A synthetic early promoter from a baculovirus: roles of the TATA box and conserved start site CAGT sequence in basal levels of transcription

Sequencing, Analysis and Organization of the Complete Genome of a Novel Baculovirus Calliteara abietis Nucleopolyhedrovirus (CaabNPV)

Baculoviridae, a virus family characterized by a single large double stranded DNA, encompasses the majority of viral bioinsecticides, representing a highly promising and environmentally friendly pesticide approach to insect control. This study focuses on the characterization of a baculovirus isolated from larvae of Calliteara abietis (Erebidae, Lymantriidae) collected in Mongolian pinaceae forests. This new isolate was called Calliteara abietis nucleopolyhedrovirus (CaabNPV). CaabNPV exhibits an irregular polyhedron shape, and significant variation in the diameter of its occlusion bodies (OBs) was observed. Nucleotide distance calculations confirmed CaabNPV as a novel baculovirus. The CaabNPV genome spans 177,161 bp with a G+C content of 45.12% and harbors 150 potential open reading frames (ORFs), including 38 core genes. A comprehensive genomic analysis categorizes CaabNPV within Group II alphabaculovirus, revealing a close phylogenetic relationship with Alphabaculovirus orleucostigmae (OrleNPV). Additionally, repeat sequence analysis identified three highly repetitive sequences consisting of 112 bp repeat units, known as homologous regions (hrs). This research contributes valuable insights into CaabNPV's phylogenetic placement, genomic structure, and its potential applications in insect biocontrol.

Genome sequence and organization of the Mythimna (formerly Pseudaletia) unipuncta granulovirus Hawaiian strain

Purified occlusion bodies (OBs) of Mythimna (formerly Pseudaletia) unipuncta (the true armyworm) granulovirus Hawaiian strain (MyunGV-A) were observed, showing typical GV morphological characteristics under scanning and transmission electron microscopy (EM). The genome of MyunGV-A was completely sequenced and analysed. The genome is 176,677 bp in size, with a G+C content of 39.79%. It contains 183 open reading frames (ORFs) encoding 50 or more amino acids with minimal overlap. Comparison of MyunGV-A with TnGV, XcGV, and HearGV genomes revealed extensive sequence similarity and collinearity, and the four genomes contain the same nine homologous regions (hrs) with conserved structures and locations. Three unique genes, 12 baculovirus repeated ORF (bro), 2 helicase, and 3 enhancin genes, were identified. In particular, two repeated genes (ORF39 and 49) are present in the genome, in reverse and complementarily orientations. Twenty-four OB proteins were identified from the putative protein database of MyunGV-A. In addition, MyunGV-A belongs to the Betabaculovirus group and is most closely related to TnGV (99% amino acid identity) according to a phylogenetic tree based on the combined amino acid sequences of 38 core gene contents.

Identification of miRNAs encoded by Autographa californica nucleopolyhedrovirus

Two Autographa californica nucleopolyhedrovirus (AcMNPV) encoded miRNAs, AcMNPV-miR-1 and AcMNPV-miR-3, have been reported by us in 2013 and 2019, respectively. Here, we present an integrated investigation of AcMNPV-encoded miRNAs, which include the above two miRNAs and three additional newly identified miRNAs. Six candidate miRNAs were predicted through small RNA deep sequencing and bioinformatics, of which, five were validated. Three miRNAs are located opposite the coding sequences, the other two are located in the coding sequences of viral genes. Targets in both virus and host were predicted and subsequently tested using dual-luciferase reporter assays. The validated targets were found mainly in AcMNPV, except for the targets of AcMNPV-miR-4, which are all host genes. Based on reporter assays, the five miRNAs predominantly function by down-regulating their targets. The transcription start sites of these miRNAs were bioinformatic screened based on known baculovirus promoter motifs. Our study reveals that AcMNPV-encoded miRNAs function as fine modulators of the interactions between host and virus by regulating viral and/or host genes.

Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae)

Matsumuraeses phaseoli is a Lepidopteran pest that primarily feeds on numerous species of cultivated legumes, such as Glycine and Phaseolus. It is widely distributed in northeast Asia. A novel granulovirus, designated as Matsumuraeses phaseoli granulovirus (MaphGV), was isolated from pathogenic M. phaseoli larvae that dwell in rolled leaves of Astragalus membranaceus, a Chinese medicinal herb. In this study, using next-generation sequencing, we report the complete genome of MaphGV. MaphGV genome comprises a double-stranded DNA of 116,875 bp, with 37.18% GC content. It has 128 hypothetical open reading frames (ORFs). Among them, 38 are baculovirus core genes, 18 are lepidopteran baculovirus conserved genes, and 5 are unique to Baculoviridae. MaphGV has one baculovirus repeat ORF (bro) and three inhibitors of apoptosis proteins (iap), including a newfound iap-6. We found two atypical baculoviral homologous regions (hrs) and four direct repeats (drs) in the MaphGV genome. Based on phylogenetic analysis, MaphGV belongs to Clade b of Betabaculovirus and is closely related to Cydia pomonellagranulovirus (CpGV) and Cryptophlebia leucotretagranulovirus (CrleGV). This novel baculovirus discovery and sequencing are invaluable in understanding the evolution of baculovirus and MaphGV may be a potential biocontrol agent against the bean ravaging pest.

Real-Time Expression Analysis of Selected Anticarsia gemmatalis multiple nucleopolyhedrovirus Gene Promoters during Infection of Permissive, Semipermissive and Nonpermissive Cell Lines

Baculovirus infection follows a transcriptionally controlled sequence of gene expression that occurs by activation of different viral gene promoter sequences during infection. This sequence of promoter activation may be disrupted by cellular defenses against viral infection, which might interfere with viral progeny formation. In this work, the activity of the ie1, gp64, lef-1, vp39, p6.9 and polh promoters of the Anticarsia gemmatalis multiple nucleopolyhedrovirus was assessed during infection of permissive, semipermissive and nonpermissive cell lines by a novel methodology that detects reporter protein luminescence in real-time. This technique allowed us to characterize in rich detail the AgMNPV promoters in permissive cell lines and revealed differential profiles of expression in cells with limited permissivity that correlate well with limitations in viral DNA replication. Semipermissive and nonpermissive cell lines presented delays and restrictions in late and very late promoter expression. Cells undergoing apoptosis did not inhibit late gene expression; however, viral progeny formation is severely affected. This work demonstrates the application of the real-time luminescence detection methodology and how the promoter expression profile may be used to diagnose cellular permissivity to baculovirus infection.

Temporal characterization of protein production levels from baculovirus vectors coding for GFP and RFP genes under non-conventional promoter control

The ease of use and versatility of the Baculovirus Expression Vector System (BEVS) has made it one of the most widely used systems for recombinant protein production However, co-expression systems currently in use mainly make use of the very strong very late p10 and polyhedron (polh) promoters to drive expression of foreign genes, which does not provide much scope for tailoring expression ratios within the cell. This work demonstrates the use of different Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) promoters to control the timing and expression of two easily traceable fluorescent proteins, the enhanced green fluorescent protein (eGFP), and a red fluorescent protein (DsRed2) in a BEVS co-expression system. Our results show that gene expression levels can easily be controlled using this strategy, and also that modulating the expression level of one protein can influence the level of expression of the other protein within the system, thus confirming the concept of genes "competing" for limited cellular resources. Plots of "expression ratios" of the two model genes over time were obtained, and may be used in future work to tightly control timing and levels of foreign gene expression in an insect cell co-expression system.

The promoter of the white spot syndrome virus immediate-early gene WSSV108 is activated by the cellular KLF transcription factor

A series of deletion and mutation assays of the white spot syndrome virus (WSSV) immediate-early gene WSSV108 promoter showed that a Krüppel-like factor (KLF) binding site located from -504 to -495 (relative to the transcription start site) is important for the overall level of WSSV108 promoter activity. Electrophoretic mobility shift assays further showed that overexpressed recombinant Penaeus monodon KLF (rPmKLF) formed a specific protein-DNA complex with the (32)P-labeled KLF binding site of the WSSV108 promoter, and that higher levels of Litopenaeus vannamei KLF (LvKLF) were expressed in WSSV-infected shrimp. A transactivation assay indicated that the WSSV108 promoter was strongly activated by rPmKLF in a dose-dependent manner. Lastly, we found that specific silencing of LvKLF expression in vivo by dsRNA injection dramatically reduced both WSSV108 expression and WSSV replication. We conclude that shrimp KLF is important for WSSV genome replication and gene expression, and that it binds to the WSSV108 promoter to enhance the expression of this immediate-early gene.

Biology, genome organization, and evolution of parvoviruses in marine shrimp

As shrimp aquaculture has evolved from a subsistent farming activity to an economically important global industry, viral diseases have also become a serious threat to the sustainable growth and productivity of this industry. Parvoviruses represent an economically important group of viruses that has greatly affected shrimp aquaculture. In the early 1980s, an outbreak of a shrimp parvovirus, infectious hypodermal and hematopoietic necrosis virus (IHHNV), led to the collapse of penaeid shrimp farming in the Americas. Since then, considerable progress has been made in characterizing the parvoviruses of shrimp and developing diagnostic methods aimed to preventing the spread of diseases caused by these viruses. To date, four parvoviruses are known that infect shrimp; these include IHHNV, hepatopancreatic parvovirus (HPV), spawner-isolated mortality virus (SMV), and lymphoid organ parvo-like virus. Due to the economic repercussions that IHHNV and HPV outbreaks have caused to shrimp farming over the years, studies have been focused mostly on these two pathogens, while information on SMV and LPV remains limited. IHHNV was the first shrimp virus to be sequenced and the first for which highly sensitive diagnostic methods were developed. IHHNV-resistant lines of shrimp were also developed to mitigate the losses caused by this virus. While the losses due to IHHNV have been largely contained in recent years, reports of HPV-induced mortalities in larval stages in hatchery and losses due to reduced growth have increased. This review presents a comprehensive account of the history and current knowledge on the biology, diagnostics methods, genomic features, mechanisms of evolution, and management strategies of shrimp parvoviruses. We also highlighted areas where research efforts should be focused in order to gain further insight on the mechanisms of parvoviral pathogenicity in shrimp that will help to prevent future losses caused by these viruses.

The transcriptome of the baculovirus Autographa californica multiple nucleopolyhedrovirus in Trichoplusia ni cells

Baculoviruses are important insect pathogens that have been developed as protein expression vectors in insect cells and as transduction vectors for mammalian cells. They have large double-stranded DNA genomes containing approximately 156 tightly spaced genes, and they present significant challenges for transcriptome analysis. In this study, we report the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5' capped transcription start sites and 3' polyadenylation sites. We identified four clusters of genes associated with distinctive patterns of mRNA accumulation through the AcMNPV infection cycle. A total of 218 transcription start sites (TSS) and 120 polyadenylation sites (PAS) were mapped. Only 29 TSS were associated with a canonical TATA box, and 14 initiated within or near the previously identified CAGT initiator motif. The majority of viral transcripts (126) initiated within the baculovirus late promoter motif (TAAG), and late transcripts initiated precisely at the second position of the motif. Analysis of 3' ends showed that 92 (77%) of the 3' PAS were located within 30 nucleotides (nt) downstream of a consensus termination signal (AAUAAA or AUUAAA). A conserved U-rich region was found approximately 2 to 10 nt downstream of the PAS for 58 transcripts. Twelve splicing events and an unexpectedly large number of antisense RNAs were identified, revealing new details of possible regulatory mechanisms controlling AcMNPV gene expression. Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle.

Helicoverpa armaigera nucleopolyhedrovirus ORF50 is an early gene not essential for virus propagation in vitro and in vivo

Homologs of Helicoverpa armigera nucleopolyhedrovirus ORF50 (HA50) are found in most alphabaculoviruses, but their functions remain unknown. Here, we characterized whether Ha50 is indispensable for virus progration. Ha50 transcript was first detected at 3 h post-infection from HearNPV-infected HzAM1 cells. 3'RACE analysis showed that Ha50 transcript was polyadenlylated. 5'RACE analysis revealed two transcription initiation sites, one of which was mapped to the canonical baculovirus early transcription initiator motif CAGT. HA50 protein could be detected from infected cells harvested at 12 h post-infection. Transient expression assays showed that GFP-fused HA50 localized in the cytoplasm and nucleus of HzAM1 cells with or without superinfection. To further examine the role of Ha50 in the virus life cycle, a Ha50 knockout bacmid and a repair bacmid carrying Ha50 under the control of its native promoter elements were constructed using bacmid technology. One-step growth curve analysis showed that the kinetics of infectious budded virus production of Ha50 knockout virus was similar to that of the parental virus or the repair virus. Analysis of the expression of viral early protein IE-1, late protein VP39 and very late protein suggested that viral protein expression was not affected by Ha50 inactivation. Electron microscopy revealed that HaBacΔ50-PH-G occluded viruses (ODVs) and occlusion bodies were indistinguishable from those of the wild-type virus. Similarly, bioassays showed no significant difference in the LC(50) values between Ha50 deletion virus and wild-type virus. Our results together demonstrate that Ha50 is an early gene dispensable for virus propagation in vitro and in vivo.

Co-expression vs. co-infection using baculovirus expression vectors in insect cell culture: Benefits and drawbacks

The baculovirus expression vector system (BEVS) is a versatile and powerful platform for protein expression in insect cells. With the ability to approach similar post-translational modifications as in mammalian cells, the BEVS offers a number of advantages including high levels of expression as well as an inherent safety during manufacture and of the final product. Many BEVS products include proteins and protein complexes that require expression from more than one gene. This review examines the expression strategies that have been used to this end and focuses on the distinguishing features between those that make use of single polycistronic baculovirus (co-expression) and those that use multiple monocistronic baculoviruses (co-infection). Three major areas in which researchers have been able to take advantage of co-expression/co-infection are addressed, including compound structure-function studies, insect cell functionality augmentation, and VLP production. The core of the review discusses the parameters of interest for co-infection and co-expression with time of infection (TOI) and multiplicity of infection (MOI) highlighted for the former and the choice of promoter for the latter. In addition, an overview of modeling approaches is presented, with a suggested trajectory for future exploration. The review concludes with an examination of the gaps that still remain in co-expression/co-infection knowledge and practice.

Autographa californica multiple nucleopolyhedrovirus me53 (ac140) is a nonessential gene required for efficient budded-virus production

me53 is a highly conserved baculovirus gene found in all lepidopteran baculoviruses that have been fully sequenced to date. The putative ME53 protein contains a zinc finger domain and has been previously described as a major early transcript. We generated an me53-null bacmid (AcDeltame53GFP), as well as a repair virus (AcRepME53:HA-GFP) carrying me53 with a C-terminal hemagglutinin (HA) tag, under the control of its native early and late promoter elements. Sf9 and BTI-Tn-5b1 cells transfected with AcDeltame53GFP resulted in a 3-log reduction in budded-virus (BV) production compared to both the parental Autographa californica multiple nucleopolyhedrosis virus and the repair bacmids, demonstrating that although me53 is not essential for replication, replication is compromised in its absence. Our data also suggest that me53 does not affect DNA replication. Cell fractionation showed that ME53 is found in both the nucleus and the cytoplasm as early as 6 h postinfection. Deletion of the early transcriptional start site resulted in a 10- to 360-fold reduction of BV yield; however, deletion of the late promoter (ATAAG) resulted in a 160- to 1,000-fold reduction, suggesting that, in the context of BV production, ME53 is required both early and late in the infection cycle. Additional Western blot analysis of purified virions from the repair virus revealed that ME53:HA is associated with both BV and occlusion-derived virions. Together, these results indicate that me53, although not essential for viral replication, is required for efficient BV production.

ac109 is required for the nucleocapsid assembly of Autographa californica multiple nucleopolyhedrovirus

ORF109 (Ac109) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a highly conserved gene in all sequenced baculovirus genomes, but its function is not known. This paper describes generation of an ac109 knockout virus (Ac-ac109-KO-GP) and analyses of the influence of ac109 deletion on the virus replication in Sf-9 cells so as to investigate the role of ac109 in the viral life cycle. Results revealed that budded virus (BV) yields and occlusion body synthesis were completely blocked in cells infected with the mutant virus. Electron microscopy demonstrated that ac109 deletion blocked nucleocapsid formation, though infection was initiated and electron-dense bodies associated with the virogenic stroma appeared. The mutant phenotype was rescued by an ac109 rescue virus. On the other hand, real-time PCR analysis indicated that ac109 is not required for viral DNA replication. Thus, these results suggested that ac109 plays an important role in AcMNPV nucleocapsid formation.

Autographa californica multiple nucleopolyhedrovirus ac66 is required for the efficient egress of nucleocapsids from the nucleus, general synthesis of preoccluded virions and occlusion body formation

Although orf66 (ac66) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is conserved in all sequenced lepidopteran baculovirus genomes, its function is not known. This paper describes generation of an ac66 knockout AcMNPV bacmid mutant and analyses of the influence of ac66 deletion on the virus replication in Sf-9 cells so as to determine the role of ac66 in the viral life cycle. Results indicated that budded virus (BV) yields were reduced over 99% in ac66-null mutant infected cells in comparison to that in wild-type virus infected cells. Optical microscopy revealed that occlusion body synthesis was significantly reduced in the ac66 knockout bacmid-transfected cells. In addition, ac66 deletion interrupted preoccluded virion synthesis. The mutant phenotype was rescued by an ac66 repair bacmid. On the other hand, real-time PCR analysis indicated that ac66 deletion did not affect the levels of viral DNA replication. Electron microscopy revealed that ac66 is not essential for nucleocapsid assembly, but for the efficient transport of nucleocapsids from the nucleus to the cytoplasm. These results suggested that ac66 plays an important role for the efficient exit of nucleocapsids from the nucleus to the cytoplasm for BV synthesis as well as for preoccluded virion and occlusion synthesis.

The Chilo iridescent virus DNA polymerase promoter contains an essential AAAAT motif

The delayed-early DNA polymerase promoter of Chilo iridescent virus (CIV), officially known as Invertebrate iridescent virus, was fine mapped by constructing a series of increasing deletions and by introducing point mutations. The effects of these mutations were examined in a luciferase reporter gene system using Bombyx mori cells transfected with promoter constructs and infected with CIV. When the size of the upstream element was reduced from position −19 to −15, relative to the transcriptional start site, the luciferase activity was reduced to almost zero. Point mutations showed that each of the 5 nt (AAAAT) located between –19 and –15 were equally essential for promoter activity. Mutations at individual bases around the transcription initiation site showed that the promoter extended until position −2 upstream of the transcription start site. South-Western analysis showed that a protein of approximately 100 kDa interacted with the −19 nt promoter fragment in CIV-infected cells. This binding did not occur with a point mutant that lacked promoter activity. The AAAAT motif was also found in the DNA polymerase promoter region of other iridoviruses and in other putative CIV delayed-early genes.

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.

Functional characterization of putative promoter elements from infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp and in insect and fish cell lines

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) of shrimp contains a linear single-stranded DNA genome of approximately 4.1kb with three putative open reading frames (ORFs) on the same DNA strand designated, the Left, Middle, and Right ORFs. The Left ORF codes for non-structural protein and the Right ORF codes for capsid protein, whereas the role of the Middle ORF is still unknown. Two putative promoters, designated P2 and P61, were detected upstream of the Left ORF and Right ORF, respectively. We evaluated the activities of these two promoters with or without a transcriptional enhancer element via the use of firefly luciferase reporter constructs in insect and fish cells, and in shrimp tail muscle. In insect and fish cells, the P2 promoter was stronger than the P61 promoter. The presence of the SV40 enhancer element negatively affected P2 but not P61 promoter activity in insect cells. However, in fish cells, the SV40 enhancer element dramatically increased the activities of both promoters. In shrimp, there was no significant difference in luciferase expression driven by these two promoters. In shrimp tail muscle, the presence of SV40 enhancer element in the construct had no significant effect on the P2 promoter and a negative effect on the P61 promoter. The IHHNV P2 and P61 promoters were found to be constitutive promoters that can drive gene expression in both invertebrate and vertebrate hosts.

Characterization of AcMNPV with a deletion of me53 gene

The Autographa Californica multiple nucleopolyhedrovirus (AcMNPV) me53 gene, which was previously reported as one of the major early-transcribed genes, was deleted through homologous recombination from an AcMNPV genome propagated as a bacmid DNA in E. coli, generating a me53 gene knockout bacmid. Green fluorescent protein (GFP) expression analysis and supernatant passage assay revealed that the me53 knockout bacmid was unable to replicate in cell culture, while me53 repair bacmid, which was generated by reinsertion of the me53 gene into the mutant at a different locus (the gentamicin locus) with ET-recombination technique, resumed viral replication ability at wild-type levels, indicating that the defective phenotype of the me53 knockout virus was directly due to the deletion of the me53-ORF. Subsequent electron microscopy revealed that the me53 knockout bacmid failed to form nucleocapsid in the nuclei of the transfected cells, though viral infection seemed to be initiated. Meanwhile, real-time PCR analysis based on SYBR Green fluorescence indicated abolishment of the viral DNA replication by me53 gene inactivation. Thus, it is demonstrated for the first time that me53 knockout blocked viral DNA replication, nucleocapsid formation, and consequent BV and ODV production.

Temporal transcription program of recombinant Autographa californica multiple nucleopolyhedrosis virus

Baculoviruses, a family of large, rod-shaped viruses that mainly infect lepidopteran insects, have been widely used to transduce various cells for exogenous gene expression. Nonetheless, how a virus controls its transcription program in cells is poorly understood. With a custom-made baculovirus DNA microarray, we investigated the recombinant Autographa californica multiple nucleopolyhedrosis virus (AcMNPV) gene expression program in lepidopteran Sf21 cells over the time course of infection. Our analysis of transcription kinetics in the cells uncovered sequential viral gene expression patterns possibly regulated by different mechanisms during different phases of infection. To gain further insight into the regulatory network, we investigated the transcription program of a mutant virus deficient in an early transactivator (pe38) and uncovered several pe38-dependent and pe38-independent genes. This study of baculovirus dynamic transcription programs in different virus genetic backgrounds provides new molecular insights into how gene expression in viruses is regulated.

Sequence analysis and organization of the Neodiprion abietis nucleopolyhedrovirus genome

Of 30 baculovirus genomes that have been sequenced to date, the only nonlepidopteran baculoviruses include the dipteran Culex nigripalpus nucleopolyhedrovirus and two hymenopteran nucleopolyhedroviruses that infect the sawflies Neodiprion lecontei (NeleNPV) and Neodiprion sertifer (NeseNPV). This study provides a complete sequence and genome analysis of the nucleopolyhedrovirus that infects the balsam fir sawfly Neodiprion abietis (Hymenoptera, Symphyta, Diprionidae). The N. abietis nucleopolyhedrovirus (NeabNPV) is 84,264 bp in size, with a G+C content of 33.5%, and contains 93 predicted open reading frames (ORFs). Eleven predicted ORFs are unique to this baculovirus, 10 ORFs have a putative sequence homologue in the NeleNPV genome but not the NeseNPV genome, and 1 ORF (neab53) has a putative sequence homologue in the NeseNPV genome but not the NeleNPV genome. Specific repeat sequences are coincident with major genome rearrangements that distinguish NeabNPV and NeleNPV. Genes associated with these repeat regions encode a common amino acid motif, suggesting that they are a family of repeated contiguous gene clusters. Lepidopteran baculoviruses, similarly, have a family of repeated genes called the bro gene family. However, there is no significant sequence similarity between the NeabNPV and bro genes. Homologues of early-expressed genes such as ie-1 and lef-3 were absent in NeabNPV, as they are in the previously sequenced hymenopteran baculoviruses. Analyses of ORF upstream sequences identified potential temporally distinct genes on the basis of putative promoter elements.

Expression of Autographa californica multiple nucleopolyhedrovirus genes in mammalian cells and upregulation of the host beta-actin gene

The gene expression of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was examined in two types of mammalian cells, human HeLa14 and hamster BHK cells. DNA microarray analysis followed by reverse transcription-PCR identified at least 12 viral genes transcribed in both HeLa14 cells and BHK cells inoculated with AcMNPV. 5' rapid amplification of cDNA ends was carried out to examine the transcriptional fidelity of these genes in HeLa14 cells. The transcription of ie-1, ie-0 and gp64 was initiated at a baculovirus early gene motif, CAGT, accompanied by a TATA motif. In addition, the same splicing observed for ie-0 mRNA in Sf9 cells occurred in HeLa14 cells. While the transcription initiation sites for pe38 and p6.9 were not located in the CAGT motif, most of them were in a typical eukaryotic RNA polymerase II promoter structure (a conventional TATA motif and/or an initiator). Interestingly, the expression of beta-actin was upregulated in the mammalian cells inoculated with AcMNPV. Subsequent experiments using UV-inactivated virus confirmed the upregulation, suggesting that de novo synthesis of viral products is not required for the event. These results indicated that the AcMNPV genome acts as a template for transcription in mammalian cells through the usual infection pathway, though there is no evidence for the functional expression of viral genes at present.

Choristoneura fumiferana Granulovirus pk-1: a baculoviral protein kinase

Open reading frame (ORF) 3 on the Choristoneura fumiferana granulovirus (ChfuGV), located in the 11 kb fragment of the BamHI genomic bank encodes a predicted 32-kDa putative kinase protein. Bioinformatics analysis on the predicted amino acid sequence of ChfuGV PK-1 revealed the existence of 11 catalytic subdomains. Sequence analysis within the 5'-untranslated region (5'-UTR) of ChfuGV pk- 1 indicates the presence of both putative early and late promoter motifs, indicating that pk-1 may be expressed throughout the infection cycle. Promoter sequence analysis reveals that pk-1 is deprived of a TATA box and appears instead to be regulated by other cis-acting transcriptional regulatory elements. Temporal transcription analysis by RT-PCR confirms the appearance of transcripts detected from 2 h p.i. until 72 h p.i. Northern blot hybridization characterizes pk-1 transcription as a 1.2 kb transcript. Homology comparisons reveal that ChfuGV PK-1 protein is most closely related to Phthorimaea operculalla granulovirus (PoGV) with 80 % amino acid identity.

Microarray and RT-PCR screening for white spot syndrome virus immediate-early genes in cycloheximide-treated shrimp

Here, we report for the first time the successful use of cycloheximide (CHX) as an inhibitor to block de novo viral protein synthesis during WSSV (white spot syndrome virus) infection. Sixty candidate IE (immediate-early) genes were identified using a global analysis microarray technique. RT-PCR showed that the genes corresponding to ORF126, ORF242 and ORF418 in the Taiwan isolate were consistently CHX-insensitive, and these genes were designated ie1, ie2 and ie3, respectively. The sequences for these IE genes also appear in the two other WSSV isolates that have been sequenced. Three corresponding ORFs were identified in the China WSSV isolate, but only an ORF corresponding to ie1 was predicted in the Thailand isolate. In a promoter activity assay in Sf9 insect cells using EGFP (enhanced green fluorescence protein) as a reporter, ie1 showed very strong promoter activity, producing higher EGFP signals than the insect Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV) ie2 promoter.

Identification and characterization of a major early-transcribed gene of Trichoplusia ni single nucleocapsid nucleopolyhedrovirus using the baculovirus expression system

An early transcribed gene (me-53) of a South Africa strain of Trichoplusia ni single nucleocapsid nucleopolyhedrovirus (TnSNPV) was sequenced and identified. It has an open reading frame of 1146 nucleotides that encodes a protein of 382 amino acids with a molecular mass of 45.2 kDa. The deduced protein sequence alignment of 13 baculovirus ME-53s indicated that the TnSNPV ME-53 shares the highest homologies with NPV subgroup II-A Spodoptera exigua multiple and Mamestra configurata (Maco) nucleopolyhedrovirus ME-53s. The zinc finger-like motifs at the C-termini of ME-53s are highly conserved with similar patterns of cysteine positions. Upon introduction of the gene and a green fluorescent protein reporter gene into the baculovirus expression vector system, the transcriptional analysis of me-53 in two cell lines infected with the Autographa californica nucleopolyhedrovirus (AcMNPV) recombinant revealed that an early TnSNPV me-53 transcript can be detected by 1 h postinfection (hpi) until 12 hpi and a late one from 18 hpi up to 48 hpi, while early and late transcripts of the AcMNPV me-53 of the recombinant can be detected at 3 and 24 hpi, respectively. This suggested that the early and late promoters of both AcMNPV and TnSNPV me-53s were recognized in recombinant virus-infected cells. The regulatory elements of the TnSNPV me-53 promoter were also analyzed.

Role of AcMNPV IE0 in baculovirus very late gene activation

IE0 is the only known baculovirus protein that is produced by splicing. In this study, we have explored the role of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) IE0 and its interaction with IE1 in the activation of very late gene expression from the polyhedrin promoter using transient assays. IE0 is co-expressed with IE1 throughout infection up to late times post-infection (p.i.) but shows peak levels of expression at early times. Significant changes in the ratios of the relative levels of IE0 to IE1 were observed throughout the course of infection. To study IE0 in the absence of IE1, we constructed a plasmid pAc-IE0(M-->A) that expressed only IE0. This was due to a mutation of the internal AUG that prevented translation of IE1 from the ie0 mRNA. Both IE0 and IE0(M-->A) were able to replace IE1 in transient assays, showing that IE0 is functional for very late gene activation and should be considered the 20th late gene expression factor (lef). In transient assays, IE0 showed that maximum very late gene expression is achieved at very low relative levels of protein. In contrast, IE1 requires higher levels of protein to obtain maximum very late gene expression. Furthermore, when the levels of IE0 become too high, very late gene expression rapidly declines. Interestingly, co-expression of IE0 and IE1 results in a mutually antagonistic affect on very late gene expression.

Functional characterization of the ecdysteroid UDP-glucosyl transferase gene of Helicoverpa armigera single-enveloped nucleopolyhedrovirus isolated in South Africa

The ecdysteroid UDP-glucosyltransferase (egt) gene of a single enveloped nucleopolyhedrovirus was located using an Hz-SNPV gene-specific probe. This SNPV was found infecting a colony of Helicoverpa armigera (HaSNPV) in the Western Cape region of South Africa. The open reading frame of the HaSNPV-SA egt is 1.548 nucleotides long and encodes a predicted protein of 516 amino acids with a Mr of 58,897-kDa. The 5'-noncoding region contained an early transcription initiation motif (CAGT) and a baculovirus late transcription motif (ATAAG). A transcription enhancer sequence (GATA) was also identified. Two possible TATA boxes together with an AT rich region were also recognized. A putative signal peptide of 20 residues was present at the N-terminus of the predicted EGT sequence. A polyadenylation signal (AATAAA) was found downstream of the translation stop codon. Five Helicoverpa NPV EGT's that have an extremely high degree of nucleotide and amino acid sequence homology were used in this study. Single nucleotide polymorphisms (SNPs) within the gene were tabulated. The Helicoverpa NPV egts seem to be closely related to the egt genes of Mamestra configurata NPV (MacoNPV), Buzura suppressaria NPV (BusuSNPV) and Spodoptera exigua NPV (SeMNPV) with amino acid identities of approximately 50%. The Helicoverpa NPV EGTs show ten conserved motifs with other EGTs. A phylogenetic tree of 27 baculovirus EGTs and a human UDP-glucoronosyltransferase was constructed using Neighbour-joining within CLUSTAL X. That a secreted and active EGT is encoded by HaSNPV-SA was confirmed by assay of infected cell culture medium.

Palmitoylation of the Autographa californica multicapsid nucleopolyhedrovirus envelope glycoprotein GP64: mapping, functional studies, and lipid rafts

Budded virions (BV) of the baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) contain a major envelope glycoprotein known as GP64, which was previously shown to be palmitoylated. In the present study, we used truncation and amino acid substitution mutations to map the palmitoylation site to cysteine residue 503. Palmitoylation of GP64 was not detected when Cys503 was replaced with alanine or serine. Palmitoylation-minus forms of GP64 were used to replace wild-type GP64 in AcMNPV, and these viruses were used to examine potential functions of GP64 palmitoylation in the context of the infection cycle. Analysis by immunoprecipitation and cell surface studies revealed that palmitoylation of GP64 did not affect GP64 synthesis or its transport to the cell surface in Sf9 cells. GP64 proteins lacking palmitoylation also mediated low-pH-triggered membrane fusion in a manner indistinguishable from that of wild-type GP64. Cells infected with viruses expressing palmitoylation-minus forms of GP64 produced infectious virions at levels similar to those from cells infected with wild-type AcMNPV. In combination, these data suggest that virus entry and exit in Sf9 cells were not significantly affected by GP64 palmitoylation. To determine whether GP64 palmitoylation affected the association of GP64 with membrane microdomains, the potential association of GP64 with lipid raft microdomains was examined. These experiments showed that: (i) AcMNPV-infected Sf9 cell membranes contain lipid raft microdomains, (ii) GP64 association with lipid rafts was not detected in infected Sf9 cells, and (iii) GP64 palmitoylation did not affect the apparent exclusion of GP64 from lipid raft microdomains.

Reduced expression of the immediate-early protein IE0 enables efficient replication of Autographa californica multiple nucleopolyhedrovirus in poorly permissive Spodoptera littoralis cells

Infection of Spodoptera littoralis SL2 cells with the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) results in apoptosis and low yields of viral progeny, in contrast to infection with S. littoralis nucleopolyhedrovirus (SlNPV). By cotransfecting SL2 cells with AcMNPV genomic DNA and a cosmid library representing the complete SlNPV genome, we were able to rescue AcMNPV replication and to isolate recombinant virus vAcSL2, which replicated efficiently in SL2 cells. Moreover, vAcSL2 showed enhanced infectivity for S. littoralis larvae compared to AcMNPV. The genome of vAcSL2 carried a 519-bp insert fragment that increased the distance between the TATA element and the transcriptional initiation site (CAGT) of immediate-early gene ie0. This finding correlated with low steady-state levels of IE0 and higher steady-state levels of IE1 (the product of the ie1 gene, a major AcMNPV transactivator, and a multifunctional protein) than of IE0. Mutagenesis of the ie0 promoter locus by insertion of the chloramphenical acetyltransferase (cat) gene yielded a new recombinant AcMNPV with replication properties identical to those of vAcSL2. Thus, the analysis indicated that increasing the steady-state levels of IE1 relative to IE0 should enable AcMNPV replication in SL2 cells. This suggestion was confirmed by constructing a recombinant AcMNPV bearing an extra copy of the ie1 gene under the control of the Drosophila hsp70 promoter. These results suggest that IE0 plays a role in the regulation of AcMNPV infection and show, for the first time, that significant improvement in the ability of AcMNPV to replicate in a poorly permissive cell line and organism can be achieved by increasing the expression of the main multiple functional protein, IE1.

Identification and characterization of a putative baculoviral transcriptional factor IE-1 from Choristoneura fumiferana granulovirus

A gene that encodes a protein homologue to baculoviral IE-1 was identified and sequenced in the genome of the Choristoneura fumiferana granulovirus (ChfuGV). The gene has an 1278 nucleotide (nt) open-reading frame (ORF) that encodes 426 amino acids with an estimated molecular weight of 50.33 kDa. At the nucleotide level, several cis-acting regulatory elements were detected within the promoter region of the ie-1 gene of ChfuGV along with other studied granuloviruses (GVs). Two putative CCAAT elements were detected within the noncoding leader region of this gene; one was located on the opposite strand at -92 and the other at -420 nt from the putative start triplet. Two baculoviral late promoter motifs (TAAG) were also detected within the promoter region of the ie-1 gene of ChfuGV. A single polyadenylation signal, AATAAA, was located 18nt downstream of the putative translational stop codon of ie-1 from ChfuGV. At the protein level, the amino acid sequence data that was derived from the nucleotide sequence in ChfuGV IE-1 was compared to those of the Cydia pomonella granulovirus (CpGV), Xestia c-nigrum granulovirus (XcGV) and Plutella xylostella granulovirus (PxGV). The C-terminal regions of the granuloviral IE-1 sequences appeared to be more conserved when compared to the N-terminal regions. A domain, similar to the basic helix-loop-helix like (bHLH-like) domain in NPVs, was detected at the C-terminal region of IE-1 from ChfuGV (residues 387 to 414). A phylogenetic tree for baculoviral IE-1 was constructed using a maximum parsimony analysis. A phylogenetic estimation demonstrates that ChfuGV IE-1 is most closely related to that of CpGV.

Transcriptional mapping of two genes encoding baculovirus envelope-associated proteins

Genes encoding two representatives of the LD130 family of baculovirus envelope-associated proteins were transcriptionally mapped. These included ld130, which encodes a low pH-induced envelope fusion protein of the Lymantria dispar multinucleocapsid nucleopolyhedrovirus, and op21, which is related to ld130 but is encoded by Orgyia pseudotsugata MNPV and appears to lack an envelope fusion activity. The size and temporal expression of mRNA of both genes were examined by Northern blot analysis of RNA extracted from infected cells at selected timepoints. In addition, 5' rapid amplification of cDNA ends (RACE) in combination with DNA sequence analysis was used to map the start sites of mRNA. Ld130 predominantly utilized its early promoter at 24 h post-infection but by 72 h post-infection ld130 expression was almost exclusively from its late promoter. In contrast, op21 was expressed predominantly from its early promoter throughout the timecourse, even though a consensus late promoter sequence was present within 100 bp of the translation start codon. A significant fraction of late transcripts that mapped to op21 were spliced transcripts originating in the op18 gene region. The 3' termini of the transcripts were also mapped using 3' RACE.

Identification and characterization of the ecdysteroid UDP-glycosyltransferase gene of Epinotia aporema granulovirus

The ecdysteroid UDP-glycosyltransferase (egt) gene of Epinotia aporema granulovirus (EpapGV) was cloned sequenced and its biological activity was assessed. It encodes a protein of 446 amino acids. Direct evidence that the cloned gene encodes an active EGT protein was obtained by transient expression assays in insect cells. The upstream untranslated region of the egt gene exhibits several consensus early promoter elements. Accordingly, the gene is expressed early upon infection of Epinotia aporema larvae and the EGT activity remains high until later times post infection. Sequence analyses indicate the presence of clusters of amino acid residues conserved among all the baculoviral EGTs, although their relation with proper protein folding, ligand binding and catalytic activity remain to be assessed. Phylogenetic trees consistently cluster the granulovirus EGTs separating them clearly from the nucleopolyhedroviruses.

Identification and in vivo characterization of the Epiphyas postvittana nucleopolyhedrovirus Ecdysteroid UDP-glucosyltransferase

The genome of Epiphyas postvittana Nucleopolyhedrovirus (EppoMNPV) contains an ecdysteroid UDP-glucosyltransferase (egt) gene. The egt gene was completely sequenced and surrounding open reading frames identified. EppoMNPV egt is 1479 nucleotides in length encoding a protein with a predicted molecular mass of 55 kDa. Analysis of upstream sequence revealed dual TATA boxes and two CGT upstream activating region motifs. Mapping of the 5' terminus of the egt transcript identified a major transcript produced from an adenine residue 29 nucleotides downstream from the distal TATA box. No transcript was detected from a late promoter motif (GTAAG). Characterization of egt transcripts showed that poly-adenylation occurs at the 3' terminus. EppoMNPV egt transcripts were first detected in infected Epiphyas postvittana larvae by Northern hybridization at 9 h post-infection (hpi) and EGT enzyme activity was detected at 9 hpi in haemolymph from infected larvae. EppoMNPV EGT can conjugate the sugars from both UDP-glucose and UDP-galactose to ecdysone in vitro. Localization assays performed using radiolabelled ecdysone demonstrated that the conjugation of glucose or galactose, from the respective UDP-sugar, led to the prevention of the uptake of ecdysone by SF-21 cells. We propose that EGT functions to prevent the uptake of ecdysone or 20-hydroxyecdysone by metabolite and target cells respectively.

Characterization of the structural gene promoter of Aedes aegypti densovirus

Aedes aegypti densonucleosis virus (AeDNV) has two promoters that have been shown to be active by reporter gene expression analysis (B. N. Afanasiev, Y. V. Koslov, J. O. Carlson, and B. J. Beaty, Exp. Parasitol. 79:322-339, 1994). Northern blot analysis of cells infected with AeDNV revealed two transcripts 1,200 and 3,500 nucleotides in length that are assumed to express the structural protein (VP) gene and nonstructural protein genes, respectively. Primer extension was used to map the transcriptional start site of the structural protein gene. Surprisingly, the structural protein gene transcript began at an initiator consensus sequence, CAGT, 60 nucleotides upstream from the map unit 61 TATAA sequence previously thought to define the promoter. Constructs with the beta-galactosidase gene fused to the structural protein gene were used to determine elements necessary for promoter function. Deletion or mutation of the initiator sequence, CAGT, reduced protein expression by 93%, whereas mutation of the TATAA sequence at map unit 61 had little effect. An additional open reading frame was observed upstream of the structural protein gene that can express beta-galactosidase at a low level (20% of that of VP fusions). Expression of the AeDNV structural protein gene was shown to be stimulated by the major nonstructural protein NS1 (Afanasiev et al., Exp. parasitol., 1994). To determine the sequences required for transactivation, expression of structural protein gene-beta-galactosidase gene fusion constructs differing in AeDNV genome content was measured with and without NS1. The presence of NS1 led to an 8- to 10-fold increase in expression when either genomic end was present, compared to a 2-fold increase with a construct lacking the genomic ends. An even higher (37-fold) increase in expression occurred with both genomic ends present; however, this was in part due to template replication as shown by Southern blot analysis. These data indicate the location and importance of various elements necessary for efficient protein expression and transactivation from the structural protein gene promoter of AeDNV.

The early baculovirus he65 promoter: On the mechanism of transcriptional activation by IE1

We have initiated studies on the mechanism of early transcriptional activation of the early he65 promoter during infection with Autographa californica multicapsid nuclear polyhedrosis virus. This analysis is based on a comparison of the sequences required for he65 promoter activation with those sequences that support specific protein binding. The he65 promoter is located immediately downstream of the homologous region (hr) 4a. The sequences of hr4a are characterized by two imperfect palindromes of 24 bp. The results of transient expression assays indicate promoter activation in the presence of both the proximal palindrome and the known viral trans-regulator IE1. The results of mobility shift assays and DNaseI footprinting analyses reveal differences in specific protein binding at and close to the proximal palindrome depending on whether the nuclear protein extracts are prepared from uninfected or infected cells. The analysis of the protein binding complex at the proximal inverted repeat with extracts from infected cells suggests the involvement of both IE1 and IE0 as oligomers. The minimal protein binding sequences include the left half-site of the 24 bp repeat with 9 additional bp of the flanking sequences. The right half-site of the repeat also directs binding although with lower affinity as confirmed by phenanthroline-copper footprinting assays. Both half-sites of the repeat are thus essential for he65 promoter activation, suggesting that IE1 acts via cooperative binding. We conclude that the proximal inverted repeat is able to interact with both IE1 and IE0 although IE1 is sufficient for activation at least in transient expression assays.

Genome organization of Xestia c-nigrum granulovirus

In order to characterize the genome organization of Xestia c-nigrum granulovirus (XcGV), mapping of putative XcGV genes was performed by construction of lambda and M13 phage libraries followed by Southern blot and nucleotide sequencing analyses. Mapping of the lambda (32 clones covering the entire XcGV genome) and M13 (133 clones made by random cloning) phage library clones was carried out by hybridization of the labeled lambda phage clone DNAs to 1) Southern blotted XcGV genomic DNA fragments cleaved with EcoRI, BamHI, or HindIII, and 2) dot blotted M13 clone DNAs. All 133 M13 clone DNAs were sequenced, and coding possibilities were investigated by computer-assisted homology search; in total, about 43 kb of the genome was sequenced. Amino acid sequence homology searches of 67 M13 clones suggested that these GV DNAs coded for previously characterized genes identified in nucleopolyhedroviruses (NPVs) and GVs. These 67 M13 clones were classified into 25 gene homolog groups (including 29 putative genes) based on their homologies to NPV and GV genes. The remaining M13 clones, except one that encoded a putative metalloproteinase, did not possess deduced amino acid sequences with significant homology to proteins in gene databases. Complete nucleotide sequences of the putative XcGV DNA polymerase and Ac144 homolog genes confirmed the reliability of our speculation of putative genes based on the M13 clones sequencing analysis. In a comparison of relative locations of putative XcGV genes with locations of their homologs in NPVs, most XcGV genes were mapped close to the corresponding locations in NPV genomes. These results suggested that XcGV, compared to NPVs, had relatively conserved gene arrangements, although about 22 kb of 43 kb of DNA sequenced randomly in the XcGV genome consisted of sequences/genes non-homologous to those of previously characterized NPVs.

In vitro transcription of pe38/polyhedrin hybrid promoters reveals sequences essential for recognition by the baculovirus-induced RNA polymerase and for the strength of very late viral promoters

In vitro transcription was used to analyze the promoter specificity of the alpha-amanitin-resistant RNA polymerase that is induced late during infection of Autographa californica multicapsid nuclear polyhedrosis virus. By modifying the preparation of crude nuclear extracts, we have established an assay that permits differentiation between weak late and strong very late viral promoters. The virus-induced RNA polymerase initiates at a TAAG sequence motif in both late and very late promoters. Based on the sensitivity of our in vitro transcription system, we have investigated the sequences responsible for a functional TAAG motif and their putative role with respect to the strength of very late promoters. By constructing hybrid promoters between the early pe38 and the very late polyhedrin promoters, we demonstrated that the replacement of 7 nucleotides upstream of the nonfunctional TAAG sequences in the pe38 promoter with the corresponding sequences of the polyhedrin promoter was sufficient for recognition by the virus-induced RNA polymerase. The strength of the very late polyhedrin promoter was established after replacing the 5' untranslated sequences of the pe38 promoter by those of the polyhedrin promoter in addition to the 7 nucleotides upstream of the TAAG motif.

A 2.9-kilobase noncoding nuclear RNA functions in the establishment of persistent Hz-1 viral infection

Differential viral gene expression during both productive and persistent infections of Hz-1 virus in insect cells was elucidated. Despite more than 100 viral transcripts being expressed during productive viral infection, massive viral gene shutoff was observed during viral persistency, leaving the 2.9-kb persistence-associated transcript 1 (PAT1) as the only detectable viral RNA. Persistence-associated gene 1 (pag1), which encodes PAT1, was cloned and found to contain no significant open reading frames. PAT1 is not associated with the cellular translation machinery and is located exclusively in the nucleus. Further experiments showed that PAT1 is functional in the establishment of persistent Hz-1 viral infection in the cells. All the evidence collectively indicates that PAT1 is a novel nuclear transcript of viral origin. Our results showed that although PAT1 and XIST RNA, a mammalian X-inactive specific transcript, are transcribed by different genes, they have interesting similarities.

Identification of two independent transcriptional activation domains in the Autographa californica multicapsid nuclear polyhedrosis virus IE1 protein

The Autographa californica multicapsid nuclear polyhedrosis virus immediate-early protein, IE1, is a 582-amino-acid phosphoprotein that regulates the transcription of early viral genes. Deletion of N-terminal regions of IE1 in previous studies (G. R. Kovacs, J. Choi, L. A. Guarino, and M. D. Summers, J. Virol. 66:7429-7437, 1992) resulted in the loss of transcriptional activation, suggesting that this region may contain an acidic activation domain. To identify independently functional transcriptional activation domains, we developed a heterologous system in which potential regulatory domains were fused with a modified Escherichia coli Lac repressor protein that contains a nuclear localization signal (NLacR). Transcriptional activation by the resulting NLacR-IE1 chimeras was measured with a basal baculovirus early promoter containing optimized Lac repressor binding sites (lac operators). Chimeras containing IE1 peptides dramatically activated transcription of the basal promoter only when lac operator sequences were present. In addition, transcriptional activation by NLacR-IE1 chimeras was allosterically regulated by the lactose analog, isopropyl-beta-D-thiogalactopyranoside (IPTG). For a more detailed analysis of IE1 regulatory domains, the M1 to T266 N-terminal portion of IE1 was subdivided (on the basis of average amino acid charge) into five smaller regions which were fused in various combinations to NLacR. Regions M1 to N125 and A168 to G222 were identified as independent transcriptional activation domains. Some NLacR-IE1 chimeras exhibited retarded migration in sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. As with wild-type IE1, this aberrant gel mobility was associated with phosphorylation. Mapping studies with the NLacR-IE1 chimeras indicate that the M1 to A168 region of IE1 is necessary for this phosphorylation-associated effect.

Baculovirus gp64 gene expression: negative regulation by a minicistron

Small upstream open reading frames (ORFs) or minicistrons located in the 5' leader of eukaryotic mRNAs have been shown to play a role in translational regulation of some eukaryotic genes, particularly mammalian proto-oncogenes. A survey of the baculovirus Autographa californica multicapsid nuclear polyhedrosis virus genome suggests that at least 10 transcripts from late genes contain potential minicistrons, and at least three of these minicistrons appear to be conserved in homologous genes of the related Orygia pseudotsugata MNPV. The position of the minicistron from one of these genes, gp64, is also conserved in gp64 genes from several baculoviruses, suggesting a potential regulatory function. To identify the potential role of the gp64 minicistron in regulating translation from gp64 late mRNAs, we generated a series of recombinant viruses containing the gp64 promoter and minicistron in combination with a chloramphenicol acetyltransferase reporter gene (cat) inserted into the polyhedrin locus. We first fused a cat reporter in frame with the minicistron coding region to demonstrate that the minicistron initiator ATG was in a context suitable for translational initiation. In subsequent experiments, a cat reporter was fused in frame to the downstream gp64 ORF, and various constructs containing point mutations that inactivated the minicistron were examined. Translational efficiency in the presence and absence of the minicistron was measured by quantitative analysis of gp64-cat RNA and the GP64-CAT protein. In the absence of a functional minicistron, translational efficiency from the downstream gp64-cat reporter ORF increased. Surprisingly, single-point mutations that inactivated the minicistron initiator ATG also resulted in utilization of an upstream in-frame ATG that is found within the minicistron coding region and that is in a poor translational initiation context. Double-point mutation constructs that inactivated both the minicistron initiator ATG and the upstream in-frame ATG also resulted in increased translational efficiency from the downstream gp64-cat ORF. Thus, the gp64 minicistron serves as a negative regulatory element that decreases translation of the gp64 ORF on late mRNAs.

Deletion analysis of four of eighteen late gene expression factor gene homologues of the baculovirus, BmNPV

Nucleotide sequence analysis of the genome of the baculovirus Bombyx mori nuclear polyhedrosis virus (BmNPV) identified 18 homologues of the Autographa californica NPV (AcNPV) lefs (late expression factor genes). These BmNPV lefs showed high (73-98%) amino acid sequence identities to AcNPV lefs and were localized to similar positions in the genome. One lef, p35, was previously characterized in AcNPV and BmNPV deletion experiments. Functional deletion of each of the BmNPV lef homologues was attempted here by insertion of a beta-galactosidase gene cassette into the coding region of each lef. Four of 18 BmNPV lef (39K, ie-2, lef-7, and p35) deletion mutants were successfully isolated, indicating that the other 14 BmNPV lefs were likely essential for viral replication in cell culture. Further analysis showed that deletion of lef-7, p35, and ie-2 resulted in lower levels of viral DNA replication, indicating that the BmNPV lef-7, p35, and ie-2 products have stimulating effects on DNA replication. Deletion of 39K resulted in a significantly lower level of late gene transcription and extremely low (over 10(2)-fold less at 48-80 hr p.i.) production of progeny budded virus in BmN cells. In contrast, the deletion did not affect viral DNA replication, indicating that BmNPV 39K is involved in late gene transcription. Reduced late gene expression presumably affected production and/or release of progeny budded virus particles. This was corroborated by transmission electron microscopy, which showed that virus replication was abnormal in BmN cells infected with a BmNPV mutant lacking 39K and virion production was low. Even though 39K deletion resulted in a loss of oral infectivity, the 39K deletion mutant replicated in silkworm larvae when injected into the body cavity, as did the ie-2, lef7, and p35 deletion mutants. In addition, a BmNPV homologue of the baculovirus very late expression factor gene (vif-1) found in AcNPV was essential, implying an essential function of the BmNPV vif-1 homologue at a step before the onset of very late gene expression.

Nucleopolyhedrovirus interactions with their insect hosts

It is clear from this brief review that our understanding of the molecular cross-talk between insects and their baculovirus pathogens is still very limited. Studies in cell culture have taught us a great deal about the basic baculovirus molecular machinery and how it is regulated, and in many cases this information has been predictive of what occurs in infected insects. Frequently, however, studies in cell culture do not adequately predict the infection process in insect hosts, as demonstrated by viral mutants (some of which were discussed in this review) that behave identically to wild-type virus in cell culture but differ markedly in larvae. More baculovirus studies, therefore, need to be conducted in vivo if we are to improve our understanding of the complex interactions between baculoviruses and their hosts. Conducting baculovirus studies in insects (or at least in primary cell culture) also offers the opportunity to address questions that reach beyond the baculovirus community in significance. For example, almost all of our knowledge of viral fusion mechanisms comes from infection of cells in culture where the pH is neutral or acidic and the temperature is constant at 27 degrees or 37 degrees C. An answer to the question of how the ODV envelope fuses with the microvillar membrane of columnar epithelial cells in the highly alkaline midgut environment at low temperatures will not only be important for an improved understanding of baculovirus infection in the natural world, but will also constitute a new chapter on viral entry mechanisms. Similarly, the answer to the question of how baculovirus nucleocapsids move basally within microvilli promises to involve factors and/or a mechanism not yet described by cell biologists, and so will constitute a valuable contribution to both baculovirology and cell biology. There are many more such examples of biological mechanisms that can be uniquely explored within the context of baculoviruses and their insect hosts, some of which have been highlighted in this review. As more and more young investigators realize the importance of combining a knowledge of virology, molecular technology, and insect biology, however, many of the outstanding mysteries will be solved.

Initiation of baculovirus DNA replication: early promoter regions can function as infection-dependent replicating sequences in a plasmid-based replication assay

From the results of transient plasmid-based replication assays, it has been postulated that homologous regions (hrs) of Autographa californica nuclear polyhedrosis virus (AcMNPV) function as origins of viral DNA replication. However, these assays vary in specificity according to the methodology used and may not be dependent solely on the presence of hr sequences. To determine the role that hrs and other sequences might play in the replication process, a series of plasmids containing specific deletions of various hrs was generated and tested in a standardized replication assay. Deletion of the AcMNPV hr2 and hr5 sequences abolished the ability of plasmids to replicate in the standard infection-dependent replication assay, while deletion of hr1, hr3, and hr4a sequences decreased but did not eliminate plasmid replication in this assay. Plasmids carrying the complete ie-2 and pe38 genes, the ie-1 gene upstream region, or a variety of baculovirus genes including 11 early promoter regions were also able to replicate in virus-infected cells, suggesting that early viral promoter sequences could also function as putative origins of replication. These data suggest that the standard infection-dependent replication assay may identify a broad range of infection-dependent replicating sequences, only one or a few of which may represent genuine viral origins used by the virus in vivo. We propose a model suggesting that the selection of replication initiation sites may be imposed directly by chromatin structure and indirectly by primary sequence and that the process of viral DNA replication may be linked with viral transcription.

The GP64 envelope fusion protein is an essential baculovirus protein required for cell-to-cell transmission of infection

To demonstrate the essential nature of the baculovirus GP64 envelope fusion protein (GP64 EFP) and to further examine the role of this protein in infection, we inactivated the gp64 efp gene of Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) and examined the biological properties of this virus in vivo. To provide GP64 EFP during construction of the recombinant GP64 EFP-null AcMNPV baculovirus, we first generated a stably transfected insect cell line (SfpOP64-6) that constitutively expressed the GP64 EFP of Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV). The AcMNPV gp64 efp gene was inactivated by inserting the bacterial lacZ gene in frame after codon 131 of the gp64 efp gene. The inactivated gp64 gene was cloned into the AcMNPV viral genome by replacement of the wild-type gp64 efp locus. When propagated in the stably transfected insect cells (Sf9OP64-6 cells), budded virions produced by the recombinant AcMNPV GP64 EFP-null virus (vAc64z) contained OpMNPV GP64 EFP supplied by the Sf9OP64-6 cells. Virions propagated in Sf9OP64-6 cells were capable of infecting wild-type Sf9 cells, and cells infected by vAc64z exhibited a blue phenotype in the presence of X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside). Using cytochemical staining to detect vAc64z infected cells, we demonstrated that this GP64 EFP-null virus is defective in cell-to-cell propagation in cell culture. Although defective in cell-to-cell propagation, vAc64z produces occlusion bodies and infectious occlusion-derived virions within the nucleus. Occlusion bodies collected from cells infected by vAc64z were infectious to midgut epithelial cells of Trichoplusia ni larvae. However, in contrast to infection by a control virus, infection by vAc64z did not proceed into the hemocoel. Analysis of vAc64z occlusion bodies in a standard neonate droplet feeding assay showed no virus-induced mortality, indicating that occluded virions produced from vAc64z could not initiate a productive (lethal) infection in neonate larvae. Thus, GP64 EFP is an essential virion structural protein that is required for propagation of the budded virus from cell to cell and for systemic infection of the host insect.

Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters

The basal elements of class II promoters are: (i) a-30 region, recognized by TATA binding protein (TBP); (ii) an initiator (Inr) surrounding the start site for transcription; (iii) frequently a downstream (+10 to +35) element. To determine the sequences that specify an Inr, we performed a saturation mutagenesis of the Inr of the SV40 major late promoter (SV40-MLP). The transcriptional activity of each mutant was determined both in vivo and in vitro. An excellent correlation between transcriptional activity and closeness of fit to the optimal Inr sequence, 5'-CAG/TT-3', was found to exist both in vivo and in vitro. Employing a neural network technique we generated from these data a weight matrix definition of an Inr that can be used to predict the activity of a given sequence as an Inr. Using saturation mutagenesis data of TBP binding sites we likewise generated a weight matrix definition of the -30 region element. We conclude the following: (i) Inrs are defined by the nucleotides immediately surrounding the transcriptional start site; (ii) most, if not all, Inrs are recognized by the same general transcription factor(s). We propose that the mechanism of transcription initiation is fundamentally conserved, with the formation of pre-initiation complexes involving the concurrent binding of general transcription factors to the -30, Inr and, possibly, downstream elements of class II promoters.

Baculovirus--insect cell interactions

Baculovirus interactions with host cells range from the physical interactions that occur during viral binding and entry, to the complex and subtle mechanisms that regulate host gene expression and modify and regulate cellular and organismal physiology and defenses. Fundamental studies of baculovirus biochemistry and molecular biology have yielded many interesting and important discoveries on the mechanisms of these virus-host interactions. Information from such studies has also resulted in exciting new strategies for environmentally sound insect pest control, and in the development and improvement of a valuable eukaryotic expression vector system. In addition a number of important and valuable model biological systems have emerged from studies of baculoviruses. These include robust systems for studies of eukaryotic transcription, viral DNA replication, membrane fusion, and apoptosis. Because functions have been identified for only a small number of baculovirus genes, we can expect many exciting new discoveries in the future and an unfolding of the complex and intricate relationship between baculoviruses and insect cells.