The 3′-Terminal Structure Required for Replication of Barley Yellow Dwarf Virus RNA Contains an Embedded 3′ End

Koev, Gennadiy; Liu, Sijun; Beckett, Randy; Miller, W. Allen

doi:10.1006/viro.2001.1268

Cited by 60 publications

(58 citation statements)

References 68 publications

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“…1C,D;Na and White 2006). Similar RSEÀ39CSS interactions are also proposed for Turnip crinkle virus (TCV) (Zhang et al 2004) and are predicted in other genera in the family Tombusviridae (Koev et al 2002;Na and White 2006). For TBSV (genus Tombusvirus, family Tombusviridae), this interaction mediates replicase complex formation in vivo and modulates negative-strand synthesis in vitro (Panaviene et al 2005;Pogany et al 2003).…”

Section: Introductionsupporting

confidence: 56%

Conformational organization of the 3′ untranslated region in the tomato bushy stunt virus genome

Hong¹,

Fabian²,

White³

2006

RNA

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The 39 untranslated regions (UTRs) of positive-strand RNA viruses often form complex structures that facilitate various viral processes. We have examined the RNA conformation of the 352 nucleotide (nt) long 39 UTR of the Tomato bushy stunt virus (TBSV) genome with the goal of defining both local and global structures that are important for virus viability. Gel mobility analyses of a 39-terminal 81 nt segment of the 39 UTR revealed that it is able to form a compact RNA domain (or closed conformation) that is stabilized by a previously proposed tertiary interaction. RNA-RNA gel shift assays were used to provide the first physical evidence for the formation of this tertiary interaction and revealed that it represents the dominant or ''default'' structure in the TBSV genome. Further analysis showed that the tertiary interaction involves five base pairs, each of which contributes differently to overall complex stability. Just upstream from the 39-terminal domain, a long-distance RNA-RNA interaction involving 39 UTR sequences was found to be required for efficient viral RNA accumulation in vivo and to also contribute to the formation of the 39-terminal domain in vitro. Collectively, these results provide a comprehensive overview of the conformational and functional organization of the 39 UTR of the TBSV genome.

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Section: Introductionsupporting

confidence: 56%

Conformational organization of the 3′ untranslated region in the tomato bushy stunt virus genome

Hong¹,

Fabian²,

White³

2006

RNA

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“…RNAs were analyzed by Northern blot hybridization as described in Koev et al (2002). A 32 P-labeled probe complementary to the 39-terminal 1.5 kb of the full-length viral RNA was used to detect the BYDV genomic and subgenomic RNA accumulation.…”

Section: Northern Blot Analysismentioning

confidence: 99%

Oscillating kissing stem–loop interactions mediate 5′ scanning-dependent translation by a viral 3′-cap-independent translation element

Rakotondrafara¹,

Polacek²,

Harris³

et al. 2006

RNA

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The 39-untranslated regions (UTRs) of a group of novel uncapped viral RNAs allow efficient translation initiation at the 59-proximal AUG. A well-characterized model is the Barley yellow dwarf virus class of cap-independent translation elements (BTE). It facilitates translation by forming kissing stem-loops between the BTE in the 39-UTR and a BTE-complementary loop in the 59-UTR. Here we investigate the mechanisms of the long-distance interaction and ribosome entry on the RNA. Upstream AUGs or 59-extensions of the 59-UTR inhibit translation, indicating that, unlike internal ribosome entry sites in many viral RNAs, the BTE relies on 59-end-dependent ribosome scanning. Cap-independent translation occurs when the kissing sites are moved to different regions in either UTR, including outside of the BTE. The BTE can even confer cap-independent translation when fused to the 39-UTR of a reporter RNA harboring dengue virus sequences that cause base-pairing between the 39 and 59 ends. Thus, the BTE serves as a functional sensor to detect sequences capable of long-distance base-pairing. We propose that the kissing interaction is repeatedly disrupted by the scanning ribosome and re-formed in an oscillating process that regulates ribosome entry on the RNA.

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“…Recent evidence obtained using several unrelated viruses suggests that RNA conformational switches may be needed to hide and expose viral 3¢ ends, which may temporally regulate (+)-and (À)-strand synthesis. Some viruses appear to activate these switches by changing the conformation of 3¢-proximal structures, a process mediated by one or more unstable base pairs between complementary short sequences located within and outside of hairpins (Olsthoorn et al 1999;Koev et al 2002;Pogany et al 2003;Zhang et al 2004b). For example, Barley yellow dwarf virus is proposed to repress (À)-strand synthesis by embedding its 3¢ end in a ''pocket'' structure, thus making it unavailable to the RdRp (Koev et al 2002).…”

Section: Introductionmentioning

confidence: 99%

“…Some viruses appear to activate these switches by changing the conformation of 3¢-proximal structures, a process mediated by one or more unstable base pairs between complementary short sequences located within and outside of hairpins (Olsthoorn et al 1999;Koev et al 2002;Pogany et al 2003;Zhang et al 2004b). For example, Barley yellow dwarf virus is proposed to repress (À)-strand synthesis by embedding its 3¢ end in a ''pocket'' structure, thus making it unavailable to the RdRp (Koev et al 2002). A similar molecular switch in the Mouse hepatitis virus genome involves sequences within a stem-loop and pseudoknot in the 3¢ untranslated region (UTR) (Goebel et al 2004).…”

Section: Introductionmentioning

confidence: 99%

Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA

Zhang

Zhang²,

George³

et al. 2005

RNA

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Synthesis of wild-type levels of turnip crinkle virus (TCV)-associated satC complementary strands by purified, recombinant TCV RNA-dependent RNA polymerase (RdRp) in vitro was previously determined to require 3¢ end pairing to the large symmetrical internal loop of a phylogenetically conserved hairpin (H5) located upstream from the hairpin core promoter. However, wildtype satC transcripts, which fold into a single detectable conformation in vitro as determined by temperature-gradient gel electrophoresis, do not contain either the phylogenetically inferred H5 structure or the 3¢ end/H5 interaction. This implies that conformational changes are required to produce the phylogenetically inferred H5 structure for its pairing with the 3¢ end, which takes place subsequent to the initial conformation assumed by the RNA and prior to transcription initiation. The DR region, located 140 nucleotides upstream from the 3¢ end and previously determined to be important for transcription in vitro and replication in vivo, is proposed to have a role in the conformational switch, since stabilizing the phylogenetically inferred H5 structure decreases the negative effects of a DR mutation in vivo. In addition, high levels of aberrant transcription correlate with a specific conformational change in the Pr while maintaining the same conformation of the 3¢ terminus. These results suggest that a series of events that promote conformational changes is needed to expose the 3¢ terminus to the RdRp for accurate synthesis of wild-type levels of complementary strands in vitro.

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The 3′-Terminal Structure Required for Replication of Barley Yellow Dwarf Virus RNA Contains an Embedded 3′ End

Cited by 60 publications

References 68 publications

Conformational organization of the 3′ untranslated region in the tomato bushy stunt virus genome

Conformational organization of the 3′ untranslated region in the tomato bushy stunt virus genome

Oscillating kissing stem–loop interactions mediate 5′ scanning-dependent translation by a viral 3′-cap-independent translation element

Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA

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