termination and subsequent alternative splicing of the two pre-mRNAs. Both eIF4B mRNAs and proteins are expressed during the entire embryogenesis and life cycle. The proteins are cytoplasmic with polarized distribution. The two isoforms bind RNA with the same affinity. eIF4B-L and eIF4B-S preferentially enhance cap-dependent over IRES-dependent translation initiation in a Drosophila cell-free translation system. RNA interference experiments suggest that eIF4B is required for cell survival, although only a modest reduction in rate of protein synthesis is observed. Overexpression of eIF4B in Drosophila cells in culture and in developing eye imaginal discs promotes cell proliferation.

Amino Acid Sequence↗

PubMed1993

The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation.

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

Amino Acid Sequence↗

PubMed2002

Molecular biology of Borna disease virus and persistence.

Borna disease virus (BDV) causes central nervous system (CNS) disease that is frequently manifested by behavioral abnormalities. Recent evidence indicates that the natural host range and geographic distribution of BDV is wider than originally thought BDV has been molecularly characterized as a non-segmented, negative single-stranded (NNS) RNA virus. Its genome (ca 8.9 kb), the smallest among known NNS RNA viruses, has an organization similar to that of other members of the order Mononegavirales. BDV has the property, unique among known animal NNS RNA viruses, of a nuclear site for the replication and transcription of its genome. The nucleocytoplasmic transport of BDV macromolecules is an essential component of the life cycle of BDV. An overlap of transcription units and transcriptive signals, overlap of ORFs, transcriptional readthrough and RNA splicing regulate expression of the BDV compact genome. The concurrent use of such diversity of strategies for the regulation of virus gene expression is unique among known NNS RNA viruses. Moreover, BDV appears to have also an unusual assembly process. Based on its unique genetic and biological features, BDV is considered to be the prototypic member of a new virus family, Bornaviridae, within the order Mononegavirales. Therefore, the investigation of the molecular biology of BDV may provide new insights about the biology of mononegaviruses, which include important human pathogens.

Animals↗

PubMed2001

Nonsense-mediated decay of mutant waxy mRNA in rice.

Two rice (Oryza sativa) waxy mutations of the Japonica background were shown to contain approximately 20% of the fully spliced mRNA relative to the wild type. Sequencing analysis of the entire waxy genes of the two mutants revealed the presence of premature translation termination codons in exon 2 and exon 7. These results indicated that the lower accumulation of fully spliced RNA in the mutants was caused by nonsense-mediated decay (NMD), which is an RNA surveillance system universally found in eukaryotes. It is interesting that levels of RNA retaining intron 1 were not changed by premature nonsense codons, suggesting that splicing may be linked with NMD in plants, as previously found in mammalian cells. Measurements of the half-lives of waxy RNAs in transfected rice protoplasts indicated that the half-life of waxy RNA with a premature nonsense codon was 3.3 times shorter than that without a premature nonsense codon. Because the wild-type waxy transcripts, which are derived from the Wx(b) gene predominantly distributed among Japonica rice, have been shown to be less efficiently spliced and their alternative splicing has been documented, we examined whether these splicing properties influenced the efficiency of NMD. However, no effects were observed. These results established that NMD occurs in rice waxy RNA containing a premature nonsense codon.

Alternative Splicing↗

PubMed2001

Differential effects of chronic ethanol treatment on N-methyl-D-aspartate R1 splice variants in fetal cortical neurons.

Functional N-methyl-D-aspartate receptors consisting of NR1 and NR2 subunits are an important site of action of ethanol. Chronic ethanol treatment increases the NR1 polypeptide levels in vivo and in vitro. Chronic ethanol treatment in vitro does not significantly alter the NR1 mRNA levels, even though under similar culture conditions ethanol (50 mm, 5 days) enhances the half-life of NR1 mRNA in fetal cortical neurons. To address this phenomenon, we determined by reverse transcription-polymerase chain reaction and Western blotting whether ethanol (50 mm, 5 days) has a splice variant-specific effect on the expression of the NR1 subunit in mouse fetal cortical neurons. This report analyzes for the first time the distribution of all NR1 splice variants in these neurons. Our data indicate the presence of NR1-3a,b and NR1-4a,b splice variants in cortical neurons. Chronic ethanol treatment significantly decreased the mRNA levels of exon 5-containing NR1 splice variants (NR1-3b and NR1-4b) (-E5/+E5 = 4.6 in untreated neurons and 6.1 in ethanol-treated neurons) and had no effect on the mRNA levels of NR1-3 (+E21/-E22) and NR1-4 (-E21/-E22) splice variants. At the polypeptide level, chronic ethanol treatment significantly reduced exon 5-containing splice variants (NR1-3b and NR1-4b). However, ethanol (50 mm, 5 days) induced a significant increase in polypeptide levels of NR1-4 (-E21/-E22), without any effect on NR1-3 (+E21/-E22) polypeptide levels. These results demonstrate that chronic ethanol treatment has a selective effect on the expression of NR1 splice variants at both the mRNA and polypeptide levels in mouse fetal cortical neurons.

Alternative Splicing↗

PubMed1993

Mechanisms for the inhibition of HIV replication by interferons-alpha, -beta, and -gamma in primary human macrophages.

Interferons (IFNs) inhibit the replication of a wide range of animal viruses by acting at various steps of the life cycle. Interferons display a particularly potent antiviral effect on HIV-1 replication in primary human macrophages. A high virus-to-cell multiplicity of infection was used to investigate which steps in a single replicative cycle in these primary human cells were affected by IFNs. Monocyte-derived macrophages from healthy seronegative donors were infected with HIV-1BaL. Virus production was assessed by immunoassay for p24 antigen. Viral DNA was detected by PCR while mRNA was detected specifically by RT-PCR with primers bracketing the 5' introns of HIV-1 to detect only spliced transcripts such as tat, rev, nef, and env mRNAs. Macrophages pretreated with IFN-alpha, -beta or -gamma had a reduced viral DNA signal while the spliced mRNA signal was essentially abolished. No virus was produced. To test whether IFNs could reduce HIV transcripts in cells with established productive infection, macrophages were infected and reinfection was then prevented by azidothymidine before starting interferon treatment. Under such conditions, the addition of interferons did not affect significantly the levels of HIV spliced transcripts. No intracellular accumulation of p24 antigen was observed. Therefore, the major effect of IFNs was at an early step of the virus life cycle and resulted in a reduced viral DNA synthesis.

Cells, Cultured↗

PubMed1987

Controlled turnover and 3' trimming of the trans splicing precursor of Trypanosoma brucei.

The maturation of mRNAs in Trypanosoma brucei involves a novel step, in which a short capped sequence is spliced in trans onto the 5' end of nascent mRNAs from a 140-nucleotide precursor. This precursor is called the mini-exon-derived RNA or medRNA. We have used drugs and ultraviolet irradiation as inhibitors to probe the synthesis and processing of medRNA in vivo. Inhibition of RNA synthesis by chloroquine shows that the half-life of medRNA is about 4 minutes. Despite this high turnover, only limited accumulation of medRNA could be achieved following a block in the synthesis of high molecular weight splice acceptor substrates by UV irradiation. This implies that there is a constraint on the steady-state levels of medRNA and that excess medRNA is degraded in the cell. A 3' shortened version of medRNA accumulates upon a block in normal medRNA processing by UV irradiation or upon treatment of the cells with actinomycin D or novobiocin but was shown not to participate in trans splicing, making it a likely candidate for an in vivo degradation intermediate.

Animals↗

PubMed1990

Translation to near the distal end of the penultimate exon is required for normal levels of spliced triosephosphate isomerase mRNA.

The translation of human triosephosphate isomerase (TPI) mRNA normally terminates at codon 249 within exon 7, the final exon. Frameshift and nonsense mutations within the TPI gene that cause translation to terminate prematurely at or upstream of codon 189, within exon 6, result in a decreased level of TPI mRNA (I.O. Daar and L.E. Maquat, Mol. Cell. Biol. 8:802-813, 1988). For all mutations in this group, the decrease is to the same extent, i.e., to approximately 20% of the normal level. We show here that a second group of nonsense mutations that cause translation to terminate prematurely at or downstream of codon 208, in exon 6, did not affect TPI mRNA abundance. Deletion analysis demonstrated that the abundance of translationally active TPI mRNA is a function of both the distance and the polarity of the nonsense codon relative to the final intron in TPI pre-mRNA. Our results indicate that if translating ribosomes are unable to progress to at least a certain position within the penultimate exon relative to the final intron, then the level of the corresponding mRNA will be abnormally low. Studies inhibiting RNA synthesis with dactinomycin demonstrated that a block in translation does not affect the half-life of mature TPI mRNA. The simplest interpretation of our data is that the translation of TPI mRNA in the cytoplasm facilitates the splicing of TPI pre-mRNA or the transport of TPI mRNA across the nuclear envelope or both.

Base Sequence↗

PubMed1998

Different forms of the mRNA encoding the heat-shock transcription factor are expressed during the life cycle of the parasitic helminth Schistosoma mansoni.

Several cDNAs and a gene encoding the heat-shock transcription factor (HSF) of schistosome were cloned, and multiple forms of the mRNA were found at different developmental stages of the parasite. The encoded protein contained a DNA-binding domain with expected sequence identity (39-58%) to other HSF molecules, and two leucine zipper motifs (LZ123 and LZ4) involved in the oligomerization of HSF. Adult worms express three isoforms of HSF mRNA generated by alternative splicing inside the coding region that contains in-frame splice signals. Introns are not involved in the process since the deleted segments (36 bp or 45 bp) are not flanked by any intron in the gene. Structural variations generated by alternative splicing (insertion of 3 amino acids or 15 amino acids) are continual with LZ4 and added hydrophobic residues are in register with the hydrophobic heptad repeats of LZ4. Structural diversity at the C-terminus of LZ4 may affect the strength of LZ4 interaction with the oligomerization domain (LZ123) and thus modulate the DNA-binding activity of HSF. The conservation of this mechanism in mouse and schistosome may reflect evolutionary pressure to generate multiple HSF species exhibiting functional diversity and capable of responding to different stress signals and physiological signals. Adult worms express HSF mRNA of 2.5 kb, in agreement with the size of the cDNA, while cercariae (developmental stage preceding adult worm) show multiple bands in the range 2.5-3 kb. Available data indicate that the HSF mRNAs of cercariae are inactive. We propose that these mRNA species are generated by an alternative splicing that incorporates introns, which inactivate the mRNA by the insertion of termination codons and/or by shifting of the reading frame. Parasite HSF protein produced in bacteria showed DNA sequence recognition similar to that of HSF in parasite extracts, i.e. the recombinant HSF reacted better with a variant heat-shock element (HSE; one base change in the third NGAAN pentamer of the ideal HSE consensus sequence) than with the ideal HSE. The size of the HSF gene is 12 kb and it is composed of ten exons and nine introns. Excluding the introns, the gene and cDNA show 100% sequence identity. A plant HSF gene contains only a single intron, which matches with the position of intron I2 of schistosome. That the position of this intron is conserved in remote species is indicative of an important function during evolution of the HSF gene.

Alternative Splicing↗