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At least 1,459 records · Page 81Linked to original sources
PubMed1993

Effect of tandem repeated AUG codons on translation efficiency of eukaryotic mRNA carrying a short leader sequence.

The effect on translation of multiple copies of the initiation codon AUG at the initiation site in a eukaryotic mRNA carrying a short leader sequence was tested in translation experiments in vitro. DNA, corresponding to a chimeric mRNA sequence consisting of the 5' leader region of brome mosaic virus (BMV) RNA4 and the goat pre-alpha-lactalbumin mRNA sequence, was prepared and transcribed in vitro using SP6 RNA polymerase. Site-directed mutagenesis was carried out to change the sequence around the initiation codon AUG. In a wheat germ translation system, the yield of protein obtained using the mRNA with a duplication of the AUG codons at the initiation site was 1.6 times that achieved when only one AUG was present. The rate of formation of the 80S initiation complex was measured by the ribosome binding assay using cycloheximide. A good correlation was observed between the ability to form the complex and translation efficiency.

Animals↗
PubMed1990

Efficient translation of the UAG termination codon in Candida species.

Clinical isolates of the dimorphic fungus Candida albicans encode a tRNA that, in a cell-free translation system prepared from the yeast Saccharomyces cerevisiae, efficiently translates the amber (UAG) termination codon. Unusually, the efficiency of this UAG read-through in the heterologous cell-free system is not further enhanced by polyamines. The suppressor tRNA is also able to efficiently translate the UAG codon in the rabbit reticulocyte cell-free system and with efficiencies approaching 100% in a homologous (C. albicans) cell-free system. That the suppressor tRNA is nuclear-encoded is demonstrated by the lack of activity in purified C. albicans mitochondrial tRNAs. Finally, UAG suppressor tRNA activity is also demonstrated in three other pathogenic Candida species, C. parapsilosis, C. guillermondii and C. tropicalis. These results suggest that some, but not all, Candida species have evolved an unusual nuclear genetic code in which UAG is used as a sense codon.

Candida albicans↗
PubMed1987

The unusual translational initiation codon AUU limits the expression of the infC (initiation factor IF3) gene of Escherichia coli.

The expression of infC, the structural gene for translational initiation factor IF3, has been studied in different constructs under the control of the lambda PL and tac promoters. The amount of synthesized IF3 has been determined by a quantitative functional test and the levels of IF3-specific mRNA have been estimated. The synthesis of IF3 is strongly enhanced when the unusual AUU initiation codon is changed to AUG by site-directed mutagenesis. Removal of the sequence upstream from the start codon including most of the Shine-Dalgarno sequence, as well as part of a 10 bp region with potential complementarity to an internal region of the 16S rRNA, which is unique to the IF3 mRNA, reduced but did not completely abolish the high expression of infC obtained after introduction of the AUG initiation codon. The level of IF3 mRNA was found to be positively influenced by the presence of the rplT gene in the plasmid downstream from the infC gene. In vivo accumulation of a large excess of IF3, obtained when the infC gene was placed under the control of an incompletely repressed tac promoter, was not accompanied by any noticeable adverse phenotype.

Base Sequence↗
PubMed1984

Codon specificity of starvation induced misreading.

Mistranslated derivatives of the coat protein of the bacteriophage MS2 were isolated from infected cells starved for asparagine. This protein contains a high level of lysine for asparagine substitutions. By peptide analysis and amino acid sequencing we show that there is a six-fold greater frequency of errors at AAU codons than at AAC codons. This ratio is the same as that found in unstarved cells where the overall error frequency is 100-fold less. We also demonstrate that, at least for AAC codons, context affects error frequency.

Amino Acid Sequence↗
PubMed1984

Comparative analysis of UV-induced mutability of ten different codon units in position 211 of the Escherichia coli trpA gene.

To study the influence of the local base composition upon UV-induced mutability the reversion frequencies of ten trpA mutants with known codon sequences at position 211 were compared. Comparison of mutant strains reverting by the same base substitution type but with different dipyrimidinic sequences reveals the mutagenic character of the pyrimidine-pyrimidine (6-4) photoproduct. The codons GAC and GAT, both reverting by AT-GC transitions and AT-CG transversions in the middle position and harboring the dipyrimidinic sequence CT in the opposite strand, differ in their reversion frequencies sixfold. This difference can only be due to the influence of the different bases in the third codon position upon the mutability of adjacent second bases.

Bacterial Proteins↗
PubMed1991

A novel point mutation at codon 146 of the K-ras gene in a human colorectal cancer identified by the polymerase chain reaction.

In this report, point mutations of the K-ras gene at codon 146 were analyzed in 25 cases of colon cancer, 4 cases of lung cancer, and 41 cases of lymphoid malignancy. A codon 146 mutation substituting threonine (ACA) for alanine (GCA) was detected in the tumor tissue of a patient with colon cancer and was not detected in the normal tissue of the same patient. Any additional mutations of the ras gene family were not detected in this patient. These results suggest that the codon 146 mutation of the K-ras gene could be involved in the development of naturally occurring human malignancies.

Antisense Elements (Genetics)↗
PubMed1993

Hemoglobin E and codon 17 nonsense: two beta-globin gene mutations common in Southeast Asia detected by the use of ARMS.

Hemoglobin E (codon 26 GAG-->AAG) and codon 17 nonsense (AAG-->TAG), two clinically important mutations of the beta-globin gene, are common in Southeast Asia. The detection of these mutations using allele-specific PCR is described. Together with the previously reported method for the detection of the common Southeast asian codon 41-42 frameshift mutation (del CTTT), it is possible to identify the vast majority of clinically important beta-globin gene mutations in Southeast Asian populations by means of nonradioactive methods.

Alleles↗
PubMed1981

Simulation of protein evolution by random fixation of allowed codons.

Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin alpha and beta chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 X 10(-10) to 10(-8) accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.

Amino Acids↗
PubMed1976

Doublet frequencies and codon weighting in the DNA of Escherichia coli and its phages.

A compilation of nucleic acid sequences from E. coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations in E. coli also appear to occur in lambda and in the coat protein gene of MS2, whereas T4 and other parts of the MS2 genome show different sequence properties. These and other findings are discussed in relation to the hypothesis that rapidity of translation of mRNAs in the E. coli system is dependent on doublet frequency and codon usage patterns.

Base Sequence↗
PubMed1987

Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons.

The population dynamics of nearly neutral mutations are studied using a single-site and a multisite model. In the latter model, the nucleotides in a sequence are completely linked and the selection schemes employed are additive, multiplicative, and additive with a threshold. Although the third selection scheme is very different from the first two, the three schemes produce identical results for a wide range of parameter values. Thus the present study provides a general theory for the population dynamics of nearly neutral mutations because the results can also be used to draw inferences about other selection schemes such as stabilizing selection and synergistic selection. It is shown that the number of slightly deleterious mutations accumulated in a sequence can be considerably larger under the multisite model than under the single-site model, particularly if the sequence is long or if the mutation rate per site is high. The results show that even a very slight selective difference between synonymous codons can produce a strong bias in codon usage. Three alternative explanations for the strong bias in codon usage in bacterial and yeast genes are considered. The implications of the present results for molecular evolution are discussed.

Biological Evolution↗
PubMedDate not supplied

A p53 codon 72 polymorphism associated with prostate cancer development and progression in Japanese.

An association between the Pro/Pro genotype of p53 codon 72 and a lower risk of prostate cancer in Caucasians was recently reported. However, the association of this polymorphism with prostate cancer risk in a Japanese population has not been clarified. We performed a case-control study consisting of 114 prostate cancer patients and 105 noncancer controls. Sixty-nine percent (79 of 114) of the patients had a positive family history. The genotypic frequencies in the controls were 39.0% for Arg/Arg, 54.3% for Arg/Pro and 6.7% for Pro/Pro; they were in Hardy-Weinberg equilibrium. When a comparison of the distribution of the p53 codon 72 polymorphism was made between patients with a first-degree family history and all control subjects, the adjusted odds ratios (ORs) for prostate cancer associated with the Arg/Arg, Arg/Pro and Pro/Pro genotypes were 1.00, 0.99 [95% confidence interval (CI) 0.53-1.88] and 2.80 (95% CI 1.04-7.53), respectively. When stratification of cases was performed based on clinical stage (localized or metastatic cancer) and pathological grade (a Gleason score of <7 or > or =7), there tended to be a greater number of patients with localized cancers among those patients with the Arg/Pro genotype than among those with the Arg/Arg genotype (overall cases: age-adjusted OR 0.36, 95% CI 0.13-1.00, p = 0.049; positive family history cases: age-adjusted OR 0.25, 95% CI 0.075-0.84, p = 0.025). In addition, there tended to be a greater number of patients with low-grade cancers among those with the Pro/Pro genotype than among those with other genotypes (overall cases: age-adjusted OR 0.41, 95% CI 0.13-1.30, p = 0.13; positive family history cases: age-adjusted OR 0.20, 95% CI 0.004-0.89, p = 0.035). The present findings suggest that the Pro/Pro genotype of p53 codon 72 played a role in prostate cancer susceptibility in a Japanese population. However, the Pro allele did not appear to worsen such clinical parameters as clinical stage or pathological grade.

Adult↗
PubMed1996

Codon usage and base composition in Rickettsia prowazekii.

Codon usage and base composition in sequences from the A + T-rich genome of Rickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21 R. prowazekii proteins with that of a homologous set of proteins from Escherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests that R. prowazekii has around 800 genes and that 60-70% of the genome may be coding.

Base Composition↗
PubMed1989

Aminoglycoside suppression at UAG, UAA and UGA codons in Escherichia coli and human tissue culture cells.

We have compared the suppression of nonsense mutations by aminoglycoside antibiotics in Escherichia coli and in human 293 cells. Six nonsense alleles of the chloramphenicol acetyl transferase (cat) gene, in the vector pRSVcat, were suppressed by growth in G418 and paromomycin. Readthrough at UAG, UAA and UGA codons was monitored with enzyme assays for chloramphenicol acetyl transferase (CAT), in stably transformed bacteria and during transient expression from the same plasmid in human 293 tissue culture cells. We have found significant differences in the degree of suppression amongst three UAG codons and two UAA codons in different mRNA contexts. However, the pattern of these effects are not the same in the two organisms. Our data suggest that context effects of nonsense suppression may operate under different rules in E. coli and human cells.

Alleles↗
PubMed2006

p53 codon 72 polymorphism in basal cell carcinoma of the skin.

Basal cell carcinoma (BCC) is the most prevalent cancer in Iran. A common polymorphism at codon 72 of exon 4 of p53 tumor suppressor gene has been reported to be associated with increased inheritable susceptibility to several cancers. In the present study the frequency of p53 codon 72 polymorphism in 91 patients with BCC of skin, compared to 465 healthy normal individuals, was investigated. In total, there was no significant difference in the p53 genotypes between patients and controls. However, there was an apparent increase in the Arg/Arg genotype among those BCC patients who had a history of occupational sun exposure, compared to non-exposed patients (46.3% vs. 23.1%, P=0.11). A trend of increase in the frequency of Arg allele among sun-exposed patients was also observed (69.4% vs. 53.8%, P=0.07). Comparison of the genotype frequencies between sunexposed patients and normal controls confirmed the accumulation of Arg/Arg genotype in these patients (46.3% vs. 34.8%, P = 0.07). In addition, the frequency of Arg allele was significantly higher in sunexposed patients compared to controls (69.4% vs. 58.2%, P=0.03). Our results suggest that Arg allele at codon 72 of p53 gene might affect the risk of ultraviolet-induced basal cell carcinoma.

Codon↗
PubMed1999

Codon bias and mutability in HIV sequences.

A survey of the patterns of synonymous codon preference in the HIV env gene reveals a correlation between the codon bias and the mutability requirements of different regions of the protein. At hypervariable regions in gp120 one finds a greater proportion of codons that tend to mutate nonsynonymously, but to a target that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective pressure placed on the virus by the induced immune response, which favors amino acid substitutions in the complementarity determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein.

Codon↗
PubMed2000

["Field cancerization"--an additional phenomenon in development of colon tumors? K-ras codon 12 mutations in normal colonic mucosa of patients with colorectal neoplasms].

INTRODUCTION: The c-K-ras2-gene (K-ras) encodes the p21ras protein, which participates in the transduction of mitogenic signals from the cell surface to the nucleus. About 40-50% of colorectal cancers bear a point mutation of the K-ras codon 12 within exon I, leading to activation of the K-ras oncogene. METHODS: Using a polymerase chain reaction (PCR)-based two-step restriction fragment length polymorphism (2sRFLP)-technique, we assessed the frequency of point mutations in the first or second base of K-ras codon 12 in patients suffering from colorectal carcinoma, adenoma, and their normal colon mucosa, respectively. RESULTS: Similar to other investigators, we found mutations in 7 out of 17 (41%) colorectal carcinomas and 1 out of 4 (25%) adenomas. Using this very sensitive 2sRFLP technique (detection level = 0.2% of mutated cells), we were able to find K-ras codon 12 mutations in normal mucosa in 4 out of 18 (22.2%) patients with colorectal neoplasia. CONCLUSIONS: This result can be explained by the phenomenon of "field cancerization" or by a local micrometastasis of K-ras-positive tumor cells.

Adenocarcinoma↗