Mutation and Recombination Frequencies Reveal a Biological Contrast within Strains of Cucumber Mosaic Virus

ABSTRACTRecentin plantastudies have shown that strains Fny and LS ofCucumber mosaic virus(CMV) display differential genetic diversities, Fny and LS having higher and lower mutation frequencies, respectively (J. S. Pita and M. J. Roossinck, J Virol 87:790–797, 2012http://dx.doi.org/10.1128/JVI.01891-12). In this article, we show that these virus strains have differential recombination frequencies as well. However, the high-diversity Fny strain is a low-recombination virus, whereas the very-low-diversity LS strain is instead a high-recombination virus. Unlike the mutation frequency that was determined by both RNAs 1 and 2, the control elements of recombination frequency reside predominantly within RNA 2, specifically within the 2a gene.IMPORTANCERecombination is an important mechanism in virus evolution that can lead to increased or decreased variation and is a major player in virus speciation events that can lead to emerging viruses. Although viral genomes show very frequent evidence of recombination, details of the mechanism involved in these events are still poorly understood. We show here that the reciprocal effects of high mutation frequency and low recombination frequency (andvice versa) involve the RNA-dependent RNA polymerase of the virus, and we speculate that these evolutionary events are related to differences in processivity for two strains of the same virus.

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Deep Sequencing of Recombinant Virus Populations in Transgenic and Nontransgenic Plants Infected with Cucumber mosaic virus

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-02-13-0057-r ◽

2013 ◽

Vol 26 (7) ◽

pp. 801-811 ◽

Cited By ~ 6

Author(s):

Marco Morroni ◽

Mireille Jacquemond ◽

Mark Tepfer

Keyword(s):

Transgenic Plants ◽

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

De Novo ◽

Recombinant Viruses ◽

Viral Genomes ◽

Large Deletions ◽

Cp Gene ◽

Viral Sequences ◽

Virus Variability

Recombination is a major source of virus variability, and the question of whether novel recombinant viruses would emerge in transgenic plants expressing viral sequences has been a biosafety issue. We describe the results of pyrosequencing the recombinant viral RNAs appearing in transgenic plants expressing the coat protein (CP) gene and 3′ noncoding region of Cucumber mosaic virus RNA3, as well as in nontransgenic controls. The populations of recombinants in both transgenic and nontransgenic plants were similar to those previously described from Sanger sequencing but many more recombinant types were observed, including a novel class of large deletions removing all or nearly the entire CP gene. These results show that populations of recombinant viral genomes arising de novo can be characterized in detail by pyrosequencing, and confirm that the transgenic plants did not harbor novel recombinants of biosafety concern.

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Behavior of RNAi suppressor protein 2b of Cucumber mosaic virus in planta in presence and absence of virus

Virus Genes ◽

10.1007/s11262-008-0232-2 ◽

2008 ◽

Vol 37 (1) ◽

pp. 96-102 ◽

Cited By ~ 9

Author(s):

Shelly Praveen ◽

Satendra K. Mangrauthia ◽

Priyanka Singh ◽

Anil K. Mishra

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

In Planta ◽

Rnai Suppressor ◽

Presence And Absence

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Cucumber mosaic virus coat protein modulates the accumulation of 2b protein and antiviral silencing that causes symptom recovery in planta

PLoS Pathogens ◽

10.1371/journal.ppat.1006522 ◽

2017 ◽

Vol 13 (7) ◽

pp. e1006522 ◽

Cited By ~ 28

Author(s):

Xiao-Peng Zhang ◽

De-Shui Liu ◽

Teng Yan ◽

Xiao-Dong Fang ◽

Kai Dong ◽

...

Keyword(s):

Coat Protein ◽

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

In Planta ◽

Virus Coat Protein ◽

2B Protein ◽

Symptom Recovery ◽

Virus Coat

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Template-Independent Repair of the 3′ End of Cucumber Mosaic Virus Satellite RNA Controlled by RNAs 1 and 2 of Helper Virus

Journal of Virology ◽

10.1128/jvi.72.6.5061-5066.1998 ◽

1998 ◽

Vol 72 (6) ◽

pp. 5061-5066 ◽

Cited By ~ 20

Author(s):

József Burgyán ◽

Fernando García-Arenal

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Sequence Comparison ◽

Rna Viruses ◽

Helper Virus ◽

Viral Rna ◽

Genome Integrity ◽

In Planta ◽

Satellite Rna ◽

Cucumber Mosaic Cucumovirus

ABSTRACT RNA viruses which do not have a poly(A) tail or a tRNA-like structure for the protection of their vulnerable 3′ termini may have developed a different strategy to maintain their genome integrity. We provide evidence that deletions of up to 7 nucleotides from the 3′ terminus of cucumber mosaic cucumovirus (CMV) satellite RNA (satRNA) were repaired in planta in the presence of the helper virus (HV) CMV. Sequence comparison of 3′-end-repaired satRNA progenies, and of satRNA and HV RNA, suggested that the repair was not dependent on a viral template. The 3′ end of CMV satRNA lacking the last three cytosines was not repaired in planta in the presence of tomato aspermy cucumovirus (TAV), although TAV is an efficient helper for the replication of CMV satRNA. With use of pseudorecombinants constructed by the interchange of RNAs 1 and 2 of TAV and CMV, evidence was provided that the 3′-end repair was controlled by RNAs 1 and 2 of CMV, which encode subunits of the viral RNA replicase. These results, and the observation of short repeated sequences close to the 3′ terminus of repaired molecules, suggest that the HV replicase maintains the integrity of the satRNA genome, playing a role analogous to that of cellular telomerases.

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Impact of Cultivated Hosts on the Recombination ofCucumber Mosaic Virus

Journal of Virology ◽

10.1128/jvi.01770-18 ◽

2019 ◽

Vol 93 (7) ◽

Cited By ~ 3

Author(s):

Rimnoma S. Ouedraogo ◽

Justin S. Pita ◽

Irenée P. Somda ◽

Oumar Traore ◽

Marilyn J. Roossinck

Keyword(s):

Mosaic Virus ◽

Rna Viruses ◽

Recombination Frequency ◽

Virus Disease ◽

Population Diversity ◽

Plant Host ◽

Content Type ◽

Defective Rnas ◽

Subgroup Ii ◽

The Impact

ABSTRACTCucumber mosaic virus(CMV) is one of the most successful viruses known, infecting over 1,200 species of plants. Like other single-stranded RNA viruses, CMV is known to have a high potential for population diversity due to error-prone replication and short generation times. Recombination is also a mechanism that allows viruses to adapt to new hosts. Host genes have been identified that impact the recombination of RNA viruses by using single-cell yeast systems. To determine the impact that the natural plant host has on virus recombination, we used a high-recombination-frequency strain of CMV, LS-CMV, which belongs to subgroup II, in three different cultivated hosts:Capsicum annuumcv. Marengo (pepper),Nicotiana tabacumcv. Xanthi nc (tobacco), andCucurbita pepocv. Black Beauty (zucchini). The recombination frequency was calculated by using an RNA 3 reporter carrying restriction enzyme sites created by introducing silent mutations. Our results show that the recombination frequency of LS-CMV is correlated with the infected host. The recombination events in pepper were 1.8-fold higher than those in tobacco and 5-fold higher than those in zucchini. Furthermore, we observed the generation of defective RNAs in inoculated pepper plants, but not in tobacco or zucchini. These results indicate that the host is involved in both intra- and intermolecular recombination events and that hosts like pepper could foster more rapid evolution of the virus. In addition, we report for the first time the production of defective RNAs in a CMV subgroup II isolate.IMPORTANCERecombination is an important mechanism used by viruses for their diversification and to adapt to diverse hosts. Understanding the host role in the mechanisms of evolution is important for virus disease management and controlling the emergence of new strains. This study shows the impact that cultivated hosts are playing in the evolution of CMV. Furthermore, our results and previous studies show how some specific hosts could be an ideal environment for the emergence of new viral strains.

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Structural and functional characterization of the 5′ region of subgenomic RNA5 of cucumber mosaic virus

Journal of General Virology ◽

10.1099/vir.0.2008/001057-0 ◽

2008 ◽

Vol 89 (7) ◽

pp. 1729-1738 ◽

Cited By ~ 11

Author(s):

Jeremy R. Thompson ◽

Emanuele Buratti ◽

Mélissanne de Wispelaere ◽

Mark Tepfer

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Functional Characterization ◽

Structural Elements ◽

Wild Type ◽

In Planta ◽

Stem Loop ◽

Conserved Sequence ◽

Subgroup Ii

The uncapped and ORF-less subgenomic RNA5 is produced in subgroup II strains of cucumber mosaic virus (CMV), but not in subgroup I strains. Its initiation nucleotide (nt 1903) is in a 21 nt conserved sequence (Box1) that is absent in CMV subgroup I. Putative non-coding RNA structural elements surrounding Box1 in the plus and minus strand were identified in silico and by in vitro RNase probing. Four main stem–loop structures (SLM, SLL, SLK and SLJ) were identified between nt 1887 and 1999 of isolate R-CMV (subgroup II), with notable differences within SLM and SLL between the two strands. Mutation of a stem–loop within SLM, even when the predicted wild-type structure was maintained, showed significant reduction in RNA5 levels in planta. Three mutants containing 3–4 nt substitutions between positions −39 and +49 showed significantly reduced levels of RNA5, while another similar mutant at positions 80–83 had RNA5 levels comparable to wild-type. Deletion of Box1 resulted in similar levels of RNA3 and 4 as wild-type, while eliminating RNA5. Insertion of Box1 into a subgroup I isolate was not sufficient to produce RNA5. However, in a mutant with an additional 21 nt of R-CMV 3′ of Box1 (positions −1 to +41), low levels of RNA5 were detected. Taken together, these results have identified regions of the viral genome responsible for RNA5 production and in addition provide strong evidence for the existence of newly identified conserved structural elements in the 5′ part of the 3′ untranslated region.

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