Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus

Abstract

Characterising the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. In dsDNA and dsRNA viruses, the packaged double-stranded nucleic acid, constrained by the rigidity of the doublehelix, adopts a liquid crystalline arrangement 1-5. Owing to the different cellular fates of DNA and RNA, the life cycles of these viruses are strikingly dissimilar. Current models suggest that dsDNA viruses predominantly display single-spooled conformations due to the lack of genome segmentation and the absence of intracapsid transcriptional machinery 6-8. As dsRNA triggers host defence mechanisms if released into the cytoplasm 9 , dsRNA viruses retain their genomes within a core particle containing the enzymes required for RNA replication and transcription 10,11,12. Their genomes vary greatly in the degree of segmentation. In reoviruses (Reoviridae, 10-12 segments) the genome organizes in nonspooled fashion and is tightly associated with the viral RNA-dependent RNA polymerases (RdRPs) 11-14. However, whether this organization is generally applicable in dsRNA viruses remains unknown. Here, we use cryogenic electron microscopy (cryo-EM) to show that dsRNA viruses

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA

“…This challenge is more formidable for dsDNA packaging motors attached to virus procapsids since there is a symmetry mismatch between the relatively small motor components and the massive icosahedral capsid on which they reside. Reconstructing such an unbalanced symmetry mismatch is still non-trivial (4,26,29,(39)(40)(41). Hence, due to its size and complexity, the most tractable path to the atomic structure of a functional viral dsDNA packaging motor is to determine atomic resolution structures of isolated components by X-ray/NMR/SPA-cryoEM, and then fit them into sub-nm cryoEM reconstructions of the entire motor complex assembled on the procapsid (42).…”

“…In a second strategy, an empty virus capsid is first assembled, and the genome is then actively translocated into this pre-formed container. This strategy is utilized by dsRNA viruses (4,5), most large ssDNA viruses (6) and virtually all dsDNA viruses such as herpes virus, pox virus, adenovirus, and all the tailed dsDNA bacteriophages (7,8). This second enapsidation strategy requires that nascent viruses overcome substantial enthalpic and entropic barriers resisting DNA compaction to condense DNA within the confined space of the capsid.…”

Interrogating helical nanorod self-assembly with fractionated cellulose nanocrystal suspensions

“…where λ is the wavelength in air, n is the average cholesteric refractive index and θ is the incidence angle to m. Cholesteric Bragg reflection can be seen in the strikingly coloured and circularly polarised reflections from cuticles of certain beetles 3,4 , and even from some fruits 5,6 , revealing their helical arrangement of fibres of chitin and cellulose, respectively. In fact, cholesteric helical self-assembly can be found across a large range of biomaterials 7 , providing advantages beyond optics for, e.g., optimised packing of DNA/RNA [8][9][10] and spectacular mechanical properties of composites built around collagen 11,12 , amyloid 13 , chitin 14,15 or cellulose 16,17 . Attempts to mimic this structuring via self-assembly in cholesteric colloidal nanorod suspensions, for instance by drying cholesteric suspensions of cellulose nanocrystals (CNCs) 18 , often yield non-uniform films reflecting a range of colours with imperfect circular polarisation, and reproducibility and tunability are challenging 1,[19][20][21][22][23][24] .…”

Morphological peculiarities of DNA-protein complexes in dormantEscherichia colicells, subjected to prolonged starvation Condensation of DNA in dormant cells ofEscherichia coli

“…The structures of this kind has been demonstrated previously in starved bacteria lacking the dps gene [3], in viruses, and spores of various origin [25]. In some bacterial viruses, the double-stranded DNA is stored inside the capsid in the form of a spool [36,37], which can have different types of coiling leading to different types of liquid-crystalline packaging [37][38][39]. This packaging can change from hexagonal, to cholesteric, to isotropic at different stages of the viral life cycle.…”

“…The cell, displayed on Fig. 4(B), possess an isotropic DNA condensation type [37][38][39], which is also characteristic for bacterial spores [25]. The DNA-Dps in the cell on Fig.…”