Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

Abstract

The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs. Communicated by Ramaswamy H. Sarma.

Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting

“…This paper is devoted to search for specific signals in the genomic ssRNA sequences related to two-staged assembly/packaging of the helical ribonucleocapsid. As has been shown previously, the icosahedral symmetry of the capsid strongly affects the large-scale quasi-periodic segmentation in the related viral genomes (Chechetkin & Lobzin, 2019). The whole ribonucleocapsid structure of coronaviruses also remains invariant under transition by one helical turn.…”

“…Then, all plots for NCF were recalculated using Equations (26) and (27) and replacing all highest harmonics in the DFT spectra by the peaks assessed by extreme value statistics (cf. Chechetkin & Lobzin, 2019 ). The initial ranges of the recalculated plots are shown in the inserts to Figures 1 and 2 .…”

“…As the periodic patterns generate equidistant series of harmonics in the DFT spectra (see, e.g. Chechetkin & Turygin, 1995 ; Lobzin & Chechetkin, 2000 ), long enough patterns can be detected by the iteration of DFT or by the discrete double Fourier transform (DDFT) (Chechetkin & Lobzin, 2017 , 2019 , 2020a , 2020b ). Although, the correlation functions are the main tools in this article, our approach is based implicitly and explicitly on DFT and DDFT.…”

“…The specific cooperative RNA-coat protein interactions play important role at the both stages. The two stages may be associated with different signals (Chechetkin & Lobzin, 2019 ) and the whole dynamic process may be called assembly/packaging. The generalization of these ideas on viruses with ribonucleocapsid within the membrane envelope like that for coronaviruses assumes three stages related to the complete packaging of the genomic RNA within the envelope: two-staged assembly/packaging of the helical ribonucleocapsid and packaging of the ribonucleocapsid within the envelope.…”

Finally, a Role Befitting A star : Strongly Conserved, Unessential Microvirus A* Proteins Ensure the Product Fidelity of Packaging Reactions

“…As demonstrated with ssRNA viruses that assemble around their genomes, (8), singlestranded viral DNA with enhanced packaging efficiency may be adaptive. Indeed, bioinformatic results suggest that the genome contains 60 degenerate consensus sequences (57,58). The role of these sequences have yet to be experimentally investigated, but they probably do not govern protein J's initial interactions with the double-stranded RF DNA by which it gains access to the procapsid.…”