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Ming Shu Wang - One of the best experts on this subject based on the ideXlab platform.

  • Characterization of Synonymous Codon Usage Bias in the Riemerella Anatipestifer OmpA/MotB Gene
    Advanced Materials Research, 2013
    Co-Authors: An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang
    Abstract:

    The analysis on Codon Usage Bias of OmpA/MotB gene of Riemerella anatipestifer (RA) may provide a basis for understanding the evolution and pathogenesis of RA and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In our study, a comparative analysis of the Codon Usage Bias in the newly discovered RA OmpA/MotB gene and the OmpA/MotB gene of 20 reference flavobacteriaceae was performed. The results of the Codon adaptation indes (CAI), effective number of Codon (ENC), and GC3s values indicated that synonymous Codon Usage Bias in the OmpA/MotB gene of flavobacteriaceae. The results showed that Codon Usage Bias in the RA OmpA/MotB 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 G+C compositional constraint is the main factor that determines the Codon Usage Bias in OmpA/MotB gene of flavobacteriaceae. Comparison of the Codon Usage in the OmpA/MotB gene of different organisms revealed that there were 31 Codons showing distinct Codon Usage differences between the RA and E. coli, 41 between the RA and humans, but 29 between the RA and yeast. Therefore the yeast expression system may be more suitable for the expression of RA OmpA/MotB gene. These results may improve our understanding of the evolution, pathogenesis and functional studies of RA, as well as contribute significantly to the area of flavobacteriaceae research.

  • Characterization of Codon Usage Bias in the UL17 Gene of Duck Enteritis Virus
    Advanced Materials Research, 2013
    Co-Authors: Ting Wen, An Chun Cheng, Ming Shu Wang
    Abstract:

    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 Codon Usage Bias in the RA Ragb/SusD Gene
    Advanced Materials Research, 2013
    Co-Authors: Si Si Yang, An Chun Cheng, De Kang Zhu, Xiao Jia Wang, Ming Shu Wang
    Abstract:

    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.

  • Characterization of Synonymous Codon Usage Bias in the UL1 Gene of Duck Plague Virus
    Advanced Materials Research, 2013
    Co-Authors: Ling Jie Zuo, An Chun Cheng, Ming Shu Wang
    Abstract:

    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 Synonymous Codon Usage Bias in the UL19 Gene of Duck Plague Virus (DPV)
    2013 International Conference on Computational and Information Sciences, 2013
    Co-Authors: Bihong Dai, An Chun Cheng, Ming Shu Wang
    Abstract:

    The Codon Usage Bias of DPV UL19 gene and 25 reference herpesviruses have been analyzed in this study. This work was performed by program CodonW 1.4, and CUSP and CHIPS of EMBOSS. The results indicated that Codons of DPV UL19 gene were strong Bias towards the synonymous Codons with A or T at the third Codon position. The Codon adaptation index (CAI), effective number of Codons (ENC), and GC3s values indicated synonymous Codon Usage Bias in the UL19 gene of herpesviruses, and this synonymous Bias was correlated with host evolution. The plot of ENC against GC3s revealed that factors other than gene composition might contribute to the Codon Usage among the different herpesviruses. The Codon Usage Bias of DPV UL19 gene was compared with that of E. coli, yeast, and Homo sapiens, which might help us understand the relevant mechanism for Biased Usage of synonymous Codons and select appropriate expression systems to improve the expression of target genes. There were 13 Codons showing distinct Usage differences between DPV and E. coli; 14, between DPV and yeast; and 25, between DPV and Human. We assumed that the DPV UL19 gene might express more efficiently in the E. coli system, yeast as well.

An Chun Cheng - One of the best experts on this subject based on the ideXlab platform.

  • Characterization of Synonymous Codon Usage Bias in the Riemerella Anatipestifer OmpA/MotB Gene
    Advanced Materials Research, 2013
    Co-Authors: An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang
    Abstract:

    The analysis on Codon Usage Bias of OmpA/MotB gene of Riemerella anatipestifer (RA) may provide a basis for understanding the evolution and pathogenesis of RA and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In our study, a comparative analysis of the Codon Usage Bias in the newly discovered RA OmpA/MotB gene and the OmpA/MotB gene of 20 reference flavobacteriaceae was performed. The results of the Codon adaptation indes (CAI), effective number of Codon (ENC), and GC3s values indicated that synonymous Codon Usage Bias in the OmpA/MotB gene of flavobacteriaceae. The results showed that Codon Usage Bias in the RA OmpA/MotB 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 G+C compositional constraint is the main factor that determines the Codon Usage Bias in OmpA/MotB gene of flavobacteriaceae. Comparison of the Codon Usage in the OmpA/MotB gene of different organisms revealed that there were 31 Codons showing distinct Codon Usage differences between the RA and E. coli, 41 between the RA and humans, but 29 between the RA and yeast. Therefore the yeast expression system may be more suitable for the expression of RA OmpA/MotB gene. These results may improve our understanding of the evolution, pathogenesis and functional studies of RA, as well as contribute significantly to the area of flavobacteriaceae research.

  • Characterization of Codon Usage Bias in the UL17 Gene of Duck Enteritis Virus
    Advanced Materials Research, 2013
    Co-Authors: Ting Wen, An Chun Cheng, Ming Shu Wang
    Abstract:

    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 Codon Usage Bias in the RA Ragb/SusD Gene
    Advanced Materials Research, 2013
    Co-Authors: Si Si Yang, An Chun Cheng, De Kang Zhu, Xiao Jia Wang, Ming Shu Wang
    Abstract:

    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.

  • Characterization of Synonymous Codon Usage Bias in the UL1 Gene of Duck Plague Virus
    Advanced Materials Research, 2013
    Co-Authors: Ling Jie Zuo, An Chun Cheng, Ming Shu Wang
    Abstract:

    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 Synonymous Codon Usage Bias in the UL19 Gene of Duck Plague Virus (DPV)
    2013 International Conference on Computational and Information Sciences, 2013
    Co-Authors: Bihong Dai, An Chun Cheng, Ming Shu Wang
    Abstract:

    The Codon Usage Bias of DPV UL19 gene and 25 reference herpesviruses have been analyzed in this study. This work was performed by program CodonW 1.4, and CUSP and CHIPS of EMBOSS. The results indicated that Codons of DPV UL19 gene were strong Bias towards the synonymous Codons with A or T at the third Codon position. The Codon adaptation index (CAI), effective number of Codons (ENC), and GC3s values indicated synonymous Codon Usage Bias in the UL19 gene of herpesviruses, and this synonymous Bias was correlated with host evolution. The plot of ENC against GC3s revealed that factors other than gene composition might contribute to the Codon Usage among the different herpesviruses. The Codon Usage Bias of DPV UL19 gene was compared with that of E. coli, yeast, and Homo sapiens, which might help us understand the relevant mechanism for Biased Usage of synonymous Codons and select appropriate expression systems to improve the expression of target genes. There were 13 Codons showing distinct Usage differences between DPV and E. coli; 14, between DPV and yeast; and 25, between DPV and Human. We assumed that the DPV UL19 gene might express more efficiently in the E. coli system, yeast as well.

Edward C Holmes - One of the best experts on this subject based on the ideXlab platform.

  • the extent of Codon Usage Bias in human rna viruses and its evolutionary origin
    Virus Research, 2003
    Co-Authors: Gareth M Jenkins, Edward C Holmes
    Abstract:

    Revealing the determinants of Codon Usage Bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of Codon Usage Bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of Codon Usage Bias in RNA viruses is low and that there is little variation in Bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and Codon Usage Bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the Codon Bias observed. However, we also detected correlations between Codon Usage Bias and some characteristics of viral genome structure and ecology, with increased Bias in segmented and aerosol-transmitted viruses and decreased Bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping Codon Usage Bias.

H Zhang - One of the best experts on this subject based on the ideXlab platform.

  • Comparative characterization analysis of synonymous Codon Usage Bias in classical swine fever virus.
    Microbial Pathogenesis, 2017
    Co-Authors: Dongliang Fei, Huansheng Han, Honggui Liu, Jiayong Zhang, Yulong Zhou, Hongbin Wang, Hongwei Cao, H Zhang
    Abstract:

    Classical swine fever virus (CSFV) is responsible for the highly contagious viral disease of swine, and causes great economic loss in the swine-raising industry. Considering the significance of CSFV, a systemic analysis was performed to study its Codon Usage patterns. In this study, using the complete genome sequences of 76 CSFV representing three genotypes, we firstly analyzed the relative nucleotide composition, effective number of Codon (ENC) and synonymous Codon Usage in CSFV genomes. The results showed that CSFV is GC-moderate genome and the third-ended Codons are not preferentially used. Every ENC values in CSFV genomes are >50, indicating that the Codon Usage Bias is comparatively slight. Subsequently, we performed the correspondence analysis (COA) to investigate synonymous Codon Usage variation among all of the CSFV genomes. We found that Codon Usage Bias in these CSFV genomes is greatly influenced by G + C mutation, which suggests that mutational pressure may be the main factor determining the Codon Usage Biases. Moreover, most of the Codon Usage Bias among different CSFV ORFs is directly related to the nucleotide composition. Other factors, such as hydrophobicity and aromaticity, also influence the Codon Usage variation among CSFV genomes. Our study represents the most comprehensive analysis of Codon Usage patterns in CSFV genome and provides a basic understanding of the mechanisms for its Codon Usage Bias.

  • Synonymous Codon Usage Bias in porcine epidemic diarrhea virus.
    Israel Journal of Veterinary Medicine, 2013
    Co-Authors: H W Cao, H Zhang
    Abstract:

    In this study, we analyzed the synonymous Codon Usage Bias in porcine epidemic diarrhea virus genome. The effective number of Codons (ENC) and the relative synonymous Codon Usage (RSCU) values are used to estimate Codon Usage variation. The plot of ENC values against GC3s and correlation analysis revealed that mutational pressure rather than translational selection is the main factor determining the Codon Usage Bias in porcine epidemic diarrhea virus. In addition, other factors, such as aromaticity, hydrophobicity of genes also influenced the Codon Usage variation among virus genomes in a minor way. Our work might contribute to the understanding of molecular evolution of Codon Usage variation in porcine epidemic diar rhea virus genome.

  • Synonymous Codon Usage Bias of spike genes of porcine epidemic diarrhea virus
    African Journal of Microbiology Research, 2011
    Co-Authors: H W Cao, H Zhang
    Abstract:

    Synonymous Codons are not used randomly. Rather, some Codons are used more frequently than others. Investigating Codon Usage Bias is essential to the understanding of viral evolution. However the factors shaping synonymous Codon Usage Bias and nucleotide composition in animal viruses have been studied only to a limited extent. In our study, using the 19 complete CDS sequences of Spike (S) genes of porcine epidemic diarrhea virus (PEDV), we analyzed synonymous Codon Usage Bias. The relative synonymous Codon Usage (RSCU) was used to estimate Codon Usage variation in each gene, and the results indicated that preferentially used Codons were A-ended, G-ended, and Uended Codons. Effective number of Codons (ENC) values varies from 48.15 to 49.52, which suggested that the Codon Usage Bias in PEDV S genes was very slightly. Correspondence analysis (COA) was further performed to study the major trend in Codon Usage variation, and the plot of ENC values against GC3s (at synonymous third Codon position) revealed that mutational pressure rather than translational selection was the main factor determining the Codon Usage Bias in PEDV S genes. Moreover, correlation analysis indicated that aromaticity and hydrophobicity of S genes also influenced the Codon Usage variation in a minor way. Our study provides the most comprehensive analysis to date of PEDV S genes’ Codon Usage patterns and provides a basic understanding of the mechanisms for Codon Usage Bias.

Hitoshi Miyasaka - One of the best experts on this subject based on the ideXlab platform.

  • Translation initiation AUG context varies with Codon Usage Bias and gene length in Drosophila melanogaster.
    Journal of Molecular Evolution, 2002
    Co-Authors: Hitoshi Miyasaka
    Abstract:

    The relationship between the Codon Usage Bias and the sequence context surrounding the AUG translation initiation Codon was examined in 1100 Drosophila melanogaster mRNA sequences. The Codon Usage Bias measured by the "Codon adaptation index" (CAI), and the effectiveness of the AUG context for translation initiation assessed by the "AUG context adaptation index" (A U G CAI), showed a significant positive relationship (correlation coefficient: r = 0.34, p < 0.0001), indicating that these two factors are evolutionally under a similar natural selection constraint at the translational level. The importance of each position of the AUG context in relation to Codon Usage Bias was examined, and the preference for the nucleotide at the -13, -12, -11, -10, -7, -6, -5, -4, -3, -2, and -1 positions showed a significant positive correlation to the Codon Usage Bias, suggesting the action of natural selection on these very specific positions of the Drosophila genome. The relationship between A U G CAI value and gene length was also examined, and a significant negative relationship was found (r = -0.15, p < 0.0001), suggesting a general tendency of higher expressivity of shorter genes, and of lower expressivity of longer genes in D. melanogaster.

  • The positive relationship between Codon Usage Bias and translation initiation AUG context in Saccharomyces cerevisiae.
    Yeast, 1999
    Co-Authors: Hitoshi Miyasaka
    Abstract:

    The relationship between the Codon Usage Bias and the sequence context surrounding the AUG translation initiation Codon was examined in 211 Saccharomyces cerevisiae mRNA sequences. The Codon Usage Bias and the number of matches to optimal AUG context, (A/U)A(A/C)AA(A/C)AUGUC(U/C), for translation initiation showed a positive relationship, indicating that these two factors are evolutionally under the similar natural selection constraint at the translation level. A new index (AUGCAI=AUG Context Adaptation Index) for the measure of optimal AUG context was devised, and the importance of each position of AUG context was also examined. Copyright © 1999 John Wiley & Sons, Ltd.