Size and map locations of early transcription products on the Autographa californica nuclear polyhedrosis virus genome

Characterization of an Autographa californica multiple nucleopolyhedrovirus dual mutant: ORF82 is required for budded virus production, and a point mutation in LEF-8 alters late and abolishes very late transcription

A temperature-sensitive (ts) Autographa californica multiple nucleopolyhedrovirus dual mutant, ts42, was generated that displayed tiny-plaque and polyhedral inclusion body (PIB)-defective phenotypes at 33 °C. The mutation responsible for the tiny-plaque phenotype was mapped to orf82, which was characterized as a late gene. Its product was not studied. The mutation responsible for the PIB-defective phenotype was mapped to a highly conserved region of lef-8, which encodes the largest subunit of the viral RNA polymerase. These mutations did not cause a global defect in viral DNA replication or a defect in the shutoff of host protein synthesis. However, the mutation in orf82 caused a dramatic defect in the production of progeny budded virus (BV) but did not decrease the infectivity of those BVs that were released. Hence, ORF82 is required for BV production. The mutation in lef-8 affected a conserved residue that is part of a highly conserved region of LEF-8. This mutation abolished very late transcription whilst altering the transcript size and level of transcription of two late genes.

Characterization of an Autographa californica multiple nucleopolyhedrovirus mutant lacking the ac39(p43) gene

Open reading frame 39 [orf39(p43)] of Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) is present in 10 isolates of the Alphabaculovirus genus. It is highly conserved in sequence and genomic location in the Group I but much less conserved in the Group II viruses. To investigate the potential role of p43 in AcMNPV infection, we constructed and characterized a p43 knockout mutant. The results showed that the p43 region was expressed as RNA from 3h post infection to at least 24h post infection, and its expression pattern was identical to the expression profile of its neighbouring gene, p47. P47 is an essential core gene component of the baculovirus RNA polymerase. The deletion of the p43 region was confirmed by PCR analysis of bacmid DNA and by RT-PCR analysis of RNA purified from p43 knockout infected cells. The results supported the hypothesis that a large transcript, initiating upstream of p47, includes the p43 ORF. Analyses of protein synthesis in p43 knockout infected cells clearly demonstrated that there were no obvious differences in the timing or amount of expression of P47, LEF-3, or VP39. Growth curves showed that infectious budded virus production and occlusion body formation were also not affected by the p43 knockout. We conclude that orf39(p43) is not essential for virus replication in cell culture.

Identification of a domain of the baculovirus Autographa californica multiple nucleopolyhedrovirus single-strand DNA-binding protein LEF-3 essential for viral DNA replication

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) lef-3 is one of nine genes required for viral DNA replication in transient assays. LEF-3 is predicted to contain several domains related to its functions, including nuclear localization, single-strand DNA binding, oligomerization, interaction with P143 helicase, and interaction with a viral alkaline nuclease. To investigate the essential nature of LEF-3 and the roles it may play during baculovirus DNA replication, a lef-3 null bacmid (bKO-lef3) was constructed in Escherichia coli and characterized in Sf21 cells. The results showed that AcMNPV lef-3 is essential for DNA replication, budded virus production, and late gene expression in vivo. Cells transfected with the lef-3 knockout bacmid produced low levels of early proteins (P143, DNA polymerase, and early GP64) and no late proteins (P47, VP39, or late GP64). To investigate the functional role of domains within the LEF-3 open reading frame in the presence of the whole viral genome, plasmids expressing various LEF-3 truncations were transfected into Sf21 cells together with bKO-lef3 DNA. The results showed that expression of AcMNPV LEF-3 amino acids 1 to 125 was sufficient to stimulate viral DNA replication and to support late gene expression. Expression of Choristoneura fumiferana MNPV lef-3 did not rescue any LEF-3 functions. The construction of a LEF-3 amino acid 1 to 125 rescue bacmid revealed that this region of LEF-3, when expressed in the presence of the rest of the viral genome, stimulated viral DNA replication and late and very late protein expression, as well as budded virus production.

Autographa californica nuclear polyhedrosis virus p143 gene product is a DNA-binding protein

We have identified the protein product of the Autographa californica nuclear polyhedrosis virus (AcMNPV) p143 gene by constructing a recombinant baculovirus overexpressing the gene product P143. The overexpressed protein exhibited a relative mobility of approximately 140 kDa and was stable for at least 12 hr after synthesis. Immunoblotting using a monoclonal antibody developed against the overexpressed protein identified a similar polypeptide in AcMNPV-infected cells which was detectable by 4 hr postinfection. P143 was present within infected cell nuclei at relatively constant amounts until at least 72 hr after infection, suggesting that P143 may perform other functions at late times after infection. P143, purified from infected cell nuclei by chromatography over hydroxylapatite and DNA cellulose, bound in a sequence-independent fashion to double-stranded but not to single-stranded DNA to form a ladder of retarded protein-DNA complexes. Together, these data are consistent with the essential role of P143 for viral DNA replication and suggest that P143 may function by direct binding to DNA.

Differential requirements for baculovirus late expression factor genes in two cell lines

A plasmid library of 18 late expression factor (LEF) genes (LEF library) from the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) supports transient expression from a late viral promoter in the SF-21 cell line, derived from Spodoptera frugiperda. We found, however, that this LEF library was unable to support expression from the same promoter in the TN-368 cell line, derived from Trichoplusia ni, which is also permissive for AcMNPV replication. To identify the additional factor(s) required for expression in TN-368 cells, we cotransfected the LEF library with clones representing portions of the AcMNPV genome not represented in the LEF library. A single additional gene was identified; this gene corresponded to ORF70 of the complete AcMNPV sequence and potentially encodes a 34-kDa cysteine-rich polypeptide. Because of its differential effect on late gene expression in the two cell lines, we renamed ORF70 hcf-1 (for host cell-specific factor 1). hcf-1 was involved in expression from reporter plasmids under late and very late but not early promoter control, indicating that it was also a LEF gene. Plasmid DNA replication assays indicated that HCF-1 was involved in virus origin-specific DNA replication in TN-368 cells. Three LEF genes, ie-2, lef-7, and p35, required for optimal virus origin-specific plasmid DNA replication or stability in SF-21 cells had little or no influence in TN-368 cells. Thus, as determined by transient-expression assays, cell line-specific and potentially host-specific factors are required for origin-specific DNA replication or stability.

The roles of eighteen baculovirus late expression factor genes in transcription and DNA replication

A set of 18 plasmid subclones of the Autographa californica nuclear polyhedrosis virus genome supports expression from a late viral promoter in transient expression assays (J. W. Todd, A. L. Passarelli, and L. K. Miller, J. Virol. 69:968-974, 1995). Using this set of plasmids, we have assigned a role for each of the 18 genes required for optimal late gene expression with respect to its involvement at the levels of transcription, translation, and/or DNA replication. RNase protection analyses demonstrated that all of the known late expression factor genes (lefs) affected the steady-state level of reporter gene RNA. Thus, none of the lefs appeared to be specifically involved in translation. A subset of the lefs supported plasmid replication; ie-1, lef-1, lef-2, lef-3, p143, and p35 were essential for plasmid replication, while ie-n, lef-7, and dnapol had stimulatory effects. The predicted sequence of lef-7 suggests that it is a homolog of herpesvirus single-stranded DNA-binding protein (UL29). The role of p35 in plasmid replication appears to be suppression of apoptosis, because p35 could be functionally replaced in the replication assay by either Cp-iap or Op-iap, two heterologous baculovirus genes which suppress apoptosis by a mechanism which appears to differ from that of p35. Thus, one or more of the replication-related lefs or the process of plasmid replication appears to induce cellular apoptosis. Our results indicate that the remaining lefs, lefs 4 through 11, p47, and 39K (pp31), function either at the level of transcription or at that of mRNA stabilization.

Identification of three late expression factor genes within the 33.8- to 43.4-map-unit region of Autographa californica nuclear polyhedrosis virus

A transient transactivation assay system was used in combination with an overlapping Autographa californica nuclear polyhedrosis virus clone library to identify genes involved in late and very late baculovirus gene expression. We have identified three genes within the 33.8- to 43.4-map-unit region of the A. californica nuclear polyhedrosis virus genome which contribute to expression from promoters of the vp39 major capsid protein and polyhedrin genes. One of these three genes corresponds to the previously identified DNA polymerase gene, while the other two genes encode previously unidentified polypeptides of 59,418 and 8,706 Da. None of these genes were required for expression from the early etl promoter.

Sequence, transcriptional mapping, and overexpression of p47, a baculovirus gene regulating late gene expression

A 2.8-kb region of the Autographa californica nuclear polyhedrosis virus genome was sequenced and found to contain an open reading frame (p47) which was capable of rescuing a previously characterized temperature-sensitive mutant, ts317 (S. Partington, H. Yu, A. Lu, and E. B. Carstens, Virology 157:91-102, 1990). Transcriptional mapping demonstrated that an early 4.2-kb RNA encoded the p47 open reading frame and probably overlapped the 39K delayed-early gene. The p47 open reading frame was cloned behind the polyhedrin promoter in a baculovirus transfer plasmid, which was then used to prepare a recombinant baculovirus overexpressing the p47 polypeptide. The overexpressed polypeptide was used to prepare p47-specific monoclonal antibodies. These antibodies detected a polypeptide of 47 kDa in A. californica nuclear polyhedrosis virus-infected cells, demonstrating that p47 is expressed as an authentic viral product. The p47 gene product was localized to the nucleus of infected cells, supporting the hypothesis that it is involved in regulating viral transcription at late times postinfection.

Transcription analysis of the EcoRI D region of the baculovirus Autographa californica nuclear polyhedrosis virus identifies an early 4-kilobase RNA encoding the essential p143 gene

We have investigated the transcriptional activity of the 60.1- to 68.3-map-unit region of the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV). Twelve transcripts mapping to this region were expressed at various times during infection. An early 4.0-kb transcript, potentially coding for a 143-kDa peptide essential for viral DNA replication, was maximally abundant at 6 h postinfection (p.i.). Transcripts of 0.5, 1.1, 1.4, 2.1, and 3.1 kb were most abundant at 12 h p.i., while two large transcripts of 5.2 and 6.8 kb were expressed maximally at 24 h p.i. In the presence of cycloheximide, and in ts8-infected cells at the nonpermissive temperature, only the 4.0-kb RNA was expressed. Northern (RNA) blot analysis using DNA subfragments from the EcoRI D fragment as probes suggested that many of the transcripts overlapped. Strand-specific cRNA probes revealed that the majority of the RNAs were transcribed in the counterclockwise direction. S1 nuclease and primer extension analysis were used to map the 5' ends of transcripts coded within the 60.1- to 64.8-map-unit region. Mapping of the 3' ends of the 1.1-, 4.0-, 5.2-, and 6.8-kb transcripts suggested that these RNAs were all coterminal at their 3' ends. A minicistron was found between the early 4.0-kb transcription start site and the predicted ATG start codon of the p143 gene. Several similar sequence motifs were identified in the promoter regions of the p143 gene and the AcMNPV DNA polymerase gene.

Nucleotide sequence of a gene essential for viral DNA replication in the baculovirus Autographa californica nuclear polyhedrosis virus

The nucleotide sequence of the 60.1- to 65.5-m.u. region of Autographa californica nuclear polyhedrosis virus (AcMNPV) was determined. Seven large open reading frames were identified. Two open reading frames potentially encoding gene products of 143 and 38 kDa were found in the counterclockwise direction upstream of the p6.9 gene. Four additional open reading frames were found in the opposite direction. Analysis of the predicted amino acid sequence of the 143-kDa gene revealed a potential leucine zipper motif, a putative nuclear localization signal, and seven amino acid motifs previously identified in a number of proteins involved in NTP binding and DNA/RNA unwinding. The mutation in a DNA replication defective temperature-sensitive mutant was fine mapped to the carboxy terminus of the ORF1(p143) gene. Sequence analysis of the mutation site identified a single base change of a guanine to an adenine, resulting in the substitution of a methionine for valine. This mutation resides seven amino acids downstream of the putative NTP-binding motif of the ORF1(p143) gene product and results in a DNA negative mutant. Together these data strongly suggest that the ORF1(p143) gene product is a baculovirus helicase.

Identification of the very early transcribed baculovirus gene PE-38

We have started to identify early viral RNAs that are transcribed at 1 h after inoculation to investigate the mechanism involved in the regulation of early gene expression of Autographa californica nuclear polyhedrosis virus (AcNPV). Cloned viral DNA fragments were hybridized to Northern (RNA) blots of polyadenylated RNA isolated from Spodoptera frugiperda cells at 1, 2, and 6 h postinfection to localize very early transcripts. Subsequently we prepared a cDNA library of polyadenylated RNA transcribed at 1 h after inoculation to analyze the cDNA clones corresponding to the major early RNAs. We identified a gene located upstream of the immediate-early gene IE-N extending in the opposite direction. Because of the very early expression during AcNPV infection and the transient expression in uninfected cells, we conclude that we found an immediate-early gene, designated PE-38. The determination of the nucleotide sequence of PE-38 revealed one open reading frame potentially encoding a gene product of 38 kDa. Results of in vitro translation experiments suggest that a PE-38-specific polypeptide of approximately 38 kDa can be expressed. We have evidence from computer analyses that the predicted amino acid sequence includes two putative DNA-binding motifs, a zinc finger, and a leucine zipper.

Nucleotide sequence and characterization of the 39K gene region of Autographa californica nuclear polyhedrosis virus

The complete nucleotide sequence of the Pstl-K fragment of the Autographa californica nuclear polyhedrosis virus (AcMNPV) genome was determined. This region of the genome contains the delayed early 39K gene and V-ubi, a viral protein with homology to ubiquitine. In addition, Pstl-K potentially encodes five other proteins. Hybrid-select translation mapped nine viral-specific proteins to this fragment. Three proteins were observed with both early and late RNA; two of them comigrated with proteins directed by transcripts made from the 39K open reading frame (ORF). One protein which was only seen with hybrid-selected late RNA comigrated with ubiquitin. A correction of previously published sequence data indicates that there is an additional AUG codon upstream of the 39K ORF. This AUG codon is located 8 nucleotides downstream of the early transcription initiation site. The methionine codon is followed by codons for three amino acids and a termination codon. The 39K ORF is located 102 nucleotides downstream of the minicistron. In vitro transcription-translation experiments confirmed that the downstream AUG serves as the initiation codon for the 39K ORF. Radioimmunoprecipitation experiments indicated that the Pstl-K-encoded 39K protein reacted with antiserum raised against a previously described nuclear matrix-associated 39K protein.

Isolation of temperature sensitive mutants of Autographa californica nuclear polyhedrosis virus: phenotype characterization of baculovirus mutants defective in very late gene expression

Temperature sensitive mutants of Autographa californica nuclear polyhedrosis virus were isolated following exposure of parental replicating virus to 5-bromo-2'-deoxyuridine. Two mutants designated ts317 and ts538 were characterized in detail. Both mutants synthesized viral DNA but were defective in infectious extracellular virus production at the nonpermissive temperature suggesting defects in late gene regulation. Pulse-labeling experiments indicated that a switch to late protein synthesis occurred but this synthesis was not maintained with either mutant since all protein synthesis was gradually inhibited by 20 hr postinfection at 33 degrees. Western blots probed with antisera directed against either extracellular virus proteins or very late proteins showed a reduction in late structural proteins, a 10-fold reduction in polyhedrin, and an absence of p10 at the nonpermissive temperature. Northern blots of total intracellular RNA showed that specific late and very late transcripts were synthesized in greatly reduced amounts at the nonpermissive temperature suggesting the absence of very late proteins was a result of inhibition of virus-specific transcription. The genetic analyses indicate that the mutations lie in two closely linked genes, both important in regulating the induction of very late transcription and translation.

Multiple early transcripts and splicing of the Autographa californica nuclear polyhedrosis virus IE-1 gene

The immediate-early IE-1 gene of Autographa californica nuclear polyhedrosis virus was cloned, and its nucleotide sequence was determined. Sequence analysis indicated that this gene would encode a protein of 582 amino acids with a predicted molecular weight of 66,822. Analysis of IE-1 gene expression during baculovirus infection identified two transcripts. One, 1.9 kilobases (kb), was expressed at constant steady-state levels throughout infection, whereas the other, 2.1 kb, was expressed only early in infection. Analysis of IE-1 cDNA clones demonstrated that the 2.1-kb transcript contained the entire 1.9-kb transcript (exon 1) plus an additional 5' end (exon 0). Genomic Southern analysis placed the exon 0 sequences on the EcoRI B fragment, 4 kilobase pairs upstream of exon 1. Sequencing of the upstream region identified an open reading frame whose 5' end was identical to the exon 0 sequences in the cDNAs. Examination of the genomic DNA sequences around the exon-exon junction revealed sequences similar to published consensus splice acceptor and donor sequences. This is the first example of splicing of any viral transcript during baculovirus infection.

Characterization of an early gene accelerating expression of late genes of the baculovirus Autographa californica nuclear polyhedrosis virus

The region of the Autographa californica nuclear polyhedrosis virus (AcMNPV) encompassing the EcoRI T fragment (29.0 to 30.1 map units) was characterized by DNA sequencing, transcriptional mapping, and site-directed mutagenesis. The largest transcript from this region, an early 1.7-kilobase (kb) poly(A)+ RNA, encompassed three tandem, nonoverlapping open reading frames (ORFs). The largest of these ORFs, ETL, was proximal to the 5' end of the transcript and had the capacity to encode a 28-kilodalton (kDa) polypeptide. A recombinant virus, vETL beta gal, containing the Escherichia coli beta-galactosidase (beta gal) gene fused to the N-terminal two-thirds of the ETL ORF, produced blue plaques in the presence of a chromogenic indicator of beta gal and wild-type levels of polyhedra in cell culture. This recombinant was also infectious in insect larvae by oral administration of occluded virus. Comparison of vETL beta gal and wild-type viral proteins pulse-labeled at various times postinfection (p.i.) revealed (i) absence of a virus-induced 28-kDa polypeptide, (ii) early expression of a large (approximately 130-kDa) polypeptide which may be the ETL-beta gal fusion protein, (iii) a delay in expression of early 35 and 40-kDa polypeptides, and (iv) a 4- to 6-h delay in the expression of late proteins in vETL beta gal-infected cells. Cycloheximide did not inhibit synthesis of the 1.7-kb RNA but did inhibit its shutoff, which occurs at 12 h p.i. in the absence of inhibitors. Thus, the ETL gene product is apparently an early 28-kDa protein which is necessary, directly or indirectly, for timely expression of many other AcMNPV genes. The promoter-leader regions of the 1.7-kDa transcript showed significant sequence similarities to the leader of the AcMNPV IE-1 gene. The middle ORF within the 1.7-kb transcript, ETM, would encode a hydrophobic polypeptide of 113 amino acid residues. ETS, a small ORF within and proximal to the 3' end of the 1.7-kb transcript, was also transcribed as a set of smaller (approximately 0.5-kb) RNAs initiated heterogeneously in the region between ETL and ETS and persisting throughout infection.

Mapping Pieris rapae granulosis virus transcripts and their in vitro translation products

Poly(A)+ RNA was isolated from Pieris rapae granulosis virus (PrGV)-infected P. rapae larvae at times early (40 h postinoculation) and late (88 h postinoculation) in larval infection. Using Northern (RNA) blot analysis, we determined the sizes, relative abundances, and map locations of over 100 PrGV transcripts. Differences were found in the transcripts which had accumulated at the two time points. Splicing of these transcripts was not detected. Evidence for the expression of overlapping RNAs in PrGV was obtained. A minimum of 35 PrGV translation products were detected via hybrid selection of poly(A)+ RNA with specific PrGV restriction endonuclease fragments, followed by in vitro translation.

Nucleotide Sequence and Temporal Expression of a Baculovirus Regulatory Gene

The nucleotide sequence of a trans -activating regulatory gene (IE-1) of the baculovirus Autographa californica nuclear polyhedrosis virus has been determined. This gene encodes a protein of 581 amino acids with a predicted molecular weight of 66,856. A DNA fragment containing the entire coding sequence of IE-1 was inserted downstream of an RNA promoter. Subsequent cell-free transcription and translation directed the synthesis of a single peptide with an apparent molecular weight of 70,000. Quantitative S1 nuclease analysis indicated that IE-1 was maximally synthesized during a 1-h virus adsorption period and that steady-state levels of IE-1 message were maintained during the first 24 h of infection. Northern blot hybridization indicated that several late transcripts which overlap the IE-1 gene were transcribed from both strands. The precise locations of the 5′ and 3′ ends of these overlapping transcripts were mapped using S1 nuclease. The overlapping transcripts were grouped in two transcriptional units. One unit was composed of IE-1 and overlapping γ transcripts which initiated upstream of IE-1 and terminated downstream of IE-1. The other unit, transcribed from the opposite strand, consisted of γ transcripts with coterminal 5′ ends and extended 3′ ends. The shorter, more abundant transcripts in this unit overlapped 30 to 40 bases of IE-1 at the 3′ end, while the longer transcripts overlapped the entire IE-1 gene. Transcription of several early A. californica nuclear polyhedrosis virus genes, in addition to 39K, was shown to be trans -activated by IE-1, indicating that IE-1 may have a central role in the regulation of β-gene expression.

Variation in the temporal expression of overlapping baculovirus transcripts

To investigate gene expression from the Autographa californica nuclear polyhydrolysis virus genome (AcNPV), complementary DNA (cDNA) was synthesized from polyadenylated RNA transcribed at 2 h and 10 h postinfection (p.i.) and then cloned into Escherichia coli using plasmid pUC-9. Eighteen 2 h cDNA plasmids were homologous to five distinct regions of the viral genome, while forty-nine 10 h cDNA plasmids were homologous to 15 regions including the five regions transcribed at 2 h. Temporal expression of polyadenylated RNA transcribed from diverse regions of the genome was examined using Northern blot hybridization with the above 2 and 10 h cDNA probes. All regions displayed overlapping sets of RNAs. In addition to HindIII-I/EcoRI-F (IF) and HindIII-B2/EcoRI-H (B2H), several, but not all, regions showed a sequential appearance of higher molecular weight RNAs as the infection progressed. Each overlapping set of RNAs exhibited unique characteristics including variations in the number of overlapping transcripts, their temporal regulation, and their relative abundance during the course of infection.

Physical mapping of temporally regulated, overlapping transcripts in the region of the 10K protein gene in Autographa californica nuclear polyhedrosis virus

We investigated transcriptional activity in the region of a gene for a major late protein (10 kilodaltons) of Autographa californica nuclear polyhedrosis virus. This 10K protein gene spans an HindIII cleavage site, with the 5' end of the gene located in the HindIII-Q fragment and the 3' end in the HindIII-P fragment. Northern blot analysis showed that there were at least four transcripts mapping in this region, two that are present maximally at 12 h (1,500 and 1,100 bases in length) and two that are present at 24 h (750 and 2,500 bases in length). Northern blot analysis also suggested that these transcripts overlap. S1 mapping identified the precise positions of the transcripts and confirmed the overlap. The 1,500- and 1,100-base transcripts share a common 5' end, about 1,056 bases upstream from the HindIII-P-Q boundary; the 750- and 2,500-base transcripts share a common 5' end, about 303 bases upstream from the HindIII-P-Q boundary. The 1,100-base transcript terminates in the Q fragment, about 234 bases from the HindIII-P-Q boundary. The other three transcripts all end in the P fragment. Both the 1,500- and the 750-base transcripts terminate approximately 240 bases from the HindIII-P-Q boundary. The 2,500-base transcript exhibits 3'-end heterogeneity, ending around 2,046 bases from the HindIII-P-Q boundary. Therefore, three different transcripts (1,500, 750, and 2,500 bases in length) contain the complete 10K protein coding region. A fourth transcript (1,100 bases in length) overlaps the 750-base 10K protein gene transcript by 70 bases.