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

Cai, Mingsheng; Cheng, Anchun; Wang, Mingshu; Zhao, Lei; Zhu, Dekang; Luo, Qihui; Liu, Fei; Chen, Xiaoyue

doi:10.1159/000231992

Cited by 47 publications

(31 citation statements)

References 111 publications

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“…Different intracellular localizations may reflect different functions of viral proteins, and the intracellular localizations of viral proteins may also vary at different times after the infection (Feng, 2002;Cai et al, 2009a). Early studies demonstrated that UL54 is a nuclear protein, which can localize exclusively to the nucleolus in the absence of other viral proteins, whereas the native UL54 in PRV-infected cells is delocalized from the nucleolus to the nucleus in a structure that might resemble the viral replication compartment during infection (Monier et al, 2000;Calle et al, 2008;Li et al, 2011b).…”

Section: Discussionmentioning

confidence: 99%

Preparation and characterization of an antiserum against truncated UL54 protein of pseudorabies virus

Li¹,

Li²,

Li³

et al. 2012

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Summary. -Pseudorabies virus (PRV) early protein UL54 is a homolog of herpes simplex virus 1 immediateearly protein ICP27, which is a multifunctional protein essential for the virus replication. However, the precise role of the PRV UL54 protein in the virus life cycle is still poorly understood. To shed more light on this problem, we considered it essential to have available an antiserum specifically detecting this protein. Since it was known that a full-length UL54 protein is a too big molecule for efficient expression in prokaryotic systems, it was truncated from 1 to 66 N-terminal amino acids, fused to EYFP-His tag and expressed in Escherichia coli through an appropriate expression vector. The truncated protein was purified by Ni-NTA affinity chromatography and used for raising an antiserum in rabbits. Western blot analysis showed that this antiserum specifically recognized the purified truncated as well as full-length UL54 protein in PRV-infected cells. Immunofluorescence assay confirmed the latter finding and also demonstrated localization of this protein first in nucleoli and later in whole nuclei of PRV-infected cells. These results indicate that the prepared antiserum could serve as a valuable tool in further studies of PRV UL54 protein function.

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Section: Discussionmentioning

confidence: 99%

Preparation and characterization of an antiserum against truncated UL54 protein of pseudorabies virus

Li¹,

Li²,

Li³

et al. 2012

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“…A phenomenon designated codon usage bias (1)(2)(3). Codon usage bias among synonymous codons has been documented for numerous genes in variant species (3)(4)(5)(6)(7)(8)(9). It is reported that synonymous codon usage bias may be connected with different biological factors (6,(10)(11)(12)(13).…”

Section: Introductionmentioning

confidence: 99%

“…Codon usage bias among synonymous codons has been documented for numerous genes in variant species (3)(4)(5)(6)(7)(8)(9). It is reported that synonymous codon usage bias may be connected with different biological factors (6,(10)(11)(12)(13). Further analysis found that synonymous codon usage pattern changed at distinct sites along a coding sequence (14), balances of strong versus weak base pair bonding (15,16), maintenance of DNA and RNA secondary structure (17), and translational efficiency and fidelity (6).…”

Section: Introductionmentioning

confidence: 99%

“…It is reported that synonymous codon usage bias may be connected with different biological factors (6,(10)(11)(12)(13). Further analysis found that synonymous codon usage pattern changed at distinct sites along a coding sequence (14), balances of strong versus weak base pair bonding (15,16), maintenance of DNA and RNA secondary structure (17), and translational efficiency and fidelity (6). Aujeszky's disease, which is provoked by the pathogenic factor of Pseudorabies virus (PRV) (also known as Suid herpesvirus 1,, is a regularly lethal disease with a global distribution that influences swine, mainly and other domestic and wild animals incidentally (18)(19)(20)(21)(22).…”

Section: Introductionmentioning

confidence: 99%

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Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene

et al. 2013

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Background: Little knowledge of synonymous codon usage pattern of pseudorabies virus (PRV) genome, especially the UL31 gene in the process for its evolution is available. Objectives: In the present study, the codon usage bias between PRV UL31 sequence and the UL31-like sequences was identified. Materials and Methods:We used a comprehensive analysis on codon usage pattern in the PRV UL31 gene and the UL31-like genes of 48 reference herpesviruses by calculating codon adaptation index, ENc, RSCU and EMBOSS assays. Results: Cluster analysis demonstrated that the codon usage bias of UL31-like genes of 49 herpesviruses had a very close relation to their gene functions. In addition, comparison of codon preferences in the UL31 gene of PRV with those of E. coli, yeast and human showed that there were 33 codons showing discrete usage differences between PRV and yeast, 24 between PRV and E. coli, but 22 between PRV and human. Although there were slightly fewer differences in codon usages between PRV and human, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV UL31. Conclusions: These results may further our comprehending of the evolution, pathogenesis and functional studies of PRV.

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“…Recently, analyses of the patterns of codon usage bias of herpesviruses are primarily focused on the pseudorabies virus (PRV) [21], herpes simplex virus type 1 (HSV-1) [22], Epstein-Barr virus [23]. However, except for UL24, UL26.5, UL35, gE, dUTPase, the codon usage bias in DPV genome was known little [2,[24][25][26][27].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Synonymous Codon Usage in the newly identified DPV UL43 Gene

He¹,

Wang²,

Cheng³

et al. 2011

IJEM

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In this paper, we analyzed the UL43 gene of duck plague virus (DPV) of codon usage bias. The results may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target gene in vitro. In this study, the synonymous codon usage bias of UL43 gene in the 24 herpesviruses have been analyzed and the results showed obvious differences by the Codon Adaptation Index (CAI), effective number of codons (ENC) and the value of G + C content at the 3rd codon position (GC 3s ). In addition, the results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL43 gene of DPV. G + C compositional constraint is the main factor that determines the codon usage bias in UL43 gene. The phylogenetic analysis suggested that DPV was evolutionarily closer to fowl herpesviruses which further clustered into Alphaherpesvirinae. Furthermore the ORF of UL43 gene has sequential rare codons. There were 25 codons showing distinct usage differences between DPV with Escherichia coli, 24 codons showing distinct usage differences between DPV with yeast, and 32 between DPV and H. sapiens. Therefore the yeast and E. coli expression system may be suitable for the expression of DPV UL43 gene if some codons could be optimized.

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

Cited by 47 publications

References 111 publications

Preparation and characterization of an antiserum against truncated UL54 protein of pseudorabies virus

Preparation and characterization of an antiserum against truncated UL54 protein of pseudorabies virus

Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene

Analysis of Synonymous Codon Usage in the newly identified DPV UL43 Gene

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