SEARCH · Search PubMed

Results for “Codons”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,369 records · Page 76Linked to original sources

PubMed1997

Dichloroacetic acid reduces Ha-ras codon 61 mutations in liver tumors from female B6C3F1 mice.

Dichloroacetic acid (DCA), a disinfection by-product of chlorination found in drinking water, is a hepatocarcinogenic in the B6C3F1 mouse. Previous studies have shown that DCA does not significantly alter the incidence of Ha-ras codon 61 mutations in male mouse liver carcinomas from that observed in spontaneous tumors (approximately 50% have Ha-ras mutations) but it alters the proportions of mutations that occur in Ha-ras codon 61. Twenty-two tumors were produced in female B6C3F1 mice after treatment with 3.5 g DCA per liter of drinking water over a period of 104 weeks. To detect potential Ha-ras mutations in the liver tumor tissue of female B6C3F1 mice, genomic DNA was isolated from tumors that had been frozen. The polymerase chain reaction (PCR) and single-stranded conformational polymorphism (SSCP) was used to screen tumor DNA for mutations in Ha-ras exon 2. In DNA from liver tumors in female B6C3F1 mice induced by DCA-treatment we found only one mutation in exon 2 among the 22 tumors analyzed (4.5%). Direct-sequencing of exon 2 revealed a CAA to CTA transversion in Ha-ras codon 61. The result of this study indicates that tumor formation in DCA-treated female B6C3F1 mice is, therefore, not associated with a mutationally activated Ha-ras codon 61. This result differs from previous results obtained in male B6C3F1 mice.

Animals↗

PubMed2001

Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease.

We previously showed that in mitochondrial tRNA(Lys) with an A8344G mutation responsible for myoclonus epilepsy associated with ragged-red fibers (MERRF), a subgroup of mitochondrial encephalomyopathic diseases, the normally modified wobble base (a 2-thiouridine derivative) remains unmodified. Since wobble base modifications are essential for translational efficiency and accuracy, we used mitochondrial components to estimate the translational activity in vitro of purified tRNA(Lys) carrying the mutation and found no mistranslation of non-cognate codons by the mutant tRNA, but almost complete loss of translational activity for cognate codons. This defective translation was not explained by a decline in aminoacylation or lowered affinity toward elongation factor Tu. However, when direct interaction of the codon with the mutant tRNA(Lys) defective anticodon was examined by ribosomal binding analysis, the wild-type but not the mutant tRNA(Lys) bound to an mRNA- ribosome complex. We therefore concluded that the anticodon base modification defect, which is forced by the pathogenic point mutation, disturbs codon- anticodon pairing in the mutant tRNA(Lys), leading to a severe reduction in mitochondrial translation that eventually could result in the onset of MERRF.

Animals↗

PubMed2003

Likelihood models of somatic mutation and codon substitution in cancer genes.

The role of somatic mutation in cancer is well established and several genes have been identified that are frequent targets. This has enabled large-scale screening studies of the spectrum of somatic mutations in cancers of particular organs. Cancer gene mutation databases compile the results of many studies and can provide insight into the importance of specific amino acid sequences and functional domains in cancer, as well as elucidate aspects of the mutation process. Past studies of the spectrum of cancer mutations (in particular genes) have examined overall frequencies of mutation (at specific nucleotides) and of missense, nonsense, and silent substitution (at specific codons) both in the sequence as a whole and in a specific functional domain. Existing methods ignore features of the genetic code that allow some codons to mutate to missense, or stop, codons more readily than others (i.e., by one nucleotide change, vs. two or three). A new codon-based method to estimate the relative rate of substitution (fixation of a somatic mutation in a cancer cell lineage) of nonsense vs. missense mutations in different functional domains and in different tumor tissues is presented. Models that account for several potential influences on rates of somatic mutation and substitution in cancer progenitor cells and allow biases of mutation rates for particular dinucleotide sequences (CGs and dipyrimidines), transition vs. transversion bias, and variable rates of silent substitution across functional domains (useful in detecting investigator sampling bias) are considered. Likelihood-ratio tests are used to choose among models, using cancer gene mutation data. The method is applied to analyze published data on the spectrum of p53 mutations in cancers. A novel finding is that the ratio of the probability of nonsense to missense substitution is much lower in the DNA-binding and transactivation domains (ratios near 1) than in structural domains such as the linker, tetramerization (oligomerization), and proline-rich domains (ratios exceeding 100 in some tissues), implying that the specific amino acid sequence may be less critical in structural domains (e.g., amino acid changes less often lead to cancer). The transition vs. transversion bias and effect of CpG dinucleotides on mutation rates in p53 varied greatly across cancers of different organs, likely reflecting effects of different endogenous and exogenous factors influencing mutation in specific organs.

Data Interpretation, Statistical↗

PubMed1978

Context effects on nonsense codon suppression in Escherichia coli.

The influence of mRNA context on nonsense codon suppression has been studied by suppression measurements at one site in the Escherichia coli trpE gene and at two sites in the trpA gene. The ratio of suppression efficiencies of amber and ochre codons at each site (homotopic pairs) has been compared using ochre suppressing derivatives of tRNATyr. This ratio is independent of differential effects of the inserted amino acid on enzyme function. We have found that mRNA context can change the ratio of suppression efficiencies of homotopic nonsense codons at the three sites in the trp gene system over a ten-fold range. The causes of such variation, and, in particular the effect of certain adjacent nucleotides on nonsense codon suppression are considered.

Anthranilate Synthase↗

PubMed1995

Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer.

Phylogenetic relationships, rates of evolution, and codon usage were investigated in a family of retrotransposons (SURL elements) found in echinoids. The phylogeny of SURL element reverse transcriptase sequences from 10 echinoid species clearly shows the phylogenetic signature of the host taxa as well as paralogous sequences that diverged prior to speciation events. Two subfamilies (1 and 5) of SURL element reverse transcriptase sequences are recognized that diverged prior to the radiation of the Echinometridae. Comparisons of synonymous versus nonsynonymous substitutions indicate that SURL elements have been active in echinoid genomes and have evolved under purifying selection for millions of years. Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons. Finally, codon usage in SURL elements is biased for codons ending in A or U relative to 42 sea urchin nuclear genes. Biased codon usage is sometimes cited as evidence for horizontal transfer, but in the case of SURL elements this bias occurs in spite of a long history of vertical transmission rather than because of horizontal transfer.

Animals↗

PubMed1998

A polymorphism of angiotensinogen gene codon 174 and coronary artery disease in Japanese subjects.

The relationship between coronary artery disease (CAD) and polymorphisms of genes encoding angiotensinogen (AGT) and angiotensin converting enzyme (ACE) was analyzed in Japanese subjects. One hundred and four patients with CAD and 170 healthy subjects were enrolled in the study. CAD was defined as having a luminal diameter stenosis > or =50% in at least one of three major coronary arteries by coronary angiography. The genotypes (determined by polymerase chain reaction) of AGT gene codon 174 were not significantly associated with CAD in the total study population. However, the frequency of T/T homozygotes of AGT codon 174 was significantly higher in CAD patients compared to controls in each of three subgroups: 1) body mass index (BMI) below the median value of 24.1 kg/m2; 2) not more than two CAD risk factors out of five (hypercholesterolemia, hypertension, diabetes mellitus, smoking, and family history of CAD); and 3) the ACE I/I genotype. The M/M genotype of AGT codon 235 was negatively associated, and the ACE D/D genotype was positively associated, with CAD in the total study population. Our results indicate that the T/T genotype of AGT codon 174 may be a risk factor for CAD in Japanese individuals with low BMI, lesser CAD risk factors, or ACE I/I genotype.

Aged↗

PubMed1998

Clinical features of fatal familial insomnia: phenotypic variability in relation to a polymorphism at codon 129 of the prion protein gene.

Fatal Familial Insomnia is a hereditary prion disease characterized by a mutation at codon 178 of the prion protein gene cosegregating with the methionine polymorphism at codon 129 of the mutated allele. It is characterized by disturbances of the wake-sleep cycle, dysautonomia and somatomotor manifestations (myoclonus, ataxia, dysarthria, spasticity). PET studies disclose severe thalamic and additionally cortical hypometabolism. Neuropathology shows marked neuronal loss and gliosis in the thalamus, especially the medio-dorsal and anterior-ventral nuclei, olivary hypertrophy and some spongiosis of the cerebral cortex. Detailed analysis of 14 cases from 5 unrelated families showed that patients ran either a short (9.1 +/- 1.1 months) or a prolonged (30.8 +/- 21.3 months) clinical course according to whether they were homozygote met/met or heterozygote met/val at codon 129. Moreover, homozygotes had more prominent oneiric episodes, insomnia and dysautonomia at onset, whereas heterozygotes showed ataxia and dysarthria at onset, earlier sphincter loss and epileptic Grand Mal seizures; they also displayed more extensive cortical involvement on PET and at postmortem examination. Our data suggest that the phenotype expression of Fatal Familial Insomnia is related, at least partly, to the polymorphism at codon 129 of the prion protein-gene.

Adult↗

PubMed2002

Distributions of p53 codon 72 polymorphism in primary open angle glaucoma.

BACKGROUND: Glaucomatous neuropathy is a type of cell death by apoptosis. The p53 gene is one of the regulatory genes of apoptosis. Recently, p53 codon 72 polymorphism has been extensively studied to determine the risk factors responsible for many diseases. In the p53 gene, a single base change from G to C causes the alternation of amino acid residue 72 from arginine to proline. In this study the association between p53 codon 72 polymorphism and primary open angle glaucoma (POAG) patients was evaluated. METHODS: 58 POAG patients and 59 healthy volunteers were enrolled in this study. Polymerase chain reaction based analysis was used to resolve the p53 codon 72 polymorphism. RESULTS: There were significant differences in the distribution of the polymorphism between the control subjects and the POAG patients (p = 0.00782) The proline form of p53 gene codon 72 appears to be a significant risk factor in the development of POAG (odds ratio 2.389, 95% confidence interval: 1.14 to 5.01). CONCLUSIONS: Retinal ganglion cells die during POAG by apoptosis. The tumour suppressor protein, p53, is one of the primary regulators steps of apoptosis, and the results of our study are compatible with this concept.

Adult↗

PubMed2005

Detection of human papillomavirus DNA and p53 codon 72 polymorphism in prostate carcinomas of patients from Argentina.

BACKGROUND: Infections with high-risk human papillomaviruses (HPVs), causatively linked to cervical cancer, might also play a role in the development of prostate cancer. Furthermore, the polymorphism at codon 72 (encoding either arginine or proline) of the p53 tumor-suppressor gene is discussed as a possible determinant for cancer risk. The HPV E6 oncoprotein induces degradation of the p53 protein. The aim of this study was to analyse prostate carcinomas and hyperplasias of patients from Argentina for the presence of HPV DNA and the p53 codon 72 polymorphism genotype. METHODS: HPV DNA detection and typing were done by consensus L1 and type-specific PCR assays, respectively, and Southern blot hybridizations. Genotyping of p53 codon 72 polymorphism was performed both by allele specific primer PCRs and PCR-RFLP (Bsh1236I). Fischer's test with Woolf's approximation was used for statistical analysis. RESULTS: HPV DNA was detected in 17 out of 41 (41.5%) carcinoma samples, whereas all 30 hyperplasia samples were HPV-negative. Differences in p53 codon 72 allelic frequencies were not observed, neither between carcinomas and hyperplasias nor between HPV-positive and HPV-negative carcinomas. CONCLUSION: These results indicate that the p53 genotype is probably not a risk factor for prostate cancer, and that HPV infections could be associated with at least a subset of prostate carcinomas.

Adenocarcinoma↗

PubMed2006

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons.

BACKGROUND: While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A. THE HYPOTHESIS: First, we hypothesize that orthologues of the E. coli K12 pseudogene prfH encode a third class-I RF that we designate RFH. Second, it is likely that RFH responds to signals other than conventional stop codons. Supporting evidence comes from the following facts: (i) A number of bacterial genomes contain prfH orthologues with no discernable interruptions in their ORFs. (ii) RFH shares strong sequence similarity with other class-I bacterial RFs. (iii) RFH contains a highly conserved GGQ motif associated with peptidyl hydrolysis activity (iv) residues located in the areas supposedly interacting with mRNA and the ribosomal decoding center are highly conserved in RFH, but different from other RFs. RFH lacks the functional, but non-essential domain 1. Yet, RFH-encoding genes are invariably accompanied by a highly conserved gene of unknown function, which is absent in genomes that lack a gene for RFH. The accompanying gene is always located upstream of the RFH gene and with the same orientation. The proximity of the 3' end of the former with the 5' end of the RFH gene makes it likely that their expression is co-regulated via translational coupling. In summary, RFH has the characteristics expected for a class-I RF, but likely with different specificity than RF1 and RF2. TESTING THE HYPOTHESIS: The most puzzling question is which signals RFH recognizes to trigger its release function. Genetic swapping of RFH mRNA recognition components with its RF1 or RF2 counterparts may reveal the nature of RFH signals. IMPLICATIONS OF THE HYPOTHESIS: The hypothesis implies a greater versatility of release-factor like activity in the ribosomal A-site than previously appreciated. A closer study of RFH may provide insight into the evolution of the genetic code and of the translational machinery responsible for termination of translation. REVIEWERS: This article was reviewed by Daniel Wilson (nominated by Eugene Koonin), Warren Tate (nominated by Eugene Koonin), Yoshikazu Nakamura (nominated by Eugene Koonin) and Eugene Koonin.

Journal Article↗

PubMed1998

Variability of Ha-ras (codon 12) proto-oncogene mutations in diverse thyroid cancers.

Structural alterations to proto-oncogene sequences may be involved in the pathogenesis of human thyroid neoplasms. We studied 128 thyroid tumours (35 benign and 93 malignant) for ras gene point mutations in three different codons (12, 13 and 61) using a restriction fragment length polymorphism technique and direct sequencing of double-stranded DNA on polymerase chain-reaction-amplified tumour DNA. We found a high frequency of ras mutation for the Ha-ras codon 12 in follicular adenomas (7 of 35), particularly in atypical adenomas (5 of 17), in follicular carcinomas (6 of 19), with a high percentage for Hurthle cell carcinomas (6 of 11), and in papillary carcinomas (4 of 66). Point mutations for other ras genes in different codons studied were weak to absent. No mutation was found in undifferentiated carcinomas (n = 8). The predominant amino acid substitution both in the adenomas and in the differentiated tumours was glycine to valine (GGC to GTC) at position 12 of the Ha-ras gene. Our results obtained on a large series confirm the frequent occurrence of Ha-ras codon 12 gene mutations both in adenomas and in carcinomas. The frequency of ras mutations is linked to the geographical origin of the population studied and varies (0-85%) from one cancer type to another according to published data. Therefore, these mutations are merely an expression of cellular transformation.

Adenocarcinoma, Follicular↗

PubMed1998

Codon 249 mutations of p53 gene in development of hepatocellular carcinoma.

AIM:To investigate the mechanisms of codon 249 mutation of p53 gene in the formation of hepatocellular carcinoma (HCC).METHODS:Codon 249 mutation accompanied by loss of heterozygosity (LOH) and its effect on translation and transcription were studied using SSCP, IHC and RT-PCR/slot hybridization.RESULTS:Codon 249 mutations were detected in 32.9%, LOH detected in 68.4% among the HCC patients.Mutations of condon 249 were accompanied by LOH in 90%.The positive rates of p53 protein and mRNA were 91.3% and 95.7%, in mutational group, both were significantly higher than those in the non-mutational group (91.3% vs 19.1% and 95.7% vs 40.4%, respectively, both P < 0.01). The translation of p53 gene was strongly related to its transcription by correlation analysis( r = 0.8208).CONCLUSION:LOH might play an important role in hepatocarcinogenesis of codon 249 mutation, which could increase both transcription and translation of p53 gene.The increased expression of p53 protein mainly depend on the increased transcription of p53 gene.

Journal Article↗

PubMed1999

Codon 249 mutations of p53 gene in non-neoplastic liver tissues.

AIM:To study the significance of p53 gene in hepatocarcinogenesis through analyzing codon 249 mutations of p53 gene in non-neoplastic liver tissues.METHODS:Codon 249 mutation was detected using single-stranded conformational polymorphism analysis and allele-specific PCR in liver tissues from 10 cases of chronic hepatitis, 5 cases of cirrhosis and 20 cases of HCCs.RESULTS:The detection rate of codon 249 mutation in chronic hepatitis, cirrhosis and pericancerous tissues was 70% (7/10), 100% (5/5) and 70% (14/20), respectively by AS-PCR. These mutations could not be detected by SSCP analysis. The detection rates were 65% (13/20) and 45% (9/20) in cancerous tissues by AS-PCR and SSCP analysis.CONCLUSION:Codon 249 mutations of p53 gene were very popular in non-neoplastic liver tissues though the number of those mutant cells was only in subsection. Those mutations in cancerous tissues might take place in the stage before the formation of tumor.

Journal Article↗

PubMed2005

Arrangement of mRNA 3' of the A site codon on the human 80S ribosome.

Positioning of mRNA 3' of the A site codon was studied with the use of short mRNA analogues carrying a UUU triplet at the 5'-termini and a perfluorophenylazide group at either the N7 atom of the guanosine or the C5 atom of the uridine 3' of the triplet. Modified nucleotides were directed to positions +7, +9 or +12 with respect to the first nucleotide of the P site codon by tRNA(Phe) cognate to the UUU triplet targeted to the P site. Mild UV-irradiation resulted in cross-linking of the mRNA analogues to the 18S rRNA and to 40S proteins, the yield of cross-linking depending on the nature of the mRNA nucleotide bearing the modified group and its position on the ribosome. In addition, the yield of cross-linking to the 18S rRNA decreased strongly when the modified nucleotide was moved from position +7 to position +12. All the mRNA analogues cross-linked to the 18S rRNA nucleotides that had been found earlier at the decoding site, namely, to the invariant dinucleotide A1824/A1825 and the variable A1823 in the 3'-minidomain of the 18S rRNA, and also to the invariant nucleotide C1698 in the 3'-minidomain and the conserved region 605-620 in the apical region of helix 18 in the 5'-domain. The results indicate that (1) the mRNA makes a sharp turn between positions +6 and +7, (2) the triplet immediately 3' of the A site codon neighbors the 18S rRNA and proteins, and (3) the codon 3' of the triplet mentioned is surrounded mainly by proteins.

Base Sequence↗

PubMed1999

A novel phenotype in familial Creutzfeldt-Jakob disease: prion protein gene E200K mutation coupled with valine at codon 129 and type 2 protease-resistant prion protein.

A novel phenotype of familial Creutzfeldt-Jakob disease (CJD) with mutated codon 200 of the prion protein gene (PRNP) coupled with the valine codon 129 (E200K-129V haplotype) has two features never observed in subjects carrying the pathogenic mutation coupled with the methionine codon 129 (E200K-129M haplotype): (1) plaque-like prion protein (PrP) deposits in the cerebellum and (2) type 2 protease-resistant prion protein (PrP(res)). This observation further underlines the role of codon 129 on the mutated PRNP allele in modulating the phenotype of familial prion diseases.

Aged↗

PubMed1989

Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purification, codon specificity and translational activity.

In response to low (approximately 1 microM) levels of selenium, Escherichia coli synthesizes tRNA(Glu) and tRNA(Lys) species that contain 5-methylaminomethyl-2-selenouridine (mnm5Se2U) instead of 5-methylaminomethyl-2-thiouridine (mnm5S2U). Purified glutamate- and lysine-accepting tRNAs containing either mnm5Se2U (tRNA(SeGlu), tRNA(SeLys] or mnm5S2U (tRNA(SGlu), tRNA(SLys] were prepared by RPC-5 reversed-phase chromatography, affinity chromatography using anti-AMP antibodies and DEAE-5PW ion-exchange HPLC. Since mnm5Se2U, like mnm5S2U, appears to occupy the wobble position of the anticodon, the recognition of glutamate codons (GAA and GAG) and lysine codons (AAA and AAG) was studied. While tRNA(SGlu) greatly preferred GAA over GAG, tRNA(SeGlu) showed less preference. Similarly, tRNA(SGlu) preferred AAA over AAG, while tRNA(SeLys) did not. In a wheat germ extract--rabbit globin mRNA translation system, incorporation of lysine and glutamate into protein was generally greater when added as aminoacylated tRNA(Se) than as aminoacylated tRNA(S). In globin mRNA the glutamate and lysine codons GAG and AAG are more numerous than GAA and AAA, thus a more efficient translation of globin message with tRNA(Se) might be expected because of facilitated recognition of codons ending in G.

Cell-Free System↗

PubMed1999

Effect of the codon following the ATG start site on the expression of ovine growth hormone in Escherichia coli.

For expression of ovine growth hormone (OGH) in inclusion bodies without an affinity histidine tag at either end of the protein, three clones, differing only in the second codon following the ATG start site, were constructed. Their expression was studied by SDS-PAGE followed by immunoblotting. Clone Ala.OGH (clone 1), beginning with Met.Ala.Phe.Pro ellipsis, did not show any expression. Clone Phe.OGH (clone 3), beginning with Met.Phe.Pro ellipsis, gave very high levels of OGH expression following IPTG induction. However, in clone Gly.OGH (clone 2), in which the Ala codon was replaced with a Gly codon at the second position after the start site, a lower level of expression was obtained. Northern hybridization analysis showed that upon IPTG induction, OGH mRNA was transcribed from all three clones. These results therefore, imply that lack of expression in clone 1 and a lower level of expression in clone 2 are not due to a failure of transcription; however, they may be due to inefficient initiation of translation. The secondary structure analysis of mRNA predicts inaccessibility of different elements of the RBS in the case of Ala.OGH (clone 1). The present study highly underscores the importance of mRNA secondary structure at the start site in regulation of expression of a cloned gene in Escherichia coli, a prokaryotic expression system.

Animals↗

PubMed1996

Codon adjustment to maximise heterologous gene expression in Streptomyces lividans can lead to decreased mRNA stability and protein yield.

The impact of the codon bias of the mouse tumour necrosis factor alpha (mTNF) gene cloned in Streptomyces lividans on the efficiency of expression and secretion was analysed. Minor codons occurring in the mTNF gene were therefore adapted to the codon bias of Streptomyces by site-directed mutagenesis. No improvement in mTNF yield could be detected. The stability of the transcript derived from the construct was shown to be more important for determining the final level of mTNF production. A strong correlation was observed between the yield of secreted biologically active mTNF and the amount of mTNF mRNA present in the cells.

Algorithms↗