Cloning and sequence analysis of genome from the Inner Mongolia strain of the endogenous betaretroviruses (enJSRV)
Cloning and sequence analysis of genome from the Inner Mongolia strain of the endogenous betaretroviruses (enJSRV)
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DOI：
10.1007/s12250-008-2876-4
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发表时间：
2008-03
影响因子：
5.5
通讯作者：
Yu Wang;Shu-Ying Liu;Jian-yun Li;Min Han;Zhenlin Wang
中科院分区：
文献类型：
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作者：
Yu Wang;Shu-Ying Liu;Jian-yun Li;Min Han;Zhenlin Wang
为了扩增enJSRV内蒙古分离株（enJSRV-NM）的全基因组，我们用enJSRV特异性DNA探针和JSRV特异性DNA探针进行斑点杂交。根据Genbank序列设计了7对引物。通过PCR获得7个片段，并将其克隆到PMD 19-T载体中。对重组质粒进行测序分析。结果表明，该基因组全长7 942 bp，包含4个与gag、pro、pol和env基因重叠的开放阅读框，以及一个与pol基因3′端重叠的开放阅读框（orf-x）。将enJSRV-NM基因座的核苷酸序列与南非enJS 56 A1株（Accession No.AF153615）和美国JSRV 21株（Accession No.AF105220）的序列进行比较。核苷酸同源性分别为99.2%和92.3%。在预测的氨基酸序列的NC区发现两个锌指。然而，YXXM基序，这是一个可靠的分子标记的感染性外源病毒，没有发现在TM区。发现enJSRV-NM区域在氨基酸水平上与大多数逆转录病毒基因组中的其外源感染性对应物具有90%-98%的同一性。这是我国首次报道的enJSRV的核苷酸序列。该资源工作不仅为表达基因组学和基因组DNA序列注释提供了广泛的信息，而且还为OPA临床诊断的进一步研究提供了有用的信息。
In order to amplify the complete genome of enJSRV from the strain of Inner Mongolia (enJSRV-NM), we used enJSRV-specific and JSRV-specific DNA probes in dot blot hybridization. Seven pairs of primers were designed based on Genbank sequences. Seven fragments were obtained by PCR and were cloned into the PMD19-T vectors. The recombinant plasmids were sequenced and analyzed. The results showed that the genome was 7 942 bp in length and contained four overlapping open reading frames corresponding to the gag, pro, pol and env genes as well as an additional open reading frame (orf-x) that overlaps the 3′ end of the pol gene. The nucleotide acid sequences of the enJSRV-NM loci were compared with the sequences of South Africa enJS56A1 strain (Accession No. AF153615) and USA JSRV21 strain (Accession No. AF105220). The nucleotide acid identities were 99.2% and 92.3% respectively. Two zinc fingers were found in the NC region in the predicted amino acid sequence. However, the YXXM motif, which is a reliable molecular marker for the infectious exogenous virus, was not found in the TM region. It was found that the enJSRV-NM region was 90%-98% identical at the amino acid level to its exogenous infectious counterparts in most of the retroviral genome. This is the first nucleotide sequence of enJSRV reported in P.R China. The resource work has provided a wide range of information useful not only for expression genomics and annotation of genomic DNA sequence, but also for further research on the clinical diagnosis of OPA.