Genus: Gammapartitivirus


Genus: Gammapartitivirus

Distinguishing features

All known members of the genus Gammapartitivirus infect ascomycetous fungi. Gammapartitiviruses have two dsRNA segments that are believed to be individually encapsidated in separate particles. The genome is typically 3.13.4 kbp in total.

Virion

Morphology

The structures of Penicillium stoloniferum virus F (PsV-F) and Penicillium stoloniferum virus S (PsV-S) have been determined by X-ray crystallography (PsV-F) and electron cryomicroscopy (PsV-F and PsV-S) (Ochoa et al., 2008, Pan et al., 2009). The outer diameter of the capsid is about 35–40 nm. The most prominent features of the capsid are 60 arch-like protrusions that decorate a spherical shell (Figure 1.Gammapartitivirus.A–C). Each particle contains 120 coat protein (CP) molecules arranged with icosahedral symmetry. The tertiary structure of each CP molecule consists of two distinct domains, one of which forms the continuous, 3 nm thick capsid, and the other that, with the corresponding domain of a neighboring CP, comprises the arch (Figure 1.Gammapartitivirus.E–F). The asymmetric unit of the icosahedron consists of two related CP molecules, CPA and CPB. The 60 CPA molecules are organized as flower-like pentamers, each centered about one of the 12 vertices of the icosahedral capsid (Figure 1.Gammapartitivirus.A). The 60 CPB molecules are arranged as trimers at the twenty icosahedral 3-fold (3f) axes of symmetry (Figure 1.Gammapartitivirus.A). The CPA-CPB dimer, defined by two monomers that form an arch, is most stable based on buried surface areas and likely functions as the assembly precursor (Figure 1.Gammapartitivirus.E–F). The two CP molecules in this dimer assume nearly identical conformations and are related by almost-perfect local 2f symmetry. Each dimer is stabilized by extensive structure swapping between the monomers and the additional intersubunit interactions mediated by the arch tip. Unlike the assembly pathway that has been described for reoviruses and other larger dsRNA viruses, PsV-F and PsV-S assembly is likely to proceed from dimers of CP dimers, each of which adopts a striking, smooth-edged diamond shape (Figure 1.Gammapartitivirus.D). The N-terminal region (approximately 40 aa) of the CP polypeptide extends radially inwards and interacts with the dsRNA viral genome. Given the large number of basic residues within this region, it may participate in RNA packaging during particle assembly, or play a role during viral transcription. Small pores in the capsid shell at the icosahedral 5f and 3f axes may facilitate the export of RNA transcripts. The dsRNA genome appears as concentric layers in icosahedrally averaged maps.

Figure 1.Gammapartitivirus. Structures of two partitiviruses. (A) Crystal structure of an isolate of Penicillium stoloniferum virus F. Two asymmetric units of the icosahedron are highlighted along with the icosahedral symmetry elements that define the boundaries of these units. One CPA monomer (in red) and one CPB monomer (in yellow) from the same CP dimer are labelled. (B-C) Cryo-EM reconstructions of PsV-F and PsV-S, both at ~0.45 nm resolution, and rendered with radial, color mapping. (D) Putative capsid assembly unit consists of a dimer of CP dimers (red–yellow, labelled A1-B1 and pink–orange, labelled A2-B2) that occupy a diamond-shaped area defined by black lines. (E) A PsV-F CP dimer. In this and the next panel (F), the arch and shell domains are highlighted green/light green and red/magenta, respectively, and the two subunits are distinguished as green or light green and red or magenta. (F) A PsV-S CP dimer. The atomic coordinates for this model were generated from a homology model derived from the PsV-F structure and constrained by its fit to the PsV-S cryo-EM reconstruction.

Physicochemical and physical properties

Penicillium stoloniferum virus S virions with double-stranded RNA have a buoyant density of ~1.36 g cm-3 in CsCl (Buck and Kempson-Jones 1973)

Nucleic acid

Viral genome comprises two dsRNA segments, which are 1.61.8 (dsRNA1) and 1.41.6 kbp (dsRNA2).

Proteins

There is a single major CP with predicted Mr ranging from 44 to 47 kDa. The Mr of the RNA-dependent RNA polymerase (RdRP), as predicted from nucleotide sequence analysis, ranges from 60 to 62 kDa. Virion-associated RNA polymerase activity is present.

Genome organization and replication

Each genome segment is monocistronic: the larger one typically encodes the RdRP and the smaller one the putative CP. Apparent RNA satellites encoding small (237303 aa) proteins, homologous to each other but not to either CP or RdRP, are present in classified gammapartitiviruses  and related, unclassified gammapartitiviruses including Aspergillus ochraceous virus (EU118279), Discula destructiva virus 1 (AF316994), Gremmeniella abietina RNA virus MS1 (AY089995) and Ustilaginoidea virens partitivirus 1 (KC503901). Moreover, RNA satellites appearing not to encode any proteins are found associated with studied isolates of Discula destructiva virus 1 and Penicillium stoloniferum virus F (AF316995 and AY738338, respectively). Gammapartitiviruses do not usually have poly(A) tracts near the plus-strand 3-terminus of their genome segments.

Biology

Members of the genus Gammapartitivirus infect ascomycetous fungi. They are transmitted intracellularly during cell division or cell fusion. The related, unclassified Aspergillus fumigatus partitivirus 1 seems to mediate reduced growth rate, conidiation and pigmentation in Aspergilllus fumigatus (Bhatti et al., 2011).

Species demarcation criteria

The species demarcation criteria within genus Gammapartitivirus are:

  • ≤ 90% aa sequence identity in the RdRP, and
  • ≤ 80% aa sequence identity in the CP

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)Isolate Abbreviation
Aspergillus ochraceous virusAspergillus ochraceous virusFA0611RNA1: EU118277; RNA2: EU118278; RNA3: EU118279Complete genomeAoV
Discula destructiva virus 1Discula destructiva virus 1247RNA1: AF316992; RNA2: AF316993RNA1: NC_002797; RNA2: NC_002800Complete genomeDdV1
Discula destructiva virus 2Discula destructiva virus 2331RNA1: AY033436; RNA2: AY033437RNA1: NC_003710; RNA2: NC_003711Complete genomeDdV2
Fusarium solani virus 1Fusarium solani virus 1ShimosakaRNA1: D55668; RNA2: D55669RNA1: NC_003885; RNA2: NC_003886Complete genomeFsV1
Gremmeniella abietina RNA virus MS1Gremmeniella abietina RNA virus MS1FinlandRNA1: AY089993; RNA2: AY089994RNA1: NC_004018; RNA2: NC_004019Complete genomeGaRNAVMS1
Gremmeniella abietina RNA virus MS1Gremmeniella abietina RNA virus MS1MS2RNA1: AY615211; RNA2: AY615212; RNA3: AY615213GaRNAVMS1
Ophiostoma partitivirus 1Ophiostoma partitivirus 1IndiaRNA1: AM087202; RNA2: AM087203Complete genomeOPV1
Penicillium stoloniferum virus FPenicillium stoloniferum virus FUSARNA1: AY738336; RNA2: AY738337RNA1: NC_007221; RNA2: NC_007222Complete genomePsV-F
Penicillium stoloniferum virus SPenicillium stoloniferum virus SKimRNA1: AY156521; RNA2: AY156522RNA1: NC_005976; RNA2: NC_005977Complete genomePsV-S
Penicillium stoloniferum virus SPenicillium stoloniferum virus SHackerRNA1: AM040148; RNA2: AM040149PsV-S

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Related, Unclassified Viruses 

Virus name*

Accession number

dsRNA1/RdRP

dsRNA2/CP

dsRNA3

dsRNA4

Ustilaginoidea virens partitivirus 1

KC503898

KC503899

KC503900

KC503901

Aspergillus fumigatus partitivirus 1 isolate 88

FN376847

FN398100

   
Colletotrichum acutatum partitivirus 1 isolate CaRV1

KC572132

KC572133

   
Ustilaginoidea virens partitivirus 2 isolate Uv0901

KF361014

KF361015

   
Verticillium dahliae partitivirus 1 strain Vd08284

KC422244

KC422243

   

Penicillium aurantiogriseum partitivirus 1

KT601103

KT601104

   
* Representative isolate of a virus with a complete published genome sequence
‡  Segment encoding a hypothetical protein with unknown function