Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 1 Barker Hall, Berkeley, CA 94720-7354, USA.
J Virol. 2010 Jun;84(12):6103-18. doi: 10.1128/JVI.02042-09. Epub 2010 Mar 31.
Dengue virus (DENV) is a member of the Flavivirus genus of positive-sense RNA viruses. DENV RNA replication requires cyclization of the viral genome mediated by two pairs of complementary sequences in the 5' and 3' ends, designated 5' and 3' cyclization sequences (5'-3' CS) and the 5' and 3' upstream of AUG region (5'-3' UAR). Here, we demonstrate that another stretch of six nucleotides in the 5' end is involved in DENV replication and possibly genome cyclization. This new sequence is located downstream of the AUG, designated the 5' downstream AUG region (5' DAR); the motif predicted to be complementary in the 3' end is termed the 3' DAR. In addition to the UAR, CS and DAR motifs, two other RNA elements are located at the 5' end of the viral RNA: the 5' stem-loop A (5' SLA) interacts with the viral RNA-dependent RNA polymerase and promotes RNA synthesis, and a stem-loop in the coding region named cHP is involved in translation start site selection as well as RNA replication. We analyzed the interplay of these 5' RNA elements in relation to RNA replication, and our data indicate that two separate functional units are formed; one consists of the SLA, and the other includes the UAR, DAR, cHP, and CS elements. The SLA must be located at the 5' end of the genome, whereas the position of the second unit is more flexible. We also show that the UAR, DAR, cHP, and CS must act in concert and therefore likely function together to form the tertiary RNA structure of the circularized DENV genome.
登革热病毒（DENV）是正链 RNA 病毒属黄病毒科的成员。DENV RNA 复制需要病毒基因组通过 5' 和 3' 末端的两对互补序列的环化来介导，这些序列分别被命名为 5' 和 3' 环化序列（5'-3' CS）和 AUG 区上游的 5' 和 3'（5'-3' UAR）。在这里，我们证明 5' 端的另一个六核苷酸序列参与了 DENV 的复制和可能的基因组环化。这个新序列位于 AUG 下游，命名为 5' 下游 AUG 区（5' DAR）；在 3' 端预测互补的序列称为 3' DAR。除了 UAR、CS 和 DAR 序列外，病毒 RNA 的 5' 端还存在另外两个 RNA 元件：5' 茎环 A（5' SLA）与病毒 RNA 依赖性 RNA 聚合酶相互作用并促进 RNA 合成，编码区的茎环称为 cHP，参与翻译起始位点选择以及 RNA 复制。我们分析了这些 5' RNA 元件与 RNA 复制之间的相互作用，我们的数据表明形成了两个独立的功能单元；一个由 SLA 组成，另一个包含 UAR、DAR、cHP 和 CS 元件。SLA 必须位于基因组的 5' 端，而第二个单元的位置则更加灵活。我们还表明，UAR、DAR、cHP 和 CS 必须协同作用，因此可能一起发挥作用，形成环状 DENV 基因组的三级 RNA 结构。
