Analysis of synonymous codon usage in foot-and-mouth disease virus

Zhou, Jinlin; Zhang, Jie; Chen, Hao-tai; Ma, Li-na; Liu, Yongsheng

doi:10.1007/s11259-010-9359-4

Cited by 42 publications

(40 citation statements)

References 40 publications

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“…In general, previous reports have indicated that many viruses, including foot-andmouth disease viruses, influenza A virus subtype H5N1, severe acute respiratory syndrome Coronavirus (SARSCoV), and human bocavirus, preferentially use codons ending in C or G (Zhao et al, 2008;Zhou et al, 2010). However, in the case of the EV71 virus, only a few studies have been performed on the synonymous codon usage pattern influencing its evolution.…”

Section: Discussionmentioning

confidence: 99%

Overall codon usage pattern of enterovirus 71

R¹,

Liu²,

Wang³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Hand, foot, and mouth disease (HFMD) is a systemic illness in children and is usually caused by enterovirus 71 (EV71). To provide new insights into the genetic features of EV71 and the relationship between the overall codon usage pattern of this virus and that of humans, values for relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and nucleotide composition were calculated and analyzed. The relationship between ENC values and (G+C) 3 % suggests that, although nucleotide composition plays an important role in shaping the overall codon usage pattern of this virus, other factors also affect this pattern. In addition, the negative correlation between the CAI value and (G+C) 3 % suggests that the secondary structure of the EV71 coding sequence caused by its nucleotide composition can affect gene expression. Moreover, there was no significant correlation between ENC and CAI, suggesting that gene expression does not play a role in shaping the overall codon usage pattern of EV71. The overall codon usage pattern of the EV71 virus is only partly similar to the general codon pattern of human, suggesting that, although EV71 has co-evolved with humans for extended periods, mutation pressure played an important role in shaping the virus's overall codon 337 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (1): 336-343 (2014) Enterovirus 71 related to hand, foot and mouth disease usage pattern. These results revealed that the EV71 virus has developed a subtle strategy during evolution for adapting to environmental changes in its host cells solely by means of mutation pressure.

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Section: Discussionmentioning

confidence: 99%

Overall codon usage pattern of enterovirus 71

R¹,

Liu²,

Wang³

et al. 2014

Genet. Mol. Res.

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“…To investigate the pattern of relative synonymous codon usage (RSCU) without the influence of amino acid composition among all samples, the RSCU values of codons in each ORF of NDV, H5N2 and DHV were calculated according to the formula of previous reports [31,32].…”

Section: Composition Analysis Of Coding Region Of 31 Ndv Strainsmentioning

confidence: 99%

Analysis of codon usage in Newcastle disease virus

et al. 2011

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In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and dinucleotide were used to investigate codon usage pattern of each protein-coding gene and genome among 31 Newcastle disease virus (NDV) isolates. The result shows that the overall extent of codon usage bias in NDV is low (mean ENC = 56.15 > 40). The good correlation between the (C + G)(12)% and (G + C)(3)% suggests that the mutational pressure, rather than natural selection, is the main factor that determines the codon usage bias and base component in NDV. It is observed that synonymous codon usage pattern in NDV genes is gene function and geography specific, but not host specific. By contrasting synonymous codon usage patterns of different NDV isolates, we suggest that more than one genotype of NDV circulates in waterfowl in USA; and gene length has no significant effect on the variations of synonymous codon usage in these virus genes. CpG under-represented is a characteristic for NDV to fit in its host. These results not only provide an insight into the variation of codon usage pattern among the genomes of NDV, but also may help in understanding the processes governing the evolution of NDV.

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“…Additionally, there is a simple method that supposes that statistically equal and random usage of all available synonymous codons is the "neutral point" (RSCU 0 = 1.00) for the development of serotype-specific codon usage (Zhou et al, 2010). CUB:…”

Section: Analysis Of Codon Usage Biasmentioning

confidence: 99%

“…It is accepted that information on protein sequences and the formation of codon usage bias (CUB) arises from the non-randomness of nucleotide compositions (Lloyd and Sharp, 1992;Xie and Ding, 1998). In general, translation selection and compositional constraints under mutational pressure are thought to be major factors accounting for codon usage variation among genomes in microorganisms (Karlin and Mrázek, 1996;Lesnik et al, 2000;Zhou et al, 2006, Zhou et al, 2010. In some microorganisms, compared with translation selection in nature, mutation pressure plays an important role in the synonymous codon usage pattern (Zhou et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis

Liu

2016

Genet. Mol. Res.

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ABSTRACT. To provide a new perspective on the evolutionary characteristics shaping the genetic diversity of Haemophilus parasuis biofilms, the relative synonymous codon usage values, codon usage bias values, effective number of codons (ENC) values, codon adaptation index (CAI) values, and the base components were calculated. Our objective was to implement a comparative analysis to evaluate the dynamic evolution of biofilm-associated genes in H. parasuis. The analysis of genetic diversity provides evidence that some biofilmassociated genes have similar genetic features. However, other genes show some variations in genetic direction. Furthermore, preferential selection of the synonymous codons and amino acids is apparent in biofilm-associated genes. Additionally, the ENC and CAI data from this study all strongly suggested that biofilm-associated genes may depend on deoptimization to adapt to environmental changes, and the mutation effect of biofilm-associated genes in H. parasuis plays an important role 2 L.Y. Wang et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 15 (2): gmr.15027226 in shaping the genetic features. Our results reveal that the mutations of biofilm-associated genes form a set of sophisticated strategies for combating the environmental changes arising from the host cell in the evolution of H. parasuis.

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Analysis of synonymous codon usage in foot-and-mouth disease virus

Cited by 42 publications

References 40 publications

Overall codon usage pattern of enterovirus 71

Overall codon usage pattern of enterovirus 71

Analysis of codon usage in Newcastle disease virus

Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis

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