Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites
Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites
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DOI：
10.1093/nar/gkp588
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发表时间：
2009-09-01
影响因子：
14.9
通讯作者：
Lukavsky, Peter J.
中科院分区：
文献类型：
--
作者：
Easton, Laura E.;Locker, Nicolas;Lukavsky, Peter J.
丙型肝炎病毒（HCV）内部核糖体进入位点（IRES）和其他HCV样IRES RNA的翻译活性取决于结构域II和III中的结构化RNA元件，其用于募集核糖体40 S亚基、真核起始因子（eIF）3和三元eIF 2/Met-tRNA（i）（Met）/GTP复合物，随后结构域II辅助亚基连接。猪捷申病毒1型塔凡病毒（PTV-1）属于小核糖核酸病毒科，具有HCV样二级结构，但只有40 S结合区的茎环IIId和IIIe与HCV IRES具有显著的序列保守性。在这里，我们使用化学探针，以显示与40 S亚基和eIF 3的相互作用位点之间的HCV和HCV样IRES保守。此外，我们揭示了一个严格保守的协变之间的嘌呤-嘌呤错配附近的假结（A-A/G）和环序列的域IIIe（GAU/CA）的功能作用。这些核苷酸参与三级相互作用，其用于稳定假结结构并与PTV-1和HCV IRES中的翻译效率相关。我们的数据表明，HCV和HCV样IRES的功能结构域的保护，包括一个更复杂的结构周围的假结比以前假设的。
The translational activity of the hepatitis C virus (HCV) internal ribosome entry site (IRES) and other HCV-like IRES RNAs depends on structured RNA elements in domains II and III, which serve to recruit the ribosomal 40S subunit, eukaryotic initiation factor (eIF) 3 and the ternary eIF2/Met-tRNA(i)(Met)/GTP complex and subsequently domain II assists subunit joining. Porcine teschovirus-1 talfan (PTV-1) is a member of the Picornaviridae family, with a predicted HCV-like secondary structure, but only stem-loops IIId and IIIe in the 40S-binding domain display significant sequence conservation with the HCV IRES. Here, we use chemical probing to show that interaction sites with the 40S subunit and eIF3 are conserved between HCV and HCV-like IRESs. In addition, we reveal the functional role of a strictly conserved co-variation between a purine-purine mismatch near the pseudoknot (A-A/G) and the loop sequence of domain IIIe (GAU/CA). These nucleotides are involved in a tertiary interaction, which serves to stabilize the pseudoknot structure and correlates with translational efficiency in both the PTV-1 and HCV IRES. Our data demonstrate conservation of functional domains in HCV and HCV-like IRESs including a more complex structure surrounding the pseudoknot than previously assumed.