Panicum Mosaic Virus and Its Satellites Acquire RNA Modifications Associated with Host-Mediated Antiviral Degradation

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.

3′ UTR is critical for viral RNA accumulation of jasmine virus H

“…Previous studies showed that LDRIs can span significant distances within viral RNA genomes, ranging from one to several thousand nucleotides (Miller and White 2006;Nicholson and White 2014;Newburn and White 2015). Viral 3′ UTRs play an important role in viral replication and translation through LDRIs, and many of which belong to the Tombusviridae (Newburn and White 2015; Pyle et al 2019;Ilyas et al 2021). Efficient translation of PLPV of the genus Pelarspovirus relies on a TED-Like CITE in the 3′ UTR that communicates with the corresponding 5′-region through LDRI (Blanco-Pérez et al 2016).…”

The Battle for Survival: The Role of RNA Non-Canonical Tails in the Virus–Host Interaction

“…Taken together, uridylation appears to be wide-spread in eukaryotic viruses. Although it is not fully clear, TUTases are more likely to attack viral RNA that lacks or with short A-tail, which may not be protected and is critical for host recognition of pathogens [ 92 , 95 , 96 , 97 ]. Consequently, uridylation promotes viral RNA degradation and protects host cells from viral invasion in some cases.…”

Brachypodium and plant viruses: entwined tools for discovery

“…The pool of polyadenylated RNA used for the above‐mentioned RNA‐seq study resulted in an intriguing follow‐up finding: alteration of PMV, SPMV and a satellite RNA (satRNA) during Brachypodium infection (Pyle et al , , ; Pyle & Scholthof, ). PMV is in the large virus family Tombusviridae , having single‐stranded RNA genomes defined, in part, by the lack of 7mG‐cap structures and 3′ ends that are not polyadenylated.…”

“…Therefore, when we discovered that the viruses in the PMV complex had polyadenylated 3′‐ends it was a surprise. Upon further investigation, we identified and defined the polyadenylation of viral and subviral RNAs in natural infections of switchgrass ( Panicum virgatum ) and St. Augustinegrass ( Stenotaphrum secundatum ) and in laboratory infections of proso millet ( Panicum miliaceum ) and Brachypodium (Pyle et al , ). A host‐dependent viral recombination mechanism may control this, as the recombination sites of the satRNAs differed in Brachypodium and proso millet plants (Pyle et al , ; Pyle & Scholthof, ).…”