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At least 109 records · Page 6Linked to original sources
PubMed1991

Codon usage divergence of homologous vertebrate genes and codon usage clock.

This paper is concerned with the divergence of synonymous codon usage and its bias in three homologous genes within vertebrate species. Genetic distances among species are described in terms of synonymous codon usage divergence and the correlation is found between the genetic distances and taxonomic distances among species under study. A codon usage clock is reported in alpha-globin and beta-globin. A method is developed to define the synonymous codon preference bias and it is observed that the bias changes considerably among species.

Animals↗
PubMed1992

Codon-anticodon pairing. A model for interacting codon-anticodon duplexes located at the ribosomal A- and P-sites.

The interaction between two codon-anticodon duplexes of the ribosomal A- and P-site-bound tRNAs is the key feature of the proposed model. This interaction prohibits non-canonical base pairing at the first and second positions of the codon and controls base pairing at the third position (wobbling rules ensuing from the model are in good accord with those generated from experiments). The model is capable of predicting codon context effects. It follows from the model that modifications of the first anticodon residue of the P-site tRNA can affect the stability of the A-site duplex, and that the translation of a DNA single chain analogue of mRNA should be accompanied by non-canonical base pairing at all three positions of the codon. These predictions of the model can be subjected to experimental tests.

Anticodon↗
PubMed1993

Double mutations at codon 180 and codon 232 of the PRNP gene in an apparently sporadic case of Creutzfeldt-Jakob disease.

Several polymorphisms of the prion protein gene are associated with the occurrence of familial Creutzfeldt-Jakob disease. We described a 84-year-old Japanese man with neuropathologically verified Creutzfeldt-Jakob disease of apparently sporadic type. His clinical presentation was atypical in point of a very late age at onset and absence of periodic synchronous discharge on electroencephalography. The patient carried double hitherto undescribed mutations of the prion protein gene; at codon 180 on one allele and at codon 232 on another. The mutation at codon 180 abolishes the Tth111I cutting site, which may be misunderstood to represent codon 178 mutation on routine restriction fragment length polymorphism study.

Aged↗
PubMed1992

Heterozygosity for the IVS-I-5 (G-->C) mutation with a G-->A change at codon 18 (Val-->Met; Hb Baden) in cis and a T-->G mutation at codon 126 (Val-->Gly; Hb Dhonburi) in trans resulting in a thalassemia intermedia.

We have analyzed the hemoglobins of a young German patient with beta-thalassemia intermedia and of his immediate family and included in these studies an evaluation of possible nucleotide changes in the beta-globin genes through sequencing of amplified DNA. One chromosome of the propositus and one of his father's carried the GTG-->GGG mutation at codon 126 leading to the synthesis of Hb Dhonburi or alpha 2 beta (2)126(H4)Val-->Gly; this variant is slightly unstable and is associated with mild thalassemic features. His second chromosome and one of his mother's had the common IVS-I-5 (G-->C) mutation that leads to a rather severe beta(+)-thalassemia and the GTG-->ATG mutation at codon 18, resulting in the replacement of a valine residue by a methionine residue. This newly discovered beta-chain variant, named Hb Baden, was present for only 2-3% in both the patient and his mother. This low amount results from a decreased splicing of RNA at the donor splice-site of the first intron that is nearly completely deactivated by the IVS-I-5 (G-->C) thalassemic mutation. The chromosome with the codon 18 (GTG-->ATG) and the IVS-I-5 (G-->C) mutations has thus far been found only in this German family; analysis of 51 chromosomes from patients with the IVS-I-5 (G-->C) mutation living in different countries failed to detect the codon 18 (GTG-->ATG) change.

Amino Acid Sequence↗
PubMed2004

Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance.

Expression patterns in Escherichia coli of two small archaeal proteins with a natural content of about 30% rare codons were analyzed. The proteins, a histone-like protein from Sulfolobus shibatae (Ssh10), and a glutaredoxin-like protein from Methanobacterium thermoautotrophicum (mtGrx), were produced with expression plasmids encoding wild-type genes, codon-optimized synthetic, and GST-fusion genes. These constructs were expressed in BL21 (DE3), its LysS derivative, and modified strains carrying copies for rare codon tRNAs or deletions in the RNAseE gene. Both Ssh10 and mtGrx expression levels were constitutively high in BL21(DE3) and its derivatives, with the exception of the LysS phenotype, which prevented high level expression of the Ssh10 wild-type gene. Surprisingly, a codon-optimized mtGrx gene construct displayed undetectable levels of protein production. The translational block observed with the synthetic mtGrx gene could be circumvented by using a synthetic mtGrx-glutathione S-transferase (GST) fusion construct or by in vitro translation. Taken together, the results underscore the importance of mRNA levels and RNA stability, but not necessarily tRNA abundance for efficient heterologous protein production in E. coli.

Archaeal Proteins↗
PubMed2004

Influences of lifestyle habits and p53 codon 72 and p21 codon 31 polymorphisms on gastric cancer risk in Taiwan.

Influences of lifestyle habits and p53 codon 72 and p21 codon 31 polymorphisms on the risk for developing primary gastric cancer were examined in 89 gastric adenocarcinoma cases (51 males, 38 females) and 192 controls (106 males, 86 females) in a hospital-based, case-control study in Taiwan. In the final regression model, Helicobacter pylori infection and substance use (cigarette smoking, areca chewing) were significant predictors of risk for developing gastric cancer. Compared with subjects negative for H. pylori infection, positive subjects were 3.65-fold (95% CI = 2.07-6.42) more likely to develop gastric cancer. Compared with non-smokers or non-chewers, subjects with more than a 15 pack-year history or more than a 498 betel-year history (about 20 betel quids/day for 25 years) were 2.27- and 4.86-fold more at risk (95% CI = 1.06-4.84 and 1.20-19.74), respectively. Frequencies of arg/arg, arg/pro and pro/pro in p53 were 11 (12.4%), 53 (59.5%) and 25 (28.1%) in carcinoma cases and 40 (20.8%), 95 (49.5%) and 57 (29.7%) in control cases, respectively. Frequencies of arg/arg, ser/arg and ser/ser in p21 were 26 (29.2%), 36 (40.5%) and 27 (30.3%) in carcinoma cases and 49 (25.5%), 94 (49.0%) and 49 (25.5%) in control cases, respectively. Neither p53, nor p21 polymorphisms were significantly different in cases and controls ( P = 0.16 and P = 0.41, respectively). Results remained insignificant after dichotomizing with respect to cigarette smoking, areca chewing and H. pylori infection. In summary, our data indicate that in Taiwan, H. pylori infection, smoking and areca chewing are significant risk predictors for developing gastric cancer. p53 codon 72 and p21 codon 31 genotypes did not modify these risks.

Adult↗
PubMed2005

The association of p53 mutations and p53 codon 72, Her 2 codon 655 and MTHFR C677T polymorphisms with breast cancer in Northern Greece.

The aim of this study was to explore a possible association between p53 codon 72, Her 2 codon 655 and MTHFR C677T polymorphisms and breast cancer in Northern Greece. We examined 42 women with breast cancer and 51 controls. A total of 42 women with breast cancer as well as healthy controls were investigated and results showed that p53 codon 72 polymorphism is statistically significantly associated with breast cancer (OR for Arg/Arg to non-Arg/Arg was 6.66, P = 0.0001 at 95% CI 2.63-16.9), but not Her 2 and MTHFR polymorphisms are associated with breast cancer (OR for Ile/Ile to non-Ile/Ile was 1.33, P = 0.54 at 95% CI 0.52-3.38 and OR for T/T versus non-T/T was 1.07, P = 0.89 at 95% CI 0.35-3.25). All subjects were examined for p53 exons 5-8 mutations. Three novel sequence variations in exons 7 and 8 of TP53 gene were found in three patients. One of them induces an amino acid change at Ser 241Gly, the second is a silent mutation Gly244Gly, and the third one results in a premature stop codon 294 (Glu294stop) and a truncated p53 protein.

Adult↗
PubMed2001

A highly prevalent polymorphism at codon 72 of HIV-1 reverse transcriptase in Argentina prevents hybridization reaction at codon 74 in the LiPA genotyping test.

The aim of this study was to compare the performance of two commercial drug-resistance HIV-1genotyping kits: LiPA (Innogenetics, Belgium) and TruGene (Visible Genetics, Canada). Samples from 103 HIV-1 infected individuals from Argentina were studied. The average correlation between the two methods was 92.81%. More codons could be analysed by TruGene than by LiPA (610/618 and 541/618 codons, respectively). The sequences of the samples and the LiPA probes were aligned showing that a silent mutation at codon 72 (AGA-->AGG) of the HIV-1 reverse transcriptase, which was not recognised by the LiPA probes, was present in 35/36 non-reactive samples for position 74. The overall prevalence of this polymorphism in the population studied was 39.81%. When sequences from different parts of the world were analysed 189/3395 (5.63%) carried the mutation at codon 72, while 23/133 (17.29%) of the sequences from Latin America (excluding Argentina) had this mutation. In both cases, the prevalence of this polymorphism in the Argentinean population was significantly higher. This highlights the importance of carrying out studies on the performance of genotyping kits outside the United States and Europe, especially in areas where non-B HIV-1 subtypes are prevalent.

Argentina↗
PubMed2002

Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli.

The SsrA or tmRNA quality control system intervenes when ribosomes stall on mRNAs and directs the addition of a C-terminal peptide tag that targets the modified polypeptide for degradation. Although hundreds of SsrA-tagged proteins can be detected in cells when degradation is prevented, most of these species have not been identified. Consequently, the mRNA sequence determinants that cause ribosome stalling and SsrA tagging are poorly understood. SsrA tagging of Escherichia coli ribokinase occurs at three specific sites at or near the C terminus of this protein. The sites of tagging correspond to ribosome stalling at the termination codon and at rare AGG codons encoding Arg-307 and Arg-309, the antepenultimate and C-terminal residues of E. coli ribokinase. Mutational analyses and studies of the effects of overexpressing the tRNA that decodes AGG reveal that the combination of a rare arginine codon at the C terminus and the adjacent inefficient UGA termination codon act to recruit the SsrA-tagging system, presumably by slowing the rate of translation elongation and termination.

Amino Acid Sequence↗
PubMed2006

Detection of two rare beta-thalassemia alleles found in the Tunisian population: codon 47 (+A) and codons 106/107 (+G).

We here present the first report of the detection of two rare beta0-thalassemia (thal) mutations in the Tunisian population: codon 47 (+A) and codons 106/107 (+G). To the best of our knowledge this is the second report of the codon 47 (+A) mutation, the first being identified in a Surinamese subject. The codons 106/107 (+G) mutation was first described in American Blacks, subsequently in Egyptians and Palestinians, and now in Tunisians. These mutations were detected by denaturing gradient gel electrophoresis (DGGE) screening followed by automated nucleotide sequencing. The former was found in two related beta-thal major patients in the homozygous state, while the latter was identified in a homozygous state in a transfusion-dependent beta-thal subject and in a sickle cell beta-thal patient. Both mutations are in linkage disequilibrium with haplotype V and sequence framework 2. Given the known wide spectrum of beta-thal alleles in the Tunisian population, the present report further confirms such heterogeneity. The knowledge of an updated spectrum of beta-thal alleles in Tunisia must allow the implementation of a more efficient screening strategy for genetic counseling and prenatal diagnosis.

Adolescent↗
PubMed1997

Small regions of preferential codon usage and their effect on overall codon bias--the case of the plp gene.

Preferential codon usage within synonymous groups (codon bias), is hypothesised to be a consequence of either mutational pressure or translational selection. This paper examines PLP and DM-20, two transcripts differentially spliced from the plp gene, using a variety of previously described indices measuring codon bias as well as a novel index for quantifying the response to directional mutation pressure. The results demonstrate that small regions of extreme codon bias may have appreciable effects on the quantification of total bias, and that this effect may be either an increase or a decrease depending which index is used.

Animals↗
PubMed1997

The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity.

In some Candida species, the universal CUG leucine codon is translated as serine. However, in most cases, the serine tRNAs responsible for this non-universal decoding (tRNA(Ser)CAG) accept in vitro not only serine, but also, to some extent, leucine. Nucleotide replacement experiments indicated that m1G37 is critical for leucylation activity. This finding was supported by the fact that the tRNA(Ser)CAGs possessing the leucylation activity always have m1G37, whereas that of Candida cylindracea, which possesses no leucylation activity, has A37. Quantification of defined aminoacetylated tRNAs in cells demonstrated that 3% of the tRNA(Ser)CAGs possessing m1G37 were, in fact, charged with leucine in vivo. A genetic approach using an auxotroph mutant of C.maltosa possessing this type of tRNA(Ser)CAG also suggested that the URA3 gene inactivated due to the translation of CUG as serine was rescued by a slight incorporation of leucine into the polypeptide, which demonstrated that the tRNA charged with multiple amino acids could participate in the translation. These findings provide the first evidence that two distinct amino acids are assigned by a single codon, which occurs naturally in the translation process of certain Candida species. We term this novel type of codon a 'polysemous codon'.

Amino Acids↗
PubMed1985

Nucleotide sequence of a macronuclear DNA molecule coding for alpha-tubulin from the ciliate Stylonychia lemnae. Special codon usage: TAA is not a translation termination codon.

The gene-sized macronuclear DNA of the hypotrichous ciliate Stylonychia lemnae contains two size classes of DNA molecules (1.85 and 1.73 kbp) coding for alpha-tubulin. Each macronucleus contains about 55000 copies of the 1.85 kbp molecules and about 17000 copies of the 1.73 kbp DNA molecules. Five macronuclear molecules of these sequences were cloned and sequenced, one, from the 1.85 kbp size class in its entirety. The 5 sequences fell into two classes suggesting that Stylonychia lemnae contains at least two different alpha-tubulin genes. All 5 clones show the codon TAA in the same nucleotide positions of the coding region. In this position the TAA codon cannot function as a translational stop codon and we suggest that this codon codes for the amino acid glutamine. The nucleotide sequence of the coding region as well as the encoded amino acid sequence is highly conserved compared to alpha-tubulin genes from vertebrates. The noncoding regions show several putative transcription-regulatory sequences as well as sequences presumably functioning as replication origins.

Base Sequence↗
PubMed1990

The effect of context on synonymous codon usage in genes with low codon usage bias.

The effect of neighbouring bases on the usage of synonymous codons in genes with low codon usage bias in yeast and E. coli is examined. The codon adaptation index is employed to identify a group of genes in each organism with low codon usage bias, which are likely to be weakly expressed. A similar pattern is found in complementary sequences with respect to synonymous usage of A vs G or of U vs C. It is suggested that this may reflect an effect of context on mutation rates in weakly expressed genes.

Base Sequence↗
PubMed1984

Yeast tRNAAsp: codon and wobble codon-anticodon interactions. A transferred nuclear Overhauser enhancement study.

The conformations of the ribotrinucleoside bisphosphates GpApC and GpApU, the codon and wobble codon for aspartic acid respectively, bound to yeast tRNAAsp in solution, have been examined by means of time-dependent transferred nuclear Overhauser enhancement measurements to determine distances between bound ligand protons. The conformations of the two bound ribotrinucleoside bisphosphates are shown to be very similar with an overall root-mean-square difference in interproton distances of 0.03 nm. The ribose conformations of all the residues are 3'-endo; the glycosidic bond torsion angles of the A and C residues of GpApC and of the A and U residues of GpApU are in the low anti range. These features are typical of an A-RNA type structure. In contrast, the G residue of both GpApC and GpApU exists as a mixture of syn and anti conformations. The overall conformation of the two bound ribotrinucleoside bisphosphates is also similar to A-RNA and the stability of the complexes is enhanced by extensive base-base stacking interactions. In addition, it is shown that the binding of the codon GpApC to tRNAAsp induces self-association into a multicomplex system consisting of four GpApC-tRNAAsp complexes, whereas the wobble codon GpApU fails to induce any observable self-association.

Anticodon↗
PubMed1985

Mutations that convert the four leucine codons of the Salmonella typhimurium leu leader to four threonine codons.

In Salmonella typhimurium, expression of the leucine operon is regulated by a transcription attenuation mechanism. According to a current model of attenuation, elevated expression of this operon requires that a ribosome stall at one of four adjacent codons for leucine on a leader RNA. We used oligonucleotide-directed mutagenesis to convert the four leucine codons of the S. typhimurium leu leader to four threonine codons. Analysis of the resulting mutant operon showed that almost all regulation by leucine had been abolished. The mutant operon was, instead, partially derepressed by a limitation for charged threonine tRNA. These results provide direct evidence for the function for the four leucine codons postulated by the attenuator model. An unexpected observation made during these studies was that the wild-type leu operon was partially derepressed by starvation for threonine.

Codon↗
PubMed2005

Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates.

In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the "effective number of codons," N(c). Several attempts have been made recently to improve Wright's estimate of N(c), but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of N(c) and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, F, turns out to be a key to the estimation of N(c). F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The N(c) methods that are based on sampling without replacement showed much better accuracy at short gene lengths than those based on sampling with replacement, indicating that Wright's homozygosity method is superior. Surprisingly, the methods based on sampling with replacement displayed a superior correlation with mRNA levels in Escherichia coli.

Codon↗
PubMed2000

K-ras codon 12 mutation induces higher level of resistance to apoptosis and predisposition to anchorage-independent growth than codon 13 mutation or proto-oncogene overexpression.

The position of the point mutation in the c-K-ras gene appears associated with different degrees of aggressiveness in human colorectal tumors. In addition, colon tumors carrying K-ras codon 12 mutations associate with lower levels of apoptosis than tumors lacking this mutation. To test the hypothesis of a distinct transforming capacity of different K-ras forms in an in vitro system, we generated stable transfectants of NIH3T3 cells expressing a plasmid containing K-ras mutated at codon 12 (K12) or at codon 13 (K13), or overexpressing the K-ras proto-oncogene (Kwt-oe). We evaluated changes in morphology, proliferative capacity, contact inhibition, and predisposition to apoptosis and anchorage-independent growth in K12, K13, and Kwt-oe transformants. In addition, we studied alterations in expression and/or activation of proteins that participate in signal transduction downstream of Ras or are involved in the regulation of apoptosis and cell-cell (E-cadherin and beta-catenin) and cell-substrate (focal adhesion kinase) interactions. We observed that K13 or Kwt-oe transformants died synchronically 24-48 h after reaching confluency. Their death was apoptotic. In contrast, K12 grew, forming bigger colonies with higher cell densities; and before reaching confluency, spontaneously formed spheroids and showed no sign of apoptosis. The enhanced resistance to apoptosis, loss of contact inhibition, and predisposition to anchorage-independent growth in the K12 transformants were associated with higher AKT/protein kinase B activation, bcl-2, E-cadherin, beta-catenin, and focal adhesion kinase overexpression, and RhoA underexpression, whereas the increased sensitivity of K13 or Kwt-oe transformants to apoptosis was associated with increased activation of the c-Jun-NH2-terminal kinase 1 pathway. All transformants showed a similar overactivation of mitogen-activated protein kinases and levels of bax expression similar to the endogenous level. Therefore, in our in vitro model, the localization of the mutation in the K-ras gene predisposes to a different level of aggressiveness in the transforming phenotype. K12 may increase aggressiveness not by altering proliferative pathways, but by the differential regulation of K-Ras downstream pathways that lead to inhibition of apoptosis, enhanced loss of contact inhibition, and increased predisposition to anchorage-independent growth. These results offer a molecular explanation for the increased aggressiveness of the tumors with K-ras codon 12 mutations observed in the clinical setting.

3T3 Cells↗