Defective and Defective Interfering RNAs of Monopartite Plus-strand RNA Plant Viruses

White, K. Andrew; Morris, T. Jack

doi:10.1007/978-3-662-09796-0_1

Cited by 41 publications

(47 citation statements)

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“…Current models of RNA recombination in carmoand tombusviruses predict that the viral RdRp jumps from the donor RNA to the acceptor RNA during viral RNA synthesis (37,39,70). Therefore, we tested the abilities of two viral RdRps, a recombinant TCV RdRp and the partially purified CNV RdRp, to switch templates in vitro.…”

Section: Resultsmentioning

confidence: 99%

“…The tombusvirus DI RNAs are mosaic types that have two or three sequence deletions (70), resulting in 80 to 90% reduced genome size for DI RNAs when compared to the parental virus genome. Sequence deletions during DI RNA formation are thought to be the consequence of viral replicase jumping on the templates, and the deletions may occur in a stepwise manner (68,70).The most popular model of RNA recombination is the template-switching (copy-choice) mechanism, which predicts that the viral RNA-dependent RNA polymerase (RdRp) switches templates during cRNA synthesis (22,26,27,33,37). After the jump from the donor to the acceptor RNA, the RdRp is assumed to continue RNA synthesis on the acceptor template, using the nascent RNA as a primer.…”

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confidence: 99%

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confidence: 99%

“…DI RNAs are mainly derived from the parent (helper) virus via sequence deletion(s). The DI RNAs are deficient in replication and/or other functions, which makes them dependent on the helper virus for their survival and spread (50,70). The best-known DI RNAs among plant viruses are those associated with tombusvirus infections.…”

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Mechanism of RNA Recombination in Carmo- and Tombusviruses: Evidence for Template Switching by the RNA-Dependent RNA Polymerase In Vitro

Cheng

Nagy

2003

J Virol

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RNA recombination occurs frequently during replication of tombusviruses and carmoviruses, which are related small plus-sense RNA viruses of plants. The most common recombinants generated by these viruses are either defective interfering (DI) RNAs or chimeric satellite RNAs, which are thought to be generated by template switching of the viral RNA-dependent RNA polymerase (RdRp) during the viral replication process. To test if RNA recombination is mediated by the viral RdRp, we used either a purified recombinant RdRp of Turnip crinkle carmovirus or a partially purified RdRp preparation of Cucumber necrosis tombusvirus. We demonstrated that these RdRp preparations generated RNA recombinants in vitro. The RdRp-driven template switching events occurred between either identical templates or two different RNA templates. The template containing a replication enhancer recombined more efficiently than templates containing artificial sequences. We also observed that AU-rich sequences promote recombination more efficiently than GC-rich sequences. Cloning and sequencing of the generated recombinants revealed that the junction sites were located frequently at the ends of the templates (end-to-end template switching). We also found several recombinants that were generated by template switching involving internal positions in the RNA templates. In contrast, RNA ligationbased RNA recombination was not detected in vitro. Demonstration of the ability of carmo-and tombusvirus RdRps to switch RNA templates in vitro supports the copy-choice models of RNA recombination and DI RNA formation for these viruses.Viral RNA recombination, a process that joins together two noncontiguous RNA segments, is an especially powerful tool in virus evolution, since it can rapidly lead to dramatic changes in virus genomes by recombining or rearranging "battle-tested" (i.e., evolutionarily successful) sequences. Accordingly, the significant role of RNA recombination in emergence of new viruses or virus strains is well documented for numerous human, animal, plant, insect, fungal, and bacterial viruses (2, 4, 12, 17, 18, 20, 21, 27-31, 51, 57, 61, 62, 64, 65, 71). In addition to increasing sequence variability, RNA recombination can be an efficient tool for viruses to repair viral genomes, thus contributing to virus fitness (6,14,35,36,53,66). In spite of its significance, our understanding of RNA recombination is incomplete. This is due to the complex nature of RNA recombination and the lack of tractable systems for mechanistic studies.RNA recombination may also play a role in the formation of subviral RNAs that include defective interfering (DI) RNAs associated with many animal and plant viruses. DI RNAs are mainly derived from the parent (helper) virus via sequence deletion(s). The DI RNAs are deficient in replication and/or other functions, which makes them dependent on the helper virus for their survival and spread (50, 70). The best-known DI RNAs among plant viruses are those associated with tombusvirus infections. The tombusvirus DI RNAs are mosai...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Mechanism of RNA Recombination in Carmo- and Tombusviruses: Evidence for Template Switching by the RNA-Dependent RNA Polymerase In Vitro

Cheng

Nagy

2003

J Virol

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“…The D-RNA retains the cis-acting components necessary for efficient replication but depends on helper virus replication and encapsidation functions (Graves et al, 1996). The presence of D-RNAs has important effects on host symptoms, ranging from amelioration to enhancement, to no effect at all (White and Morris, 1999).…”

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Analysis of external factors that affect formation and accumulation of D-RNAs in Bromovirus infections

Sandoval

Llamas

Romero³

2008

Span. j. agric. res.

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Defective RNA molecules (D-RNAs) are being studied in several plant RNA virus groups. In the genus Bromovirus, D-RNAs have been described for Broad bean mottle virus (BBMV), they are formed by a single internal deletion in the RNA2 and have been generated de novo by serial passages. In contrast, in Brome mosaic virus (BMV) D-RNAs are generated by a single or double internal deletion in the RNA3 without serial passages in their hosts. In this work the external effects of the host and the growth temperature in the generation and accumulation of D-RNAs in BBMV, BMV and Cowpea chlorotic mottle virus (CCMV) are studied. The BBMV and BMV D-RNAs were generated and accumulated with or without serial passages of the viruses in different hosts and cultivars. Plants grown at 12, 16, 20 and 24°C in a growth chamber and in a greenhouse (22 ± 5°C) generated D-RNAs after being inoculated with virusfree D-RNAs, with and without passages. The D-RNAs observed in BBMV and BMV presented some common characteristics: both were formed de novo after serial passages or without passages, their deletion borders had short repeated and palindrome sequences that favour recombination. In addition, growing inoculated plants at lower temperatures greatly facilitated the generation and accumulation of D-RNAs. The CCMV did not generate defective molecules in cowpea (Vigna unguiculata) and Nicotiana benthamiana plants after several serial passages or without passages. This is the first time that D-RNAs have been generated in BBMV without passages and BMV with serial passages.Additional key words: BBMV, BMV, CCMV, host effects, temperature conditions. Resumen Análisis de los factores externos que afectan a la formación y acumulación de los D-RNAs en infecciones de BromovirusLos RNAs defectivos (D-RNAs) están siendo estudiados en diversos virus RNA de plantas. En el género Bromovirus se han descrito D-RNAs en el virus del moteado del haba (BBMV), formados mediante una delección interna en el RNA2, que se generan de novo mediante pases seriados del virus sobre un nuevo huésped. En contraste, en el virus del mosaico del bromo (BMV), los D-RNAs se forman por una o dos delecciones en el RNA3 sin necesidad de pases en sus huéspedes. En este trabajo estudiamos algunos factores externos, como los huéspedes, las inoculaciones y las temperaturas de crecimiento en la generación y acumulación de D-RNAs en BBMV, BMV y en el virus del moteado clorótico de la carilla (CCMV). Los D-RNAs de BBMV y BMV fueron generados y acumulados mediante pases seriados y sin pases de los virus en diferentes huéspedes y cultivares. Plantas inoculadas con BBMV y BMV sin D-RNAs, mantenidas a 12, 16, 20 y 24°C en cámaras de crecimiento a temperatura constante o en un invernadero (22 ± 5°C), generaron D-RNAs con o sin pases sobre nuevos huéspedes. Los D-RNAs observados en ambos virus presentan algunas características en común: son formados de novo mediante pases seriados o purificados de hojas infectadas algunas semanas después de la inoculación; los bordes de la delección tie...

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Using Vectors Derived from Tomato Bushy Stunt Virus (TBSV) and TBSV Defective Interfering RNAs (DIs)

Qiu

Scholthof

2007

CP Microbiology

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This unit describes principles and protocols for expressing a gene of interest in plant cells using gene vectors that are derived from an infectious full‐length cDNA plasmid of the tomato bushy stunt virus (TBSV) genomic RNA, and from defective interfering RNAs (DIs). The TBSV gene vector system permits convenient cloning, allows modification and abundant expression of the gene of interest, and facilitates biosecure containment of the gene vectors. These vectors can be employed for functional genomics studies and for analyzing the biochemical properties and subcellular distribution of expressed RNAs and/or their cognate proteins. As with other plant virus gene vectors, recombination and deletion of the gene of interest during virus multiplication limits the application of the TBSV gene vectors to the inoculated cells or leaves. Curr. Protoc. Microbiol. 7:16I.4.1‐16I.4.16. © 2007 by John Wiley & Sons, Inc.

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Defective and Defective Interfering RNAs of Monopartite Plus-strand RNA Plant Viruses

Cited by 41 publications

References 63 publications

Mechanism of RNA Recombination in Carmo- and Tombusviruses: Evidence for Template Switching by the RNA-Dependent RNA Polymerase In Vitro

Mechanism of RNA Recombination in Carmo- and Tombusviruses: Evidence for Template Switching by the RNA-Dependent RNA Polymerase In Vitro

Analysis of external factors that affect formation and accumulation of D-RNAs in Bromovirus infections

Using Vectors Derived from Tomato Bushy Stunt Virus (TBSV) and TBSV Defective Interfering RNAs (DIs)

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