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At least 649 records · Page 36Linked to original sources
PubMed2000

Selenoprotein W: a review.

Purification of selenoprotein W (Se-W) from rat and monkey muscles was shown to exist in multiple forms: with or without reduced glutathione and/or a 41-Da moiety (identity still unknown). TGA is located at coding position 13 in Se-W complementary DNA (cDNA) from all five species studied (rats, mice, sheep, human and monkey). TGA is also the stop codon in the rodents and sheep cDNA, but TAA is the stop codon in primates. There is an 80% homology of the nucleotide sequence in the coding region among the five species of animals, and the predicted amino acid sequences are 83% identical (rodents identical and primates identical). Se-W levels are highest in muscle, heart and brain from sheep and primates, but very low in rodent hearts. Studies with tissue cultures of muscle and brain cells indicated that selenium influenced Se-W levels. Although the metabolic function of Se-W is unknown, preliminary data suggest that it has an antioxidant function.

Amino Acid Sequence↗
PubMed2003

Mutations in the HLA class II genes leading to loss of expression of HLA-DR and HLA-DQ in diffuse large B-cell lymphoma.

Loss of expression of human leukocyte antigen (HLA) class II molecules on tumor cells affects the onset and modulation of the immune response through lack of activation of CD4+ T lymphocytes. Previously, we showed that the frequent loss of expression of HLA class II in diffuse large B-cell lymphoma (DLBCL) of the testis and the central nervous system (CNS) is mainly due to homozygous deletions in the HLA region on chromosome band 6p21.3. A minority of cases showed hemizygous deletions or mitotic recombination, implying that mutation of the remaining copy of the class II genes might be involved. Here, we studied three DLBCLs with loss of HLA-DQ expression for mutations in the DQB1 and DQA1 genes and three tumors with loss of HLA-DR expression for mutations in the DRB1 and DRA genes. In one case, a point mutation in exon 2 of the DQB1 gene, leading to the formation of a stop codon, was detected at position 47. In a second case, a stop codon was found at position 11 due to a deletion of 19 bp in exon 1 of the DRA gene. No mutations were found in the promoter sequences of the DRA, DQA1 and DQB1 genes. We conclude that both homozygous deletions and hemizygous deletions or mitotic recombination with mutations of the remaining allele may lead to loss of expression of the HLA class II genes, which is comparable to the mechanisms affecting HLA class I expression in solid cancers.

Base Sequence↗
PubMed1992

[Mollicute Acholeplasma florum possesses a gene of phosphoenolpyruvate sugar phosphotransferase system and it uses UGA as tryptophan codon].

Acholeplasmas are mollicutes which do not require sterol for growth and do not possess a phosphoenolpyruvate-dependent sugar-phosphotransferase system. In contrast to spiroplasmas, mycoplasmas and ureaplasmas, they utilize UGA as a stop codon and not as a tryptophan codon. Acholeplasma florum, because of its metabolic properties and its close phylogenetic relationship to members of the genera Spiroplasma and Mycoplasma, does not seem to be an acholeplasma senso stricto. Here, we present molecular data to support this hypothesis. We have detected a gene coding for one of the components of the phosphotransferase system (PTS) in A. florum. In addition we demonstrate that the organism uses UGA as a tryptophan codon and not as a stop codon. These findings offer strong evidence, along with an earlier phylogenetic proposal, that A. florum is not a member of the genus Acholeplasma.

Acholeplasma↗
PubMed1994

Deficiency in the A-subunit of coagulation factor XIII: two novel point mutations demonstrate different effects on transcript levels.

Congenital deficiency in coagulation factor XIII is a rare autosomal recessive bleeding disorder. Although the defect was characterized over 30 years ago, little is known about the molecular basis of the disorder. Here, we show two novel point mutations in the gene of the A-subunit of factor XIII in the genetically isolated population of Finland. All eight factor XIII-deficient families identified in Finland were studied. The exons of the gene of A-subunit were amplified individually by polymerase chain reaction and subsequently screened by single-strand conformation polymorphism. Sequence analysis of the abnormally migrating fragments showed two point mutations resulting in an amino acid alteration. A C-to-T transition at Arg-661 in exon XIV created a premature stop codon. This mutation was detected in six of the eight families, thus being the major alteration causing FXIII deficiency in Finland. In two of the six families, the patients were compound heterozygotes with the Arg-661-Stop mutation in one allele and either a T-to-C point mutation in exon VI or a thus far uncharacterized mutation in the other allele. The T-to-C transition in exon VI resulted in a substitution of threonine for methionine 242. The transition was found in one family only, where it was in the heterozygote form combined with the Arg-661-Stop mutation. To evaluate the consequences of these mutations, steady-state FXIII mRNA levels were quantitated by solid-phase minisequencing. In addition to the termination of translation 70 amino acids before the initial stop codon, the Arg-661-Stop mutation causes a 10- to 30-fold reduction in FXIII mRNA levels. This is also likely to result in a low translation level in the truncated polypeptide. In contrast, Met-242-Thr mutation does not seem to affect the level of mRNA. Here, the absence of a functional and immunodetectable protein is probably caused by an altered conformation of the mutant polypeptide, resulting in early degradation of the defective protein.

Adolescent↗
PubMed1994

Versatile Escherichia coli expression vectors for production of truncated proteins.

Several expression vector plasmids containing the tac promoter, the rrnBT1T2 terminator, and the pUC ori sequence were constructed. Some of them, the pES series, have a start codon in all three reading frames and multiple cloning sites downstream of the tac promoter and have stop codons also in all three frames and additional stop codons accompanying restriction sites. They are designed for versatile expression of truncated proteins which are produced by deleting portions of the inserted DNA.

Amino Acid Sequence↗
PubMed1989

Single base substitution between human intestinal and hepatic apolipoprotein B mRNA detected by ribonuclease cleavage analysis.

The molecular mechanism of human intestinal apolipoprotein (apo) B-48 synthesis has been elucidated by a combination of sequencing of cloned complementary DNAs and RNase cleavage analysis of RNA heteroduplex. All intestinal cDNA clones contained a single C to T base substitution in the codon CAA encoding Gln2153 in apoB-100 cDNA, resulting in a translational stop. One of the our intestinal apoB cDNA clones was polyadenylated 106 bases downstream from the stop codon, possibly producing a 7-kb apoB message in the intestine. RNase cleavage analysis of the RNA heteroduplex between hepatic or intestinal RNA and apoB cDNA-directed anti-sense RNA showed that this single C to U substitution may occur in most of intestinal apoB mRNA. These results suggested that human apoB-48 is mostly produced by apoB mRNA with an in-frame stop codon in the intestine.

Apolipoproteins B↗
PubMed1989

RNA editing: a novel mechanism for regulating lipid transport from the intestine.

Human apolipoprotein (apo)-B mRNA undergoes a novel tissue specific editing reaction which replaces a genomically templated cytidine with uridine. This substitution converts codon 2153 from glutamine (CAA) in apo-B100 mRNA to a stop codon (UAA) in apo-B48 mRNA. This novel RNA editing process is responsible for the generation of hepatic apo-B100 and intestinal apo-B48. We have established the following concerning this process: (1) by transfection of a series of deletion mutants into the rat hepatoma cell line McArdle 7777, which makes both apo-B100 and apo-B48, we have defined a minimum sequence of 26 nucleotides that is required for apo-B mRNA editing. The sequence containing the modified nucleotide forms a 26 nucleotide highly conserved stem loop with the modified nucleotide occurring in an 8-base loop. (2) Conversion in vitro of apo-B mRNA has been established, using cell free S100 cytoplasmic extract and synthetic RNA templates. Activity was abolished by protease treatment. (3) Transgenic mice were created which expressed a human apo-B construct spanning the stop codon. Apo-B mRNA was found in all tissues examined and this was shown to undergo editing. (4) In the rat liver, which produces apo B-100 and apo-B48, modulation of the relative proportion of these proteins by thyroxine was demonstrated to be mediated at the level of the RNA editing mechanism. It is concluded that apo-B mRNA is edited by a generally expressed protein and editing is highly regulated.

Animals↗
PubMed2000

Molecular analysis of the hydroxymethylbilane synthase (HMBS) gene in Italian patients with acute intermittent porphyria: report of four novel mutations.

Acute intermittent porphyria (AIP) is an autosomal disorder caused by molecular abnormalities in the hydroxymethylbilane synthase (HMBS) gene coding for the third enzyme in the heme biosynthetic pathway. So far, more than 160 different mutations responsible for AIP have been identified in this gene. We have now identified seven mutations in eight unrelated Italian patients with AIP: two splicing defects (IVS7+2T-->C, 612G-->T), three small deletions (308-309delTG, 730-731delCT, 182delA) and two missense mutations (134C-->A, 541C-->T). The splicing defects were responsible for activation of splicing cryptic sites respectively within intron 7 (15 bp insertion) and exon 10 (9 bp deletion). The small deletions resulted in frameshifts leading to the formation of premature stop codons. The 134C-->A and 541C-->T mutations caused the formation of stop codons likely to be responsible for drastic disruption of the HMBS structure (Ser45Ter, Gln181Ter). This is the first molecular study in AIP patients of Italian origin leading to the identification of four new mutations and three molecular defects that have already been described.

Adult↗
PubMed2006

The distribution of constitutional and somatic mutations in the neurofibromatosis 2 gene.

Constitutional heterozygous inactivating mutations in the neurofibromatosis 2 (NF2) tumor suppressor gene cause the autosomal dominant disease NF2, and biallelic inactivating somatic NF2 mutations are found in a high proportion of unilateral sporadic vestibular schwannoma (USVS) and sporadic meningioma. We surveyed the distributions of constitutional NF2 mutations in 823 NF2 families, 278 somatic NF2 mutations in USVS, and 208 somatic NF2 mutations in sporadic meningioma. Based on the available NF2 mutation data, the most dominant influence on the spectra of mutations in exons 1-15 are C>T transitions that change arginine codons (CGA) to stop codons (TGA) due to spontaneous deamination of methylcytosine to thymine in CpG dinucleotides. The paucity of reported mutations in exon 9 and the absence of reported mutations in exons 16 and 17 may be related to structure-function relationships in the NF2 protein.

Codon, Nonsense↗
PubMed1986

Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins.

We have determined the nucleotide sequences of two genes from Klebsiella pneumoniae, nifA, the nif-specific activator of transcription and ntrC, the bifunctional regulatory protein involved in 'nitrogen control'. These sequences differ significantly from those previously published. In particular, nifA extends 40 codons beyond the stop codon reported earlier. This extension encodes a putative DNA-binding domain strongly homologous to the Rhizobium meliloti nifA protein and to some extent to the ntrC protein. In all three proteins this domain is linked by a segment of variable length to a strongly conserved central domain of 240 residues. A short segment having the properties of an interdomain linker joins the central region to an N-terminal domain, which is weakly related in the case of the two nifA proteins. This homology is not shared by the N-terminal domain of ntrC, which is clearly but unexpectedly related to the N-terminal domains of a diverse set of procaryotic pleiotropic control proteins, including ompR, dye and nusA from Escherichia coli and spoOA and spoOF from Bacillus subtilis.

Amino Acid Sequence↗
PubMed1993

Identification and characterization of the ctaC (coxB) gene as part of an operon encoding subunits I, II, and III of the cytochrome c oxidase (cytochrome aa3) in the cyanobacterium Synechocystis PCC 6803.

The gene (coxII = coxB = ctaC) encoding subunit II of Synechocystis PCC 6803 cytochrome c oxidase has been isolated by screening a genomic DNA library in pUC18 with a 17-bp oligonucleotide probe (probe C) derived from coxI of Paracoccus denitrificans after Southern blots with a 19-kb oligonucleotide (probe A) derived from coxII of P. denitrificans had given equivocal results. A 2.2 kb PstI-KpnI restriction fragment was subcloned into pUC 18 and the resulting plasmid pDAUV26, which contained the probe C-binding site near the downstream end was found also to contain the whole coxII gene upstream of this site. The novel plasmid pDAUV 26 was used to transform competent E. coli cells, propagated therein, and the sequence determined. The 2.2 kb insert contained the entire coding region for the coxII gene together with a GAG start codon, a TAA stop codon, and a putative Shine-Dalgarno sequence. The deduced COII polypeptide is composed of 319 aa (calculated molecular mass of 32,800) plus a N-terminal leader sequence of 20 aa. The hydropathy plot suggests two lipophilic transmembrane domains near the N-terminus connected with an extremely hydrophilic aa stretch on the cytosolic side, while an unusually long (> 50 aa) aa stretch on the periplasmic (= intrathylakoidal) side leads to a typical cyanobacterial threonine in place of the first conserved glutamate of the cytochrome c-binding region in all other COII proteins. Together with a considerably shortened and interrupted aromatic aa stretch in this region, these differences are discussed in terms of the peculiar affinity of cyanobacterial cytochrome oxidases for acidic c-type cytochromes. Other invariant features such as the strictly conserved CuA-binding aa, however, are found in correct positions.

Amino Acid Sequence↗
PubMed2002

The identification of the inhibitory gamma-subunits of the type 6 retinal cyclic guanosine monophosphate phosphodiesterase in non-retinal tissues: differential processing of mRNA transcripts.

Here, we report that mouse lung expresses gamma-subunit (PDEgamma) transcripts of the rod and cone photoreceptor cGMP phosphodiesterase genes (Pde6g and Pde6h, respectively). Moreover, a major 14-kDa protein (p14) in lung membranes was immunostained with antibodies that react with both rod and cone PDEgamma. We show that p14 is, in fact, a mixture of rod and cone PDEgamma, based on three additional lines of evidence. First, p14 was also immunostained with antibodies specific for the cone PDEgamma isoform. Second, the expression of p14 immunostained with antibodies recognizing both rod and cone PDEgamma was substantially reduced in lung membranes from Pde6g-/- mice. In contrast, the fraction of p14 stained with cone PDEgamma-specific antibodies was not altered in the Pde6g-/- mice. Third, the absence of the Pde6g transcript was correlated with reduced levels of p14 in Pde6g-/- mice. We have also found that mouse lung contains a small Pde6h transcript that has a 41-bp deletion resulting in a frame change, derived by differential mRNA processing of exon 3 of Pde6h. BLAST searches also revealed a rat ovary EST that has the same 41-bp deletion causing the same frame change. However, the premature in-frame stop codon seen in the short Pde6h transcript is absent and the regular stop codon is out of frame leading to a predicted ORF extension into the 3' UTR. These findings show that rod and cone PDEgamma isoforms are expressed in lung and seem to have a critical role in regulating p42/p44 mitogen-activated protein kinase signaling.

3',5'-Cyclic-GMP Phosphodiesterases↗
PubMed1995

Aberrations of the p53 tumor suppressor gene in human epithelial ovarian carcinoma.

Aberrations of the p53 gene in 26 surgical specimens of human epithelial ovarian carcinomas were examined by single-strand conformation polymorphism (SSCP) analysis of polymerase chain reaction (PCR) products. Seven (27%) of the tumors demonstrated a SSCP band shift in exons 4 to 9 of the gene, including 5 in the region encompassing exons 5 and 6, 1 in exon 7, and 1 in the region encompassing exons 8 and 9. Mutations were clustered in exon 5 in highly conserved regions of the p53 gene. All of the abnormal DNA fragments have been further characterized by direct DNA sequencing. These include five missense mutations (five transitions), a one-base-pair deletion introducing, by frameshift, a stop codon further downstream, and a two-base-pair insertion introducing a stop codon downstream by frameshift. Most mutations were base substitutions, and were clustered in exon 5 (71%), especially codons 175 and 179. The aberrations of the p53 gene were only found in tumors of FIGO stages III and IV. Histologic grading was also reviewed with respect to p53 aberrations. The aberrations were absent in well-differentiated carcinomas. The more undifferentiated the primary tumor, the more frequent p53 mutation (P < 0.05). Our results indicated that the aberrations of the p53 gene were common in epithelial ovarian cancers and p53 aberration may occur late during ovarian cancer evolution.

Base Sequence↗
PubMed1994

A nonsense mutation in the alpha4 subunit of the nicotinic acetylcholine receptor (CHRNA4) cosegregates with 20q-linked benign neonatal familial convulsions (EBNI)

Benign Familial Neonatal Convulsions (BFNC) is an epileptic disorder with an autosomal dominant mode of transmission. It has been shown that about 80% of BFNC pedigrees are linked to a genetic defect on chromosome 20q13.3. A candidate gene for the epilepsies, the gene coding for the alpha4 subunit of the nicotinic cholinergic receptor (CHRNA4), has previously been localized on chromosome 20. Here we report a single point mutation converting a serine codon to a stop codon in the exon 5 of CHRNA4, in one BFNC family. Identification of CHRNA4 as the defective gene in 20q-BFNC represents the first example of a human idiopathic epilepsy caused by a mutation directly affecting a neurotransmitter receptor in the central nervous system.

DNA Probes↗
PubMed1991

Recurrent mutation at aa 792 in the LDL receptor gene in a French patient.

Many mutations in the low density lipoprotein receptor gene (LDLR) have been characterized at the molecular level in individuals with familial hypercholesterolemia. Most of the mutations that have been reported are large deletions or insertions in the gene, it being much more difficult to identify point mutations. In this study, 139 unrelated French familial hypercholesterolemia subjects were screened for the presence of three different previously described LDLR point mutations, employing the polymerase chain reaction and allele-specific oligonucleotide hybridization. Only one subject carried a point mutation at amino acid position 792, which substituted a Trp codon for a Stop codon. The same mutation has previously been described in a subject originating from Saudi Arabia. Haplotype analysis of LDLR associated with each mutation was performed. The haplotypes were totally different, suggesting that this mutation has occurred more than once.

Base Sequence↗
PubMed1991

Recurrence of a nonsense mutation in the NF1 gene causing classical neurofibromatosis type 1.

The gene responsible for von Recklinghausen neurofibromatosis (NF1) has recently been identified, and several point mutations and deletions have been described. The availability of intron-exon boundaries of several exons of the NF1 gene facilitates the search for mutations in affected patients. We have analysed 38 patients for mutations in exon 4 of the NF1 gene, and found one patient with a C----T transition at base position 1087 of the cDNA, changing an arginine codon to a stop codon, at amino acid position 365. Sequencing of other members of the family, including both parents, did not show the mutation, confirming that this mutation is responsible for this sporadic NF1 case. As the mutation described here was previously identified in an independent case by others, this case represents a recurrence of this mutation and suggests that codon 365 might be a hot spot for mutations in the NF1 gene. Thus, a specific search for this mutation should be performed when studying NF1 sporadic or familiar cases for genetic analysis.

Amino Acid Sequence↗
PubMed1992

Mutational analysis of SRY: nonsense and missense mutations in XY sex reversal.

XY females (n = 17) were analysed for mutations in SRY (sex-determining region Y gene), a gene that has recently been equated with the testis determining factor (TDF). SRY sequences were amplified by the polymerase chain reaction (PCR) and analysed by both the single strand conformational polymorphism assay (SSCP) and DNA sequencing. The DNA from two individuals gave altered SSCP patterns; only these two individuals showed any DNA sequence variation. In both cases, a single base change was found, one altering a tryptophan codon to a stop codon, the other causing a glycine to arginine amino acid substitution. These substitutions lie in the high mobility group (HMG)-related box of the SRY protein, a potential DNA-binding domain. The corresponding regions of DNA from the father of one individual and the paternal uncle of the other, were sequenced and found to be normal. Thus, in both cases, sex reversal is associated with de novo mutations in SRY. Combining this data with two previously published reports, a total of 40 XY females have now been analysed for mutations in SRY. The number of de novo mutations in SRY is now doubled to four, adding further strength to the argument that SRY is TDF.

Base Sequence↗
PubMed1994

Nonsense mutations at Arg-1947 in two cases of familial neurofibromatosis type 1 in Japanese.

We report two familial cases of NF1 presenting as C to T transitions changing an Arg-1947 codon to a stop codon. In one of the two families, cosegregation of the mutation with NF1 was demonstrated, indicating this mutation causes the disease in this family. As the same mutation at Arg-1947 has been reported previously in three cases of unrelated Caucasians (two are sporadic; the origin of the other is not reported), the codon at Arg-1947 (CGA) in the NF1 gene is considered to be a hotspot common among different ethnic groups and also among familial and sporadic cases.

Adult↗