Department of Biology, University of Victoria, PO Box 3020, Victoria, British Columbia, Canada V8W 3N51
Author for correspondence: David B. Levin.Fax +1 250 472 4075. e-mail dlevin{at}uvic.ca
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Abstract |
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Introduction |
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A second type of putative baculovirus origin of replication, referred to as non-hr origins (non-hr oris), has been described in AcMNPV (Kool et al., 1994 ), OpMNPV (Pearson et al., 1993
) and SeMNPV (Heldens et al., 1997
). Non-hr oris contain unique palindromic and repetitive sequences that are not found in baculovirus hr sequences and are relatively complex in their organization. Only one copy of a non-hr sequence was identified in the genome of AcMNPV (Kool et al., 1994
; Lee & Krell, 1994
). Sequences in the AcMNPV HindIII-K region, also referred to as oriK and located between 84·987·3 map units (m.u.) of the AcMNPV genome, support replication of plasmids in transient replication assays (Kool et al., 1994
) and become enriched in defective AcMNPV genomes (Lee & Krell, 1994
). Deletion analysis of the HindIII-K fragment indicated that the sequences required for optimal replication are contained within a relatively large region within the p94 gene. The function of oriK in vivo is unknown, but its conservation in defective AcMNPV genomes (Lee & Krell, 1994
) and in the genome of BmNPV, which is closely related but lacks the p94 gene (Kool et al., 1994
), suggests that non-hr elements may play an important role in the replication of NPVs.
Deletion analysis of the OpMNPV non-hr sequence, located within the HindIII-N fragment (7·011·3 m.u. of the OpMNPV genome), revealed a complex organization, since deletion of any portion of the HindIII-N fragment resulted in reduced replication efficiency, suggesting that sequences affecting ori activity were distributed throughout the fragment. Sequence analysis identified a variety of direct and inverted repeat sequences and palindromic sequences (Pearson et al., 1993 ). The non-hr sequence of SeMNPV (Heldens et al., 1997
) was mapped to 1052 bp within the XbaI-F fragment (60·762·3 m.u. of the SeMNPV genome). Sequence analysis revealed a unique distribution of six different imperfect palindromes, several polyadenylation consensus motifs, multiple direct repeats and several putative transcription factor-binding sites.
SpliNPV is a member of the Baculoviridae (Volkman et al., 1995 ) and appears distantly related to AcMNPV and other more extensively studied baculoviruses. Phylogenetic analyses (Hu et al., 1997
; Levin et al., 1997
; Smith & Goodale, 1998
) have suggested that SpliNPV represents a more ancient lineage of NPVs that is distantly related to more commonly studied NPVs that cluster together in a clade referred to as the Group I NPVs (Zannotto et al., 1993
). Nucleotide sequence analyses of five SpliNPV genes and their flanking regions [polh (Croizier & Croizier, 1994
; Faktor et al., 1997a
), egt (Faktor et al., 1995
), p10 (Faktor et al., 1997b
), lef-3 (Wolff et al., 1998
) and lef-8 (Faktor & Kamensky, 1997
)] have revealed a number of unique and unusual features about this virus that are not found in other NPVs studied to date. In this study, we have described the identification and characterization of a putative non-hr origin of SpliNPV DNA replication.
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Methods |
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Recombinant plasmids.
SpliNPV DNA was prepared as described by O'Reilly et al. (1992) and digested with the restriction endonucleases EcoRI, SacI, XhoI, PstI and HindIII (New England Biolabs) individually. The viral DNA fragments were cloned into the EcoRI, SacI, XhoI or HindIII sites of plasmid pUC18 (New England Biolabs) to generate a partial SpliNPV genomic library. Plasmid pE4 was found to contain a 344 bp EcoRI fragment (the `E4 fragment') that enabled the plasmid to replicate in SpliNPV-infected cells by transient replication assays (see below). Plasmids with the E4 fragment in both `forward' and `reverse' orientations were recovered and designated pE4 and pE4R, respectively (Fig. 1a)
. In the forward orientation, the HinfI restriction endonuclease sites within the E4 sequence are proximal to the SmaI and SalI sites of pUC18. In the reverse orientation, the HinfI sites are distal to the SmaI and SalI sites of pUC18. The plasmid pGL2-Basic was purchased from Promega. The luciferase gene (bp 182744) was excised from pGL2-Basic after cleavage with SmaI and SalI, and inserted into pE4 and pE4R, creating the plasmids pE4-luc and pE4R-luc, respectively (Fig. 1 a
).
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Transient replication assay.
Plasmid DNA (5 µg) was transfected into 5x106 cells by calcium phosphate precipitation. After 24 h at 27 °C, cells were mock-infected or infected with SpliNPV at an m.o.i. of 10 for 2 h. The infectious media were then replaced by fresh medium and the cultures were further incubated at 27 °C for 72 h. The cells were harvested and the DNA was extracted following the protocol of Sarisky & Hayward (1996) . To test for replication in cells, 10 µg DNA was digested in a 100 µl reaction volume overnight at 37 °C, with 30 U HindIII to linearize the plasmid and with 30 U DpnI, which cleaves in the sequence 5' CAGT 3' only if the A is methylated. To monitor DpnI activity, 5 µl DpnI reaction mix was removed and incubated simultaneously with 500 ng pUC18 DNA overnight at 37 °C. Complete cleavage of the pUC18 DNA indicated that experimental DNA was also completely digested. After electrophoresis in a 0·7% agarose gel, the DNA was transferred to nylon membranes (Hybond-N; Amersham Life Science) and hybridized with [32P]dCTP-labelled pUC18 plasmid DNA. The plasmid DNA was labelled by random primed PCR according to the protocols specified in the Tag-It kit (Bios). All transfection replication assays were repeated at least three times. Replicated plasmid DNAs were subjected to partial digestion with HindIII followed by electrophoresis on agarose gels to determine if a `step-ladder' of fragments, indicative of high-molecular-mass concatameric DNAs, was detectable.
DNA sequence analysis.
The E4 fragment (in pBS-E4) was sequenced by the dideoxy chain-termination method (Sanger et al., 1977 ). DNA sequencing reactions were performed with the fmol DNA Sequencing system (Promega) according to the manufacturer's protocol. Sequences of both strands were obtained by bidirectional sequencing of plasmid DNA using T3 and T7 primers. Sequences were assembled and analysed with the aid of computer programs from the Lasergene package (DNASTAR). The E4 sequence was compared with DNA and amino acid sequences in GenBank using the BLAST and FASTA network service programs (Altschul et al., 1990
). Nucleotide sequence alignments were performed using the Clustal W multiple sequence alignment program (Thompson et al., 1994
). Direct and inverted repeat sequences were identified by using the Align program (DNASTAR). A weight matrix search program, MatInspector (Quandt et al., 1995
), was used to search for putative transcription factor-binding sites. The helical stability of the E4 fragment sequence was analysed by use of the algorithm Oligo program (National BioSciences). The -
G values across the entire sequence were plotted using Microsoft Excel.
Luciferase assays.
Mock-infected and SpliNPV-infected (m.o.i. of 10) Sf9 and CLS79 cells (106) were transfected at 2 h post-infection (p.i.) with 2 µg plasmid-containing luciferase gene, by calcium phosphate precipitation. At 4 h post-transfection, the culture medium was removed, the cells were washed twice with PBS and then provided with fresh medium. Cells were harvested at 48 h post-transfection. The cell pellets were resuspended in 100 µl lysis buffer (25 mM Trisphosphate, pH 7·8, 2 mM DTT, 2 mM 1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid, 10% glycerol, 1% Triton X-100) and then incubated at room temperature for 10 min. The Luciferase Assay system (Promega) was used according to the manufacturer's protocol. Assays were performed using a Liquid Scintillation Counter (model 1410; Wallac). All samples were measured within 2 min of the addition of the luciferase assay reagent.
Preparation of nuclear extracts and gel mobility shift assays.
Extracts of nuclear protein were prepared following the methods of Parker & Topol (1984) . Protein concentrations of 520 mg/ml were determined by the method of Bradford (1976)
, with BSA as a standard (Bio-Rad). Gel-purified dsDNA probes were radioactively labelled by the use of Klenow and [
-32P]ATP. Unlabelled dsDNAs were used as specific (E4 DNA) and non-specific (poly[dIdC]) competitors in the gel mobility shift assays. Binding reactions with nuclear extracts from uninfected and infected cells were carried out by incubating various amounts of nuclear extract with 1 ng radiolabelled E4 DNA, in a buffer containing 20 mM HEPES (pH 7·9), 50 mM NaCl, 5 mM MgCl2, 0·1% BSA, 6% glycerol, 1 mM DTT and 3 µg poly[dIdC] (Pharmacia) at 25 °C for 40 min. Two types of labelled probe were used. The preliminary experiments were conducted with intact labelled E4 fragments. Later experiments were conducted with HinfI-cleaved E4 fragments to observe the pattern of proteinDNA complex formation with different regions of the E4 sequence. HinfI cleaves the E4 fragment at bp 176 and bp 274, generating fragments of 176, 98 and 70 bp. ProteinDNA complexes were separated by electrophoresis in 6% polyacrylamide (37·5:1 acrylamide/bisacrylamide) gels prepared and run in 0·5x TrisborateEDTA buffer at 4 °C.
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Results |
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The SpliNPV E4 sequence aligned with regions within each of the AcMNPV HindIII-K (bp 11901592; Kool et al., 1994 ; GenBank accession no. M16821), OpMNPV HindIII-N (bp 517899; Pearson et al., 1993
; GenBank accession no. D17353) and SeMNPV XbaI-F (bp 213598; Heldens et al., 1997
) non-hr ori fragments. While the SpliNPV non-hr ori sequence shared 57% sequence identity in the region of alignment with the AcMNPV non-hr ori, and approximately 50% sequence identity with the regions to which it aligned in the SeMNPV and OpMNPV non-hr sequences, no common sequences (other than consensus putative transcription factor-binding motifs) were identified. No sequence similarities to hr oris of other baculoviruses were detected and no open reading frames could be identified in any of the three possible reading frames in the putative SpliNPV non-hr origin fragment.
Functional analysis of cis-acting sequences in the E4 fragment
We investigated the ability of the SpliNPV E4 fragment to act as an enhancer of SpliNPV early gene promoter-mediated gene expression using transient expression assays. In both uninfected and SpliNPV-infected cells, luciferase expression from constructs containing the E4 fragment (pE4-lef3-luc and pE4R-lef3-luc; see Fig.1 b), was lower than luciferase expression from the plef3-luc control plasmid, indicating that the E4 fragment repressed, rather than enhanced, lef-3 promoter-mediated luciferase expression in both Sf9 and CLS79 cells (Fig. 1a
).
We further tested the E4 fragment for potential ability to promote expression of the luciferase gene. In uninfected cells, transfection of the pE4-luc and pE4R-luc plasmids (Fig. 1a) resulted in basal luciferase gene expression in an orientation-independent manner. Transfection of plasmids into SpliNPV-infected cells resulted in an approximately 10-fold increase in luciferase gene expression and was also orientation-independent (Fig. 4b)
. However, the level of E4-mediated luciferase expression from pE4-luc and pE4R-luc (i.e. in the absence of the lef-3 promoter) was much lower than SpliNPV lef-3 promoter-mediated luciferase expression (compare Fig. 4a
and b
). Transient expression assays in SpliNPV-infected Sf9 and CLS79 cells resulted in approximately the same pattern of activity, although the level of E4-mediated luciferase expression was higher in SpliNPV-infected CLS79 cells than in virus-infected Sf9 cells. Transient expression assays with pBluescript II KS(+) containing the luciferase gene alone (pBS-luc) resulted in only background levels of luciferase expression (Fig. 4b
).
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Incubation of nuclear extracts from uninfected or virus-infected cells with the E4 fragment cut with HinfI (176, 98 and 70 bp fragments) also resulted in the formation of three discrete proteinDNA complexes (Fig. 5d, lanes 69). Incubation of nuclear extracts from uninfected or virus-infected cells with the gel-purified 98 and 70 bp fragments resulted in the formation of only one proteinDNA complex (Fig. 5d
, lanes 24). We could not detect a difference in proteinDNA complex formation between the E4 fragment and extracts prepared from uninfected or virus-infected cells using the gel mobility shift assay.
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Discussion |
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Firstly, the SpliNPV E4 fragment supported SpliNPV-infection-dependent plasmid replication in transient replication assays. Recombinant plasmids containing the E4 fragment did not replicate in uninfected cells and the parent plasmid (pUC18) did not replicate in uninfected or SpliNPV-infected cells. Thus, replication of the recombinant plasmid in SpliNPV-infected cells was due to the presence of the E4 fragment. Comparison of the E4 nucleotide sequence with sequences in GenBank failed to reveal any similarities with reported baculovirus hr sequences and no known baculovirus promoters were detected. Baculovirus early gene promoters, such as the ie-1 gene promoter, are known to be capable of supporting plasmid replication in transient replication assays (Wu & Carstens, 1996 ). Thus, the ability of the E4 fragment to support plasmid replication is not due to the presence of an hr-like ori or a baculovirus early promoter sequence.
Secondly, the SpliNPV E4 sequence displayed limited alignment with known non-hr ori sequences of other NPVs. The E4 fragment shared 57% DNA sequence identity with the AcMNPV non-hr element in the region of alignment, which occurred at the 3' end of the AcMNPV HindIII-K fragment. It also shared approximately 50% DNA identity with both the OpMNPV HindIII-N fragment and the SeMNPV XbaI-F fragment. The region to which the SpliNPV E4 fragment aligned in AcMNPV oriK is contained completely within the AcMNPV EcoRI-S fragment of HindIII-K, which by itself was shown to be unable to support plasmid replication in AcMNPV-infected cells. Deletion analyses revealed that sequences between 84·9 and 85·9 m.u. of the AcMNPV genome (approximately 1300 bp of the HindIII-K fragment) were required to support plasmid replication. Thus, sequences essential for replication of AcMNPV oriK are distributed over a much larger region of DNA than that to which the SpliNPV E4 sequence aligned. Transient replication assays revealed that deletion clones of OpMNPV HindIII-N were replication-competent only if they contained a central region that spanned bp 17862342. The SpliNPV E4 sequence aligned to a location well upstream of this essential region. Thus, while the SpliNPV E4 sequence aligned with sequences within the AcMNPV and OpMNPV non-hr ori elements, the locations of alignment in these elements did not correspond to regions that, by themselves, are replication-competent. The region to which the SpliNPV E4 fragment aligned in the SeMNPV non-hr, however, did lay within an 800 bp SspI fragment that was shown to be replication-competent by deletion analyses (Heldens et al., 1997 ).
The lengths of NPV non-hr oris are 1052 bp (SeMNPV XbaI-F), 1300 bp (AcMNPV HindIII-K) and 4000 bp (OpMNPV HindIII-N). Thus, the putative SpliNPV non-hr ori is the shortest baculovirus non-hr ori identified to date. The lack of common sequence elements within each non-hr ori (other than consensus motifs of putative transcription factor-binding sites) and the fact that sequences required for replication competence for the AcMNPV, OpMNPV and SeMNPV non-hr oris are distributed over large regions of DNA suggest that the SpliNPV E4 fragment is, so far, unique among baculovirus non-hr elements.
Thirdly, the complex structure of direct repeats, palindrome sequences, A+T-rich regions, and putative transcription factor-binding sites in the SpliNPV E4 sequence has much in common with the non-hr oris identified in AcMNPV, OpMNPV and SeMNPV (Kool et al., 1994 ; Pearson et al., 1993
; Heldens et al., 1997
). Fig. 6
displays the distribution of putative transcription factor-binding sites and A+T-rich domains in the four non-hr oris within the regions of alignment of the SpliNPV sequence with the AcMNPV, OpMNPV and SeMNPV non-hr ori elements. We have not shown the numerous direct and inverted repeat sequences that are also found in these elements. While there are common putative transcription factor-binding sites, as well as A+T-rich domains, in the four non-hr oris, each element has a unique distribution of these sequences. The role of host proteins in the replicative ability of non-hr oris, and the importance of palindrome sequences, direct repeat sequences and putative transcription factor-binding sites within non-hr sequences are unknown.
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Comparison of the non-hr oris from AcMNPV, OpMNPV, SeMNPV and SpliNPV with the consensus oris of vertebrate viruses revealed some intriguing structural similarities. Origins of replication among prokaryotes, viruses and multicellular organisms possess a number of common features which variably include simple tri-, tetra- or higher dispersed repetitions of nucleotides, A+T-rich tracts, inverted repeats, initiator protein-binding sites, intrinsically curved DNAs, DNase I-hypersensitive sites and/or binding sites for transcription factors (Boulikas, 1996 ). Analyses of viral DNA replication in vertebrate cell lines have demonstrated that the oris of most vertebrate viruses consist of two components: (1) an essential core sequence that recruits origin-recognition proteins and specifies the replication initiation site; and (2) auxiliary regions, which contain transcription factor-binding sites and modulate the efficiency of replication initiated at the core (DePamphilis, 1988
, 1993
, 1996
). It is well established that virus replication often depends on sequence elements and proteins that also activate transcription (Herendeen et al., 1989
; DePamphilis, 1988
, 1996
).
Transcription factors are known to play an essential role in replication of vertebrate viruses such as adenovirus (Jones et al., 1987 ; Pruijn et al., 1988
; Mul et al., 1990
), simian virus 40 (Cheng & Kelly, 1989
) and herpes simplex virus (Nguyen-Huynh & Schaffer, 1998
) by recruiting replication proteins to the origin and modulating the efficiency of replication initiation. The SpliNPV E4 fragment was able to activate transcription when it was cloned upstream of a reporter gene (luciferase). The absence of a known baculovirus promoter element in the E4 sequence and the observation that expression from the E4 fragment was orientation-independent suggest that the transcriptional activity detected (indirectly as a function of luciferase activity) may have been a consequence of host and/or virus-encoded transcription factors that bind to the E4 element. Alternatively, there may have been an increase in the copy number of the luciferase gene as a result of infection-dependent plasmid replication. Gel mobility shift assays support the contention that there are proteins in nuclear extracts from both uninfected and virus-infected cells that bind specifically to DNA sequence elements in the E4 fragment.
In some cases, however, origins of replication have been demonstrated to act as transcription silencers (Rivier & Rine, 1992 ). In our transient expression assays, luciferase expression was repressed when the E4 fragment was placed immediately upstream of the lef-3 promoter. It is possible that lef-3 promoter-mediated luciferase expression was reduced due to competition between the E4 fragment and the lef-3 promoter for transcription factors. An alternative explanation might be that it was due to steric constraints placed upon the transcription complex during plasmid replication that render the lef-3 promoter inactive. However, we feel that this is unlikely. Some hr sequences have been demonstrated to act as origins of DNA replication in infection-dependent transient replication assays, as well as cis-acting enhancers of early baculovirus promoters, such as 39K, ie-2, p35 and p145 (Guarino & Summers, 1986
; Nissen & Friesen, 1989
; Carson et al., 1991
; Lu & Carstens, 1993
). hr-containing plasmids replicated in AcMNPV-infected cells were shown to consist of high-molecular-mass DNA, possibly in the form of a linear concatamer containing multiple copies of the plasmid (Leisy & Rohrmann, 1993
). Despite this replication-dependent change in plasmid DNA structure, hr sequences still enhanced transcription in an orientation- and position-independent manner.
Restriction endonuclease analysis of replicated pE4 plasmid indicated that it did not form high-molecular-mass DNAs, suggesting that it does not form concatamers. Thus, repression of lef-3 promoter-mediated luciferase expression by the E4 fragment is not likely to have occurred as a consequence of steric constraints due to plasmid replication. Moreover, unlike transcription of the AcMNPV lef-3 gene, which reaches its peak at 6 h p.i. and then decreases to a low level by 24 h (Li et al., 1993 ), the SpliNPV lef-3 gene is first detected approximately 4 h p.i. and steadily increases up to 56 h p.i. (Wolff et al., 1998
). Thus, the decreased luciferase expression we observed in SpliNPV-infected cells was not due to a reduction in lef-3 promoter activity as a consequence of the kinetics of lef-3 transcription. Further characterization of the putative SpliNPV non-hr ori will resolve the role of these sequence motifs in viral DNA replication.
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Acknowledgments |
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References |
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![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.[Medline]
Ayres, M. D., Howard, S. C., Kuzio, J., Lopez-Ferber, M. & Possee, R. D. (1994). The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology 202, 586-605.[Medline]
Blissard, G. W. & Rohrmann, G. F. (1990). Baculovirus diversity and molecular biology. Annual Review of Entomology 35, 127-155.[Medline]
Boulikas, T. (1996). Common structural features of replication origins in all life forms. Journal of Cellular Biochemistry 60, 297-316.[Medline]
Bradford, M. M. (1976). Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of proteindye binding. Analytical Biochemistry 72, 248-254.[Medline]
Broer, R., Heldens, J. G. M., van Strien, E. A., Zuidema, D. & Vlak, J. M. (1998). Specificity of multiple homologous genomic regions in Spodoptera exigua nucleopolyhedrovirus DNA replication. Journal of General Virology 79, 1563-1572.[Abstract]
Carson, D. D., Summers, M. D. & Guarino, L. A. (1991). Molecular analysis of a baculovirus regulatory gene. Virology 182, 279-286.[Medline]
Cheng, L. & Kelly, T. J. (1989). Transcriptional activator nuclear factor I stimulates the replication of SV40 minichromosomes in vivo and in vitro. Cell 59, 541-551.[Medline]
Croizier, L. & Croizier, G. (1994). Nucleotide sequence of the polyhedrin gene of Spodoptera littoralis multiple nucleocapsid nuclear polyhedrosis virus. Biochimica et Biophysica Acta 1218, 457-459.[Medline]
Croizier, G., Boukhoudmi-Amiri, K. & Croizier, L. (1989). A physical map of Spodoptera littoralis B-type nuclear polyhedrosis virus genome. Archives of Virology 104, 145-151.[Medline]
DePamphilis, M. L. (1988). Transcriptional elements as components of eukaryotic origin of DNA replication. Cell 52, 635-638.[Medline]
DePamphilis, M. L. (1993). Eukaryotic DNA replication: anatomy of an origin. Annual Review of Biochemistry 62, 29-63.[Medline]
DePamphilis, M. L. (1996). Eukaryotic replication origins. In DNA Replication in Eukaryotic Cells, pp. 45-86. Edited by M. L. DePamphilis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Faktor, O. & Kamensky, B. (1997). Genomic location and nucleotide sequence of a lef-8 gene of the Spodoptera littoralis nucleopolyhedrovirus. Virus Genes 15, 9-15.[Medline]
Faktor, O., Toister-Achituv, M. & Kamensky, B. (1995). Identification and nucleotide sequence of an ecdysteroid UDP-glucosyltransferase gene of Spodoptera littoralis multicapsid nuclear polyhedrosis virus. Virus Genes 11, 47-52.[Medline]
Faktor, O., Toister-Achituv, M. & Nahum, O. (1997a). Enhancer element, repetitive sequences, and gene organization in an 8-kbp region containing the polyhedrin gene of the Spodoptera littoralis nucleopolyhedrovirus. Archives of Virology 142, 1-15.[Medline]
Faktor, O., Toister-Achituv, M., Nahum, O. & Kamensky, B. (1997b). The p10 gene of Spodoptera littoralis nucleopolyhedrovirus: nucleotide sequence, transcription analysis and unique gene organization in the p10 locus. Journal of General Virology 78, 2119-2128.[Abstract]
Guarino, L. A. & Summers, M. D. (1986). Interspersed homologous DNA of Autographa californica nuclear polyhedrosis virus enhances delayed-early gene expression. Journal of Virology 60, 215-223.
Heldens, J. G. M., Broer, R., Zuidema, D., Goldbach, R. W. & Vlak, J. M. (1997). Identification and functional analysis of a non-hr origin of DNA replication in the genome of Spodoptera exigua multicapsid nucleopolyhedrovirus. Journal of General Virology 78, 1497-1506.[Abstract]
Herendeen, D. R., Kassavetis, G. A., Barry, J., Alberts, B. M. & Geiduschek, E. P. (1989). Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus. Science 245, 952-958.[Medline]
Hu, Z., Broer, R., Westerlaken, J., Martens, J. W. M., Jin, F., Wang, L. M. & Vlak, J. M. (1997). Identification and nucleotide sequence of the ecdysteroid UDP-glycosyltransferase gene of the Buzura suppressaria nucleopolyhedrovirus. Virus Research 47, 91-97.[Medline]
Jones, K. A., Kadonaga, J. T., Rosenfeld, P. J., Kelly, T. J. & Tjian, R. (1987). A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell 73, 1207-1221.
Kogan, P. H. & Blissard, G. W. (1994). A baculovirus gp64 early promoter is activated by host transcription factor binding to CACGTG and GATA elements. Virology 119, 219-222.
Kool, M., Goldbach, R. W. & Vlak, J. M. (1994). A putative non-hr origin of DNA replication in the HindIII-K fragment of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus. Journal of General Virology 75, 3345-3352.[Abstract]
Kool, M., Ahrens, C. H., Vlak, J. M. & Rohrmann, G. F. (1995). Replication of baculovirus DNA. Journal of General Virology 76, 2103-2118.[Medline]
Lee, H. J. & Krell, P. J. (1994). Reiterated DNA fragments in defective genomes of Autographa californica nuclear polyhedrosis virus are competent for AcMNPV-dependent DNA replication. Virology 202, 418-429.[Medline]
Leisy, D. J. & Rohrmann, G. F. (1993). Characterization of the replication of plasmids containing hr sequences in baculovirus-infected Spodoptera frugiperda cells. Virology 196, 722-730.[Medline]
Leisy, D. J., Rasmussen, C., Kim, H. T. & Rohrmann, G. F. (1995). The Autographa californica nuclear polyhedrosis virus homologous region 1a: identical sequences are essential for DNA replication activity and transcriptional enhancer function. Virology 208, 742-752.[Medline]
Levin, D. B., Laitinen, A. M., Clarke, T. C., Lucarotti, C. J., Morin, B. & Otvos, I. S. (1997). Characterization of nuclear polyhedrosis viruses from three subspecies of Lambdina fiscellaria. Journal of Invertebrate Pathology 69, 125-134.[Medline]
Li, Y., Passarelli, A. L. & Miller, L. K. (1993). Identification, sequence, and transcriptional mapping of lef-3, a baculovirus gene involved in late and very late gene expression. Journal of Virology 67, 5260-5268.[Abstract]
Lu, A. & Carstens, E. B. (1993). Immediate-early baculovirus genes transactivate the p143 gene promoter of Autographa californica nuclear polyhedrosis virus. Virology 195, 710-718.[Medline]
Lu, A., Krell, P. J., Vlak, J. M. & Rohrmann, G. F. (1997). Baculovirus DNA replication. In The Baculoviruses, pp. 171-191. Edited by L. K. Miller. New York: Plenum.
Majima, K., Kobara, R. & Maeda, S. (1993). Divergence and evolution of homologous regions of Bombyx mori nuclear polyhedrosis virus. Journal of Virology 67, 7513-7521.[Abstract]
Mul, Y. M., Verrijzer, C. P. & van der Vliet, P. C. (1990). Transcription factors NFI and NFIII/OCT-1 function independently, employing different mechanisms to enhance adenovirus DNA replication. Journal of Virology 64, 5510-5518.[Medline]
Nguyen-Huynh, A. T. & Schaffer, P. A. (1998). Cellular transcription factor enhance herpes simplex virus type 1 oriS-dependent DNA replication. Journal of Virology 72, 3635-3645.
Nissen, M. S. & Friesen, P. D. (1989). Molecular analysis of the transcriptional regulatory region of an early baculovirus gene. Journal of Virology 63, 493-503.[Medline]
O'Reilly, D. R., Miller, L. K. & Luckow, V. A. (1992). Baculovirus Expression Vectors. A Laboratory Manual. New York: W. H. Freeman.
Parker, C. S. & Topol, J. (1984). A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity. Cell 36, 357-369.[Medline]
Pearson, M. N. & Rohrmann, G. F. (1995). Lymantria dispar nuclear polyhedrosis virus homologous regions: characterization of their ability to function as replication origins. Journal of Virology 69, 213-221.[Abstract]
Pearson, M. N., Bjornson, R. M., Ahrens, C. & Rohrmann, G. F. (1993). Identification and characterization of a putative origin of DNA replication in the genome of a baculovirus pathogenic for Orgyia pseudotsugata. Virology 197, 715-725.[Medline]
Pruijn, G. J. M., van Miltenburg, R. T., Claessens, J. A. J. & van der Vliet, P. C. (1988). Interaction between the octamer-binding protein nuclear factor III and the adenovirus origin of DNA replication. Journal of Virology 62, 3092-3102.[Medline]
Quandt, K., Frech, K., Karas, H., Wingender, E. & Werner, T. (1995). MatInd and MatInspector new fast and versatile tools for detection of consensus matches in nucleotide sequences. Nucleic Acids Research 23, 4878-4884.[Abstract]
Rivier, D. H. & Rine, J. (1992). An origin of DNA replication and a transcription silencer require a common element. Science 256, 659-663.[Medline]
Rodems, S. M. & Friesen, P. D. (1993). The hr5 transcriptional enhancer stimulates early expression from the Autographa californica nuclear polyhedrosis virus genome but is not required for virus replication. Journal of Virology 67, 5776-5785.[Abstract]
Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain terminating inhibitors. Proceedings of the National Academy of Sciences, USA 74, 5463-5468.[Abstract]
Sarisky, R. T. & Hayward, G. S. (1996). Evidence that the UL84 gene product of human cytomegalovirus is essential for promoting oriLyt-dependent DNA replication and formation of replication compartments in cotransfection assays. Journal of Virology 70, 7398-7413.[Abstract]
Smith, I. & Goodale, C. (1998). Sequence and in vivo transcription of Lacanobia oleracea granulovirus egt. Journal of General Virology 79, 405-413.[Abstract]
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.[Abstract]
van der Vliet, P. C. (1996). Roles of transcription factors in DNA replication. In DNA Replication in Eukaryotic Cells, pp. 87-118. Edited by M. L. DePamphilis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Volkman, L. E., Blissard, G. W., Freisen, P. D., Possee, R. D. & Theilmann, D. A. (1995). The Baculoviridae. In Virus Taxonomy. Sixth Report of the International Committee on Taxonomy of Viruses, pp. 104-113. Edited by F. A. Murphy, C. M. Fauquet, D. H. L. Bishop, S. A. Ghabrial, A. W. Jarvis, G. P. Martelli, M. A. Mayo & M. D. Summers. Vienna & New York: Springer-Verlag.
Wolff, J.-L. C., Herzog, L. M., Sun, L. & Levin, D. B. (1998). Identification and Characterization of the Spodoptera littoralis nucleopolyhedrovirus lef-3 gene. Archives of Virology 143, 743-767.[Medline]
Wu, Y. & Carstens, E. B. (1996). Initiation of baculovirus DNA replication: early promoter regions can function as infection-dependent replicating sequences in a plasmid-based replication assay. Journal of Virology 70, 6967-6972.[Abstract]
Xie, W. D., Arif, B., Dobos, P. & Krell, P. J. (1995). Identification and analysis of a putative origin of DNA replication in the Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus genome. Virology 209, 409-419.[Medline]
Zannotto, P. M., Kessing, B. D. & Maruniak, J. E. (1993). Phylogenetic interrelationships among baculoviruses: evolutionary rates and host associations. Journal of Invertebrate Pathology 62, 147-164.[Medline]
Received 23 February 1999;
accepted 1 April 1999.