Department of Animal Sciences, 210 Upchurch Hall, Auburn University, Auburn, AL 36849-5415, USA.
Virus Res. 2011 Sep;160(1-2):136-42. doi: 10.1016/j.virusres.2011.06.002. Epub 2011 Jun 12.
The internal ribosomal entry site (IRES) RNA of bovine viral diarrhea virus (BVDV) has been implicated in virus propagation. To gain insight into the structure and potential function of the BVDV IRES RNA, we collected and aligned 663 of its sequences. Compensatory Watson-Crick and wobble G·U pairs were investigated to establish phylogenetically supported secondary structures for each of the BVDV IRES RNA sequences. The extensively folded BVDV IRES RNAs were composed of helices 2, 3 and 4. Helix 2 consisted of five helical sections. Helix 3 contained sections 3a to 3j as well as six helical insertions 3.1-3.6. Sections 3a and 3b together with helices 3.6 and 4 formed an RNA pseudoknot. Two highly variable regions corresponded to hairpins 3j and 3.4. Three-dimensional modeling of the BVDV-1b strain Osloss IRES RNA predicted an elongated structure with approximate dimensions of 170 Å by 65 Å by 90 Å. The model of the IRES RNA-ribosome complex suggested proximity between helix 2 of the BVDV IRES and ribosomal proteins S5 and S25.
牛病毒性腹泻病毒（BVDV）的内部核糖体进入位点（IRES）RNA 与病毒的增殖有关。为了深入了解 BVDV IRES RNA 的结构和潜在功能，我们收集并对齐了 663 个序列。通过调查补偿性 Watson-Crick 和 wobble G·U 对，为每个 BVDV IRES RNA 序列建立了系统发育支持的二级结构。广泛折叠的 BVDV IRES RNA 由 2、3 和 4 号螺旋组成。2 号螺旋由五个螺旋段组成。3 号螺旋包含 3a 到 3j 以及六个螺旋插入 3.1-3.6。3a 和 3b 段与 3.6 号螺旋和 4 号螺旋共同形成一个 RNA 假结。两个高度可变区对应于 3j 和 3.4 号发夹。BVDV-1b 株 Osloss IRES RNA 的三维建模预测了一个长约 170 Å 乘 65 Å 乘 90 Å 的拉长结构。IRES RNA-核糖体复合物的模型表明，BVDV IRES 的 2 号螺旋与核糖体蛋白 S5 和 S25 接近。
