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

Musto, Héctor; Romero, Héctor; Zavala, Alejandro

doi:10.1099/mic.0.26063-0

Cited by 29 publications

(19 citation statements)

References 37 publications

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“…The average GCcontent of the total of 2,744 C. perfringens genes investigated was 29.9% (below the average AU content), while the average GC3s content was lower at 25.6%. These results are consistent with the GC and AU contents of C. acetobutylicum [15].…”

Section: Discussionsupporting

confidence: 81%

Analysis of Codon Bias on Clostridium Perfringens Del1 Genome

Chen¹,

Bai²,

Wang³

et al. 2018

Proceedings of the 2017 2nd International Conference on Biological Sciences and Technology (BST 2017)

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Abstract. Clostridium perfringens is a conditional pathogen, which widely exists in the nature water, soil, intestinal tract, and serious threat to public health and safety. In this study, the codon usage of Clostridium perfringens was examined. CDS sequences of 2744 high confidence protein coding genes were selected from Clostridium perfringens Genome Database. Their GC content of these genes ranged from 14.7% to 41.9%, with the average of 29.9% for whole genome. The frequency of G or C in the third position of synonymous codon was 25.6%, which was lower than that of A or T. The effective number of codon(ENC) of Clostridium perfringens genome ranged from 26.9 to 61.0,with the average of 39.9. Clostridium perfringens prefer codons ending in A/T. The ENC values of each gene significantly positive correlated with its C3s, G3s, GC3s and GC content (r=0.674, 0.738, 0.780 and 0.368, respectively, p<0.01). However, ENC showed significant negative correlations with T3s, respectively, p<0.01). A total of 27 optimal codons were found from Clostridium perfringens genome, all of which the third position of synonymous codon was A or T.

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Section: Discussionsupporting

confidence: 81%

Analysis of Codon Bias on Clostridium Perfringens Del1 Genome

Chen¹,

Bai²,

Wang³

et al. 2018

Proceedings of the 2017 2nd International Conference on Biological Sciences and Technology (BST 2017)

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“…In other words, codons with high frequencies in low-expression genes are not the same as the ones preferred in high-expression genes. Along with explaining these previously described patterns (35)(36)(37), we quantify the changes in codon frequencies with gene expression.…”

Section: Resultsmentioning

confidence: 99%

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

Shah

Gilchrist

2011

Proc. Natl. Acad. Sci. U.S.A.

155

180

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The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved. Using a nested model of protein translation and population genetics, we show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation. The correlation between observed codon counts within individual genes and our model predictions is 0.96. Although a variety of factors shape patterns of CUB at the level of individual sites within genes, our results suggest that selection for efficient ribosome usage is a central force in shaping codon usage at the genomic scale. In addition, our model allows direct estimation of codon-specific mutation rates and elongation times and can be readily applied to any organism with highthroughput expression datasets. More generally, we have developed a natural framework for integrating models of molecular processes to population genetics models to quantitatively estimate parameters underlying fundamental biological processes, such a protein translation.ribosome overhead cost | protein production rate F or many organisms, the preferential usage of certain codons, commonly referred to as codon usage bias (CUB), is strongly correlated with corresponding tRNA abundances and expression levels (1, 2). Explanations for these correlations abound; the most favored ones include selection against translational errors (3-5), selection for translational efficiency (6-8), effects on protein folding (9), and stability of mRNA secondary structures (10, 11). Because different combinations of these factors could lead to very similar patterns of codon usage, their relative importance in shaping the evolution of CUB is unknown (10, 12, 13). We believe that this uncertainty over their relative importance is, in large part, attributable to a lack of mechanistic models of processes hypothesized to give rise to these patterns (exceptions are found in refs. 5, 6, 13, and 14). Although most theories of codon usage predict that the degree of bias in codon usage should increase with gene expression (1, 4, 15), they lack any specific quantitative predictions about the rate and nature of these changes. This is because most commonly used indices of CUB, such as frequency of optimal codons (F op ) (1), codon adaptation index (CAI) (16), and codon bias index (CBI) (17), are both heuristic and aggregate measures of CUB and fail to define explicitly the factors responsible for the evolution of CUB. In contrast, we show that a mechanistic model of protein translation that explicitly includes the effects of biased mutation, genetic drift, and selection for efficient ribosome usage...

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“…Third, for some amino acids, the identity of the translationally optimal codon varies among species. For example, in Clostridium perfringens, the codons heavily used in highly expressed genes (Musto et al 2003) differ from those in E. coli (table 1) for six amino acids. These differences are correlated with changes in tRNA populations.…”

Section: Variation In Codon Usage Bias Among Bacteriamentioning

confidence: 99%

Forces that influence the evolution of codon bias

Sharp

Emery

Zeng

2010

Phil. Trans. R. Soc. B

322

246

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The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the variation among species appears to be due to biased patterns of mutation. The strength of selection on codon usage can be estimated by two different approaches. First, the extent of bias in favour of translationally optimal codons in highly expressed genes, compared to that in genes where selection is weak, reveals the longterm effectiveness of selection. Here we show that the strength of selected codon usage bias is highly correlated with bacterial growth rate, suggesting that selection has favoured translational efficiency. Second, the pattern of bias towards optimal codons at polymorphic sites reveals the ongoing action of selection. Using this approach we obtained results that were completely consistent with the first method; importantly, the frequency spectra of optimal codons at polymorphic sites were similar to those predicted under an equilibrium model. Highly expressed genes in Escherichia coli appear to be under continuing strong selection, whereas selection is very weak in genes expressed at low levels.

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

Cited by 29 publications

References 37 publications

Analysis of Codon Bias on Clostridium Perfringens Del1 Genome

Analysis of Codon Bias on Clostridium Perfringens Del1 Genome

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

Forces that influence the evolution of codon bias

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