Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation. (Q39939460)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19822731%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

title

Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation (English)

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9 February 2020

2

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9 February 2020

author name string

Michael A Gilchrist

series ordinal

1

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9 February 2020

Russell Zaretzki

series ordinal

3

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9 February 2020

language of work or name

English

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publication date

12 October 2009

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9 February 2020

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9 February 2020

volume

183

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9 February 2020

issue

4

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9 February 2020

page(s)

1493-1505

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A review of techniques for parameter sensitivity analysis of environmental models

9 February 2020

cites work

1 reference

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Fidelity at the molecular level: lessons from protein synthesis

22 September 2017

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The impact of the nucleosome code on protein-coding sequence evolution in yeast

22 September 2017

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22 September 2017

Selection on Codon Bias

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Investigating protein-coding sequence evolution with probabilistic codon substitution models

22 September 2017

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Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

22 September 2017

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Recent and ongoing selection in the human genome

22 September 2017

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Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster

22 September 2017

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Synonymous codon usage in Escherichia coli: selection for translational accuracy.

22 September 2017

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Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

22 September 2017

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Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes

22 September 2017

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Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans

22 September 2017

1 reference

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Hearing silence: non-neutral evolution at synonymous sites in mammals

22 September 2017

1 reference

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Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

22 September 2017

1 reference

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The application of statistical physics to evolutionary biology

22 September 2017

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Dissecting eukaryotic translation and its control by ribosome density mapping

22 September 2017

1 reference

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

22 September 2017

1 reference

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Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons

22 September 2017

1 reference

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Tissue-specific codon usage and the expression of human genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon usage between genomes is constrained by genome-wide mutational processes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Translational selection and yeast proteome evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Ribosome recycling, diffusion, and mRNA loop formation in translational regulation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Population, evolutionary and genomic consequences of interference selection

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Gradients in nucleotide and codon usage along Escherichia coli genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Predicted highly expressed genes of diverse prokaryotic genomes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Studies on codon usage in Entamoeba histolytica

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Shutdown in protein synthesis due to the expression of mini-genes in bacteria.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Maximizing transcription efficiency causes codon usage bias

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

The effects of mutation and natural selection on codon bias in the genes of Drosophila

22 September 2017

1 reference

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A codon-based model of nucleotide substitution for protein-coding DNA sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

22 September 2017

Codon selection in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon usage and tRNA content in unicellular and multicellular organisms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Compositional constraints and genome evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

The 'effective number of codons' used in a gene

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

The selection-mutation-drift theory of synonymous codon usage

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Translational accuracy and the fitness of bacteria

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Synthesis and degradation of termination and premature-termination fragments of β-galactosidase in vitro and in vivo

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

The signature of selection mediated by expression on human genes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

The accumulation as peptidyl-transfer RNA of isoaccepting transfer RNA families in Escherichia coli with temperature-sensitive peptidyl-transfer RNA hydrolase

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Selective charging of tRNA isoacceptors explains patterns of codon usage.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Reduced natural selection associated with low recombination in Drosophila melanogaster.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Rates of aminoacyl-tRNA selection at 29 sense codons in vivo.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Processivity errors of gene expression in Escherichia coli.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon usage divergence of homologous vertebrate genes and codon usage clock

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Nearly neutrality and the evolution of codon usage bias in eukaryotic genomes

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Genomic choice of codons in 16 microbial species.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

20 August 2018

1 reference

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Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Codon adaptation index as a measure of dominating codon bias.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: compositional constraints and translational selection.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2787434

Factors affecting the efficiency of protein synthesis in Escherichia coli. Production of a polypeptide of more than 6000 amino acid residues.

20 August 2018

1 reference

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Translational selection and molecular evolution

20 August 2018

1 reference

12 December 2020

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting tran

1 reference

12 December 2020

The evolution of base composition and phylogenetic inference

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12 December 2020

A model of protein translation including codon bias, nonsense errors, and ribosome recycling

1 reference

12 December 2020

Inferring lifestyle from gene expression patterns

1 reference

12 December 2020

Translational selection on codon usage in Xenopus laevis

1 reference

12 December 2020

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

1 reference

12 December 2020

Free fitness that always increases in evolution

1 reference

12 December 2020

Energy constraints on the evolution of gene expression

1 reference

12 December 2020

10.1534/GENETICS.109.108209

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19822731%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19822731%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

19822731

1 reference