Replication of the RNA Segments of a Bipartite Viral Genome Is Coordinated by a Transactivating Subgenomic RNA

Eckerle, Lance D.; Ball, L. Andrew

doi:10.1006/viro.2002.1377

Cited by 49 publications

(65 citation statements)

References 34 publications

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“…Long-distance RNA-RNA interactions have been identified for several viruses for the regulation of subgenomic RNAs, as in the case of Red clover necrotic mosaic virus (Sit et al, 1998) and TBSV (Zhang et al, 1999). With FHV, the replication of subgenomic RNA3, which is synthesized by transcription from FHV RNA1, is necessary for the replication of RNA2 (Eckerle & Ball, 2002;Eckerle et al, 2003). We speculate that a similar interaction regulates the replication of CymRSV sat RNA.…”

Section: Discussionmentioning

confidence: 80%

Expression of tombusvirus open reading frames 1 and 2 is sufficient for the replication of defective interfering, but not satellite, RNA

Rubino¹,

Pantaleo²,

Navarro³

et al. 2004

Journal of General Virology

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Yeast cells co-expressing the replication proteins p36 and p95 of Carnation Italian ringspot virus (CIRV) support the RNA-dependent replication of several defective interfering (DI) RNAs derived from either the genome of CIRV or the related Cymbidium ringspot virus (CymRSV), but not the replication of a satellite RNA (sat RNA) originally associated with CymRSV. DI, but not sat RNA, was replicated in yeast cells co-expressing both DI and sat RNA. Using transgenic Nicotiana benthamiana plants constitutively expressing CymRSV replicase proteins (p33 and p92), or transiently expressing either these proteins or CIRV p36 and p95, it was shown that expression of replicase proteins alone was also not sufficient for the replication of sat RNA in plant cells. However, it was also shown that replicating CIRV genomic RNA deletion mutants encoding only replicase proteins could sustain replication of sat RNA in plant cells. These results suggest that sat RNA has a replication strategy differing from that of genomic and DI RNAs, for it requires the presence of a cis-replicating genome acting as a trans-replication enhancer. INTRODUCTIONTombusviruses are small isometric plant viruses belonging to the genus Tombusvirus, family Tombusviridae. Their genome is a monopartite, single-stranded, positive-sense RNA of 4800 nt containing five ORFs. ORF1 and -2 encode the replicase proteins of 33 or 36 kDa (p33 or p36), depending on the species, and the corresponding readthrough products, p92 and p95. ORF3 encodes the coat protein (CP), and two nested ORFs (ORF4 and -5) encode two proteins involved in virus movement and pathogenesis Silhavy et al., 2002). Tombusvirus infections are often associated with small parasitic RNAs, which can be either defective interfering (DI) or satellite (sat) RNAs. DI RNAs are shortened forms of genomic RNA deprived of all viral genes required for replication, encapsidation and movement of the viral genome. They are generated by errors of the viral replicase, which bypasses local intramolecular base-paired regions of genomic RNA, thus leading to the synthesis of deletion mutants. All described tombusvirus DI RNA molecules contain segments of viral RNA, derived from the 59 leader sequence, the replicase and movement protein genes and the 39 noncoding sequence. Tombusviruses can support the replication of homologous or heterologous DI RNA in plant (Havelda et al., 1998) or yeast cells (Pantaleo et al., 2003(Pantaleo et al., , 2004Panavas & Nagy, 2003). Tombusvirus DI RNAs have been widely used for the analysis of cis-acting factors directing the replication of viral RNA both in vivo Chang et al., 1995;Ray & White, 1999White & Morris, 1994;Wu & White, 1998;Wu et al., 2001) and in vitro (Nagy & Pogany, 2000; Panavas et al., 2002a, b;Panavas & Nagy, 2003).The molecular biology of tombusvirus sat RNAs has been much less studied. So far, the best characterized sat RNA is the 621 nt sat RNA of Cymbidium ringspot virus (CymRSV) whose cis-acting sequence requirements essential for replication and the significance and ...

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Section: Discussionmentioning

confidence: 80%

Expression of tombusvirus open reading frames 1 and 2 is sufficient for the replication of defective interfering, but not satellite, RNA

Rubino¹,

Pantaleo²,

Navarro³

et al. 2004

Journal of General Virology

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“…These include elements at the 5¢ ends that may be required for genome circularization (Barton et al 2001;Frolov et al 2001;Herold and Andino 2001;Khromykh et al 2001;You et al 2001), and internal elements such as repressors, enhancers, and other replication-required elements, which function either in cis (Kim and Makino, 1995;Klovins et al 1998;Nagy et al 1999;Ray andWhite 1999, 2003;Murray and Barton 2003;Panavas and Nagy 2003;Pogany et al 2003;Zhang and Simon 2003;Zhang et al 2004b) or in trans (Sit et al 1998;Eckerle and Ball 2002). Enhancers are generally found on viral (À)-strands, need not be proximal to the core promoter, contain sequence and/or structural features of core promoters, and can promote transcription in the presence of sequences resembling the transcription initiation site (Nagy et al 1999;Panavas and Nagy 2003;Ray and White 2003).…”

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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“…Both B1 and B2 are dispensable for FHV RNA replication in some mammalian cells, and B2 is dispensable for FHV RNA replication in yeast cells (5,13,33). However, a mutant FHV RNA1 unable to synthesize B2 exhibits phenotypic defects in RNA replication in cultured Drosophila cells (21,27).…”

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confidence: 99%

Nodamura Virus Nonstructural Protein B2 Can Enhance Viral RNA Accumulation in both Mammalian and Insect Cells

Johnson

Price

Eckerle

et al. 2004

J Virol

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During infection of both vertebrate and invertebrate cell lines, the alphanodavirus Nodamura virus (NoV) expresses two nonstructural proteins of different lengths from the B2 open reading frame. The functions of these proteins have yet to be determined, but B2 of the related Flock House virus suppresses RNA interference both in Drosophila cells and in transgenic plants. To examine whether the NoV B2 proteins had similar functions, we compared the replication of wild-type NoV RNA with that of mutants unable to make the B2 proteins. We observed a defect in the accumulation of mutant viral RNA that varied in extent from negligible in some cell lines (e.g., baby hamster kidney cells) to severe in others (e.g., human HeLa and Drosophila DL-1 cells). These results are consistent with the notion that the NoV B2 proteins act to circumvent an innate antiviral response such as RNA interference that differs in efficacy among different host cells.Nodamura virus (NoV) is the type species of the genus Alphanodavirus of the Nodaviridae, a family of small riboviruses with bipartite, positive-strand RNA genomes that also includes Flock House virus (FHV). NoV is unique among alphanodaviruses in its ability to lethally infect both insects and mammals, including the mosquitoes Aedes aegypti, Aedes albopictus, and Toxorhynchites amboinensis (4, 36, 41), suckling mice, and suckling hamsters (17,35,36). NoV infects cultured mosquito cells from Aedes pseudoscutellaris, A. aegypti, and A. albopictus (1, 3, 41) and cultured baby hamster kidney BHK21 cells (3,23,30). When NoV genomic RNAs are introduced by transfection, they can replicate in a wide range of cultured cells (6).The divided nodavirus genome naturally separates the replicative and packaging functions onto two different positivesense RNA molecules, RNA1 and RNA2, respectively. These two genomic RNAs are copackaged into the same virion, and both are required for infectivity (24,30,38). RNA1 encodes protein A, the RNA-dependent RNA polymerase (RdRp) that catalyzes the replication of both genome segments. RNA2 encodes the viral capsid precursor protein, ␣. RNA2 and protein ␣ are dispensable for RNA1 replication. Protein A also catalyzes the synthesis of a single subgenomic RNA3 from an RNA1 template. RNA3 is not packaged into virus particles. For FHV, RNA3 encodes two small proteins, B1 and B2, in overlapping reading frames. Protein B1 is in the same reading frame as protein A and thus represents its C-terminal fragment, whereas protein B2 is in the ϩ1 reading frame relative to protein A (11). For NoV, the first and second AUG codons of RNA3 initiate the translation of two forms of B2 (B2-137 and B2-134) that differ only at the N terminus, whereas B1 initiates at the third AUG codon. As for FHV, the B2 proteins are in the ϩ1 reading frame relative to the A/B1 open reading frame (ORF) (23). All three proteins are detected in cells transfected with NoV RNA1 (NoV1), which replicates autonomously and leads to the synthesis of RNA3 (23).The functions of the nodavirus B1 and B2 prote...

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Replication of the RNA Segments of a Bipartite Viral Genome Is Coordinated by a Transactivating Subgenomic RNA

Cited by 49 publications

References 34 publications

Expression of tombusvirus open reading frames 1 and 2 is sufficient for the replication of defective interfering, but not satellite, RNA

Expression of tombusvirus open reading frames 1 and 2 is sufficient for the replication of defective interfering, but not satellite, RNA

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

Nodamura Virus Nonstructural Protein B2 Can Enhance Viral RNA Accumulation in both Mammalian and Insect Cells

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