State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, PR China.
Virol J. 2011 Oct 21;8:476. 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.
猪繁殖与呼吸综合征病毒（PRRSV）是一种新出现的病原体，严重影响了全球的猪群。PRRSV 的复制受到病毒基因表达的严格控制，每个基因翻译起始区的密码子使用情况可能调节翻译速率。因此，更好地了解起始翻译区的密码子使用模式将有助于了解 PRRSV 基因表达的调控。
在这项研究中，比较了 PRRSV ORF1a 和 ORFs2-7 中翻译起始区和整个编码序列的密码子使用情况。为了研究密码子使用对翻译起始速率的潜在影响，我们建立了 PRRSV 翻译起始区的密码子使用模型。我们观察到，在特定的 ORFs 中，一些非偏好性密码子在翻译起始区被优先使用。尽管一些位置随密码子而变化，但它们倾向于使用具有负 CUB 的密码子。此外，我们的密码子使用模型表明，CUB 的保守模式与保守序列并不完全一致，而是在翻译选择的作用下形成的。
核糖体扫描的 PRRSV 翻译起始区的非变化模式与负 CUB 被认为是翻译过程中的限速步骤。
