Factors influencing codon usage bias in genomes

Salim, Hannah M. W.; Cavalcanti, André R. O.

doi:10.1590/s0103-50532008000200008

Cited by 41 publications

(40 citation statements)

References 40 publications

(62 reference statements)

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“…Thus, codons that have the potential to form OSCs tend to be AT-rich and consequently are disproportionately prevalent in organisms with AT-rich genomes. Given that other selective forces or mutational biases determine the GC content of an organism [8,10-12], this implies that the relationship found between a codon’s usage and its propensity to form OSCs is a poor test of the predictions of the Ambush Hypothesis, as it is easily explained by the high AT content of stop codons.…”

Section: Resultsmentioning

confidence: 99%

“…Codon usage bias is known to vary between organisms and several hypotheses have been proposed to explain these differences [8]. The selection for OSCs predicted by the Ambush Hypothesis should be a very weak selective force as translational frameshifts affect a single protein product at a time, and regardless of the hypothesis, some level of OSCs is expected by chance.…”

Section: Introductionmentioning

confidence: 99%

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Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes

2013

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BackgroundIn this paper, we address the evidence for the Ambush Hypothesis. Proposed by Seligmann and Pollock, this hypothesis posits that there exists a selection for off-frame stop codons (OSCs) to counteract the possible deleterious effects of translational frameshifts, including the waste of resources and potential cytotoxicity. Two main types of study have been used to support the hypothesis. Some studies analyzed codon usage and showed that codons with more potential to create OSCs seem to be favored over codons with lower potential; they used this finding to support the Ambush Hypothesis. Another study used 342 bacterial genomes to evaluate the hypothesis directly, finding significant excesses of OSCs in these genomes.ResultsWe repeated both analyses with newer datasets and searched for other factors that could explain the observed trends. In the first case, the relative frequency of codons with the potential to create OSCs is directly correlated with the GC content of organisms, as stop codons are GC-poor. When evaluating the frequency of OSCs directly in 1,976 bacterial genomes we also detected a significant excess. However, when comparing the excess of OSCs with similarly obtained results for the frequency of out-of-frame sense codons, some sense codons have a more significant excess than stop codons.ConclusionsTwo avenues of study have been used to support the Ambush Hypothesis. Using the same methods as these previous studies, we demonstrate that the evidence in support of the Ambush Hypothesis does not hold up against more rigorous testing.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes

2013

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“…The synonymous codons are not used at equal frequencies in coding sequences in many organisms [1]. This phenomenon called 'synonymous codon usage bias (SCUB)' reflects non-uniform usage of synonymous codons encoding the same amino acid during the translation of genes to proteins [2,3].The degree of SCUB divergence varies greatly among different species and genes [4][5][6][7]. SCUB was affected by many factors, including directional mutation, neutral selection [8], GC content, synonymous substitution rate [9], tRNA abundance [10], selection for efficient translation initiation [11], codon hydropathy and DNA replication initiation site [12], gene length [13] and expression level [14], etc.…”

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confidence: 99%

“…The degree of SCUB divergence varies greatly among different species and genes [4][5][6][7]. SCUB was affected by many factors, including directional mutation, neutral selection [8], GC content, synonymous substitution rate [9], tRNA abundance [10], selection for efficient translation initiation [11], codon hydropathy and DNA replication initiation site [12], gene length [13] and expression level [14], etc.…”

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confidence: 99%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

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“…Codon usage can differ widely not only between organisms, but also within a genome and within a single gene [16,25]. A lot of factors might cause different codon usage bias and the selective forces influencing it, such as selection for optimized translation, expression, location within genes, rate of evolution, secondary structure, nucleotide composition, protein length and environment [30]. It was demonstrated that many bacteria and yeast undergo translational selection, with highly expressed genes preferentially using codons assumed to be translated faster and/or more accurately by the ribosome [11,2].…”

Section: Introductionmentioning

confidence: 99%

Codon usage bias in prokaryotic genomes and environmental adaptation

Arella

Dilucca

Giansanti

2020

Preprint

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In each genome, some codons are favored over others by selection likely because they are translated more efficiently and accurately. The selectively favored codons tend to correspond to the most highly expressed tRNAs. It has been recognized that this codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the codon usage bias of 615 prokaryotes. We found that the extent of codon usage corresponds to the environment in witch the prokaryotes live. In particular, measuring the degree of codon usage bias by the tRNA adaptation index (tAI), we obtained that organisms living in a specialized habitat have high extents of codon usage bias, consistent with their need to adapt efficiently to specific environmental constraints. Differently, organisms able to live in multiple habitats exhibit low codon usage bias as they need to adapt to various physical and chemical conditions. Our results suggest the importance of co-evolution between tRNA availability and codon usage of an organism, in relation with the environmental adaptation.

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Factors influencing codon usage bias in genomes

Cited by 41 publications

References 40 publications

Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes

Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes

Genome-wide analysis of codon usage bias in four sequenced cotton species

Codon usage bias in prokaryotic genomes and environmental adaptation

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