Differential segregation of nodaviral coat protein and RNA into progeny virions during mixed infection with FHV and NoV

Abstract

Nodaviruses are icosahedral viruses with a bipartite, positive-sense RNA genome. The two RNAs are packaged into a single virion by a poorly understood mechanism. We chose two distantly related nodaviruses, Flock House virus and Nodamura virus, to explore formation of viral reassortants as a means to further understand genome recognition and encapsidation. In mixed infections, the viruses were incompatible at the level of RNA replication and their coat proteins segregated into separate populations of progeny particles. RNA packaging, on the other hand, was indiscriminate as all four viral RNAs were detectable in each progeny population. Consistent with the trans-encapsidation phenotype, fluorescence in situ hybridization of viral RNA revealed that the genomes of the two viruses co-localized throughout the cytoplasm. Our results imply that nodaviral RNAs lack rigorously defined packaging signals and that coencapsidation of the viral RNAs does not require a pair of cognate RNA1 and RNA2.

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

“…NGS analysis was conducted to determine the identity of host RNA species encapsidated by pCNVCPpBin(ϩ) VLPs and by WT CNV virions during infection. RNA was extracted from RNasetreated VLPs and from WT CNV particles that were either not treated (CNV-nr) or treated (CNV-r) with RNase (18). After quality control analyses, approximately 8.1 million reads from pCNVCPpBin(ϩ) VLP RNA, 9.1 million reads from CNV-nr RNA, and 372 million reads from CNV-r RNA were obtained.…”

“…In many cases, virus capsid proteins have been found to bind specific high-affinity sequences and/or structures on viral RNA, which helps to preclude encapsidation of host RNAs (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). In the case of the satellite tobacco necrosis virus (STNV) and MS2 bacteriophage, specific RNA sequences may not exist; rather, the genome may contain numerous distinct but functionally similar packaging sites (e.g., small stem-loops) that are bound simultaneously but independently by multiple coat protein (CP) subunits (4,18,19). In addition, it has been suggested for some viruses that assembly occurs within viral factories consisting predominantly of viral RNA, thus making encapsidation of host RNA less likely.…”

Recent advances in coarse-grained modeling of virus assembly

“…Experiments and simulations suggest that the physical features of viral RNAs (e.g. charge, and size due to tertiary structure) are optimized for assembly of their capsid [33,48,[51][52][53][54][55]. Secondly, interactions between capsid proteins and specific sequences within the genome called packaging sites (PSs) have been identified for a number of viruses (e.g.…”