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Vascular variant of prion protein cerebral amyloidosis with tau-positive neurofibrillary tangles: the phenotype of the stop codon 145 mutation in PRNP.

Deposition of PrP amyloid in cerebral vessels in conjunction with neurofibrillary lesions is the neuropathologic hallmark of the dementia associated with a stop mutation at codon 145 of PRNP, the gene encoding the prion protein (PrP). In this disorder, the vascular amyloid in tissue sections and the approximately 7.5-kDa fragment extracted from amyloid are labeled by antibodies to epitopes located in the PrP sequence including amino acids 90-147. Amyloid-laden vessels are also labeled by antibodies against the C terminus, suggesting that PrP from the normal allele is involved in the pathologic process. Abundant neurofibrillary lesions are present in the cerebral gray matter. They are composed of paired helical filaments, are labeled with antibodies that recognize multiple phosphorylation sites in tau protein, and are similar to those observed in Alzheimer disease. A PrP cerebral amyloid angiopathy has not been reported in diseases caused by PRNP mutations or in human transmissible spongiform encephalopathies; we propose to name this phenotype PrP cerebral amyloid angiopathy (PrP-CAA).

Adult↗

Nearby stop codons in exons of the neurofibromatosis type 1 gene are disparate splice effectors.

Stop mutations are known to disrupt gene function in different ways. They both give rise to truncated polypeptides because of the premature-termination codons (PTCs) and frequently affect the metabolism of the corresponding mRNAs. The analysis of neurofibromin transcripts from different neurofibromatosis type 1 (NF1) patients revealed the skipping of exons containing PTCs. The phenomenon of exon skipping induced by nonsense mutations has been described for other disease genes, including the CFTR (cystic fibrosis transmembrance conductance regulator) gene and the fibrillin gene. We characterized several stop mutations localized within a few base pairs in exons 7 and 37 and noticed complete skipping of either exon in some cases. Because skipping of exon 7 and of exon 37 does not lead to a frameshift, PTCs are avoided in that way. Nuclear-scanning mechanisms for PTCs have been postulated to trigger the removal of the affected exons from the transcript. However, other stop mutations that we found in either NF1 exon did not lead to a skip, although they were localized within the same region. Calculations of minimum-free-energy structures of the respective regions suggest that both changes in the secondary structure of the mRNA and creation or disruption of exonic sequences relevant for the splicing process might in fact cause these different splice phenomena observed in the NF1 gene.

Alternative Splicing↗

'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation.

Certain restriction endonucleases recognise target sequences that contain the stop triplet TAG and are commonly either 4 or 6 bp in length. Interestingly, these restriction targets do not occur at the frequency expected on the basis of base composition and size. For example, the tetranucleotide MaeI recognition sequence (CTAG) occurs considerably less commonly (5-8-fold) in the genome of Escherichia coli (and many other eubacteria) than expected from mononucleotide frequencies. This surprising rarity is particularly evident in protein-encoding genes and is largely dictated by codon usage. Thus, amber (TAG) nonsense mutations frequently give rise to novel MaeI (CTAG) sites which are unique within a translated region. Such amber/MaeI sites, whether arising spontaneously or created in vitro by site-directed mutagenesis, act as a useful physical marker for the presence of the nonsense mutation and are a convenient startpoint for a range of diverse procedures. These features provide a useful supplement to protein engineering methods which use nonsense suppression to mediate amino acid replacements.

Bacteria↗

Factor XIII ABristol 1: detection of a nonsense mutation (Arg171-->stop codon) in factor XIII A subunit deficiency.

Molecular analysis has been performed on a patient with coagulation factor XIII A subunit deficiency. A previously published genomic sequence indicates that exon 4 of the factor XIII A subunit gene contains two TaqI restriction sites within which arginine (CGA)-->stop (TGA) nonsense mutations are possible. Oligonucleotide primers were therefore used to amplify exon 4 by the polymerase chain reaction. TaqI digestion of the 326 base pair (bp) product derived from normal genomic DNA yielded expected fragments of 244, 73 and 9 bp in size. In the case of the patient, however, an additional fragment of 253 bp was present. Direct sequence analysis showed that the 5' TaqI site had been lost from one allele by a C-->T transition at nucleotide 598. Family studies demonstrated the mutation in the patient's father but no other first-degree relatives. This is the third independent mutation described in the factor XIII A subunit gene and the first to be identified in a patient compound heterozygous for the disorder.

Adult↗

Three different premature stop codons lead to skipping of exon 7 in neurofibromatosis type I patients.

Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder affecting one in 3,500 individuals. The mutation rate in the NF1 gene is one of the highest known for human genes. Compared to other methods, the protein truncation test (PTT) provides improved efficiency in detecting NF1 mutations which are dispersed throughout the gene which spans 350 kilobases of genomic DNA. We have applied the PTT and subsequent sequence analysis of cloned cDNA to identify mutations in NF1 patients. We report here the identification of two novel (W336X and Q315X), and one recurrent (R304X) mutation located in exon 7 and show that all three premature termination codons lead to skipping of exon 7 in a proportion of the transcripts derived from the mutated allele. Possible mutation-induced alterations of the RNA secondary structure and their impact on skipping of exon 7 of the NF1 gene are explored and discussed.

Base Sequence↗

A stop codon mutation in COL11A2 induces exon skipping and leads to non-ocular Stickler syndrome.

Mutations in COL11A2 cause a spectrum of phenotypes affecting chondrogenic tissues. We analyzed this gene by conformation sensitive gel electrophoresis (CSGE) and sequencing in a family with non-ocular Stickler syndrome, and found a heterozygous C --> T mutation in exon 57 + 13 in affected members, resulting in Arg893Stop codon. Since heterozygous nonsense mutations in COL11A2 do not usually lead to any obvious phenotype, all exons and exon boundaries of COL11A2 in the sample of the propositus were sequenced. Because no disease-associated alterations were found, we performed RT-PCR analysis on the RNA. Analysis showed skipping of exon 57 in one allele, resulting in an inframe deletion of 54 bp or 18 amino acids, which would explain the phenotype observed in the family. Thus, the exon skipping resulted from a nonsense-associated altered splicing (NAS). This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/suppmat/index.html.

Abnormalities, Multiple↗

Five novel mutations in the C1 inhibitor gene (C1NH) leading to a premature stop codon in patients with type I hereditary angioedema.

Hereditary angioedema (HAE) is a disorder characterised by recurrent attacks of localized subcutaneous or submucosal edema. It is inherited in an autosomal dominant fashion and caused by a deficiency of C1 inhibitor (C1 inh, or C1NH). Most patients with HAE have an absolute deficiency of C1 inh (type I HAE) while the rest (15% of kindreds) synthetize a dysfunctional C1 inh protein (type II HAE). In this report a novel use of denaturing gradient gel electrophoresis (DGGE) followed by direct sequencing of the C1 inhibitor gene is presented. Five novel mutations, one nonsense (p.S48X) and four small deletions resulting in frameshifts (g.2264-2265delAG, g.2304delC, g.8493-8494delCC and g.16676-16677delTG) have been identified in the C1 inhibitor gene in five families with type I HAE. All of these mutations lead to premature termination of translation and thus can be considered causative of the C1 inh deficiency. Moreover, two previously described mutations in the reactive center of C1 inh, p.R444C and p.R444H, have been detected in four unrelated patients with type II HAE.

Angioedema↗

Initiation of translation at a UAG stop codon in the aldolase gene of Plasmodium falciparum.

The gene coding for the key glycolytic enzyme fructose-1,6-diphosphate aldolase of the human malaria parasite Plasmodium falciparum lacks a functional AUG initiation codon for translation. Protein sequences of natural or in vitro translated aldolase include the candidate start methionine residue at internal positions. No additional AUG start codon is found in genomic DNA, cDNA or mRNA sequences. Instead, a UAG chain termination codon is recognized as the start signal of protein synthesis in vivo and in vitro.

Amino Acid Sequence↗

Characteristics of core promoter and precore stop codon mutants of hepatitis B virus in Vietnam.

In Asia, genotypes B and C are the most common genotypes of hepatitis B virus (HBV); and genotype C causes more severe liver disease. Core promoter/precore (CP/PC) mutants, known to be linked to these genotypes, could have an impact on the progression and severity of liver disease. Sera of 115 patients, including 39 acute and 76 chronic Vietnamese HBV infected patients, were tested for their liver profile, HBeAg, HBV genotypes, and HBV DNA level. Fragments of 282 nucleotides covering CP/PC were amplified, sequenced, and analysed. In the acute group, CP/PC mutants accounted for 38.4 and 25.6%, respectively. Genotype B was found to be predominant (74.3%, P < 0.05) and linked to the PC mutant (A1896) (P < 0.05). In the chronic group, CP/PC mutants accounted for 61.7 and 32.8%. CP mutants, especially the T1762/A1764 double mutant, were found to correlate with genotype C (81%, P < 0.001), liver cirrhosis, and hepatocellular carcinoma (P < 0.05). Therefore, genotype C in Vietnam, which carried high rate of C-1858 (70%), could play an important role in causing severe chronic liver disease.

Adolescent↗

Hepatitis B virus genotypes, core promoter variants, and precore stop codon variants in patients infected chronically in North-Eastern Italy.

The hepatitis B virus (HBV) genotypes distribution and the core promoter (CP)/precore (PC) variability were evaluated by a line probe assay in 272 patients infected chronically enrolled consecutively in an area of the North-Eastern Italy. Seven out of the eight genotypes were detected. Italian subjects (83% of the sample) were infected mainly by genotype D (73%) and A (26%); genotype F, and genotype H, were detected only in one subject. In foreigners, the genotype distribution reflected the distribution described for the areas of origin, that is, in Asia genotypes B, C, and D; in Africa genotypes A and E. CP and PC variants prevalence rates were 51% and 60%, respectively, and were significantly higher in Italian patients, probably in relation to their older age. In the analysis restricted to genotypes A and D, PC wild type was linked strongly to genotype A (OR = 4.08, 95% CI = 3.07-5.43, P < 0.0001). In genotype A-infected patients, only e seroconversion was associated significantly with CP variants. In genotype D-infected subjects, CP variants were linked significantly to older age and to a higher e seroconversion rate, while PC variants also showed a strong relationship with an ALT lower activity and a lower viral load. In multivariate analysis, HBeAg positivity was associated strongly and independently with younger age, genotype A and CP wild type. Independent determinants of higher viral loads were recognized by increasing age, in male gender and concomitant presence of HBeAg and the CP wild type virus.

Adult↗

Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes.

During protein translation, a variety of quality control checks ensure that the resulting polypeptides deviate minimally from their genetic encoding template. Translational fidelity is central in order to preserve the function and integrity of each cell. Correct termination is an important aspect of translational fidelity, and a multitude of mechanisms and players participate in this exquisitely regulated process. This review explores our current understanding of eukaryotic termination by highlighting the roles of the different ribosomal components as well as termination factors and ribosome-associated proteins, such as chaperones.

Animals↗

The naturally occurring silent invertase structural gene suc2 zero contains an amber stop codon that is occasionally read through.

The yeast invertase structural gene SUC2 has two naturally occurring alleles, the active one and a silent allele called suc2 zero. Strains carrying suc2 zero are unable to ferment sucrose and do not show detectable invertase activity. We have isolated suc2 zero and found an amber codon at position 232 of 532 amino acids. However, transformants carrying suc2 zero on a multicopy plasmid were able to ferment sucrose and showed detectable invertase activity. Full-length invertase was found in gels stained for active invertase and in immunoblots. Therefore we concluded that the amber codon is occasionally read as an amino acid. The calculated frequency of read-through is about 4% of all translation events.

Alleles↗