The structure of a plant-specific partitivirus capsid reveals a unique coat protein domain architecture with an intrinsically disordered protrusion

Abstract

Persistent plant viruses may be the most common viruses in wild plants. A growing body of evidence for mutualism between such viruses and their hosts, suggests that they play an important role in ecology and agriculture. Here we present the capsid structure of a plant-specific partitivirus, Pepper cryptic virus 1, at 2.9 Å resolution by Cryo-EM. Structural features, including the T = 1 arrangement of 60 coat protein dimers, are shared with fungal partitiviruses and the picobirnavirus lineage of dsRNA viruses. However, the topology of the capsid is markedly different with protrusions emanating from, and partly comprising, the binding interface of coat protein dimers. We show that a disordered region at the apex of the protrusion is not required for capsid assembly and represents a hypervariable site unique to, and characteristic of, the plant-specific partitiviruses. These results suggest a structural basis for the acquisition of additional functions by partitivirus coat proteins that enables mutualistic relationships with diverse plant hosts.

Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density

“…The CafeMol 3.1 program [8] was used for all coarse-grained (CG) operations. In its representation, a nucleotide contains three interaction sites: one corresponding to the sugar moiety, the second one corresponding to the base, and third one corresponding to the phosphate linkage.…”

“…The problem is particularly challenging for large biomolecular systems, such as entire viruses or cellular organelles, because typical algorithms are usually incapable of fitting the whole structure at once and non-trivial approaches are needed to fit parts of the system and build a coherent complete structure. The structure of virus particles has been measured for a number of different viruses recently [3][4][5][6][7][8][9][10]. In the majority of the published data, however, only the protein capsid of the virus is measured.…”

“…The structures of virus particles have been measured for a number of different viruses recently. [3][4][5][6][7][8][9][10] In the majority of the published data, however, only the protein capsid of the virus is measured. This is because the resolution of the measured cryo-EM map for the interior of the virus is typically insufficient for tting the atomistic structure.…”

Global genetic diversity and evolutionary patterns among Potato leafroll virus populations

“…Several studies have been performed to predict and validate the disordered protein regions in the proteins of plant-infecting RNA viruses (Charon et al, 2016(Charon et al, , 2018Walter et al, 2019;Byrne et al, 2021;. In our study, the probability of protein disorder was predicted for P0, P1, RdRp, CP, CP-RTD, MP, and RTD proteins using the Protein DisOrder prediction System (PrDOS; Ishida and Kinoshita, 2007).…”

Capsid structure of a metazoan fungal dsRNA megabirnavirus reveals its uniquely acquired structures

“…Some metazoan dsRNA viruses might have acquired surface features for another reason. One fungus-infecting member of the family Partitiviridae has a surface arch, possibly for enhancing capsid stability and assembly (28), while in another plant partitivirus, the disordered protrusion apex might serve as a permissive site for enabling symbiotic relationships between viruses and hosts (29).…”