Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene
Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene
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伪狂犬病病毒 UL31 基因同义密码子使用偏差的鉴定
DOI：
10.5812/ijb.13811
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发表时间：
2013-10
影响因子：
1.3
通讯作者：
Meili Li
中科院分区：
文献类型：
--
作者：
Jianhong Chen;Bingyun Wang;Zi Li;Meili Li
背景：对伪狂犬病毒（PRV）基因组的同义密码子使用模式，尤其是UL31基因在其进化过程中的使用模式了解甚少。目的：本研究鉴定了PRV UL31序列和UL31样序列之间的密码子使用偏差。材料与方法：通过计算密码子适应指数、ENc、RSCU和EMBOSS等方法，对48种参考疱疹病毒UL31基因和UL31样基因的密码子使用模式进行综合分析。结果：聚类分析表明，49种疱疹病毒ul31样基因的密码子使用偏向性与其基因功能密切相关。此外，将PRV UL31基因的密码子偏好与大肠杆菌、酵母菌和人的密码子偏好进行比较，发现PRV与酵母菌之间有33个密码子使用差异，PRV与大肠杆菌之间有24个，PRV与人之间有22个。虽然PRV和人类在密码子使用上的差异略小，但差异不太可能具有统计学意义，需要通过实验研究来建立最适合PRV UL31的表达体系。结论：这些结果有助于我们进一步了解PRV的进化、发病机制和功能研究。
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. Conclusion: These results may further our comprehending of the evolution, pathogenesis and functional studies of PRV.
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影响因子：
5
作者：
Gu W;Zhou T;Ma J;Sun X;Lu Z
通讯作者：
Lu Z
影响因子：
--
作者：
T. Burland
通讯作者：
T. Burland
DOI：
10.1098/rstb.1995.0108
发表时间：
1995-09-29
影响因子：
6.3
作者：
SHARP, PM;AVEROF, M;PEDEN, JF
通讯作者：
PEDEN, JF
影响因子：
3.9
作者：
BERNARDI, G;BERNARDI, G
通讯作者：
BERNARDI, G
影响因子：
5.4
作者：
Gonnella, R;Farina, A;Faggioni, A
通讯作者：
Faggioni, A