Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses

Autographa californica multiple nucleopolyhedrovirus ac106 is required for the nuclear egress of nucleocapsids and intranuclear microvesicle formation

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) orf106 (ac106) is highly conserved in baculoviruses. Previous studies have shown that ac106 is required for the production of infectious budded virions (BVs). However, the functional role of ac106 in virion morphogenesis remains unknown. In this report, an ac106 knockout virus and an ac106 repair virus were constructed. The effect of ac106 deletion on virion morphogenesis was investigated, and the expression and subcellular localization of the Ac106 protein were characterized. Our data indicated that ac106 is required for the nuclear egress of nucleocapsids and intranuclear microvesicle formation, as well as subsequent BV and occlusion-derived virion (ODV) production and the embedding of ODVs into polyhedra. Ac106 is a baculovirus late protein that is concentrated in discrete foci of virus-induced membrane structures in the intranuclear ring zone of virus-infected cells. Further studies on the relationship between Ac106 and four other proteins that are also required for intranuclear microvesicle formation, Ac75, Ac76, Ac93, and P48 (Ac103), revealed that Ac106 is associated with Ac75, Ac76, Ac93, P48, and itself. Ac106 is required for Ac75, Ac93, and P48 accumulation in foci of virus-induced intranuclear membrane structures and the intranuclear transport of Ac76. Analysis of the subcellular localization of ODV integral envelope proteins upon deletion of the genes required for intranuclear microvesicle formation indicated that intranuclear microvesicle formation may be essential for ODV integral envelope protein transport into the nucleus, supporting the hypothesis that intranuclear microvesicles originate from the nuclear membrane.IMPORTANCEBaculovirus occlusion-derived virions (ODVs) are known to acquire their envelopes from virus-induced intranuclear microvesicles within the nucleoplasm, and this strategy of intranuclear envelopment of nucleocapsids to form virions is unique among viruses. However, the mechanism of ODV morphogenesis, particularly intranuclear microvesicle formation, remains unclear. In this study, we identified ac106 as the fifth gene, in addition to ac75, ac76, ac93, and p48 (ac103), which are required for intranuclear microvesicle formation. Further studies on the relationship between ac106 and the other four genes, as well as the effect of ac106 or ac75 deletion on the localization of ODV integral envelope proteins, indicated that intranuclear microvesicle formation may be essential for the transport of ODV integral envelope proteins into the nucleus, which strongly supports the hypothesis that intranuclear microvesicles originate from the nuclear membrane. These findings greatly enhance our understanding of the molecular mechanism of baculovirus ODV morphogenesis.

Virus-host coevolutionary analyses of an Alphabaculovirus with a wide host range

Baculoviruses are highly host specific, and their host range is usually restricted to a single or a few closely related insect species, except for few virus species, e.g. Alphabaculovirus aucalifonicae and Alphabaculovirus mabrassicae. In this study, two new alphabaculovirus isolates were isolated from the larvae of Mamestra brassicae and Mythimna separata, which were named as Mamestra brassicae multiple nucleopolyhedrovirus isolate QD (MbMNPV-QD) and Mythimna separata multiple nucleopolyhedrovirus isolate Hb (MyseMNPV-Hb), respectively. The Kimura two-parameter values based on the concatenated 38 core genes of baculovirus revealed that MbMNPV (isolates QD/CHb1/K1/CTa), MyseMNPV-Hb, Helicoverpa armigera multiple nucleopolyhedrovirus (HearMNPV) and Mamestra configurata nucleopolyhedrovirus B (MacoNPV-B) were different isolates of a same virus species. A phylogenetic tree of baculoviruses and nudiviruses constructed from their 20 homologous gene sequences, and that of their isolated hosts constructed from 13 protein-coding genes of the insect mitochondrial genomes, were used to analyse the coevolution of baculoviruses with their isolated hosts. The results showed that M. brassicae was the most likely ancestral host of these virus isolates, included MbMNPV isolates, MyseMNPV-Hb, HearMNPV, and MacoNPV-B. Therefore, we concluded that these virus isolates belong to the existing virus species - Alphabaculovirus mabrassicae with M. brassicae as their ancestral host.

Complete genome sequence analysis and genome organization of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1) from Turkey

The economically important pale tussock moth Dasychira pudibunda L. (Lepidoptera: Lymantriidae), known as a beech pest in Europe, primarily inflicts damage on beech leaves. In the present study, we aim to reveal the genome characteristics of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1), which was detected for the first time in Turkey and compare it with the reference genome and other baculovirus genomes. The DapuNPV-T1 genome was determined to be a circular, double-stranded DNA molecule with 136,920 bp and a nucleotide distribution of 54.4% G + C. Bioinformatics analysis showed that the DapuNPV-T1 genome contains 163 open reading frames with more than 150 nucleotides. Fifty-four ORFs of unknown function, 6 homologous regions (hrs), 1 AC-rich region, and 3 bro genes (bro-a, bro-b, and bro-c) were determined in the genome sequence. Comparative analysis with other baculovirus strains revealed distinctions in the DapuNPV-T1 genome based on ORF. The gene parity plot and phylogenetic analysis confirmed that DapuNPV-T1 belongs to the alphabaculovirus group Ib. In addition, the DapuNPV-T1 isolate was found to be close to the nucleopolyhedrovirus Poland isolate in Dasychira pudibunda and Orgyia pseudotsugata multiple nucleopolyhedrovirus. With this study, the first genome analysis of DapuNPV from Turkey became the second in the world to enter the literature. Comprehensive information on a wide range of isolates will provide a more detailed overview of baculoviruses and help overcome their shortcomings as biocontrol agents.

The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase

We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.

The Bombyx mori Nucleopolyhedrovirus GP64 Retains the Transmembrane Helix of Signal Peptide to Contribute to Secretion across the Cytomembrane

Bombyx mori nucleopolyhedrovirus (BmNPV) is the primary pathogen of silkworms that causes severe economic losses in sericulture. GP64 is the key membrane fusion protein that mediates budded virus (BV) fusion with the host cell membrane. Previously, we found that the n-region of the GP64 signal peptide (SP) is required for protein secretion and viral pathogenicity; however, our understanding of BmNPV GP64 remains limited. Here, we first reported that BmNPV GP64 retained its SP in the mature protein and virion in only host cells but did not retain in nonhost cells. Uncleaved SP mediates protein targeting to the cytomembrane or secretion in Bombyx mori cells. The exitance of the n-region extended the transmembrane helix length, which resulted in the cleavage site to be located in the helix structure and thus blocked cleavage from signal peptidase (SPase). Without the n-region, the protein fails to be transported to the cytomembrane, but this failure can be rescued by the cleavage site mutation of SP. Helix-breaking mutations in SP abolished protein targeting to the cytomembrane and secretion. Our results revealed a previously unrecognized mechanism by which SP of membrane fusion not only determines protein localization but also determines viral pathogenicity, which highlights the escape mechanism of SP from the cleavage by SPase. IMPORTANCE BmNPV is the primary pathogen of silkworms, which causes severe economic losses in sericulture. BmNPV and Autographa californica multiple nucleopolyhedrovirus (AcMNPV) are closely related group I alphabaculoviruses, but they exhibit nonoverlapping host specificity. Recent studies suppose that GP64 is a determinant of host range, while knowledge remains limited. In this study, we revealed that BmNPV GP64 retained its SP in host cells but not in nonhost cells, and the SP retention is required for GP64 secretion across the cytomembrane. This is the first report that a type I membrane fusion protein retained its SP in mature proteins and virions. Our results unveil the mechanism by which SP GP64 escapes cleavage and the role of SP in protein targeting. This study will help elucidate an important mechanistic understanding of BmNPV infection and host range specificity.

Ac106/107 affects production of infectious progeny BV by regulating transcription of late viral genes and host cell energy metabolism

BACKGROUND

AcMNPV is a model organism of baculovirus, and Spodoptera frugiperda is one of its hosts. Disclosing the role of ac106/107 in AcMNPV infecting Spodoptera frugiperda 9 (Sf9) cells is of great significance for modifying AcMNPV as a microbial insecticide. This work constructed recombinant baculovirus that knocking out, repairment and overexpression of ac106/107 and explored the effects of Ac106/107 on the proliferation of progeny viruses. Moreover, the potential mechanism and targets of ac106/107 were further revealed.

RESULTS

First, compared with the Bacmid-EGFP transfection group, the progeny virus does not proliferate after knocking out of ac106/107, and the proliferation ability increases by 14.5% at 72 h post transfection (h p.t.) when overexpression of ac106/107. However, knockout, repairment and overexpression of ac106/107 have no effect on viral DNA replication. Secondly, Ac106/107-EGFP was located in the cytoplasm and nucleus. Transcription level of late viral genes and viral RNA polymerase subunit genes in the Bacmid^ac106/107KO -EGFP transfection group and Bacmid-Ac106/107-EGFP transfection group was reduced and increased, respectively. Thirdly, AcMNPV would increase the glucose utilization and lactate consumption of the host Sf9 cells, and Bacmid^ac106/107KO -EGFP transfection group had lower glucose consumption and lactic acid accumulation than Bacmid-EGFP, Bacmid^ac106/107KO -Ac106/107(rep)-EGFP and Bacmid-Ac106/107-EGFP transfection groups.

CONCLUSION

Ac106/107 can enter the nucleus and affect transcription of viral RNA polymerase subunit genes, which in turn affects the transcription of late genes, and ultimately affects virus proliferation and energy metabolism in host cells. © 2021 Society of Chemical Industry.

Systematic Analysis of 42 Autographa Californica Multiple Nucleopolyhedrovirus Genes Identifies An Additional Six Genes Involved in the Production of Infectious Budded Virus

Baculoviruses have been widely used as a vector for expressing foreign genes. Among numerous baculoviruses, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most frequently used and it encodes 155 open reading frames (ORFs). Here, we systematically investigated the impact of 42 genes of AcMNPV on the production of infectious budded viruses (BVs) by constructing gene-knockout bacmids and subsequently conducting transfection and infection assays. The results showed that among the 39 functionally unverified genes and 3 recently reported genes, 36 are dispensable for infectious BV production, as the one-step growth curves of the gene-knockout viruses were not significantly different from those of the parental virus. Three genes (ac62, ac82 and ac106/107) are essential for infectious BV production, as deletions thereof resulted in complete loss of infectivity while the repaired viruses showed no significant difference in comparison to the parental virus. In addition, three genes (ac13, ac51 and ac120) are important but not essential for infectious BV production, as gene-knockout viruses produced significantly lower BV levels than that of the parental virus or repaired viruses. We then grouped the 155 AcMNPV genes into three categories (Dispensable, Essential, or Important for infectious BV production). Based on our results and previous publications, we constructed a schematic diagram of a potential mini-genome of AcMNPV, which contains only essential and important genes. The results shed light on our understanding of functional genomics of baculoviruses and provide fundamental information for future engineering of baculovirus expression system.

Genome sequence analysis of a Helicoverpa armigera single nucleopolyhedrovirus (HearNPV-TR) isolated from Heliothis peltigera in Turkey

The entire genome of Helicoverpa armigera single nucleopolyhedrovirus (HearNPV-TR) was sequenced, and compared to genomes of other existing isolates. HearNPV-TR genome is 130.691 base pairs with a 38.9% G+C content and has 137 open reading frames (ORFs) of ≥ 150 nucleotides. Five homologous repeated sequences (hrs) and two baculovirus repeated ORFs (bro-a and bro-b) were identified. Phylogenetic analysis showed that HearNPV-TR is closer to HaSNPV-C1, HaSNPV-G4, HaSNPV-AU and HasNPV. However, there are significant differences in hr3, hr5 regions and in bro-a gene. Pairwise Kimura-2 parameter analysis of 38 core genes sequences of HearNPV-TR and other Helicoverpa NPVs showed that the genetic distances for these sequences were below 0.015 substitutions/site. Genomic differences as revealed by restriction profiles indicated that hr3, hr5 regions and bro-a gene may play a role in the virulence of HearNPV-TR.

Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing

Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features

Background

The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, polh, lef-8 and lef-9, the underlying virus did not belong to any known nucleopolyhedrovirus (NPV) species. Therefore, this NPV was provisionally named “TraeNPV”. To understand this NPV, the nucleotide sequence of the whole TraeNPV genome was determined using next-generation sequencing (NGS) technology.

Results

The genome of TraeNPV is 125,477 bp in length with 144 putative open reading frames (ORFs) and its GC content is 40.45%. A phylogenetic analysis based on the 37 baculoviral core genes suggested that TraeNPV is a Group I NPV that is closely related to Autographa californica nucleopolyhedrovirus (AcMNPV). A genome-wide analysis showed that TraeNPV has some different features in its genome compared with other NPVs. Two novel ORFs (Ta75 and Ta139), three truncated ORFs (pcna, he65 and bro) and one duplicated ORF (38.7 K) were found in the TraeNPV genome; moreover, there are fewer homologous regions (hrs) than there are in AcMNPV, which shares eight hrs within the TraeNPV genome. TraeNPV shares similar genomic features with AcMNPV, including the gene content, gene arrangement and gene/genome identity, but TraeNPV lacks 15 homologous ORFs from AcMNPV in its genome, such as ctx, host cell-specific factor 1 (hcf-1), PNK/PNL, vp15, and apsup, which are involved in the auxiliary functions of alphabaculoviruses.

Conclusions

Based on these data, TraeNPV would be clarified as a new NPV species with defective AcMNPV genomic features. The precise relationship between TraeNPV and other closely related NPV species were further investigated. This report could provide comprehensive information on TraeNPV for evolutionary insights into butterfly-infected NPV.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5713-2) contains supplementary material, which is available to authorized users.

Characterization and functional assay of apsup (Lyxy105) from Lymantria xylina multiple nucleopolyhedrovirus (LyxyMNPV)

The baculoviral anti-apoptotic genes, p35 and iap (inhibitor of apoptosis), play important roles in the initiation of viral infection. Recently, a new anti-apoptotic gene (apoptosis suppressor, apsup) was identified in Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV). An apsup homolog gene, Lyxy105 (ly-apsup), was also predicted in the Lymantria xylina multiple nucleopolyhedrovirus (LyxyMNPV) genome. In this study, we attempt to perform a gene expression analysis and a functional assay of ly-apsup to demonstrate its anti-apoptotic activity and identify the functional domain of this protein. The transcription of the ly-apsup gene region was detected from 12 h post-infection (hpi) and increased significantly after 24-72 hpi. Comparison of the putative amino acid sequences to those of 18 baculoviral homolog proteins showed high amino acid identity to the LdMNPV sequences. Moreover, five conserved protein domains (named as domains I-V) were found. Therefore, protein functional assays were conducted on full-length proteins and different truncation clones. The overexpression of each clone was confirmed by western blot analysis, and the data revealed that a cleavage of ~ 5 kDa at the N-terminal region of the full-length, domains I-IV (1-241) and I-III (1-178), proteins occurred. The results of the functional analysis showed that full-length Ly-apsup and Ly-apsup with domain I (1-70) could inhibit Drosophila-RPR protein (D-RPR)-induced and actinomycin D (ActD)-induced apoptoses. In addition, the domains I and I-II (1-126) regions showed higher anti-apoptotic activity than the other domains in both D-RPR-induced and ActD-induced cell apoptoses. In conclusion, domain I of Ly-apsup may play an important role in the anti-apoptotic activity of this protein; cleavage of the Ly-apsup N-terminus may lead to decreased anti-apoptotic activity.

Lacanobia oleracea nucleopolyhedrovirus (LaolNPV): A new European species of alphabaculovirus with a narrow host range

During an insect sampling program in alfalfa crops near Montpellier, France in 2011, Lacanobia oleracea larvae were collected that died due to nucleopolyhedrovirus infection (LaolNPV). This virus was subjected to molecular and biological characterization. The virus was a multiple nucleocapsid NPV that showed similar restriction profiles to Mamestra configurata NPV-A (MacoNPV-A) but with significant differences. Polypeptide analysis demonstrated similar proteins in occlusion bodies and occlusion derived virions, to those observed in NPVs from Mamestra spp. Terminal sequencing revealed that the genome organization shared similarity with that of MacoNPV-A. The most homologous virus was MacoNPV-A 90/2 isolate (95.63% identity and 96.47% similarity), followed by MacoNPV-A 90/4 strain (95.37% and 96.26%), MacoNPV-B (89.21% and 93.53%) and M. brassicae MNPV (89.42% and 93.74%). Phylogenetic analysis performed with lef-8, lef-9, polh and a concatenated set of genes showed that LaolNPV and the Mamestra spp. NPVs clustered together with HaMNPV, but with a closer genetic distance to MacoNPV-A strains. The Kimura 2-parameter (K-2-P) distances of the complete genes were greater than 0.05 between LaolNPV and the MbMNPV/MacoNPV-B/HaMNPV complex, which indicates that LaolNPV is a distinct species. K-2-P distances were in the range 0.015–0.050 for comparisons of LaolNPV with MacoNPV-A strains, such that additional biological characteristics should be evaluated to determine species status. While MacoNPV-A was pathogenic to seven lepidopteran species tested, LaolNPV was only pathogenic to Chrysodeixis chalcites. Given these findings, Lacanobia oleracea nucleopolyhedrovirus should be considered as a new species in the Alphabaculovirus genus.

The genome of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lymantriidae family

Background

DapuNPV (Dasychira pudibunda nucleopolyhedrovirus), presented in this report, belongs to Alphabaculovirus group Ib. Its full, newly sequenced genome shows close relationship to baculovirus OpMNPV isolated from douglas-fir tussock moth Orgyia pseudotsugata. Baculovirus DapuNPV is a natural limiter of pale tussock moth Dasychira pudibunda L. (syn. Calliteara pudibunda L.)(Lepidoptera, Lymantriidae), which can occur in a form of an outbreak on many species of deciduous trees and may cause significant economic losses in the forests.

Methods

Late instars dead larvae of pale tussock moth were mechanically homogenized and polyhedra were purified during series of ultracentrifugation. Viral DNA was extarcted and sequenced using Miseq Illumina platform. 294,902 paired reads were used for de novo assembling. Genome annotation, multiple allingment to others baculoviruses and phylogegentic analises were perform with the use of multiple bioinformatic tools like: Glimmer3, HMMER web server, Geneious 7 and MEGA6.

Results

The genome of DapuNPV is 136,761 bp long with AT pairs content 45.6 %. The predicted number of encoded putative open reading frames (ORFs) is 161 and six of them demonstrate low or no homology to ORFs previously found in baculoviruses. DapuNPV genome shows very high similarity to OpMNPV in a nucleotide sequence (91.1 % of identity) and gene content (150 homologous ORFs), though some major differences (e.g. lack of he65 in OpMNPV) have also been noted.

Conclusions

Similarly to other members of the Baculoviridae family, DapuNPV baculovirus possesses highly conserved core genes. Among them, there is a second copy of occluded derived virus envelope 27 protein (odv-e27), which was previously found only in a member of Alphabaculovirus group II – LyxyMNPV (Lymantria xylina MNPV). Surprisingly enough, DapuNPV and LyxyMNPV genomes share also another feature. Phylogenetic analysis of chitin binding family protein (cbpl) indicates significant similarity of those two baculoviruses from distinct evolutionary groups which infect the same hosts from Lymantriidae. The ubiquitin like family gene (ubil), which has not been described until now, is another characteristic component of DapuNPV genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1963-9) contains supplementary material, which is available to authorized users.

Complete Genome Sequence of the Autographa californica Multiple Nucleopolyhedrovirus Strain E2

Many vectors that are commonly used in the baculovirus/insect cell system (BICS) are derived from the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) strain E2. To facilitate work with these vectors, we sequenced the E2 genome, compared it to that of the AcMNPV C6 strain, and found that they are very similar overall.

Homologous region 1 of Plutella xylostella granulovirus functions as an enhancer for early gene expression

Homologous regions (hrs) contained in genomes of baculoviruses have been shown to function as origins of viral DNA replication in alphabaculoviruses and betabaculoviruses, and as enhancers for early gene expression in alphabaculoviruses. The hr sequences of betabaculoviruses differ substantially from the ones of alphabaculoviruses. The enhancing property of betabaculovirus hrs has not been reported. In this study, transient assays were performed to investigate the effects of Plutella xylostella granulovirus (PlxyGV) hr1 on early gene expression of the virus. It was shown that hr1 stimulated reporter gene expression from the promoters of four early genes--ie1, dnapol, lef1, and lef9--independent of additional viral gene expression. The PlxyGV ie1 was shown to repress reporter gene expression from all four early gene promoters in a Trichoplusia ni cell line, both in the presence and absence of hr.

Identification of a conserved non-protein-coding genomic element that plays an essential role in Alphabaculovirus pathogenesis

Highly homologous sequences 154-157 bp in length grouped under the name of "conserved non-protein-coding element" (CNE) were revealed in all of the sequenced genomes of baculoviruses belonging to the genus Alphabaculovirus. A CNE alignment led to the detection of a set of highly conserved nucleotide clusters that occupy strictly conserved positions in the CNE sequence. The significant length of the CNE and conservation of both its length and cluster architecture were identified as a combination of characteristics that make this CNE different from known viral non-coding functional sequences. The essential role of the CNE in the Alphabaculovirus life cycle was demonstrated through the use of a CNE-knockout Autographa californica multiple nucleopolyhedrovirus (AcMNPV) bacmid. It was shown that the essential function of the CNE was not mediated by the presumed expression activities of the protein- and non-protein-coding genes that overlap the AcMNPV CNE. On the basis of the presented data, the AcMNPV CNE was categorized as a complex-structured, polyfunctional genomic element involved in an essential DNA transaction that is associated with an undefined function of the baculovirus genome.

The sf32 unique gene of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) is a non-essential gene that could be involved in nucleocapsid organization in occlusion-derived virions

A recombinant virus lacking the sf32 gene (Sf32null), unique to the Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV), was generated by homologous recombination from a bacmid comprising the complete viral genome (Sfbac). Transcriptional analysis revealed that sf32 is an early gene. Occlusion bodies (OBs) of Sf32null contained 62% more genomic DNA than viruses containing the sf32 gene, Sfbac and Sf32null-repair, although Sf32null DNA was three-fold less infective when injected in vivo. Sf32null OBs were 18% larger in diameter and contained 17% more nucleocapsids within ODVs than those of Sfbac. No significant differences were detected in OB pathogenicity (50% lethal concentration), speed-of-kill or budded virus production in vivo. In contrast, the production of OBs/larva was reduced by 39% in insects infected by Sf32null compared to those infected by Sfbac. The SF32 predicted protein sequence showed homology (25% identity, 44% similarity) to two adhesion proteins from Streptococcus pyogenes and a single N-mirystoylation site was predicted. We conclude that SF32 is a non-essential protein that could be involved in nucleocapsid organization during ODV assembly and occlusion, resulting in increased numbers of nucleocapsids within ODVs.

Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering

Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach.

Genomic sequencing and analyses of HearMNPV--a new Multinucleocapsid nucleopolyhedrovirus isolated from Helicoverpa armigera

Background

HearMNPV, a nucleopolyhedrovirus (NPV), which infects the cotton bollworm, Helicoverpa armigera, comprises multiple rod-shaped nucleocapsids in virion(as detected by electron microscopy). HearMNPV shows a different host range compared with H. armigera single-nucleocapsid NPV (HearSNPV). To better understand HearMNPV, the HearMNPV genome was sequenced and analyzed.

Methods

The morphology of HearMNPV was observed by electron microscope. The qPCR was used to determine the replication kinetics of HearMNPV infectious for H. armigera in vivo. A random genomic library of HearMNPV was constructed according to the “partial filling-in” method, the sequence and organization of the HearMNPV genome was analyzed and compared with sequence data from other baculoviruses.

Results

Real time qPCR showed that HearMNPV DNA replication included a decreasing phase, latent phase, exponential phase, and a stationary phase during infection of H. armigera. The HearMNPV genome consists of 154,196 base pairs, with a G + C content of 40.07%. 162 putative ORFs were detected in the HearMNPV genome, which represented 90.16% of the genome. The remaining 9.84% constitute four homologous regions and other non-coding regions. The gene content and gene arrangement in HearMNPV were most similar to those of Mamestra configurata NPV-B (MacoNPV-B), but was different to HearSNPV. Comparison of the genome of HearMNPV and MacoNPV-B suggested that HearMNPV has a deletion of a 5.4-kb fragment containing five ORFs. In addition, HearMNPV orf66, bro genes, and hrs are different to the corresponding parts of the MacoNPV-B genome.

Conclusions

HearMNPV can replicate in vivo in H. armigera and in vitro, and is a new NPV isolate distinguished from HearSNPV. HearMNPV is most closely related to MacoNPV-B, but has a distinct genomic structure, content, and organization.

Complete sequence, analysis and organization of the Orgyia leucostigma nucleopolyhedrovirus genome

The complete genome of the Orgyia leucostigma nucleopolyhedrovirus (OrleNPV) isolated from the whitemarked tussock moth (Orgyia leucostigma, Lymantridae: Lepidoptera) was sequenced, analyzed, and compared to other baculovirus genomes. The size of the OrleNPV genome was 156,179 base pairs (bp) and had a G+C content of 39%. The genome encoded 135 putative open reading frames (ORFs), which occupied 79% of the entire genome sequence. Three inhibitor of apoptosis (ORFs 16, 43 and 63), and five baculovirus repeated ORFs (bro-a through bro-e) were interspersed in the OrleNPV genome. In addition to six direct repeat (drs), a common feature shared among most baculoviruses, OrleNPV genome contained three homologous regions (hrs) that are located in the latter half of the genome. The presence of an F-protein homologue and the results from phylogenetic analyses placed OrleNPV in the genus Alphabaculovirus, group II. Overall, OrleNPV appears to be most closely related to group II alphabaculoviruses Ectropis obliqua (EcobNPV), Apocheima cinerarium (ApciNPV), Euproctis pseudoconspersa (EupsNPV), and Clanis bilineata (ClbiNPV).

Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues

Cyclobutane pyrimidine dimer (CPD) photolyases repair ultraviolet (UV)-induced DNA damage using blue light. To get insight in the origin of baculovirus CPD photolyase (phr) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized. Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well-supported clade within the insect photolyases. This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host. A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene. Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses (NPVs), including those that infect noctuids of the Plusiinae subfamily.

Comparative genomic sequence analysis of novel Helicoverpa armigera nucleopolyhedrovirus (NPV) isolated from Kenya and three other previously sequenced Helicoverpa spp. NPVs

A newly cloned Helicoverpa armigera nucleopolyhedrovirus (HearNPV) from Kenya, HearNPV-NNg1, has a higher insecticidal activity than HearNPV-G4, which also exhibits lower insecticidal activity than HearNPV-C1. In the search for genes and/or nucleotide sequences that might be involved in the observed virulence differences among Helicoverpa spp. NPVs, the entire genome of NNg1 was sequenced and compared with previously sequenced genomes of G4, C1 and Helicoverpa zea single-nucleocapsid NPV (Hz). The NNg1 genome was 132,425 bp in length, with a total of 143 putative open reading frames (ORFs), and shared high levels of overall amino acid and nucleotide sequence identities with G4, C1 and Hz. Three NNg1 ORFs, ORF5, ORF100 and ORF124, which were shared with C1, were absent in G4 and Hz, while NNg1 and C1 were missing a homologue of G4/Hz ORF5. Another three ORFs, ORF60 (bro-b), ORF119 and ORF120, and one direct repeat sequence (dr) were unique to NNg1. Relative to the overall nucleotide sequence identity, lower sequence identities were observed between NNg1 hrs and the homologous hrs in the other three Helicoverpa spp. NPVs, despite containing the same number of hrs located at essentially the same positions on the genomes. Differences were also observed between NNg1 and each of the other three Helicoverpa spp. NPVs in the diversity of bro genes encoded on the genomes. These results indicate several putative genes and nucleotide sequences that may be responsible for the virulence differences observed among Helicoverpa spp., yet the specific genes and/or nucleotide sequences responsible have not been identified.

Identification of a novel apoptosis suppressor gene from the baculovirus Lymantria dispar multicapsid nucleopolyhedrovirus

Ld652Y cells from Lymantria dispar readily undergo apoptosis upon infection with a variety of nucleopolyhedroviruses (NPVs), while L. dispar multicapsid NPV (LdMNPV) infection of Ld652Y cells results in the production of a high titer of progeny viruses. Here, we identify a novel LdMNPV apoptosis suppressor gene, apsup, which functions to suppress apoptosis induced in Ld652Y cells by infection with vAcΔp35, a p35-defective recombinant Autographa californica MNPV. apsup also suppresses apoptosis of Ld652Y cells induced by actinomycin D and UV exposure. Apsup is expressed in LdMNPV-infected Ld652Y cells late in infection, and RNA interference-mediated apsup ablation induces apoptosis of LdMNPV-infected Ld652Y cells.

Sequence comparison between three geographically distinct Spodoptera frugiperda multiple nucleopolyhedrovirus isolates: Detecting positively selected genes

The complete genomic sequence of a Nicaraguan plaque purified Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV) genotype SfMNPV-B was determined and compared to previously sequenced isolates from United States (SfMNPV-3AP2) and Brazil (SfMNPV-19). The genome of SfMNPV-B (132,954bp) was 1623bp and 389bp larger than that of SfMNPV-3AP2 and SfMNPV-19, respectively. Genome size differences were mainly due to a deletion located in the SfMNPV-3AP2 egt region and small deletions and point mutations in SfMNPV-19. Nucleotide sequences were strongly conserved (99.35% identity) and a high degree of predicted amino acid sequence identity was observed. A total of 145 open reading frames (ORFs) were identified in SfMNPV-B, two of them (sf39a and sf110a) had not been previously identified in the SfMNPV-3AP2 and SfMNPV-19 genomes and one (sf57a) was absent in both these genomes. In addition, sf6 was not previously identified in the SfMNPV-19 genome. In contrast, SfMNPV-B and SfMNPV-19 both lacked sf129 that had been reported in SfMNPV-3AP2. In an effort to identify genes potentially involved in virulence or in determining population adaptations, selection pressure analysis was performed. Three ORFs were identified undergoing positive selection: sf49 (pif-3), sf57 (odv-e66b) and sf122 (unknown function). Strong selection for ODV envelope protein genes indicates that the initial infection process in the insect midgut is one critical point at which adaptation acts during the transmission of these viruses in geographically distant populations. The function of ORF sf122 is being examined.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

BACKGROUND

The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.

RESULTS

In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).

CONCLUSIONS

The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Genetic and biological variation among nucleopolyhedrovirus isolates from the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)

A PCR-based method was used to identify and distinguish among 40 uncharacterized nucleopolyhedrovirus (NPV) isolates from larvae of the moth Spodoptera frugiperda that were part of an insect virus collection. Phylogenetic analysis was carried out with sequences amplified from two strongly conserved loci (polh and lef-8) from the 40 isolates in the collection and from eight previously studied S. frugiperda NPV (SfMNPV) isolates. To further distinguish these isolates, analysis was also carried out with sequences from two less-conserved loci, hr4 and hr5. Phylogenetic inference from the sequence data could distinguish among several of the individual isolates and between different groups of isolates from Georgia (USA) and Colombia, South America. A stronger degree of bootstrap support for the phylogenetic trees was obtained with the hr4 and hr5 homologous repeat sequences. Sequencing and phylogenetic analysis detected a relatively high degree of larva-to-larva sequence divergence occurring among isolates of SfMNPV collected from the same field in Missouri, USA. Restriction endonuclease analysis of viral DNA from larvae infected with five isolates from Georgia, Missouri, Louisiana, Florida (USA), and Colombia allowed for further comparison with other previously reported isolates of SfMNPV. Bioassays with these five geographically distinct isolates detected minor differences in virulence. This study highlights the use of PCR to rapidly distinguish and characterize large numbers of historical baculovirus isolates from the same host using minimal quantities of material, and the use of sequences from homologous repeat regions to distinguish closely related isolates of the same NPV species.

Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus

BACKGROUND

Outbreaks of the casuarina moth, Lymantria xylina Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of host plants to include more than 65 species of broadleaf trees. LyxyMNPV (L. xylina multiple nucleopolyhedrovirus) is highly virulent to the casuarina moth and has been investigated as a possible biopesticide for controlling this moth. LdMNPV-like virus has also been isolated from Lymantria xylina larvae but LyxyMNPV was more virulent than LdMNPV-like virus both in NTU-LY and IPLB-LD-652Y cell lines. To better understand LyxyMNPV, the nucleotide sequence of the LyxyMNPV DNA genome was determined and analysed.

RESULTS

The genome of LyxyMNPV consists of 156,344 bases, has a G+C content of 53.4% and contains 157 putative open reading frames (ORFs). The gene content and gene order of LyxyMNPV were similar to those of LdMNPV, with 151 ORFs identified as homologous to those reported in the LdMNPV genome. Two genes (Lyxy49 and Lyxy123) were homologous to other baculoviruses, and four unique LyxyMNPV ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified in the LyxyMNPV genome, including a gag-like gene that was not reported in baculoviruses. LdMNPV contains 23 ORFs that are absent in LyxyMNPV. Readily identifiable homologues of the gene host range factor-1 (hrf-1), which appears to be involved in the susceptibility of L. dispar to NPV infection, were not present in LyxyMNPV. Additionally, two putative odv-e27 homologues were identified in LyxyMNPV. The LyxyMNPV genome encoded 14 bro genes compared with 16 in LdMNPV, which occupied more than 8% of the LyxyMNPV genome. Thirteen homologous regions (hrs) were identified containing 48 repeated sequences composed of 30-bp imperfect palindromes. However, they differed in the relative positions, number of repeats and orientation in the genome compared to LdMNPV.

CONCLUSION

The gene parity plot analysis, percent identity of the gene homologues and a phylogenetic analysis suggested that LyxyMNPV is a Group II NPV that is most closely related to LdMNPV but with a highly distinct genomic organisation.

A new nucleopolyhedrovirus strain (LdMNPV-like virus) with a defective fp25 gene from Lymantria xylina (Lepidoptera: Lymantriidae) in Taiwan

A new multiple nucleopolyhedrovirus strain was isolated from casuarina moth, Lymantria xylina Swinhoe, (Lepidoptera: Lymantriidae) in Taiwan. This Lymantria-derived virus can be propagated in IPLB-LD-652Y and NTU-LY cell lines and showed a few polyhedra (occlusion bodies) CPE in the infected cells. The restriction fragment length polymorphism (RFLP) profiles of whole genome indicated that this virus is distinct from LyxyMNPV and the virus genome size was approximately 139 kbps, which was smaller than that of LyxyMNPV. The molecular phylogenetic analyses of three important genes (polyhedrin, lef-8 and lef-9) were performed. Polyhedrin, LEF-8 and LEF-9 putative amino acid analyses of this virus revealed that this virus belongs to Group II NPV and closely related to LdMNPV than to LyxyMNPV. The phylogenetic distance analysis was further clarified the relationship to LdMNPV and this virus provisionally named LdMNPV-like virus. A significant deletion of a 44bp sequence found in LdMNPV-like virus was noted in the fp25k sequences of LdMNPV and LyxyMNPV and may play an important role in the few polyhedra CPE. In ultrastructural observations, the nuclei of the infected LD host cells contained large occlusion bodies (OBs), and few OBs, which presented as one or two OBs in a nucleus that was otherwise filled with free nuclocapsids and virions. We concluded that this LdMNPV-like virus is a new LdMNPV strain from L. xylina.

Structural divergence among genomes of closely related baculoviruses and its implications for baculovirus evolution

Baculoviruses are members of a large, well-characterized family of dsDNA viruses that have been identified from insects of the orders Lepidoptera, Hymenoptera, and Diptera. Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, some sequenced baculovirus genomes from closely related viruses are structurally very similar and share overall nucleotide sequence identities in excess of 95%. This review focuses on the comparative analysis of partial and complete nucleotide sequences from two groups of closely related baculoviruses with broad host ranges: (a) group I multiple nucleopolyhedroviruses (MNPVs) from a cluster including Autographa californica (Ac)MNPV, Rachiplusia ou (Ro)MNPV, and Plutella xylostella (Plxy)MNPV; and (b) granuloviruses (GVs) from a cluster including Xestia c-nigrum (Xecn)GV and Helicoverpa armigera (Hear)GV. Even though the individual viruses in these clusters share high nucleotide sequence identities, a significant degree of genomic rearrangement (in the form of insertions, deletions, and homologous recombination resulting in allelic replacement) is evident from alignments of their genomes. These observations suggest an important role for recombination in the early evolution and biological characteristics of baculoviruses of these two groups.

Evidence of a major role of GP64 in group I alphabaculovirus evolution

Previous investigations suggest that the divergence of the group I alphabaculoviruses was later than that of the group II alphabaculoviruses, however, there is no quantitative data to support this hypothesis. To examine this theory, the evolutionary rates of the 30 core genes that are conserved among all baculoviruses and the 11 unique genes among group I alphabaculoviruses were estimated in this report. For core genes, the synonymous and nonsynonymous substitution rates (Ks and Ka) were found to be significantly different among different groups, with the rates being granulovirus>group II>group I. Among the 11 unique genes, gp64 was found to have the highest amino acid identity and the lowest omega (Ka/Ks) and Ka values. The significant difference in the selection pressure was found in the F-like protein. These analyses suggests the following interpretation: (i) group I evolved from an ancestral group II alphabaculovirus that had 11 genes not present in other members of this group; (ii) the acquisition of the gp64 gene may have stimulated or initiated the formation of the group I as a major lineage distinct from group II; and (iii) after being functionally displaced by gp64, the F-like gene of group I evolved under a relaxed selection pressure that lead to the partial lost of its function.

Baculovirus-expressed virus-like particles of Pea enation mosaic virus vary in size and encapsidate baculovirus mRNAs

Pea enation mosaic virus (PEMV: family Luteoviridae) is transmitted in a persistent, circulative manner by aphids. We inserted cDNAs encoding the structural proteins of PEMV, the coat protein (CP) and coat protein-read through domain (CPRT) into the genome of the baculovirus Autographa californica multiple nucleopolyhedrovirus with and without a histidine tag or an upstream Kozak consensus sequence. The Sf21 cell line provided the highest level of CP expression of the cell lines tested and resulted in production of virus-like particles (VLPs). The CPRT was not detected in recombinant baculovirus-infected cells by Western blot. Addition of a Kozak sequence increased the yield of baculovirus produced VLPs. Baculovirus-expressed VLPs purified on a nickel NTA column were of variable size (13-30 nm) and contained CP mRNA. The purified VLPs were also shown by RT-PCR to contain 70% of 154 baculovirus mRNAs, indicative of non-specific RNA encapsidation in the absence of viral RNA replication. When fed to the pea aphid, Acyrthosiphon pisum (Harris), the VLPs entered the aphid hemocoel, demonstrating that CPRT is not required for uptake of PEMV from the aphid gut. Baculovirus expression of PEMV VLPs provides a useful tool for future analysis of RNA encapsidation requirements and molecular aphid-virus interactions.

Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus

The complete genome of the Maruca vitrata nucleopolyhedrovirus (MaviNPV) isolated from the legume pod borer, Maruca vitrata (Lepidoptera: Pyralidae), was sequenced. It was found to be 111 953 bp in length, with an overall 39 % G+C content, and contained 126 open reading frames (ORFs) encoding predicted proteins of over 50 aa. The gene content and gene order of MaviNPV have the highest similarity to those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and their shared homologous genes are 100 % collinear. In fact, MaviNPV seems to be a mini-AcMNPV that is native to Taiwan and possesses a smaller genome with fewer auxiliary genes than the AcMNPV type species. Except for one ORF (Mv74), all of the MaviNPV ORFs have homologues in the AcMNPV genome. MaviNPV is the first lepidopteran-specific baculovirus to lack homologues of vfgf and odv-e66. In addition, MaviNPV lacks the baculovirus repeat ORF (bro) gene that corresponds to AcMNPV ORF2. Five homologous regions (hrs) were located within the MaviNPV genome, and these contained a total of 44 imperfect palindromes. Phylogenetic analysis of the whole genome revealed that MaviNPV was separated from the common ancestor of AcMNPV and Bombyx mori nucleopolyhedrovirus before these two viral species diverged from each other. Moreover, replication of MaviNPV in several cell lines and an egfp-MaviNPV infection assay revealed that IPLB-LD-652Y cells are only partially permissive to MaviNPV, which supports our conclusion that MaviNPV is a distinct species of the group I lepidopteran NPVs.

Cytopathological process by multiple nucleopolyhedrovirus in the testis of Bombyx mori L., 1758 (Lepidoptera: Bombycidae)

A cytopathological methodology was used to analyze infection by Bombyx mori multiple nucleopolyhedrovirus (BmMNPV), a geographic isolate of the family Baculoviridae, in the caterpillar testes of the B. mori. Japanese B. mori strain caterpillar, fifth instar, were inoculated with BmMNPV and their testes were collected and processed for light and transmission electronic microscopy. Epithelial coating cells and interfollicular septa in testes were susceptible to BmMNPV. The first evidence of infection was detected on the 6th day post-inoculation (p.i.) in the external epithelium, and on the 7th day p.i. in the internal epithelium and interfollicular septa. Cytopathological characteristics consisted of hypertrophied nuclei, the formation of virogenic stroma, and the occlusion of virions in polyhedron protein crystals in several stages of development. At the end of the infectious process, cell lysis and release of polyhedra into the extracellular medium occurred. Histopathology revealed early infection foci in the surrounding regions of tracheal insertions, thus underlining the role of the trachea as an infection-spreading organ in insects. This spreading occurs through penetration of the basal lamina, which facilitates entry of the budded virus into the testis. Additionally, an alignment of a partial sequence of the ORF 14 of the BmMNPV geographic isolate with other NPV certified the virus genera.

Genomic sequence analysis of a granulovirus isolated from the Old World bollworm, Helicoverpa armigera

The genome of a granulovirus isolated from the Old World bollworm, Helicoverpa armigera, was completely sequenced. The size of the Helicoverpa armigera granulovirus (HearGV) genome is 169,794 nt containing 179 open reading frames (ORFs), making it the second largest baculovirus genome analyzed to date. The genomes of HearGV and the Xestia c-nigrum GV (XecnGV) exhibit extensive sequence similarity and co-linearity, with both genomes containing the same nine homologous regions (hrs) with conserved structure and locations and sharing 167 open reading frames (ORFs). Phylogenetic inference and pairwise analysis of Kimura-2-parameter nucleotide distances for the lef-8, lef-9, and granulin genes indicate that HearGV is part of a cluster of granuloviruses typified by XecnGV. The HearGV genome contains all 62 ORFs found in common among other fully sequenced lepidopteran baculovirus genomes, as well as seven ORFs unique to HearGV. In addition, HearGV and XecnGV genomes share 20 ORFs not found among other baculovirus genomes sequenced to date. In addition to possessing ten ORFs with sequence similarity to baculovirus repeated ORFs (bro), the HearGV genome contains members of two other gene families with homologues in ascovirus, nucleopolyhedrovirus, and entomopoxvirus genomes. Alignment of the HearGV and XecnGV genome sequences revealed that HearGV is missing approximately 16.6 kbp of XecnGV-homologous sequence and contains approximately 8.2 kbp of sequence not found in the XecnGV genome.

AcMNPV ac143 (odv-e18) is essential for mediating budded virus production and is the 30th baculovirus core gene

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ac143 (odv-e18) is a late gene that encodes for a predicted 9.6 kDa structural protein that locates to the occlusion derived viral envelope and viral induced intranuclear microvesicles [Braunagel, S.C., He, H., Ramamurthy, P., and Summers, M.D. (1996). Transcription, translation, and cellular localization of three Autographa californica nuclear polyhedrosis virus structural proteins: ODV-E18, ODV-E35, and ODV-EC27. Virology 222, 100-114.]. In this study we demonstrate that ac143 is actually a previously unrecognized core gene and that it is essential for mediating budded virus production. To examine the role of ac143 in the baculovirus life cycle, we used the AcMNPV bacmid system to generate an ac143 knockout (KO) virus (AcBAC(ac142)(REP-ac143KO)). Fluorescence and light microscopy showed that infection by AcBAC(ac142)(REP-ac143KO) is limited to a single cell and titration assays confirmed that AcBAC(ac142)(REP-ac143KO) was unable to produce budded virus (BV). Progression to very late phases of the viral infection was evidenced by the development of occlusion bodies in the nuclei of transfected cells. This correlated with the fact that viral DNA replication was unaffected in AcBAC(ac142)(REP-ac143KO) transfected cells. The entire ac143 promoter, which includes three late promoter motifs, is contained within the ac142 open reading frame. Different deletion mutants of this region showed that the integrity of the ac142-ac143 core gene cluster was required for the bacmids to display wild-type patterns of viral replication, BV production and RNA transcription.

The genome sequence of the multinucleocapsid nucleopolyhedrovirus of the Chinese oak silkworm Antheraea pernyi

The complete genome sequence of the Liaoning isolate of the Antheraea pernyi multinucleocapsid nucleopolyhedrovirus (AnpeMNPV) was determined. The viral genome size is 126,246 bp, relatively GC-rich (53.5% G+C), with 145 predicted open reading frames (ORFs) of more than 50 amino acids, accounting for more than 97% of the genome. 97% of the ORFs have predicted functions or homologues in other baculoviruses. There are six homologous repeat regions (hrs) and two bro homologues, which are associated with regions of genome instability. The virus lacks the p35 homologue but encodes two members of the inhibitors of apoptosis (iap) gene family. The presence of a gp64 homologue in the AnpeMNPV genome and results from gene parity plot and phylogenetic analysis using the 29 core baculovirus genes clearly classify AnpeMNPV as a group I NPV. The divergence of genome sequences in two geographical NPV isolates suggests of great genetic heterogeneity of baculovirus populations in nature.

Functional and structural characterisation of AgMNPV ie1

We have located and cloned the Anticarsia gemmatalis multicapsid nucleopolyhedrovirus isolate 2D (AgMNPV-2D) genomic DNA fragment containing the immediate early 1 ORF and its flanking regions. Computer assisted analysis of the complete ie1 locus nucleotide sequence information was used to locate regulatory signals in the upstream region and conserved nucleotide and amino acid sequences. Comparative studies led to the identification of several characteristic protein motifs and to the conclusion that AgMNPV-2D is more closely related to Choristoneura fumiferana defective NPV than to other Group I nucleopolyhedrovirus. We have also shown that the AgMNPV IE1 protein was able to transactivate an early Autographa californica MNPV promoter and its own promoter in transient expression assays. In order to investigate the biological functionality of the ie1 promoter, the ie1 upstream activating region (UAR) was molecularly dissected and cloned upstream of the E. coli lacZ ORF. The results obtained, after transfection of UFL-AG-286 insect cells, leading us to find that the -492 and -357 versions contains sequence motifs important for the level of the lacZ reporter gene expression.

Genomic sequence analysis of a nucleopolyhedrovirus isolated from the diamondback moth, Plutella xylostella

The CL3 plaque isolate of Plutella xylostella multiple nucleopolyhedrovirus (PlxyMNPV-CL3) exhibits a high degree of genetic similarity with the Autographa californica MNPV (AcMNPV) but is significantly more virulent against the diamondback moth, P. xylostella, than AcMNPV. To identify genetic differences between PlxyMNPV-CL3 and AcMNPV that may account for the difference in virulence against P. xylostella, the genome sequence of the CL3 plaque isolate of PlxyMNPV was determined and compared to the genome sequence of AcMNPV isolate C6. The PlxyMNPV genome is 134,417 bp, 523 bp larger than the AcMNPV-C6 genome, and the nucleotide sequence is almost completely co-linear with that of AcMNPV-C6. Of the 153 open reading frames (ORFs) identified in PlxyMNPV, 151 had homologues in AcMNPV-C6, with a mean amino acid sequence identity of 98.5%. The PlxyMNPV genome possessed two features previously reported for other variants of AcMNPV: (1) an extra baculovirus repeated orf (bro) sequence located between the plxy29/ac30 and sod ORFs, and (2) the deletion of the AcMNPV pnk/pnl polynucleotide kinase/ligase gene. In addition, an 817 bp insert of unknown origin located between the fp25K and lef-9 genes was discovered. This insert contained two small ORFs and was detected in both tissue culture- and larvae-derived PlxyMNPV DNA by PCR. Finally, the PlxyMNPV-CL3 ie-2 gene encodes a product with a low level (37.3%) of amino acid sequence identity with the AcMNPV-C6 ie-2 product. PlxyMNPV-CL3 apparently acquired this variant ie2 gene by recombination with an undescribed nucleopolyhedrovirus.

Identification and functional analysis of the origins of DNA replication in the Cydia pomonella granulovirus genome

The entire genome of Cydia pomonella granulovirus (CpGV) was systematically screened for origins of DNA replication, using an infection-dependent DNA replication assay in the granulovirus-permissive Cydia pomonella cell line, Cp14R. All seven cosmids in an overlapping library that covered the CpGV genome were found to replicate in the assay. A genomic library of 32 overlapping plasmids was subsequently screened. Plasmids that replicated were in turn subcloned into 1-2 kbp overlapping fragments. Eleven subclones replicated, each containing at least one of the 13 single-copy 74-76 bp imperfect palindromes, previously identified in the CpGV genome as possible origins of replication. Genome fragments of 156 bp, each containing one of the 13 palindromes, were cloned to verify replication and provided confirmation that these 13 palindromes are the only origins of replication in the genome. A real-time PCR method was developed for the quantification of DNA replication, which eliminated the need for Southern blotting and hybridization. A set of deletion clones allowed further quantitative characterization of one of the palindromes. The previously proposed non-homologous region origin of replication did not replicate in the assay.

Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

BACKGROUND

One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.

RESULTS

The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families.

CONCLUSION

With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.

The Homingbac baculovirus cloning system: An alternative way to introduce foreign DNA into baculovirus genomes

An in vitro baculovirus cloning system has been developed for direct cloning of foreign DNA into baculovirus genomes. This system is called the "Homingbac system" because it uses homing endonucleases. The Homingbac system was engineered into the baculoviruses AcMNPV, BmNPV, PxMNPV, RoMNPV, HaSNPV and HzSNPV. All Homingbac viruses were designed to retain the polyhedra phenotype so that they could be inoculated per os to insects. This is the first time a common in vitro baculovirus cloning system has been made for multiple baculovirus species that include both groups I and II nucleopolyhedroviruses (NPVs). In this study, the Homingbac system was demonstrated by directly cloning a PCR-amplified beta-glucuronidase gene cassette into a parent Homingbac virus. This new collection of groups I and II NPV Homingbac viruses are a significant expansion of in vitro cloning technology and are new tools for making recombinant baculoviruses.