title: A conserved secondary structure in the hypervariable region at the 5' end of Bamboo mosaic virus satellite RNA is functionally interchangeable.
abstract: Satellite RNA (satRNA) associated with Bamboo mosaic virus (BaMV) is dependent on BaMV for replication and encapsidation. Molecular analyses of total RNA extracted from bamboo species collected worldwide revealed that 26 out of 61 BaMV isolates harbored satBaMV. Among them, two phylogenetically distinguishable groups, A and B, with a genetic diversity of 6.9 +/- 0.7% were identified. Greatest sequence diversity occurred in the 5' untranslated region (UTR) that contained one hypervariable region with variations of up to 20.7%. Concurrent covariations in the 5' hypervariable sequences support the existence of a conserved apical hairpin stem-loop structure, which was earlier mapped by enzymatic probings and functional analyses [Annamalai, P., Hsu, Y.H., Liu, Y.P., Tsai, C.H., Lin, N.S., 2003. Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus. Virology 311 (1), 229-239]. Furthermore, chimeric satBaMVs generated by interchanging the hypervariable region between groups A and B demonstrated the replication competence of satBaMV isolates in Nicotiana benthamiana protoplasts co-inoculated with BaMV RNA. The results suggest that an evolutionarily conserved secondary structure exists in the hypervariable region of 5' UTR of satBaMV.
authors.affiliation: Department of Biology, Kaoshiung Medical University, Kaoshiung, Taiwan 807, Republic of China.
authors.forename: Wen-Bin
authors.initials: WB
authors.lastname: Yeh
authors.forename: Yau-Heiu
authors.initials: YH
authors.lastname: Hsu
authors.forename: Hsin-Chuan
authors.initials: HC
authors.lastname: Chen
authors.forename: Na-Sheng
authors.initials: NS
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D014644:Genetic Variation; D008969:Molecular Sequence Data; D009029:Mosaic Viruses / Q000145:classification / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D019244:RNA, Satellite / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D031787:Sasa / Q000821:virology*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D019244:RNA, Satellite; D012367:RNA, Viral