Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus

Abstract

Filamentous fungus Fusarium poae is a worldwide cause of the economically important disease Fusarium head blight of cereal grains. The fungus is itself commonly infected with a bisegmented dsRNA virus from the family Partitiviridae. For this study, we determined the structure of partitivirus Fusarium poae virus 1 (FpV1) to a resolution of 5.6Å or better by electron cryomicroscopy and three-dimensional image reconstruction. The main structural features of FpV1 are consistent with those of two other fungal partitiviruses for which high-resolution structures have been recently reported. These shared features include a 120-subunit T=1 capsid comprising 60 quasisymmetrical capsid protein dimers with both shell and protruding domains. Distinguishing features are evident throughout the FpV1 capsid, however, consistent with its more massive subunits and its greater phylogenetic divergence relative to the other two structurally characterized partitiviruses. These results broaden our understanding of conserved and variable elements of fungal partitivirus structure, as well as that of vertebrate picobirnavirus, and support the suggestion that a phylogenetic subcluster of partitiviruses closely related to FpV1 should constitute a separate taxonomic genus.

Fig. 1

Protein and RNA gels of purified PsV-F and FpV1 virions. (A) SDS/polyacrylamide gel stained with Coomassie blue. Molecular weight (MW) markers were run in one lane as shown, with approximate masses in kDa labeled at left. Positions of the PsV-F (middle lane) or FpV1 (right lane) CP are labeled at right. (B) Agarose gel stained with ethidium bromide. Positions of the PsV-F (left lane) or FpV1 (right lane) genomic dsRNA1 (R1), genomic dsRNA2 (R2), or satellite RNA (sat) are labeled. (C) Nondenaturing 5% polyacrylamide gel stained with ethidium bromide. Labeling as in panel B.

Fig. 2

Transmission electron micrograph of vitrified sample of purified FpV1 virions. Most particles exhibit circular profiles, but some are more angular (black arrows). Short surface projections are visible on some particles (white arrow). Many capsid regions have a beaded appearance suggestive of morphological capsomers (dashed arc), and some particles exhibit RNA fingerprints in the central regions (open arrows). Scale bar, 500 Å.

Fig. 3

Cryo-reconstruction of FpV1. (A) Equatorial section with density values coded in grayscale (lowest density in white). Icosahedral symmetry axes (2, 3, 5) are labeled in the upper right quadrant. Scale bar, 100 Å. (B) Radial density plot. Evident layers in FpV1 are labeled at top. (C, D) Same as for panel A except for partitiviruses PsV-F (C) and PsV-S (D).

Fig. 4

FpV1 capsid structure. (A) Stereo view of the outer surface along an I2 axis. A model icosahedron is superimposed (black lines). The capsid is radially depth-cued, from yellow (innermost); through rust, blue, and purple; to white (outermost) (also applies to panels B and C). The density threshold for this display is 1σ. Scale bar, 100 Å. (B) Magnified stereo view of the outer surface. The density threshold for this display is 2 σ to reveal additional features of the capsid densities (also applies to panels C and D). Encompassed I2, I3, and I5 axes are respectively marked by ellipse, triangle, and pentagon symbols (also applies to panels C and D), and one Q2 axis is also labeled. Scale bar, 50 Å (also applies to panel C). (C) Stereo view of the inner surface. (D) Stereo view of the inner surface with modeled helices for the CP dimers in two adjacent asymmetric units (CPA, blue; CPB, red). Scale bar, 50 Å.

Fig. 5

Comparisons of FpV1, PsV-F, PsV-S, and raPBV capsids. CryoTEM maps of the partitiviruses and a simulated density map of raPBV were used to generate the images (see Materials and methods). (A) Surface views of maps all rendered at 8-Å resolution. (B) Threshold-rendered equatorial sections. (C–E) Density-coded radial sections at the indicated radii through the capsid regions of each virus. The different radii were chosen to allow side-by- side comparison of morphologically analogous regions of the different capsids: protruding domains (C), upper part of the shell domains (D), and lower part of the shell domains (E).

Fig. 6

Further comparisons of CP dimers in PsV-F, PsV-S, and raPBV. (A) Side views of the backbone trace of the CP dimer of each virus (CPA, blue; CPB, red), which occupies the asymmetric unit of the T=1 icosahedron. (B) Same as in panel A, but rotated by 90° (horizontal axis) to place the protruding domains closest to the viewer. Each dimer is also rotated by 37° counterclockwise on the page to match the angular orientation of the left front dimer in panel C. (C) Outside view of the capsid of each virus, constructed from only the Cα atoms of the CP shell domains (see Materials and methods). The two front CP dimers in each capsid are shown in cyan and pink instead of blue and red. The respective front dimers are labeled A–B and a–b.