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目的:通过生物信息学的手段,预测SARS病毒的基因组包装信号序列,为反义核酸和干扰核酸药物的设计提供有效的靶序列。方法:结合已报道的有关MHV和BCoV的基因组包装信号的一级结构和二级结构特点等信息,把SARS病毒的基因组和MHV,BCoV,PEDV,HCoV的基因组序列进行多序列比对;使用RNA二级结构预测软件对它们的RNA二级结构进行了预测和比较。在此基础上,根据冠状病毒识别基因组包装信号的机理,对来自这五种病毒的N蛋白、M蛋白序列也进行了多序列比对,探讨基因组包装信号与这两个蛋白质的进化关系。结果:SARS病毒的基因组包装信号位于接近ORFlb的3’端的位置,和MHV、BCoV的基因组包装序列一起位于ORFlb基因的核酸序列高突变区,但是其RNA二级结构与MHV、BCoV的基因组包装信号的二级结构很相似。对PEDV和HCoV的基因组包装信号序列的预测获得了类似的结果,而且三者的包装信号序列的位置在多序列比对的结果中互相重叠。突变频率的分析表明,基因组包装信号序列的突变频率高于N蛋白,而N蛋白高于M蛋白。结论:SARS病毒的基因组包装信号序列靠近ORFlb基因的3’端,其二级结构与MHV、BCoV的包装信号相似。基因组包装信号所在的基因组序列具有很高的突变性,这对与之相互作用的N蛋白和M蛋白也产生了影响。
OBJECTIVE: To predict the genomic packaging signal sequence of SARS virus by means of bioinformatics and to provide an effective target sequence for the design of antisense and interfering nucleic acid drugs. Methods: The genomes of SARS virus and the genome sequences of MHV, BCoV, PEDV and HCoV were multiple sequence alignment based on the reported primary structure and secondary structure characteristics of MHV and BCoV genome packaging signals. Using RNA Secondary structure prediction software predicts and compares their RNA secondary structure. Based on this, according to the mechanism of coronavirus recognizing genome packaging signal, multiple sequence alignment of N protein and M protein sequence from these five viruses was also conducted to explore the evolutionary relationship between the genome packaging signal and these two proteins. Results: The genome packaging signal of SARS virus was located close to the 3 ’end of ORF1b, together with the genomic packaging sequences of MHV and BCoV in the high mutation region of the nucleotide sequence of ORF1b gene. However, its RNA secondary structure was associated with the genome packaging signals of MHV and BCoV The secondary structure is very similar. Similar results were obtained for the prediction of the genomic packaging signal sequences of PEDV and HCoV, and the positions of the packaging signal sequences of the three overlapped each other in the results of the multiple sequence alignments. Mutational frequency analysis showed that the genomic packaging signal sequence mutation frequency higher than the N protein, while the N protein is higher than the M protein. Conclusion: The SARS virus genome packaging signal sequence is close to the 3 ’end of ORF1b gene, and its secondary structure is similar to that of MHV and BCoV. Genomic packaging signal where the genomic sequence has a high mutation, which interact with the N protein and M protein also had an impact.