▪ Abstract This article summarizes studies of viral coat (capsid) proteins (CPs) of RNA plant viruses. In addition, we discuss and seek to interpret the knowledge accumulated to date. CPs are named for their primary function; to encapsidate viral genomic nucleic acids. However, encapsidation is only one feature of an extremely diverse array of structural, functional, and ecological roles played during viral infection and spread. Herein, we consider the evolution of viral CPs and their multitude of interactions with factors encoded by the virus, host plant, or viral vector (biological transmission agent) that influence the infection and epidemiological facets of plant disease. In addition, applications of today's understanding of CPs in the protection of crops from viral infection and use in the manufacture of valuable compounds are considered.

The red clover necrotic mosaic virus genome is composed of two single-stranded RNA components, RNA-1 and RNA-2. The viral capsid protein is translated from a subgenomic RNA (sgRNA) that is transcribed from genomic RNA-1. Here, a 34-nucleotide sequence in RNA-2 is shown to be required for transcription of sgRNA. Mutations that prevent base-pairing between the RNA-1 subgenomic promoter and the 34-nucleotide trans-activator prevent expression of a reporter gene. A model is proposed in which direct binding of RNA-2 to RNA-1 trans-activates sgRNA synthesis. This RNA-mediated regulation of transcription is unusual among RNA viruses, which typically rely on protein regulators.

Climate changes, emerging species of plant pests, and deficits of clean water and arable land have made availability of food to the ever-increasing global population a challenge. Excessive use of synthetic pesticides to meet ever-increasing production needs has resulted in development of resistance in pest populations, as well as significant ecotoxicity, which has directly and indirectly impacted all life-forms on earth. To meet the goal of providing safe, sufficient, and high-quality food globally with minimal environmental impact, one strategy is to focus on targeted delivery of pesticides using eco-friendly and biodegradable carriers that are derived from naturally available materials. Herein, we discuss some of the recent approaches to use biodegradable matrices in crop protection, while exploring their design and efficiency. We summarize by discussing associated challenges with the existing approaches and future trends that can lead the world to more sustainable agricultural practices.

Significance: Folded RNA elements are essential for diverse biological processes. Recently discovered examples include viral xrRNAs, which co-opt the cellular RNA decay machinery within a novel noncoding RNA production pathway. Here we characterize an xrRNA with no apparent evolutionary link or sequence homology to those described previously. Our results show that xrRNAs are an authentic class of functional RNAs that have arisen independently in different contexts, suggesting that they may be widespread. The detailed 3D structure of one of these xrRNAs reveals that an underlying structural topology may be the key feature that confers exoribonuclease resistance to diverse xrRNAs.

The structure of Red clover necrotic mosaic virus (RCNMV), an icosahedral plant virus, was resolved to 8.5 Å by cryoelectron microscopy. The virion capsid has prominent surface protrusions and subunits with a clearly defined shell and protruding domains. The structures of both the individual capsid protein (CP) subunits and the entire virion capsid are consistent with other species in the Tombusviridae family. Within the RCNMV capsid, there is a clearly defined inner cage formed by complexes of genomic RNA and the amino termini of CP subunits. An RCNMV virion has approximately 390 ± 30 Ca ²⁺ ions bound to the capsid and 420 ± 25 Mg ²⁺ ions thought to be in the interior of the capsid. Depletion of both Ca ²⁺ and Mg ²⁺ ions from RCNMV leads to significant structural changes, including (i) formation of 11- to 13-Å-diameter channels that extend through the capsid and (ii) significant reorganization within the interior of the capsid. Genomic RNA within native capsids containing both Ca ²⁺ and Mg ²⁺ ions is extremely resistant to nucleases, but depletion of both of these cations results in nuclease sensitivity, as measured by a significant reduction in RCNMV infectivity. These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell.