Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Stop codon”

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 1,045 records · Page 58Linked to original sources
PubMed2005

A statistical analysis of random mutagenesis methods used for directed protein evolution.

We have developed a statistical method named MAP (mutagenesis assistant program) to equip protein engineers with a tool to develop promising directed evolution strategies by comparing 19 mutagenesis methods. Instead of conventional transition/transversion bias indicators as benchmarks for comparison, we propose to use three indicators based on the subset of amino acid substitutions generated on the protein level: (1) protein structure indicator; (2) amino acid diversity indicator with a codon diversity coefficient; and (3) chemical diversity indicator. A MAP analysis for a single nucleotide substitution was performed for four genes: (1) heme domain of cytochrome P450 BM-3 from Bacillus megaterium (EC 1.14.14.1); (2) glucose oxidase from Aspergillus niger (EC 1.1.3.4); (3) arylesterase from Pseudomonas fluorescens (EC 3.1.1.2); and (4) alcohol dehydrogenase from Saccharomyces cerevisiae (EC 1.1.1.1). Based on the MAP analysis of these four genes, 19 mutagenesis methods have been evaluated and criteria for an ideal mutagenesis method have been proposed. The statistical analysis showed that existing gene mutagenesis methods are limited and highly biased. An average amino acid substitution per residue of only 3.15-7.4 can be achieved with current random mutagenesis methods. For the four investigated gene sequences, an average fraction of amino acid substitutions of 0.5-7% results in stop codons and 4.5-23.9% in glycine or proline residues. An average fraction of 16.2-44.2% of the amino acid substitutions are preserved, and 45.6% (epPCR method) are chemically different. The diversity remains low even when applying a non-biased method: an average of seven amino acid substitutions per residue, 2.9-4.7% stop codons, 11.1-16% glycine/proline residues, 21-25.8% preserved amino acids, and 55.5% are amino acids with chemically different side-chains. Statistical information for each mutagenesis method can further be used to investigate the mutational spectra in protein regions regarded as important for the property of interest.

Amino Acid Substitution↗
PubMed1992

Hepatitis B virus precore mutants are identical in carriers from various ethnic origins and are associated with a range of liver disease severity.

Hepatitis B virus carriers in Israel are mostly HBeAg negative, of whom 5% to 10% have circulating hepatitis B virus. Recently, a hepatitis B virus variant with a stop codon in the precore region was identified, and it was suggested that specific mutations are associated with fulminant or severe chronic active hepatitis. We have analyzed serum samples from HBeAg-positive and HBeAg-negative patients by polymerase chain reaction, using primers spanning the precore/core region. Nucleotide sequence analysis (by direct sequencing) from amplified hepatitis B virus DNA demonstrated that viral genomes from all HBeAg-negative patients contain G to A mutation (nucleotide 1896), leading to the formation of a stop codon. An additional G to A mutation was identified three nucleotides downstream (nucleotide 1899). These patients are of various ethnic origins, with no unique clinical characteristics and with normal liver histology, chronic hepatitis or cirrhosis. No mutation at the precore/core region was observed in the HBeAg-positive patients. In conclusion, the precore mutations identified in hepatitis B virus carriers in Israel are identical regardless of the carrier's ethnic origin and are associated with mild-to-severe liver disease.

Adult↗
PubMed2004

Identification of SQSTM1 mutations in familial Paget's disease in Australian pedigrees.

We have conducted a genome-wide scan on a pedigree containing 372 adult members, of whom 49 have PDB. In the present study, we report linkage of a large pedigree to the PDB3 region on chromosome 5q35-qter with a peak multipoint LOD score of 6.77. Sequestosome 1 (SQSTM/p62) has been identified as the causative PDB gene in this region. Six sequestosome 1 mutations have been described to date. Four mutations have been identified in exon 8, 1210delT and 1215delC both resulting in premature stop codon at amino acid 394, 1215C to T (P392L), 1224insT (E396X), one mutation in exon 7, 1200C to T (P387L) and a G to A splice junction mutation at IVS7+1. These mutations cluster in the C terminus of the protein and are predicted to disrupt the ubiquitin binding properties of sequestosome 1. Sequence analysis of the gene encoding sequestosome 1 revealed a single base pair deletion (1215delC) segregating with the majority of affected members in the pedigree. This deletion introduces a stop codon at position 394, resulting in premature termination of the protein (L394X) and loss of the ubiquitin-associated binding domain. Screening of affected members from 10 further PDB families identified the previously reported P392L mutation in one family. No SQSTM1/p62 coding mutations were found in the remaining 9 families or in 113 age-matched controls.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Impact of new mutations in the methylenetetrahydrofolate reductase gene assessed on biochemical phenotypes: a familial study.

Methylenetetrahydrofolate reductase (MTHFR) deficiency was identified in two out of four children born from nonconsanguineous parents. One of the affected children exhibited some clinical findings suggesting cystathionine beta-synthase deficiency; MTHFR activity was extremely reduced. In addition, hyperhomocysteinaemia, hypomethioninaemia, low total folate, especially methylfolate in red blood cells, and a reduced methylfolate/total folate ratio were found. Two mutations not yet reported, one on exon 1 of the gene changing an arginine to stop codon and one other on exon 9 changing an arginine to tryptophan were identified in both children in the compound heterozygous state associated with a common polymorphism, 1298A>C, also in the heterozygous state. The mother, homozygous for the mutation on exon 9 and for the polymorphism 1298A>C on exon 7, was clinically and biochemically normal, with normal folate status, mainly methylfolate levels in red blood cells, although MTHFR activity was moderately decreased. The father, heterozygous for the transition arginine to stop codon and for the common polymorphism 677C>T on exon 4, exhibited major biochemical abnormalities, hyperhomocysteinaemia and low methylfolate levels in red blood cells, but was clinically normal. The unaffected children had a biochemical pattern close to that of their mother and were heterozygous for the mutation on exon 9 and also for the two common polymorphisms, 677C>T and 1298A>C. In the affected children, some biochemical abnormalities, including folate status, especially methylfolate levels, were improved with treatment combining methyltetrahydrofolic acid, hydroxocobalamin, pyridoxine and betaine; however, homocysteine concentrations remained high and methionine concentrations were lowered. The father was treated with folic acid, which partially improved biochemical abnormalities. The impact of these mutations is discussed.

Adult↗
PubMed1997

Isolation of ALU1-P gene encoding a protein with aluminum tolerance activity from Arthrobacter viscosus.

We isolated a DNA fragment (ALU1-P) encoding a protein with an activity of aluminum tolerance from an Al tolerant soil microorganism, Arthrobacter viscosus. This microorganism was isolated from acidic tea field soils. The cloned DNA is composed of 1090 nucleotides, which has one open-reading frame without any stop codon. However, when the DNA fragment was transferred into Escherichia coli, a microorganism susceptible to Al toxicity, it endowed E. coli with Al tolerance. The deduced amino acid sequence of the DNA showed 65% identity with the protein of YbaX gene in Escherichia coli, and 51.1% identity with YB91 Haein hypothetical protein of HI1191 gene in Haemophilus influenzae. The ALU1-P gene in the expression vector produced a protein of 192 amino acids deriving a molecular weight of 21.3 kDa by using the stop codon in vector. The ALU1-P gene is a new one that has the characteristic of Al tolerance.

Aluminum↗
PubMed1997

Two previously unrecognized splicing mutations of GCH1 in Dopa-responsive dystonia: exon skipping and one base insertion.

We describe two previously unrecognized splice site mutations of GCH1 in Dopa responsive dystonia (DRD). Both mutations affect consensus splice acceptor (AG) sites. The first mutation is an A-->G transition at position -2 of intron 1 of GCH1. This mutation results in skipping of exon 2. Fusion of exons 1 and 3 causes a frame shift that generates a premature stop codon. The second mutation is an A-->G transition at position -2 of intron 2. The mutation generates a new splice acceptor site AG one base pair upstream of the wild-type splice site. This, together with a pyrimidine stretch upstream of the new splice site, renders this site functional and generates a transcript with the insertion of one base, i.e. the G of the wild-type splice site. This in turn causes a frame shift including the introduction of a premature stop codon. The two different mutations generate truncated GTP cyclohydrolase polypeptides.

Adolescent↗
PubMed2003

Novel mutations identified in the human multidrug resistance-associated protein 2 (MRP2/ABCC2) gene in a Japanese patient with Dubin-Johnson syndrome.

A 39-year-old Japanese women who has been jaundiced since childhood and indicative of Dubin-Johnson syndrome (DJS) underwent MRP2/ABCC2 mutation analysis. The results of the analysis revealed two novel mutations, C298T and C3928T, and two single nucleotide polymorphisms (SNPs), C3972T and C-24T. One of the two mutations (C298T) is in the transmembrane domain. The other mutation (C3928T) and the SNP (C3972T) are in the cytoplasmaic domain which are concentrated in the second adenosine triphosphate (ATP)-binding cassette. Both of the mutations, C298T and C3928T, are immature stop codons. C298T, C-24T and C3972T (originating from the mother) and C3928T (from the father) were observed to be heterozygous in this patient. Light-microscopy examination of the liver biopsy specimens revealed the accumulation of dark pigment granules in most of the hepatocytes. In the immunohistochemistry using pAb recognizing the C-terminal of the human MRP2, no staining of MRP2 in the canalicular membrane domain was observed in the liver sections from this patient. In this patient, the mutations with immature stop codons presumably resulted in instability of MRP2 mRNA and/or defective synthesis of the truncated protein, which may underlie the loss of the expression of functional MRP2 protein.

Journal Article↗
PubMed1999

Molecular biological aspects of inhibitor development.

Mutation genotype studies have led to a number of interesting observations about the role of the different types of mutations in inhibitor development. Searchable information on mutations, phenotype data, models, etc., are available on the internet at http://europium.mrc.rpms.ac.uk. A relatively high incidence of inhibitors occurs in patients with deletion mutations. Stop mutations are also associated with a high incidence of inhibitors, although there is anomalous distribution of the inhibitors associated with different stop codons. Inhibitors have been associated with a small number of missense mutations. Missense mutations are of great interest from the structure/function viewpoint; in many instances, a missense mutation which results in reduced function of a circulating protein can be mapped onto a model structure and inferences can be made about the effects on the functionality of the protein. A model of the A domains of FVIII is available, but as yet, no structure is available on which to model the C domain of FVIII. Stop codons appear to have a different incidence of inhibitor formation compared to other types of mutations. It is concluded that while genotype mutation studies have led to a number of interesting observations about the role of the different types of mutations in inhibitor development, though more questions have been raised than answers provided to date.

Databases, Factual↗
PubMed2005

Transcription of the Rickettsia felis ompA gene in naturally infected fleas.

Rickettsia felis is maintained transovarially in Ctenocephalides felis fleas in a widespread geographic distribution and is transmitted to humans and animals, including opossums. This rickettsia is phylogenetically a member of the spotted fever group, most closely related to Rickettsia akari and R. australis. An unusual feature of this rickettsia is that the gene for the outer membrane protein A (OmpA) is interrupted by stop codons. To determine if this putatively dying gene is expressed, mRNA was extracted from laboratory-maintained, R. felis-infected cat fleas. Reverse transcriptase-polymerase chain reaction amplification of three segments of the ompA gene indicated that mRNA of ompA is actively transcribed in fleas. The cDNA sequences expressed represented mRNA of the first 1860-basepair segment of ompA, which includes domains I and II, part of domain III, the region from site 1836 to site 2180, despite the presence of several stop codons, and the open reading frame from site 2788 to site 3837. The detected sequences showed several differences in the amino acid composition when compared with the previously reported sequence.

Animals↗
PubMed2006

Automated sequence screening of the entire dystrophin cDNA in Duchenne dystrophy: point mutation detection.

This is the first report of direct sequencing of the complete 11 kb coding sequence of the dystrophin gene affording high sensitivity for all types of mutations of both coding sequence and splicing. Direct automated capillary gel sequence analysis of dystrophin reverse-transcribed polymerase chain reaction (RT-PCR) products was carried out in 15 Duchenne muscular dystrophy (DMD) patient muscle biopsies (170,000 bp sequenced). We identified mutations in 67% of patients tested (10/15); including premature stop codons (n = 5) and small deletions/duplications (n = 5). Mutation-negative patients (n = 5) were also negative for promoter mutations. All were tested for the possibility of transcription abnormalities using quantitative multiplex fluorescence polymerase chain studies (QMF-PCR), however, equal ratios of mRNA transcripts were identified at the 5'and 3' regions, with mild reduction in overall quantity, suggesting that transcription abnormalities were less likely. We suggested that such patients might have a problem with the 3.5 kb 3' UTR, polyA site or undetected stop codons. It is also possible that splicing defects could result in addition of intron sequence which could lead to preferential amplification of low level residual normal transcript skipping.

Base Sequence↗
PubMed1989

Impact of altered protein structures on the intracellular traffic of a mutated vasopressin precursor from Brattleboro rats.

The rat vasopressin precursor, synthesized in the reticulocyte lysate system under the direction of in vitro transcribed mRNA, is processed and correctly delivered to the lumen of added microsomal vesicles. Translation of mRNA for the mutant (Brattleboro) vasopressin precursor which lacks a translational stop codon as a consequence of a frame-shift mutation, gives rise to a mutated protein (B-mutant precursor) with a C-terminal poly(lysine) sequence encoded by the poly(A) tail. Upon addition of microsomal membranes, the mutated precursor has access to the lumen of the vesicles as indicated by removal of the signal peptide; however, the C-terminal part with the poly(lysine) tail remains outside the vesicles as shown by its sensitivity to proteinase K. When a modified RNA, including a stop codon located similarly to that found in the cDNA encoding the normal precursor, is translated in the presence of microsomal membranes, the resulting product (S-mutant precursor) is refractory to proteolysis by exogenously added proteinase K. Analysis of the microsomal membranes indicates, however, that the C-terminus of the S-mutant precursor is still anchored within membranes. For studying the intracellular transport of the mutated precursor Xenopus laevis oocytes were injected with various RNA constructs. To monitor the transport steps from the endoplasmic reticulum to the Golgi compartment an RNA encoding a glycosylation site within the S-mutant precursor sequence was constructed. The resulting GS-mutant precursor is synthesized in the oocyte but not secreted into the incubation medium, completely in contrast to the normal vasopressin precursor which can be detected in the incubation bath 4 h after injection of the respective RNA. The sensitivity of the GS-mutant precursor carbohydrate side chain to endoglycosidase H treatment suggests that the mutated precursor does not reach the Golgi apparatus.

Acetylglucosaminidase↗
PubMed1993

A truncated form of herpes simplex virus type 1 immediate-early protein Vmw110 is expressed in a cell type dependent manner.

Herpes simplex virus type 1 (HSV-1) encodes five immediate-early (IE) genes, at least three of which are involved in the regulation of gene expression. Gene IE-1 is one of the few HSV-1 genes whose pre-mRNAs are spliced; the IE-1 pre-mRNA contains two introns, the second of which contains an in-frame stop codon which would terminate IE-1 translation if the intron were not excised. Previous work has shown that plasmids which have been constructed so as to express only the first two exons of Vmw110 can inhibit gene expression in transfection assays, whereas the normal intact protein is an activator of gene expression. In this paper we show that this predicted truncated Vmw110 protein is expressed during normal HSV-1 infection, and that it must be translated from IE-1 pre-mRNAs which retain the in-frame stop codon in the second intron. This truncated product is produced in amounts which depend upon the cell type infected. The possible consequences of these observations are discussed.

Animals↗
PubMed1992

Point mutations and polymorphisms in the human dystrophin gene identified in genomic DNA sequences amplified by multiplex PCR.

About one third of Duchenne muscular dystrophy (DMD) patients have no gross DNA rearrangements in the dystrophin gene detectable by Southern blot analysis or multiplex exon amplification. Presumably, in these cases, the deficiency is caused by minor structural lesions of the dystrophin gene. However, to date, only a single human DMD case has been described where a point mutation, producing a stop codon, accounts for the DMD phenotype. To screen for microheterogeneities in the dystrophin gene, we applied analysis by chemical mismatch cleavage to thirteen exons amplified in multiplex sets by the polymerase chain reaction. This analysis covers approximately 20% of the dystrophin-coding sequence. Sixty DMD patients without detectable deletions or duplications were investigated, leading to the identification of two point mutations and four polymorphisms with a frequency higher than 5%. Both point mutations are frameshift mutations in exons 12 and 48, respectively, and are closely followed by stop codons, thus explaining the functional deficiency of the dystrophin gene products in both patients.

Base Sequence↗
PubMed2005

A specific haplotype in the 3' end of estrogen-receptor alpha gene is associated with low bone mineral density in premenopausal women and increased risk of postmenopausal osteoporosis.

It is well established that the development of postmenopausal osteoporosis is under genetic influence. We have recently identified a synonymous single nucleotide polymorphism (SNP) in exon 8 of estrogen receptor-alpha (ERalpha) gene in the vicinity of the stop codon (G2014A) that is associated with an increased risk of postmenopausal osteoporosis. In the present study, we attempted to locate SNPs in the 3'-unstranslated region (3'UTR) of the ERalpha gene that are in linkage disequilibrium with the exon 8 SNP and assessed their utilization in the risk assessment of postmenopausal osteoporosis in 352 Thai postmenopausal women. The association with bone mineral density (BMD) in premenopausal women was also investigated in 202 premenopausal women. A C to A SNP 1,748 nucleotides distal to the end of the stop codon (C3768A) was identified. The C3768A SNP was not overrepresented in subjects with osteoporosis. However, the presence of the A-C haplotype allele based on the A2014 and C3768 alleles was significantly related to the risk of osteoporosis independently of age, body weight, the G2014A and C3768A SNPs (odds ratio 2.36, 95% CI 1.42-3.91). Moreover, the presence of the A-C haplotype allele was associated with lower femoral neck BMD in premenopausal women ( P =0.05). We concluded that a specific haplotype in the 3' end of the ERalpha gene is associated with lower BMD in premenopausal women and is associated with a higher risk of osteoporosis in postmenopausal women. It is likely that the haplotype allele exerts its influence on bone as early as during young adulthood to increase the risk of osteoporosis later in life.

3' Untranslated Regions↗
PubMed1995

Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells.

In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding rules between the yeast Saccharomyces cerevisiae and mammalian cells by establishing a versatile vector that can be used to study recoding in both species. We first assessed this vector by analysing the site of +1 frameshift of the Ty1 transposon. Two sequences from higher organisms were then tested in both yeast and mammalian cells: the gag-pol junction of human immunodeficiency virus type 1 (HIV-1) (a site of -1 frameshift), and the stop codon region of the replicase cistron from the tobacco mosaic virus (a site of UAG read through). We show that both sequences direct a high level of recoding in yeast. Furthermore, different mutations of the target sequences have similar effects on recoding in yeast and in mouse cells. Most notably, a strong decrease of frameshifting was observed in the absence of the HIV-1 stem-loop stimulatory signal. Taken together, these data suggest that mechanisms of some recoding events are conserved between lower and higher eukaryotes, thus allowing the use of S. cerevisiae as a model system to study recoding on target sequences from higher organisms.

Animals↗
PubMed2000

A survey of liver pathology in needle biopsies from HBsAg and anti-HBe positive individuals.

AIMS: To use laboratory data and liver biopsies, prospectively obtained from hepatitis B surface antigen (HBsAg) and anti hepatitis B e antigen (anti-HBe) positive patients, for the assessment of: (1) the relation between biopsy length/number of portal tracts and sampling error; (2) the relation between the severity of piecemeal necrosis and the new grading terminology (minimal, mild, moderate, and severe chronic hepatitis); and (3) liver pathology, which has not been studied in patients with this specific serological profile. METHODS: The study group (n = 174) included 104 patients with normal aminotransferase concentrations and no cases with clinically apparent cirrhosis. The specimen length and number of portal tracts were measured at light microscopy examination. Sampling error analysis was related to the discrepancies between aminotransferase concentrations versus histological grade. Detailed histological scorings were undertaken by the reference pathologist and compared with laboratory and hepatitis B virus (HBV) DNA precore sequence data. RESULTS: Sampling error seemed to be a constant feature, even for biopsies > or = 20 mm, but increased dramatically in biopsies < 5 mm long and/or containing less than four portal tracts. Between 25% and 30% of biopsies, graded as "mild" or "moderate" activity showed features of moderate and severe piecemeal necrosis, respectively. Ten per cent of the patients with normal aminotransferase values had stage III-IV hepatic fibrosis, and 20% had piecemeal necrosis. Only cytoplasmic, not nuclear, core antigen expression was a strong predictor of high hepatitis B viraemia. There was no association between precore stop codon mutations, grade/stage of liver disease, and hepatitis B core antigen (HBcAg) expression. CONCLUSIONS: The specimen available for light microscopical examination should be > 5 mm long and should contain more than four portal tracts. In addition, the new grading terminology might give the clinician an inappropriately mild impression of the severity of piecemeal necrosis. Furthermore, even in the presence of normal aminotransferase concentrations, considerable liver pathology can be found in 10-20% of HBsAg and anti-HBe positive individuals; such pathology is not associated with the occurrence of precore stop codon mutations.

Biopsy, Needle↗
PubMed2004

C-terminal truncated dystrophin identified in skeletal muscle of an asymptomatic boy with a novel nonsense mutation of the dystrophin gene.

Mutations that cause premature stop codons in the dystrophin gene lead to a complete loss of dystrophin from skeletal muscle, resulting in severe Duchenne muscular dystrophy. Here, a C-terminally truncated dystrophin resulting from a novel nonsense mutation is shown for the first time to be localized to the muscle plasma membrane. An asymptomatic 8-y-old boy was examined for dystrophin in skeletal muscle because of high serum creatine kinase activity. Remarkably, no dystrophin labeling was seen with an MAb against the C-terminal domain, suggesting the presence of an early stop codon in the dystrophin gene. Labeling with an antibody specific to the N-terminal domain, however, revealed weak, patchy, and discontinuous staining, suggesting limited production of a truncated form of the protein. Molecular analysis revealed a novel nonsense mutation (Q3625X) as a result of a single nucleotide change in the patient's genomic DNA (C10873T), leaving 1.6% of dystrophin gene product unsynthesized at the C terminus. Dystrophin mRNA analysis did not show rescue of the nonsense mutation as a result of exon-skipping by an alternative splicing mechanism. This is the first report of an asymptomatic dystrophinopathy with a nonsense mutation in the dystrophin gene.

Child↗
PubMed1997

[Hepatitis B virus mutants--clinical significance].

Hepatitis B virus (HBV) mutants have recently been identified in patients with acute or fulminant as well as chronic infections. Naturally occurring mutations have been identified in all viral genes and regulatory elements, most notably in the genes coding for the structural envelope and nucleocapsid proteins. Mutations in the gene coding for the hepatitis B surface antigen (HBsAg) may result in infection or viral persistence despite the presence of antibodies against HBsAg (anti-HBs) ("vaccine escape" or "immune escape"). Mutations in the gene encoding the pre-core/ core protein (pre-core stop codon mutant) result in a loss of hepatitis B e antigen (HBeAg) and seroconversion to antibodies to HBeAg (anti-HBe) with persistence of HBV replication (HBeAg minus mutant). Mutations in the core gene may lead among others to an "immune escape" due to a T cell receptor antagonism. Mutations in the gene coding for the polymerase/reverse transcriptase can be associated with viral persistence or resistance to nucleoside analogues. Thus, HBV mutations may affect the natural course of infection, viral clearance and response to antiviral therapy. Apart from the precore/core stop codon mutations, the exact contribution of specific mutations to diagnosis and therapy of HBV infection as well as patient management in clinical practice remain to be established.

Antibody Formation↗