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Virology Journal
Published in: Virology Journal 1/2011

Open Access 01-12-2011 | Research

Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

Authors: Jun-hong Su, Xiao-xia Ma, Ya-li He, Ji-dong Li, Xu-sheng Ma, Yong-xi Dou, Xue-nong Luo, Xue-peng Cai

Published in: Virology Journal | Issue 1/2011

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Abstract

Background

Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression.

Results

In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection.

Conclusions

The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.
Appendix
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Metadata
Title
Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome
Authors
Jun-hong Su
Xiao-xia Ma
Ya-li He
Ji-dong Li
Xu-sheng Ma
Yong-xi Dou
Xue-nong Luo
Xue-peng Cai
Publication date
01-12-2011
Publisher
BioMed Central
Published in
Virology Journal / Issue 1/2011
Electronic ISSN: 1743-422X
DOI
https://doi.org/10.1186/1743-422X-8-476

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