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At least 1,135 records · Page 63Linked to original sources
PubMed2003

In-phase implies large likelihood for independent codon model: distinguishing coding from non-coding sequences.

It is proven that under the independent codon model, the likelihood of a DNA coding sequence read according to the correct frame is asymptotically larger than that read with an incorrect frame. Based on this proposition, a single set of probabilities of the codon usage is enough for discriminating the six frames of coding sequences under the independent codon model. The direct coding sequence of Escherichia coli genome is taken as an example to examine the codon independency by using the mutual information and chi2 analysis. The contrast between the coding frame and the two offset frames is evident. A self-learning approach for generating training set is proposed to estimate probability parameters.

Codon↗
PubMed1987

Translation rate modification by preferential codon usage: intragenic position effects.

We present a model for calculating the protein production rate as a function of the translation rate. The model takes into account that the elongation rate along an mRNA molecule is non-uniform as a result of different tRNA availabilities for different codons. Initiation of ribosomes on an mRNA is normally the rate-limiting step in the translation process, and blocking of the initiation site can be avoided if the codons closest to this site allow fast translation by the ribosome. Hence, different selective forces may act on the choice of synonymous codons in the initiation region than elsewhere on a given mRNA. We show that the elongation rate along the whole mRNA influences the production rate of abundant proteins, whereas only the elongation rate in the initiation region is of importance for the production rate of rare proteins. We also present an analysis of the codon distribution along known mRNAs coding for abundant and rare proteins.

Bacterial Proteins↗
PubMed1997

UV-induced mutations affecting codon 12 of the K-ras gene are suppressed by interferon-alpha in human RSa cells.

K-ras gene sequences mutant at codon 12 were recovered following differential dot-blot hybridization of genomic DNA from human RSa cells up to 12 days after the cells had been irradiated with far-UV (principally 254 nm). By contrast, no mutant codon 12 sequences were recovered from cells which had been treated with 50 IU/ml human interferon (HuIFN)-alpha for 24 h prior to their UV exposure. HuIFN-alpha treatment in combination with anti-HuIFN-alpha antibody did not lead to the loss of mutant sequences. However, culture of interferon-pretreated cells with medium containing the protease inhibitor antipain (0.01 mM) for 6 h immediately after UV irradiation led to the recovery of mutant codon 12 sequences. Thus, while treatment with HuIFN-alpha appeared to prevent any UV-induced mutations affecting codon 12 of the K-ras gene from being recovered, the putative antipain-sensitive protease responsible for this suppressive affect appeared to be significantly affected by the protease inhibitor antipain.

Cell Line↗
PubMed1997

The mouse lymphoma L5178Y Tk+/- cell line is heterozygous for a codon 170 mutation in the p53 tumor suppressor gene.

The p53 tumor suppressor protein plays an important role in regulating the cellular response to DNA damage, including cell cycle arrest and apoptosis induction. Normal p53 function is critical for the maintenance of genomic stability. The mouse lymphoma L5178Y/TK(+/-)-3.7.2C cell line is widely used in genetic toxicology for mutagenesis and clastogenesis testing. A related line L5178Y-R, has previously been shown to react with antibodies specific for mutant as well as wild-type p53 protein and to exhibit delayed cell death after radiation. For this reason, as well as the mouse lymphoma assay's reputation for high sensitivity of detection for genotoxic agents but low specificity, we examined several clones of L5178Y cells for mutations in the conserved core domain (exons 5-8) of the p53 gene. Using single-strand conformational polymorphism analysis, we found evidence for the same mutation in exon 5 of p53 in L5178Y-R, L5178Y-S and L5178Y/TK(+/+)-3.7.2C cells. The mutation was identified by sequencing of exon 5 as a TGC (Cys) to CGC (Arg) transition in codon 170 (= codon 176 in humans). Sequencing showed approximately equivalent signals for the mutant and normal alleles for all 3 lines. The mutation in codon 170 is adjacent to a mutation hotspot of the human p53 gene (codon 175) and eliminates a critical zinc-coordinating cysteine residue such that the mutant protein is likely to be denatured and have a dominant negative effect on normal p53 function. Western blots showed approximately 100-fold higher levels of p53 protein in unirradiated L5178Y cells as compared to induced levels of p53 in normal mouse splenocytes 4 h after 5 Gy of gamma radiation. The high levels of p53 protein in L5178Y cells were not further inducible by radiation, whereas an 11-fold induction was seen in the irradiated splenocytes. These results indicate that p53 protein in L5178Y cells is dysfunctional and suggest that this line may therefore be abnormally susceptible to the induction of genetic alterations.

Animals↗
PubMed1998

Biological consequences of a point mutation at codon 969 of the FMS gene.

The FMS proto-oncogene encodes the cell surface receptor for colony stimulating factor-1 (CSF-1). Mutations of the FMS gene at codon 969, in the C-terminal region of the gene, have been detected in haematological malignancies. To ascertain the biological significance of a mutation at this codon, we have used a murine haematopoietic cell line, FDC-P1, containing a mutation at codon 969 that results in a phenylalanine replacing a tyrosine. FMS 969 mutant cells and v-fms transfected cells conferred interleukin 3 (IL-3) independent stimulation of FDC-P1 cells, whereas cells transfected with a wild-type FMS construct required exogenous IL-3 for growth. FDC-P1 cells containing a FMS 969 mutation and v-fms transfected cells were tumorigenic in nude mice. Binding studies with radioidonated CSF-1 revealed saturable specific binding in FMS wild-type cells with a Km of 0.9 mM; however, mutant FMS-containing cells did not display saturation kinetics, but instead exhibited a linear relationship between ligand concentration and amount bound. Constitutive expression of FOS was detected in 969 mutant cells in the absence of exogenous CSF-1, a phenotype that was only inducible in wild-type cells in response to CSF-1. FOS and JUNB expression by v-FMS transfected cells showed a similar pattern to FMS wild-type cells. This mutation has been detected in patients with haematological malignancies, and illustrates that the pathway of FMS 969 phenylalanine mutations and v-fms induced pathogenesis can be distinguished. These data indicate that there is a biological role for FMS codon 969 phenylalanine mutation which results in transformation of FDC-P1 cells.

Animals↗
PubMed1998

7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria.

In mitochondria of the squid, Loligo bleekeri, both the AGA and AGG codons are considered to correspond to serine instead of arginine as in the universal genetic code, and its genome encodes a single tRNA(Ser) gene with the anticodon GCT. Therefore, this gene product, tRNA(Ser)GCU, should be able to translate all four AGN (N; U, C, A, and G) codons as serine. To elucidate this recognition mechanism, the tRNA(Ser)GCU was isolated from squid liver and its complete nucleotide sequence determined. The tRNA(Ser)GCU was found to possess 7-methylguanosine (m7G) at the wobble position of the anticodon. This suggests that in the squid mitochondrial system, tRNA(Ser)GCU with the anticodon m7GCU can recognize not only the usual serine codons AGU and AGC, but also the unusual serine codons AGA and AGG, as in the case of starfish mitochondria (Matsuyama et al., J. Biol Chem. 273 (1988) 3363-3368).

Animals↗
PubMed2003

A transformation system for the nonuniversal CUG(Ser) codon usage species Candida rugosa.

Since Candida rugosa utilizes a nonuniversal serine codon CUG rather than leucine, no vectors have been constructed to transform this organism. Moreover, it is difficult to design a new transformation system because no selection markers and promoters are available. In this study, Zeocin (400 microg/ml) was demonstrated to inhibit the growth of C. rugosa. The dominant selectable marker bleomycin-resistant determinant (ble) gene containing five CUG codons in an open-reading frame of 375 bp was synthesized by replacing its CUG codons into leucine codons (zeo-n). This marker conferred resistance to Zeocin. GAL1 promoter, transcription elongation factor 1 (TEF1) promoter from Saccharomyces cerevisiae and LIP3 promoter from C. rugosa were then used to drive zeo-n and to examine the function of promoter in C. rugosa. The resulting vectors enabled selection of Zeocin-resistant clones after transformation by LiCl method and electroporation. These results demonstrate that transformation into C. rugosa is feasible under the operation of GAL1, TEF1, and LIP3 promoters. The development of the transformation system for C. rugosa is essential to the genetic analysis of gene regulation and biochemical features of this fungal species and the expression of recombinant proteins in C. rugosa.

Amino Acid Sequence↗
PubMed1981

Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model.

Neither a dynamic nor an energetic approach of the translation process has taken into account that intracellular levels of iso-tRNA species are adapted or adjusted to the codon frequency of mRNA being decoded (Bombyx mori silk gland, rabbit reticulocyte). A critical study of available experimental data suggests that the average elongation rate of a protein is maximized in the presence of an adapted tRNA population, usually an homologous tRNA. In addition, the amount of synthesized protein parallels that of corresponding mRNA. Other evidences--including in vitro and in vivo elongation assays with fibroin mRNA--show that individual elongation rates are not uniform. Pauses occur at certain sites of the mRNA chain. The relative lifetime of these pauses depends on the tRNA pool used. Finally, it appears that translation accuracy also depends on the balanced tRNA population. We propose to explain these different effects by using a codon-anticodon recognition model, called "trial and error system" based on a stochastic processing of the ribosome. Accordingly, various acylated tRNA species which surround a ribosome randomly encounter the receptor A site. Every trapped tRNA species is tested for a proper pairing with the codon to be recognized at the level of a comparator or discriminator function. If the pairing is correct, transpeptidation becomes irreversible. If not, the aminoacyl-tRNA is rejected and another randomly trapped tRNA is processed in turn. Mathematical analysis of this model shows that the mean number of trials used for translating the whole sequence of a mRNA is minimized when the proportion of different iso-tRNA species is correlated with the square root of codon frequency. Quantitations of reticulocyte tRNA support such a parabolic relation. Our translation system model brings some light into the role of tRNA adaptation for optimizing translation efficiency, i.e. maximizing both speed and accuracy. Some consequences of the model are discussed.

Codon↗
PubMed2003

p53 Codon 72 polymorphism and urothelial cancer risk.

The p53 tumor suppressor gene is often mutated in various human cancers. Recently, the p53 codon 72 polymorphism has been extensively studied to determine the risk factors responsible for cancer formation. We investigated the genotype distribution of the p53 codon 72 polymorphism in 112 male urothelial cancer cases and 175 male unrelated non-cancer controls. The allelic frequencies in Japanese non-cancer controls were 0.58 (Arg) and 0.42 (Pro). There was no significant difference in the three genotype frequencies (Arg/Arg, Arg/Pro, Pro/Pro) of the p53 codon 72 between the urothelial cancer cases and the controls. However, stratifying by smoking status, we found that the frequency of the Pro/Pro genotype for smokers was significantly more than that for never-smokers (odds ratio (OR)=2.28, 95% confidence interval (95%CI)=1.12-4.66). Furthermore, we divided smoking status (pack-years) into quartiles (<20, 20-40, 40-60, >60). OR (Pro/Pro vs. Arg/Arg) for the lighter smokers (<20 pack-years) was higher than in other groups (OR=6.83). Our results suggest that the Pro/Pro genotype of the p53 codon 72 polymorphism increases the risk of urothelial cancer in smokers.

Aged↗
PubMed2003

Frequent loss of p53 codon 72 Pro variant in hepatitis C virus-positive carriers with hepatocellular carcinoma.

Codon 72 exon 4 polymorphism of the p53 gene has been implicated in cancer risk and it has been suggested that it may have an impact on the clinical outcome of the disease. Our objective was to evaluate the association between p53 polymorphism at codon 72 and hepatocellular carcinoma. The p53 codon 72 genotype was examined in 97 biopsy samples from 67 Basque patients histologically diagnosed with hepatocellular carcinoma. Blood samples collected from 111 Basque residents were examined as a control group. The polymorphism was examined by both single strand conformation polymorphism analysis and allele specific polymerase chain reaction. Fisher's exact test was used to evaluate the data. The results showed that there were no statistically significant differences in the frequency of codon 72 polymorphism genotype between patients with liver cancer and healthy controls. We found a frequent loss of proline allele in hepatitis C virus (HCV)-positive carriers. In conclusion, the lack of a significant relationship between this polymorphism and risk of hepatocellular carcinoma suggests that it does not predispose towards hepatocarcinogenesis in this population. We suggest that the frequent loss of the proline allele in HCV-associated carcinogenesis of the liver plays some role in hepatocarcinogenesis.

Adult↗
PubMed2003

H-ras mutations at codon 61 or 13 in tumors initiated with a NO donor in mouse skin.

The tumor-initiating activity of nitric oxide (NO) in carcinogenesis was assessed using (+/-)-(E)-4-methyl-2-[(E)-hydroxyimino]-5-nitro-6-methoxy-3-hexenamide (NOR1), a synthetic NO donor. Topical application of NOR1 followed by 12-O-tetradecanoylphorbol 13-acetate (TPA) treatment twice a week for 20 weeks resulted in the development of papillomas in mice. All of the papillomas examined contained H-ras mutations at codons 61 or 13. At codon 61, CAA-CTA and CAA-TTA mutations were seen in 42/46 and 1/46 of the papillomas, respectively. Three papillomas without a mutation at codon 61 were mutated at codon 13. A GGC-CGC mutation was found in two of these samples while the third possessed a GGC-GTC mutation. These results suggest that NO possesses tumor-initiating activity through a process that induces mutation in H-ras.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2000

A functional significance for codon third bases.

Most amino acids are specified by more than one trinucleotide codon. Here we show that amino acids of differing functional importance may be distinguished by the pattern of synonymous codon usage. GC-rich genes tend to be of a greater transcriptional (p<0.01) and mitogenic (p<0.0001) significance than AT-rich genes, consistent with GC-->AT mutational drift in methylated genomic regions. Third-base GC retention also identifies critical amino acids within individual proteins, as indicated by non-random patterns of codon variation between gene homologs and also by differential sequelae of site-directed mutagenesis. Sequence analysis of human receptor tyrosine kinase genes confirms that functionally important transmembrane hydrophobic amino acids are specified by codons containing GC third bases more often than are transmembrane neutral amino acids (chi(2)=134.2). Amino acids encoded by GC third bases thus appear more tightly linked to cell function and survival than are those encoded by AT third bases.

Amino Acids↗
PubMed2001

The Candida albicans gene encoding the cytoplasmic leucyl-tRNA synthetase: implications for the evolution of CUG codon reassignment.

In a number of Candida species the 'universal' leucine codon CUG is decoded as serine. To help understand the evolution of such a codon reassignment we have analyzed the Candida albicans leucyl-tRNA synthetase (CaLeuRS) gene (CaCDC60). The predicted CaLeuRS sequence shows a significant level of amino acid identity to LeuRS from other organisms. A mitochondrial LeuRS (ScNAM2) homologue, which shared low identity with the CaLeuRS, was also identified in C. albicans. Antigenically-related LeuRSs were identified in a range of Candida species decoding the CUG codon as both serine and leucine, using an antibody raised against the N-terminal 15 amino acids of the CaLeuRS. Complementation experiments demonstrated that the CaLeuRS was able to functionally complement a Saccharomyces cerevisiae cdc60::kanMX null mutation. We conclude that there is no alteration in tRNA recognition and aminoacylation by the C. albicans LeuRS, which argues against it having a role in codon reassignment. The nucleotide sequences of the CaCDC60 and CaNAM2 genes were deposited at GenBank under Accession numbers AF293346 and AF352020, respectively.

Amino Acid Sequence↗
PubMed2002

Synonymous codon usage in Pseudomonas aeruginosa PA01.

Pseudomonas aeruginosa PA01 has a large (6.7 Mbp) genome with a high (67%) G+C content. Codon usage in this species is dominated by this compositional bias, with the average G+C content at synonymously variable third positions of codons being 83%. Nevertheless, there is some variation of synonymous codon usage among genes. The nature and causes of this variation were investigated using multivariate statistical analyses. Three trends were identified. The major source of variation was attributable to genes with unusually low G+C content that are probably due to horizontal transfer. A lesser trend among genes was associated with the preferential use of putatively translationally optimal codons in genes expressed at high levels. In addition, genes on the leading strand of replication were on average more G+T-rich. Our findings contradict the results of two previous analyses, and the reasons for the discrepancies are discussed.

Amino Acids↗
PubMed2003

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.

Each prokaryote has a unique genomic signature as evidenced by a set of species-specific frequencies of short oligonucleotides. With respect to genomic signatures a bacterial genome is homogenous and the variation within a genome is smaller than the variations between genomes of different species. This study quantifies the species-specificity of genomic signatures in the complete genomes of 57 prokaryotes. The species-specificity in the genomic signature was related to the quantification of other sequence biases, such as G+C content, synonymous codon choice and amino acid usage. The results confirm that the genomic signature is genome-wide with high species-specificity in both coding and non-coding regions. In coding regions the species-specific bias in synonymous codon choice was comparable to the genomic signature, while the bias in amino acid usage only captured about 50% of the species-specific bias in the genomic signature. A correlation between the species-specificity in synonymous codon choice and amino acid usage was identified, in which proteins with species-specific amino acid usage were also coded with species-specific synonymous codon choice. However, we demonstrated that the G+C content captures only approximately 40% of the species-specificity in the genomic signature, and is insufficient to explain the species specificity in the non-coding regions. Thus, the species-specific bias in non-coding regions remains largely unknown. Further, we compared the genomic signature in relation to phylogenetic distance. This was performed in order to illustrate the feasibility of a hierarchical classification scheme in future applications of the described classification methodology in screening for horizontal gene transfer and biodiversity studies.

Amino Acids↗
PubMed2003

The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti.

The genome of the nitrogen-fixing bacterium Sinorhizobium meliloti is composed of three replicons of 3.65 (chromosome), 1.35 (pSymA) and 1.68 Mb (pSymB), respectively. While the chromosome encodes for most of the housekeeping functions, the three elements may contribute to symbiosis, though pSymA is absolutely necessary for nodulation and nitrogen fixation, since it harbours all the characterized nodulation and symbiotic fixation genes. On the other hand, the majority of the sequences located in this megaplasmid are probably not expressed during the free-living stage of the organism. Since most of the sequences located in pSymA are transcribed only at the stage of bacteroids when most probably the fate of the bacterium is to die, the mutations occurring at this stage will not be fixed in the population. Therefore, if natural selection contributes to the codon usage pattern in this species, its effect will be much weaker for the genes placed in pSymA. A codon usage analysis of the genes comprising the three replicons is consistent with the conclusion that selection for translational speed shapes the codon usage of the two replicons which are important for competitive cell growth while the codon usage of the third replicon reflects primarily the mutational bias.

Base Sequence↗
PubMed2003

mRNA 5' region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

5' Untranslated Regions↗
PubMed1997

Codon usage and nucleotide composition in Coxiella burnetii.

Coxiella burnetii, the causative agent of Q fever, is an obligate intracellular bacterium. With the development of molecular biology techniques, there have been increasing efforts on gene cloning and other genetic analyses of this organism. In this report, we tabulate the codon usage (CU) and nucleotide (nt) co-occurrence in C. burnetii, based on available nt sequence data. The average G+C content of the C. burnetii genome is 42.4%, where the G+C content is 42.7% for the chromosome and 38.7% for the plasmid. In comparison to Escherichia coli, there is biased CU. Some codons are frequently used in C. burnetii, but rarely used in E. coli and vice versa. Plasmid genes prefer A or T at the first or third position of a codon. However, TAA remains the most used stop codon. In the AT-rich DNA of C. burnetii, A or T tend to occur together, forming A or T tracks.

Bacterial Proteins↗