Genomic analysis of an Argentinean isolate of Spodoptera frugiperda granulovirus reveals that various baculoviruses code for Lef-7 proteins with three F-box domains

Abstract

A new isolate of the Spodoptera frugiperda granulovirus, SfGV ARG, was completely sequenced and analyzed. The SfGV ARG genome is 139,812 bp long and encodes 151 putative open reading frames. Of these ORFs, 56 were found in betabaculoviruses, 19 of which are present only in GVs closely related to SfGV. Seven ORFs found homologs in this small GV group and also in noctuid NPVs. ORF066 codes a 74 amino acid protein, overlapped with nudix gene, with several homologs in baculovirus, found by tblastn search. Comparison with the genome of the Colombian isolate SfGV VG008 resulted in SfGV being 1101 bp smaller and lacking a homologue of VG008 ORF084, which codes for Lef-7. However, we found that ORF051 shows remote homology to Lef-7 proteins. Moreover, analysis of ORF051 along with Lef-7 proteins coded by a group of noctuid specific GVs and NPVs indicated that Lef-7 proteins coded by these viruses include three F-box domains in contrast to the single one reported for AcMNPV Lef-7. SfGV ARG genome also contains a split photolyase as a distinct feature not found in VG008. BlastX analysis revealed that a complete photolyase is coded considering a putative frameshift in a poly-A tract, which resembles known slippery sequences involved in programmed ribosome frameshifting.

Fig 1. Linear map of SfGV-ARG.

Arrows represent orientations of predicted ORFs. Each ORF is designated by its number in the genome annotation. Those numbers that belong to well conserved baculovirus orthologs have been replaced by the particular descriptive names. ORFs categories are indicated in the figure with different colors. Transcription products corresponding to some ORFs (indicated by asterisks) were checked and detected by RT-PCR (S1 Appendix). Homologous repeat regions (hrs) are represented by black lines.

Fig 2. Betabaculovirus phylogenetic tree.

Neighbor-Joining cladogram based on a concatemer of 37 core protein sequences obtained from 41 betabaculovirus genomes. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. Virus genomes accession numbers are listed in S2 Table.

Fig 3. F-box proteins.

(a) Multiple alignment of Lef-7 proteins from noctuid betabaculovirus and alphabaculovirus containing 3 F-box motifs, along with the paralogs found in SfGV genomes. F-box motifs are boxed. (b) Multiple alignment of F-box 1, 2 and 3 from proteins aligned in (a). (c) Phylogenetic analysis of baculovirus lef-7 ORFs shown in (a) along with their SfGV ARG paralog ORF051 (and its homolog in VG008, ORF049), by Maximum Likelihood method. AcMNPV Lef-7 was used as an outgroup. Boostrap values (>50%, 100 replicates) are indicated for each node. Uniprot IDs of the proteins used are listed in S3 Table.

Fig 4. SfGV ARG Photolyase.

(a) Schematic representation of two overlapping ORFs predicted automatically. (b) Homology to photolyase fragments obtained by BlastX. (c) Nucleotide sequence of the direct DNA strand of photolyase locus fragment and three reading frames f1, f2 and f3. Automatically detected ORFs 053a and 053b are shaded in yellow and blue in accordance with the schematic in panel (a). The translation product of combined f2 and f3 is boxed in red and the 8 consecutive adenine residues where frameshift would occur are underlined. (d) Phylogenetic analysis of baculovirus photolyases by Maximum Likelihood method. For SfGV ARG, ClbiNPV and ApciNPV photolyase we considered the complete polypeptides obtained after translation of combined frames (S3 Appendix). Uniprot IDs of the rest of the proteins are indicated. Boostrap values (>50%, 100 replicates) are indicated for each node. The sequence of Mythimna separata entmopoxvirus (MySEV) photolyase was included as an outgroup.

Fig 5. Percentage of ORFs in SfGV ARG according to their classification.

Slices of the pie chart are colored according to ORFs classification depicted in Fig 1.