Lipid composition of Sindbis virus

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.

Structural mutants of dengue virus 2 transmembrane domains exhibit host-range phenotype

BACKGROUND

There are over 700 known arboviruses and at least 80 immunologically distinct types that cause disease in humans. Arboviruses are transmitted among vertebrates by biting insects, chiefly mosquitoes and ticks. These viruses are widely distributed throughout the world, depending on the presence of appropriate hosts (birds, horses, domestic animals, humans) and vectors. Mosquito-borne arboviruses present some of the most important examples of emerging and resurgent diseases of global significance.

METHODS

A strategy has been developed by which host-range mutants of Dengue virus can be constructed by generating deletions in the transmembrane domain (TMD) of the E glycoprotein. The host-range mutants produced and selected favored growth in the insect hosts. Mouse trials were conducted to determine if these mutants could initiate an immune response in an in vivo system.

RESULTS

The DV2 E protein TMD defined as amino acids 452SWTMKILIGVIITWIG467 was found to contain specific residues which were required for the production of this host-range phenotype. Deletion mutants were found to be stable in vitro for 4 sequential passages in both host cell lines. The host-range mutants elicited neutralizing antibody above that seen for wild-type virus in mice and warrant further testing in primates as potential vaccine candidates.

CONCLUSIONS

Novel host-range mutants of DV2 were created that have preferential growth in insect cells and impaired infectivity in mammalian cells. This method for creating live, attenuated viral mutants that generate safe and effective immunity may be applied to many other insect-borne viral diseases for which no current effective therapies exist.

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to the mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.

Lipids and membrane microdomains in HIV-1 replication

Several critical steps in the replication cycle of human immunodeficiency virus type 1 (HIV-1) - entry, assembly and budding - are complex processes that take place at the plasma membrane of the host cell. A growing body of data indicates that these early and late steps in HIV-1 replication take place in specialized plasma membrane microdomains, and that many of the viral and cellular components required for entry, assembly, and budding are concentrated in these microdomains. In particular, a number of studies have shown that cholesterol- and sphingolipid-enriched microdomains known as lipid rafts play important roles in multiple steps in the virus replication cycle. In this review, we provide an overview of what is currently known about the involvement of lipids and membrane microdomains in HIV-1 replication.

Lipid of white-spot syndrome virus originating from host-cell nuclei

The hypothesis that white-spot syndrome virus (WSSV) generates its envelope in the nucleoplasm is based on electron microscopy observations; however, as yet there is no direct evidence for this. In the present study, the lipids of WSSV and the nuclei of its host, the crayfish Procambarus clarkii, were extracted and the neutral lipid and phospholipid contents were analysed by high-performance liquid chromatography, thin-layer chromatography and gas chromatography/mass spectrometry. Phosphatidylcholine (PC) and phosphatidylethanolamine comprised 62.9 and 25.8 %, respectively, of WSSV phospholipids, whereas they comprised 58.5 and 30 %, respectively, of crayfish nuclei phospholipids. These two phospholipids were the dominant phospholipids, and amounts of other phospholipids were very low in the total WSSV and crayfish nuclei phospholipids. The data indicate that the phospholipid profile of WSSV and crayfish nuclei are similar, which is in agreement with the model that the lipids of WSSV are from the host-cell nuclei. However, the fatty acid chains of PC were different between the WSSV virions and crayfish nuclei, and the viral neutral lipid component was also found to be somewhat more complicated than that of the host nuclei. The number of species of cholesterol and hydrocarbon in virus neutral lipid was increased compared with that in host-cell nuclei neutral lipid. It is suggested that the differences between WSSV and its host are either due to selective sequestration of lipids or reflect the fact that the lipid metabolism of the host is changed by WSSV infection.

The role of lipid microdomains in virus biology

Many of the highly pathogenic viruses including influenza virus, HIV and others of world wide epidemiological importance are enveloped and possess a membrane around the nucleocapsid containing the viral genome. Viral membrane is required to protect the viral genome and provide important functions for attachment, morphogenesis and transmission. Viral membrane is essentially composed of lipids and proteins. While the proteins on the viral envelope are almost exclusively virally encoded, lipids, on the other hand, are all of host origin and recruited from host membrane. However, lipids on the viral membrane are not incorporated randomly and do not represent average lipid composition of the host membrane. Recent studies support that specific lipid microdomains such as lipid rafts play critical roles in many aspects of the virus infectious cycle including attachment, entry, uncoating, protein transport and sorting as well as viral morphogenesis and budding. Lipid microdomains aid in bringing and concentrating viral components to the budding site. Similarly, specific viral protein plays an important role in organizing lipid microdomains in and around the assembly and budding site of the virus. This review deals with the specific role of lipid microdomains in different aspects of the virus life cycle and the role of specific viral proteins in organizing the lipid microdomains.

Lipid composition and fluidity of the human immunodeficiency virus envelope and host cell plasma membranes

Previous studies have indicated that human immunodeficiency virus (HIV) is enclosed with a lipid envelope similar in composition to cell plasma membranes and to other viruses. Further, the fluidity, as measured by spin resonance spectroscopy, is low and the viral envelope is among the most highly ordered membranes analyzed. However, the relationship between viral envelope lipids and those of the host cell is not known. Here we demonstrate that the phospholipids within the envelopes of HIV-1RF and HIV-2-L are similar to each other but significantly different from their respective host cell surface membranes. Further, we demonstrate that the cholesterol-to-phospholipid molar ratio of the viral envelope is approximately 2.5 times that of the host cell surface membranes. Consistent with the elevated cholesterol-to-phospholipid molar ratio, the viral envelopes of HIV-1RF and HIV-2-L were shown to be 7.5% and 10.5% more ordered than the plasma membranes of their respective host cells. These data demonstrate that HIV-1 and HIV-2-L select specific lipid domains within the surface membrane of their host cells through which to emerge during viral maturation.

Interaction of polyunsaturated fatty acids with animal cells and enveloped viruses

Essential unsaturated fatty acids such as oleic, linoleic, or arachidonic were incorporated into the phospholipids of animal cells and induced in them a change in the fluidity of their membranes. Exposure of enveloped viruses such as arbo-, myxo-, paramyxo-, or herpesviruses to micromolar concentrations of these fatty acids (which are not toxic to animal cells) caused rapid loss of infectivity of these viruses. Naked viruses such as encephalomyocarditis virus, polio virus or simian virus 40 were not affected by incubation with linoleic acid. The loss of infectivity was attributed to a disruption of the lipoprotein envelope of these virions, as observed in an electron microscope.

Fatty acid composition of rubella virus and BHK21/13S infected cells

The rubella virus is composed of RNA (2.4 per cent dry weight of the virus), proteins (74.8 per cent), carbohydrates (4:2.5 per cent of which are present as aminosugars, 1.5 per cent as neutral sugars) and lipids (18.8 per cent). The analysis of fatty acids in rubella virus was done at the same time as the analysis of control cells and infected cells. In the virus, the main fatty acids are: palmitic (26 per cent), stearic (15 per cent), oleic (15 per cent). Rubella virus differs from other togaviruses by the presence of fatty acids with odd-numbers of atoms of C (C15, C17, C19) which represent 23 per cent of total acids and of an hydroxyacid. In the cells, the acids oleic, palmitic, stearic and linoleic represent 90 per cent of total fatty acids. The infection of the BHK21/13S cells by rubella virus leads essentially to an increase (35 per cent) of the amount of linoleic acid with a decrease of palmitic and oleic acids.

Base composition of rubella virus RNA. Brief report

The base composition of 32P-labelled RNA of rubella virus was shown to be; Gp:31.1, Ap:21.9, Cp:34.3 and Up:12.8 per 100 nucleotides. The result demonstrates that the virus is distinct from other members of family Togaviridae in that it possesses RNA with relatively high contents of Gp and Cp, and low content of Up. Viral RNA adsorbed to oligo (dT)-cellulose column was shown to be infectious, whereas no infectivity of RNA appearing in the void volume was found. This may indicate that viral RNA needs to carry a minimal length of poly(A) to be infectious.

Mutants of Sindbis virus. III. Host polypeptides present in purified HR and ts103 virus particles

The amounts of host-encoded protein present in purified Sindbis virions of both the HR strain and of a mutant (ts103) which makes multicored particles were examined. Cells were labeled with [35S]methionine before infection and with [3H]methionine postinfection. Virions were purified by velocity sedimentation and isopycnic banding, and their polypeptides were examined by polyacrylamide gels in a sodium dodecyl sulfate-containing discontinuous buffer system. Host prelabeled material was found principally in a small number of discrete polypeptides in HR virions, which contained as little as 0.2% host-encoded protein. Virus-sized particles of mutant ts103 contained significantly more host material, and multiploid particles from ts103 infection contained up to 12% host prelabeled protein.

Susceptibility of chick neural retina to viral multiplication in vitro during embryonic development

Decrease in the susceptibility of embryonic chick neural retina cultures to the multiplication of various viruses was observed with increasing age of the embryo. In contrast the retinal cells supported the multiplication of Sindbis virus irrespective of the age when they were infected with the viral RNA. These results suggest that the restricted multiplication of the viruses observed is due to the modulated inability of the cell to process the adsorbed viruses for subsequent replication.

Purification and composition of the proteins from Sindbis virus grown in chick and BHK cells

Procedures are described for the purification of the Sindbis virus structural proteins. The amino acid and carbohydrate compositions of the purified proteins are presented for virus grown in BHK-21/13 and chicken embryo cells. Glycoprotein E1 from virus grown in BHK cells is deficient in a mannose-rich glycopeptide found on that glycoprotein when virus is grown in chicken embryo cells. The complex glactose-containing glycopeptides appear similar for virus grown in both hosts. However, when virus is grown in BHK cells, both glycoproteins are enriched in those glycopeptides containing more sialic acid. Since the two viral glycoproteins are difficult to separate cleanly during purification, it is suggested that there may be strong, but noncovalent, interactions between glycoproteins E1 and E2. It is also suggested that there may be an interaction between glycoprotein E2 and a component of the nucleocapsid.

Phospholipids of Semliki Forest virus grown in cultured mosquito cells

The phospholipids of Semliki Forest virus grown in mosquito cells (Aedes albopictus) were analyzed radiochemically. The ratio of 32P-labeled phospholipids to total 32P-label in the virus grown in mosquito cells equilibrated with radiophosphorus was 0.558 +/- 0.021. This value was similar to the lipid phosphorus: total phosphorus ratio (0.539 +/- 0.025) of the virus grown in the BHK cells. It is concluded that an average virion of the two types of Semliki Forest virus contains approximately the same number of phospholipid molecules. Phosphatidylethanolamine (62%), phosphatidylcholine (14%), phosphatidylserine (10%) and the ethanolamine analogue of sphingomyelin, ceramide phosphoethanolamine (9%) were the principal phospholipids in the mosquito cell-grown virus. Comparison with the lipids of virus grown in hamster cells (BHK cells) revealed that two-thirds of the polar structures were dissimilar. Surface labeling with formylmethionyl [35S] sulfone methylphosphate suggests that a relatively large fraction of ceramide phosphoethanolamine is located in the outer half of the lipid bilayer of the viral membrane.

Phospholipid and cholesterol composition of rubella virus and its host cell BHK 21 grown in suspension cultures

Analysis of total lipid, phospholipid and cholesterol distribution has been conducted in parallel on BHK 21/13S cells grown in suspension cultures, on purified Rubella virus and on cells infected by the virus. Extracellular virus was purified by use of a previously described procedure (3,4). A higher content of lipid and phospholipid was found in infected cells (versus control cells) which were characterized by the presence of an unidentified nonphosphorylated lipid fraction that was detected neither in the control cells nor in the purified virus. The level and the nature of phospholipids and cholesterol of BHK 21/13S cells (infected or not) were compared to those of various clones of BHK 21cells. The same phospholipids were detected in the virus and in the cells but phosphatidyl choline level was much higher than in the control cells and lower than in the infected cells, while phosphatidyl ethanolamine content was lower than in the cells (infected or not). The presence of cardiolipin (4.4 per cent), the amount of sphingomyelin (6.9 per cent) and the molar ratio of cholesterol to phospholipids (0.26) in varions seem to favor a rubella virus maturation site in the cells.

Sindbis virus glycoproteins: effect of the host cell on the oligosaccharides

Sindbis virus was grown in four different host cells and the carbohydrate portions of the glycoproteins were analyzed. Sindbis virus grown in BHK-21 cells has more sialic acid and galactose than Sindbis virus grown in chicken embryo cells. In other respects the carbohydrates from virus grown in these two hosts are very similar. Sindbis virus grown either in chick cells transformed by Rous sarcoma virus or in BHK cells transformed by polyoma virus was also examined. In comparisons of virus from normal and transformed cells, differences in the amount of sialic acid were observed; but otherwise the carbohydrate structures appeared basically similar. The growth conditions used for the host cell also affected the degree of completion of the carbohydrate chains of the viral glycoproteins.

Adaptation of BHK-21 cells to growth in shaker culture and subsequent challenge by Japanese encephalitis virus

Baby hamster kidney (BHK-21) cells were adapted to grow in shaker culture using Waymouth medium 752/1 containing 20 mM N-2-hydroxyethyl-piperazine-N'-2'-ethanesulfonic acid buffer and supplemented with 2.5% (vol/vol) calf serum, 0.002% (wt/vol) sodium oleate, and 0.2% fatty acid-free bovine serum albumin (WO2.5). Infectivity of Japanese encephalitis virus grown in the cells adapted to WO2.5 approached 2 x 10(8) plaque-forming units per ml. The culture volume of infected cells was reduced fivefold 12 h after infection. This step resulted in a 10-fold increase in infectivity over that obtained from infected cultures not subjected to volume reduction.

Paramagnetic spin label interactions with the envelope of a group A arbovirus. Lipid organization

Electron paramagnetic resonance observations were made on nitroxide spin- labeled molecules which were bound to the TC-83 vaccine strain of Venezuelan equine-encephalomyelitis virus. Paramagnetic resonance parameters derived from the observations and their dependence on sample temperature were similar but not identical to those which have been reported for these labels dissolved in lipid bilayer membranes of mammalian and bacterial origin. The data has a mechanical rigidity substantially greater than that of bilayers in cellular membranes. A model is presented which assumes the location of the lipid bilayer outside the nucleoprotein capsid and inside a spherical layer of envelope proteins. The model is in accord with Harrison's X-ray diffraction results for Sindbis virus. The model is discussed in terms of its implications with respects to the role played by lipid in viral maturation and infectivity.

Phospholipids in Newcastle Disease Virus infected cells

Infection of chicken cells with Newcastle Disease Virus modifies phosphatidylserine and phosphatidylcholine synthesis in the host cell. The virion contains cellular phospholipids synthesized both before and after infection. Relative concentration of various labeled phospholipids in the virus differ from those in the corresponding cells and their surface membranes. Late in infection, fragments of membranes with a distribution of labeled phospholipids similar but not identical to that of the virus can be found in the supernatant of infected cells. The significance of these findings is discussed in relation to the origin of viral phospholipids and the intervention of the host cell membrane in the assembly of the viral envelope.

Glycoproteins of Sindbis virus: priliminary characterization of the oligosaccharides

The carbohydrate content of Sindbis virus was determined by gas chromatographic analysis. The two viral glycoproteins were found to be approximately 8% carbohydrate by weight. Mannose is the sugar present in the largest amount. Smaller amounts of glucosamine, galactose, sialic acid, and fucose were also detected. Each of the two viral glycoproteins appears to contain two structurally unrelated oligosaccharides. Two of the three Sindbis-specific glycoproteins found in infected chick cells were shown to contain short, unfinished oligosaccharides.

Formation of Sindbis virus capsid protein in mammalian cell-free extracts programmed with viral messenger RNA

Extracts from Krebs II ascites cells and rabbit reticulocytes effectively synthesize viral proteins with Sindbis viral mRNA isolated from Sindbis-infected BHK cells. The major product is identical to Sindbis capsid protein on the basis of its electrophoretic mobility in sodium dodecyl sulfate-acrylamide gels and two-dimensional tryptic-peptide fingerprints. Various amounts of several additional discrete polypeptides are formed, depending on the components of the cell-free extracts. One of these polypeptides may be a prematurely terminated part of the viral-capsid protein, while another is larger in molecular weight than capsid protein but contains the capsid tryptic peptides. Several of the proteins formed in vitro also are detected in extracts of Sindbis-infected BHK cells labeled with [(35)S]methionine. The three proteins found in Sindbis virions are postulated to originate by proteolytic cleavage from a larger molecular weight polypeptide precursor that is translated from a polycistronic mRNA presumed to contain a single site for initiation of protein synthesis. The two in vitro systems appear to translate this polycistronic viral mRNA to yield specific viral capsid although no evidence was found for post-translational proteolysis. Other mechanisms for production of the capsid protein in the cell-free extracts are considered, and some of these may function in the viral-infected cell where unusually large amounts of viral capsid proteins are frequently detected.

Membrane proteins of uninfected and Rous sarcoma virus- transformed avian cells

A method for preparing large membrane fragments and cell ghosts was developed for uninfected and Rous sarcoma virus-transformed chicken embryo fibroblasts in culture. Membrane proteins were analyzed by electrophoresis in acrylamide gels containing sodium dodecyl sulfate. A major amino-acid-containing component of uninfected cell membranes was greatly diminished in amount or absent in membranes of virus-transformed cells. This component, called MP-1, had an electrophoretic mobility in sodium dodecyl sulfate-containing gels similar to that of a protein of a mol wt of 1.42 x 10(5). MP-1 was not altered by changes in cell growth rate or in cells infected with the nontransforming virus RAV-1.

Enzymatic iodination of Sindbis virus proteins

Sindbis virus was iodinated by using the enzyme lactoperoxidase, an iodination technique which labels only surface proteins. By this technique, the two viral glycoproteins are labeled, and the internal viral protein is not. The two glycoproteins are iodinated to strikingly different extents. This difference in susceptibility to iodination apparently is due to the position or conformation of the glycoproteins in the envelope spikes of the virion and not to differing contents of tyrosine, the amino acid substrate of lactoperoxidase. Both viral glycoproteins are iodinated by lactoperoxidase on the surface of Sindbis-infected chicken cells. Here, as in the virion, the glycoproteins are iodinated unequally, with the smaller glycoprotein again being preferentially iodinated. Another virus-specific protein found in large amounts in infected cells, and from which the preferentially iodinated virion glycoprotein is produced by a proteolytic cleavage, is not iodinated by lactoperoxidase. Thus it appears that the viral glycoproteins are present on the cell surface and that the precursor protein is not.

Thermal inactivation of Newcastle disease virus. I. Coupled inactivation rates of hemagglutinating and neuraminidase activities

The thermal stability of Newcastle disease virus has been characterized in terms of the rate constants for inactivation of hemagglutinating activity (HA), neuraminidase activity (NA), and infectivity. Inactivation of HA results in the concomitant loss of NA. Infectivity, however, is much more thermolabile. Disintegration of the virus particle is not responsible for the identical rate constants for inactivation of HA and NA, nor is their parallel inactivation uncoupled in envelope fragments produced by pretreating the virus with phospholipase-C. The data indicate that a common envelope factor(s) can influence the thermal stability of both activities.

Lipids in Viruses

This chapter discusses lipids in viruses. Lipid forms an integral part of many viruses and exists either in the form of a continuous envelope or in lipoprotein complexes that surround a nucleoprotein core or helix. In general, the envelope can be described as a molecular container for the genetic material of the virus. Viruses are obligate intracellular parasites and are not known to carry genetic coding for enzymes involved in lipid synthesis. Hence, they generally contain the same classes of lipid as are found in the host cell or their membrane of assembly. Lipids make up 20–35% by weight of most viruses; however, there are exceptions such as vaccinia virus, which has only 5% lipid despite having a complex multimembrane envelope structure. Naked herpesvirus capsids closely resemble non-lipid-containing viruses such as adenovirus or polyoma virus, which are also assembled in the nucleus but show full infectivity without any envelope. Both naked and enveloped herpesvirus particles are found in infected cells; however, only enveloped particles are found in extracellular fluids.

Fatty chains of different lipid classes of Semliki forest virus and host cell membranes

Semliki Forest virus was grown in BHK-21 cells. The major classes of phospho-and glycolipids of the virus were analyzed for the compositions of fatty acids, aldehydes, and sphingosine bases, and the major glycerophospholipids were analyzed for the relative proportions of alkenyl-acyl, alkyl-acyl, and diacyl forms. All viral lipid classes proved to be mixtures of several molecular species. Each class contained a characteristic mixture of fatty chains, which was different in all other classes. All viral lipid classes resembled their counterparts of the host plasma membrane and also those of the endoplasmic reticulum. The gangliosides of the virus and the plasma membrane proved to be similar even at the level of individual molecular species. The number of certain lipid molecules in an average virion was less than the number of the protein molecules.