3D structures of fungal partitiviruses

Abstract

Partitiviruses constitute one of the nine currently recognized families of viruses with encapsidated, double-stranded (ds)RNA genomes. The partitivirus genome is bisegmented, and each genome segment is packaged inside a separate viral capsid. Different partitiviruses infect plants, fungi, or protozoa. Recent studies have shed light on the three-dimensional structures of the virions of three representative fungal partitiviruses. These structures include a number of distinctive features, allowing informative comparisons with the structures of dsRNA viruses from other families. The results and comparisons suggest several new conclusions about the functions, assembly, and evolution of these viruses.

FIGURE 1

Taxonomy and properties of encapsidated dsRNA viruses. Taxa that include fungal viruses are bolded. Icosahedral symmetries of the viral capsids are indicated; for T=1 capsids, the number in parentheses indicates whether there are 60 or 120 subunits in each capsid. Cystoviruses and reoviruses have two concentric icosahedral capsids with different symmetries as indicated; the T=1 capsid of each of these viruses is the one that encloses the genome (inner capsid). Viruses in certain reovirus genera may lack parts of the T=13 outer capsid. The T=1(120) capsid structure of partitiviruses is boxed to emphasize the focus of this review, and the particular partitiviruses for which structures are described (PsV-S, etc.) are indicated beside the box.

FIGURE 2

Fungal partitivirus virion structures obtained by cryo-TEM and icosahedral 3-D image reconstruction. Radially color-coded surface views are shown for (A) PsV-S, (B) PsV-F, and (C) FpV1 (Pan et al., 2009; Tang et al., 2010a; Tang et al., 2010b). The structures are shown at the same scale (see bar at lower left), with the same radial color map (lower right; radii in Å) applied to each.

FIGURE 3

Fungal partitivirus capsid and CP structures obtained by X-ray crystallography or by cryo-TEM and homology modeling. (A) Cα trace of the PsV-F capsid structure viewed along an I2 axis. A and B subunits are colored red and yellow, respectively. I2, I3, and I5 axes are marked with symbols (oval, triangles, and pentagons) and connected by lines. (B) A CP dodecamer with two quasisymmetric A–B dimers (A₁–B₁ and A₂–B₂) differentially colored (red:yellow and magenta:orange, respectively). A₁–B₁ and A₂–B₂ extend in antiparallel fashion along either side of an I2 axis, forming a dimer of dimers (tetramer) that is largely confined within the diamond shape formed by lines connecting the I3 and I5 axes. (C–F) Views of the PsV-F quasisymmetric A–B dimer Cα trace (C, D) and the PsV-S quasisymmetric A–B dimer Cα trace (E, F) as viewed from the side (C, E) and from beneath (i.e., from inside the particle) (D, F). A and B subunits are colored red and yellow, respectively. In C and E, visible N-and C-termini are labeled. Red and yellow arrows point toward β-strands involved in domain swapping, as discussed in the text. Cα traces for PsV-F and PsV-S are respectively from Pan et al. (2009) and Tang et al. (2010b).

FIGURE 4

Comparison of reovirus, totivirus, and partitivirus inner capsid or capsid organizations. Shown are crystallography-derived Cα traces of (A) Bluetongue virus (family Reoviridae) inner capsid (Grimes et al., 1998), (B) Saccharomyces cerevisiae virus L-A (family Totiviridae) capsid (Naitow et al., 2002), and (C) PsV-F (family Partitiviridae) capsid (Pan et al., 2009). In each virus, A and B subunits are colored red and yellow, respectively. In addition, a chosen A subunit is labeled and colored magenta in each virus, and the three adjacent B subunits are colored green (B₁), cyan (B₂), and blue (B₃). The A–B₁ and A–B₂ dimers are asymmetric and the A–B₃ dimers are quasisymmetric in each case. Note: different capsids are not shown at the same scale.

FIGURE 5

Views of genomic dsRNA in fungal partitivirus virions. Equatorial cross-sections are shown for PsV-F, PsV-S, and FpV1 cryo-TEM maps. (A, B) These panels have been reproduced from Pan et al. (2009). The Cα trace of PsV-F (A subunits, red; B subunits, yellow) is fitted into the cryo-TEM reconstruction of the PsV-F virion at 8.0-Å resolution. Magenta arcs highlight three rings of RNA density that are evident in the particle interior. Cryo-TEM densities corresponding to the disordered N termini of both subunits (not visible in the Cα traces) are indicated by cyan arrows. A close-up view of the boxed region in A is shown in B. The ordered N-terminal ends of the A and B subunit Cα traces are indicated by red and yellow stars, respectively. The disordered N-termini from two adjacent A–B dimers, indicated by cyan and blue arrows, respectively, extend as tube-like densities from the end of the Cα traces into the underlying outer ring of RNA density. (C, D) Density projection images of thin, planar sections encompassing the equatorial regions of (C) PsV-S (Tang et al., 2010b) and (D) FpV1 (Tang et al., 2010a) are shown. Magenta arcs highlight two or three rings of RNA density evident in PsV-S or FpV1, respectively. Blue arrowheads indicate examples of close approach between the capsid undersurface and the outer RNA ring in both viruses.

FIGURE 6

Comparison of picobirnavirus and partitivirus capsid organizations and CP folds. Shown are crystallography-derived Cα traces of (A) Rabbit picobirnavirus (RaPBV) virus-like particles (Duquerroy et al., 2009) and (B) partitivirus PsV-F virions (Pan et al., 2009). A and B subunits are colored red and yellow, respectively. I2, I3, and I5 axes are marked with symbols and connected with lines as in Fig. 3. The two capsids are shown at the same scale. Also shown are side views of the Cα traces of the quasisymmetric A–B dimer of (C) RaPBV and (D) PsV-F. The B subunit is colored gray in each. In the A subunit, the shell domain is colored red and the protruding/arch domain is colored green. Visible N-and C-termini are labeled for the A subunit of each virus. Red arrows point toward an α-helix involved in domain swapping in each virus, as discussed in the text.

FIGURE 7

Neighbor-joining phylogenetic tree for the family Partitiviridae. The tree was constructed from complete aa sequences of RdRps of representative members and probable members of the family. The aa sequences were aligned using the program CLUSTAL X2, and the tree was generated for codon positions using the MEGA5 phylogenetic package. Bootstrap percentages out of 2000 replicates are indicated at the nodes. Green, blue, and yellow shading respectively highlight the assignments of individual viruses to the current genera Alphacryptovirus, Partitivirus, and Cryspovirus. The divisions of the Alphacryptovirus and Partitivirus regions into two sections each (I, II) reflect the four new genera, obtained by dividing the current genera, that are suggested by these and previous phylogenetic results as cited in the text. Red boxes indicate the three fungal partitiviruses for which 3-D structures are described in recent reports and this review. GenBank accession numbers for the viruses in this figure are, top to bottom: YP_086754, ABN71237, ACL93278, YP_002308574, BAC23065, AF473549, NP_604475, YP_001936016, NP_620659, YP_00310476, AET80948, NP_624349, YP_227355, YP_392480, BAD32677, ACJ76981, ABC96789, BAA34783, ABU55400, AAB27624, AAY51483, ABB04855, AAZ06131, ABZ10945, YP_271922, BAA09520, ABV30675, AAN8683, NP_659027, CAJ31886, YP_001686789, AAG59816, NP_620301, and AAC47805.