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PubMed1992

[Identification of two different genetic mutation associated with silent phenotypes for human serum cholinesterase in Japanese].

Two different gene mutations associated with the silent phenotype for human serum cholinesterase were demonstrated. DNA from five individuals with silent gene phenotype of three unrelated Japanese families was amplified by the polymerase chain reaction (PCR) and analyzed by direct sequencing. The first instance demonstrated a G----C transversion at codon 365 from GGA (Gly) to CGA (Arg), which was seen in three individuals of the two families. This mutation was resulted to create a new Taq 1 restriction site (TCGA). The second mutation was shown by a double heterozygous condition with two different silent gene mutations in two members of remaining one family. These mutations were as follows: 1) one type was a frameshift mutation, in which an extra A was inserted in codon 315 (ACC----AACC) to create a new stop codon at position 322 and 2) the other was the same point mutation at codon 365 as seen in the first instance. These results indicated that many silent variants can be distinguished by direct sequence analyses of genomic DNA.

Asian People↗
PubMed1992

Truncated phenylalanine ammonia-lyase expression in tomato (Lycopersicon esculentum).

Southern blot analyses of genomic DNA fragments suggest there are five different classes of phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) genomic sequence in tomato (Lycopersicon esculentum). Isolation and subsequent sequence analysis of three examples from genomic libraries reveal highly homologous coding sequences but also a surprisingly high frequency of single point mutations which would truncate protein synthesis. The nucleotide sequence for one of the genes (PAL5) encodes a normal polypeptide of 721 amino acids, interrupted by a 710-base pair intron in the codon for amino acid 139. In contrast, premature stop codons, 363 triplets from the end in PAL1 and 304 triplets from the end in PAL3 would result in substantially (51-43%) shorter polypeptides that are consistent with the protein polymorphism, recently reported in alfalfa (Jorrin, J., and Dixon, R. A. (1990) Plant Physiol. 92, 447-445) but ascribed to protein degradation. S1 mapping of the mRNA termini and polymerase chain reaction analysis of cDNA transcripts indicate that at least one of these truncated coding sequences is expressed, strongly suggesting that at least some of the shorter polypeptides constitute original gene products with a potentially important function.

Amino Acid Sequence↗
PubMed2006

The mismatch repair gene hPMS2 is mutated in primary breast cancer.

Mismatch repair (MMR) genes play a fundamental role in the correction of replication errors and their mutation leads to cancer development. In the present study we have analyzed the hPMS2 MMR gene for mutation using 20 primary breast cancers and seven breast tissues obtained from areas adjacent to breast cancer. For this purpose we have used cDNA sequence analysis and Western blotting using the specific antibody against the amino-terminal domain E-19. In primary breast cancers we found that the hPMS2 gene had 9 missense mutations [codons: 513 (by change of Ser x Asp) in 14 tumors, 520 (Ala x Val) in 8 tumors, 573 (by change of Thr x Ser in 19 tumors), 578 (by change of Arg x Leu in 9 tumors), 587 (by change of Ser x Asp in 7 tumors), 590 (by change of Ile x Leu in 12 tumors), 598 (by change of Gln x His in 5 tumors), 601 (by change of Ser x Leu in 13 tumors), 608 (by change of Ala x Ser in 9 tumors. Nine out of 20 breast cancers had a non-sense mutation in nucleotide 1862 by changing Adenine by Thymine (AAG x TAG), which corresponded with a change in codon 613 by a change of Lys by stop codon. This non-sense mutation is responsible for the premature truncation of the protein hPMS2, which is reflected in the Western blotting by two bands, one corresponding with the wild-type form (100 kDa) and a lower one (75 kDa) corresponding with the truncated form of the hPMS2 MMR protein. This truncated protein and the mutations in the hPMS2 gene were also detected in two samples of normal-appearing tissue adjacent to their corresponding cancerous lesion. Altogether the present report demonstrates that primary breast cancers harbor mutations in this MMR gene and that normal-appearing breast tissue adjacent to the primary lesion also harbors the same mutations before the neoplastic process is manifested.

Adenosine Triphosphatases↗
PubMed1991

Catalytic triad residue mutation (Asp156----Gly) causing familial lipoprotein lipase deficiency. Co-inheritance with a nonsense mutation (Ser447----Ter) in a Turkish family.

We studied the molecular basis of familial Type I hyperlipoproteinemia in two brothers of Turkish descent who had normal plasma apolipoprotein C-II levels and undetectable plasma post-heparin lipoprotein lipase (LPL) activity. We cloned the cDNAs of LPL mRNA from adipose tissue biopsies obtained from these individuals by the polymerase chain reaction and directional cloning into M13 vectors. Direct sequencing of pools of greater than 2000 cDNA clones indicates that their LPL mRNA contains two mutations: a missense mutation changing codon 156 from GAU to GGU predicting an Asp156----Gly substitution and a nonsense mutation changing the codon for Ser447 from UCA to UGA, a stop codon, predicting a truncated LPL protein that contains 446 instead of 448 amino acid residues. Both patients were homozygous for both mutations. Analysis of genomic DNAs of the patients and their family members by the polymerase chain reaction, restriction enzyme digestion (the GAT----GGT mutation abolishes a TaqI restriction site), and allele-specific oligonucleotide hybridization confirms that the patients were homozygous for these mutations at the chromosomal level, and the clinically unaffected parents and sibling were true obligate heterozygotes for both mutations. In order to examine the functional significance of the mutations in this family, we expressed wild type and mutant LPLs in vitro using a eukaryotic expression vector. Five types of LPL proteins were produced in COS cells by transient transfection: (i) wild type LPL, (ii) Asp156----Gly mutant, (iii) Ser447----Ter mutant, (iv) Gly448----Ter mutant, and (v) Asp156----Gly/Ser447----Ter double mutant. Both LPL immunoreactive mass and enzyme activity were determined in the culture media and intracellularly. Immunoreactive LPLs were produced in all cases. The mutant LPLs, Asp156----Gly and Asp156----Gly/Ser447----Ter, were devoid of enzyme activity, indicating that the Asp156----Gly mutation is the underlying defect for the LPL deficiency in the two patients. The two mutant LPLs missing a single residue (Gly448) or a dipeptide (Ser447-Gly448) from its carboxyl terminus had normal enzyme activity. Thus, despite its conservation among all mammalian LPLs examined to date, the carboxyl terminus of LPL is not essential for enzyme activity. We further screened 224 unrelated normal Caucasians for the Ser447----Ter mutation and found 36 individuals who were heterozygous and one individual who was homozygous for this mutation, indicating that it is a sequence polymorphism of no functional significance. Human LPL shows high homology to hepatic triglyceride lipase and pancreatic lipase.(ABSTRACT TRUNCATED AT 400 WORDS)

Adipose Tissue↗
PubMed1990

Characterization of the apolipoprotein B mRNA editing activity in enterocyte extracts.

Apolipoprotein B (apoB) circulates in human plasma as two isoforms, apoB-100 (512 kDa) and apoB-48 (242 kDa). ApoB-48 is generated by a novel RNA editing mechanism which post-transcriptionally modifies apoB mRNA in the intestine by converting cytidine at nucleotide 6666 to uridine. This converts codon 2153 from glutamine (CAA) to a premature stop codon (UAA). To characterize the activity which edits apoB mRNA, extracts were prepared from enterocytes isolated from baboon small intestine. These extracts efficiently edit synthetic apoB RNA in vitro. Editing was detected by primer extension, and the specificity of the reaction was confirmed by DNA sequencing. Extracts prepared from other baboon tissues did not edit apoB RNA in vitro. The editing activity was partially purified by chromatography of the enterocyte extracts on DEAE-cellulose. The activity is sensitive to proteinase K but resistant to micrococcal nuclease and has an average molecular mass of 125 kDa when analyzed by gel filtration chromatography.

Animals↗
PubMed1994

The MTS1 gene is frequently mutated in primary human esophageal tumors.

Homozygous and heterozygous deletions involving chromosome 9p21 have been reported in a variety of primary human tumors in vivo, and point mutations have been reported in melanoma cell lines in vitro within a probable tumor suppressor gene, MTS1, located at chromosome 9p21. We describe six sequence alterations occurring among twenty-four primary esophageal squamous carcinomas and nineteen primary esophageal adenocarcinomas analyzed by DNA sequencing of MTS1 exon 2. Nucleotide substitutions were observed in five squamous cell carcinomas and in one adenocarcinoma. Two occurred in the germline, while four were somatic alterations. All six nucleotide changes resulted in marked alterations in amino acid sequence. Four were nonsense mutations leading to premature termination codons; nucleotide substitutions identical to two of these stop codons were previously reported in other tumor types. Loss of heterozygosity occurred in all five informative (constitutionally heterozygous) cases in which a sequence alteration was present. Esophageal cancer is one primary human tumor in which MTS1 constitutes an apparent target of heterozygous or homozygous deletions occurring at chromosome 9p21.

Base Sequence↗
PubMedDate not supplied

The third zinc finger of the WT1 gene is mutated in Wilms' tumour but not in a broad range of other urogenital tumours.

Aberrations in the WT1 tumour suppressor gene have been documented in a fraction of Wilms' tumours (WTs). Encoding a protein with four zinc fingers, the WT1 gene is expressed in the developing kidney, gonads, uterus, spleen, mesothelium and brain. Using polymerase chain reaction (PCR), single strand conformation polymorphism (SSCP) analysis and direct DNA sequencing, we analysed 156 diverse tumours for abnormalities of zinc finger 3 (ZF3), a mutational hotspot in WT1. Only one sample (WT) exhibited PCR-SSCP mobility shift. A CGA to TGA nonsense mutation at codon 390 with arginine being substituted with a stop codon was detected and predicted to encode a faulty WT1 protein in this WT, out of 8 WTs studied. Our results are consistent with the presence of WT1 ZF3 mutations in a subset of WTs, but not in other tumours of urogenital nor of WT1-related origin.

Base Sequence↗
PubMed1995

Synchronous multifocal bone sarcomas--a case report and molecular pathologic investigation.

A case of a 54-year-old woman is described who developed synchronously two malignant bone tumors: a dedifferentiated chondrosarcoma in the olecranon and a malignant fibrous histiocytoma (MFH) in the lower tibia. The anaplastic part of the dedifferentiated chondrosarcoma revealed an MFH-like pattern. Myogenous differentiations were not observed in the anaplastic sarcoma cells. The MFH in the tibia showed a storiform-pleomorphic pattern. Single tumor cells showed positivity for M-actin and desmin pointing to myogenous differentiation. DNA-cytophotometry of the dedifferentiated chondrosarcoma showed an aneuploid stem cell line. The MFH in the tibia did not reveal aneuploid stem cells. Staining for p53 protein was negative in both tumors. SSCP analysis and sequencing of the p53 gene in both tumors revealed in the dedifferentiated chondrosarcoma a mutation in exon-8 with the transversion from G to T in codon 294 resulting in a substitution of a stop codon for GLU. The mutation was not observed in the MFH. From these immunohistologic, DNA-cytometric and molecular biologic investigations, we consider it probable that the tumor in the lower tibia is a second highly malignant bone tumor and not the metastasis of the dedifferentiated portion of the dedifferentiated chondrosarcoma in the olecranon.

Bone Neoplasms↗
PubMed1998

A non-sense mutation at Arg95 is predominant in complement 9 deficiency in Japanese.

Deficiency of the ninth component of complement (C9D) is one of the most common genetic abnormalities in Japan, with an incidence of one homozygote in 1000. Although C9D individuals are usually healthy, it has been shown that they have an significantly increased risk of developing meningococcal meningitis. In the present study we report the molecular bases for C9D in 10 unrelated Japanese subjects. As a screening step for mutations, exons 2 to 11 of the C9 gene were analyzed using exon-specific PCR/single-strand conformation polymorphism analysis, which demonstrated aberrantly migrating DNA bands in exon 4 in all the C9D subjects. Subsequent direct sequencing of exon 4 of the C9D subjects revealed that eight of the 10 C9D subjects were homozygous for a C to T transition at nucleotide 343, the first nucleotide of the codon CGA for Arg95, leading to a TGA stop codon (R95X). R95X is a novel mutation different from those recently identified in a Swiss family with C9D. Cases 6 and 7 were heterozygous for the R95X mutation. Family study in case 10 confirmed the genetic nature of the defect. In case 6, the second mutation for C9D of the C9 gene was identified to be the substitution of Cys to Tyr at amino acid residue 507 (C507Y), while the genetic defect(s) in the other allele in case 7 remains unknown. Our results indicate that a novel mutation, R95X, is present in most cases of C9D in Japan.

Adult↗
PubMed1992

Mutations in severe, type III von Willebrand's disease in the Dutch population: candidate missense and nonsense mutations associated with reduced levels of von Willebrand factor messenger RNA.

The von Willebrand factor (vWF) genes of nine unrelated, severe, type III von Willebrand's disease (vWD) patients (six of Dutch origin) and four unrelated Dutch type I vWD patients were screened for mutations in exons that contain CGA codons (Arg), which are liable to mutation to TGA stop codons. The nine exons of the vWF gene (3, 8, 9, 10, 28, 31, 32, 43 and 45) that contain all the CGA codons (11 in total) of the vWF cDNA were amplified by the polymerase chain reaction and screened for mutations by single-strand conformation polymorphism analysis, restriction enzyme - and/or nucleotide sequence analysis. Three of the severe vWD patients were found to be heterozygous for a nonsense mutation: CGA Arg 2535-->TGA Stop. Three other severe vWD patients were homozygous for a single nucleotide substitution, AAC Asn 2546-->TAC Tyr. The transcription of these mutated alleles was tested by cDNA dependent amplification of platelet RNA. The level of transcription product was strongly reduced for either mutant allele.

Alleles↗
PubMed2003

Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency.

Pyrimidine 5' nucleotidase-I (P5N-I) deficiency is a rare autosomal recessive disorder associated with hemolytic anemia, marked basophilic stippling, and accumulation of high concentrations of pyrimidine nucleotides within the erythrocyte. Recently, the structure and location of the P5N-I gene have been published. This paper presents the results of a study characterizing the molecular pathologies of P5N-I deficiency in a total of 6 Turkish patients from 4 unrelated families of consanguineous marriages. Mutation analysis in the P5N-I gene led to the identification of 3 novel mutations in these patients. In 4 patients from 2 families, a homozygous insertion of double G at position 743 was detected in exon 9 (743-744insGG), leading to premature termination of translation 23 bp downstream. In one family, a homozygous T to G transition at position 543 (543T>G) in exon 8 resulted in the replacement of tyrosine (Tyr) with a stop codon (Tyr181Stop). In another family, a homozygous insertion of a single A in exon 7 (384-385insA) created a stop signal at the codon nearby. In all families, the parents were heterozygous for the relevant mutations. None of these changes was detected in 200 chromosomes from a healthy Turkish population. These mutations were not correlated with any particular phenotype.

5'-Nucleotidase↗
PubMed1993

Identification of a nonsense mutation at codon 128 of the Norrie's disease gene in a male infant.

OBJECTIVE: Norrie's disease (ND) is a rare X-linked hereditary disorder characterized by congenital blindness. A putative gene for ND has been isolated and mapped to Xp11.3. Four point mutations in this gene have been identified recently in patients with ND, thus providing strong evidence that this gene is associated with the disease. We report a new mutation. DESIGN: Clinical findings from the proband were correlated with results from DNA analysis. The proband's DNA was compared with that from his mother, an unaffected brother, and four unrelated normal males. PATIENT: The proband was a male infant referred for ocular evaluation at 3 months of age. INTERVENTIONS: The patient was evaluated with a general ocular examination at 4 months of age, a computed tomographic scan at 8 months of age, and then periodic follow-up examinations over the next 7 years. Blood samples were also collected from the proband, his family, and four unrelated normal males. DNA was extracted, amplified using polymerase chain reactions, and then cloned and sequenced. RESULTS/CONCLUSIONS: We identified a new mutation at codon 128 of the ND gene, a dinucleotide GC-to-AA substitution that changed the normal codon for cysteine, TGC, to TAA, which is a stop codon. Thus, this patient lacks the last six amino acids of the carboxyl terminus of the ND protein. The normal ND protein has 11 cysteines in conserved positions that are proposed to be functionally significant. The mutation at codon 128 occurs at the 10th cysteine and might be expected to alter the function of the ND protein. Since the phenotype of this patient is similar to those of other patients with point mutations in the ND gene, this mutation is likely to be the molecular basis of the phenotype.

Amino Acid Sequence↗
PubMed1999

Identification of a novel R21X mutation in the liver-type arginase gene (ARG1) in four Portuguese patients with argininemia.

Argininemia is a rare autossomal recessive disorder caused by deficiency in the cytosolic liver-type arginase enzyme (L-arginine urea-hydrolase; E.C. 3.5.3.1). In order to investigate the molecular basis for argininemia in four unrelated Portuguese patients (two from northern Portugal and two from Madeira Island) we performed a DNA sequence analysis of all the exons and exon/intron boundaries of the liver-type arginase gene (ARG1). All patients were found to be homozygous for a newly identified C ->T transition in codon 21 (exon 2) substituting arginine for a premature stop codon (R21X: CGA to TGA) and generating a NlaIII restriction site. Restriction digestion following PCR amplification of ARG1 exon 2 confirmed the presence of the mutation.

Amino Acid Metabolism, Inborn Errors↗
PubMed1999

Missense and nonsense mutations in codon 659 of MLH1 cause aberrant splicing of messenger RNA in HNPCC kindreds.

Germline mutations that give rise to premature termination codons in mRNAs have frequently been associated with aberrant processing of the nascent transcripts. This can take the form either of nonsense-mediated mRNA decay or of aberrant splicing of the pre-mRNA. In a family affected by hereditary nonpolyposis colorectal cancer, a two-nucleotide deletion in codon 659, which introduces a frameshift and a new stop codon in exon 17 of the DNA mismatch repair gene MLH1, has been reported to lead to skipping of the exon. We now report that this phenomenon occurs also when there are missense or nonsense mutations in this codon. Our results thus suggest that in aberrant splicing the nature of the mutation may be less important than its position within the exon. These findings are of importance to mutation interpretation, as they imply that aberrant splicing could be associated even with silent mutations that do not lead to amino acid substitutions. Genes Chromosomes Cancer 26:372-375, 1999.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Structural analysis of the mouse prosaposin (SGP-1) gene reveals the presence of an exon that is alternatively spliced in transcribed mRNAs.

SGP-1/prosaposin can be secreted or targeted to the lysosomes where it is processed into smaller saposins A, B, C, and D required for the hydrolysis of glycosphingolipids. The deficiency of saposins B and C results in variant forms of metachromatic leukodystrophy and Gaucher's disease, respectively, which are characterized by lysosomal storage of undegraded glycosphingolipids. A required step to correct these genetic defects, or to understand the targeting mechanism of SGP-1 to the lysosomes, or to the extracellular space as well as its interaction with specific glycosphingolipids, is the analysis of the gene encoding this protein. Thus our investigation dealt with the molecular cloning of the mouse SGP-1 gene. Sequence analysis revealed that the mouse SGP-1 gene consists of 15 exons ranging from nine base pairs to 298 base pairs and 14 introns, which ranged from 89 base pairs to >8 kb in length. Our data show that saposin A is encoded by the exons 3, 4, and 5, saposin B by exons 6, 7, 8, and 9, saposin C by exons 10 and 11, and saposin D by exons 12, 13, and 14. The translation start codon is located within exon 1, and the translation stop codon is located within exon 15. The exon/intron boundaries were in accordance to the AG/GT consensus sequences. Our data also revealed that the SGP-1 gene has an exon consisting of the nine base pairs (CAG GAT CAG) encoding the three amino acids of saposin B, which may be alternatively spliced in the SGP-1 mRNA. The presence of the different forms of alternatively spliced mRNAs in various tissues was analyzed by RT-PCR. This approach demonstrated that prosaposin mRNAs of brain, heart, and muscle contain the nine base pairs of exon 8, whereas the transcripts from testis, lung, pancreas, spleen, and kidney do not contain this exon 8. Sequence comparison between the human and mouse prosaposin showed that exon 11 of mouse SGP-1 consists of 279 base pairs, whereas the human prosaposin gene consists of 187 base pairs. The extra 93 base pairs encode 31 amino acids corresponding to a proline-rich region located between saposin C and saposin D in the mouse prosaposin molecule. Finally, the availability of these genomic clones provides a starting point for further studies on the genetic role of specific sequences on the structure and function of SGP-1/prosaposin and its derived saposin proteins. In conclusion, we cloned and sequenced the mouse prosaposin (SGP-1) gene. The structural analysis of this gene revealed the presence of an exon that is alternatively spliced in transcribed mRNAs in a tissue-specific manner.

Alternative Splicing↗
PubMed1993

Overexpression in Escherichia coli of soluble aristolochene synthase from Penicillium roqueforti.

Aristolochene synthase, a fungal cyclase which has been isolated from Aspergillus terreus and Penicillium roqueforti, catalyzes the cyclization of farnesyl diphosphate to the sesquiterpene hydrocarbon aristolochene. The aristolochene synthase gene (Ari1) of P. roqueforti has previously been cloned and expressed at low levels as a protein A-aristolochene synthase fusion protein in Escherichia coli. We have now used the polymerase chain reaction to amplify the aristolochene synthase coding sequence using engineered primers which produced dsDNA carrying an EcoRI restriction site and the T7 gene 10 ribosome binding site and translational spacer element immediately upstream of the ATG start codon and a BamHI site adjacent to the TAA stop codon. The PCR product was digested with EcoRI and BamHI and inserted into the multiple cloning site of the expression vector pLM1 which carried the promoter and translational leader sequence from T7 gene 10 and the E. coli rrnBT1T2 tandem transcription terminator. Cloning of the resulting construct into E. coli XL1-Blue and subcloning into the expression host E. coli BL21 (DE3) gave transformants which expressed aristolochene synthase at levels up to 40% of soluble protein when induced with isopropyl beta-D-thiogalactoside. Purification of the recombinant protein by ammonium sulfate precipitation, ion-exchange chromatography on Q Sepharose, and affinity dye chromatography on Reactive Blue 4-agarose gave homogenous aristolochene synthase which had the expected N-terminal sequence, ATSTE, mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and steady-state kinetic parameters when compared to native fungal protein.

Base Sequence↗
PubMed1999

Sequence elements required for apolipoprotein B mRNA editing enhancement activity from chicken enterocytes.

Mammalian intestinal apolipoprotein B (apoB) mRNA edits codon 2153 from CAA in apoB100 mRNA to a stop codon (UAA) in apoB48 mRNA. By contrast, chicken intestinal apoB mRNA contains a CAA codon at the corresponding site, but is not edited. Chicken enterocyte S100 extracts fail to edit mammalian apoB RNA, but contain factor(s) which enhance the mammalian enterocytes editing activity. By converting the chicken apoB mooring sequences to the conserved mammalian sequences, the study confirmed that this 11-nucleotide stretch was necessary and sufficient for minimal RNA editing. Using rat and chicken apoB chimeric constructs, the study revealed that mammalian apoB sequences were required for editing enhancement. In concert with the 29-nucleotide conserved cassette, the 5' rat apoB element (nucleotides 6615-6629) increased editing at C-6666, and was necessary for editing enhancement of chicken enterocyte S100 extracts. Similarly, the 3' rat apoB element (nucleotides 6726-6752) was required for editing enhancement of chicken enterocyte S100 extracts, but to a lesser extent in efficiency, compared to the 5' region. In conclusion, this study identified the sequences required for editing enhancement activity from chicken enterocyte S100 extracts.

Animals↗
PubMed1998

Functional interaction between tRNA2Gly2 at the ribosomal P-site and RF1 during termination at UAG.

The glycine codons GGA or GGG, on the 5' side of stop codons UAG and UGA, are associated with a uniquely low termination efficiency in Escherichia coli, as compared to other codons, including the two glycine codons GGU and GGC. In contrast to the wild-type strain, all four glycine codons have a similar effect on termination at UAG in a strain with a mutant release factor 1 (RF1). Thus, these two glycine codon pairs, when present at the ribosomal P-site, affect termination efficiency of mutant or wild-type RF1 at UAG differently. If reading of GGA/G by tRNAGly2 is eliminated in the RF1 wild-type strain and replaced by a mutant form of tRNAGly3, termination efficiency is increased to the same level as for GGU/C, normally read by tRNAGly3. The results suggest an unusual interaction between the P-site tRNAGly2 and wild-type RF1 at the ribosomal A-site that is not present with mutant RF1.

Codon, Terminator↗