A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon
A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon
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DOI：
10.1074/jbc.m210291200
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发表时间：
2003-03-28
影响因子：
4.8
通讯作者：
Berkhout, B
中科院分区：
文献类型：
--
作者：
Abbink, TEM;Berkhout, B
5'-非翻译区（5'-UTR）是HIV-1 RNA基因组中最保守的部分，它包含介导病毒生命周期中各个步骤的调控基序。先前的研究表明，HIV-1 RNA的5'端290个核苷酸采用两种互斥的二级结构，长距离相互作用（LDI）和分枝多发夹（BMH）。BMH有多个发夹，包括介导RNA二聚化的二聚体起始信号（DIS）发夹。LDI包含一个长距离的碱基配对相互作用，它遮挡了DIS区域。因此，这两种构象形成RNA二聚体的能力不同。在本研究中，我们提出了全长5'-UTR也采用LDI和BMH构象的证据。下游290-352区域，包括Gag起始密码子，在LDI和BMH结构的背景下折叠不同。这些核苷酸在LDI构象中形成延伸的发夹结构，但相同的序列在BMH构象中与上游的U5序列产生新的长距离相互作用。计算机辅助RNA结构预测、生化分析和不同病毒分离株的系统发育调查证实了这种U5-AUG双链的存在。U5-AUG双链可能影响Gag蛋白的翻译，因为它阻断了Gag开放阅读框的起始密码子。
The 5'-untranslated region (5'-UTR) is the most conserved part of the HIV-1 RNA genome, and it contains regulatory motifs that mediate various steps in the viral life cycle. Previous work showed that the 5'-terminal 290 nucleotides of HIV-1 RNA adopt two mutually exclusive secondary structures, long distance interaction (LDI) and branched multiple hairpin (BMH). BMH has multiple hairpins, including the dimer initiation signal (DIS) hairpin that mediates RNA dimerization. LDI contains a long distance base-pairing interaction that occludes the DIS region. Consequently, the two conformations differ in their ability to form RNA dimers. In this study, we have presented evidence that the full-length 5'-UTR also adopts the LDI and BMH conformations. The downstream 290-352 region, including the Gag start codon, folds differently in the context of the LDI and BMH structures. These nucleotides form an extended hairpin structure in the LDI conformation, but the same sequences create a novel long distance interaction with upstream U5 sequences in the BMH conformation. The presence of this U5-AUG duplex was confirmed by computer-assisted RNA structure prediction, biochemical analyses, and a phylogenetic survey of different virus isolates. The U5-AUG duplex may influence translation of the Gag protein because it occludes the start codon of the Gag open reading frame.