Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure.

The complete genomic sequence of kelp fly virus (KFV), originally isolated from the kelp fly, Chaetocoelopa sydneyensis, has been determined. Analyses of its genomic and structural organization and phylogeny show that it belongs to a hitherto undescribed group within the picorna-like virus superfamily. The single-stranded genomic RNA of KFV is 11,035 nucleotides in length and contains a single large open reading frame encoding a polypeptide of 3,436 amino acids with 5' and 3' untranslated regions of 384 and 343 nucleotides, respectively. The predicted amino acid sequence of the polypeptide shows that it has three regions. The N-terminal region contains sequences homologous to the baculoviral inhibitor of apoptosis repeat domain, an inhibitor of apoptosis commonly found in animals and in viruses with double-stranded DNA genomes. The second region contains at least two capsid proteins. The third region has three sequence motifs characteristic of replicase proteins of many plant and animal viruses, including a helicase, a 3C chymotrypsin-like protease, and an RNA-dependent RNA polymerase. Phylogenetic analysis of the replicase motifs shows that KFV forms a distinct and distant taxon within the picorna-like virus superfamily. Cryoelectron microscopy and image reconstruction of KFV to a resolution of 15 A reveals an icosahedral structure, with each of its 12 fivefold vertices forming a turret from the otherwise smooth surface of the 20-A-thick capsid. The architecture of the KFV capsid is unique among the members of the picornavirus superfamily for which structures have previously been determined.

Replication-independent assembly of an insect virus (Tetraviridae) in plant cells.

Infectious virions of the insect RNA virus Helicoverpa armigera stunt virus (HaSV; Omegatetravirus, Tetraviridae) were assembled in cultured plant protoplasts of Nicotiana plumbaginifolia in the absence of detectable replication. Assembly of the virus, which has not been grown in cell culture, required cotransfection of a DNA plasmid expressing the HaSV capsid gene in combination with either genomic RNA or with DNA plasmids carrying the complete cDNAs to the two HaSV genomic RNAs. Each cDNA was placed under the control of the cauliflower mosaic virus 35S promoter and followed by a cis-acting ribozyme so that the resultant transcripts corresponded precisely to the two genomic RNAs. Protoplast assembly of infectious particles was confirmed by EM and bioassay of host insect larvae, which became diseased and produced virus particles confirmed as HaSV. Variant transcripts carrying nonviral sequences at either or both termini of the RNAs showed no infectivity, except for RNA2 carrying only a 3' terminal extension. No replication of HaSV in protoplasts was detected in pulse-labeling and blotting experiments. Insects showed less severe disease symptoms when fed protoplasts transfected with only the RNA1 and coat protein plasmids. The symptomatic larvae contained only RNA1 and failed to yield infectious progeny virus, suggesting that RNA1 is capable of self-replication. This novel plasmid-based system confirms that the reported sequence of HaSV represents an infective genome and establishes a procedure for the reverse genetics of a tetravirus.

Large conformational changes in the maturation of a simple RNA virus, nudaurelia capensis omega virus (NomegaV).

An assembly intermediate of a small, non-enveloped RNA virus has been discovered that exhibits striking differences from the mature virion. Virus-like particles (VLPs) of Nudaurelia capensis omega virus (NomegaV), a T=4 icosahedral virus infecting Lepidoptera insects, were produced in insect cells using a baculovirus vector expressing the coat protein. A procapsid form was discovered when NomegaV VLPs were purified at neutral pH conditions. These VLPs were fragile and did not undergo the autoproteolytic maturation that occurs in the infectious virus. Electron cryo-microscopy (cryoEM) and image analysis showed that, compared with the native virion, the VLPs were 16% larger in diameter, more rounded, porous, and contained an additional internal domain. Upon lowering the pH to 5.0, the VLP capsids became structurally indistinguishable from the authentic virion and the subunits autoproteolyzed. The NomegaV protein subunit coordinates, which were previously determined crystallographically, were modelled into the 28 A resolution cryoEM map of the procapsid. The resulting pseudo-atomic model of the NomegaV procapsid demonstrated the large rearrangements in quaternary and tertiary structure needed for the maturation of the VLPs and presumably of the virus. Based on this model, we propose that electrostatically driven rearrangements of interior helical regions are responsible for the large conformational change. These results are surprising because large structural rearrangements have not been found in the maturation of any other small RNA viruses. However, similarities of this conformational change to the maturational processes of more complex DNA viruses (e.g. bacteriophages and herpesvirus) and to the swelling of simple plant viruses suggest that structural changes in icosahedral viruses, which are integral to their function, have similar strategies and perhaps mechanisms.

Reverse transcription of a naturally occurring nonretroviral RNA produces a precise deletion in the majority of its cDNA products.

A precise, reproducible deletion made during in vitro reverse transcription of RNA2 from the icosahedral positive-stranded Helicoverpa armigera stunt virus (Tetraviridae) is described. The deletion, located between two hexamer repeats, is a 50-base sequence that includes one copy of the hexamer repeat. Only the Moloney murine leukemia virus reverse transcriptase and its derivative Superscript I, carrying a deletion of the carboxy-terminal RNase H region, showed this response, indicating a template-switching mechanism different from one proposed that involves a RNase H-dependent strand transfer. Superscript II, however, which carries point mutations to reduce RNase H activity, does not cause a deletion. A possible mechanism involves the enzyme pausing at the 3' side of a stem-loop structure and the 3' end of the nascent DNA strand separating from the template and reannealing to the upstream hexamer repeat.

The specificity of Helicoverpa armigera stunt virus infectivity.

Helicoverpa armigera stunt virus (HaSV) is a member of the Tetraviridae family of RNA viruses whose replication and expression strategies are not well understood due to the absence of an in vitro cell culture system. We set out to find such a system for HaSV by screening an array of 13 insect and 1 mammalian cell culture lines with both virus particle infection and genomic RNA transfection. No cell line was found to be permissive for replication, although entry of genomic RNA was verified. The apparent specificity of this virus for its in vivo midgut target site was strongly corroborated by studies involving Northern blots of RNA extracted from infected insects. Only larval midgut RNA showed the presence of virus after hosts were infected per os or by injection which exposed other host cell types to the virus. The absence of replication in cell culture was due to a lack, or presence, of host factors important to replicase activity and also the likely absence of virus particle binding and entry. We thus provide both in vitro- and in vivo-based evidence demonstrating that this virus is extremely specific in the type of cells in which it will initiate an infection.

A novel capsid expression strategy for Thosea asigna virus (Tetraviridae).

This paper presents evidence that Thosea asigna virus (TaV) has a unique capsid expression strategy and is a member of the Nudaurelia beta-like genus of the Tetraviridae. Electron microscopy of TaV particles indicated a 38 nm, T = 4 icosahedral capsid similar in structure to that of Nudaurelia beta virus (NbetaV). TaV particles have a buoyant density of 1.296 g/cm3 in CsCl and consist of two capsid proteins of 56 and 6 kDa. The virus genome contains a genomic RNA molecule of 6.5 kb and a subgenomic molecule of 2.5 kb. Northern blotting of TaV RNA indicated a genomic organization similar to that of NbetaV. The capsid gene of TaV is carried on both the genomic and subgenomic RNA molecules, while the RNA polymerase gene is present only on the genomic RNA. Cloning and sequencing of the TaV capsid gene identified an open reading frame that could potentially encode a capsid precursor protein of up to 82.5 kDa. The N-terminal sequences of the capsid proteins were compared with the nucleotide sequence of the capsid open reading frame. The sequences indicate that the pre-protein is cleaved at two positions to produce the 56 and 6 kDa capsid proteins as well as a predicted third protein that was not detected in the mature virion. Phylogenetic analysis of the capsid proteins indicated that TaV is more closely related to NbetaV than to the Nudaurelia omega-like viruses. The eight beta-sheets that make up a jelly roll structure in the TaV capsid protein were identified by computer analysis.

Sequence of the genomic RNA of nudaurelia beta virus (Tetraviridae) defines a novel virus genome organization.

The monopartite genome of Nudaurelia beta virus, the type species of the Betatetravirus genus of the family Tetraviridae, consists of a single-stranded positive-sense RNA (ss+RNA) of 6625 nucleotides containing two open reading frames (ORFs). The 5' proximal ORF of 5778 nucleotides encodes a protein of 215 kDa containing three functional domains characteristic of RNA-dependent RNA polymerases of ss+RNA viruses. The 3' proximal ORF of 1836 nucleotides, which encodes the 66-kDa capsid precursor protein, overlaps the replicase gene by more than 99% (1827 nucleotides) and is in the +1 reading frame relative to the replicase reading frame. This capsid precursor is expressed via a 2656-nucleotide subgenomic RNA. The 3' terminus of the genome can be folded into a tRNA-like secondary structure that has a valine anticodon; the tRNA-like structure lacks a pseudoknot in the aminoacyl stem, a feature common to both genera of tetraviruses. Comparison of the sequences of Nudaurelia beta virus and another member of the Tetraviridae, Helicoverpa armigera stunt virus, which is in the genus Omegatetravirus, shows identities of 31.6% for the replicase and 24.5% for the capsid protein. The viruses in the genera Betatetravirus and Omegatetravirus of the Tetraviridae are clearly related but show significant differences in their genome organization. It is concluded that the ancestral virus with a bipartite genome, as found in the genus Omegatetravirus, likely evolved from a virus with an unsegmented genome, as found in the genus Betatetravirus, through evolution of the subgenomic RNA into a separate genomic component, with the accompanying loss of the capsid gene from the longer genomic RNA.

The larger genomic RNA of Helicoverpa armigera stunt tetravirus encodes the viral RNA polymerase and has a novel 3'-terminal tRNA-like structure.

In this paper we report the complete nucleotide sequence of the larger segment (5312 nucleotides) of the bipartite RNA genome of Helicoverpa armigera stunt tetravirus (HaSV). HaSV therefore becomes the first member of the Tetraviridae, a virus family with a host range restricted to lepidopteran insects, whose genome has been completely sequenced. HaSV RNA 1 encodes a 187K protein which includes three domains conserved in RNA-dependent RNA polymerases of RNA viruses in the alpha-like superfamily. Analysis of the replicase sequence confirms the status of the Tetraviridae as a distinct family within this superfamily, which includes animal, plant, and insect viruses, and shows the least-distantly related replicase for all three domains to be that of the hepatitis E virus. Another feature of the nonpolyadenylated HaSV genomic RNAs is a well-conserved 3'-terminal tRNA-like structure, the first such structure discerned in an animal virus. However, in contrast to the tRNA-like structures on some plant virus RNAs, the HaSV structure, which has a valine anticodon (CAU), appears to form without a pseudoknot and therefore resembles authentic tRNA(Val) more closely than do the plant viral structures. The implications of these observations for our understanding of RNA virus evolution are discussed.

Sequence of RNA2 of the Helicoverpa armigera stunt virus (Tetraviridae) and bacterial expression of its genes.

The complete nucleotide sequence of RNA2 of Helicoverpa armigera stunt virus (HaSV), a member of the Tetraviridae, was determined by characterization of cloned cDNA and PCR products and direct sequencing of genomic RNA. The capped, positive sense, single-stranded RNA is 2478 nucleotides in length and has two overlapping open reading frames (ORFs) likely to be cistrons which are situated between terminal non-coding regions of 282 and 168 bases, 5' and 3', respectively. Extensive secondary structure of the RNA strand is indicated, including a tRNA-like structure at the 3' terminus which is the first such structure discerned in an animal virus. The first ORF encodes a 17 kDa PEST protein (p17) of unknown function while the second ORF encodes the 71 kDa coat protein precursor (p71) that is cleaved at an Asn-Phe site into the 64 kDa and 7 kDa coat proteins. The precursor coat protein is 66% identical to that of another tetravirus, the Nudaurelia omega virus, with most of the difference residing in a 165 amino acid region located in the middle of the sequence. Despite the extensive similarity, no serological relationship was observed between the two viruses, suggesting that the dissimilar region is exposed on the capsid exterior. Expression in bacteria of the two RNA2 gene products shows they are likely to be expressed by a leaky scan-through mechanism. Bacterial expression of p71 did not produce virus-like particles while expression of p17 produced large arrays of mostly hollow, hexagonal tube-like structures.

A novel small RNA virus isolated from the cotton bollworm, Helicoverpa armigera.

A small RNA virus with novel characteristics has been isolated from laboratory-bred larvae of Helicoverpa armigera. Infection by the H. armigera stunt virus causes severe retardation of larval development and subsequent death. Its particles are isometric, 38 nm in diameter, and have a buoyant density of 1.296 g/ml in caesium chloride. The viral capsid has two major non-glycosylated protein components with M(r)s of 65,000 and 6000, and contains a genome composed of two non-polyadenylated single-stranded RNA molecules with lengths of 2.4 kb and 5.5 kb. The 5' termini of these RNAs are capped; their 3' termini are unblocked. In vitro translations of the viral RNAs showed synthesis of large proteins of sizes near the maximum coding capacity of each strand along with synthesis of numerous smaller proteins; no evidence for processing of precursors was seen. The physicochemical properties of the virus are most similar to those of the Nudaurelia omega virus, a provisional member of the Tetraviridae, although no antigenic relationship was observed between the two viruses. The bipartite genome and distinct capsid structure of these two viruses indicate the existence of a previously unrecognized virus group.

Insecticidal effects of an insect-specific neurotoxin expressed by a recombinant baculovirus.

The scorpion Androctonus australis has a peptide (AaIT) which selectively targets the insect sodium channel. This mode of action is similar to that of many widely used chemical insecticides. When Bombyx mori larvae were infected with a recombinant baculovirus carrying a synthetic AaIT gene, the expressed protein was secreted into the hemolymph and caused symptoms consistent with sodium channel blocking, including tremors and feeding cessation at 40 hr p.i. followed by paralysis and death by 60 hr p.i. Larvae infected with control virus died by 96 hr p.i. These results indicate that foreign genes can be used in recombinant baculoviruses to reduce insect feeding damage and increase the rate of insect kill.

Regulation of juvenile hormone esterase gene expression in the tobacco budworm (Heliothis virescens).

The tissue distribution, developmental control, and induction of juvenile hormone esterase (JHE) mRNA was examined in Heliothis virescens using an 800-base pair fragment of a JHE cDNA clone. Northern hybridization analysis of poly(A)+RNA from fat body and integument of fifth stadium larvae indicated the presence of a single JHE mRNA species having an estimated length of 3 kilobases. On Day 2 of the fifth stadium (L5D2), basal JHE mRNA levels were 3-fold higher in the integument than the fat body, which correlated with the higher specific activity of the enzyme in the integument at this time. However, JHE mRNA levels in the fat body on Day 4 of the fifth stadium were 9-fold higher than on Day 2, while mRNA levels in the integument remained the same. This endogenous increase in JHE mRNA and activity in the fat body occurred at the time of peak hemolymph JHE activity. JHE mRNA was not detected in third stadium larvae which have very low levels of JHE activity. Treatment of L5D2 larvae with the juvenile hormone mimic epofenonane resulted in a 7- and 14-fold increase in the level of JHE mRNA in the integument and fat body, respectively. The mRNA induced in both tissues was of the same estimated length as the constitutively expressed message. The data indicate that the developmental regulation and induction of JHE can occur at the level of mRNA. There is evidence that the fat body secretes more JHE than does the integument and could be the major source of hemolymph JHE.

Isolation and sequencing of cDNA clones coding for juvenile hormone esterase from Heliothis virescens. Evidence for a catalytic mechanism for the serine carboxylesterases different from that of the serine proteases.

Three cDNA clones containing the entire coding sequence for JH esterase from the noctuid moth Heliothis virescens have been isolated from an expression library using specific antibodies and oligonucleotide probes. The complete sequence of one of the clones shows a 2989-base pair insert that is approximately the length of the single 3.0-kilobase pair mRNA transcript detected by Northern blotting. The clone has an open reading frame of 1714 base pairs that predicts a mature protein (minus signal peptide 19 residues long) of 61,012 Da. The 3'-nontranslated region has three signals for polyadenylation although only one apparently is used. Edman degradation of purified juvenile hormone lesterase indicates two slightly different proteins (one being 75% of the total) while the three cDNA clones differ at three bases in their 5' region causing their predicted sequence to differ at one or two residues of the 35 amino acids sequenced from the major form. Comparison of the predicted protein sequence to other carboxylesterase sequences indicates extensive similarity in the NH2-terminal half of the protein and the active site serine to be at position 201. The lack of conserved histidine and aspartate residues and the presence of conserved arginine and glutamate residues in appropriate positions in the NH2-terminal half of the homologous serine carboxylesterases suggests a catalytic mechanism for the serine carboxylesterases that is different from that of the serine proteases.

Characterization of affinity-purified juvenile hormone esterase from Trichoplusia ni.

Juvenile hormone (JH) esterase was purified greater than 1000-fold in one step from hemolymph and whole larval homogenates from the last larval instar of Trichoplusia ni to give a single diffuse band that migrates at Mr = 64,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purification was based on an affinity chromatography procedure that employs trifluoromethyl ketone ligands. Isoelectric focusing of the purified preparations resulted in multiple bands that coincided to all significant hydrolysis of juvenile hormone detected in this manner. Kinetic experiments using optically pure enantiomers of JH II as substrates showed the two main electromorphs of JH esterase from the hemolymph to have apparently identical kinetic parameters as well as a similar capability to distinguish between substrates that differ in the orientation of the epoxide moiety of JH. However, the enzyme could hydrolyze esters lacking the JH structure. The proteins were shown to be monomers and to have asparagine-linked oligosaccharides, most likely of hybrid structure. Immunochemical and other evidence showed that the affinity-purified proteins were responsible for all significant JH esterase activity during periods of rapid esterolysis in vivo.

In-vitro biosynthesis of 1-(4'-hydroxyphenyl)-2-nitroethane and production of cyanogenic compounds in osmotically stressed cell suspension cultures of Eschscholtzia californica Cham.

Cell suspension cultures of Eschscholtzia californica produce one or more cyanogenic compounds when placed under osmotic stress. The nature of the compound(s) has not yet been established but they are not identical with the cyanogenic glucosides triglochinin and dhurrin, which occur in the intact plant. Microsomal fractions isolated from stressed cell cultures catalyze the synthesis of 1-(4'-hydroxyphenyl)-2-nitroethane from L-tyrosine. Both NADPH and molecular oxygen are required as cosubstrates, and 4-hydroxyphenylacetaldoxime is an intermediate in the synthesis of the nitrocompound. This observation indicates that the biosynthetic pathways leading from L-tyrosine to 1-(4'-hydroxyphenyl)-2-nitroethane and to the L-tyrosine-derived cyanogenic glucosides are closely related. A glucosyltransferase which glucosylates the nitrocompound in the presence of uridine diphosphate glucose appears in the osmotically stressed cultures in a time pattern similar to that for production of the nitrocompound.