Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 The effect of context on synonymous codon usage in genes with low codon usage bias.

Literature DB >> 2190183

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

Abstract

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.

Entities: Species

Mesh：

Substances：
Codon
RNA, Messenger

Year: 1990 PMID： 2190183 PMCID： PMC330812 DOI： 10.1093/nar/18.10.2869

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

19 in total

1. Nonrandom utilization of codon pairs in Escherichia coli.

Authors: G A Gutman; G W Hatfield
Journal: Proc Natl Acad Sci U S A Date: 1989-05 Impact factor: 11.205

2. Coevolution of codon usage and transfer RNA abundance.

Authors: M Bulmer
Journal: Nature Date: 1987 Feb 19-25 Impact factor: 49.962

3. Directional mutation pressure and neutral molecular evolution.

Authors: N Sueoka
Journal: Proc Natl Acad Sci U S A Date: 1988-04 Impact factor: 11.205

4. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

Authors: P M Sharp; W H Li
Journal: Nucleic Acids Res Date: 1987-02-11 Impact factor: 16.971

5. Sense codons are found in specific contexts.

Authors: M Yarus; L S Folley
Journal: J Mol Biol Date: 1985-04-20 Impact factor: 5.469

6. Codon contexts in enterobacterial and coliphage genes.

Authors: M Gouy
Journal: Mol Biol Evol Date: 1987-07 Impact factor: 16.240

7. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

Authors: D C Shields; P M Sharp
Journal: Nucleic Acids Res Date: 1987-10-12 Impact factor: 16.971

8. An evolutionary perspective on synonymous codon usage in unicellular organisms.

Authors: P M Sharp; W H Li
Journal: J Mol Evol Date: 1986 Impact factor: 2.395

9. Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation.

Authors: E G Shpaer
Journal: J Mol Biol Date: 1986-04-20 Impact factor: 5.469

10. Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis.

Authors: G J Phillips; J Arnold; R Ivarie
Journal: Nucleic Acids Res Date: 1987-03-25 Impact factor: 16.971

20 in total

1. The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?

Authors: N G Smith; L D Hurst
Journal: Genetics Date: 1999-06 Impact factor: 4.562

2. Expression of the Staphylococcus hyicus lipase in Lactococcus lactis.

Authors: S Drouault; G Corthier; S D Ehrlich; P Renault
Journal: Appl Environ Microbiol Date: 2000-02 Impact factor: 4.792

Review 3. Codon context.

Authors: R H Buckingham
Journal: Experientia Date: 1990-12-01

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

1. Nonrandom utilization of codon pairs in Escherichia coli.

2. Coevolution of codon usage and transfer RNA abundance.

3. Directional mutation pressure and neutral molecular evolution.

4. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

5. Sense codons are found in specific contexts.

6. Codon contexts in enterobacterial and coliphage genes.

7. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

8. An evolutionary perspective on synonymous codon usage in unicellular organisms.

9. Constraints on codon context in Escherichia coli genes. Their possible role in modulating the efficiency of translation.

10. Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis.

1. The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?

2. Expression of the Staphylococcus hyicus lipase in Lactococcus lactis.

Review 3. Codon context.

4. Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes.

5. Selection on GGU and CGU codons in the high expression genes in bacteria.

6. Decoding with the A:I wobble pair is inefficient.

7. Codon bias in Escherichia coli: the influence of codon context on mutation and selection.

8. Evidence of bias towards buffered codons in human transcripts.

9. Synonymous substitution rates in enterobacteria.

10. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases.