Translational selection and molecular evolution

Akashi, Hiroshi; Eyre‐Walker, Adam

doi:10.1016/s0959-437x(98)80038-5

Cited by 291 publications

(310 citation statements)

References 66 publications

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“…Akashi has reported significantly higher frequency of preferred codons at conserved amino acids than at non-conserved ones in fruit flies [41]. Akashi [42] has also shown that in yeast there is a correlation between tRNA concentration and corresponding amino acid content that is stronger in highly expressed genes than in genes with low expression levels. Based on those findings, the translation accuracy hypothesis states that variations in the translation accuracy of different codons lead to selection of amino acids with better (or optimal) codons [42] and to counter-selecting non-synonymous changes leading to sub-optimal codons [43]; this in turn reduces the rate of protein evolution.…”

Section: R E T R a C T E Dmentioning

confidence: 99%

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Park

Choi

2009

FEBS Letters

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Edited by Takashi Gojobori Keywords:Protein evolutionary rate Functional hypothesis Mistranslation-induced protein misfolding hypothesis Translational robustness Expression abundance a b s t r a c t Protein evolutionary rates have been presumed to be mostly determined by the density of functionally important amino acids in a given protein. They have been shown to correlate with variables intuitively related to functional importance of proteins, such as protein dispensability and protein-protein interactions. Surprisingly, the best correlate of the evolutionary rates has turned out to be not the functional importance of a protein, but the expression level of the protein. Drummond and Wilke suggest that the dominant role of expression levels in slowing the rate of protein evolution stems from a selection pressure against mistranslation-induced protein misfolding. We will review current evidence for and against different hypotheses on determining evolutionary rates.

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Section: R E T R a C T E Dmentioning

confidence: 99%

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Park

Choi

2009

FEBS Letters

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“…This was expected, as GC3 content and codon usage are known to be correlated. It should be noted, that both synonymous and non-synonymous features of the ORF are known to be related to protein function and expression [31][32][33][37][38][39][40][41] ; thus, our choice of CUFS attempts to capture and integrate as many as possible of the underlying signals in the coding sequence, for a better representation of the functional interactions between genes.…”

Section: Resultsmentioning

confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

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“…Codon bias. Codon bias is thought to enhance the efficiency and/or accuracy of translation [99][100][101] and seems to be maintained by mutation-selection-drift balance [101][102][103][104] . Across the 12 Drosophila genomes, there is more codon bias in the Sophophora subgenus than in the Drosophila subgenus, and a previously noted [105][106][107][108][109] striking reduction in codon bias in D. willistoni 110,111 (Fig.…”

Section: Articlesmentioning

confidence: 99%

Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,816

1,041

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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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Translational selection and molecular evolution

Cited by 291 publications

References 66 publications

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

RETRACTED: Why proteins evolve at different rates: The functional hypothesis versus the mistranslation‐induced protein misfolding hypothesis

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Evolution of genes and genomes on the Drosophila phylogeny

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