Diverse Mechanisms of RNA Recombination

Gmyl, Anatoly P.; Agol, Vadim I.

doi:10.1007/s11008-005-0069-x

Cited by 13 publications

(15 citation statements)

References 150 publications

(182 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Subsequently, it was observed in other picornaviruses (191,192) as well as in flaviviruses (193)(194)(195)(196). As discussed elsewhere (197), this mechanism may also be responsible for certain earlier observed cases of recombination between alphaviruses (198) and rubiviruses (199) (both belonging to the Togaviridae family) and hence appears to be a general phenomenon.…”

Section: Insertions Deletions and Replacementsmentioning

confidence: 76%

Emergency Services of Viral RNAs: Repair and Remodeling

Agol

Gmyl

2018

Microbiol Mol Biol Rev

View full text Add to dashboard Cite

Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.

show abstract

Section: Insertions Deletions and Replacementsmentioning

confidence: 76%

Emergency Services of Viral RNAs: Repair and Remodeling

Agol

Gmyl

2018

Microbiol Mol Biol Rev

View full text Add to dashboard Cite

show abstract

“…In animal RNA viruses, in addition to copy-choice mechanism, nonreplicative mechanisms were indicated as a possible source of their genetic diversity (53). This has been confirmed in the absence of viral replication (48), based on transesterification among RNAs (27), on the rescue from RNAse cleavage (66) or on crossovers with nonreplicative precursors (110).…”

Section: Final Remarksmentioning

confidence: 95%

“…Two models are suggested to account for RNA-RNA recombination: the cleavage-religation of precursor RNAs supporting the formation of nonhomologous recombinants and the replicative mechanism, where the RdRp-nascent chain complex switches mid-replication from one RNA template to another, acceptor RNA template (53). Studying in vitro RNA recombination of Qβ bacteriophage, Chetverin et al (27) proposed the idea of the cleavage-religation model where a breakage of the same or different precursor RNA molecules at two distinct sites followed by their religation supports the formation of nonhomologous recombinants.…”

Section: Replication and Recombinationmentioning

confidence: 99%

RNA-RNA Recombination in Plant Virus Replication and Evolution

Sztuba-Solińska

Urbanowicz

Figlerowicz

et al. 2011

Annu. Rev. Phytopathol.

150

110

View full text Add to dashboard Cite

RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence for recombination, not only between related viruses but also among distantly related viruses, and even with host RNAs, suggests that plant viruses unabashedly test recombination with any genetic material at hand.

show abstract

“…Nevertheless, the involvement of host factors cannot be excluded. Several variants of nascent-strand transfer are conceivable (Gmyl & Agol, 2005;Nagy & Simon, 1997), but experimental evidence is still lacking. Important structural factors of the template or nascent strand that are used for classification have been identified in these model viruses and can be subdivided into primary factors, such as sequence similarity, AU-rich motifs, sequence complementarity and replicative cis elements, and secondary structures, such as stem-loops (Bruyere et al, 2000;Nagy & Bujarski, 1993Olsthoorn et al, 2002;Shapka & Nagy, 2004).…”

Section: Introductionmentioning

confidence: 99%

Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination

Draghici

Varrelmann

2009

Journal of General Virology

View full text Add to dashboard Cite

Virus RNA recombination, one of the main factors for genetic variability and evolution, is thought to be based on different mechanisms. Here, the recently described in vivo potato virus X (PVX) recombination assay . J Virol 83, 7761-7769] was applied to characterize structural parameters of recombination. The assay uses an Agrobacterium-mediated expression system incorporating a PVX green fluorescent protein (GFP)-labelled full-length clone. The clone contains a partial coat protein (CP) deletion that causes defectiveness in cell-to-cell movement, together with a functional CP+39 non-translated region (ntr) transcript, in Nicotiana benthamiana leaf tissue. The structural parameters assessed were the length of sequence overlap, the distance between mutations and the degree of sequence similarity. The effects on the observed frequency of reconstitution and the composition of the recombination products were characterized. Application of four different type X intact PVX CP genes with variable composition allowed the estimation of the junction sites of precise homologous recombination. Although one template switch would have been sufficient for functional reconstitution, between one and seven template switches were observed. Use of PVX-GFP mutants with CP deletions of variable length resulted in a linear decrease of the reconstitution frequency. The critical length observed for homologous recombination was 20-50 nt. Reduction of the reconstitution frequency was obtained when a phylogenetically distant PVX type Bi CP gene was used. Finally, the prediction of CP and 39-ntr RNA secondary structure demonstrated that recombination-junction sites were located mainly in regions of stem-loop structures, allowing the recombination observed to be categorized as similarity-assisted.

show abstract

Diverse Mechanisms of RNA Recombination

Cited by 13 publications

References 150 publications

Emergency Services of Viral RNAs: Repair and Remodeling

Emergency Services of Viral RNAs: Repair and Remodeling

RNA-RNA Recombination in Plant Virus Replication and Evolution

Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination

Contact Info

Product

Resources

About