1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
2 Great Lakes Forestry Centre, Sault Ste Marie, Ontario, Canada, P6A 2E5
3 Department of Microbiology and Immunology, Queens University, Kingston, Ontario, Canada, K7L 3N6
Correspondence
Peter J. Krell
pkrell{at}uoguelph.ca
![]() |
ABSTRACT |
---|
![]() ![]() ![]() ![]() ![]() ![]() |
---|
The GenBank/EMBL/DDBJ accession number of the complete genome sequence of CfMNPV reported in this paper is AF512031.
![]() |
INTRODUCTION |
---|
![]() ![]() ![]() ![]() ![]() ![]() |
---|
The genome sequences of 22 baculoviruses are published and 26 are currently listed in GenBank. Herniou et al. (2003) identified 30 core baculovirus genes common to 13 analysed baculovirus genomes. With the addition of the complete genome sequences of Neodiprion lecontei NPV (NeleNPV; Lauzon et al., 2004
) and Neodiprion sertifer NPV (NeseNPV; Garcia-Maruniak et al., 2004
) the core set of baculoviral genes has dropped to 29 as both hymenopteran baculoviruses lacked an identified F protein. Based on phylogenetic analysis, using the 29 core genes, baculoviruses segregate into five major groups, the GVs, the group I and group II NPVs, a group of the dipteran virus, Culex nigripalpus NPV (CuniNPV; Afonso et al., 2001
) and a group containing the hymenopteran viruses. The five published GV genomes include those for Xestia c-nigrum GV (XecnGV; Hayakawa et al., 1999
), Plutella xylostella GV (PlxyGV; Hashimoto et al., 2000
), Cydia pomonella GV (CpGV; Luque et al., 2001
), Adoxophyes orana GV (AdorGV; Wormleaton et al., 2003
) and Cryptophlebia leucotreta GV (CrleGV; Lange & Jehle, 2003
). Based on phylogeny of the 30 core genes and the presence (group I) or absence (group II) of the gp67/gp64 fusion protein gene (Pearson et al., 2000
), 14 published NPV genomes include six group I NPVs; Autographa californica MNPV (AcMNPV; Ayres et al., 1994
), Bombyx mori NPV (BmNPV; Gomi et al., 1999
), Choristoneura fumiferana defective NPV, Epiphyas postvittana NPV (EppoNPV; Hyink et al., 2002
), Orgyia pseudotsugata MNPV (OpMNPV; Ahrens et al., 1997
) and Rachiplusia ou NPV (RoMNPV; Harrison & Bonning, 2003
), and eight group II NPVs, Helicoverpa armigera NPV (HearNPV G4; Chen et al., 2001
), Helicoverpa zea single NPV (HzSNPV; Chen et al., 2002
), Lymantria dispar MNPV (LdMNPV; Kuzio et al., 1999
), Mamestra configurata NPV A (MacoNPV A; Q. Li et al., 2002
), Mamestra configurata NPV B (MacoNPV B; L. Li et al., 2002
), Spodoptera exigua MNPV (SeMNPV; IJkel et al., 1999
), Spodoptera litura NPV (SpltNPV; Pang et al., 2001
) and Adoxophyes honmai NPV (AdhoNPV; Nakai et al., 2003
).
Choristoneura fumiferana MNPV (CfMNPV) is a group I multiple encapsidated NPV, infectious to the eastern spruce budworm, Choristoneura fumiferana, which historically has been one of the most destructive forest insect pest species in North America destroying up to 35 million hectares of forest per year. Arif et al. (1984) constructed a physical map for the CfMNPV genome estimated at 124·4126·4 kb in size. The sequences of CfMNPV genes p143, lef-3, iap-2, vlf-1 (Chen et al., 2004
), ie-1, ie-2, pe38 (Carstens et al., 2002
), pkip, p47, lef-12, gta (Lapointe et al., 2000
), p48, p82 (Li et al., 1997
, 1999
), slp (Liu & Carstens, 1996
), DNApol (Liu & Carstens, 1995
), cathepsin, gp67/gp64 (Hill et al., 1993
, 1995
) and p10 (Wilson et al., 1995
) have been published and clustered with those of OpMNPV by phylogenetic analysis. This paper describes the complete CfMNPV genome sequence and organization, compares it to that of other published baculovirus genomes and places it in the context of baculovirus phylogeny.
![]() |
METHODS |
---|
![]() ![]() ![]() ![]() ![]() ![]() |
---|
Sequence analysis.
Sequence data were compiled into contigs using GeneRunner (www.generunner.com). Open reading frames (ORFs) were identified using ORF finder (http://www.ncbi.nlm.nih.gov/gorf). The criterion for defining an ORF was a size of at least 50 aa with minimal overlap. All BLAST searches were done through the national centre for biotechnology information (ncbi) website using BLAST 2.2.3. Multiple alignments and percentage identities were generated by using the alignX package from Vector NTI (Invitrogen). Genome parity plots were generated using GenBank data and as described previously (Hu et al., 1998).
![]() |
RESULTS AND DISCUSSION |
---|
![]() ![]() ![]() ![]() ![]() ![]() |
---|
A total of 146 methionine-initiated ORFs, with no or minimal overlap and encoding putative proteins of 50 aa or more were identified (Fig. 1, Table 1
). Exceptions regarding overlap were made for CfORFs 2, 40, 51 and 76 based on the identity and length of their homologues in other baculoviruses. The CfMNPV ORFs demonstrated no preference to orientation (49 % forward and 51 % reverse) or clustering based on function or expression, which was consistent with other baculovirus genomes. Of the 146 identified ORFs, 139 had homologues in at least one other baculovirus and seven were unique to CfMNPV. Five regions that resembled baculovirus homologous regions (hrs) were also identified. hrs have been implicated as origins of DNA replication (Ahrens & Rohrmann, 1995
; Kool et al., 1995
; Lee & Krell, 1994
) and transcriptional enhancers (Theilmann & Stewart, 1992
). ORFs accounted for 117 551 bp, hrs for 2762 bp and the remaining 9280 bp represented intergenic or unidentified regions. Most of the intergenic regions ranged from 0 to 200 bp in length, but were as long as 762 bp (Cf97/Cf98). However, some contiguous ORFs also overlapped, in 29 cases by as little as 279 bp, but longer overlaps of 119 (Cf76/Cf77), 152 (Cf51/Cf52), 199 (Cf2/Cf3) and 416 bp (Cf40/Cf41) were also observed (Table 1
).
|
|
Compared to the group II NPVs, CfMNPV shared the highest number of ORFs with MacoNPV A (94 ORFs) and the least with LdMNPV and SpltMNPV (84 ORFs). A total of 74 baculovirus ORFs were present in all lepidopteran NPVs, including CfMNPV. Some of these ORFs were also present in one or more GVs. Of the 74 ORFs, eight were found exclusively in lepidopteran NPVs, [ac17, ac21 (actin rearrangement inducing factor, arif-1), ac34, ac55, ac57, ac59, ac104, ac108] of which only arif-1 (Cf19, ac21) was studied in detail. CfMNPV shared 69, 65 and 68 ORFs with the granuloviruses CpGV, PlxyGV and XecnGV, respectively.
CfMNPV had homologues of two ORFs identified as unique to EppoNPV. Multiple alignment of Cf11 to EppoNPV ORF9 (15·2 % amino acid identity) revealed areas of high conservation including a strongly conserved C terminus (71·2 % over the last 12 aa). Cf103 was 34·5 % identical at the amino acid level to Eppo98. Both Cf103 and Eppo98 had a 23 residue C-4 zinc finger motif (aa 79101 in CfMNPV and aa 7597 in EppoNPV). The percentage identity within these regions (78·3 %) was much higher than the overall amino acid identity (34·5 %), indicating that this region may be functionally important.
Genes involved in DNA replication
Six baculovirus genes, lef-1, lef-2, lef-3, DNApol, p143 (hel) and ie-1, are essential in transient assays for DNA replication in AcMNPV and OpMNPV and exist in all lepidopteran baculoviruses including CfMNPV (Kool et al., 1995; Lu & Miller, 1995
; Ahrens & Rohrmann, 1995
). Only four are conserved among all sequenced baculovirus genomes as CuniNPV lacks recognizable ie-1 and lef-3 homologues (Afonso et al., 2001
). CuniNPV infects a dipteran, rather than a lepidopteran host, which might account for these differences. DNApol was the most highly conserved gene involved in DNA replication with a mean identity of 43·6 % at the amino acid level when the CfMNPV DNApol was compared with those from all sequenced baculovirus genomes. This high degree of conservation of DNApol may reflect the need to conserve its functional domains (e.g. nucleotide binding/5'-3' polymerization) (Liu & Carstens, 1995
). The least conserved gene product of this group was lef-3 (identity of 28 %), a protein with single-stranded DNA binding abilities (Chen et al., 2004
; Hang et al., 1995
) and thought to be a chaperone for the transport of P143 helicase to the nucleus (Wu & Carstens, 1998
; Chen et al., 2004
). Homologues of an additional single-stranded DNA-binding protein (ssdbp/ac25) (Mikhailov et al., 1998
) and immediate-early gene me53/ac139, both of which have been implicated in DNA replication, were also found in CfMNPV (Cf38 and Cf132). Homologues of the non-essential DNA replication stimulatory genes ie-2, lef-7 and pe38 (Kool et al., 1994
) were found in CfMNPV (Carstens et al., 2002
). Several baculoviruses, including OpMNPV, MacoNPV A, MacoNPV B, LdMNPV, SeMNPV, SpltMNPV and CpGV encode ribonucleotide reductase subunits and/or a dUTPase, which are involved in nucleotide metabolism. These genes may allow the viruses to replicate in non-dividing cells in which the nucleotide biosynthesis pathways have been shut-off (Ahrens et al., 1997
). However, no homologues to rr1, rr2 or dutpase or any other gene involved in nucleotide metabolism were found in CfMNPV.
Genes regulating transcription
Baculovirus gene transcription occurs in a temporal cascade for the immediate-early, delayed-early, late and very late genes. Immediate-early and delayed-early gene expression occurs prior to DNA replication and utilizes host RNA polymerase II while late and very late gene expression occurs after initiation of DNA replication and is driven by a viral encoded RNA polymerase (Miller, 1997). In AcMNPV the viral RNA polymerase comprises four subunits encoded by lef-4, lef-8, lef-9 and p47 (Guarino et al., 1998
) and these are present in all fully sequenced baculovirus genomes, including that of CfMNPV. These were highly homologous with mean amino acid identities of 40·462·3 % when compared with those from CfMNPV. The most highly conserved transcriptional protein was lef-9 (mean identity of 62·3 %), which is the subunit containing the polymerization domain. Homologues of both lef-5 and vlf-1, which are present in all baculovirus genomes sequenced to date, were also found in CfMNPV. Although the function of lef-5 is unclear, vlf-1 is essential for the burst in very late gene expression seen for p10 and polyhedrin (Yang & Miller, 1998
, 1999
).
In addition to the six transcriptional genes described above, CfMNPV encodes homologues of 39K/pp31, lef-6 and lef-11, which are present in all sequenced lepidopteran baculoviruses (Herniou et al., 2003). The early gene transactivators me53, ie-0 and ie-1, also present in CfMNPV, were generally less conserved with mean identities of 30, 37 and 35 %, respectively. Since the corresponding proteins interact with host factors, such as host RNA polymerase, rather than viral factors, they may have evolved to be more host specific, resulting in a greater degree of variation among these genes from different baculoviruses (IJkel et al., 1999
).
Inhibitors of apoptosis
Like both OpMNPV and EppoNPV, CfMNPV encoded homologues of iap-1, iap-2 and iap-3, but lacked the p35 caspase inhibitor homologue found in AcMNPV, RoMNPV and BmNPV. This absence is not surprising as other members of the iap family are functionally equivalent to p35 from AcMNPV (Crook et al., 1993). The CfMNPV iap gene products had high sequence identity to IAPs from OpMNPV, Hyphantria cunea NPV (HycuNPV) and EppoNPV. CfMNPV IAP-1, -2 and -3 possess C-terminal zinc RING-finger domains common to IAPs (Crook et al., 1993
). CfMNPV iap-3 also had two tandem copies of the baculovirus iap repeat (BIR) sequence and iap-1 had one BIR sequence (Birnbaum et al., 1994
). CfMNPV lacked iap-4, which is present in both OpMNPV and EppoNPV, the viruses that are most closely related to CfMNPV.
Structural genes
Herniou et al. (2003) identified nine structural genes common to 13 sequenced baculovirus genomes, all of which were found in CfMNPV (ld130, gp41, odv-e27, odv-e56, p6·9, p74, vp91, vp39, vp1054). Furthermore, CfMNPV has six additional structural protein genes found in all lepidopteran baculoviruses (fp25K, odv-e18, odv-e25, odv-e66, pk-1, polyhedrin/granulin). Also found in CfMNPV were several NPV-specific genes including polyhedron envelope protein (pep) (Cf124), vp80/87 (Cf97) and slp (Cf60) and the group I specific gp67.
Auxiliary genes
Baculovirus genomes typically encode auxiliary genes that are non-essential for replication but otherwise provide a selective advantage to the virus (Miller, 1997). Several of these auxiliary genes have homologues in CfMNPV, including protein tyrosine phosphatase-1 (ptp-1), ptp-2, ecdysteroid UDP glucosyltransferase (egt), arif, ubiquitin, fibroblast growth factor (fgf), superoxide dismutase (sod), viral enhancing factor (vef), proliferating cell nuclear antigen (pcna), viral chitinase (v-chi), viral cathepsin (v-cath), alkaline exonuclease and conotoxin-like peptide. The only auxiliary gene conserved among all baculoviruses is alkaline exonuclease, which interacts with lef-3 and can degrade both single- and double-stranded DNA in a 5'-3' direction and possesses both endo- and exonuclease activities (Mikhailov et al., 2003
). The alkaline exonuclease may be involved in the processing of replicative intermediates (Li & Rohrmann, 2000
) and/or repair and recombination of viral genomes (Mikhailov et al., 2003
) during infection. fgf and ubiquitin are also conserved among all lepidopteran baculoviruses, however their roles in baculovirus infection are unknown.
Unique ORFs found in CfMNPV
Seven CfMNPV ORFs had no recognizable baculovirus or other GenBank homologues (Table 2). Of these ORFs, Cf143 had an upstream late promoter motif (TTAAG) 25 nt upstream of the start codon. Six ORFs had conserved baculovirus early promoter motifs (CAKT) 200 bases or less upstream of their ATGs, while no baculovirus promoter motif was detected upstream of Cf133.
|
Repeated sequences
With the exception of CpGV, AdhoGV and NeleNPV, most baculoviruses contain hr regions composed of direct repeats with an imperfect palindromic core. hrs have been implicated as origins of DNA replication in transient assays (Ahrens & Rohrmann, 1995; Kool et al., 1995
; Lee & Krell, 1994
) and as enhancers of RNA polymerase II-mediated transcription (Theilmann & Stewart, 1992
). We have identified five hrs in the CfMNPV genome, which is one more than reported earlier (Xie et al., 1995
) (Fig. 2
). The number of repeats per hr ranged from seven in hr1 and hr3, eight in hr4, to 10 in both hr5 and hr2 and accounted for 2·3 % of the genome. The five hrs were dispersed randomly in the genome with 3988 bp separating hr1 and hr2, 42 710 bp separating hr2 and hr3, 32 606 bp separating hr3 and hr4, 21 327 bp separating hr4 and hr5 and 26 609 bp separating hr5 and hr1. The multiple alignment of the CfMNPV hrs (Fig. 2a
) showed a high degree of conservation within and between the hrs. The derived consensus repeat of the CfMNPV hrs, with an imperfect palindrome (shown in bold, Fig. 2b
) demonstrated a high degree of similarity to the repeats found in the consensus OpMNPV hrs and to the consensus hr repeat from HycuNPV. Even though the hrs were dispersed randomly, the group I NPVs showed conserved genomic locations for certain hrs. hr1 and hr2 from CfMNPV were in the same relative genomic location as OpMNPV hr2, EppoNPV hr2, AcMNPV hr2, RoMNPV hr2 and BmNPV hr2L and 2R (near fgf). EppoNPV hr5, OpMNPV hr5, AcMNPV hr1, RoMNPV hr1, BmNPV hr1 and CfMNPV hr5 also shared the same relative genomic locations, between odv-e56 and ie-2 (Carstens et al., 2002
). Furthermore, all group I NPVs, with the exception of EppoNPV, had an hr near the p95-cg30 loci. The relative location of CfMNPV hr4 between lef-7 and chitinase is identical to that of hr4 of OpMNPV, while the hr3 of EppoNPV is only about 1 kb away from chitinase. CfMNPV hr4 is the only hr overlapping an ORF (Cf116), suggesting that this ORF may not be functional.
|
|
|
Variations among group I NPV genomes
To date, a vef gene has been identified only in the GVs and type II NPVs (MacoNPV A, MacoNPV B and LdMNPV). VEFs are metalloproteinases that target the intestinal mucin of invertebrates leading to the degradation of the peritrophic membrane, thereby enhancing virus infectivity (Wang & Granados, 1997; Bischoff & Slavicek, 1997
). CfMNPV is the first group I NPV to have a vef homologue. While multiple alignments revealed that CfMNPV VEF (Cf29) showed low similarity to other enhancing factors, a metalloproteinase zinc-binding signature domain (HEXXH) was identified. This signature pattern suggested that CfMNPV VEF may belong to the metalloproteinase superfamily (Jongeneel et al., 1989
).
That vef was not found in any other group I baculovirus suggested that CfMNPV acquired it through horizontal gene transfer. Furthermore, the genomic location of CfMNPV vef was in one of two regions of variability found among the type I baculoviruses identified by Hyink et al. (2002). Alignment of these genomic regions between Op26 and Op38, or their corresponding homologues revealed a high degree of variation in ORF content between the AcMNPV, OpMNPV, EppoNPV, CfDEFNPV and CfMNPV genomes (Fig. 3a
). Hyink et al. (2002)
suggested that the common EppoNPV/OpMNPV ancestral virus at one point contained the Op2837 cluster and that EppoNPV lost Op2834 including sod. Considering that the EppoNPV/OpMNPV split occurred prior to the OpMNPV/CfMNPV split in the phylogenetic trees and that the CfMNPV vef falls within the Op2837 cluster in CfMNPV (Fig. 3a
) vef might also have been part of this gene cluster in a shared ancestor. Alternatively, this region might have more readily acquired new genes through recombination with other viruses or hosts. Both OpMNPV and EppoNPV genomes have unique ORFs in this region, which may have been acquired in this way (Fig. 3a
, EppoU2 and Op28).
Hyink et al. (2002) identified a second region of variability around the odv-e56 and ie-2 gene loci suggesting that OpMNPV acquired the Op147150 cluster based on the orientation of ie-2 which is reversed to that in AcMNPV and EppoNPV (Fig. 3b
). The Op147150 cluster was not present in CfMNPV and the orientation of the CfMNPV ie-2 gene was consistent with that in AcMNPV and EppoNPV thereby supporting the hypothesis presented by Hyink et al. (2002)
. Although CfMNPV lacked the Op147150 cluster, a CfMNPV unique gene (Cf143) was immediately downstream of ie-2 (Fig. 1
), and may have been incorporated due to a high rate of recombination in this area (Carstens et al., 2002
). Additionally, CfDEFNPV has a unique gene within this genomic region (Fig. 3b
).
Alignment of several hr genomic regions from group I NPV further supports the theory of recombination within these areas (Fig. 3ae). Within the genomic region encompassing Op86Op89, CfMNPV lost Op88, while EppoNPV lacked Op87, Op88 and the hr associated with this region. Additionally, AcMNPV retained Op86 (p95) to Op89, the hr and has two genes, ac84 and ac86, not found in OpMNPV, CfMNPV or EppoNPV (Fig. 3c
). BmNPV, which is closely related to AcMNPV, had lost Op87 and does not have ac84 or ac86. CfDEFNPV shares the same genomic organization as OpMNPV for this region. The genomic region spanning Op120 to chitinase also demonstrated variability (Fig. 3d
). CfMNPV retained the Op120chitinase cluster, however it lost the hr region and, instead, has two genes in its place, one of which is unique (Cf114, Cf116). EppoNPV lost a single gene, Op121, while AcMNPV retained the entire Op120chitinase cluster, the hr and has two genes, ac121 and pk-2, not found in CfMNPV, EppoNPV or OpMNPV. Both BmNPV and RoMNPV retained the Op120chitinase cluster, as well as pk-2, however both lack ac121, and BmNPV lacks the hr in this region. Like CfMNPV, a Cf114 homologue is found within this region in CfDEFNPV, however CfDEFNPV also acquired a unique gene between Op120 and Op121. The final region shown (Fig. 3e
) is the p74ie-0 genomic region in which EppoNPV, OpMNPV and CfDEFNPV have hrs, while CfMNPV, BmNPV, AcMNPV and RoMNPV do not. However, both CfMNPV and AcMNPV have genes (Fig. 3e
, black arrows, Cf133 and ac140) in this area not found in the other viruses used in this analysis. Moreover, despite both having retained hrs in this area, OpMNPV, EppoNPV and CfDEFNPV, differ as EppoNPV and CfDEFNPV have lost Op135ctl-1. Given the high degree of variability within these selected regions, the hrs may play a key role in viralviral and viralhost DNA recombination.
CfMNPV is also distinguished from other group I baculoviruses by the presence of two copies of p26 (Cf7 and Cf128), a feature previously found only in the group II NPVs, MacoNPV A, MacoNPV B and SeMNPV. As in other group I NPVs, Cf128 (p26b) was immediately upstream of p10. In addition, Cf128 showed a relatively high amino acid identity (50·464·4 %) to other group I P26s while demonstrating lower identity to group II P26s. Conversely, Cf7 (p26a) was more homologous to group II p26s and less to group I p26s. This copy of p26 was immediately upstream of ptp-2 and downstream of a small ORF (68 aa) that demonstrated limited identity (69 % identity over 22 aa) to ac2, a bro gene. Considering the homology and genomic locations of the two copies of p26, it appears that Cf128 (p26b) may have been conserved from a common group I NPV ancestor, and that Cf7 (p26a) was acquired separately and not by gene duplication. The role of p26 is unknown, however homologues for it have been identified in all NPVs sequenced to date except SpltMNPV (Pang et al., 2001) and the two hymenopteran baculoviruses NeleNPV and NeseNPV (Lauzon et al., 2004
; Garcia-Maruniak et al., 2004
). Since one MacoNPV A p26 had an early promoter and the second a late promoter in their respective upstream regions, Li & Rohrmann (2000)
suggested that p26 is required both early and late in infection and that having two copies fulfil this function. The CfMNPV p26a had a consensus early promoter within the first 150 bp, while p26b had both early and late promoters within the upstream 150 bp.
Interestingly a small remnant of a bro gene (ac2) was located adjacent to Cf7 (p26a), and bro genes have been implicated in recombination. In MacoNPV A, bro genes flanked regions of the genome containing unique genes or inversions and insertions when compared with other baculoviruses (Q. Li et al., 2002). Kuzio et al. (1999)
also noted that a region of the LdMNPV genome, which contained five contiguous bro sequences, was an area of frequent recombination. Given these observations, Cf7 may have been acquired through recombination via bro-like sequences.
As mentioned above, CfMNPV did not have an iap-4 homologue as found in OpMNPV and EppoNPV. In these genomes, iap-4 occupies the same genomic location as he65 in AcMNPV, RoMNPV and BmNPV, all of which lack iap-4. While CfMNPV lacked a full copy of he65, short contiguous sequences, in different reading frames, which displayed similarity to portions of he65, were found at the corresponding genomic location, accounting for much of the intergenic region between p87 (Cf97) and Cf98 (Table 1). This suggested that a CfMNPV ancestor may have had a functional he65 but had lost most of it, and what remained was rearranged and may be non-functional. Additionally, in OpMNPV and EppoNPV, which are quite closely related to CfMNPV, iap-4 may have been acquired at the he65 locus. Interestingly, in this genomic location in CfDEFNPV, there are two ORFs corresponding to the 3' and 5' ends of he65 and a single copy of iap-4, adjacent to an hr element, further suggesting extensive recombination in this area.
In conclusion, based on concatenated protein phylogeny (Lauzon et al., 2005) and gene parity plots, CfMNPV was most closely related to OpMNPV and to a lesser extent to EppoNPV. In phylogenetic trees, CfMNPV clusters with the group I NPVs and contains the entire group I-specific genes identified by Herniou et al. (2003)
. Despite its close relatedness to OpMNPV, the CfMNPV genome has several distinct features including the presence of a vef gene previously identified only in GVs and group II NPVs and contains two copies of the p26 gene as found in several group II viruses. Herniou et al. (2003)
proposed a possible model for the evolution of baculovirus gene content, whereby the ancestral lepidopteran virus acquired up to 45 genes beyond the 30 common baculovirus genes. Furthermore, the GVs and 14 of the lepidopteran NPVs had acquired 27 genes (Herniou et al., 2003
). The entire group I NPVs acquired an additional 12 genes (ptp1, ac5, ac16, ac30, iap-1, gta, ac73, ac114, ac124, gp64/67, ac132 and ie-2). The AcMNPV, BmNPV and RoMNPV acquired five genes (ac39, ac45, ac149, ac150 and ac154), while losing iap-3 and the other group I NPV viruses acquired four genes (Cf2, Cf31, Cf32 and Cf104) while losing ac52. Moreover, CfMNPV acquired vef, a second copy of p26, and the unique ORFs presented in Table 2
, compared with all other group I viruses and either never acquired, or lost, iap-4, Op4 and Op106, relative to OpMNPV. These differences identified between baculovirus genomes might provide insight into their evolution, host specificity and pathogenicity.
![]() |
ACKNOWLEDGEMENTS |
---|
![]() |
REFERENCES |
---|
![]() ![]() ![]() ![]() ![]() ![]() |
---|
Ahrens, C. H. & Rohrmann, G. F. (1995). Replication of Orgyia pseudotsugata baculovirus DNA: lef-2 and ie-1 are essential and ie-2, p34, and Op-iap are stimulatory genes. Virology 212, 650662.[CrossRef][Medline]
Ahrens, C. H., Russell, R. L. Q., Funk, C. J., Evans, J. T., Harwood, S. H. & Rohrmann, G. F. (1997). The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 229, 381399.[CrossRef][Medline]
Arif, B. M., Kuzio, J., Faulkner, P. & Doerfler, W. (1984). The genome of Choristoneura fumiferana nuclear polyhedrosis virus: molecular cloning and mapping of the EcoRI, BamHI, SmaI, XbaI and BglII restriction sites. Virus Res 1, 605614.[CrossRef]
Ayres, M. D., Howard, S. C., Kuzio, J., Lopez-Ferber, M. & Possee, R. D. (1994). The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology 202, 586605.[CrossRef][Medline]
Birnbaum, M. J., Clem, R. J. & Miller, L. K. (1994). An apoptosis-inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs. J Virol 68, 25212528.[Abstract]
Bischoff, D. S. & Slavicek, J. M. (1997). Molecular analysis of an enhancin gene in the Lymantria dispar nuclear polyhedrosis virus. J Virol 71, 81338140.[Abstract]
Blissard, G. W., Black, B., Crook, N., Keddie, B. A., Possee, R., Rohrmann, G., Theilmann, D. & Volkman, L. (2000). Family Baculoviridae. In Virus Taxonomy. The Seventh Report of the International Committee on Taxonomy of Viruses, pp. 195202. Edited by M. H. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner. San Diego: Academic Press.
Carstens, E. B., Liu, J. J. & Dominy, C. (2002). Identification and molecular characterization of the baculovirus CfMNPV early genes: ie-1, ie-2 and pe38. Virus Res 83, 1330.[CrossRef][Medline]
Chen, X., IJkel, W. F., Tarchini, R. & 8 other authors (2001). The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome. J Gen Virol 82, 241257.
Chen, X., Zhang, W. J., Wong, J. & 9 other authors (2002). Comparative analysis of the complete genome sequences of Helicoverpa zea and Helicoverpa armigera single-nucleocapsid nucleopolyhedroviruses. J Gen Virol 83, 673684.
Chen, T., Sahri, D. & Carstens, E. B. (2004). Characterization of the interaction between P143 and LEF-3 from two different baculovirus species: Choristoneura fumiferana nucleopolyhedrovirus LEF-3 can complement Autographa californica nucleopolyhedrovirus LEF-3 in supporting DNA replication. J Virol 78, 329339.
Crook, N. E., Clem, R. J. & Miller, L. K. (1993). An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif. J Virol 67, 21682174.[Abstract]
Garcia-Maruniak, A., Maruniak, J. E., Zanotto, P. M., Doumbouya, A. E., Liu, J. C., Merritt, T. M. & Lanoie, J. S. (2004). Sequence analysis of the genome of the Neodiprion sertifer nucleopolyhedrovirus. J Virol 78, 70367051.
Gomi, S., Majima, K. & Maeda, S. (1999). Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol 80, 13231337.[Abstract]
Guarino, L. A., Xu, B., Jin, J. & Dong, W. (1998). A virus-encoded RNA polymerase purified from baculovirus-infected cells. J Virol 72, 79857991.
Hang, X., Dong, W. & Guarino, L. A. (1995). The lef-3 gene of Autographa californica nuclear polyhedrosis virus encodes a single-stranded DNA-binding protein. J Virol 69, 39243928.[Abstract]
Harrison, R. L. & Bonning, B. C. (2003). Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses. J Gen Virol 84, 18271842.
Hashimoto, Y., Hayakawa, T., Ueno, Y., Fujita, T., Sano, Y. & Matsumoto, T. (2000). Sequence analysis of the Plutella xylostella granulovirus genome. Virology 275, 358372.[CrossRef][Medline]
Hayakawa, T., Ko, R., Okano, K., Seong, S. I., Goto, C. & Maeda, S. (1999). Sequence analysis of the Xestia c-nigrum granulovirus genome. Virology 262, 277297.[CrossRef][Medline]
Hayakawa, T., Rohrmann, G. F. & Hashimoto, Y. (2000). Patterns of genome organization and content in lepidopteran baculoviruses. Virology 278, 112.[CrossRef][Medline]
Herniou, E. A., Olszewski, J. A., Cory, J. S. & O'Reilly, D. R. (2003). The genome sequence and evolution of baculoviruses. Annu Rev Entomol 48, 211234.[CrossRef][Medline]
Hill, J. E., Kuzio, J., Wilson, J. A., MacKinnon, E. A. & Faulkner, P. (1993). Nucleotide sequence of the p74 gene of a baculovirus pathogenic to the spruce budworm, Choristoneura fumiferana multicapsid nuclear polyhedrosis virus. Biochim Biophys Acta 1172, 187189.[Medline]
Hill, J. E., Kuzio, J. & Faulkner, P. (1995). Identification and characterization of the v-cath gene of the baculovirus, CfMNPV. Biochim Biophys Acta 1264, 275278.[Medline]
Hu, Z. H., Arif, B. M., Jin, F., Martens, J. W., Chen, X. W., Sun, J. S., Zuidema, D., Goldbach, R. W. & Vlak, J. M. (1998). Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome. J Gen Virol 79, 28412851.[Abstract]
Huang, J. & Levin, D. B. (2001). Expression, purification and characterization of the Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) DNA polymerase and interaction with the SpliNPV non-hr origin of DNA replication. J Gen Virol 82, 17671776.
Hyink, O., Dellow, R. A., Olsen, M. J., Caradoc-Davies, K. M., Drake, K., Herniou, E. A., Cory, J. S., O'Reilly, D. R. & Ward, V. K. (2002). Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus. J Gen Virol 83, 957971.
IJkel, W. F., van Strien, E. A., Heldens, J. G., Broer, R., Zuidema, D., Goldbach, R. W. & Vlak, J. M. (1999). Sequence and organization of the Spodoptera exigua multicapsid nucleopolyhedrovirus genome. J Gen Virol 80, 32893304.
Jongeneel, C. V., Bouvier, J. & Bairoch, A. (1989). A unique signature identifies a family of zinc-dependent metallopeptidases. FEBS Lett 242, 211214.[CrossRef][Medline]
Kool, M., Ahren, C. H., Goldbach, R. W., Rohrmann, G. F. & Vlak, J. M. (1994). Identification of genes involved in DNA replication of the Autographa californica baculovirus. Proc Natl Acad Sci U S A 91, 1121211216.
Kool, M., Ahrens, C. H., Vlak, J. M. & Rohrmann, G. F. (1995). Replication of baculovirus DNA. J Gen Virol 76, 21032118.[Medline]
Kost, T. A. & Condreay, J. P. (1999). Recombinant baculoviruses as expression vectors for insect and mammalian cells. Curr Opin Biotechnol 10, 428433.[CrossRef][Medline]
Kuzio, J., Pearson, M. N., Harwood, S. H., Funk, C. J., Evans, J. T., Slavicek, J. M. & Rohrmann, G. F. (1999). Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology 253, 1734.[CrossRef][Medline]
Lange, M. & Jehle, J. A. (2003). The genome of the Cryptophlebia leucotreta granulovirus. Virology 317, 220236.[CrossRef][Medline]
Lapointe, R., Back, D. W., Ding, Q. & Carstens, E. B. (2000). Identification and molecular characterization of the Choristoneura fumiferana multicapsid nucleopolyhedrovirus genomic region encoding the regulatory genes pkip, p47, lef-12, and gta. Virology 271, 109121.[CrossRef][Medline]
Lauzon, H. A. M., Lucarotti, C. J., Krell, P. J., Feng, Q., Retnakaran, A. & Arif, B. M. (2004). Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome. J Virol 78, 70237035.
Lauzon, H. A. M., Jamieson, P. B., Krell, P. J. K. & Arif, B. M. (2005). Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome. J Gen Virol 86, 945961.
Lee, H. & Krell, P. J. (1994). Reiterated DNA fragments in defective genomes of Autographa californica nuclear polyhedrosis virus are competent for AcMNPV-dependent DNA replication. Virology 202, 418429.[CrossRef][Medline]
Li, L. & Rohrmann, G. F. (2000). Characterization of a baculovirus alkaline nuclease. J Virol 74, 64016407.
Li, X., Pang, A., Lauzon, H. A., Sohi, S. S. & Arif, B. M. (1997). The gene encoding the capsid protein P82 of the Choristoneura fumiferana multicapsid nucleopolyhedrovirus: sequencing, transcription and characterization by immunoblot analysis. J Gen Virol 78, 26652673.[Abstract]
Li, X., Lauzon, H. A., Sohi, S. S., Palli, S. R., Retnakaran, A. & Arif, B. M. (1999). Molecular analysis of the p48 gene of Choristoneura fumiferana multicapsid nucleopolyhedroviruses CfMNPV and CfDEFNPV. J Gen Virol 80, 18331840.[Abstract]
Li, L. & Rohrmann, G.F. (2000). Characterization of a baculovirus alkaline nuclease. J Virol 74, 64016407.
Li, L., Donly, C., Li, Q., Willis, L. G., Keddie, B. A., Erlandson, M. A. & Theilmann, D. A. (2002). Identification and genomic analysis of a second species of nucleopolyhedrovirus isolated from Mamestra configurata. Virology 297, 226244.[CrossRef][Medline]
Li, Q., Donly, C., Li, L., Willis, L. G., Theilmann, D. A. & Erlandson, M. (2002). Sequence and organization of the Mamestra configurata nucleopolyhedrovirus genome. Virology 294, 106121.[CrossRef][Medline]
Liu, J. J. & Carstens, E. B. (1993). Infection of Spodoptera frugiperda and Choristoneura fumiferana cell lines with the baculovirus Choristoneura fumiferana nuclear polyhderosis virus. Can J Microbiol 39, 932939.
Liu, J. J. & Carstens, E. B. (1995). Identification, localization, transcription, and sequence analysis of the Choristoneura fumiferana nuclear polyhedrosis virus DNA polymerase gene. Virology 209, 538549.[CrossRef][Medline]
Liu, J. J. & Carstens, E. B. (1996). Identification, molecular cloning, and transcription analysis of the Choristoneura fumiferana nuclear polyhedrosis virus spindle-like protein gene. Virology 223, 396400.[CrossRef][Medline]
Lu, A. & Miller, L. K. (1995). The roles of eighteen baculovirus late expression factor genes in transcription and DNA replication. J Virol 69, 975982.[Abstract]
Luque, T., Finch, R., Crook, N., O'Reilly, D. R. & Winstanley, D. (2001). The complete sequence of the Cydia pomonella granulovirus genome. J Gen Virol 82, 25312547.
Maguire, T., Harrison, P., Hyink, O., Kalmakoff, J. & Ward, V. K. (2000). The inhibitors of apoptosis of Epiphyas postvittana nucleopolyhedrovirus. J Gen Virol 81, 28032811.
Mikhailov, V. S., Mikhailova, A. L., Iwanaga, M., Gomi, S. & Maeda, S. (1998). Bombyx mori nucleopolyhedrovirus encodes a DNA-binding protein capable of destabilizing duplex DNA. J Virol 72, 31073116.
Mikhailov, V. S., Okano, K. & Rohrmann, G. F. (2003). Baculovirus alkaline nuclease possesses a 5'3' exonuclease activity and associates with the DNA-binding protein LEF-3. J Virol 77, 24362444.
Miller, L. K. (1997). Introduction to the Baculoviruses. In The Baculoviruses, pp. 16. Edited by L. K. Miller. New York: Plenum.
Monsma, S. A., Oomens, A. G. & Blissard, G. W. (1996). The GP64 envelope fusion protein is an essential baculovirus protein required for cell-to-cell transmission of infection. J Virol 70, 46074616.[Abstract]
Nakai, M., Goto, C., Kang, W., Shikata, M., Luque, T. & Kunimi, Y. (2003). Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai. Virology 316, 171183.[CrossRef][Medline]
Pang, Y., Yu, J., Wang, L. & 7 other authors (2001). Sequence analysis of the Spodoptera litura multicapsid nucleopolyhedrovirus genome. Virology 287, 391404.[CrossRef][Medline]
Pearson, M. N., Groten, C. & Rohrmann, G. F. (2000). Identification of the Lymantria dispar nucleopolyhedrovirus envelope fusion protein provides evidence for a phylogenetic division of the Baculoviridae. J Virol 74, 61266131.
Slack, J. M., Ribeiro, B. M. & de Souza, M. L. (2004). The gp64 locus of Anticarsia gemmatalis multicapsid nucleopolyhedrovirus contains a 3' repair exonuclease homologue and lacks v-cath and ChiA genes. J Gen Virol 85, 211219.
Theilmann, D. A. & Stewart, S. (1992). Tandemly repeated sequence at the 3' end of the IE-2 gene of the baculovirus Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus is an enhancer element. Virology 187, 97106.[Medline]
Wang, P. & Granados, R. R. (1997). An intestinal mucin is the target substrate for a baculovirus enhancin. Proc Natl Acad Sci U S A 94, 69776982.
Wilson, J. A., Hill, J. E., Kuzio, J. & Faulkner, P. (1995). Characterization of the baculovirus Choristoneura fumiferana multicapsid nuclear polyhedrosis virus p10 gene indicates that the polypeptide contains a coiled-coil domain. J Gen Virol 76, 29232932.[Abstract]
Wormleaton, S., Kuzio, J. & Winstanley, D. (2003). The complete sequence of the Adoxophyes orana granulovirus genome. Virology 311, 350365.[CrossRef][Medline]
Wu, Y. & Carstens, E. B. (1998). A baculovirus single-stranded DNA binding protein, LEF-3, mediates the nuclear localization of the putative helicase P143. Virology 247, 3240.[CrossRef][Medline]
Xie, W. D., Arif, B., Dobos, P. & Krell, P. J. (1995). Identification and analysis of a putative origin of DNA replication in the Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus genome. Virology 209, 409419.[CrossRef][Medline]
Yang, S. & Miller, L. K. (1998). Control of baculovirus polyhedrin gene expression by very late factor 1. Virology 248, 131138.[CrossRef][Medline]
Yang, S. & Miller, L. K. (1999). Activation of baculovirus very late promoters by interaction with very late factor 1. J Virol 73, 34043409.
Yang, D.-H., de Jong, J. G., Makhmoudova, A., Arif, B. M. & Krell, P. J. (2004). Choristoneura fumiferana nucleopolyhedrovirus encodes a functional 3'-5' exonuclease. J Gen Virol 85, 35693573.
Received 30 July 2004;
accepted 12 November 2004.