SEQUENCE AND SECONDARY STRUCTURE-ANALYSIS OF THE 5'-TERMINAL REGION OF FLAVIVIRUS GENOME RNA
SEQUENCE AND SECONDARY STRUCTURE-ANALYSIS OF THE 5'-TERMINAL REGION OF FLAVIVIRUS GENOME RNA
复制标题
DOI：
10.1016/0042-6822(88)90468-0
复制
发表时间：
1988-02-01
期刊：
影响因子：
3.7
通讯作者：
DISPOTO, JH
中科院分区：
文献类型：
--
作者：
BRINTON, MA;DISPOTO, JH
用与西尼罗病毒（WNV）RNA株编码区5“-末端互补的单一合成cDNA引物测定了7株圣路易斯脑炎病毒（SLEV）和1株西尼罗病毒（WNV）基因组RNA的5”-末端非编码区序列。将SLEV和WNV RNA的5“-末端序列与黄热病病毒（YFV）、墨累谷脑炎病毒（MVEV）和登革热病毒的已发表序列进行比较。虽然在不同的黄病毒RNA中只有5“-非编码序列内的短区域是保守的，但在同一黄病毒亚组的成员中观察到该区域的显著同源性，并且在同一病毒的不同毒株之间观察到几乎完全的保守性。例如，在17年的时间里，从不同的地理位置分离的7种SLE菌株，其神经毒力表型不同，在5“-非编码区仅含有2至4个核苷酸变化。 有趣的是，三个低毒力菌株中的每一个都在位置16处共享相同的独特碱基替换。预测由每个不同黄病毒基因组RNA的5“-末端形成的二级结构具有相似的大小和形状，在每种情况下由具有小的顶环和较大的侧环的茎组成。尽管缺乏广泛的序列同源性，但在许多不同的黄病毒中预测出一个共同的结构，这表明这种二级结构在功能上是重要的。预测在跨越翻译起始密码子的区域中形成另外的茎环结构。该结构的大小和形状的保守性明显低于5 ''末端二级结构。
The 5''-terminal noncoding region sequences were determined for the genome RNAs of seven strains of St. Louis encephalitis virus (SLEV) and one strain of West Nile virus (WNV) using a single synthetic cDNA primer complementary to the 5''-terminus of the coding region of a strain of WNV RNA. The 5''-terminal sequences obtained for the SLEV and WNV RNAs were compared with published sequences for yellow fever viurs (YFV), Murray Valley encephalitis virus (MVEV), and dengue virus. While only short regions within the 5''-noncoding sequence were conserved among different flavivirus RNAs, significant homology was observed in this region among members of the same flavivirus subgroup and almost complete conservation was observed between different strains of the same virus. For example, seven strains of SLE, isolated from different geographic locations over a 17-year period and differing in their neurovirulence phenotype, contained only two to four nucleotide changes in the 5''-noncoding region. Interestingly, each of three low-virulence strains shared the same unique base substitution at position 16. Secondary structures predicted to be formed by the 5''-termini of each of the different flavivirus genome RNAs were of similar size and shape, in each case consisting of a stem with a small top loop and a larger side loop. The prediction of a common structure among a number of different flaviviruses, despite the lack of extensive sequence homology, suggests that this secondary structure is functionally important. An additional stem and loop structure is predicted to be formed in the region spanning the translation initiation codon. This structure showed significantly less conservation of size and shape than the 5''-terminal secondary structure.