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At least 1,495 records · Page 83Linked to original sources
PubMed1976

On the possible modulating role of the isoleucine AUA-codon in bacteriophage MS2 RNA.

A set of MS2 mutants were shown to have an additional silent mutation met --> ile at position 108 of the coat protein. As transitions are more frequent than transversions one would have expected an AUA codon in this position in the mutant RNAs. As the AUA codon is one of the best candidates for a modulation role in the control of translation in E. coli, the presence of this AUA in the gene for the protein made in major amounts upon viral infection would impose serious doubt on the theory of modulation. We have directly proven by minifinger-printing of mutant RNA and further analysis of the relevant spots that, in fact, the isoleucine residue at position 108 of the coat protein gene is specified by the non-rate-limiting AUU codon, in agreement with a modulation type of control of protein synthesis.

Base Sequence↗
PubMed1989

Absence of mutations in codon 61 of the Ha-ras oncogene in epithelial cells transformed in vitro by 7,12-dimethylbenz(a)anthracene.

Epithelial cells of the respiratory tract of rats were transformed in vitro by 7,12-dimethylbenz(a)anthracene (DMBA) which has been reported to cause A----T transversion mutations of the second position of Ha-ras in codon 61 in several biological models. In this study Ha-ras exon 2 was amplified by the polymerase chain reaction (PCR) and then sequenced directly. In 10 transformed cell lines, of which 5 are known to be tumorigenic, no mutations in codon 61 were found. The results suggest that Ha-ras codon 61 mutations are not associated with cell transformation initiated with DMBA in this particular cell transformation system. These data imply that other genes (oncogenes) are responsible for transformation of these cells. The results are discussed in relation to observations in various transformation systems in vivo and in vitro.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1990

Human urate oxidase gene: cloning and partial sequence analysis reveal a stop codon within the fifth exon.

Using the cDNA and selected genomic probes of rat urate oxidase, we have screened the human genomic library and isolated seven clones; one clone (clone 13) contained exonic regions which correspond to the exons 5, 6, and 7 of rat urate oxidase gene. The nucleotide sequence was determined for these three exons and exon/intron junctions, and compared with the sequence from the rat gene. A mutation resulting in a stop codon TGA was found in the fifth exon of the human urate oxidase gene. Sequence analysis of the polymerase chain reaction amplified DNA, corresponding to the fifth exon of urate oxidase from DNA samples from four different individuals, confirmed the same TGA stop codon in all. This single stop codon mutation and/or other mutation(s) in this gene may be responsible for the lack of urate oxidase activity in the human.

Amino Acid Sequence↗
PubMed1990

Codon usage pattern in alpha 2(I) chain domain of chicken type I collagen and its implications for the secondary structure of the mRNA and the synthesis pauses of the collagen.

A stability map of local secondary structure of the mRNA of the triple-helical alpha 2(I) chain domain of chicken type I collagen was obtained by plotting the free energy of the optimal secondary structure of a local segment in mRNA against the segment position along a base sequence of the mRNA. It was found that the positions of the minima of free energy in the plot coincide with the positions where synthesis pauses of the alpha-chain polypeptides of the corresponding sizes translated from the mRNA have been reported to occur (1). The codon usage pattern of each of the three major amino acids of the alpha-chain domain of the collagen, Gly, Pro and Ala, fluctuates considerably along the base sequence segments of the mRNA and a deviation of the pattern from that of the average of the whole alpha 2(I) chain domain mRNA, particularly for Gly codons, leads to a loss of the stability of the local secondary structure of the mRNA. The results suggest that selection has operated on the codon usage to optimize the secondary structure characteristic of the mRNA of the chicken collagen alpha 2(I) chain domain which leads to a nonuniform polypeptide elongation pattern.

Animals↗
PubMed1996

Lack of mutations in K-ras codons 12 and 13 in human atherosclerotic lesions.

In the framework of a project investigating the possible involvement of cancer biomarkers in human atherogenesis, we evaluated the occurrence of K-ras mutations in the DNA extracted from smooth muscle cells of abdominal aorta atherosclerotic lesions. The molecular analysis of the DNA from 32 surgical specimens, using PCR-based denaturing gradient gel electrophoresis (DGGE), did not reveal any variant in K-ras codons 12 and 13, which are the most frequently involved codons among the ras genes mutated in various types of human tumors. Analysis of the DNA extracted from four cell lines carrying known K-ras mutational alleles showed typically positive DGGE patterns. Thus, on the whole, the conclusions of this study and of previous studies using the same biological material are consistent with the occurrence of DNA adducts in human atherosclerotic lesions but in the absence of p53 involvement or of K-ras mutations in codons 12 and 13. The search for candidate genes which may possibly be involved in the atherogenetic process warrants further studies.

Aged↗
PubMed1995

A trinucleotide deletion together with a base duplication event at codon 439 in the human tyrosinase gene identifies a mutational hotspot.

Molecular analysis of the human tyrosinase gene in two patients suffering from a temperature-sensitive form of albinism has identified a thymine triplet deletion at codon 439 which is accompanied by a duplication of the immediately preceding cytosine residue. This results in a two base pair frame shift leading to premature termination at codon 448, giving a truncated protein. Its relationship to other mutations in tyrosinase and the possible cause are discussed. The temperature-sensitive phenotype is due to the guanine to adenine mutation at codon 422, known to generate a temperature-sensitive enzyme. The CTTT at F439 in tyrosinase is also present at F508 in CFTR, the main mutation causing cystic fibrosis.

Adolescent↗
PubMed1989

The yeast pyruvate kinase gene does not contain a string of non-preferred codons: revised nucleotide sequence.

The sequence of the gene encoding pyruvate kinase from Saccharomyces cerevisiae was re-determined because of failures with oligonucleotide-directed mutagenesis experiments involving a region thought to contain a string of five contiguous non-preferred codons. This region was found to be difficult to sequence and was shown to have three extra bases when compared with the published sequence [(1983) J. Biol. Chem. 258, 2193-2201]. The revised sequence demonstrates that the yeast pyruvate kinase gene does not have a cluster of non-preferred codons, and that it therefore is not an example of the class of genes which possibly exhibit translational control by the presence of non-preferred codons.

Amino Acid Sequence↗
PubMed1990

Influence of the second and third codon on the expression of recombinant hirudin in E. coli.

The effect of all possible codons corresponding to the second and third amino acid (isoleucine and threonine) on the expression level of hirudin in E. coli has been analysed. These levels could not be correlated with changes in primary and secondary mRNA structure. A decrease in the rate of synthesis and of product accumulation follows the introduction for ile of the ATA codon which is of very low usage, and for thr of the ACC codon, which results in homology of the mRNA with the 3'-end of 16S rRNA. The results are discussed according to current concepts of protein expression in E. coli.

Base Sequence↗
PubMed1994

Detection of a single base deletion in codon 424 of the low density lipoprotein receptor gene in a Danish family with familial hypercholesterolemia.

We performed a screening of exon 9 of the low density lipoprotein receptor (LDLR) gene in 14 Danish families with familial hypercholesterolemia (FH) using the denaturing gradient gel electrophoresis (DGGE) technique. In one of the probands from these families an abnormal band pattern in the gradient gel was detected. Subsequent DGGE analysis of the family of this index patient revealed that the DGGE pattern cosegregated with the disease in this family. Sequencing of the exon showed a deletion of a C in codon 424 of the LDLR gene resulting in a frame shift with the introduction of a stop codon 5 codons further downstream. The mutation is referred to as FH-Odense. The predicted truncated receptor protein consists of the 428 amino terminal amino acids. Consequently, the cytosolic and membrane spanning parts of the mature LDL receptor, which normally secure the receptor in the plasma membrane, are missing. The FH-Odense mutation results in severe premature coronary atherosclerosis as shown by the clinical expression in 5 generations of the affected family.

Adolescent↗
PubMed1986

Normal yeast tRNA(CAGGln) can suppress amber codons and is encoded by an essential gene.

We have isolated a gene that can encode yeast tRNA(CAGGln). When present on a multicopy plasmid, this gene suppresses the phenotype of a number of amber mutants, but has no effect on the ocher mutants tested. We therefore conclude that the anticodon CUG in tRNA(CAGGln) can decode the amber codon UAG by G-U mispairing, possibly by wobble base-pairing in the first codon position. This represents the second example we have observed in this laboratory of nonsense suppression in yeast by natural tRNA(Gln), involving G-U mispairing in the first codon position. Replacing the genomic copy of the cloned gene with a disrupted tRNA gene results in recessive lethality in heterozygous diploids and is lethal to haploid cells. This lethality can be rescued by transformation of cells with a single copy plasmid containing the tRNA(CAGGln) gene. Thus, the gene encoding tRNA(CAGGln) is apparently essential for viability in yeast, suggesting that it is normally present as a single copy gene.

Animals↗
PubMed1987

At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells.

Sequences flanking the AUG initiator codon influence its recognition by eukaryotic ribosomes. From a comparison of several hundred mRNA sequences, CCA/GCCAUGG emerged as the consensus sequence for initiation in higher eukaryotes. Systematic mutagenesis of a cloned preproinsulin gene confirmed the facilitating effect of A or G in position -3 (i.e. 3 nucleotides upstream from the AUG codon), C in positions -1 and -2, and G immediately following the AUG codon. The analysis of a new set of mutants now reveals that sequences slightly farther upstream are also influential, the optimal context for initiation being (GCC)GCCA/GCCAUGG. Possible mechanistic implications of the repeating GCC motif are discussed.

Base Sequence↗
PubMed1988

Evidence for a unique first position codon-anticodon mismatch in vivo.

The Ser68(AGC) codon of the beta-lactamase gene was changed to the glycine codons GGA and GGC. With glycine at position 68, beta-lactamase is inactive because it does not have a nucleophilic side-chain to function in the reaction mechanism. The mutant SG68(GGA) allele had no detectable beta-lactamase activity; however, the mutant SG68(GGC) did produce a small amount of activity. Both mutant alleles produce comparable amounts of beta-lactamase protein in a maxi-cell system. To identify why these two "same-sense" beta-lactamase mutants differ phenotypically, we introduced the alleles into Escherichia coli strains with mutations that affect translational fidelity. The rpsD mutation, which decreases fidelity, significantly increased activity with the SG68(GGC) allele, while the rpsL mutation, which increases translational fidelity, had little effect on the beta-lactamase activity. The rpsD and rpsL alleles had no effect on the SG68(GGA) allele. From the allele specificity of the activity produced by the bla mutants, and from the differential effect of translational fidelity on the activity of the SG68(GGC) allele, we infer that tRNA(GCU)Ser, the AGU/C reading tRNA(Ser), mistranslates SG68(GGC) at a frequency of about 0.1%, and subsequently produces active beta-lactamase. This is the first observation of an A/G wobble with a wild-type tRNA at the first position of the codon-anticodon interaction.

Amino Acid Sequence↗
PubMed1991

An apparent rare-codon effect on the rate of translation of a Neurospora gene.

As the result of two mutually compensating frameshift mutations, three successive codons with third-position A were generated in the Neurospora crassa am (NADP-specific glutamate dehydrogenase: GDH) gene. These codons do not occur at all elsewhere in the gene and only infrequently in other highly expressed Neurospora genes. The double-frameshift strain produces only 25 to 35% of the normal level of GDH, whether measured as enzyme activity or as immunoprecipitable protein, but its level of GDH mRNA is normal. Although the modified enzyme is somewhat more heat-sensitive than the wild-type in vitro, its stability in vivo was found to be indistinguishable from that of the wild-type. It is concluded that the introduction of consecutive rare codons reduces the efficiency of translation of the mRNA. The possible mechanisms of such an effect are discussed.

Amino Acid Sequence↗
PubMed1992

Translation inhibition by an mRNA coding region secondary structure is determined by its proximity to the AUG initiation codon.

In the present study we investigate the impact of highly stable coding region secondary structures on mRNA translation efficiency. By introducing antisense segments into the 3'non-translated region of human alpha-globin mRNA we are able to synthesize a series of transcripts in which site-specific secondary structures are introduced without altering the primary structure of the 5' non-translated region, the coding region, or the encoded protein product. Coding region duplexes in close proximity to the AUG initiation codon are found to inhibit translation severely to a degree equal to that of a duplex that extends into the 5' non-translated region. In contrast, mRNAs containing duplexes positioned further 3' in the coding region translate at levels that are significantly higher although are still below those of native alpha-globin mRNA. The primary determinant of translation inhibition by coding region duplexes appears to be the proximity of the duplex to the AUG initiation codon and reflects a parallel inhibition of monosome formation. These data demonstrate that extensive coding region secondary structures suppress translation to a minimal or to a substantial degree depending on their distance from the initiation codon.

Base Sequence↗
PubMed1983

A thermodynamic theory of codon bias in viral genes.

The relationship between degeneracy in the genetic code and the occurrence of a strong codon bias is examined, with particular reference to a group of viral genomes. The present paper shows how codon bias may have been imposed by thermodynamic considerations at the time the primitive DNA first formed in the primordial soup. Using a four-state Ising-like model with stacking interactions between successive base pairs, we show how primeval periodic DNA polymers could have arisen the remnants of which are still observed in codon biases today.

Base Composition↗
PubMed1993

Separation of transforming N-ras mutations in codons 12, 13 and 61 by denaturing gradient gel electrophoresis: investigation based on a set of phagemid constructs.

In the present study we have introduced 19 activating base pair substitutions into N-ras cDNA by use of an in vitro site-directed mutagenesis system. Six mutants were constructed for N-ras codon 12 (exon 1), six for codon 13 (exon 1), and seven for codon 61 (exon 2). Fifteen out of 19 PCR-amplified mutation sequences showed a clear separation from the wild type on denaturing gradient gel electrophoresis runs as homoduplex band, and the rest could be separated after heteroduplex formation with wild-type DNA. These constructs can be used as controls in many screening systems for analyzing activating point mutations of the N-ras gene.

Base Sequence↗
PubMed1981

The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons.

Cross hybridization between maize mitochondrial DNA fragments and a specific yeast mitochondrial DNA probe from the oxi 1 gene has been used to identify and isolate the maize mitochondrial gene coding cytochrome oxidase subunit II, mox 1. The DNA sequence reveals two coding regions separated from each other by a single centrally located intervening sequence. Hybridization of mox 1 DNA probes to mitochondrial RNA from plants shows that te gene is transcribed and indicates that several transcripts are spliced. TGA codons, which code Trp in the mitochondria of all species examined to date, do not occur in this gene. However, alignment of the mox 1 gene sequence with the amino acid sequences of subunit II from other organisms strongly suggests that codon CGG (normally Arg) codes for Trp in maize mitochondria, in addition to the standard Trp codon TGG.

Base Sequence↗
PubMed1992

Rare point mutation at codon 301 and 969 of FMS/M-CSF receptor in acute myelomonocytic and monocytic leukemia.

We have investigated whether point mutations occurred at codon 301 or 969 of FMS (M-CSF receptor) in 19 patients with acute myelomonocytic (M4) and monocytic leukemia (M5). Nineteen peripheral blood and bone marrow blood samples collected from M4 and M5 patients were examined by using polymerase chain reaction and hybridization to allele specific oligonucleotide probes. Mutations at codon 301 and 969 of FMS were not detected in any samples. FMS gene mutations at codon 301 and 969 were rarely involved in M4 and M5 patients in Japan.

Amino Acid Sequence↗