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

• Published in: Virology journal Vol. 8; no. 1; p. 476
• Main Authors: Su, Jun-hong, Ma, Xiao-xia, He, Ya-li, Li, Ji-dong, Ma, Xu-sheng, Dou, Yong-xi, Luo, Xue-nong, Cai, Xue-peng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.10.2011; BioMed Central; BMC
• Subjects: Bias; Causes of; Chromosome mapping; Codon; codon usage bias; Efficiency; Gene Expression Regulation, Viral; Genetic aspects; Genetic regulation; Genetics; Genome, Viral; Genomes; Life sciences; Open Reading Frames; Peptide Chain Initiation, Translational; Polypeptides; Porcine reproductive and respiratory syndrome; Porcine respiratory and reproductive syndrome virus - genetics; Proteins; PRRSV; R&D; Research & development; Ribonucleic acid; Ribosomes - metabolism; RNA; RNA polymerase; translation efficiency; translation initiation region; translation selection; Viral Proteins - biosynthesis; China
• ISSN: 1743-422X; 1743-422X
• DOI: 10.1186/1743-422X-8-476

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. 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. 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.