Analysis of Synonymous Codon Usage in the US5 Gene of Duck Plague Virus

2013 ◽  
Vol 641-642 ◽  
pp. 606-614
Author(s):  
Xiao Huan Hu ◽  
Ming Shu Wang ◽  
An Chun Cheng
Keyword(s):  
Codon Usage ◽  
Genomic Library ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
Yeast Expression System ◽  
Synonymous Codons ◽  
Duck Plague Virus ◽  
Compositional Constraint ◽  
On Line

The Duck Plague Virus (DPV) US5 gene was identified by constructing the DPV genomic library, the synonymous codon usage in the US5 gene of DPV and 11 reference herpesviruses have been investigated by using the CodonW 1.4 program, CUSP (create a codon usage table) program and CHIPS (calculated ENC value) of EMBOSS (The European Molecular Biology Open Software Suite). The results reveals that the synonymous codons with A and T at the third codon positon have widely usage in the codon of US5 gene of DPV. G + C compositional constraint is the main factor that determines the codon usage bias in US5 gene. In addition, rare condons analysis showed that there are 75 rare condons (13.9%) in the ORF of the DPV US5 gene on line (http//:www.kazusa.or.jp/codon), There were 20 codons showing distinct usage differences between DPV with Escherichia coli, 19 between DPV and yeast, 25 between DPV and Human. Therefore the yeast expression system may be suitable for the expression of DPV US5 gene.

Characterization of Synonymous Codon Usage Bias in the UL1 Gene of Duck Plague Virus

2013 ◽  
Vol 641-642 ◽  
pp. 693-700
Author(s):  
Ling Jie Zuo ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
E Coli ◽  
Synonymous Codons ◽  
Compositional Constraint ◽  
Main Factor

In this study, we calculated the codon usage bias in DPV CHv UL1 gene and performed a comparative analysis of synonymous codon patterns in UL1 of DPV CHv strain and other 19 reference herpesviruses. The results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL1 gene of DPV CHv. G + C compositional constraint was the main factor that determined the codon usage bias in UL1 gene. In addition, the codon usage bias of DPV CHv UL1 gene was compared with those of E. coli, yeast and human. There are 25 codons showing distinct usage differences between DPV and E. coli, 26 codons between DPV and yeast, and 21 codons between DPV and human. Therefore, the Human expression system is more suitable for heterologous expression of the DPV UL1 gene.

Analysis of Synonymous Codon Usage in the US2 Gene of Duck Plague Virus

2013 ◽  
Vol 647 ◽  
pp. 220-226
Author(s):  
Jie Gao ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
Eukaryotic Expression ◽  
Eukaryotic Expression System ◽  
Duck Plague Virus

The codon usage bias of DPV-CHv US2 gene (GenBank Accession No. EU195086) will be analysed in this study, and a comparative analysis of DPV-CHv US2 gene and those of other 15 alphaherpesvirus US2 genes was performed. We also analysed the RSCU, ENC, GC3s value of those US2 genes in herpesvirus, some data were analysed specifically in the article. Consequently, we found that the eukaryotic expression system——the yeast is more suitable for the expression of DPV US2 gene.

Characterization of Codon Usage Bias in the RA Ragb/SusD Gene

2013 ◽  
Vol 641-642 ◽  
pp. 654-665
Author(s):  
Si Si Yang ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Target Genes ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
Effective Number ◽  
E Coli ◽  
Synonymous Codons ◽  
Effective Number Of Codons

The analysis on codon usage bias of Riemerella anatipestifer (RA) RagB/SusD gene (GenBank accession No. NC_017045.1) may improve our understanding of the evolution and pathogenesis of RA and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. In this study, the synonymous codon usage in the RagB/SusD gene of RA and 19 reference bacteroidetes have been investigated. The results showed that codon usage bias in the RagB/SusD gene was strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in RagB/SusD gene of bacteroidetes was constrained by the G + C content. The codon adaptation index (CAI), effective number of codons (ENC), and GC3S values indicated synonymous codon usage bias in the RagB/SusD gene of bacteroidetes, and this synonymous bias was correlated with host evolution. The phylogentic analysis suggested that RagB/SusD was evolutionarily closer to Ornithobacterium rhinotracheale and that there was no significant deviation in codon usage in different bacteroidetes. There are 25 codons showing distinct usage differences between RA RagB/SusD and E. coli, 30 between RA RagB/SusD and Homo sapiens, 26 codons between RA RagB/SusD and yeast. Therefore the yeast and E. coli expression system may be suitable for the expression of RA RagB/SusD gene if some codons could be optimized.

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.

Analysis of Synonymous Codon Usage in the UL14 Gene of Duck Enteritis Virus

2012 ◽  
Vol 424-425 ◽  
pp. 680-689
Author(s):  
Fang Jie Li ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Synonymous Codon ◽  
Expression System ◽  
Synonymous Codon Usage ◽  
Its Gene ◽  
Close Relationship ◽  
Enteritis Virus ◽  
High Level

The codon usage of DEV UL14 gene was analyzed by using CAI, CHIPS and CUSP program of EMBOSS. The results showed that codon usage bias in the DEV UL14 gene was a high level of diversity in codon usage bias towards the synonymous with C and G at the third codon position existed for coding the Glu, Gly, Asn and Tyr amino acids. The cluster analysis demonstrated that the codon usage bias of DEV UL14 gene has a very close relationship with its gene function and gene type. In addition, the E.coli expression system is more suitable for heterologous expression of the DEV UL14 gene.

Characterization of Codon Usage Bias in UL13 Gene of the Duck Plague Virus

2011 ◽  
Vol 393-395 ◽  
pp. 641-650
Author(s):  
Xi Xia Hu ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Expression System ◽  
Expression Systems ◽  
Yeast Expression System ◽  
E Coli ◽  
Synonymous Codons ◽  
Suitable Expression

A comprehensive analysis of codon usage bias of DPV UL13 gene (GenBank Accession No. EU195098) was performed to provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting suitable expression systems to improve the expression of UL13 genes. Our study showed that codon usage bias of DPV UL13 gene strongly prefered to the synonymous with A and T at the third codon position. And ENC value and GC3s contents of the codon usage bias of UL13 gene in DPV were significantly different compared with those in other 21 reference herpesviruses. The phylogentic analysis about the putative protein of DPV UL13 and the 21 reference herpesviruses revealed that DPV was evolutionarily closer to the AnHV-1. In addition, the codon usage bias of DPV UL13 gene was compared with those of E. coli, yeast and human. There are 23 codons showing distinct usage differences between DPV and E. coli, 12 codons between DPV and yeast, 21 codons between DPV and human. Therefore, the yeast expression system is more appropriate for heterologous expression of the DPV UL13 gene.

scholarly journals Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene

Intervirology ◽  
2009 ◽  
Vol 52 (5) ◽  
pp. 266-278 ◽  
Author(s):  
Ming-Sheng Cai ◽  
An-Chun Cheng ◽  
Ming-Shu Wang ◽  
Li-Chan Zhao ◽  
De-Kang Zhu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Duck Plague Virus ◽  
Synonymous Codon Usage Bias
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