Viral RNAs Are Unusually Compact

Abstract

A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.

Single Particle Observation of SV40 VP1 Polyanion-Induced Assembly Shows That Substrate Size and Structure Modulate Capsid Geometry

“…In general, viral RNA is substantially more compact than nonviral sequences; Gopal and co-workers observed that large RNAs formed ellipsoidal structures. The hydrodynamic radius, R h , of a nonviral RNA was about half the radius of gyration one would calculate based on its length, and the R h for nonviral RNA was as much as twice that of viral RNA 39, 40 . Our data support the concept that compactness matters.…”

“…PSS has a persistence length similar to that of a hypothetical ssRNA that lacks base-pairs but PSS has a smaller excluded volume due to the hydrophobic styrene side chains 38 . Conversely viral RNA, in general, has a pronounced tendency to form compact structures based on its density of base-pairing 39, 40 , thus our source of RNA is the P1 region of Bovine Enterovirus 41 . We found the particle yield and uniformity were sensitive to both substrate length and structure.…”

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

“…Others, such as HOTAIR and NRON, are important regulators of gene expression (9)(10)(11) linked to diverse human diseases (12). Furthermore, a vast number of important pathogenic viruses including HIV, SARS coronavirus, poliovirus, Dengue fever virus, and many others utilize long RNAs as genetic material, which also play structural roles during virus assembly and genome packaging (13)(14)(15)(16)(17)(18)(19)(20). Previous studies have established the importance of local secondary and three-dimensional structure in the biological function of RNA (21,22).…”

“…Previous studies have established the importance of local secondary and three-dimensional structure in the biological function of RNA (21,22). However, the effects of the secondary structure on the large-scale properties (e.g., size) of long RNAs remain poorly understood, even while its importance for virus assembly has been demonstrated (13)(14)(15)(16)(17)(18)(19)(20).…”

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

“…STMV RNA is exceptionally extended, in contrast to the compactness predicted (Yoffe et al 2008) and observed (Gopal et al 2012(Gopal et al , 2014 for the RNA genomes of other spherical viruses. Compactness facilitates packaging into the small volume of the capsid for some viruses (Yoffe et al 2008;Cadena-Nava et al 2012;Gopal et al 2012;Garmann et al 2014a,b), and compactness has also been suggested as a basis for protection against RNA interference and other innate intracellular responses.…”