Complete mitochondrial DNA genome of Bemisia tabaci cryptic pest species complex Asia I (Hemiptera: Aleyrodidae)

The complete length of the Asia I member of the Bemisia tabaci species complex mitochondrial DNA genome (mitogenome) is 15,210 bp (GenBank accession no. KJ778614) with an A-T biased nucleotide composition (A: 32.7%; T: 42.4%; G: 14.0%; C: 10.8%). The mitogenome consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA (rRNAs) and a 467 bp putative control region which also includes the A+T rich repeat region. All PCGs have an ATA (n = 8) or ATG (n = 5) start codon. Gene synteny of Asia I is overall similar to B. afer and two other members of the B. tabaci species complex Mediterranean and New World 1, and contains the tRNA-Ser2 located between the Cytb and ND1 genes found in Mediterranean and New World 1, but which is absent in B. afer. The orientation of the tRNA-Arg in Asia I is on the "plus" strand and differed from Mediterranean which is found on the "minus" strand. The Asia I mitogenome size is currently ranked the second smallest after B. afer (14,968 bp) followed by New World 1 (15,322 bp) and Mediterranean (15,632 bp).

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.

Exploring a benzyloxyaniline linker utilizing ceric ammonium nitrate (CAN) as a cleavage reagent: solid-phase synthesis of N-unsubstituted beta-lactams and secondary amides

[figure: see text] A novel benzyloxyaniline linker that uses ceric ammonium nitrate (CAN) as a cleavage reagent is described. Its application in the solid-phase synthesis of N-unsubstituted beta-lactams and secondary amides furnishes compounds in moderate to excellent yield (45-91%) and high purity (93-99%).

Analysis of the structure and electrophysiological actions of halitoxins: 1,3 alkyl-pyridinium salts from Callyspongia ridleyi

We have chemically characterized a preparation of halitoxins, (1,3 alkyl-pyridinium salts) isolated from the marine sponge Callyspongia ridleyi. At concentrations of 50 and 5 microg/ml the halitoxin preparation caused irreversible membrane potential depolarization, decreased input resistance and inhibited evoked action potentials when applied to cultured dorsal root ganglion neurones. Under whole cell voltage clamp the halitoxins produced an increase in cation conductance that was attenuated by replacing sodium with N-methyl-d-glucamine. Fura-2 fluorescence ratiometric calcium imaging was used to directly measure calcium flux into neurones after exposure to halitoxins. Calcium influx, evoked by the halitoxins, persisted when the neurones were bathed in medium containing the voltage-activated calcium channel antagonists cadmium and nickel. Experiments on undifferentiated F-11 cells showed little or no calcium influx in response to depolarizing concentrations of potassium and indicated that halitoxins evoked massive calcium influx in the absence of voltage-activated calcium channels. The halitoxins also produced transient increases in intracellular calcium when F-11 cells were bathed in calcium-free medium suggesting that the toxins could release calcium from intracellular stores. The pore-forming action of the halitoxins was identified when the toxins were applied to artificial lipid bilayers composed of phosphatidylcholine and cholesterol. Halitoxins evoked channel-like activity in the lipid bilayers, with estimated unitary conductances of between 145pS and 2280pS, possibly indicating that distinct channels could be produced by the different components in the preparation of halitoxins.

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.

Were RNA replication and translation directly coupled in the RNA (+protein?) World?

The ribosome is proposed to have evolved from an ancestor that simultaneously replicated and translated template RNA. At its decoding site, this ancestor to the ribosome carried a ribozyme that assembled product RNA by sequentially ligating anticodon triplets excised from tRNAs. This ribozyme was the ancestor of the Group I introns, which are still present on some ribosomal RNA precursors. Coupling of reversible RNA replication by transesterification with the thermodynamically favourable process of transpeptidation provides a rationale for the evolution of the complete ribosome as a replicase for large RNAs in the RNA (+protein?) world. A detailed and experimentally verifiable mechanism can be proposed for simultaneous replication and translation. Sequence requirements for recognition of the decoding complex as a substrate helix by these ribozymes are consistent with earlier models for the origin of the genetic code, but require an indirect mode for ribosomal self-replication. This proposal has the potential to explain the location of Group I introns in the anticodon loops of some tRNAs.

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.

Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses

The nucleotide sequence of the 3035 residues of RNA 2 (Mr 1.03 X 10(6) ) of the Q strain of cucumber mosaic virus (CMV) was determined by sequencing M13 clones of the RNA 2 cDNA and by dideoxy sequencing using primers prepared either from M13 clones or by chemical synthesis. A single long open reading frame starts at the second AUG from the 5' end of RNA 2 and encodes 839 amino acids (Mr 94333). This frame has flanking regions of 92 nucleotides at the 5' terminus and 423 nucleotides at the 3' terminus. Computer analysis of the nucleotide sequence showed that CMV RNA 2 has a significant homology with RNA 2 of brome mosaic virus (BMV) and alfalfa mosaic virus (AMV) and also with a region for tobacco mosaic virus (TMV) RNA encoding the read-through part of the 183-kDa protein. About 400 amino acids in the central region of the CMV RNA 2 translation product have a striking homology with the corresponding proteins encoded by BMV and AMV and with the read-through part of the TMV 183-kDa protein. Hydrophobicity plots of CMV and BMV RNA translation products also had apparent similarities. It is concluded that CMV is related to BMV, AMV and TMV in order of increasing evolutionary divergence.

Construction of the physical map of the chloroplast DNA of Phaseolus vulgaris and localization of ribosomal and transfer RNA genes

Construction of a physical map of the chloroplast DNA from Phaseolus vulgaris showed that this circular molecule is segmentally organized into four regions. Unlike other chloroplast DNAs which have analogous organization, two single-copy regions that separate two inverted repeats have been demonstrated to exist in both relative orientations, giving rise to two populations of DNA molecules. Hybridization studies using individual rRNA and tRNA species revealed the location of a set of rRNA genes and at least seven tRNA genes in each inverted repeat region, a minimum of 17 tRNA genes in the large single-copy region and one tRNA gene in the small single-copy region. The tRNA genes code for 24 tRNA species corresponding to 16 amino acids. Comparison of this gene map with those of other chloroplast DNAs suggests that DNA sequence rearrangements, involving some tRNA genes, have occurred.

Satellite RNA of cucumber mosaic virus forms a secondary structure with partial 3'-terminal homology to genomal RNAs

Sat-RNA is one of several replicating satellite RNAs which have been isolated from RNA encapsidated in cucumber mosaic virus (CMV) and which are totally dependent on CMV for replication. The 336 residue sequence of Sat-RNA obtained using the dideoxynucleotide chain termination and partial enzymic digestion procedures shows only a few short stretches (up to 11 residues) of sequence homology with one of the three CMV genomal RNAs so far sequenced. Sat-RNA has 88% sequence homology with another, previously sequenced, satellite RNA of CMV, CARNA 5. Analysis of partial digests of 5'- or 3' -32P-Sat-RNA with nuclease S1 or RNase T1 under non-denaturing conditions showed that only about 10% of the residues in Sat-RNA were cleaved. Further data on base-paired segments of Sat-RNA were obtained using digestion with RNase T1 followed by electrophoretic fractionation of the resulting fragments under both non-denaturing and denaturing conditions. On the basis of this data, a complete secondary structure model is proposed for Sat-RNA with 52% of its residues involved in base pairs. A prominent hairpin at the 3'-terminus of Sat-RNA shows considerable sequence and structural homology with parts of the 3'-terminal tRNA-like structure of the CMV genomal RNAs.

Physical mapping of differences in chloroplast DNA of the five wild-type plastomes in Oenothera subsection Euoenothera

1) DNA has been isolated from the five genetically distinguishable plastid types of Oenothera, subsection Euoenothera. DNA of plastomes I to IV was obtained from plants with identical nuclear backgrounds containing the genotype AA of Oenothera hookeri whereas the DNA of plastome V came from Oenothera argillicola (genotype CC). 2) The DNAs of the five basic Euoenothera wild-type plastomes can be distinguished by restriction endonuclease analysis with Sal I, Pst I, Kpn I, Eco RI and Bam HI. The fragment patterns exhibit distinct common features as well as some degree of variability. 3) Physical maps for the circular DNAs of plastome I, II, III and V could be constructed using the previously detailed map of plastome IV DNA (Gordon et al. 1981). This has been achieved by comparing the cleavage products generated by restriction endonucleases Sal I, Pst I and Kpn I which collectively result in 36 sites in each of the five plastome DNAs, and by hybridization of radioactively labelled chloroplast rRNA or chloroplast cRNA probes of spinach to Southern blots of appropriate restriction digests. The data show that the overall fragment order is the same for all five plastome DNAs. Each DNA molecule is segmentally organized into four regions represented by a large duplicated sequence in inverted orientation whose copies are separated by two single-copy segments. 4) The alterations in position of restriction sites among the Euoenothera plastome DNAs result primarily from insertions/deletions. Eleven size differences of individual fragments in the Sal I, Pst I and Kpn I patterns measuring 0.1-0.8 Md (150-1,200 bp) relative to plastome IV DNA have been located. Most changes were found in the larger of the two single-copy regions of the five plastomes. Changes in the duplication are always found in both copies. This suggests the existence of an editing mechanism that, in natural populations, equalizes or transposes any change in one copy of the repeat to the equivalent site of the other copy. 5) Detailed mapping of the two rDNA regions of the five plastomes, using the restriction endonucleases Eco RI and Bam HI which each recognize more than 60 cleavage sites per DNA molecule, disclosed a 0.3 Md deletion in plastome III DNA and a 0.1 Md insertion in plastome V DNA relative to DNA of plastome IV, I and II. These changes are most probably located in the spacer between the genes for 16S and 23S rRNA and are found in both rDNA units.

Restriction endonuclease cleavage site map of chloroplast DNA from Oenothera parviflora (Euoenothera plastome IV)

1) More than 50 cleavage sites produced by the restriction endonucleases Sal I, Pst I, Kpn I, Sma I and Eco RI have been physically mapped on the 47 μm circular DNA molecule of the Euoenothera plastome IV. This plastome (= plastid genome) is considered to be the phylogenetically oldest of the subsection. 2) The DNA molecule is segmentally organized into four regions represented by a large duplicated sequence in inverted orientation whose copies are separated by two single-copy segments. The single-copy regions comprise about 14 and 57 Md in size, respectively. 3) The size of the inverted repeat, about 15 Md, was determined by restriction site mapping, by mapping of genes for ribosomal RNAs and by hybridization of a cRNA transcribed from a homologous part of Spinacia oleracea chloroplast DNA which appears to be phylogenetically conserved. 4) Hybridization of radio-iodinated spinach 16S, 23S and 5S chloroplast rRNA species to Southern blots of restricted plastome IV DNA has localized the rDNA to the inverted repeat regions, in the order given. The genes for 16S and 23S rRNA are separated by a 2.4 kbp spacer. 5) The physical map of the plastome IV DNA serves as basis for comparison with the DNA from the four other, closely related Euoenothera plastomes.

Compositional heterogeneity of the chloroplast DNAs from Euglena gracilis and Spinacia oleracea

The chloroplast genomes of Euglena gracilis and Spinacia oleracea were investigated in their compositional heterogeneity, by using different experimental approaches. Euglena chloroplast DNA has a dG + dC content of 28%. Preparations averaging 20 x 10(6) in molecular weight exhibit a gross heterogeneity in their elution profiles from hydroxyapatite and in their buoyant densities because the rRNA genes have a high rG + rC content. Finer analysis by melting, buoyant density of restriction fragments and micrococcal nuclease degradation have revealed an extended compositional heterogeneity. From micrococcal nuclease digestion data, approximately 30% of the chloroplast genome is as low as 12% in its dG + dC content, whereas 10% is higher than 60% dG + dC. Since the average dG + dC content of large restriction endonuclease fragments varied to a lesser extent, most of dA + dT-rich sequences must occur in short stretches interspersed with dG + dC-rich stretches. Spinach chloroplast DNA (dG + dC = 36.5%) did not exhibit any gross compositional heterogeneity in its hydroxyapatite elution or in its buoyant density profile. But the higher resolution methods of melting, bouyant densities of restriction fragments and micrococcal nuclease degradation revealed a high degree of heterogeneity which appears to be due to interspersion of short DNA stretches of different base composition. About 30% of genome is as low as 22% in dG + dC, while 10% is higher than 60% in dG + dC.

Homologies among ribosomal RNA and messenger RNA genes in chloroplasts, mitochondria and E. coli

Labelled chloroplast rRNAs from Spinacia oleracea were hybridized to restriction endonuclease digests of chloroplast DNA from Oenothera hookeri and Euglena gracilis, to mitochondrial DNA of Acanthamoeba castellanii, and to DNA of the E. coli rrn B operon in the transducing phage lambda rifd 18. The degree of homology is greatest for the 16S rRNA gene. Greater than 90% occurs between the two higher plant genes, 80% homology to the lower plant gene, 60%-70% homology to the bacterial gene, and 20% homology to the mitochondrial gene. The degree of hybridization varied considerably for the 23S and the 5S rRNA genes. Very high homology exists between the two higher plant genes, only about 50% homology for both the Euglena and bacterial genes, and no significant homology for the mitochondrial genes. These results show that any chloroplast (or E. coli) rRNA may be used as a probe to identify rRNA genes in other ctDNAs. Two RNA populations, each enriched for a different ctDNA-encoded mRNA, proved useful in the location of these genes on both higher plant ctDNAs. No significant hybridization was obtained using these probes to the Euglena ctDNA which seems to be too distantly related.

Analysis of the plastid DNA in an Oenothera plastome mutant deficient in ribulose bisphosphate carboxylase

Plastid DNA of the light green Oenothera plastome mutant sigma, from plastome I, which is deficient in ribulose bisphosphate carboxylase, has been compared with wild-type chloroplast DNA from plastome I and the related plastome IV. For this, double digestions with the restriction endonucleases Sal I, Pst I and Kpn I were used. Chloroplast DNA from plastomes I and IV differs in the sizes of several fragments, with the changes being from under 0.1 to about 0.6 Md in size. In the cleavage patterns of the mutant DNA compared to the wild-type DNA from plastome I, the only differences observed are two possible deletions of less than 0.1 Md from a fragment known to partly cover the genes for the ribosomal RNAs and from a fragment located in the small single-copy region of the molecule. It is concluded that the ribulose bisphosphate carboxylase deficiency in this mutant is not caused by a major deletion in the plastid DNA.