Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
PLoS Pathog. 2013;9(4):e1003294. doi: 10.1371/journal.ppat.1003294. Epub 2013 Apr 4.
RNA secondary structure plays a central role in the replication and metabolism of all RNA viruses, including retroviruses like HIV-1. However, structures with known function represent only a fraction of the secondary structure reported for HIV-1(NL4-3). One tool to assess the importance of RNA structures is to examine their conservation over evolutionary time. To this end, we used SHAPE to model the secondary structure of a second primate lentiviral genome, SIVmac239, which shares only 50% sequence identity at the nucleotide level with HIV-1NL4-3. Only about half of the paired nucleotides are paired in both genomic RNAs and, across the genome, just 71 base pairs form with the same pairing partner in both genomes. On average the RNA secondary structure is thus evolving at a much faster rate than the sequence. Structure at the Gag-Pro-Pol frameshift site is maintained but in a significantly altered form, while the impact of selection for maintaining a protein binding interaction can be seen in the conservation of pairing partners in the small RRE stems where Rev binds. Structures that are conserved between SIVmac239 and HIV-1(NL4-3) also occur at the 5' polyadenylation sequence, in the plus strand primer sites, PPT and cPPT, and in the stem-loop structure that includes the first splice acceptor site. The two genomes are adenosine-rich and cytidine-poor. The structured regions are enriched in guanosines, while unpaired regions are enriched in adenosines, and functionaly important structures have stronger base pairing than nonconserved structures. We conclude that much of the secondary structure is the result of fortuitous pairing in a metastable state that reforms during sequence evolution. However, secondary structure elements with important function are stabilized by higher guanosine content that allows regions of structure to persist as sequence evolution proceeds, and, within the confines of selective pressure, allows structures to evolve.
RNA 二级结构在所有 RNA 病毒（包括 HIV-1 等逆转录病毒）的复制和代谢中起着核心作用。然而，具有已知功能的结构仅代表 HIV-1（NL4-3）报道的二级结构的一部分。评估 RNA 结构重要性的一种工具是检查它们在进化时间上的保守性。为此，我们使用 SHAPE 对第二种灵长类慢病毒基因组 SIVmac239 的二级结构进行建模，该基因组与 HIV-1NL4-3 的核苷酸水平只有 50%的序列同一性。在这两个基因组中，只有大约一半的配对核苷酸配对，并且在整个基因组中，只有 71 个碱基对与两个基因组中的同一配对伙伴形成配对。平均而言，RNA 二级结构的进化速度比序列快得多。Gag-Pro-Pol 框架转换位点的结构得以维持，但形式发生了显著改变，而维持蛋白质结合相互作用的选择对 Rev 结合的小 RRE 茎中配对伙伴的保守性产生了影响。在 SIVmac239 和 HIV-1（NL4-3）之间保守的结构也出现在 5' 多聚腺苷酸化序列、正链引物位点 PPT 和 cPPT 以及包括第一个剪接受体的茎环结构中。这两个基因组富含腺苷，而胞嘧啶含量低。结构区域富含鸟嘌呤，而未配对区域富含腺苷，功能重要的结构比非保守结构具有更强的碱基配对。我们得出结论，大部分二级结构是在不稳定状态下偶然配对的结果，这种配对在序列进化过程中重新形成。然而，具有重要功能的二级结构元件通过更高的鸟嘌呤含量得到稳定，允许结构区域在序列进化过程中持续存在，并且在选择压力的限制内，允许结构进化。
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