scholarly journals Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes

2021 ◽  
Author(s):  
Brian R. Morton
Keyword(s):  
Codon Usage ◽  
Significant Role ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Context Effects ◽  
Chloroplast Genes ◽  
Mutation Bias ◽  
Highly Expressed Genes ◽  
Context Dependent ◽  
Mutation Dynamics

AbstractTwo competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between the observed and expected codon usage when context effects are taken into consideration, with psbA being a notable exception. Overall, the data support the model that selection is not a widespread factor affecting the codon usage of angiosperm chloroplast genes and highlight the need to have an accurate model of mutational dynamics.

scholarly journals Codon usage of highly expressed genes affects proteome-wide translation efficiency

2018 ◽  
Vol 115 (21) ◽  
pp. E4940-E4949 ◽  
Author(s):  
Idan Frumkin ◽  
Marc J. Lajoie ◽  
Christopher J. Gregg ◽  
Gil Hornung ◽  
George M. Church ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Protein Translation ◽  
Translation Efficiency ◽  
Synonymous Codons ◽  
Codon Composition ◽  
Theoretical Predictions ◽  
Highly Expressed Genes

Although the genetic code is redundant, synonymous codons for the same amino acid are not used with equal frequencies in genomes, a phenomenon termed “codon usage bias.” Previous studies have demonstrated that synonymous changes in a coding sequence can exert significantciseffects on the gene’s expression level. However, whether the codon composition of a gene can also affect the translation efficiency of other genes has not been thoroughly explored. To study how codon usage bias influences the cellular economy of translation, we massively converted abundant codons to their rare synonymous counterpart in several highly expressed genes inEscherichia coli. This perturbation reduces both the cellular fitness and the translation efficiency of genes that have high initiation rates and are naturally enriched with the manipulated codon, in agreement with theoretical predictions. Interestingly, we could alleviate the observed phenotypes by increasing the supply of the tRNA for the highly demanded codon, thus demonstrating that the codon usage of highly expressed genes was selected in evolution to maintain the efficiency of global protein translation.

Analysis of codon usage bias of chloroplast genes in Oryza species

Planta ◽  
2020 ◽  
Vol 252 (4) ◽  
Author(s):  
Supriyo Chakraborty ◽  
Sophiarani Yengkhom ◽  
Arif Uddin
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Oryza Species ◽  
Chloroplast Genes

scholarly journals Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis

2010 ◽  
Vol 7 (1) ◽  
pp. 131-135 ◽  
Author(s):  
Laura R. Emery ◽  
Paul M. Sharp
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Trna Genes ◽  
Strongly Correlated ◽  
Methanococcus Maripaludis ◽  
E Coli ◽  
Moderate Growth ◽  
Optimal Codons ◽  
Genome Wide ◽  
Highly Expressed Genes

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis . Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli , the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli : in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.

scholarly journals Codon Usage Bias in Two Hemipteran Insect Species: Bemisia tabaci and Homalodisca coagulata

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Jyotika Sharma ◽  
Supriyo Chakraborty ◽  
Arif Uddin
Keyword(s):  
Codon Usage ◽  
Bemisia Tabaci ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Insect Species ◽  
Codon Usage Pattern ◽  
Mutation Pressure ◽  
Homalodisca Coagulata ◽  
Highly Expressed Genes ◽  
Hemipteran Insect

Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species.

scholarly journals Comparisons of Coding and Noncoding Sequences to infer the Origin of Codon usage Bias

2017 ◽  
Author(s):  
Prashant Mainali ◽  
Sobita Pathak
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Mutation Bias ◽  
Translation Process ◽  
Noncoding Regions ◽  
Coding Regions ◽  
Synonymous Codons ◽  
Shed Light

ABSTRACTCodon usage bias is the preferential use of the subset of synonymous codons during translation. In this paper, the comparisons of normalized entropy and GC content between the sequence of coding regions of Escherichia coli k12 and noncoding regions (ncRNA, rRNA) of various organisms were done to shed light on the origin of the codon usage bias.The normalized entropy of the coding regions was found significantly higher than the noncoding regions, suggesting the role of the translation process in shaping codon usage bias. Further, when the position specific GC content of both coding and noncoding regions was analyzed, the GC2 content in coding regions was lower than GC1 and GC2 while in noncoding regions, the GC1, GC2, GC3 contents were approximately equal. This discrepancy is explained by the biased mutation coupled with the presence and absence of selection pressure. The accumulation of CG content occurs in the sequences due to mutation bias in DNA repair and recombination process. In noncoding regions, the mutation is harmful and thus, selected against while due to the degeneracy of codons in coding regions, a mutation in GC3 is neutral and hence, not selected. Thus, the accumulation of GC content occurs in coding regions, and thus codon usage bias occurs.

scholarly journals A New Look at Codon Usage and Protein Expression

10.29007/d4tz ◽  
2019 ◽  
Author(s):  
Gabriel Wright ◽  
Anabel Rodriguez ◽  
Patricia Clark ◽  
Scott Emrich
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Empirical Data ◽  
Codon Usage Bias ◽  
Elongation Rate ◽  
Translation Rate ◽  
Translation Elongation ◽  
Promising Alternative ◽  
Highly Expressed Genes ◽  
Adaptation Index

%MinMax, a model of intra-gene translational elongation rate, relies on codon usage frequencies. Historically, %MinMax has used tables that measure codon usage bias for all genes in an organism, such as those found at HIVE-CUT. In this paper, we provide evidence that codon usage bias based on all genes is insufficient to accurately measure absolute translation rate. We show that alternative ”High-φ” codon usage tables, generated by another model (ROC-SEMPPR), are a promising alternative. By creating a hybrid model, future codon usage analyses and their applications (e.g., codon harmonization) are likely to more accurately measure the ”tempo” of translation elongation. We also suggest a High- φ alternative to the Codon Adaptation Index (CAI), a classic metric of codon usage bias based on highly expressed genes. Significantly, our new alternative is equally well correlated with empirical data as traditional CAI without using experimentally determined expression counts as input.

Schistosoma mansoni: patterns of codon usage and bias

Parasitology ◽  
1995 ◽  
Vol 110 (1) ◽  
pp. 53-60 ◽  
Author(s):  
J. T. Ellis ◽  
D. A. Morrison
Keyword(s):  
Multidimensional Scaling ◽  
Schistosoma Mansoni ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Significant Heterogeneity ◽  
Metric Multidimensional Scaling

Codon usage and bias has been examined in 20 genes ofSchistosoma mansoni. Significant heterogeneity was detected in the patterns of codon usage and bias among genes by metric multidimensional scaling and three general indictors of bias (GC3S, Ncand B). In keeping with observations on sporozoan parasites, codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were over or under-represented in the sequences.

scholarly journals Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Viruses ◽  
2013 ◽  
Vol 5 (1) ◽  
pp. 162-181 ◽  
Author(s):  
Daniel Cardinale ◽  
Kate DeRosa ◽  
Siobain Duffy
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Plant Viruses ◽  
Translational Selection
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