Crowning Touches in Positive-Strand RNA Virus Genome Replication Complex Structure and Function

Abstract

Positive-strand RNA viruses, the largest genetic class of eukaryotic viruses, include coronaviruses and many other established and emerging pathogens. A major target for understanding and controlling these viruses is their genome replication, which occurs in virus-induced membrane vesicles that organize replication steps and protect double-stranded RNA intermediates from innate immune recognition. The structure of these complexes has been greatly illuminated by recent cryo-electron microscope tomography studies with several viruses. One key finding in diverse systems is the organization of crucial viral RNA replication factors in multimeric rings or crowns that among other functions serve as exit channels gating release of progeny genomes to the cytosol for translation and encapsidation. Emerging results suggest that these crowns serve additional important purposes in replication complex assembly, function, and interaction with downstream processes such as encapsidation. The findings provide insights into viral function and evolution and new bases for understanding, controlling, and engineering positive-strand RNA viruses. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Nodavirus RNA Replication Crown Architecture Reveals Proto-Crown Precursor and Viral Protein A Conformational Switching

“…8A) appear inconsistent with (+)RNA synthesis, due to their physical separation from the dsRNA template beneath the crown floor and other issues. Rather, the requirements of (+)RNA synthesis appear to demand an alternate state of protein A near the 7 nm central channel of the crown floor to access the viral dsRNA template inside the spherule (1, 10). In keeping with this, strong electron density spanning the central channel of the mature crown floor has been consistently observed in all cryo-EM studies of replication-active nodavirus crowns ((9–11) and this paper).…”

“…8A) are blocked by the crown floor from accessing the spherule-protected dsRNA template, and therefore incompatible with (+)RNA synthesis. These considerations implied that crowns must contain another form of Pol with direct access to the dsRNA (1, 10, 12), which a Pol in the central channel would provide. As summarized in the next section, emerging results on CHIKV crowns strongly support this hypothesis.…”

“…5 and 7). Moreover, despite even greater evolutionary differences, coronaviruses also form membrane-spanning multimeric crowns that channel release of progeny RNAs to the cytosol (1, 10, 15, 16). The crown and RC features revealed here also underscore and further illuminate multiple parallels with the replicative cores of dsRNA virus and retrovirus virions (1).…”

“…1A) in membrane-bounded, organelle-like RNA replication complexes (RC’s) that organize RNA replication factors and templates, protect dsRNA replication intermediates from innate immune recognition and responses, and release new (+)RNA genomes for translation, further replication and encapsidation. The two known RC classes are ~ 50-150 nm spherular invaginations or spherules, and ~ 200-300 nm double membrane vesicles or DMVs (1).…”

“…Recent results imply that similar crown-like complexes of viral RNA replication proteins play crucial roles in the RCs of many, if not most, (+)RNA viruses ((1, 10, 12) and references therein). CHIKV nsP1, which as noted above is related to protein A’s A N segment (Fig.…”