| Cucumber mosaic virus (Cucumber mosaic virus, CMV) is a typical +ssRNA virus with tripartite genome. Mutation, recombination and reassortment are the principal forms of variation and evolution for CMV to adapt new environments and new hosts. Thus, CMV is considered to be a good model for studying the pathogenesis of RNA virus. According to their evolution discrepancy of genes and untraslated regions (UTR), CMV strains were divided into Subgroup I and Subgroup II for apparent differences in pathogenicity, whilst, Subgroup I has been further divideded into IA and IB.In this study, a new strain of CMV (namely CMV-Mb) was detected from natural-infected Musa basjoo sampled from Hangzhou, Zhejiang Province, China in 2008. After double stranded RNA analysis, RT-PCR and gene clone, it is found that the 5'partial sequence of CMV-Mb RNA1, containing 1381 nucleotides (nts), encods the 1a protein conposed of 460 amino acids (aa), corresponding to the sequence from 119 to 1500. CMV-Mb RNA2 contains 3034 nts, encoding 2a protein composted of 858 aa and 2b protein composted of 111 aa, corresponding to the sequences from 86 to 2659 and 2418 to 2750 respectively. RNA3 contains 2189 nts, encoding 3a protein of 280 aa and CP of 219 aa, corresponding to the sequences from 97 to 936 and 1229 to 1885 respectively. RNA1 of CMV-Mb showed 96.0% nucleotide sequence identity with those of Q strain identified from Australia and over 97.0% with those of CMV-Tsh and CMV-Tagetes identified recently from China. The comparison of the CMV-Mb RNA2 nucleotide sequence to those of CMV-Fny, CMV-Sd and CMV-Q revealed that CMV-Mb was more closer to CMV-Q (with over 97.0% sequence identity) than to CMV-Fny and CMV-Sd (less than 85.0% identity). Interestingly, the 2b nucleotide sequence of CMV-Mb was more closely related to Subgroup II strain, CMV-Q, but less than 50.0% identity with CMV-Fny and CMV-Sd representing IA and IB strains. The nucleotide sequences of CMV-Mb RNA3 3a and CP showed over 98% sequence identity with those of CMV-Q, but less than 85% identities with those of CMV-Fny and CMV-Sd. These results indicated that CMV-Mb RNA1, RNA2 and RNA3 were all derived from CMV Subgroup II strain. The results of phylogenetic analysis of the five ORFs between CMV-Mb and other 21 CMV strains also revealed that CMV-Mb is a natural Subgroup II strains. Therefore, this is the first reported of a Subgroup II homozygous from M. basjoo infected by CMV.Using sequence alignment to analyze 5′terminal sequence of RNA3 independently, we found that the sequence of Subgroup I and Subgroup II showed a certain similarity. CMV-Mb is characterized for belonging to Subgroup II, but with 12-14nt deleted at the 5'UTR of this segment. Two natural mutations in the region 8 ~ 33 nt and 50 ~ 63 nt were found, for a possible specific condition to fit transmission, host interactions or environment. It could also be considered that the deletion and rearrangement of regions at RNA3 5′UTR of CMV-Mb is part of its evolution.The infectious clone of CMV-Mb RNA3 has been constructed with addition of a T7 promoter by PCR. Infectious RNA transcripts of CMV-Mb RNA3 was generated by in vitro transcription. Along with the transcripts of CMV-Fny RNA1 and RNA2, the RNA transcripts were combined to reform pseudorecombinant between CMV-Fny RNA1 and RNA2 and CMV-Mb RNA3 (namely F1F2M3). The artificial recombinant (F1F2M3) was found to be infectious to Nicotiana glotinosa as a systemic host.
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