scholarly journals Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias

2018 ◽  
Vol 10 (2) ◽  
pp. 562-576 ◽  
Author(s):  
Saurabh Mahajan ◽  
Deepa Agashe
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Translational Selection ◽  
Selection For

scholarly journals Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Wenqi Ran ◽  
David M. Kristensen ◽  
Eugene V. Koonin
Keyword(s):  
Codon Usage ◽  
Protein Level ◽  
Codon Usage Bias ◽  
Protein Sequence ◽  
Gc Content ◽  
Protein Sequences ◽  
Microbial Evolution ◽  
Fine Tuning ◽  
Selection For ◽  
Genomic Gc Content

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

Reduced Selection for Codon Usage Bias in Drosophila miranda

2007 ◽  
Vol 64 (5) ◽  
pp. 586-590 ◽  
Author(s):  
Doris Bachtrog
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Selection For

The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti

Gene ◽  
2003 ◽  
Vol 320 ◽  
pp. 109-116 ◽  
Author(s):  
Lucı́a Peixoto ◽  
Alejandro Zavala ◽  
Héctor Romero ◽  
Héctor Musto
Keyword(s):  
Codon Usage ◽  
Sinorhizobium Meliloti ◽  
Translational Selection ◽  
Selection For

Evidence for translational selection in codon usage in Echinococcus spp.

Parasitology ◽  
2001 ◽  
Vol 123 (2) ◽  
pp. 203-209 ◽  
Author(s):  
V. FERNÁNDEZ ◽  
A. ZAVALA ◽  
H. MUSTO
Keyword(s):  
Codon Usage ◽  
Correspondence Analysis ◽  
Mutational Bias ◽  
Expression Levels ◽  
Translational Selection ◽  
Synonymous Sites ◽  
Highly Expressed Genes ◽  
Selection For ◽  
Almost All ◽  
Echinococcus Spp

We analysed the intragenomic variation in codon usage in Echinococcus spp. by correspondence analysis. This approach detected a trend among genes which was correlated with expression levels. Among the (presumed) highly expressed sequences we found an increased usage of a subset of codons, almost all of them G- or C- ending. Since an increase in these bases at the synonymous sites is against the mutational bias (these genomes are slightly A+T- rich), we conclude that codon usage in Echinococcus is the result of an equilibrium between compositional pressure and selection, the latter acting at the level of translation, mainly on highly expressed genes. This is the first report where translational selection for codon usage is detected among Platyhelminthes.

scholarly journals Variation and selection on codon usage bias across an entire subphylum

2019 ◽  
Author(s):  
Abigail L. Labella ◽  
Dana A. Opulente ◽  
Jacob L. Steenwyk ◽  
Chris Todd Hittinger ◽  
Antonis Rokas
Keyword(s):  
Codon Usage ◽  
Genetic Drift ◽  
Codon Usage Bias ◽  
Budding Yeast ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutational Bias ◽  
Translational Efficiency ◽  
Translational Selection ◽  
Yeast Genomes

AbstractVariation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid, between genes in a genome, and between genomes of different species. It is now well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural selection for translational efficiency and genetic drift, but how these processes shape patterns of codon usage bias across entire lineages remains unexplored. To address this question, we used a rich genomic data set of 327 species that covers nearly one third of the known biodiversity of the budding yeast subphylum Saccharomycotina. We found that, while genome-wide relative synonymous codon usage (RSCU) for all codons was highly correlated with the GC content of the third codon position (GC3), the usage of codons for the amino acids proline, arginine, and glycine was inconsistent with the neutral expectation where mutational bias coupled with genetic drift drive codon usage. Examination between genes’ effective numbers of codons and their GC3 contents in individual genomes revealed that nearly a quarter of genes (381,174/1,683,203; 23%), as well as most genomes (308/327; 94%), significantly deviate from the neutral expectation. Finally, by evaluating the imprint of translational selection on codon usage, measured as the degree to which genes’ adaptiveness to the tRNA pool were correlated with selective pressure, we show that translational selection is widespread in budding yeast genomes (264/327; 81%). These results suggest that the contribution of translational selection and drift to patterns of synonymous codon usage across budding yeasts varies across codons, genes, and genomes; whereas drift is the primary driver of global codon usage across the subphylum, the codon bias of large numbers of genes in the majority of genomes is influenced by translational selection.Lay Summary / Significance statementSynonymous mutations in genes have no effect on the encoded proteins and were once thought to be evolutionarily neutral. By examining codon usage bias across codons, genes, and genomes of 327 species in the budding yeast subphylum, we show that synonymous codon usage is shaped by both neutral processes and selection for translational efficiency. Specifically, whereas codon usage bias for most codons appears to be strongly associated with mutational bias and largely driven by genetic drift across the entire subphylum, patterns of codon usage bias in a few codons, as well as in many genes in nearly all genomes of budding yeasts, deviate from neutral expectations. Rather, the synonymous codons used within genes in most budding yeast genomes are adapted to the tRNAs present within each genome, a result most likely due to translational selection that optimizes codons to match the tRNAs. Our results suggest that patterns of codon usage bias in budding yeasts, and perhaps more broadly in fungi and other microbial eukaryotes, are shaped by both neutral and selective processes.

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

scholarly journals Codon usage bias in animals: disentangling the effects of natural selection, effective population size and GC-biased gene conversion

2017 ◽  
Author(s):  
N. Galtier ◽  
C. Roux ◽  
M. Rousselle ◽  
J. Romiguier ◽  
E. Figuet ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Codon Usage Bias ◽  
Effective Population ◽  
Translational Selection ◽  
Wide Range ◽  
Biased Gene Conversion

AbstractSelection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

scholarly journals Dissimilation of synonymous codon usage bias in virus–host coevolution due to translational selection

2020 ◽  
Vol 4 (4) ◽  
pp. 589-600 ◽  
Author(s):  
Feng Chen ◽  
Peng Wu ◽  
Shuyun Deng ◽  
Heng Zhang ◽  
Yutong Hou ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Translational Selection ◽  
Synonymous Codon Usage Bias

scholarly journals Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli

2016 ◽  
Vol 7 ◽  
Author(s):  
Shixiang Sun ◽  
Jingfa Xiao ◽  
Huiyong Zhang ◽  
Zhang Zhang
Keyword(s):  
Escherichia Coli ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Translational Selection ◽  
Core Genes
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