Kaesberg P, Dasgupta R, Sgro J Y, Wery J P, Selling B H, Hosur M V, Johnson J E
Institute for Molecular Virology, University of Wisconsin, Madison 53706.
J Mol Biol. 1990 Jul 20;214(2):423-35. doi: 10.1016/0022-2836(90)90191-N.
The genomic RNA2s of nodaviruses encode a single gene, that of protein alpha, the precursor of virion proteins beta and gamma. We compared the sequences of the RNA2s of the nodaviruses, black beetle virus (BBV), flock house virus, boolarra virus and nodamura virus, with the objective of identifying homologies in the primary and secondary structure of these RNAs and in the structure of their encoded protein. The sequences of the four RNAs were found to be similar, so that homologous regions relating to translation and RNA replication were readily identified. However, the overall, secondary structures in solution, deduced from calculations of optimal Watson-Crick base-pairing configurations, were very different for the four RNAs. We conclude that a particular, overall, secondary structure in solution within host cells is not required for virus viability. The partially refined X-ray structure of BBV (R = 26.4% for the current model) was used as a framework for comparing the structure of the encoded proteins of the four viruses. Mapping of the four protein sequences onto the BBV capsid showed many amino acid differences on the outer surface, indicating that the exteriors of the four virions are substantially different. Mapping in the beta-barrel region showed an intermediate level of differences, indicating that some freedom in choice of amino acid residues is possible there although the basic framework of the capsids is evidently conserved. Mapping onto the interior surface of the BBV capsid showed a high degree of conservation of amino acid residues, particularly near the protein cleavage site, implying that that region is nearly identical in all four virions and has an essential role in virion maturation, and also suggests that all four capsid interior surfaces have similar surfaces exposed to the viral RNA. Apart from a small portion of the C promoter, the amino terminus of the BBV protein (residues 1 to 60) is crystallographically disordered and the amino acid residues in that region are not well conserved. The disordered portion of the BBV protein clearly projects from the capsid inner surface into the interior of the virion, the region occupied by the viral RNA. In all four viruses, residues 1 to 60 had a high proportion of basic residues, suggesting a virus-specific interaction of the amino terminus with the virion RNA.
诺达病毒的基因组RNA2编码一个单一基因，即蛋白质α基因，它是病毒粒子蛋白质β和γ的前体。我们比较了诺达病毒（黑甲虫病毒（BBV）、禽呼肠孤病毒、博拉病毒和诺达木拉病毒）的RNA2序列，目的是确定这些RNA的一级和二级结构以及它们编码的蛋白质结构中的同源性。发现这四种RNA的序列相似，因此与翻译和RNA复制相关的同源区域很容易识别。然而，根据最佳沃森-克里克碱基配对构型计算推导得出的这四种RNA在溶液中的整体二级结构却非常不同。我们得出结论，宿主细胞内溶液中的特定整体二级结构并非病毒生存所必需。BBV的部分精制X射线结构（当前模型的R值为26.4%）被用作比较这四种病毒编码蛋白质结构的框架。将这四种蛋白质序列映射到BBV衣壳上显示，外表面存在许多氨基酸差异，这表明这四种病毒粒子的外部有很大不同。在β桶区域的映射显示差异处于中等水平，这表明尽管衣壳的基本框架显然是保守的，但在该区域氨基酸残基的选择仍有一定自由度。映射到BBV衣壳的内表面显示氨基酸残基高度保守，特别是在蛋白质切割位点附近，这意味着该区域在所有四种病毒粒子中几乎相同，并且在病毒粒子成熟过程中起重要作用，还表明所有四种衣壳内表面都有类似的暴露于病毒RNA的表面。除了一小部分C启动子外，BBV蛋白质的氨基末端（第1至60位残基）在晶体学上是无序的，该区域的氨基酸残基保守性不佳。BBV蛋白质的无序部分显然从衣壳内表面伸入病毒粒子内部，即病毒RNA占据的区域。在所有四种病毒中，第1至60位残基有很高比例的碱性残基，这表明氨基末端与病毒粒子RNA存在病毒特异性相互作用。
