scholarly journals Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts

2018 ◽  
Vol 19 (12) ◽  
pp. 3872 ◽  
Author(s):  
Jian Tian ◽  
Qingbin Li ◽  
Xiaoyu Chu ◽  
Ningfeng Wu
Keyword(s):  
High Frequency ◽  
Synonymous Codon ◽  
Low Frequency ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Evolutionary Information ◽  
Specific Expression ◽  
Synonymous Codons ◽  
New Genes ◽  
And Function

In the natural host, most of the synonymous codons of a gene have been evolutionarily selected and related to protein expression and function. However, for the design of a new gene, most of the existing codon optimization tools select the high-frequency-usage codons and neglect the contribution of the low-frequency-usage codons (rare codons) to the expression of the target gene in the host. In this study, we developed the method Presyncodon, available in a web version, to predict the gene code from a protein sequence, using built-in evolutionary information on a specific expression host. The synonymous codon-usage pattern of a peptide was studied from three genomic datasets (Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae). Machine-learning models were constructed to predict a selection of synonymous codons (low- or high-frequency-usage codon) in a gene. This method could be easily and efficiently used to design new genes from protein sequences for optimal expression in three expression hosts (E. coli, B. subtilis, and S. cerevisiae). Presyncodon is free to academic and noncommercial users; accessible at http://www.mobioinfor.cn/presyncodon_www/index.html.

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.

Synonymous codon usage pattern analysis of Hepatitis D virus

2013 ◽  
Vol 173 (2) ◽  
pp. 350-353 ◽  
Author(s):  
Arghya Kamal Bishal ◽  
Rashmi Mukherjee ◽  
Chandan Chakraborty
Keyword(s):  
Codon Usage ◽  
Pattern Analysis ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Hepatitis D ◽  
Hepatitis D Virus

scholarly journals The selection-mutation-drift theory of synonymous codon usage.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 897-907 ◽  
Author(s):  
M Bulmer
Keyword(s):  
Codon Usage ◽  
Genetic Model ◽  
Synonymous Codon ◽  
Growth Yield ◽  
Synonymous Codon Usage ◽  
Synonymous Codons ◽  
Drift Theory ◽  
Highly Expressed Genes ◽  
Unicellular Organisms ◽  
Selection For

Abstract It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in highly expressed genes reflecting stronger selection for efficiency of translation. A population genetic model is developed taking into account population size and selective differences between synonymous codons. A biochemical model is then developed to predict the magnitude of selective differences between synonymous codons in unicellular organisms in which growth rate (or possibly growth yield) can be equated with fitness. Selection can arise from differences in either the speed or the accuracy of translation. A model for the effect of speed of translation on fitness is considered in detail, a similar model for accuracy more briefly. The model is successful in predicting a difference in the degree of bias at the beginning than in the rest of the gene under some circumstances, as observed in Escherichia coli, but grossly overestimates the amount of bias expected. Possible reasons for this discrepancy are discussed.

Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

2011 ◽  
Vol 204-210 ◽  
pp. 649-662 ◽  
Author(s):  
Ying Wu ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Yue Chen
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Duck Enteritis Virus ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
E Coli ◽  
Usage Patterns ◽  
Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus specific and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

scholarly journals Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 991
Author(s):  
Huiguang Wu ◽  
Zhengyu Bao ◽  
Chunxiao Mou ◽  
Zhenhai Chen ◽  
Jingwen Zhao
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Similarity Index ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Broad Host Range ◽  
Mutation Pressure ◽  
Porcine Astrovirus ◽  
Usage Patterns

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

scholarly journals A code within the genetic code: codon usage regulates co-translational protein folding

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Yi Liu
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Genetic Code ◽  
Synonymous Codon ◽  
Protein Structures ◽  
Translation Efficiency ◽  
Intrinsically Disordered ◽  
Synonymous Codons ◽  
Eukaryotic Organisms ◽  
And Function

Abstract The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding.

scholarly journals Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

2018 ◽  
Vol 19 (12) ◽  
pp. 4010
Author(s):  
Zhaocai Li ◽  
Wen Hu ◽  
Xiaoan Cao ◽  
Ping Liu ◽  
Youjun Shang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Family Members ◽  
Synonymous Codon Usage ◽  
Amino Acid Usage ◽  
Codon Usage Pattern ◽  
Evolutionary Trend ◽  
Mutation Pressure ◽  
Wide Range

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

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