Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses

Abstract

We synthesized the cDNAs of an insect picornavirus, infectious flacherie virus of silkworm (IFV), genomic RNA and inserted it into a bacterial plasmid (pUC119). The 9,650 nucleotides (nts) sequence except for the poly(A) tail was obtained from the cloned cDNAs, and the sequence integrity was confirmed by primer extension and direct RNA sequencing. The sequence has a large open reading frame (ORF) of 9,255 nts (3,085 codons) flanked by the short 5' non-coding region (156 nts) and by the rather long 3' non-coding (239 nts). The structural proteins VP3, 4, 1 and 2 were located at the N-terminus of the polyprotein in this order and were preceded by a tentative small peptide. Computer analysis identified the sequences similar to the consensus sequences of 2C (helicase?), 3C (protease), and 3D (RNA polymerase) conserved among mammalian and plant picorna(-like) viruses. In addition, the predicted genome organization of IFV was quite similar to those of picornaviruses. Further analyses of the characteristics of the genome structure and a tentative phylogenetic tree constructed on the basis of the amino acid sequence similarity emphasized the evolutionary relationships among the insect and plant viruses.

Molecular and Biological Characterization of Deformed Wing Virus of Honeybees ( Apis mellifera L.)

“…The VP3 protease site (AIPE 901 GEES) conforms to the classic pattern for viral 3C proteases that cut after either glutamine (Q) or glutamic acid (E) (37,58). The flanking amino acids are usually also conserved for individual 3C proteases (37,41,58), with the glycine (G), proline (P), and alanine (A) residues common in the shown positions (16,58,59). Using the positions of these residues as a guide, we found several putative recognition sites for the DWV 3C protease in the polyprotein (Fig.…”

“…Prior to DWV VP2 is a putative leader polypeptide (L protein), also found in other iflaviruses (41,75) and cardio-and aphthopicornaviruses (37,58). The DWV L protein has two motifs ( 123 CIFx 7 V 133 and 172 HL 173 ) that weakly resemble the catalytic sites of papain-like cysteine proteases found in some aphthoviruses (34,38,40,43).…”

“…Originally classified as picorna-like insect viruses (52,53), these viruses now fall largely into two groups: the genus Cripavirus, family Dicistroviridae (51), with separate open reading frames for the structural and nonstructural polyproteins (in the 3Ј and 5Ј halves of the genome, respectively), and the genus Iflavirus, with a typical picornavirus genome organization consisting of a single open reading frame in which the structural proteins are N-terminal to the nonstructural proteins. In both genera, the viral RNA is polyadenylated and the open reading frame is flanked by nontranslated regions (NTR) containing replication and translation control elements (41,71,74,75). Among the honeybee viruses, BQCV, ABPV, and KBV are cripaviruses, while SBV, Kakugo virus (KV), and Varroa destructor virus 1 (VDV-1) are iflaviruses (25,28,30,35,46,57).…”

A Perina nuda cell line(NTU-Pn-HF) from pupal ovary that is persistently infected with a picorna-like virus(PnPV).

“…These five viruses are recognized as a new genus, the "CrPV-like virus," distinct from the family Picornaviridae (van Regenmortel et al, 1999). In contrast, infectious flacheries virus (IFV, Isawa et al, 1998) and Sacbrood virus (SBV, Ghosh et al, 1999) have a genomic organization similar to that of typical picornaviruses (Stanway, 1990). PnPV has a genomic organization similar to that of IFV and SBV (paper in preparation, Genebank accession no.…”

A case for “StopGo”: Reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go)

“…It is 89% identical at the amino acid level to Ectropis obliqua picorna-like virus (Wang et al 2004;Lu et al 2006), and less so (25%) to Infectious flacherie virus (Isawa et al 1998). From the 59 end of the PnPV ORF there are 319 codons in the position corresponding to the 202 codons in FMDV that encode its leader protease.…”