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

Authors

  • Bingyun Wang Department of Veterinary Medicine, Foshan Science and Technology University, Foshan, China
  • Jianhong Chen Department of Veterinary Medicine, Foshan Science and Technology University, Foshan, China
  • Juny Zhu Department of Pathogenic Biology and Immunology, Guangzhou Medical University, Guangzhou, China
  • Meili Li Department of Pathogenic Biology and Immunology, Guangzhou Medical University, Guangzhou, China
  • Mingsheng Cai Department of Pathogenic Biology and Immunology, Guangzhou Medical University, Guangzhou, China and Department of Veterinary Medicine, Foshan Science and Technology University, Foshan, China
  • Zhiyao Zhao Department of Pathogenic Biology and Immunology, Guangzhou Medical University, Guangzhou, China
  • Zi Li Department of Pathogenic Biology and Immunology, Guangzhou Medical University, Guangzhou, China
Abstract:

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.

Upgrade to premium to download articles

Sign up to access the full text

Already have an account?login

similar resources

identification of synonymous codon usage bias in the pseudorabies virus ul31 gene

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 a...

full text

Synonymous Codon Usage Bias in Porcine Epidemic Diarrhea Virus

ABST RACT 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 ...

full text

Characterization of synonymous codon usage bias in the duck plague virus UL35 gene.

OBJECTIVE The aim was to identify the codon usage bias between the newly identified duck plague virus (DPV) UL35 gene (GenBank accession No. EF643558) and the UL35-like genes of 27 other reference herpesviruses. METHODS A comparative analysis of the codon usage bias of the 28 herpesviruses was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (T...

full text

The Selective Advantage of Synonymous Codon Usage Bias in Salmonella.

The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is referred to as synonymous codon usage bias. The genomes of free-living unicellular organisms such as bacteria have an extreme codon usage bias...

full text

The effect of context on synonymous codon usage in genes with low codon usage bias.

The effect of neighbouring bases on the usage of synonymous codons in genes with low codon usage bias in yeast and E. coli is examined. The codon adaptation index is employed to identify a group of genes in each organism with low codon usage bias, which are likely to be weakly expressed. A similar pattern is found in complementary sequences with respect to synonymous usage of A vs G or of U vs ...

full text

Molecular cloning and characterization of the pseudorabies virus UL31 gene.

We amplified a 816-bp sequence of the UL31 gene from the pseudorabies virus (PRV) Becker strain genome. Evidence that this was the UL31 gene was confirmed by cloning and sequencing. The PRV UL31 gene encodes a putative protein of 271-amino acid residues, which was designated the UL31 protein. Bioinformatic analysis indicated that PRV UL31 contains a conserved PHA03328 domain, closely related wi...

full text

My Resources

Save resource for easier access later

Save to my library Already added to my library

{@ msg_add @}


Journal title

volume 11  issue 4

pages  214- 222

publication date 2013-10-01

By following a journal you will be notified via email when a new issue of this journal is published.

Hosted on Doprax cloud platform doprax.com

copyright © 2015-2023