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.

Characterization of Codon Usage Bias in the UL17 Gene of Duck Enteritis Virus

2013 ◽  
Vol 641-642 ◽  
pp. 666-674
Author(s):  
Ting Wen ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Expression System ◽  
Duck Enteritis Virus ◽  
Yeast Expression System ◽  
E Coli ◽  
Synonymous Codons ◽  
Enteritis Virus

The analysis on codon usage bias of UL17 gene of duck enteritis virus (DEV) may provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting appropriate host expression systems to improve the expression of DEV UL17 gene. In this study the results indicate that codon usage bias of DEV UL17 gene strongly preferred to the synonymous with A and T at third codon position. The ENC values and GC3S contents of the codon usage bias of UL17 genes in DEV and the 20 reference herpesviruses were obviously different. In addition, we compared the codon usage bias of DEV UL17 gene with E.coli, yeast and human. There are 25 codons showing distinct usage differences between DEV and E. coli, 17 codons between DEV and yeast, 23 codons between DEV and human. Therefore, the yeast expression system is more suitable for heterologous expression of the DEV UL17 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.

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.

Analysis of Codon Usage Pattern in the DNA Polymerase Gene of Porcine Cytomegalovirus

2011 ◽  
Vol 271-273 ◽  
pp. 514-520
Author(s):  
Yan Qun Wang ◽  
Zhi Wen Xu ◽  
Wan Zhu Guo ◽  
Feng Qin Li ◽  
Ling Zhu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Position ◽  
Expression System ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Polymerase Gene ◽  
Expression Systems ◽  
Porcine Cytomegalovirus ◽  
Synonymous Codons ◽  
Usage Preference

The analysis of the codon usage pattern of Porcine Cytomegalovirus (PCMV) DPOL gene has both theoretical and practical value in understanding the basics of molecular biology and selecting appropriate expression systems to improve the expression level. In this study, the codon usage pattern of PCMV DPOL gene and other 36 reference herperviruses were analyzed, the results showed that the codon of PCMV DPOL gene was strong bias toward the synonymous codons with G or C at the third codon position, and was closer relatively to these viruses which were classified in Betaherpesvirinae. Correlation analysis indicated that there was no obvious correlation between PCMV DPOL gene and it’s host swine, and 13 codons showed distinct usage preference between PCMV DPOL gene and H.sapiens, whereas 16 in the E.coli and 27 in the yeast. Thus the mammal expression system may be more appropriate for the expression of PCMV DPOL gene.

scholarly journals Codon Usage Bias of the Wheat Flower Development Gene WAG-2 and Other AGAMOUS Group Genes

2017 ◽  
Vol 9 (9) ◽  
pp. 56
Author(s):  
Wenhan Hu ◽  
Shuhong Wei
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Target Genes ◽  
Expression System ◽  
Functional Studies ◽  
Codon Preference ◽  
Synonymous Codons ◽  
The Difference ◽  
Relationship Of

Analyzing codon usage bias of WAG-2 gene in wheat three-pistil (TP) mutant may provide a basis for selecting the appropriate host expression systems to improve the expression of target genes. In the present study, we analyzed the codon bias of the complete coding sequence (CDS) of the WAG-2 gene in TP using Codon W program, and compared the results with AGAMOUS (AG) group genes of other plant species. Results showed that the WAG-2 gene in TP and other monocot AG group genes preferably used codons ending with G/C bases, but Arabidopsis thaliana, Nicotiana tabacum, and other dicot crops were biased toward the synonymous codons with A/T. The clustering results based on codon bias were consistent with those based on CDS of the AG group genes, indicating that the difference in codon preference of AG group genes sequences was closely associated with the genetic relationship of the species. The Euclidean distance coefficients of WAG-2 with A. thaliana and N. tabacum were 9.255 and 5.730, respectively, indicating that N. tabacum may be more suitable for the expression of WAG-2. There were 37 codons showing distinct usage differences between WAG-2 and genome of yeast, 23 between WAG-2 and Escherichia coli. Therefore, the E. coli was the superior protein expression system. These results may improve our understanding of codon usage bias and functional studies of WAG-2.

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 Synonymous Codon Usage in the R1 Gene of Duck Enteritis Virus

2013 ◽  
Vol 641-642 ◽  
pp. 701-711
Author(s):  
Guo Fu Lu ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Large Subunit ◽  
Expression System ◽  
Evolutionary Relationship ◽  
Duck Enteritis Virus ◽  
Yeast Expression System ◽  
R1 Gene ◽  
Enteritis Virus

In this paper, a corresponding analysis of the codon usage bias in the large subunit of ribonucleotide reductase (R1), encoded by UL39 gene from duck enteritis virus (DEV) CHv strain (Assigned Accession No.: EU071042) and 33 other reference herpesviruses was performed by using CAI, CHIPS and CUSP program of EMBOSS, aims to provide a basis for understanding the evolution and pathogenesis of DEV and for selecting appropriate host expression systems. The results showed that codon usage bias of DEV R1 gene strongly preferred to the synonymous with A and T at the third codon position; the phylogentic analysis revealed that DEV had a close evolutionary relationship with the avian Alphaherpesvirinae. In addition, the codon usage bias of DEV R1 gene was compared with those of E.coli, yeast and human. There are 17 codons showing distinct usage differences between DEV and E.coli, 13 codons between DEV and yeast, 20 codons between DEV and human. Therefore, the yeast expression system is more suitable for the target gene’s expression. The extent of codon usage bias in the DEV R1 gene was highly correlated with the gene expression level, therefore the results may provide useful information for the study of classification and function of the target gene.

Analysis of Codon Usage in Herpesvirus Glycoprotein B (gB) Gene

2011 ◽  
Vol 343-344 ◽  
pp. 721-728
Author(s):  
Long Jiang ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Ren Yong Jia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Pearson Correlation ◽  
Gc Content ◽  
Correlation Coefficients ◽  
Mutational Bias ◽  
Synonymous Codons ◽  
Base Position ◽  
Two Factors

Due to the degeneracy of genetic code, most amino acids are coded by more than one codon (synonymous codons). The synonymous codons are not used at equal frequencies both within and between organisms. Of the total 33 herpesvirus gB genes, approximately 9.1% of the total gB genes had low codon bias (ENC<35), 72.7% of the gB genes had high ENC values (ENC>50), indicating that these gB genes had random codon usage in herpesviruses. There might be no direct correlation between the codon usage bias and the host, which indicates that the tRNA abundance of the host was not the main factor influencing the codon usage bias. A plot of ENC vs. GC3 indicates that mutational bias may be a more important factor than tRNA abundance in determining codon usage bias of herpesvirus gB genes. Pearson correlation coefficients between the ENC value and corresponding GC%, cumulative GC% in 2nd (GC2%) and 3rd codon position (GC3%) of each herpesvirus gB gene were -0.621 (p<0.01), -0.656 (p<0.01) and -0.712 (p<0.01), respectively, which implies that significant correlations existed between them. But no significant correlations existed between ENC and cumulative GC% in 1st codon position of each herpesviral gB gene. Furthermore, significant correlations also existed between GC% and GC3% of 33 herpesvirus gB genes (r=0.856, p<0.01). So it seems that, GC content, and particularly GC content at the 3rd base position, contributing greatly to the effective number of codons, indicating that the mutational bias dominates over translational selection. Further analysis on the relationship between gene length and ENC of 33 herpesvirus gB genes demonstrated that the two factors were not correlated. Significant correlations were found between the gene expression levels assessed by CAI value and ENC (r = -0.424, p<0.05) and GC3 values (r = 0.644, p<0.01).

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.

scholarly journals Analysis of Mutation Bias in Shaping Codon Usage Bias and Its Association with Gene Expression Across Species

10.29007/87r9 ◽  
2020 ◽  
Author(s):  
Zhixiu Lu ◽  
Michael Gilchrist ◽  
Scott Emrich
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutation Bias ◽  
Protein Coding ◽  
E Coli ◽  
Synonymous Codons ◽  
Computation Efficiency

Codon usage bias has been known to reflect the expression level of a protein-coding gene under the evolutionary theory that selection favors certain synonymous codons. Although measuring the effect of selection in simple organisms such as yeast and E. coli has proven to be effective and accurate, codon-based methods perform less well in plants and humans. In this paper, we extend a prior method that incorporates another evolutionary factor, namely mutation bias and its effect on codon usage. Our results indicate that prediction of gene expression is significantly improved under our framework, and suggests that quantification of mutation bias is essential for fully understanding synonymous codon usage. We also propose an improved method, namely MLE-Φ, with much greater computation efficiency and a wider range of applications. An implementation of this method is provided at https://github.com/luzhixiu1996/MLE- Phi.

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