Perspectives on Viral RNA Genomes and the RNA Folding Problem

Abstract

Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles. These structurally dynamic RNA shapeshifters present a challenging RNA folding problem, because the RNA sequence adopts multiple structures and may sometimes contain regions of partial disorder. Recent advances in high resolution asymmetric cryoelectron microscopy and chemical probing provide new ways to probe the degree of structure and disorder, and have identified more than one conformation in dynamic equilibrium in viral RNA. Chemical probing and the Detection of RNA Folding Ensembles using Expectation Maximization (DREEM) algorithm has been applied to studies of the dynamic equilibrium conformations in HIV RNA in vitro, in virio, and in vivo. This new type of data provides insight into important questions about virus assembly mechanisms and the fundamental physical forces driving virus particle assembly.

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

“…The E RMSD (with a cutoff of 100), which enforces the secondary structure, increases by around 5% in both cases, which expresses that the structure of the restrained stems is minimally affected. An optimal determination of the 3D encapsidated structure of the RNA genome goes beyond the capabilities of the current RNA-protein interaction modeling, which was discussed and conceptualized under different hypotheses, specifically for virus assemblies [44][45][46][47]. Nevertheless, we aim to present a systematic and reasonable model, which brings a new methodology, to structurally interpret, explain and evaluate the feasibility of the chemically probed secondary structures and the further microscopic characteristics of confined RNA inside virus capsids.…”

Evaluating RNA Structural Flexibility: Viruses Lead the Way

“…Apart from this, the genome remains largely disordered. This contrasts with the MS2 genome, where 80% of nucleotides can be individually resolved (multiple conformers still exist, however) [67], implying a much higher degree of structural order to the RNA within the virion in the latter.…”

“…A field of study that high-resolution cryo-EM is particularly useful for is imaging the RNA packaging structure within the nucleocapsid of viruses. Asymmetric reconstructions of Brome mosaic virus (BMV) and MS2 bacteriophage have been completed and revealed differing levels of RNA packaging [67]. Analysis of BMV at 3.9 angstrom resolution showed that the capsid protein interacts with the gRNA at the two-and threefold vertices, with the RNA forming different conformations.…”

RNA secondary structure regulates fragments’ adsorption onto flat substrates

“…The lack of a solid understanding of the connection between self-assembled structures of biopolymers such as RNA, 37,38 induced by specific internucleotide interactions, and their modification as a result of the adsorption process, induced by less specific interactions with the adsorbing substrate, is a challenge whose general aspects we aim to address in this work.…”