Phylogenetic analysis and possible function of bro
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Phylogenetic analysis and possible function of bro
Journal of General Virology (2003), 84, 2531–2544 DOI 10.1099/vir.0.19256-0 Phylogenetic analysis and possible function of brolike genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria Dennis K. Bideshi,1,2 Sylvaine Renault,3 Karine Stasiak,1,3 Brian A. Federici1 and Yves Bigot1,3 1 Department of Entomology and Interdepartmental Graduate Program in Genetics, University of California, Riverside, CA 92521, USA Correspondence Yves Bigot (at Université François Rabelais) 2 [email protected] 3 Received 26 March 2003 Accepted 1 May 2003 Baculovirus repeated open reading frame (bro) genes and their relatives constitute a multigene family, typically with multiple copies per genome, known to occur among certain insect dsDNA viruses and bacteriophages. Little is known about the evolutionary history and function of the proteins encoded by these genes. Here we have shown that bro and bro-like (bro-l) genes occur among viruses of two additional invertebrate viral families, Ascoviridae and Iridoviridae, and in prokaryotic class II transposons. Analysis of over 100 sequences showed that the N-terminal region, consisting of two subdomains, is the most conserved region and contains a DNA-binding motif that has been characterized previously. Phylogenetic analysis indicated that these proteins are distributed among eight groups, Groups 1–7 consisting of invertebrate virus proteins and Group 8 of proteins in bacteriophages and bacterial transposons. No bro genes were identified in databases of invertebrate or vertebrate genomes, vertebrate viruses and transposons, nor in prokaryotic genomes, except in prophages or transposons of the latter. The phylogenetic relationship between bro genes suggests that they have resulted from recombination of viral genomes that allowed the duplication and loss of genes, but also the acquisition of genes by horizontal transfer over evolutionary time. In addition, the maintenance and diversity of bro-l genes in different types of invertebrate dsDNA viruses, but not in vertebrate viruses, suggests that these proteins play an important role in invertebrate virus biology. Experiments with the unique orf2 bro gene of Autographa californica multicapsid nucleopolyhedrovirus showed that it is not required for replication, but may enhance replication during the occlusion phase of reproduction. California Baptist University, 8432 Magnolia Avenue, Riverside, CA 92504-3297, USA Laboratoire d’Etude des Parasites Génétiques, FRE CNRS 2535, Université François Rabelais, UFR des Sciences et Techniques, Parc de Grandmont, 37200 Tours, France INTRODUCTION A common feature of many eukaryotic dsDNA viruses is the presence of multigene families (MGFs) composed of related repeated open reading frames (ORFs) dispersed along the genome. MGFs are abundant in viruses of the family Phycodnaviridae (Van Etten & Meints, 1999), Asfarviridae (Almendral et al., 1990; De la Vega et al., 1990; Gonzalez et al., 1990; Vydelingum et al., 1993; Rodriguez et al., 1994; Yozawa et al., 1994; Yanez et al., 1995; Pires et al., 1997), Herpesviridae (Gompels et al., 1995), Chordopoxviridae (Goebel et al., 1990; Massung et al., 1994) and vertebrate The sequences reported here have been deposited in the DDBJ/ EMBL/GenBank sequence database under accession nos AJ292546– AJ292551. 0001-9256 G 2003 SGM Iridoviridae (Schnitzler et al., 1987), where they occur in the terminal regions of the genomes. MGFs also occur in insect dsDNA viruses with large genomes. One of these families, the Baculoviridae, contains viruses in which repeated genes called baculovirus repeated open reading frames (bro) occur commonly among different nucleopolyhedroviruses (NPVs) and granuloviruses (GVs) (Goto et al., 1998; Ahrens et al., 1999; Gomi et al., 1999; Kang et al., 1999; Kuzio et al., 1999; Iyer et al., 2002). Baculovirus bro genes vary in number and length from one virus to another, even among closely related viruses. For example, only one copy of a bro gene (orf2) is present in Autographa californica multicapsid NPV (AcMNPV) (Ayres et al., 1994), whereas three, five, sixteen and seven are present in, respectively, the baculoviruses from Orgyia Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Printed in Great Britain 2531 D. K. Bideshi and others pseudotsugata (OpMNPV; Ahrens et al., 1999), Bombyx mori (BmNPV; Gomi et al., 1999), Lymantria dispar (LdMNPV; Kuzio et al., 1999) and Xestia c-nigrum (XcGV; Goto et al., 1998; Hayakawa et al., 1999). Though prevalent among many baculoviruses, bro genes are absent in Plutella xylostella (Px) GV (Hashimoto et al., 2000) and in Anagrapha falcifera MNPV (Federici & Hice, 1997) and Rachiplusia ou MNPV (Harrison & Bonning, 1999), both of which are closely related to AcMNPV. Homologues of bro genes have also been reported from more distantly related baculoviruses, such as the Culex nigripalpus NPV, which contains six bro genes (Afonso et al., 2001), but are absent in the Hz-1 virus (Cheng et al., 2002) and the shrimp white spot bacilliform virus (Yang et al., 2001). Although reported originally from baculoviruses, homologues of bro genes have been identified in other insect dsDNA viruses, including the entomopoxviruses (subfamily Entomopoxvirinae) of Amsacta moorei (AmEPV) and Melanoplus sanguinipes (MsEPV), where they are referred to as the ALI family (Bawden et al., 2000; Afonso et al., 1999). They have also been reported in Chilo iridescent virus (CIV), family Iridoviridae, an iridovirus from the lepidopteran Chilo suppressalis (Jakob et al., 2001). Only a few invertebrate dsDNA viral genomes have been fully sequenced, but the occurrence of bro genes in baculovirus, entomopoxvirus and entomoiridovirus genomes suggests that these genes may be widespread among insect dsDNA viruses. Interestingly, bro genes have been reported to show homology with genes in bacteriophages, probacteriophages and in the phycodnavirus Ectocarpus siliculosus virus (ESV) (Afonso et al., 1999; Kang et al., 1999; Iyer et al., 2002). Here we refer to these homologues as ‘bro-like’ (bro-l) to distinguish them from baculovirus bro genes. With respect to length, BRO and BRO-like (BRO-l) proteins vary from about 88 to 450 amino acid residues. A characteristic of these proteins is that the first 100–150 N-terminal residues are highly conserved and contain a nucleic acid binding domain, BRO-N (Zemskov et al., 2000; Iyer et al., 2002). The BRO-N domain is widely distributed, being found alone or in conjunction with domains in proteins encoded by eukaryotic and prokaryotic viruses (Iyer et al., 2002). A less conserved C-terminal domain, BRO-C, is also present in BRO proteins, but this domain appears to be restricted to baculoviruses and viruses that constitute the recently identified nucleo-cytoplasmic large DNA viruses (NCLDV), a monophyletic clade of eukaryotic viruses, which includes poxviruses, phycodnaviruses, asfarviruses and iridoviruses (Iyer et al., 2001, 2002). Due to high levels of divergence in the C-terminal regions, the major criterion therefore required for identifying BRO and BRO-l proteins is the presence of the BRO-N domain. Despite their common occurrence among insect dsDNA viruses, little is known about the factors influencing the expression of bro genes or the function(s) of BRO proteins. Kang et al. (1999) showed that the five bro genes (bro a–e) in BmNPV are expressed early, about 2–4 h after initiation of 2532 virus replication, and that transcription initiates 50– 70 nucleotides upstream from the translation start codon at the characteristic baculovirus early gene promoter motif, (C/T)AGT. In addition, no significant differences in pathobiology were observed for wild-type virus or certain bro deletion mutants grown in B. mori cells (BmN-4) or larvae (Kang et al., 1999). Nevertheless, Kang et al. (1999) were unable to isolate mutants deficient in bro-d or mutants that contained double deletions in bro-a and bro-c, which suggests that these genes could play significant roles in BmNPV pathogenesis. More recently, Zemskov et al. (2000) showed that BRO-a, BRO-c and BROd are associated with the histone H1 fraction from the BmN-4 cell line and provided evidence that about 80 residues in the conserved N-terminal region are required for a non-specific nucleic acid binding activity. They proposed that BRO-a and BRO-c could function as DNA binding proteins that influence host DNA replication and/ or transcription by regulating chromatin structure in the host chromosomes (Zemskov et al., 2000; Iyer et al., 2002). The presence of bro and bro-l genes in different insect dsDNA virus families, along with evidence that BRO proteins could potentially play a role in virus replication, has suggested that the bro MGF may be larger and more extensively distributed than currently realized. Here we have reported the identification and sequences of bro genes from a crustacean virus belonging to the family Iridoviridae, as well as among viruses of the Ascoviridae (Federici et al., 2000). We have also shown that bro-l genes are not restricted to bacteriophages, but occur in certain bacterial transposable elements belonging to the IS3 and IS5 families. At least eight BRO lineages were identified by phylogenetic analysis using the sequences of 114 BRO and BRO-l N-terminal domains. These data suggest that the bro MGF has evolved by genetic processes of gene duplication and loss and horizontal transfer among viruses belonging to different families. Lastly, we have shown that the unique AcMNPV orf2 bro gene is not required for infection or replication of this virus in lepidopteran cells or larvae, although it may enhance replication during the occlusion phase of reproduction. METHODS Virus strains. The ascoviruses used, SfAV1a and HvAV3c, were isolated initially from the noctuid hosts Spodoptera frugiperda and Heliothis virescens, respectively (Federici et al., 1990). DpAV4 was isolated from its wasp host, Diadromus pulchellus (family Ichneumonidae), and from pupae of its lepidopteran host, Acrolepiopsis assectella (Family Yponeumonidae; Bigot et al., 1997). The iridovirus (IIV; iridovirus type 31, so-called IV31) was isolated from the terrestrial isopod Armadillidium vulgare, and has been described previously (Federici, 1980). Propagation and preparation of viral DNA were performed as described previously (Bigot et al., 1997; Federici et al., 1990). Genomic DNA libraries. Fifty mg of SfAV1, HvAV3c and IIV DNA were sheared by sonication (20 W for 2?5 min with 1 s pulses) to produce fragments ranging in size from 0?5 to 3 kbp. DNA fragments Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes were blunted with SI nuclease and T4 DNA polymerase (New England Biolabs) and EcoRI linkers were ligated at both ends. Fragments of approximately 0?85–1?1 kbp were purified from agarose gel using a QIAquick gel extraction kit (Qiagen) and ligated to the EcoRI site in pUC18. DNA sequencing. Plasmids were isolated and purified by standard protocols (Ausubel et al., 1994). Nucleotide sequences were determined by dideoxy-nucleotide sequencing (Sanger et al., 1977) using the Sequitherm long-read cycle sequencing kit with universal and reverse IRD800 fluorescent-labelled primers (Epicentre Technologies). DNAs were amplified by PCR (25 cycles of denaturation at 94 uC for 30 s, annealing at 50 uC for 15 s and polymerization at 70 uC for 1 min). Nucleotide sequences for both strands were generated using a DNA Sequencer Long Reader model 4200 (Li-cor). Sequences were determined for 500 cloned fragments of SfAV1a, 50 of HvAV3c and 50 of iridovirus IIV. Database searches and sequence analyses. The Infobiogen facilities were used for database searches (GenBank release 132, updated 10/15/2001; Swissprot release 40 and TrEMBL 21, both updated 12/06/2002), sequence alignments and calculations. Due to the presence of numerous deletions and insertions (1–250 amino acids) between the regions conserved between BRO and BRO-l proteins, the alignment of their amino acid sequences was performed in three steps. First, 12 groups of related sequences identified from BLAST searches were aligned using CLUSTAL W (Thompson et al., 1994). Taking into account data described previously (Iyer et al., 2002), the 12 alignments were then aligned to each other. Finally, ambiguities were identified by pair sequence alignments using Kanehisa’s program for sequence comparison, and the quality of the sequence alignment of the C-terminal domain of the BRO and BRO-l was verified by comparison with their structural profiles determined by hydrophobic cluster analysis (HCA) (http://smi.snv. jussieu.fr/hca/hca-seq.html). At each step, the sequences were manually adjusted to facilitate the quality of alignment. The aligned sequences have been deposited in DDBJ/EMBL/GenBank (DS43784). Phylogenetic analyses were performed using the PHYLIP package, version 3.5c (Felsenstein, 1993). DNA probes and Southern blot hybridization. DNA probes (SfAV1a-bro-12, HvAV3c-bro-l1 and orf2, chl r and tet r; see below) were prepared using a Dig DNA labelling and detection kit (Boehringer Mannheim). Hybridization was performed at 65 uC in 0?1 % SDS, 0?5 M Na2HPO4/NaH2PO4 buffer, pH 7, and posthybridization washes were performed at 65 uC using 0?56 SSC (high stringency) or 26 SSC (low stringency). Disruption of the AcMNPV orf2 (bro) in E. coli BJ5183. The recombinant AcMNPV bacmid AcBacP+1 and methods used for baculovirus gene disruption by homologous recombination in E. coli BJ5183 (recBC sbsBC; Hanahan 1983; Chartier et al., 1996) have been described previously (Bideshi & Federici, 2000). The AcMNPV orf2 (Ayres et al., 1994) was obtained as a 2?2 kbp fragment by PCR with Taq DNA polymerase (Promega), using primers ORF2a (59-AAGCGAGGATCTACAACGTT-39) and ORF2b (59-TAAAATGTTTCCCGCGCGTT-39) and AcBacP+1 as the DNA source. The PCR product was cloned in pGEM-T Easy to generate pGEMT-orf2. The restriction sites used for orf2 disruption were SwaI and BstEII located at, respectively, positions +23 and +677 relative to the translation initiation codon of orf2. pGEM-Bro/tet, which retained the BRO-N domain coding sequence, was generated by inserting the 1?6 kbp SspI–MscI fragment with the tetracycline resistance gene (tetr) from pBR322 (Biolabs) into the blunted BstEII site in pGEMT-orf2. pGEM-Bro/chl was constructed by inserting the blunted 1?2 kb BspHI–XmnI fragment with the chloramphenicol resistance marker (chlr) from pBCSK(2) (Stratagene) in the blunted BstEII and SwaI sites in pGEM-T-orf2. The 3?9 kb and 2?8 kb fragments http://vir.sgmjournals.org in, respectively, pGEM-Bro/tet and pGEM-Bro/chl were obtained by PCR with the ORF2a and ORF2b primers and used to disrupt the orf2 in AcBacP+1 harboured in E. coli BJ5183. E. coli BJ5183 strains with recombinant bacmids AcP+4M:T12 and AcBacP+1:brochlABD were recovered on LB agar containing, respectively, tetracycline (15 mg ml21) and kanamycin (45 mg ml21) or chloramphenicol (15 mg ml21) and kanamycin (45 mg ml21). Disruption of orf2 was confirmed by PCR using the ORF2a and ORF2b primers and by Southern blot hybridization with the orf2 probe. In vitro and in vivo replication of recombinant AcMNPV bacmids. DNAs from AcBacP+1 (polh+, kanr, chl s, tet s, orf2+), AcP+4M:T12 (polh+, kanr, chls, orf2 disrupted with tetr) and AcBacP+1:brochlABD (polh+, kanr, tets, orf2 disrupted with chlr) were purified using the Nucleobond AX kit (Clontech). Insect cells were grown in TC-100 medium (Gardiner & Stockdale, 1975) with 10 % foetal bovine serum (TC-100/FBS). Cells of Trichoplusia ni (BTI-TN5-B1-4; Invitrogen) or S. frugiperda (SF21; Pharmingen) were transfected in triplicate with approximately 1 mg viral DNA, or mock-transfected using the Cellfectin liposome reagent (Gibco BRL). Transfected cell cultures of AcBacP+1, AcP+4M:T12 and AcBacP+1:brochlABD were incubated at 28 uC for 7 days after which the percentage of cells containing polyhedra was assessed. A total of 300 cells was counted in each of the transfected cultures. Two ml of each transfected culture medium was collected by centrifugation at 1000 r.p.m. for 5 min, diluted 1 : 100 in TC-100/FBS and used to infect T. ni and S. frugiperda cells. After incubation for 4 days at 28 uC, budded virions were collected from the culture medium and viral DNAs were isolated. The presence of recombinant bacmids was confirmed by PCR using the ORF2a and ORF2b primers and by Southern blot hybridization using the orf2 probe. Larvae of T. ni were grown on a semi-defined medium (Shorey & Hale, 1965). For insect inoculation, 100 ml culture medium from BTI-TN5-B1-4 cells infected with AcBacP+1, AcP+4M:T12, AcBacP+1:brochlABD, or mock-infected cells were mixed with 100 ml Grace’s insect cell culture medium (Gibco BRL). Two ml of the mixture was injected into 10 early fourth instar T. ni using the Microapplicator model M microinjector (Instrumentation Specialities Company). To determine whether the virus was infectious by feeding, BTI-TN5-BI-4 cells containing polyhedra were suspended in 1 ml Grace’s medium. Twenty ml of this suspension was added to 0?5 mg of growth medium, which was then fed to 10 early fourth instars of T. ni. RESULTS Cloning of bro-l genes from the genomes of ascoviruses and the crustacean iridovirus IIV Based on BLAST searches with sequences generated from our ascovirus and iridovirus genomic libraries and from DpAV4 sequences reported previously (Bigot et al., 1997, 2000; Stasiak et al., 2000), several bro and bro-l sequences were identified, with the quality of the observed similarities based on smallest sum probabilities ranging from 1.e2200 to 1.e210 (30–45 % similar to the most closely related BRO proteins). Eleven bro-l ORFs were identified in SfAV1a (SfAV1a-bro-l1 to -l11), three in DpAV4 (DpAV4-bro-l1 to -l3), two in HvAV3c (HvAV3c-bro-l1 and -l2) and one in iridovirus IIV (IIV-bro-l) (Table 1). The bro-l genes present in the HvAV3c and IIV genomes were confirmed by Southern blot hybridization. Several HvAV3c fragments hybridized with the HvAV3c-bro-l1 Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2533 D. K. Bideshi and others Table 1. bro and bro-like genes found in invertebrate and bacterial viruses Name of bro or bro-like genes Ac-bro-B40781 Ac-bro-B38477 Ag-bro-a Ag-bro-b AmEPV-bro-la AmEPV-bro-lb AmEPV-bro-lc AmEPV-bro-ld AmEPV-bro-le Bm-bro-a Bm-bro-b Bm-bro-c Bm-bro-d Bm-bro-e CIV-bro-la CIV-bro-lb CIV-bro-lc Cn-bro-a Cn-bro-b Cn-bro-c Cn-bro-d Cn-bro-e Cn-bro-f DpAV4-bro-l1 DpAV4-bro-l2 DpAV4-bro-l3 Ha-bro-a Ha-bro-b Ha-bro-c Ha-bro-d Ha-bro-e Ha-bro-f HaEPV-bro-l HvAV3c-bro-l1 HvAV3c-bro-l2 Hz-bro-a Hz-bro-b Hz-bro-c Hz-bro-d Hz-bro-e IIV-bro-l Ld-bro-a Ld-bro-b Ld-bro-c Ld-bro-d Ld-bro-e Ld-bro-f Ld-bro-g Ld-bro-h Ld-bro-i Ld-bro-j Ld-bro-k Ld-bro-l 2534 Virus or transposons Virus or transposon family Host name Gene accession no. Protein accession no. AcMNPV " AgMNPV " AmEPV " " " " BmMNPV " " " " CIV (IV6) " " CuniNPV " " " " " DpAV4 " " HaNPV " " " " " HaEPV HvAV3c " HzMNPV " " " " IIV (IV31) LdMNPV " " " " " " " LsMNPV " " " Baculoviridae " Baculoviridae " Poxviridae " " " " Baculoviridae " " " " Iridoviridae " " Baculoviridae " " " " " Ascoviridae " " Baculoviridae " " " " " Poxviridae Ascoviridae " Baculoviridae " " " " Iridoviridae Baculoviridae " " " " " " " Baculoviridae " " " Autographa californica " Anticarsia gemmatalis " Amsacta moorei " " " " Bombyx mori " " " " Chilo suppressalis " " Culex nigripalpus " " " " " Diadromus pulchellus " " Helicoverpa armigera " " " " " Heliothis armigera Heliothis virescens " Helicoverpa zea " " " " Armadillidium vulgare Lymantria dispar " " " " " " " Lymantria dispar " " " L22858 " Y17753 " AF250284 " " " " L33180 " " " " AF003534 " " AF403738 " " " " " X85006 AJ279818 AJ279813 AF303045 " " " " " AF022176 AJ292549 AJ292550 " " " " AF275264 AJ292551 AF081810 " " " " " " " AF081810 " " " B40781 B38477 – – – – – – O92398 O92457 O92458 O92507 O92508 – – Q91FW9 Q91FN5 Q919R4 Q919G9 Q919G8 Q919R0 Q919I2 Q919R1 – – – Q8QMF6 Q99GY7 Q99GY8 Q8QMF5 Q91BV2 Q91BA1 – – – Q8V5T5 Q8V5T7 Q9E231 Q8V5T6 – – Q9YMU2 Q9YMU1 Q9YMQ6 Q9YMQ5 Q9YMQ4 Q9YMQ3 Q9YMQ2 Q9YML5 Q9YML4 Q9YML3 Q9YML2 Q9YMI2 Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes Table 1. (cont.) Name of bro or bro-like genes Virus or transposons Virus or transposon family Host name Gene accession no. Protein accession no. Ld-bro-m Ld-bro-n Ld-bro-o Ld-bro-p Ls-bro Mc-bro-c Mc-bro-d Mc-bro-e Mc-bro-f Mc-bro-g MsEPV bro-l1 MsEPV bro-l2 MsEPV bro-l3 MsEPV bro-l4 MsEPV bro-l5 MsEPV bro-l6 MsEPV bro-l7 Op-bro PuGV-bro Se-bro Sl-bro-a Sl-bro-b Sl-bro-c SfAV1a-bro-l1 SfAV1a-bro-l2 SfAV1a-bro-l3 SfAV1a-bro-l4 SfAV1a-bro-l5 SfAV1a-bro-l6 SfAV1a-bro-l7 SfAV1a-bro-l8 SfAV1a-bro-l9 SfAV1a-bro-l10 SfAV1a-bro-l11 TnGV-bro-1 TnGV-bro-2 TnGV-bro-3 XcGV bro-a XcGV bro-c XcGV bro-e XcGV bro-f XcGV bro-g XcGV bro-j ESV-bro-l " " " " LsMNPV MacoNPV " " " " MsEPV " " " " " " OpMNPV PuGV SeMNPV SlMNPV " " SfAV1a " " " " " " " " " " TnGV " " XcGV ‘‘ " " " " ESV " " " " Baculoviridae Baculoviridae " " " " Poxviridae " " " " " " Baculoviridae Baculoviridae Baculoviridae Baculoviridae " " Ascoviridae " " " " " " " " " " Baculoviridae " " Baculoviridae " " " " " Phycodnaviridae " " " " Leucania separata Mamestra configurata " " " " Melanoplus sanguinipes " " " " " " Orgyia pseudotsugata Pseudaletia unipuncta Spodoptera exigua Spodoptera littura " " Spodoptera frugiperda " " " " " " " " " " Trichoplusia ni " " Xestia c-nigrum " " " " " Ectocarpus siliculosus " " " " AB009612 AF467808 " " " " AF063866 " " " " " " U75930 D14871 AF169823 AF143953 AF325155 " AJ292546 AJ292547 AJ292547 AJ312700 AJ312700 AJ312701 AJ312702 AJ312702 AJ312703 AJ312699 AJ292548 D58376 D58375 D58377 AF162221 " " ‘‘ ‘‘ " AF204951 Q9YMH8 Q9YMH5 Q9YMH4 Q9YMG7 – – – – – – – – – – – – – – – Q9J8C2 Q9JAD6 Q91BA1 Q91BA9 – – – – – – – – – – – – – – Q9PYY3 Q9PYT4 Q9PYR5 Q9PYR4 Q9PYN7 – – probe (Fig. 1a). An HpaII restriction sites was present at position 196 in the sequence of the probe used, but DraI and EcoRV sites were absent. The two hybridizing fragments observed in the DraI and EcoRV DNA digests indicated that another sequence homologous to the HvAV3c-bro-l1 was present in the HvAV3c genome (Fig. 1a, lanes 1 and 2). Due to its nucleic acid sequence similarity to HvAV3c-bro-l1 http://vir.sgmjournals.org (less than 65 %), probing with HvAV3c-bro-l2 did not reveal the same bands (data not shown). The results suggested that at least three bro-l genes were present in this genome. Similar studies were carried out with iridovirus IIV. Two to three fragments were detected in IIV DNA digested with restriction enzymes with sites absent in the nucleotide sequence of the probe (Fig. 1b, lanes 1 and 2). This indicated Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2535 D. K. Bideshi and others (a) 1 2 3 kbp 21.7 5.5 4.9 3.5 (b) 1 2 3 kbp 21.7 (c) 1 2 3 kbp 21.7 5.5 4.9 5.5 4.9 3.5 3.5 2.0 2.0 1.5 0.9 2.0 1.5 1.5 Fig. 1. Identification of bro genes in ascovirus and iridovirus genomes by Southern hybridization. (a) Hybridization of bro-l1 cloned from HvAV3c to HvAV3c genomic DNA digested with DraI (lane 1), EcoRV (lane 2) and HpaII (lane 3). (b) Hybridization of bro-l1 cloned from the IIV (type 31) genome to IIV DNA digested with ClaI (lane 1), EcoRI (lane 2) and EcoRV (lane 5). (c) Hybridization of SfAV1a-bro-l2 to the genome of three different variants of SfAV1, SfAV1a (lane 1), SfAV1b (lane 2) and SfAV1c (lane 3), each digested with BamHI/ HindIII. The four SfAV1a fragments that hybridized with bro-l2 are indicated by arrows in the left margin. Molecular masses are indicated in the right margins. that at least three related copies of bro-l genes were present in the IIV genome. Eleven genes with their 59 and 39 flanking regions encoding BRO-l proteins ranging from 70 to 370 amino acids were found in the 500 SfAV1a genomic sequences. Five of them, SfAV1a-bro-l5, -l7, -l8, -l9 and -l10, presented cardinal features of functional genes. One, SfAV1a-bro-l2, lacked a start codon and SfAV1a-bro-l3 and -l4 lacked sequences encoding approximately 150 N-terminal residues. SfAV1abro-l1, -l6 and -l11 corresponded to partial bro-l gene sequences. SfAV1a-bro-l2, -l3 and -l4 were apparently nonfunctional based on their small size and coding capacity, suggesting the presence of functional and non-functional bro-l genes in the SfAV1a genome. Comparison of the SfAV1a-bro-l1 to -l11, or HvAV3c-brol1 and -l2 nucleotide sequences showed that they were about 65 % similar to each other and shared no significant homology with the 3?1 kbp and 1?1 kbp repeated sequences (accession nos AJ279828 and AJ279829) described previously for SfAV1a and HvAV3c (Bigot et al., 2000). In contrast, the three bro-l sequences from DpAV4a were 80–89 % identical to each other and were located within three different 980 bp repeated sequences (accession nos 2536 X85006, nt 410–1400; AJ27918, nt 680–1675; AJ279813, nt 5290–6250, respectively; Bigot et al., 1997, 2000). In DpAV4a, these bro-l genes included at least 80 % of the 980 bp repeated sequences and analysis of their sequence revealed that they were non-functional bro-l genes since the ORF was interrupted by frame shifts or stop codons. We therefore classified the bro-l genes that could be aligned as being either ‘fossil’ or ‘active’, depending on whether the ORFs were interrupted by frame shifts or stop codons, or not. When SfAV1a-bro-l2 was used to probe BamHI–HindIII fragments of three SfAV1 variants (SfAV1a, -1b and -1c; Stasiak et al., 2000), the probe hybridized to three fragments ranging in size from 15 to 20 kbp in SfAV1a (Fig. 1c, lane1). However, only one fragment of about 1?5 kbp in SfAV1b (Fig. 1c, lane 2) and in SfAV1c (Fig. 1c, lane 3) hybridized with the probe. Similar polymorphisms were observed in 12 different HvAV3 isolates (data not shown). Ubiquity of bro and bro-l genes in large dsDNA viruses, bacterial phages and transposons Using sequences reported in this study and by Iyer et al. (2002), 128 BRO and BRO-l proteins were identified by BLAST searches. These sequences were restricted to invertebrate viruses and prokaryotic genetic elements (Tables 1 and 2). Ninety-six were encoded by ascoviruses, baculoviruses, insect iridoviruses and entomopoxviruses, one by the phycodnavirus ESV (ORF 117) and 31 were found in bacteriophage or prophages integrated in bacterial genomes. In agreement with Iyer et al. (2002), sequences with significant homology to bro-l genes were not identified in eukaryotic genomes, including those of Caenorhabditis elegans, Drosophila melanogaster and Anopheles gambiae for which complete genome sequences are known, or in vertebrate viruses or their mobile genetic elements. Additionally, five bro-l sequences, not previously described, were identified in bacterial class II transposons. In Pseudomonas alcaligenes, a bro-l gene was located in Tn5563, a transposon related to ISXc5 and ISXc4 (IS3 family; Mahillon & Chandler, 1998), upstream from the transposase A ORF in a different coding frame (accession no. U88088, nt 30716–31717). In Pseudomonas putida, four bro-l genes were present in Tn5542, a transposable element related to ISPs1 (IS5 family, IS427 group; Mahillon & Chandler, 1998). One of these was found upstream from the transposase A gene and was fused in the same coding frame (accession no. AF148496, nt 4724–5110) and the other three were interrupted by several frame shifts and stop codons. We also identified sequences in O. pseudotsugata MNPV, Pseudaletia unipuncta GV, T. ni GV and X. c-nigrum GV (XcGV-bro-j) that contained bro-l sequences interrupted by several stop codons and frame shifts. Two bro-l sequences with regions encoding a truncated N-terminal domain were present in Leucania separata MNPV (Table 1) and in Epiphyas postvittana MNPV (Hyink et al., 2002). Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes Table 2. bro-like genes found in genomes of bacteriophage and in bacterial transposons Name of bro-like gene Virus or transposons Virus or transposon family A2-bro-l BIL309-bro-l BK5T-bro-l CP-933N-bro-l LLH-bro-l Mx8-bro-l N15-bro-l P27-bro-l phiPV83-bro-l phi11-bro-l r1t-bro-l Hi-bro-l1 TnpPa-bro-l Ll-bro-l TnpPp-bro-l Bm-bro-l1 Bm-bro-l2 Cl-bro-l Li-bro-l Ng-bro-l Se-bro-l1 Se-bro-l2 Sp-bro-l1 Sp-bro-l2 Sp-bro-l3 Sc-bro-l Xf-bro-l-1 Xf-bro-l-2 Xf-bro-l-3 Xf-bro-l-4 Yp-bro-l A2 BIL309 BKT5 CP-933N LLH Mx8 N15 P27 PhiPV83 Phi11 r1t Unnamed ISP1 Unnamed Tn5542 Unnamed " " " " " " " " " " " " " " " Bacteriophage " " " " " " " " " " " IS5 Bacteriophage IS5 Prophage " " " " " " " " " " " " " " " Host name Gene accession no. Protein accession no. Lactobacillus casei Lactococcus lactis " Lactobacillus delbrueckii Myxococcus sp. Escherichia coli " Staphylococcus aureus " Lactococcus lactis Haemophilus influenzae Lactococcus lactis Pseudomonas alcaligenes Pseudomonas putita Brucella melitensis " Clostridium perfringens Listeria inoculata Neisseria gonorrhoeae Staphylococcus epidermidis " Streptococcus pyogenes " " Streptomyces coelicolor Xylella fastidiosa " " " Yersinia pestis Y12813 A323670 L44593 AE005325 L42315 AF396866 U63086 AJ298298 AB044554 AF424781 U38906 U32821 A47218 U88088 AF148496 AE009530 AE009601 AP003189 AL596163 AJ004687 AF269322 AF269376 AE10005 AE00979 Ae006544 AF096822 AE003912 AE004059 AE003992 AE003985 AJ414151 – Q9AZQ4 – Q8X797 – Q94MQ6 – Q8W644 – – – P44189 – – – Q8YHA3 Q8YF64 Q8XLD2 Q92FM4 – – – – – – – Q9FHP4 Q9PCU2 Q9PAJ2 Q9PAK9 Q8ZEN5 Sequence relationships between BRO and BRO-l proteins and their coding genomes The high level of polymorphism and repetition of the bro MGF in invertebrate viruses makes it difficult to determine orthological relationships between bro genes and their respective genomes. None the less, we attempted to assess whether bro genes have co-evolved with their respective viruses or within viral families by inferring phylogenetic relationships using complete N-terminal domain (BRO-N) sequences (Iyer et al., 2002) from 114 BRO and BRO-l proteins. Three analytic methods – parsimony, neighbourjoining and unweighted pair-group with arithmetic means – each with 1000 bootstrap replicates, were used for analyses. The topologies of the trees generated by these methods were similar, but bootstrap values obtained by parsimony were more significant and were used to construct the tree shown in Fig. 2. Eight groups (Groups 1–8) composed of 103 of the 114 sequences used were clearly defined in the tree. Other notable characteristics of the tree were that the bootstrap values at the intergroup nodes were lower than 50 %, http://vir.sgmjournals.org whereas the values at the terminal nodes in each group were more robust, typically >50 %, and that Group 2, 3, 5 and 6 contained BRO-N domains encoded by viruses belonging to different virus families. In view of data previously published on baculovirus evolution (Bulach et al., 1999), the relationships between N-terminal domains in groups 1, 2 and 5 indicate that numerous horizontal transfers have also occurred between the genomes of these viruses. Finally, Group 8 was composed of closely related bro-l genes from bacteriophages and bacterial transposons. Surprisingly, this group also contained phycodnavirus ESV-bro-l, suggesting that this eukaryotic sequence has a prokaryotic origin. These results reflect the evolutionary relationships of BRO and BRO-l N-terminal domains. In an attempt to verify whether they also reflect the evolutionary history of C-terminal domains and therefore that of complete BRO and BRO-l proteins, psi-BLAST searches were carried out with each of the C-terminal domains and the BLOSUM45 as a starting matrix. At equilibrium, the first scores for all searches indicated that each C-terminal domain was always Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2537 D. K. Bideshi and others Fig. 2. Consensus unrooted tree illustrating the phylogenetic relationships of BRO and BRO-l proteins. The tree is based on amino acid sequences from aa 1 to 160, as shown in Fig. 3. Due to the large number of protein sequences used in this analysis, bootstrap values at nodes (1000 replicates) are represented by red, violet, blue and green spots that are scaled in the left margin. All the references for each protein are given in the Tables 1 and 2. Depending on their origin, the names of different BRO and BRO-l proteins are identified with different colours as follows: NPVs (dark green), GVs (green), Culex nigripalpus NPV (light blue), entomopoxviruses (red), iridoviruses (dark blue), ascoviruses (pink), bacteriophages (orange), bacterial transposon (brown) and the phycodnavirus ESV (black). The different groups of BRO and BRO-l proteins are identified by grey ellipses and numbered from 1 to 8. The putative BRO and BRO-l proteins that are encoded by truncated genes or a pseudogenes are typed within boxes filled in yellow. more related to the C-terminal domains of BRO proteins with N-terminal domains present in the same group. This, therefore, indicated that N- and C-terminal domains of the BRO proteins belonging to each of the seven invertebrate groups have co-evolved together. However, our results also indicated that the 11 unclassified proteins (Ag-bro-b, 2538 CIV-bro-l1, CIV-bro-l2, Ha-bro-a, Hz-bro-b, Ld-bro-m, Mc-bro-c, Mc-bro-g, Mc-bro-f, Se-bro and SfAV1-bro-l5) were probably chimeric proteins resulting from fusion of the N-terminal BRO domain from one group with the C-terminal domain of a different group. In agreement with the results of Iyer et al. (2002), we observed that the Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes Fig. 3. Alignment of the consensus sequences deduced from amino acid sequence analyses of each of the eight groups (G1–G8) of BRO and BRO-l proteins identified in dsDNA genomes of invertebrate viruses and bacteriophages. In each conserved motif, empty columns indicate short sequences of the complete alignment that corresponded to insertions or deletions that were deleted. Conserved positions between the eight consensus sequences are indicated in white, with identical positions occurring in at least 50 % of the positions in black boxes and those that are similar are in grey boxes. The residues in clear grey boxes correspond to positions that are identical or similar in more than 75 % of the BRO sequences used to define the consensus of each group. The matrix of substitutions used was that described by Nevill-Manning et al. (1998). Only one substitution group was added: R=K=H. The residues proposed by Zemskov et al. (2000) as corresponding to the conserved motif responsible of the non-specific DNA binding activity in BRO proteins are indicated below the alignment at aa 9–62. The two subdomains contained in the conserved N-terminal region of the BRO and BRO-l proteins are located by boxes filled in light grey, whereas the hinge region is located by grey hatching. C-terminal domain of the BRO-l protein from bacteriophages was the most diverse from the others. This indicated that the N- and C-terminal domains of these proteins http://vir.sgmjournals.org were probably more mobile and thus subject to greater chimerization than those of their homologues contained in the genomes of the invertebrate DNA viruses. Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2539 D. K. Bideshi and others Conservation of the BRO-N and BRO-C domains among invertebrate BRO proteins Consensus sequences for invertebrate BRO and BRO-l proteins were assembled for each of the groups and then aligned with each other (Fig. 3). Analysis of the alignment confirmed that BRO-N (aa 1–150) was the most conserved. This analysis, however, also revealed that this feature varied from that proposed previously. Indeed, only the second half of the motif proposed by Zemskov et al. (2000) as being the origin of the structure responsible for the non-specific DNA binding activity – [K/R]-X2–5-[K/R]-X4–12-[F/Y]-X2–14[F/Y]-X6–13-[F/Y]-X1–19-[K/R]-X3–26-[F/Y/W]-X6–12-[K/R] – was found to be significantly conserved. Moreover, conserved residues at positions 49, 52–54, 60–61 and 64–65 (Fig. 3) suggested that the DNA binding domain of BRO and BRO-l proteins might be different from that proposed. HCA analyses confirmed this and also revealed that the N-terminal domain contains two subdomains separated by a hinge, which varied in size from approximately 1 to 40 amino acids (Fig. 3, aa 78–95; unpublished data). As a result, our data and those of Iyer et al. (2002) suggested that the folding of the N-terminal domain of the BRO proteins might correspond to a structure yet to be determined through crystallographic studies. In contrast to BRO-N, alignments of the consensus sequences showed that the BRO-C domain was less conserved among BRO proteins in Groups 1, 2, 3, 5 and 7 (Fig. 3); the C-terminal sequences of the Group 4 proteins were unrelated to BRO-C. BRO protein encoded by AcMNPV orf2 is not required for replication Previous studies of bro genes in BmNPV suggested that BRO-a, BRO-c and BRO-d play an important role in the biology of this virus, since mutants with single or double deletions in these genes could not be recovered from BmN-4 cells (Kang et al., 1999). However, it is not known whether disruption of these genes is deleterious to BmNPV, or whether bro-a and bro-c compensate for their deletion. Because bro-d and the unique bro gene (orf2) in the AcMNPV share a high level of homology, we disrupted orf2 to determine its effect on AcMNPV replication in insect cells and larvae. PCR, Southern blot and sequence analyses confirmed that the unique bro orf2 was disrupted in the two mutant AcMNPV. Specifically, using the ORF2a and ORF2b primers and viral DNAs prepared from budded virions, PCR products of 2?2, 3?9 and 2?8 kb were obtained from, respectively, the intact orf2 in the control AcBacP+1 (Fig. 4a, b, lanes 1 and 3), orf2 disrupted with tetr (orf2-tetr) in AcP+4M:T12 (Fig. 4a, lanes 2 and 4) and orf2 disrupted with chlr (orf2-chlr) in AcBacP+1:brochlABD (Fig. 4b, lanes 2 and 4). All of the PCR fragments hybridized with the orf2 probe (Fig. 4a, b, lanes 3 and 4). All of the bacmid strains replicated in BTI-TN5-B1-4 and 2540 (a) kbp (b) 1 2 3 4 2 4 kbp 1 2 3 4 3 2 Fig. 4. Gel analysis illustrating disruption of the AcMNPV bro orf2 gene. (a) PCR products from budded virions obtained using ORF2a and ORF2b primers with DNA from AcBacP+1 containing the intact orf2 (lanes 1 and 3) and AcP+4M:T12 containing orf2 disrupted with the tetracycline resistance gene (lanes 2 and 4). (b) PCR products obtained from AcBacP+1 (lanes 1 and 3) and AcBacP+1:brochlABD (lanes 2 and 4). Results of hybridization with the orf2 probe are shown in lane 3 and 4 (a, b). SF21 cells, and budded virions produced in these cells were lethal for T. ni and Spodoptera exigua fourth instar larvae. None of the larvae injected with budded virions survived. However, significant differences were observed in the polyhedra production in cells transfected or infected with the different bacmid strains, at 7 days post-infection (Fig. 5). For example, 5 days after transfection, approximately 61 % and 46 % of BTI-TN5-B1-4 cells transfected with AcBacP+1 and AcP+4M:T12, respectively, contained numerous polyhedra in the nuclei (more than 100 per nuclei), whereas the percentage value was markedly reduced to 11 % for AcBacP+1:brochlABD (Fig. 5). Furthermore, relatively few polyhedra, generally between 5 and 25 and occasionally only one, were observed in nuclei of cells infected with AcBacP+1:brochlABD. DISCUSSION Previous studies have identified and partially characterized the bro MGF in baculoviruses, poxviruses and bacteriophages (Afonso et al., 1999; Hayakawa et al., 1999; Kang et al., 1999; Kuzio et al., 1999; Bawden et al., 2000; Iyer et al., 2002). In this study, we have shown that the bro and bro-l MGF is present in two other invertebrate virus families, Ascoviridae and Iridoviridae, and in at least two bacterial class II transposons. Although the list of sequences used in the present study was more extensive than previously reported, our sequence analyses are in general agreement with Iyer et al. (2002) that BRO proteins encoded by invertebrate viruses contain a conserved N-terminal DNA binding domain (BRO-N) associated with a highly variable C-terminal domain (BROC). In BRO-l proteins of prokaryotic origin, BRO-N appears to be more homogeneous than those encoded by invertebrate viruses and is linked to highly variable BRO-C domains from at least seven different origins (Iyer et al., 2002). Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes Fig. 5. Polyhedra observed in BTI-TN5-B1-4 cells at 7 days post-transfection. Cells were mock transfected (A), or transfected with 1 mg bacmid DNA (A), or transfected with AcBacP+1 (polh+, kanr, chls, tets, orf2+) (B), AcP+4M:T12 (polh+, kanr, chls, orf2 disrupted with tet r) (C) or AcBacP+1:brochlABD (polh+, kanr, tets, orf2 disrupted with chl r) (D). For each of the three virus mutants, three assays were performed. In B, C and D, white arrows indicate the polyhedra in the infected cells. Interestingly, bro gene homologues appear to be absent from vertebrate genomes, vertebrate viruses and transposons of invertebrates including C. elegans, An. gambiae and D. melanogaster for which complete genome sequences are known, and from prokaryotic genomes with the exception of those found in prophages. Thus, it is tempting to propose that bro genes, like genes that encode capsid proteins, are native components of invertebrate dsDNA viruses. In this regard, contrary to the proposal that many virus-encoded proteins, such as those involved in DNA metabolism or in anti-apoptotic pathways (Domingo et al., 1999; Huang et al., 2000), have been pirated from host chromosomes, the unique characteristics of BRO proteins, particularly the N-terminal domain, and the apparent absence of these proteins in eukaryotes suggest that the evolution of bro genes has not been mediated by genetic exchanges between invertebrate viruses and their hosts. Previous data (Lopez-Ferber et al., 2001) and ours indicate that both intra- and interspecific polymorphisms in bro and bro-l genes are a general feature of insect dsDNA viruses. One of the major factors that could explain the high level of polymorphism and redundancy of the bro MGF in viral genomes is the process of gene duplication and differentiation. However, it is interesting to note that the relatedness http://vir.sgmjournals.org of many bro genes and therefore their evolutionary origin and differentiation was not related to the virus genomes in which they occurred. Thus, the main process that is responsible for the plasticity of the bro and bro-l gene is very probably a result of the recombination events that occur within viral genomes and between different viruses that infect the same invertebrate hosts. Regardless of the mechanisms that maintain bro diversity, our analysis revealed that the differentiation of the bro MGF was largely independent of the evolutionary history of invertebrate viruses. The presence of non-functional or ‘fossil’ bro genes in several invertebrate viruses and bacteriophages is somewhat unexpected, since it would be presumed that the lack of selective pressure would lead to elimination of these sequences during viral genome evolution. However, it is possible that these ‘fossil’ sequences are maintained in viral populations by processes such as intertypic recombination between different viruses or by horizontal transfer of bro sequences, as noted above. The high degree of variation among BRO proteins encoded by different viruses, and even among BRO proteins encoded by the same virus, for example those of LdMNPV and Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2541 D. K. Bideshi and others BmNPV, suggests that these proteins constitute a multifunctional or diversified protein family, the function of which could be to initiate and terminate transcription, translation or replication at different stages during virus pathogenesis. However, early expression of the five BmNPV bro genes by 2–4 h post-infection (Kang et al., 1999; Suzuki et al., 2001) and the DNA binding activity of the BRO protein (Zemskov et al., 2000) in B. mori cells infected with BmNPV suggest that their functions might be limited to early events, including infection and replication, in virus pathogenesis. The BmNPV BRO-a, BRO-c and BRO-d proteins appear to play important roles in the biology of this virus, potentially being involved in transcription of virus genes and BmNPV replication (Kang et al., 1999; Zemskov et al., 2000). Here we have shown that disruption of the BRO-c domain (recombinant AcP+M4:BT12) in the unique AcMNPV BRO (orf2), a homologue of BmNPV BRO-d, had little detrimental effect on replication and pathogenesis of this virus in cells of S. frugiperda and T. ni, or in T. ni and S. exigua larvae infected with budded virus or per os with polyhedra. Instead, we found that disruption of BRO-N in orf2 in the recombinant AcBacP+1:brochlABD affected the terminal stage of AcMNPV replication by markedly reducing the number of polyhedra produced in infected nuclei. In this regard, orf2 could function, directly or indirectly, in maximizing polyhedra formation in infected larvae, thereby maintaining high numbers of infective virions in the field following larval death. Further studies are required to determine the exact role orf2 plays in AcMNPV replication. The function of orf2 homologues may not be essential for other baculoviruses that are closely related to AcMNPV. For example, the A. falcifera MNPV and R. ou MNPV, variants of the AcMNPV, which replicate efficiently in the same lepidopteran hosts, apparently lack orf2 (Federici & Hice, 1997; Harrison & Bonning, 1999). This indicates that the role of BRO proteins might be host dependent. The absence of bro genes in P. xylostella GV (Hashimoto et al., 2000) provides additional support that BRO function may not be essential for all baculoviruses. Whether there are bro homologues present in insect hosts that compensate for deficiency in BRO function in these baculoviruses is not known. In conclusion, the structural features of ‘active’ bro genes and BRO proteins in different viral species, which include putative motifs for temporal bro expression and BRO function (Kang et al., 1999; Zemskov et al., 2000; Iyer et al., 2002), suggest that BRO proteins mediate specific virus– host interactions during virus pathogenesis. Taking into account the plasticity, variability and putative host-specific function of BRO proteins, it is tempting to propose that bro and bro-like genes have the features of a genetic system resulting from the evolution of the virus–host relationship. They may provide a general mechanism to maintain the ‘virulence’ of these viruses within specific 2542 hosts, resulting from host resistance to viruses and bacteriophages with a large dsDNA genome that is common to many invertebrates and bacteria. ACKNOWLEDGEMENTS We thank Dr M. V. Demattei and J. J. Johnson for their assistance throughout our investigations. This work was supported by grants from the CNRS (UPRES-A 6035), NATO and the Ministère de l’Education Nationale, de la Recherche et de la Technologie to Y. Bigot and from US National Science Foundation Grant INT-9726818 to B. A. Federici. REFERENCES Afonso, C. L., Tulman, E. R., Lu, Z., Oma, E., Kutish, G. F. & Rock, D. L. (1999). The genome of Melanoplus sanguinipes entomopoxvirus. J Virol 73, 533–552. Afonso, C. L., Tulman, E. R., Lu, Z., Balinsky, C. A., Moser, B. A., Becnel, J. J., Rock, D. L. & Kutish, G. F. (2001). Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J Virol 75, 11157–11165. Ahrens, C. H., Russell, R. L. Q., Funk, C. J., Evans, T. J., Harwood, S. H. & Rohrmann, G. F. (1999). The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 229, 381–399. Almendral, J. M., Almazan, F., Blasco, R. & Vinuela, E. (1990). Multigene families in African swine fever virus: family 110. J Virol 64, 2064–2072. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. (editors) (1994). Current Protocols in Molecular Biology, vols 1 and 2. New York: John Wiley & Sons. 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. Bawden, A. L., Glassberg, K. J., Diggans, J., Shaw, R., Farmerie, W. & Moyer, R. W. (2000). Complete genomic sequence of the Amsacta moorei: analysis and comparison with other poxviruses. Virology 274, 120–139. Bideshi, D. K. & Federici, B. A. (2000). The Trichoplusia ni granulovirus helicase is unable to support replication of Autographa californica multicapsid nucleopolyhedrovirus in cells and larvae of T. ni. J Gen Virol 81, 1593–1599. Bigot, Y., Rabouille, A., Sizaret, P. Y., Hamelin, M. H. & Periquet, G. (1997). Particle and genomic characterization of a new member of the Ascoviridae, Diadromus pulchellus ascovirus. J Gen Virol 78, 1139–1147. Bigot, Y., Stasiak, K., Rouleux-Bonnin, F. & Federici, B. A. (2000). Characterization of repetitive DNA regions and methylated DNA in ascovirus genomes. J Gen Virol 81, 3073–3082. Bulach, D. M., Kumar, A., Zaia, A., Liang, B. & Tribe, D. E. (1999). Group II nucleopolyhedrovirus subgroups revealed by phylogenetic analysis of polyhedrin and DNA polymerase gene sequences. J Invertebr Pathol 73, 59–73. Chartier, C., Degryse, E., Gantzer, M., Dieterle, A., Pavirani, A. & Mehtali, M. (1996). Efficient generation of recombinant adenovirus vectors by homologous recombination in Escherichia coli. J Virol 70, 4805–4810. Cheng, C. H., Liu, S. M., Chow, T. Y., Hsiao, Y. Y., Wang, D. P., Huang, J. J. & Chen, H. H. (2002). Analysis of the complete genome Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84 bro and bro-like genes sequence of the Hz-1 virus suggests that it is related to members of the Baculoviridae. J Virol 76, 9024–9034. (2002). Whole genome analysis of the Epiphyas postvittana nucleopolyhedrosisvirus. J Gen Virol 83, 957–971. De la Vega, I., Vinuela, E. & Blasco, R. (1990). Genetic variations Iyer, L. M., Aravind, L. & Koonin, E. V. (2001). Common origin of and multigene families in African swine fever virus. Virology 179, 234–246. four diverse families of large eukaryotic DNA viruses. J Virol 75, 11720–11734. Domingo, E., Webster, R. & Holland, J. (1999). Origins and Evolution Iyer, L. M., Koonin, E. V. & Aravind, L. (2002). Extensive domain of Viruses. New York: Academic Press. shuffling in transcription regulators of DNA viruses and implications for the origins of fungal APSES transcription factors. Genome Biol 3, 1–11. Federici, B. A. (1980). Isolation of an iridovirus from two terrestrial isopods, the pillbug, Armadillidium vulgare, and the sow bug, Porcellio dilatatus. J Invertebr Pathol 36, 373–381. Jakob, N. J., Müller, K., Bahr, U. & Darai, G. (2001). Analysis of characterization of genes in the polyhedrin region of Anagrapha falcifera multinucleocapsid NPV. Arch Virol 142, 333–348. the first complete DNA sequence of an invertebrate iridovirus: coding strategy of the genome of Chilo iridescent virus. Virology 286, 182–196. Federici, B. A., Vlak, J. M. & Hamm, J. J. (1990). Comparative study Kang, W., Suzuli, M., Evgueni, Z., Okano, K. & Maeda, S. (1999). of virion structure, protein composition and genomic DNA of three ascovirus isolates. J Gen Virol 71, 1661–1668. Characterization of baculovirus repeated open reading frames (bro) in Bombyx mori nucleopolyhedrovirus. J Virol 73, 10339–10345. Federici, B. A., Bigot, Y., Granados, R. R., Hamm, J. J., Miller, L. K. & Vlak, J. M. (2000). Family Ascoviridae. In Viral Taxonomy. Seventh Kuzio, J., Pearson, M. N., Harwood, S. H., Funk, C. J., Evans, J. T., Slavicek, J. M. & Rohrmann, G. F. (1999). Sequence and analysis of Report of the International Committee on Taxonomy of Viruses, pp. 261–265. Edited by M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner. San Diego: Academic Press. the genome of a baculovirus pathogenic for Lymantria dispar. Virology 253, 17–34. Diversity, distribution, and mobility of bro gene in Bombyx mori nucleopolyhedrovirus. Virus Genes 22, 247–254. Felsenstein, J. (1993). PHILIP: phylogeny inference package, version Mahillon, J. & Chandler, M. (1998). Insertion sequences. Microbiol Federici, B. A. & Hice, R. H. (1997). Organization and molecular 3.5c. University of Washington, Seattle, WA, USA. Gardiner, G. R. & Stockdale, H. (1975). Two tissue-culture media for production of lepidopteran cells and nuclear polyhedrosis viruses. J Invertebr Pathol 25, 363–370. Goebel, S. J., Johnson, G. P., Perkus, M. E., Davis, S. W., Winslow, J. P. & Paoletti, E. (1990). The complete DNA sequence of vaccinia virus. Virology 179, 247–266. Gomi, S., Majima, K. & Maeda, S. (1999). Sequence analysis of the genome of Bombyx mori nucleopolyhedrosis virus. J Gen Virol 80, 1323–1337. Gompels, U. A., Nicholas, J., Lawrence, G., Jones, M., Thomson, B. J., Martin, M. E. D., Efstathiou, S., Craxton, M. & Macaulay, H. A. (1995). The DNA sequence of human herpesvirus-6, coding content, and genome evolution. Virology 209, 29–51. Gonzalez, A., Calvo, V., Almazan, F., Almendral, J. M., Ramirez, J. C., De la Veda, I., Blasco, R. & Vinuela, E. (1990). Multigene families in African swine fever virus: family 360. J Virol 64, 2073–2081. Goto, C., Hayakawa, T. & Maeda, S. (1998). Genome organization of Xestia c-nigrum granulovirus. Virus Genes 16, 199–210. Hanahan, D. (1983). Studies on the transformation of Escherichia coli with plasmids. J Mol Biol 166, 557–580. Harrison, R. L. & Bonning, B. C. (1999). The nucleopolyhedroviruses of Rachiplusia ou and Anagrapha falcifera are isolates of the same virus. J Gen Virol 80, 2793–2798. Hashimoto, Y., Hayakawa, T., Ueno, Y., Fujita, T., Sano, Y. & Matsumoto, T. (2000). Sequence analysis of the Plutella xylostella granulovirus genome. Virology 275, 358–372. Lopez Ferber, M., Argaud, O., Croizier, L. & Croizier, G. (2001). Mol Biol Rev 62, 725–774. Massung, R. F., Liu, L., Qi, J., Knight, J. C., Yuran, T. E., Kerlavage, A. R., Parsons, J. M., Venter, J. C. & Esposito, J. J. (1994). Analysis of the complete genome of smallpox variola major virus strain Bangladesh-1975. Virology 201, 215–240. Nevill-Manning, C. G., Wu, T. D. & Brutlag, D. L. (1998). Highly specific protein sequence motifs for genome analysis. Proc Natl Acad Sci U S A 95, 5865–5871. Pires, S., Ribeiro, G. & Costa, J. V. (1997). Sequence and organization of left multigene family 110 region of the veroadapted L60V strain of African swine fever virus. Virus Genes 15, 271–274. Rodriguez, J. M., Yanez, R. J., Pan, R., Rodriguez, J. F., Salas, M. L. & Vinuela, E. (1994). Multigene families in African swine fever virus: family 505. J Virol 68, 2746–2751. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-termination inhibitors. Proc Natl Acad Sci U S A 74, 5463–5467. Schnitzler, P., Delius, H., Schollz, J., Touray, M., Orth, E. & Darai, G. (1987). Identification and nucleotide sequence analysis of the repetitive DNA element in the genome of fish lymphocystis virus. Virology 161, 570–578. Shorey, H. H. & Hale, R. L. (1965). Mass-rearing of the larvae of nine noctuid species on a simple artificial medium. J Econ Entomol 58, 522–524. Stasiak, K., Demattei, M. V., Federici, B. A. & Bigot, Y. (2000). Hayakawa, T., Ko, R., Okano, K., Seong, S. I., Goto, C. & Maeda, S. (1999). Nucleotide sequence analysis of the Xestia c-nigrum Molecular analyses of the DNA polymerase gene confirms the classification of DpAV4 among the ascoviruses. J Gen Virol 81, 3059–3072. granulovirus genome. Virology 30, 277–297. Suzuki, M. G., Kang, W. K. & Maeda, S. (2001). An element Huang, Q., Deveraux, Q. L., Maeda, S., Salvensen, G. S., Stennicke, H. R., Hammock, B. D. & Reed, J. C. (2000). Evolutionary downstream of the transcription start site is required for activation of Bombyx mori nucleopolyhedrovirus bro-c promoter. Arch Virol 146, 495–506. conservation of apoptosis mechanisms: lepidopteran and baculoviral inhibitor of apoptosis proteins are inhibitors of caspase-9. Proc Natl Acad Sci U S A 97, 1427–1432. Hyink, O., Dellow, R. A., Olsen, M. J., Caradoc-Davies, K. M. B., Drake, K., Herniou, E. A., Cory, J. S., O’Reilly, D. R. & Ward, V. K. http://vir.sgmjournals.org Thompson, J. D., Higgins, D. G. & Gibson, J. J. (1994). CLUSTAL W. Improving the sensitivity of progressive multiple alignment through sequence weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680. Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 2543 D. K. Bideshi and others Van Etten, J. L. & Meints, R. H. (1999). Giant viruses infecting algae. Yang, F., He, J., Lin, X., Pan, D., Zhang, X. & Xu, X. (2001). Complete Annu Rev Microbiol 53, 447–494. genome sequence of the shrimp white spot bacilliform virus. J Virol 75, 11811–11820. Vydelingum, S., Baylis, S. A., Bistow, C., Smith, G. L. & Dixon, L. K. (1993). Duplicated genes within the variable right end of the genome of a pathogenic isolate of African swine fever virus. J Gen Virol 74, 2125–2130. Yozawa, T., Kutish, G. F., Afonso, C. L., Lu, Z. & Rock, D. L. (1994). Two novel multigene families, 530 and 300, in the terminal variable regions of African swine fever virus genome. Virology 202, 997–1002. Yanez, R. J., Rodriguez, J. M., Nogal, M. L., Yuste, L., Enriquez, C., Rodriguez, J. F. & Vinuela, E. (1995). Analysis of the complete Zemskov, E. A., Kang, W. & Maeda, S. (2000). Evidence for nucleic nucleotide sequence of African swine fever virus. Virology 208, 249–278. acid binding ability and nucleosome association of Bombyx mori nucleopolyhedrovirus BRO proteins. J Virol 74, 6784–6789. 2544 Downloaded from www.microbiologyresearch.org by IP: 78.47.27.170 On: Mon, 24 Oct 2016 08:14:30 Journal of General Virology 84