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At least 199 records · Page 11Linked to original sources
PubMed2003

Mitochondrial myopathy and complex III deficiency in a patient with a new stop-codon mutation (G339X) in the cytochrome b gene.

A 19-year-old woman complained of life-long exercise intolerance and had chronic lactic acidosis. Neurological examination was normal, but muscle biopsy showed cytochrome c oxidase-positive fibers and marked complex III deficiency. Sequence analysis showed a novel stop-codon mutation (G15761A) in the mitochondrial DNA (mtDNA)-encoded cytochrome b gene, resulting in loss of the last 41 amino acids of the protein. By PCR/restriction fragment-length polymorphism (RFLP) analysis, the G15761A mutation was very abundant (73%) in the patient's muscle, barely detectable (less than 1%) in her urine, and absent in her blood; it was also absent in muscle, urine and blood from the patient's mother. This mutation fulfills all accepted criteria for pathogenicity.

Acidosis, Lactic↗
PubMed2005

Homozygosity for premature stop codon of the MHC class I chain-related gene A (MIC-A) is associated with early activation of islet autoimmunity of DR3/4-DQ2/8 high risk DAISY relatives.

We hypothesized that homozygosity for the major histocompatibility complex (MHC) class I chain-related gene A (MIC-A)5.1 allele with premature stop codon would increase diabetes risk of individuals followed from infancy in the DAISY study (Diabetes Autoimmunity Study in the young). Forty five percent (10/22) of relatives (siblings and offspring cohort, SOC) who developed anti-islet autoantibodies were MIC-A5.1/5.1 homozygous. Of SOC individuals without autoantibodies, 12/58 (19%, p = 0.02) were MIC-A5.1 homozygous. By life table analysis of expression of autoantibodies, DR3-DQ2/ DR4-DQ8 more than 50% of MIC-A5.1 homozygous children became autoantibody positive by 7 years of age, compared to delayed development of autoantibodies for non-MIC-A5.1/5.1 DR3-DQ2/ DR4-DQ8 children (p = 0.005). For DR3-DQ2/DR4-DQ8 nonrelatives, the risk of activating anti-islet autoimmunity remained low even with MIC-A5.1 homozygosity suggesting that there are additional factors contributing to the marked risk of relatives compared to the general population with the DR3-DQ2/DR4-DQ8 genotype.

Adolescent↗
PubMed1997

Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine.

The mitochondrial DNA of the chytridiomycete fungus Spizellomyces punctatusen codes only eight tRNAs, although a minimal set of 24-25 tRNAs is normally found in fungi. One of these tRNAs has a CAU anticodon and is structurally related to leucine tRNAs, which would permit the translation of the UAG 'stop' codons that occur in most of its protein genes. The predicted structures of all S. punctatus tRNAs have the common feature of containing one to three mis-pairings in the first three positions of their acceptor stems. Such mis-pairing is expected to impair proper folding and processing of tRNAs from their precursors. Five of these eight RNAs were shown to be edited at the RNA level, in the 5'portion of the molecules. These changes include both pyrimidine to purine and A to G substitutions that restore normal pairing in the acceptor stem. Editing was not found at other positions of the tRNAs, or in the mitochondrial mRNAs of S. punctatus. While tRNA editing has not been observed in other fungi, the editing pattern inS.punctatus is virtually identical to that described in the amoeboid protozoan Acanthamoeba castellanii. If this type of mitochondrial tRNA editing has originated from their common ancestor, one has to assume that it was independently lost in plants, animals and in most fungi. Alternatively, editing might have evolved independently, or the genes coding for the components of the editing machinery were laterally transferred.

Amino Acid Sequence↗
PubMed2001

A novel 4-bp deletion creates a premature stop codon and dramatically decreases HEXB mRNA levels in a severe case of Sandhoff disease.

We present the molecular genetic analysis of an infantile-onset Sandhoff disease patient. Genomic DNA amplification, heteroduplex analysis, cloning and sequencing revealed a 4-bp deletion in exon 4 (497 DeltaAGTT). The result is a frameshift mutation that leads to a stop codon in exon 5. This mutation is associated with a dramatic decrease of HEXB mRNA levels.

Base Sequence↗
PubMed1990

Frameshifting at the internal stop codon within the mRNA for bacterial release factor-2 on eukaryotic ribosomes.

A translational frameshift is necessary in the synthesis of Escherichia coli release factor 2 (RF-2) to bypass an in-frame termination codon within the coding sequence. High-efficiency frameshifting around this codon can occur on eukaryotic ribosomes as well as prokaryotic ribosomes. This was determined from the relative efficiency of translation of RF-2 RNA compared with that for the other release factor RF-1, which lacks the in-frame premature stop codon. Since the termination product is unstable an absolute measure of the efficiency of frameshifting has not been possible. A gene fusion between trpE and RF-2 was carried out to give a stable termination product as well as the frameshift product, thereby allowing a direct determination of frameshifting efficiency. The extension of RF-2 RNA near its start codon with a fragment of the trpE gene, while still allowing high efficiency frameshifting on prokaryotic ribosomes, surprisingly gives a different estimate of frameshifting on the eukaryotic ribosomes than that obtained with RF-2 RNA alone. This paradox may be explained by long distance context effects on translation rates in the frameshift region created by the trpE sequences in the gene fusion, and may reflect that pausing and translation rate are fundamental factors in determining the efficiency of frameshifting.

Base Sequence↗
PubMed2004

A novel stop codon mutation in the PMP22 gene associated with a variable phenotype.

The most frequent inherited peripheral neuropathy is the peripheral myelin protein 22 (PMP22) gene related disease. Duplication, deletion, and point mutations in that gene are associated with phenotypic variability. Here we report a family carrying a novel mutation in the PMP22 gene (c. 327C>A), which results in a premature stop codon (Cys109stop). The family members who carry this mutation have a Charcot-Marie-Tooth type 1 variable phenotype, ranging from asymptomatic to severely affected. These findings suggest that the fourth transmembrane domain of the PMP22 gene may play an important role, although the intrafamilial clinical variability reinforces the observation that pathogenic mutations are not always phenotype determinant and that other factors (genetic or epigenetic) modulate the severity of the clinical course.

Adolescent↗
PubMed2005

Prenatal diagnosis of recessive congenital methaemoglobinaemia type II: novel mutation in the NADH-cytochrome b5 reductase gene leading to stop codon read-through.

A case of type II recessive congenital methaemoglobinaemia (RCM) observed in a Lebanese subject with a novel mutation in NADH-cytochrome b5 reductase gene is described. A homozygous mutation CAC to AA identified at Thr 295 with an out-of-frame 1-bp deletion leads to a frameshift with translational read-through of the natural stop codon. The molecular mechanism is demonstrated by an in vitro translation study. The model of mutated cytochrome b5 reductase protein possessing 46 additional amino acids was obtained by homology modelling. The mutation causes an alteration of hydrophobicity in the carboxyl-terminal portion, resulting in the conformation being drastically disturbed by the presence of 46 supplementary amino acids. The identical mutation was found in the heterozygous state in the patient's parents and sister. Identification of this new mutation enabled us to perform the molecular prenatal diagnosis of type II RCM at the DNA level.

Amino Acid Sequence↗
PubMed2002

Homozygous hereditary C3 deficiency due to a premature stop codon.

C3 deficiency in humans is a rare disorder characterized by severe recurrent infections. We identified the mutations responsible for a complete homozygous C3 deficiency. Sequencing of the proband C3 cDNA (5067 bp) revealed the following alterations: (a) a silent G-->A transition at nucleotide 972; (b) a T-->C substitution at nucleotide 1001 resulting in a L314P transition; and (c) a stop codon in exon 13 caused by a G-->A substitution at position 1716. The presence of the same premature termination codon was confirmed in approximately half the clones obtained from the proband's paternal and maternal genomic DNAs. Finally, the proband produced approximately 20-fold less C3 mRNA than the normal control. Therefore, in addition to the fact that no functional protein will be synthesized in the deficient cells, this nonsense mutation may be associated with the low C3 mRNA levels.

Adolescent↗
PubMed1998

Two isoforms of a human intersectin (ITSN) protein are produced by brain-specific alternative splicing in a stop codon.

Using selected trapped exons with homology to specific protein domains, we identified a new full-length cDNA encoding a protein containing many motifs for protein-protein interactions. There are two major mRNA transcripts, a ubiquitously expressed mRNA of 5.3 kb and a brain-specific transcript of approximately 15 kb, encoding proteins of 1220 and 1721 amino acids, respectively. The stop codon of the ORF of the shorter transcript is split between adjacent exons. In brain tissues the last exon of the short transcript is skipped, and an alternative downstream exon, the first of several additional, is used to produce the 15-kb mRNA. The putative human protein is highly homologous to Xenopus intersectin (81% identical) and to Drosophila dynamin-associated protein, Dap160 (31% identical) and was termed intersectin (ITSN). Both human proteins contain five SH3 (Src homology 3) domains, two EH (Eps15 homology) domains, and an alpha-helix-forming region. The brain-specific long transcript encodes for three additional domains: a GEF (guanine-nucleotide exchange factors), a PH (pleckstrin homology), and a C2 domain. The Drosophila homologue is associated with dynamin, a protein family involved in the endocytic pathway and/or synaptic vesicle recycling. The structure of the human ITSN protein is consistent with its involvement in membrane-associated molecular trafficking and signal transduction pathways. The human ITSN gene has been mapped to 21q22. 1-q22.2 between markers D21S319 and D21S65, and its importance in Down syndrome and monogenic disorders is currently unknown.

Adaptor Proteins, Vesicular Transport↗
PubMed2002

Recognizing shorter coding regions of human genes based on the statistics of stop codons.

With the quick progress of the Human Genome Project, a great amount of uncharacterized DNA sequences needs to be annotated copiously by better algorithms. Recognizing shorter coding sequences of human genes is one of the most important problems in gene recognition, which is not yet completely solved. This paper is devoted to solving the issue using a new method. The distributions of the three stop codons, i.e., TAA, TAG and TGA, in three phases along coding, noncoding, and intergenic sequences are studied in detail. Using the obtained distributions and other coding measures, a new algorithm for the recognition of shorter coding sequences of human genes is developed. The accuracy of the algorithm is tested based on a larger database of human genes. It is found that the average accuracy achieved is as high as 92.1% for the sequences with length of 192 base pairs, which is confirmed by sixfold cross-validation tests. It is hoped that by incorporating the present method with some existing algorithms, the accuracy for identifying human genes from unannotated sequences would be increased.

Algorithms↗
PubMed2003

Evaluation of the diagnostic accuracy of the stop codon (SC) assay for identifying protein-truncating mutations in the BRCA1and BRCA2genes in familial breast cancer.

Screening for protein-truncating mutations of the BRCA1 and BRCA2 genes is useful in genetic testing for familial breast cancer because, first, the methods are usually simple and not expensive, and second, the detected mutations indicate pathogenic mutations in general. We evaluated the diagnostic accuracy of the stop codon (SC) assay for detecting protein-truncating mutations in the BRCA1 and BRCA2 genes by comparing the results with DNA sequencing in samples from 29 patients with breast cancer from 24 Japanese families with a history of breast cancer. Protein-truncating mutations were detected in 5 of the 24 families (20.8%; two in the BRCA1 gene and three in the BRCA2 gene). Among the 176 DNA fragments examined using the SC assay, the existence of three protein-truncating mutations (one in the BRCA1 gene and two in the BRCA2gene) was predicted correctly by the assay. Only one reverse transcriptase-polymerase chain reaction fragment was positive for the SC assay but was negative using DNA sequencing. Our study showed clearly that the SC assay is sensitive (3 of 3, 100%) and specific (172 of 173, 99%) for detecting pathogenic protein-truncating mutations in the BRCA1 and BRCA2 genes, and that it could be useful for screening larger populations.

Biological Assay↗
PubMed1992

The intronless mouse gene for the tissue specific splicing protein SmN is a processed pseudogene containing a stop codon after thirty-one amino acids.

The SmN protein is a component of small ribonucleoprotein particles which is closely related to the ubiquitously expressed splicing proteins SmB and B' but is expressed in only a small number of cells and tissues. We have isolated a mouse SmN-related sequence which lacks introns and contains multiple changes from the SmN cDNA sequence including a stop codon after thirty-one amino acids which would prevent it encoding functional SmN protein. This indicates that this intronless gene is a processed pseudogene and that the functional gene has yet to be isolated. In agreement with this southern blotting of mouse DNA with SmN probes reveals bands, additional to those derived from the pseudogene, which are characteristic of an intron-containing SmN gene. The relationship of the pseudogene to the functional SmN gene and to an intronless SmN-related sequence in the rat genome is discussed.

Amino Acid Sequence↗
PubMed2003

A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires' disease.

Although Toll-like receptors (TLRs) are critical mediators of the immune response to pathogens, the influence of polymorphisms in this gene family on human susceptibility to infection is poorly understood. We demonstrated recently that TLR5 recognizes flagellin, a potent inflammatory stimulus present in the flagellar structure of many bacteria. Here, we show that a common stop codon polymorphism in the ligand-binding domain of TLR5 (TLR5392STOP) is unable to mediate flagellin signaling, acts in a dominant fashion, and is associated with susceptibility to pneumonia caused by Legionella pneumophila, a flagellated bacterium. We also show that flagellin is a principal stimulant of proinflammatory cytokine production in lung epithelial cells. Together, these observations suggest that TLR5392STOP increases human susceptibility to infection through an unusual dominant mechanism that compromises TLR5's essential role as a regulator of the lung epithelial innate immune response.

Codon, Terminator↗
PubMed2003

Growth at low temperature suppresses readthrough of the UGA stop codon during the expression of Bacillus subtilis flgM gene in Escherichia coli.

The efficient production of recombinant proteins in Escherichia coli requires a proper termination of translation to ensure the synthesis of only the desired product. During the recombinant production of Bacillus subtilis flgM in E. coli, we detected an additional polypeptide of molecular mass higher than the expected, corresponding to a product of a translational readthrough of the UGA stop codon. In this paper we show that the readthrough was abolished when the synthesis of the recombinant protein was carried out at 25 degrees C. The possible causes that contribute to reduce the proportion of readthrough protein species against the correct terminated product are discussed.

Bacillus subtilis↗
PubMed1988

A homozygous point mutation results in a stop codon in the C1q B-chain of a C1q-deficient individual.

Southern blot analysis of the B-chain genes in one of eight C1q-deficient individuals revealed an abnormal banding pattern. The defect, which was homozygous, could be localized by restriction mapping to a single Taq I site within residue 150 in the coding region of the B-chain gene. DNA sequencing across the site revealed a stop codon that would cause premature termination of the protein product. No material corresponding to the A or C chains, or a truncated B chain, could be identified by antigenic analysis of the patient's serum, indicating that a complete B chain is required for secretion of a C1q molecule.

Codon↗
PubMed2000

High expression of the second lysine decarboxylase gene, ldc, in Escherichia coli WC196 due to the recognition of the stop codon (TAG), at a position which corresponds to the 33th amino acid residue of sigma38, as a serine residue by the amber suppressor, supD.

Escherichia coli WC196, which was obtained from the strain W3110 by nitrosoguanidine mutagenesis as an overproducer of lysine, produced approximately twenty times more cadaverine than did W3110, and had a twenty fold higher level of rpoS gene product, sigma38, than in W3110. Both WC196 and W3110 had a stop codon (TAG) in rpoS at position which corresponds to the 33th residue of sigma38 protein. In addition, WC196 but not W3110 had a mutation in the gene encoding Ser-tRNA (SerU), called, supD. Analysis of the amino acid sequence of a sigma38 preparation from WC196 showed that the 33th residue of sigma38 is a serine residue. The deltarpoS deltacadA mutant of E. coli W3110 harboring the plasmid containing rpoS, in which the TAG codon was converted to a TCG codon for serine-33 residue of sigma38, expressed a significant amount of Ldc and accumulated a large amount of sigma38. However, the deltarpoS deltacadA mutant of W3110 with the plasmid containing the intact rpoS from W3110 could synthesize neither sigma38 nor Ldc significantly.

Amino Acid Sequence↗
PubMed1994

Protein C deficiency found in a patient with acute myocardial infarction: a single base mutation 157 Arg (CGA) to stop codon (TGA).

Protein C has an important role in the regulatory mechanisms of coagulation and fibrinolysis. In patients with heterozygous protein C deficiency, there is an increased risk for thromboembolic disease, especially in the venous system. We describe a patient with protein C deficiency presenting with an acute myocardial infarction (AMI). Direct sequence analysis of the whole protein C gene detected a single base mutation at exon 7; 157 [Arg(CGA) to stop codon (TGA): 6182 C to T]. Thus, the patient was suspected to have a deficiency of the protein C heavy chain molecule, resulting in both a low protein C antigen and activity level. The mutation was also found in the propositus' son and was confirmed by differential termination of the primer extension (DTPE).

Base Sequence↗
PubMed1985

An active variant of the prokaryotic transposable element IS903 carries an amber stop codon in the middle of an open reading frame.

The prokaryotic mobile genetic element IS903.B is an active variant of IS903. It differs from IS903 and IS102 by 34 and 61 nucleotide substitutions, respectively. The large open reading frame (ORFI) which probably encodes the transposase is conserved in all three IS elements, whereas the smaller open reading frame (ORFII), which codes on the opposite DNA strand and entirely overlaps ORFI, contains an amber stop codon past the middle of ORFII in IS903.B. Experiments using Escherichia coli K12 strains permissive or non-permissive for amber mutations revealed no difference in the cointegration frequency mediated by IS903.B. Therefore, a possible peptide encoded by ORFII on the IS903-related element is unlikely to be necessary for transposition.

Base Sequence↗