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Publication Abstract from PubMed

Members of the Tombusviridae family have highly similar structures and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the Tombusviridae family have ssRNA genomes with T=3 icosahedral protein shells with a maximum diameter of approximately 340A. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P(protruding). Between the R and S domain is the 'arm' region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the Tombusviridae viral lifecycles, the structures of cucumber leaf spot virus (CLSV, genus Aureusvirus) and red clover necrotic mosaic (RCNMV, genus Dianthovirus) were determined to resolutions of 3.2A and 2.9A, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the Tombusviridae family are likely correlated with differences in the size and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the beta-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased inter-subunit beta-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have co-evolved to package different genomes within the conserved and rigid shell.Importance Members of the Tombusviridae family have nearly identical shells and yet they package genomes that range from 4.6kb (monopartite) to 5.3 kb (bi-partite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high resolution cryo-EM structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the 'arm', seems to have also co-evolved with the R domain to allow for particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.

Near atomic resolution cryo-electron microscopy structures of cucumber leaf spot virus and red clover necrotic mosaic virus; evolutionary divergence at the icosahedral three-fold axes.,Sherman MB, Guenther R, Reade R, Rochon D, Sit T, Smith TJ J Virol. 2019 Nov 6. pii: JVI.01439-19. doi: 10.1128/JVI.01439-19. PMID:31694952^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.