Nonhomologous Recombination between Defective Poliovirus and Coxsackievirus Genomes Suggests a New Model of Genetic Plasticity for Picornaviruses

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, B; Joffret, Marie-Line; Delpeyroux, Françis

doi:10.1128/mbio.01119-14

Cited by 53 publications

(81 citation statements)

References 44 publications

(82 reference statements)

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“…Although an increase in IRES size might be attributable to replicative “stuttering” or non-templated incorporation of nucleotides, picornavirus polymerases are not known to be prone to such errors. However, recent studies have identified mechanisms, including non-homologous, non-replicative recombination (Gmyl et al, 2003; Holmblat et al, 2014) and an imprecise replicative recombinational process (Lowry et al, 2014) that could result in partial duplication of picornavirus genome fragments. Duplicated sequences present in a region of the genome that is not under strong selective pressure could diversify rapidly by nucleotide substitution or by partial deletion (Lowry et al, 2014) and might be particularly permissive for insertion of ‘captured’ domains, such as the “8-like” motif discussed above.…”

Section: Discussionmentioning

confidence: 99%

Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae

2015

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Picornavirus genomes contain internal ribosomal entry sites (IRESs) that promote end-independent translation initiation. Five structural classes of picornavirus IRES have been identified, but numerous IRESs remain unclassified. Here, previously unrecognized Type IV IRESs were identified in members of three proposed picornavirus genera (Limnipivirus, Pasivirus, Rafivirus) and four recognized genera (Kobuvirus, Megrivirus, Sapelovirus, Parechovirus). These IRESs are ∼230–420 nucleotides long, reflecting heterogeneity outside a common structural core. Closer analysis yielded insights into evolutionary processes that have shaped contemporary IRESs. The presence of related IRESs in diverse genera supports the hypothesis that they are heritable genetic elements that spread by horizontal gene transfer. Recombination likely also accounts for the exchange of some peripheral subdomains, suggesting that IRES evolution involves incremental addition of elements to a pre-existing core. Nucleotide conservation is concentrated in ribosome-binding sites, and at the junction of helical domains, likely to ensure orientation of subdomains in an active conformation.

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Section: Discussionmentioning

confidence: 99%

Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae

2015

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“…It is possible that the replication of this remaining wild-type population of viruses could generate, by a presently unknown mechanism, a majority of viruses with terminally deleted genomic RNAs in cardiomyocytes that are unable to replicate by themselves and a minority of wild-type viruses capable of maintaining a low-level chronic infection. The wild-type virus could also play the role of helper virus, allowing TD viruses to replicate by providing, in trans or through genomic recombination events, the elements necessary for their replication (50)(51)(52). Wild-type and TD viruses could reproduce in vivo by using a mode of viral persistence known to occur in cell culture via defective interfering (DI) particles (53).…”

Section: Discussionmentioning

confidence: 99%

Functional Consequences of RNA 5′-Terminal Deletions on Coxsackievirus B3 RNA Replication and Ribonucleoprotein Complex Formation

Lévêque

Garcia

Bouin

et al. 2017

J Virol

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Group B coxsackieviruses are responsible for chronic cardiac infections. However, the molecular mechanisms by which the virus can persist in the human heart long after the signs of acute myocarditis have abated are still not completely understood. Recently, coxsackievirus B3 strains with 5=-terminal deletions in genomic RNAs were isolated from a patient suffering from idiopathic dilated cardiomyopathy, suggesting that such mutant viruses may be the forms responsible for persistent infection. These deletions lacked portions of 5= stem-loop I, which is an RNA secondary structure required for viral RNA replication. In this study, we assessed the consequences of the genomic deletions observed in vivo for coxsackievirus B3 biology. Using cell extracts from HeLa cells, as well as transfection of luciferase replicons in two types of cardiomyocytes, we demonstrated that coxsackievirus RNAs harboring 5= deletions ranging from 7 to 49 nucleotides in length can be translated nearly as efficiently as those of wild-type virus. However, these 5= deletions greatly reduced the synthesis of viral RNA in vitro, which was detected only for the 7-and 21-nucleotide deletions. Since 5= stem-loop I RNA forms a ribonucleoprotein complex with cellular and viral proteins involved in viral RNA replication, we investigated the binding of the host cell protein PCBP2, as well as viral protein 3CD pro , to deleted positive-strand RNAs corresponding to the 5= end. We found that binding of these proteins was conserved but that ribonucleoprotein complex formation required higher PCBP2 and 3CD pro concentrations, depending on the size of the deletion. Overall, this study confirmed the characteristics of persistent CVB3 infection observed in heart tissues and provided a possible explanation for the low level of RNA replication observed for the 5=-deleted viral genomes-a less stable ribonucleoprotein complex formed with proteins involved in viral RNA replication.IMPORTANCE Dilated cardiomyopathy is the most common indication for heart transplantation worldwide, and coxsackie B viruses are detected in about one-third of idiopathic dilated cardiomyopathies. Terminal deletions at the 5= end of the viral genome involving an RNA secondary structure required for RNA replication have been recently reported as a possible mechanism of virus persistence in the human heart. These mutations are likely to disrupt the correct folding of an RNA secondary structure required for viral RNA replication. In this report, we demonstrate that transfected RNAs harboring 5=-terminal sequence deletions are able to direct the synthesis of viral proteins, but not genomic RNAs, in human and murine cardiomyocytes. Moreover, we show that the binding of cellular and viral replication factors to viral RNA is conserved despite genomic deletions but that the impaired RNA synthesis as-

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“…The strategy initially used involved cotransfecting or co-infecting cells and then studying the recombination events occurring between different viruses in permissive cells. Using such a strategy, we recently showed that a defective type 2 cVDPV genome with a small deletion at the 3′ end could be rescued by the cotransfection of cells with defective or infectious CV-A17 RNAs23. Many homologous or nonhomologous recombinants were obtained, with recombination hotspots in three regions encoding nonstructural proteins.…”

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confidence: 99%

Exchanges of genomic domains between poliovirus and other cocirculating species C enteroviruses reveal a high degree of plasticity

Bessaud

Joffret

Blondel

et al. 2016

Sci Rep

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The attenuated Sabin strains contained in the oral poliomyelitis vaccine are genetically unstable, and their circulation in poorly immunized populations can lead to the emergence of pathogenic circulating vaccine-derived polioviruses (cVDPVs). The recombinant nature of most cVDPV genomes and the preferential presence of genomic sequences from certain cocirculating non-polio enteroviruses of species C (EV-Cs) raise questions about the permissiveness of genetic exchanges between EV-Cs and the phenotypic impact of such exchanges. We investigated whether functional constraints limited genetic exchanges between Sabin strains and other EV-Cs. We bypassed the natural recombination events by constructing 29 genomes containing a Sabin 2 capsid-encoding sequence and other sequences from Sabin 2 or from non-polio EV-Cs. Most genomes were functional. All recombinant viruses replicated similarly in vitro, but recombination modulated plaque size and temperature sensitivity. All viruses with a 5′UTR from Sabin 2 were attenuated in mice, whereas almost all viruses with a non-polio 5′UTR caused disease. These data highlight the striking conservation of functional compatibility between different genetic domains of cocirculating EV-Cs. This aspect is only one of the requirements for the generation of recombinant cVDPVs in natural conditions, but it may facilitate the generation of viable intertypic recombinants with diverse phenotypic features, including pathogenicity.

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Nonhomologous Recombination between Defective Poliovirus and Coxsackievirus Genomes Suggests a New Model of Genetic Plasticity for Picornaviruses

Cited by 53 publications

References 44 publications

Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae

Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae

Functional Consequences of RNA 5′-Terminal Deletions on Coxsackievirus B3 RNA Replication and Ribonucleoprotein Complex Formation

Exchanges of genomic domains between poliovirus and other cocirculating species C enteroviruses reveal a high degree of plasticity

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