Abstract
Positive-sense RNA viruses in the Tombusviridae family have genomes lacking a 5' cap structure and prototypical 3' polyadenylation sequence. Instead, these viruses utilize an extensive network of intramolecular RNA-RNA interactions to direct viral replication and gene expression. Here we demonstrate that the genomic RNAs of Panicum mosaic virus (PMV) and its satellites undergo sequence modifications at their 3' ends upon infection of host cells. Changes to the viral and subviral genomes arise de novo within Brachypodium distachyon (herein called Brachypodium) and proso millet, two alternative hosts of PMV, and exist in the infections of a native host, St. Augustinegrass. These modifications are defined by polyadenylation [poly(A)] events and significant truncations of the helper virus 3' untranslated region-a region containing satellite RNA recombination motifs and conserved viral translational enhancer elements. The genomes of PMV and its satellite virus (SPMV) were reconstructed from multiple poly(A)-selected Brachypodium transcriptome data sets. Moreover, the polyadenylated forms of PMV and SPMV RNAs copurify with their respective mature icosahedral virions. The changes to viral and subviral genomes upon infection are discussed in the context of a previously understudied poly(A)-mediated antiviral RNA degradation pathway and the potential impact on virus evolution.IMPORTANCE The genomes of positive-sense RNA viruses have an intrinsic capacity to serve directly as mRNAs upon viral entry into a host cell. These RNAs often lack a 5' cap structure and 3' polyadenylation sequence, requiring unconventional strategies for cap-independent translation and subversion of the cellular RNA degradation machinery. For tombusviruses, critical translational regulatory elements are encoded within the 3' untranslated region of the viral genomes. Here we describe RNA modifications occurring within the genomes of Panicum mosaic virus (PMV), a prototypical tombusvirus, and its satellite agents (i.e., satellite virus and noncoding satellite RNAs), all of which depend on the PMV-encoded RNA polymerase for replication. The atypical RNAs are defined by terminal polyadenylation and truncation events within the 3' untranslated region of the PMV genome. These modifications are reminiscent of host-mediated RNA degradation strategies and likely represent a previously underappreciated defense mechanism against invasive nucleic acids.
Highlights
Positive-sense RNA viruses in the Tombusviridae family have genomes lacking a 5= cap structure and prototypical 3= polyadenylation sequence
In order to validate the transcriptome changes by reverse transcription (RT)-PCR, total RNA was converted to cDNA using an oligo(dT) primer, followed by PCR of selected genes [32, 36]
Because Panicum mosaic virus (PMV) and SPMV are presumably nonpolyadenylated, we were surprised to find that multiple PMV and SPMV gene-specific products were readily amplified using the oligo(dT)-primed cDNA in the RT-PCR assay (Fig. 2A)
Summary
Positive-sense RNA viruses in the Tombusviridae family have genomes lacking a 5= cap structure and prototypical 3= polyadenylation sequence. IMPORTANCE The genomes of positive-sense RNA viruses have an intrinsic capacity to serve directly as mRNAs upon viral entry into a host cell These RNAs often lack a 5= cap structure and 3= polyadenylation sequence, requiring unconventional strategies for cap-independent translation and subversion of the cellular RNA degradation machinery. Tombusvirus genomes must serve directly as mRNAs to initiate infection, yet they do not contain prototypical eukaryotic 5= m7GpppN cap structures or 3= polyadenylation [poly(A)] sequences [3,4,5] To overcome this issue, tombusviruses encode a diverse suite of structured RNAs for cap-independent translation, most of which are located in the 3= untranslated region (UTR) of the viral genomes [6,7,8,9,10,11,12,13,14]. During mechanical transmission to a new host, the satellite RNAs are preferentially packaged by the 17-kDa capsid protein of SPMV, promoting maintenance of the tripartite pathosystem in nature (Fig. 1) [30, 34]
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