Lipid composition of frog virus 3

Computational virology: From the inside out

Viruses typically pack their genetic material within a protein capsid. Enveloped viruses also have an outer membrane made up of a lipid bilayer and membrane-spanning glycoproteins. X-ray diffraction and cryoelectron microscopy provide high resolution static views of viral structure. Molecular dynamics (MD) simulations may be used to provide dynamic insights into the structures of viruses and their components. There have been a number of simulations of viral capsids and (in some cases) of the inner core of RNA or DNA packaged within them. These simulations have generally focussed on the structural integrity and stability of the capsid and/or on the influence of the nucleic acid core on capsid stability. More recently there have been a number of simulation studies of enveloped viruses, including HIV-1, influenza A, and dengue virus. These have addressed the dynamic behaviour of the capsid, the matrix, and/or of the outer envelope. Analysis of the dynamics of the lipid bilayer components of the envelopes of influenza A and of dengue virus reveals a degree of biophysical robustness, which may contribute to the stability of virus particles in different environments. Significant computational challenges need to be addressed to aid simulation of complex viruses and their membranes, including the need to integrate structural data from a range of sources to enable us to move towards simulations of intact virions. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

Frog virus 3 replication: induction and intracellular distribution of polypeptides in infected cells

The synthesis of the polypeptides induced in frog virus 3-infected cells was analyzed by high-resolution sodium dodecyl sulfate-polyacrylamide gel electrophoresis of radiolabeled cell extracts. Purified frog virus 3 contained 22 polypeptides, with molecular weights in the range 9 x 10(3) to 114 x 10(3). All of the structural and an additional seven nonstructural polypeptides were detected in infected cell lysates. The following three classes of induced polypeptides (under temporal control) were observed in BHK cells: at 2 h, four alpha polypeptides; at 4 h, 13 beta polypeptides; and at 6 h, the remaining 12 gamma polypeptides. The total molecular weight of the infected cell-specific polypeptides (ICPs) was approximately 1.5 x 10(6), which accounts for about 30% of the coding capacity of the viral genome. At least 10 of the induced polypeptides were phosphorylated, but none was glycosylated or sulfated. No evidence for posttranslation cleavage of polypeptides in pulse-chase and inhibition experiments was obtained. The synthesis of gamma polypeptides was not detected in the presence of the viral DNA replication inhibitors cytosine arabinoside and hydroxyurea, but halogenated nucleotides apparently had no effect. These results suggest that alpha and beta polypeptides are "early" events and that detectable gamma polypeptide synthesis is dependent on the production of progeny viral DNA. The regulation of frog virus 3-induced polypeptide synthesis in infected BHK cells was examined by using inhibitors of protein and RNA synthesis and amino acid analogs. These experiments confirmed the existence of three sequentially synthesized, coordinately regulated classes of polypeptides, designated alpha, beta, and gamma. The requirements for the synthesis of each class were as follows: (i) alpha polypeptides did not require previous cell protein synthesis; (ii) beta polypeptides required a prescribed period of alpha polypeptide synthesis and new mRNA synthesis; and (iii) gamma polypeptides required prior synthesis of functional beta polypeptides and new mRNA synthesis. alpha polypeptide synthesis was controlled by beta and gamma polypeptides, and alpha and beta polypeptides were involved in the suppression of host cell polypeptide synthesis. Indirect evidence was obtained for the temporal regulation of frog virus 3 transcription. The intracellular distribution of virus-induced polypeptides in cells infected with frog virus 3 was investigated by using standard cell fractionation techniques. Most of the 29 induced polypeptides were bound to structures within the nucleus, and only two ICPs were not associated with purified nuclei. When isolated nuclei were incubated in an infected cell cytoplasm preparation, all of the nuclear ICPs were incorporated in vitro. All of the ICPs were associated with ribosomal and rough endoplasmic reticulum fractions of infected cells, and a number of ICPs were found on smooth intracellular membranes. Most of the ICPs were also associated with purified plasma membranes of infected cells, and one polypeptide (ICP 58) was highly enriched in the plasma membrane compared with whole cell extracts or purified frog virus 3.

Lipidomic study of intracellular Singapore grouper iridovirus

Singapore grouper iridoviruses (SGIV) infected grouper cells release few enveloped extracellular viruses by budding and many unenveloped intracellular viruses following cell lysis. The lipid composition and function of such unenveloped intracellular viruses remain unknown. Detergent treatment of the intracellular viruses triggered the loss of viral lipids, capsid proteins and infectivity. Enzymatic digestion of the viral lipids with phospholipases and sphingomyelinase retained the viral capsid proteins but reduced infectivity. Over 220 lipid species were identified and quantified from the viruses and its producer cells by electrospray ionization mass spectrometry. Ten caspid proteins that dissociated from the viruses following the detergent treatments were identified by MALDI-TOF/TOF-MS/MS. Five of them were demonstrated to be lipid-binding proteins. This is the first research detailing the lipidome and lipid–protein interactions of an unenveloped virus. The identified lipid species and lipid-binding proteins will facilitate further studies of the viral assembly, egress and entry.

Isolation of lymphocystis disease virus from sole, Solea senegalensis Kaup, and blackspot sea bream, Pagellus bogaraveo (Brunnich)

Two viruses were isolated from cultured sole, Solea senegalensis, and wild blackspot sea bream, Pagellus bogaraveo, and preliminarily characterized as lymphocystis disease viruses (LCDVs). Viral isolates were characterized by morphological, biochemical and biophysical properties. In addition, the susceptibility of four fish cell lines was also tested. LCDV isolates developed cytopathic effects on the SAF-1 cell line at 5 and 6 days post-infection and reached titres of 10(6) TCID50 mL(-1). The antigenic and structural protein analysis of the two new LCDV isolates showed identical profiles to that obtained for LCDV strain Leetown NFH (ATCC VR-342), used as a reference viral strain, and for an LCDV isolate collected from gilt-head sea bream, Sparus aurata, cultured in southern Spain. Molecular confirmation was performed by polymerase chain reaction. Specific primers for LCDV produced a 270-bp DNA fragment, the expected size for LCDV.

Sensitivity of Invertebrate iridescent virus 6 to organic solvents, detergents, enzymes and temperature treatment

The sensitivity of Invertebrate iridescent virus 6 (IIV-6) to a selection of organic solvents, detergents, enzymes and heat treatment was assayed in Spodoptera frugiperda (Sf9) cells and by injection of inoculum into larvae of Galleria mellonella. In several cases, the degree of sensitivity of the virus depended on the method of assay; cell culture assays indicated greater losses of activity than insect bioassay. IIV-6 was sensitive to chloroform but sensitivity to ether was only detected by cell culture assay. Sensitivity (defined as a reduction of at least 1 log activity) was detected following treatment by 1 and 0.1% SDS, 1% Triton-X100, 70% ethanol, 70% methanol, 1% sodium deoxycholate, pH 11.1 and 3.0. No sensitivity was detected to 1% Tween 80, 1 M MgCl2, 100 mM EDTA, lipase, phospholipase A2, proteinase K, or trypsin at the concentrations tested. Viral activity was reduced by approximately 4 logs following heating to 70 degrees C for 60 min or 80 degrees C for 30 min. The above observations highlight the need for studies on the role of the virus lipid component in the process of particle entry into cells, and may explain why vertebrate and invertebrate iridoviruses have been reported to differ in their sensitivity to organic solvents and enzymes.

Molecular anatomy of Chilo iridescent virus genome and the evolution of viral genes

Chilo iridescent virus (CIV) or Insect iridescent virus 6 (IIV-6) is the type species of the genus iridovirus, a member of the Iridoviridae family. CIV is highly pathogenic for a variety of insect larvae and this implicates a possible use as a biological insecticide. CIV progeny and assembly occur in the cytoplasm of the infected cell and accumulate in the fatbody of the infected insects. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure and the amino acid sequences of different viral gene products. The elucidation of the coding capacity and strategy of CIV was the first step towards understanding the underlying mechanisms of viral infection, replication and virus-host interaction. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The coding capacity of the CIV genome was determined by the analysis of the complete DNA nucleotide sequence consisting of 212,482 bp that represent 468 open reading frames encoding for polypeptides ranging from 40 to 2432 amino acid residues. The analysis of the coding capacity of the CIV genome revealed that 50% (234 ORFs) of all identified ORFs (468 ORFs) were non-overlapping. The identification of several putative viral gene products including a DNA ligase and a viral antibiotic peptide is a powerful tool for the investigation of the phylogenetic relatedness of this evolutionary and ecologically relevant eukaryotic virus.

Electron microscopic observations of a marine fish iridovirus isolated from brown-spotted grouper, Epinephelus tauvina

The morphogenesis and the ultrastructure of a marine fish iridovirus isolated from diseased grouper, Epinephelus tauvina were studied by electron microscopy. The virus was grown on a marine fish cell line (GP) at 25 degrees C. After appearance of advanced cytopathic effect (CPE), various morphogenetic stages of virus amplification, maturation and assembly were detected in the cytoplasm of virus-infected cells. The matured nucleocapsids were probably formed by insertion of electron-dense core material into a partly forming empty capsid just before completely sealed. The nucleocapsids were located at the assembly sites as pseudocrystalline arrays or scattered individually. In the late phase of infection, the nucleocapsids were enveloped and released by budding from the plasma membrane. The budding virus particles could directly enter neighbouring cells by endocytosis to start the next round infection. Ultrastructure of the grouper iridovirus was studied using the methods of enzymatic digestions and detergent degradations. The purified iridovirus particles showed a three-layered membrane including an external lipoprotein envelope, an inner periodic protein capsid and a lipid-containing membrane. The regular array of surface capsid subunits was observed after degradation with detergent.

Inactivation of frog virus 3 and channel catfish virus by esculentin-2P and ranatuerin-2P, two antimicrobial peptides isolated from frog skin

While it is clear that some amphibian populations have recently experienced precipitous declines, the causes of those die-offs are complex and likely involve multiple variables. One theory suggests that environmental factors may trigger events that result in depressed immune function and increased susceptibility to infectious disease. Here we examine one aspect of innate immunity in amphibians and show that esculentin-2P (E2P) and ranatuerin-2P (R2P), two antimicrobial peptides isolated from Rana pipiens, inactivate frog virus 3, a potentially pathogenic iridovirus infecting anurans, and channel catfish herpesvirus. In contrast to mammalian antimicrobial peptides, E2P and R2P act within minutes, at temperatures as low as 0 degrees C, to inhibit viral infectivity. Moreover, these compounds appear to inactivate the virus directly and do not act by inhibiting replication in infected cells. This is the first report linking amphibian antimicrobial peptides with protection from an amphibian viral pathogen and suggests that these compounds may play a role in maintaining amphibian health.

Fatty acid profiles of invertebrate iridescent viruses

Eight invertebrate iridescent viruses (IVs) from diverse host taxa were grown in a common lepidopteran host, Galleria mellonella. The lipid composition of purified virus was assessed by fatty acid methyl esterase (FAME) analysis using a gas-liquid chromatograph. IV fatty acid profiles were markedly different from those of the host tissues. The interrelationships among the IVs did not follow previous serological and genetic findings. We conclude that FAME analysis is not a useful technique for revealing phylogenetic relationships among these viruses.

Ultrastructure of lymphocystis disease virus (LDV) as compared to frog virus 3 (FV3) and chilo iridescent virus (CIV): effects of enzymatic digestions and detergent degradations

Ultrastructure of fish lymphocystis disease virus (LDV), the largest of all known icosahedral viruses, has been studied under electron microscopy using enzymatic digestions and detergent degradations. LDV structure appeared roughly the same as those of frog virus 3 (FV3) and chilo iridescent virus (CIV), two other well known viruses of the family Iridoviridae, although the great flexibility of its capsid as observed on negatively stained and shadow cast particles, and its three electron dense layers visualized in ultrathin sections, differed from observations made with the two other viruses. Specific degradation of the virions with enzymes or detergents revealed that the composition of the three iridoviruses was very much alike. In fact, their capsid was composed of two layers as observed in negative staining: an external one, which was removed following digestion with proteinase K, and an internal one which could be digested with phospholipase A2. Thus, the outermost layer is probably made of surface protein units, more or less tightly bound to each other, while the internal one would be a lipoprotein membrane. Consequently, these three iridoviruses appeared structurally related.

Infectivity of vesicles prepared from chilo iridescent virus inner membrane: evidence for recombination between associated DNA fragments

Treatment of CIV particles with octylglucoside at high ionic strength leads to the solubilization of the inner viral membrane. Incubation of permissive cells (Cf124 cells) with vesicles obtained after dialysis of the detergent shows that this fraction is infectious. This infectivity, which is very low, could only be detected after two serial passages on permissive cells. This phenomenon is, however, reproducible. Isopycnic centrifugation analysis shows that some DNA cosediments with the vesicles. Extraction and purification of this DNA confirm the presence of a large DNA fragment of about 50.10(6) Da. Digestion with restriction endonucleases demonstrated that this DNA did not correspond to a particular fragment but to a population of DNA fragments of homogeneous size arising from various regions of the viral genome. Purified viral DNA was not infectious, the presence of DNA in the vesicles could not account therefore for their infectivity. Experiments of non-genetic reactivation of purified CIV DNA by UV-irradiated virus suggest that one (or several) structural component(s) of CIV particles must be involved in the first stages of the viral replication cycle. In addition, transfection of cells with large overlapping DNA fragments could generate infectious particles when the cells were superinfected with UV-irradiated virus. It can be supposed that the vesicle suspensions, which probably contain the reactivating factor, are composed of a population of vesicles which are all different in their DNA content. Infectivity of such suspensions would be the consequence of a recombination between large overlapping DNA fragments.

Analysis of the structure of fish lymphocystis disease virions from skin tumours of pleuronectes

Virions of fish lymphocystis disease (FLDV) from tumour-carrying-fishes (flounder, dab, plaice and gurnard) collected in the North Sea were isolated directly from the tumours and purified by sucrose and subsequent caesium chloride gradient centrifugation. They were studied by electron microscopy using embedding methods, negative staining and using metal shadowing methods. Tumours of dermal connective fish tissue showed particles with hexagonal outlines. Occasionally, an "empty structure" was observed. Subunits of the virus membrane were identified after 3 per cent phosphotungstic acid (PTA) or 0.2 per cent Ruthenium red (RR) staining. FLDV measures 199-227 nm in diameter.

Polypeptides and structure of African swine fever virus

Extracellular and intracellular African swine fever virus (ASFV) was purified using a two-phase aqueous polymer system. Both the structure of the virus and the polypeptides present during the purification procedure were studied. After PEG/dextran phase separation and centrifugation through 20% (w/v) Ficoll, 79% of input infectivity was recovered as semi-purified virus. The density of the virus after equilibrium centrifugation in sucrose was 1.19 g/ml. The envelope of the virion consisting of a unit membrane was removed from the virion after centrifugation in sucrose. Removal of envelope was associated with the loss of a 230 kilodalton (kd) glycoprotein from the virion. Disruption of the viral surface structure resulted in a loss of infectivity. Eighteen of the most prominent of the 33 polypeptides of extracellular or cell free (CF) virus were those with molecular weights of 230, 195, 165, 155, 150, 125, 116, 97, 92, 73, 62, 58, 50, 45, 35, 33, 25 and 11 kd, while the fourteen most prominent polypeptides in intracellular or cell associated (CA) virus were 103, 97, 92, 84, 73, 62, 58, 54, 47, 45, 35, 33, 25 and 17 kd. The 45 kd polypeptide may be actin which copurifies with the virus. No major differences were found in the number or size of proteins among three isolates of ASFV. Electron micrographs of thin sections of ASFV show the capsid to consist of a distinct double layer of closely packed capsomeres enclosed on both sides with a semi-transparent layer. Cell associated virus measured from side-to-side 188 nm and vertex-to-vertex 212 nm. The capsid encloses an inner core composed of a dense nucleoid surrounded by a 40-48 nm layer of core protein.

The organization of frog virus 3 as revealed by freeze-etching

A variety of freeze-fracture techniques has been employed in this study with the aim of dissecting the frog virus 3 virion and obtaining further information about its architecture. The icosahedral capsid has a skew symmetry with a triangulation number of 133 or 147. The capsomers are closely packed with a center-to-center spacing of 72 A. The inner membrane contains transmembrane proteins which appear as intra-membranous particles on both fracture faces. Rod-like structures (about 100 A in diameter) are present in the virus interior suggesting that the DNA-protein complex is highly organized.

Ultrasonic absorption evidence for structural fluctuations in frog virus 3 and its subparticles

The structural fluctuations specific to self-assemblies of biological molecules have been investigated further with ultrasonic techniques by using frog virus 3 (FV3). We compared the ultrasonic properties of complete FV3 virions and of several subparticles that may be obtained from this DNA virus: (i) the central nucleoprotein core versus its component DNA and proteins in a dissociated state; (ii) the core versus the capsidless subparticle, consisting of the core surrounded by the lipid membrane; and (iii) the complete virus versus the capsidless subparticle. The ultrasonic absorption by the core particle was quite large compared with the absorption by other nucleoprotein assemblies, suggesting that the core contains some organized structure. Both the core and the complete virus absorbed ultrasound more than did the capsidless subparticle. The difference spectrum for the virion relative to the capsidless subparticle may represent a single relaxation and is analyzed, by using a recent model, in terms of volume fluctuations due to radial movements in the virion. These fluctuations are much smaller than can be detected in virus crystals with present-day x-ray techniques.

Lipid composition of an iridescent virus type 6 (CIV)

The Chilo Iridescent Virus (CIV) is a lipid-containing virus propagated in vitro in choristoneura fumiferana cell cultures. We have analysed the individual lipids of the viral membrane which appeared interesting in their relative amounts and mainly in the high proportion of phosphatidylinositol. This fraction represented about 27 per cent of the phospholipid extract. The lipid composition of the viral membrane was unchanged whether the virus was propagated in vivo in larvae or in vitro in invertebrate cell cultures and was clearly different from that of the hosts.