Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome.
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.
State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China.
Jun-hong
JH
Su
Xiao-xia
XX
Ma
Ya-li
YL
He
Ji-dong
JD
Li
Xu-sheng
XS
Ma
Yong-xi
YX
Dou
Xue-nong
XN
Luo
Xue-peng
XP
Cai
D003062:Codon; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational; D019316:Porcine respiratory and reproductive syndrome virus / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism; D014764:Viral Proteins / Q000096:biosynthesis
D003062:Codon; D014764:Viral Proteins