Abstract
Solenopsis invicta virus 3 (SINV-3) is a positive-sense single-stranded RNA virus that infects the red imported fire ant, Solenopsis invicta. We show that the second open reading frame (ORF) of the dicistronic genome is expressed via a frameshifting mechanism and that the sequences encoding the structural proteins map to both ORF2 and the 3' end of ORF1, downstream of the sequence that encodes the RNA-dependent RNA polymerase. The genome organization and structural protein expression strategy resemble those of Acyrthosiphon pisum virus (APV), an aphid virus. The capsid protein that is encoded by the 3' end of ORF1 in SINV-3 and APV is predicted to have a jelly-roll fold similar to the capsid proteins of picornaviruses and caliciviruses. The capsid-extension protein that is produced by frameshifting, includes the jelly-roll fold domain encoded by ORF1 as its N-terminus, while the C-terminus encoded by the 5' half of ORF2 has no clear homology with other viral structural proteins. A third protein, encoded by the 3' half of ORF2, is associated with purified virions at sub-stoichiometric ratios. Although the structural proteins can be translated from the genomic RNA, we show that SINV-3 also produces a subgenomic RNA encoding the structural proteins. Circumstantial evidence suggests that APV may also produce such a subgenomic RNA. Both SINV-3 and APV are unclassified picorna-like viruses distantly related to members of the order Picornavirales and the family Caliciviridae. Within this grouping, features of the genome organization and capsid domain structure of SINV-3 and APV appear more similar to caliciviruses, perhaps suggesting the basis for a "Calicivirales" order.
Highlights
Acyrthosiphon pisum virus (APV) is an unclassified picorna-like positive-sense single-stranded RNA virus that infects the pea aphid, Acyrthosiphon pisum [1,2]
We show that expression of ORF2 depends on frameshifting, and we show that a subgenomic RNA (sgRNA) encoding the structural proteins is produced in Solenopsis invicta virus 3 (SINV-3)-infected ants
Sequence analysis suggests that APV expresses its structural proteins from a subgenomic RNA
Summary
Acyrthosiphon pisum virus (APV) is an unclassified picorna-like positive-sense single-stranded RNA virus that infects the pea aphid, Acyrthosiphon pisum [1,2]. The approximately 10-kb genomic RNA is polyadenylated and contains two long ORFs (Fig. 1). The 5’ ORF (ORF1) is predicted to encode the nonstructural proteins since its product contains canonical motifs for helicase, protease and RNA-dependent RNA polymerase (RdRp) domains. Purified virions contain proteins with estimated masses of approximately 66, 33, 24 and 23 kDa, where the most abundant protein, 33K, is estimated to occur at 5- to 10-fold excess relative to the other capsid-associated proteins [1]. The genomic regions encoding the capsid proteins have been partially mapped via Edman degradation of five internal peptides. The presence of canonical motifs (a U_UUA_AAC slippery site and 3’-proximal predicted RNA stem-loop structure; Fig. 1) [3] for programmed -1 ribosomal frameshifting in the short region where ORF1 and ORF2 overlap, strongly suggests that the mechanism by which the 66K transframe protein is produced is ribosomal frameshifting [2]
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