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.

Crucial Role of the 5′ Conserved Structure ofBamboo Mosaic VirusSatellite RNA in Downregulation of Helper Viral RNA Replication

“…The 5Ј UTR of the satBaMV genome exhibits significant genetic heterogeneity within an HV region, which allows for diversity of up to 20% variation for adaptation (57). A number of cis-acting elements important for satBaMV replication have been identified within HV regions in protoplast and wholeplant assays (1).…”

“…A number of cis-acting elements important for satBaMV replication have been identified within HV regions in protoplast and wholeplant assays (1). Strikingly, the 5Ј HV region folds into an evolutionarily conserved AHSL secondary structure whose intramolecular base pairing is more important for satBaMV replication than the primary sequence (57). Taking advantage of the AHSL structure being functionally interchangeable between the two phylogenetic satBaMV groups (57), the HV region was further mapped as the key downregulating determinant by exchanging the HV region between the BSL6 and BSF4 satBaMVs (Fig.…”

“…P20 is an RNA-binding protein (49) but is dispensable for satBaMV replication (25). The satBaMV isolates collected worldwide were classified into two major phylogenetic groups, A and B, in which one hypervariable (HV) region with divergence of up to 20% was identified in the 5Ј UTRs of those satBaMV isolates (57). Enzymatic probing and mutational analysis revealed that the 5Ј UTR of prototype BSF4 satBaMV RNA folds into a long stem loop (LSL) and a small stem loop (1).…”

Mimicry of molecular pretenders: The terminal structures of satellites associated with plant RNA viruses

“…However, how these specific sequences or the structures involved in these sequences interacts with the helper virus or host protein and subsequently replication of satBaMV RNAs. 43,58 Some covariation occurs in the satBaMV 5' and 3' UTRs for maintaining the stem formation, which also provides conclusive evidence that the structure exists in the 5' and 3' UTRs of satBaMV RNA.…”

“…51,63 Despite the vast sequence diversity in the AHSL region among satBaMV isolates, the secondary structure of a conserved AHSL was identified and found to be required for satBaMV replication. 58,59 Also, the AHSL of BaMV, BSF4 and BSL6 share similarities in structures and functions (Fig. 3).…”