Comparisons among the larger genome segments of six nodaviruses and their encoded RNA replicases

Abstract

The Nodaviridae are a family of isometric RNA viruses that infect insects and fish. Their genomes, which are among the smallest known for animal viruses, consist of two co-encapsidated positivesense RNA segments : RNA1 encodes the viral contribution to the RNA-dependent RNA polymerase (RdRp) which replicates the viral genome, whereas RNA2 encodes the capsid protein precursor. In this study, the RNA1 sequences of two insect nodaviruses -Nodamura virus (the prototype of the genus) and Boolarra virus -are reported as well as detailed comparisons of their encoded RdRps with those of three other nodaviruses of insects and one of fish. Although the 5h and 3h untranslated regions did not reveal common features of RNA sequence or secondary structure, these divergent viruses showed similar genome organizations and encoded RdRps that had from 26 to 99 % amino acid sequence identity. All six RdRp amino acid sequences contained canonical RNA polymerase motifs in their C-terminal halves and conserved elements of predicted secondary structure throughout. A search for structural homologues in the protein structure database identified the poliovirus RdRp, 3D pol , as the best template for homology modelling of the RNA polymerase domain of Pariacoto virus and allowed the construction of a congruent three-dimensional model. These results extend our understanding of the relationships among the RNA1 segments of nodaviruses and the predicted structures of their encoded RdRps.

Complete sequence of RNA1 and subgenomic RNA3 of Atlantic halibut nodavirus (AHNV)

“…A similar comparison of protein A sequences within the insect nodaviruses revealed a much lower level of similarity within that genus (Table 1, and Johnson et al 2001). In fact, the identities between the geographically and biologically separated insect nodavirus PaV and the other insect nodaviruses (approximately 23%) are as low as the variation between the fish and insect nodaviruses (approximately 24%).…”

“…The sequence identity between protein A of GGNNV and SJNNV, in viruses that infect geographically and biologically closer related species of fish, was also 89%. The differences in the protein A encoding-region between the fish nodaviruses were all due to nucleotide substitutions, except two 3-nucleotide deletions in the AHNV RNA1 sequence which made the 119 Dis Aquat Org 58: [117][118][119][120][121][122][123][124][125] 2004 deduced protein A 1 aa shorter than GGNNV and 2 aa shorter than the SJNNV protein A sequence.A similar comparison of protein A sequences within the insect nodaviruses revealed a much lower level of similarity within that genus (Table 1, and Johnson et al 2001). In fact, the identities between the geographically and biologically separated insect nodavirus PaV and the other insect nodaviruses (approximately 23%) are as low as the variation between the fish and insect nodaviruses (approximately 24%).…”

“…This ORF, called ORF-B2, showed significant sequence similarities with the B2 ORF identified in the RNA1 sequence of GGNNV (85% identity) and SJNNV (79% identity). Alignments with the much longer insect nodavirus B2 proteins (Johnson et al 2001) showed no obvious sequence similarities. The B2 protein encoded by FHV has recently been identified as a potent RNAsilencing inhibitor (Li et al 2002).…”

“…The AHNV RNA1 sequence had a 5' UTR of 79 nt and 3' UTR of 76 nt, identical in length to that of GGNNV (Tan et al 2001) and 1 nt shorter at the 3' UTR than SJNNV RNA1 (Iwamoto et al 2001). Compared to the insect nodaviruses 5' UTRs, which vary from 21 to 39 nt (Johnson et al 2001), the 5' UTRs of fish nodaviruses are relatively long. The 3' UTR of the fish nodaviruses' RNA1 are all very C-rich (41%) and the average % GC is 63.…”

“…The RdRp signature sequence has been defined as DX 3 (FYWLCA)X 0-1 DX n (STM)GX 3 TX 3 (NE)X n (GS)DD (Koonin & Dolja 1993), where X denotes any residue, residues in parentheses are amino acids allowed in this position, and subscripts denote the number of residues present. As discussed by Johnson et al (2001), this signature was precisely matched by alignment of each of the 5 insect nodaviruses and the SJNNV protein A sequence. Addition of the AHNV (and GGNNV) protein A sequences to this alignment also resulted in a precise match of the RdRp signature in the C-terminal part of the molecules (core residues in the RdRp signature are boxed in Fig.…”