scholarly journals Codon usage bias and environmental adaptation in microbial organisms

2021 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Principal Component ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

Codon usage bias in prokaryotic genomes and environmental adaptation

2020 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Environmental Adaptation ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
The Impact

AbstractIn each genome synonymous codons are used with different frequencies; this phenomenon is known as codon usage bias. The preferred codons tend to correspond to the most highly expressed tRNAs. It had been known that 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 relationship between codon usage bias and the phenotypic traits of 615 prokaryotic organisms. Principal component analysis revealed that prokaryotes with a specific phenotypic characteristic and living in similar environmental conditions have similar codon preferences, accessed by the Relative Synonymous Codon Usage (RSCU), and a similar tRNA availability gauged by the tRNA gene copy number (tGCN). In addition, by measuring the average tRNA adaptation index (tAI) for each genome, we discovered that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, exhibit lower extents of translational efficiency, consistent with their need to adapt to different environments.This is the first large-scale study that examines the role of translational efficiency in the environmental adaptation of prokaryotes. Our results show that synonymous codon choices might be under strong translational selection, adapting the codons to the tRNA pool to different extents depending on the organism’s lifestyle needs.

scholarly journals Analysis of codon usage bias of classical swine fever virus

2021 ◽  
pp. 1450-1458
Author(s):  
Sharanagouda S. Patil ◽  
Uma Bharathi Indrabalan ◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Bibek Ranjan Shome
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Principal Component ◽  
Infectious Agent ◽  
Classical Swine Fever ◽  
Economic Loss ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Coding Regions

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

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.

Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains

2011 ◽  
Vol 57 (12) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xue Lian Luo ◽  
Jian Guo Xu ◽  
Chang Yun Ye
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Shigella Flexneri ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Mutational Pressure ◽  
E Coli ◽  
Shigella Flexneri 2A ◽  
Usage Patterns

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

scholarly journals Characteristics of synonymous codon usage bias in the beginning region of West Nile virus

2014 ◽  
Vol 13 (3) ◽  
pp. 7347-7355 ◽  
Author(s):  
X.X. Ma ◽  
Y.P. Feng ◽  
J.L. Liu ◽  
L. Chen ◽  
Y.Q. Zhao ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
West Nile ◽  
In The Beginning ◽  
Synonymous Codon Usage Bias

scholarly journals Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1087 ◽  
Author(s):  
Sheng-Lin Shi ◽  
Run-Xi Xia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Effective Number ◽  
Bias Analysis ◽  
The Family ◽  
Usage Patterns ◽  
Codon Positions ◽  
Effective Number Of Codons

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

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