Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Codon, Terminator”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed2004

Premature termination codons enhance mRNA decapping in human cells.

Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance process that promotes selective degradation of imperfect messages containing premature translation termination codons (PTCs). In yeast, PTCs trigger both deadenylylation-independent mRNA decapping, thereby allowing their rapid degradation by a 5' to 3' exonuclease, and to a smaller extent accelerated deadenylylation. It is not clear to what extent this decay pathway is conserved in higher eukaryotes. We used a transcriptional pulse strategy relying on a tetracycline-regulated promoter to study the decay of a PTC- containing beta-globin mRNA in human cells. We show that a PTC destabilizes the mRNA and decreases its half-life from >16 h to 3 h. The deadenylylation rate is increased, but not sufficiently to account for the decreased half-life on its own. Using a circularization RT-PCR (cRT-PCR) strategy, we could detect decapped degradation intermediates and measure simultaneously their poly(A) tail length. This allowed us to show that a PTC enhances the rate of mRNA decapping and that decapped products have been deadenylylated to a certain extent. Thus the major feature of the NMD pathway, enhanced decapping, is conserved from yeast to man even though the kinetic details might differ between various mRNAs and/or species.

Codon, Nonsense↗
PubMed1992

Lipoprotein lipase genotypes for a common premature termination codon mutation detected by PCR-mediated site-directed mutagenesis and restriction digestion.

We have developed a procedure for the determination of a common mutation in exon 9 of the human lipoprotein lipase (LPL) gene. The mutation is due to a C-G transversion which creates a premature termination codon (Ser447-Ter) and results in a truncated LPL molecule lacking the C-terminal dipeptide SER-GLY. The mutation can be detected by polymerase chain reaction (PCR) amplification of exon 9 using a modified 3' amplimer that produces a 140 bp product containing a site for the restriction enzyme Hinf-1 in the presence of the mutation (G allele). The G allele was in strong linkage disequilibrium with a Hind-III restriction fragment length polymorphism (RFLP) allele in intron 8. Genotype determinations for the mutation can be performed by PCR amplification of genomic DNA, digestion with Hinf-1, and analysis of the products by polyacrylamide gel electrophoresis. The allelic frequency of the Ser447-Ter mutation in normal male Caucasian controls was 0.11. The frequency of the mutation was lower in a group of subjects with primary hypertriglyceridemia compared to normolipidemic controls.

Adult↗
PubMed1994

The T-->C mutation at position +96 of the untranslated region 3' to the terminating codon of the beta-globin gene is a rare polymorphism that does not cause a beta-thalassemia as previously ascribed.

We have observed a T-->C mutation at position +96 of the untranslated region 3' to the terminating codon of the beta-globin gene in members of two Czech families and one black family. Data from initial studies suggested that this change was the cause of a beta-thalassemia, but continued analyses have provided convincing evidence that this mutation is a simple polymorphism.

Adult↗
PubMed1994

Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2.

Retroviruses whose gag and pol genes are in the same reading frame depend upon approximately 5% read-through of the gag UAG termination codon to make the gag-pol polyprotein. For murine leukemia virus, this read-through is dependent on a pseudoknot located eight nucleotides 3' of the UAG. Other retroviruses whose gag and pol genes are in the same frame can potentially form similar pseudoknots 3' of their UAG codons. Beyond the similar secondary structures, there is strong sequence conservation in the spacer region and in loop 2 of the pseudoknots. The detrimental effects of substitutions of several of these conserved spacer and loop 2 nucleotides in the murine leukemia virus sequence show their importance for the read-through process. The importance of specific nucleotides in loop 2 of the pseudoknot contrasts with the flexibility of sequence in loop 2 of the most intensively studied frameshift-promoting pseudoknot which occurs in infectious bronchitis virus. Two nucleotides in loop 2 of the murine leukemia virus pseudoknot, which were shown to be important by mutagenic analysis, display hypersensitivity to the single-strand specific nuclease, S1. They are likely to be particularly accessible or are in an unusually reactive conformation.

Base Sequence↗
PubMed1975

The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon.

Translation of the RNA from the wild-type bacteriophages R17, MS2, and f2 in bacterial cell-free extracts containing an amber suppressor yields 30-40% of the synthetase with an approximate molecular weight of 63 500, slightly larger than the major synthetase product (63 000 daltons). The occurrence of the 63 500 dalton in vitro product is dependent on the presence of an amber suppressor, and we predict that it is due to read-through of a UAG termination codon at the end of the synthetase gene. Previous results of Capecchi and Klein (Nature, 226, 1029-1033, 1070) showed that antibodies to both release factors RF1 and RF2 are required to block release of synthetase, suggesting that synthetase is released at a UAA codon. If the interpretations of both experiments are correct, the termination and release may not be synonomous and may be spatially separated. In addition there is the unexplained fact that 7% of the synthetase made in vitro in both su+ and su- extracts with either R17, MS2 or f2 as template has an apparent molecular weight of 66 000.

Autoradiography↗
PubMed1990

Efficient translation of the UAG termination codon in Candida species.

Clinical isolates of the dimorphic fungus Candida albicans encode a tRNA that, in a cell-free translation system prepared from the yeast Saccharomyces cerevisiae, efficiently translates the amber (UAG) termination codon. Unusually, the efficiency of this UAG read-through in the heterologous cell-free system is not further enhanced by polyamines. The suppressor tRNA is also able to efficiently translate the UAG codon in the rabbit reticulocyte cell-free system and with efficiencies approaching 100% in a homologous (C. albicans) cell-free system. That the suppressor tRNA is nuclear-encoded is demonstrated by the lack of activity in purified C. albicans mitochondrial tRNAs. Finally, UAG suppressor tRNA activity is also demonstrated in three other pathogenic Candida species, C. parapsilosis, C. guillermondii and C. tropicalis. These results suggest that some, but not all, Candida species have evolved an unusual nuclear genetic code in which UAG is used as a sense codon.

Candida albicans↗
PubMed1985

Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon.

We have purified from Moloney murine leukemia virus (Mo-MuLV) a protease that has the capacity of accurately cleaving the polyprotein precursor Pr65gag into the mature viral structural proteins. Both the NH2- and COOH-terminal amino acid sequences have been determined and aligned with the amino acid sequence deduced from the DNA sequence of Mo-MuLV by other workers. The results show that: (i) the protease is located at the 5' end of the pol gene, and the first four amino acids are overlapped with the 3' end of the gag gene; (ii) the fifth amino acid residue is glutamine, which is inserted by suppression of the UAG termination codon at the gag-pol junction; and (iii) the protease is composed of 125 amino acids with calculated Mr = 13,315, and the COOH terminus of the protease is adjacent to the NH2 terminus of reverse transcriptase. The map order of the gag-pol gene is proposed to be 5'-p15-p12-p30-p10-protease-reverse transcriptase-endonuclease-3'.

Amino Acid Sequence↗
PubMed2006

Targeted skipping of a single exon harboring a premature termination codon mutation: implications and potential for gene correction therapy for selective dystrophic epidermolysis bullosa patients.

This study examined the feasibility of antisense oligoribonucleotide (AON) therapy for dystrophic epidermolysis bullosa (DEB). AON was designed to induce skipping of a targeted exon containing a premature termination codon mutation, resulting in restoration of the open reading frame. We targeted exon 70 of COL7A1, as a recurrent mutation 5818delC in Japanese DEB patients was localized to exon 70. We found that one AON induced effective skipping of normal exon 70 containing 16 amino acids. Attachment and migration analyses showed that recombinant collagen without contribution of exon 70 was similar in effect to normal type VII collagen. Next, we synthesized mutation-specific AON by deleting cytosine at 5818. Introduction of this AON into DEB keratinocytes harboring 5818delC showed that the AON induced skipping of exon 70 in the abnormal 5818delC allele. Furthermore, 6.2% of DEB keratinocytes started to express type VII collagen in vitro after application of the mutation-specific AON. Injection of the AON into rat model grafted with DEB keratinocytes and fibroblasts induced a low amount of type VII collagen expression. We conclude that skipping of targeted exons using mutation-specific AON may show potential for future gene therapy for DEB patients.

Animals↗
PubMed1989

Reversion of trpA nonsense mutations by deletion of the chain-termination codons.

This paper describes a novel mechanism for reversion of nonsense mutations in the trpA gene of Escherichia coli. This mechanism, deletion of the nonsense codon, was discovered in the course of selecting for missense revertants of trpA(UGA211) and for catalytically active tryptophan synthetase alpha chain revertants of trpA(UAA234) and trpA(UAG234). Each type of revertant trpA was cloned and its DNA sequence determined. trpA(UGA211) gave rise to two previously unidentified types of missense revertant. The first type was expected, namely trpA(CGA211), the result of a base substitution event. The other type, representing approximately 1% of the missense revertants, was unexpected on the basis of single base substitutions and an understanding of which amino acids are functional at alpha chain position 211. It was found to be the result of a 21 base-pair deletion of a region containing codon 211. The tryptophan-independent revertants of both position 234 nonsense mutants occurred at a frequency of approximately 2 per 10(9) viable cells. They were identical in that they both resulted from a 3 base-pair deletion, namely deletion of the chain-terminating codon at position 234. One of them, however, also displayed an A instead of the normal G in the third position of codon 235. The revertants were characterized according to growth in different media and tryptophan synthetase assays performed on crude extracts. These types of mutants should prove interesting and important for the elucidation of alpha chain structure-function relationships, for insight into the assembly and interaction of subunits in this model multienzyme complex, and for the study of mechanisms by which deletions can be generated.

Base Sequence↗
PubMed1992

The leaky UGA termination codon of tobacco rattle virus RNA is suppressed by tobacco chloroplast and cytoplasmic tRNAs(Trp) with CmCA anticodon.

RNA-1 molecules from tobacco rattle virus (TRV) and pea early-browning virus (PEBV), two members of the tobravirus group, have recently been shown to contain internal, in-frame UGA termination codons which are suppressed in vitro. Our results suggest that a UGA stop codon also exists in RNA-1 of pepper ringspot virus (PRV), another tobravirus. UGA suppression may therefore be a universal feature of the expression of tobravirus genomes. We have isolated two natural suppressor tRNAs from uninfected tobacco plants on the basis of their ability to promote readthrough over the leaky UGA codon of TRV RNA-1 in a wheat germ extract depleted of endogenous mRNAs and tRNAs. Their amino acid acceptance and nucleotide sequences identify the two UGA-suppressor tRNAs as chloroplast (chl) and cytoplasmic (cyt) tryptophan-specific tRNAs with the anticodon CmCA. These are the first UGA suppressor tRNAs to be identified in plants. They have several interesting features. (i) Chl tRNA(Trp) suppresses the UGA stop codon more efficiently than cyt tRNA(Trp). (ii) Chl tRNA(Trp) contains an A24:U11 pair in the D-stem as does the mutated Escherichia coli UGA-suppressor tRNA(Trp) which is a more active suppressor than wild-type tRNA(Trp). (iii) The suppressor activity of chl tRNA(Trp) is dependent on the nucleotides surrounding the stop codon because it recognizes UGA in the TRV context but not the UGA in the beta-globin context.

Animals↗
PubMed1985

Translational readthrough of an amber termination codon during synthesis of feline leukemia virus protease.

Feline leukemia virus contains a protease which apparently has the same specificity as murine leukemia virus protease. It cleaves in vitro the Pr65gag of Gazdar-mouse sarcoma virus into the constituent p15, p12, p30, and p10 proteins. We purified the protease and determined its NH2-terminal amino acid sequence (the first 15 residues). Alignment of this amino acid sequence with the nucleotide sequence (I. Laprevotte, A. Hampe, C. H. Sherr, and F. Galibert, J. Virol. 50:884-894, 1984) reveals that the protease is a viral-coded enzyme and is located at the 5' end of the pol gene. As previously found for murine leukemia virus (Y. Yoshinaka, I. Katoh, T. D. Copeland, and S. Oroszlan, Proc. Natl. Acad. Sci. U.S.A. 82:1618-1622, 1985), feline leukemia virus protease is synthesized through in-frame suppression of the gag amber termination codon by insertion of a glutamine in the fifth position, and the first four amino acids are derived from the gag gene.

Amino Acid Sequence↗
PubMed1991

A C----G mutation at nt position 6 3' to the terminating codon may be the cause of a silent beta-thalassemia.

We describe the hematological and clinical data for a young Greek patient with beta-thalassemia intermedia and for several members of her family. The patient had inherited the common IVS-I-1 (G----A) mutation from her mother, while the second beta-globin gene had a C----G mutation at position 6 3' to the terminating codon (term. + 6). Her father and three additional relatives with a heterozygosity for this newly discovered mutation had no hematological abnormalities, normal Hb A2 values, and a nearly normal in vitro chain synthesis ratio. Analyses of nearly 500 additional beta-thalassemia and normal chromosomes failed to detect this mutation which eliminates it as a common polymorphism. Although our findings may indicate a rare polymorphism, the probability that it represents the cause of diminished beta chain synthesis is very high indeed. We suggest that the C----G mutation in this untranslated region of the beta-globin gene causes a slight decrease in the stability of the mRNA which becomes clinically important only in situations when beta chain synthesis in trans is eliminated.

Base Sequence↗
PubMed1985

Characterization of two class I major histocompatibility rat cDNA clones, one of which contains a premature termination codon.

A cDNA clone that shares considerable homology with mRNA for class-I major-histocompatibility (MHC) antigens has been isolated from a cDNA library constructed from an insulin-secreting tumor of the NEDH rat (RIN). Although there is very strong homology between the third extracellular domain of this gene, and other class-I antigen genes, a stop codon was noticed at the junction between the external and transmembrane regions of its protein. Thus, this gene codes for a truncated class-I antigen that lacks both transmembrane and cytoplasmic domains but has hydrophilic amino acids towards its C-terminus and therefore resembles a soluble protein. This gene was found to be transcribed at significant levels in the rat testis and an insulin-secreting tumor, but transcription was negligible in liver and kidney. The partial nucleotide sequence of this gene in a Wistar rat genomic clone indicates that the cDNA clone is represented in the rat genome complete with premature termination codon, thus eliminating the possibility of artifactual origins for the clone.

Animals↗
PubMed2004

Does the position of the premature termination codon in COL7A1 correlate with the clinical severity in recessive dystrophic epidermolysis bullosa?

Recessive dystrophic epidermolysis bullosa (RDEB) is an inherited skin disease caused by mutations in the gene encoding type VII collagen (COL7A1). The mutations are highly variable and this greatly complicates the study of the genotype-phenotype relationships. To date, three recurrent mutations, specific to Japanese RDEB patients have been reported. By comparing the phenotypes of RDEB patients with different recurrent mutations, the upstream positions of the premature termination codons (PTCs) showed strong correlation with the RDEB clinical disease severity. However, such correlations have not been supported by patients with mutations that were different from these recurrent Japanese patients mutations. In this study, we report a case of RDEB with a very mild clinical phenotype, who was a compound heterozygote harbouring both a recurrent Japanese mutation and a novel deletion mutation resulting in a more upstream PTC. The patient and his mother were shown to have a recurrent donor splice site mutation within intron 81 (6573 + 1G > C), a recurrent Japanese mutation that activates a cryptic donor splicing site and results in a downstream PTC. The patient and his father shared a single-nucleotide deletion within exon 64 (5504delA), which causes a downstream frame shift in five amino acids before creating a PTC. Occurrence of the PTCs in mRNA was confirmed by reverse transcription-polymerase chain reaction (RT)-PCR. The patient's skin showed reduced immunofluorescence staining for COL7A1 and reduced number of abnormal or short anchoring fibrils by electron microscopy. Although the position of the mutation 5504delA PTC was located upstream of the previous mutations reported in combination with the 6573 + 1G > C mutation, the two mutations together give an apparently milder clinical phenotype. Therefore, genotype-phenotype relationships in RDEB cannot be explained purely by the position of PTC.

Base Sequence↗
PubMed1993

RNA editing of rapeseed mitochondrial atp9 transcripts: RNA editing changes four amino acids, but termination codon is already encoded by genomic sequence.

The gene encoding subunit 9 of Fo-ATPase of rapeseed mitochondria has been isolated. The complete genomic DNA sequence and cDNA sequence corresponding to the atp9 gene transcript have been determined by a method involving cDNA synthesis, using specific oligonucleotides as primers, followed by PCR amplification, cloning and sequencing of the amplification products. In comparison of cDNA sequences to genomic one, four modifications, C-to-U conversions, have been found. When compared with RNA editing patterns of atp9 transcripts among plant mitochondria, that of rapeseed atp9 transcript is more simple; there are only four editing sites on the coding region, and its termination codon is already encoded by genomic sequence.

Amino Acid Sequence↗
PubMed1993

A variant of metabotropic glutamate receptor subtype 5: an evolutionally conserved insertion with no termination codon.

We herein report the presence of a variant of the rat metabotropic glutamate receptor subtype 5 (mGluR5) cDNA. In this variant, named mGluR5b, an extra 96 bp sequence is inserted into the originally reported mGluR5 cDNA. The position of this insertion corresponds to that of the 85 bp insertion reported for the alternative form of mGluR1, another subtype of the receptors (designated as mGluR1 beta). No sequence-similarity was found between the additional sequences of the mGluR1 beta and the mGluR5b. While the additional sequence of the mGluR1 beta cDNA contains a translation termination codon in the frame, that of the mGluR5b cDNA does not. This identical 96 bp insertion was also found in a human mGluR5 cDNA clone. Northern blot analyses with the mGluR5b-specific probe showed that the expression of mRNA for this species is regulated in a region-specific manner in the rat brain.

Amino Acid Sequence↗
PubMed1982

Origin of life: a hypothesis for the origin of adaptor-mediated ordered synthesis of proteins and an explanation for the choice of terminating codons in the genetic code.

Life can be defined as a system of self-sustained chemical processes springing from the ordered synthesis of proteins directed by nucleic acids. To the notoriously difficult problem of the origin of this basic process of nucleic acid-directed protein synthesis, we give a solution of molecular interactions between pentanucleotides and amino acids. A particular conformation of a pentanucleotide forms a double sided template, with its 'inside' capable of nestling an amino acid while the 'outside' acts as an adaptor to a 'codon' triplet on long-chain nucleic acids. This serves as a primitive decoding system. An important aspect of our postulate is that a dynamic interaction is triggered, by this decoding system, through which amino acids are brought to juxtaposition facilitating peptide bond formation. Almost all the important and unique features of contemporary protein-synthesizing machinery are seen to be a direct and natural consequence of our postulate. The emergence of the termination codons also fits in, as a natural consequence of this molecular mechanism.

Animals↗
PubMed2004

Homozygosity for a severe novel medium-chain acyl-CoA dehydrogenase (MCAD) mutation IVS3-1G > C that leads to introduction of a premature termination codon by complete missplicing of the MCAD mRNA and is associated with phenotypic diversity ranging from sudden neonatal death to asymptomatic status.

Virtually all patients with medium-chain acyl-CoA dehydrogenase deficiency (MCADD) are homozygous or compound heterozygous for the 985A > G mutation, which limits the study of a possible genotype/phenotype correlation. A newborn Palestinian infant died suddenly on the second day of life. A previous sibling had also died in similar circumstances aged 3 weeks. Urine organic acid and bloodspot acylcarnitine analysis were consistent with MCADD. He was homozygous for a novel MCAD splice mutation, IVS3-1G > C. This mutation leads to deletion of 7 bp and introduction of a premature termination codon as a result of complete missplicing of MCAD mRNA. This misspliced MCAD mRNA encodes a non-functional protein and is furthermore reduced in amounts due to nonsense-mediated decay, resulting in total lack of functional MCAD enzyme. This is the first molecular identification of MCADD in an Arab patient and the first reported splice mutation in the MCAD gene that has been functionally characterized. The association of homozygosity for a null mutation with lethal neonatal presentation in the index patient and presumably the previous infant suggested a genotype/phenotype correlation. However, a 6-year-old completely asymptomatic sibling also had the characteristic MCADD biochemical phenotype and was homozygous for the same IVS3-1G > C mutation. As a first candidate to modify the disease presentation, by modulating the overlapping enzyme activity, we tested the entire family for the prevalent SCAD gene 625G > A susceptibility variant. Interestingly, all family members were 625G > A homozygous. Additional genetic and/or environmental factors must play a major role in determining the phenotypic diversity of MCADD.

Acyl-CoA Dehydrogenase↗