Encapsidation of Host RNAs by Cucumber Necrosis Virus Coat Protein during both Agroinfiltration and Infection

Ghoshal, Kankana; Theilmann, Jane; Reade, Ron; Maghodia, Ajay B.; Rochon, D’Ann

doi:10.1128/jvi.01466-15

Cited by 26 publications

(27 citation statements)

References 63 publications

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“…In summary, our work reveals that genome-encoded circRNAs carrying a self-cleaving ribozyme like the HHR are frequent molecules in plant transcriptomes, and constitute a feasible source for the origin of some virus satellites and viroids. In this regard, host RNAs derived from Ty3-gypsy retroelements are known to be efficiently encapsidated by the coat protein of a plant virus [ 56 ], and also Ty1-copia retrotransposons have already been proposed as the origin of non-HHR viroids of the family Pospiviroidae [ 57 ]. Finally, a plethora of splicing-derived circRNAs with diverse biological functions have been recently reported in eukaryotes [ 58 – 64 ] and, consequently, future research will be focused on deciphering the possible roles and biotechnological applications of genome-encoded circRNAs with HHRs.…”

Section: Discussionmentioning

confidence: 99%

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

2016

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BackgroundCatalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA pathogens. Recent data, however, indicate that small self-cleaving ribozymes are widespread in genomes, although their functions are still unknown.ResultsWe reveal that hammerhead ribozyme sequences in plant genomes form part of a new family of small non-autonomous retrotransposons with hammerhead ribozymes, referred to as retrozymes. These elements contain two long terminal repeats of approximately 350 bp, each harbouring a hammerhead ribozyme that delimitates a variable region of 600–1000 bp with no coding capacity. Retrozymes are actively transcribed, which gives rise to heterogeneous linear and circular RNAs that accumulate differentially depending on the tissue or developmental stage of the plant. Genomic and transcriptomic retrozyme sequences are highly heterogeneous and share almost no sequence homology among species except the hammerhead ribozyme motif and two small conserved domains typical of Ty3-gypsy long terminal repeat retrotransposons. Moreover, we detected the presence of RNAs of both retrozyme polarities, which suggests events of independent RNA-RNA rolling-circle replication and evolution, similarly to that of infectious circular RNAs like viroids and viral satellite RNAs.ConclusionsOur work reveals that circular RNAs with hammerhead ribozymes are frequently occurring molecules in plant and, most likely, metazoan transcriptomes, which explains the ubiquity of these genomic ribozymes and suggests a feasible source for the emergence of circular RNA plant pathogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1002-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

2016

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“…To assess the latter possibility, we analyzed the level of VLPs that accumulated in the above-described experiment at 6 dpai. We recently found that pCNVCPpBin(ϩ)-agroinfiltrated plants accumulate VLPs that harbor host RNA (65). The particles consist of both Tϭ3 and Tϭ1 icosahedra and intermediate-sized (IS) spherical particles of unknown icosahedral symmetry (unpublished observations).…”

Section: Resultsmentioning

confidence: 90%

“…N. benthamiana plants were agroinfiltrated with pCNVCPpBin(ϩ), which is a binary vector that expresses the CNV CP, as described previously (65). Agroinfiltration was performed in the presence of pNbHsc70-2/pBin(ϩ), which encodes N. benthamiana Hsc70-2 (see below), or pGFP/pBin(ϩ), which expresses green fluorescent protein (GFP) as a control.…”

Section: Methodsmentioning

confidence: 99%

Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection

Alam

Rochon

2016

J Virol

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RNA viruses often depend on host factors for multiplication inside cells due to the constraints of their small genome size and limited coding capacity. One such factor that has been exploited by several plant and animal viruses is heat shock protein 70 (HSP70) family homologs which have been shown to play roles for different viruses in viral RNA replication, viral assembly, disassembly, and cell-to-cell movement. Using next generation sequence analysis, we reveal that several isoforms of Hsp70 and Hsc70 transcripts are induced to very high levels during cucumber necrosis virus (CNV) infection of Nicotiana benthamiana and that HSP70 proteins are also induced by at least 10-fold. We show that HSP70 family protein homologs are co-opted by CNV at several stages of infection. We have found that overexpression of Hsp70 or Hsc70 leads to enhanced CNV genomic RNA, coat protein (CP), and virion accumulation, whereas downregulation leads to a corresponding decrease. Hsc70-2 was found to increase solubility of CNV CP in vitro and to increase accumulation of CNV CP independently of viral RNA replication during coagroinfiltration in N. benthamiana. In addition, virus particle assembly into virus-like particles in CP agroinfiltrated plants was increased in the presence of Hsc70-2. HSP70 was found to increase the targeting of CNV CP to chloroplasts during infection, reinforcing the role of HSP70 in chloroplast targeting of host proteins. Hence, our findings have led to the discovery of a highly induced host factor that has been co-opted to play multiple roles during several stages of the CNV infection cycle. IMPORTANCEBecause of the small size of its RNA genome, CNV is dependent on interaction with host cellular components to successfully complete its multiplication cycle. We have found that CNV induces HSP70 family homologs to a high level during infection, possibly as a result of the host response to the high levels of CNV proteins that accumulate during infection. Moreover, we have found that CNV co-opts HSP70 family homologs to facilitate several aspects of the infection process such as viral RNA, coat protein and virus accumulation. Chloroplast targeting of the CNV CP is also facilitated, which may aid in CNV suppression of host defense responses. Several viruses have been shown to induce HSP70 during infection and others to utilize HSP70 for specific aspects of infection such as replication, assembly, and disassembly. We speculate that HSP70 may play multiple roles in the infection processes of many viruses. C ucumber necrosis virus (CNV) is a positive-strand RNA virus in the genus Tombusvirus, family Tombusviridae (1). The CNV genome is monopartite and consists of ϳ4.7 kb of positive polarity single-stranded RNA. The genome contains five open reading frames (ORFs) which encode five different proteins: the auxiliary replicase factor (p33), the RNA-dependent RNA polymerase (RdRp) (p92), the coat protein (CP; p41), the movement protein (p21), and the silencing suppressor (p20) (Fig. 1A). The UAG stop codon of the p...

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“…In plants, Ghoshal et al. [28] showed that cucumber necrosis virus can encapsidate TEs from their host (Nicotiana benthamiana). These three possible routes of HTs are schematized in Fig.…”

Section: Mechanisms Of Horizontal Transfersmentioning

confidence: 99%

Horizontal transfers of transposable elements in eukaryotes: The flying genes

Panaud

2016

Comptes Rendus. Biologies

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Transposable elements (TEs) are the major components of eukaryotic genomes. Their propensity to densely populate and in some cases invade the genomes of plants and animals is in contradiction with the fact that transposition is strictly controlled by several molecular pathways acting at either transcriptional or post-transcriptional levels. Horizontal transfers, defined as the transmission of genetic material between sexually isolated species, have long been considered as rare phenomena. Here, we show that the horizontal transfers of transposable elements (HTTs) are very frequent in ecosystems. The exact mechanisms of such transfers are not well understood, but species involved in close biotic interactions, like parasitism, show a propensity to exchange genetic material horizontally. We propose that HTTs allow TEs to escape the silencing machinery of their host genome and may therefore be an important mechanism for their survival and their dissemination in eukaryotes.

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Encapsidation of Host RNAs by Cucumber Necrosis Virus Coat Protein during both Agroinfiltration and Infection

Abstract: Next

Cited by 26 publications

References 63 publications

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs

Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection

Horizontal transfers of transposable elements in eukaryotes: The flying genes

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