Properties of Semliki forest virus nucleocapsid. II. An irreversible contraction by acid pH

The regulation of disassembly of alphavirus cores

Alphaviruses are used as model viruses for structure determination and for analysis of virus entry. They are used also as vectors for protein expression and gene therapy. Virus particles are assembled by budding, using preformed cores and a modified cellular membrane. During entry, alphaviruses release the viral core into the cytoplasm. Cores are disassembled during virus entry and accumulate in the cytoplasm during virus multiplication. The regulation of core disassembly is the subject of this review. A working model compatible with all experimental data is formulated. This model comprises the following steps: (1) The incoming core is present in the cytoplasm in a metastable state, primed for disassembly. A core structure containing the so-called linker region of the core protein in an exposed position susceptible to proteolytic cleavage on the core surface might represent the primed state. (2) The primed core allows access of cellular proteins to the viral genome RNA, e.g. initiation factors of protein synthesis. (3) In a following step, ribosomal 60S subunits bind to the complex and lead to core disassembly with a concomitant transfer of core protein or of core protein fragments to the 28S rRNA. The linker region may be involved in this transfer. (4) During the later stages of virus multiplication, cellular components involved in step (2) and/or in step (3) are inactivated. This inactivation might involve the binding of newly synthesised core protein to 28S rRNA. (5) Unprimed cores, e.g. core particles containing the linker region in an unexposed position, are assembled during virus multiplication. Priming of cores and inactivation of host-cell factors each represent a complete mechanism of regulation of core disassembly. Future experiments will show whether or not both processes are actually used. Since alphaviruses, e.g. Chikungunya virus, Ross River virus, Semliki Forest virus, and Sindbis virus, are human pathogens, these experiments are of practical relevance, since they might identify targets for antiviral chemotherapy.

In vitro analysis of factors involved in the disassembly of Sindbis virus cores by 60S ribosomal subunits identifies a possible role of low pH

Disassembly of alphavirus cores early in infection involves interaction of the core with 60S ribosomal subunits. This interaction might be subjected to regulatory processes. We have established an in vitro system of core disassembly in order to identify cellular proteins involved in the regulation of disassembly. No evidence for the existence of such proteins was found, but it became apparent that certain organic solvents and detergents or a high proton concentration (pH 6.0) stimulated core disassembly. Alphaviruses infect cells by an endosomal pathway. The low pH in the endosome activates a fusion activity of the viral surface protein E1 and leads to fusion of the viral membrane with the endosomal membrane, followed by release of the core into the cytoplasm. Since the presence of the E1 protein in the plasma membrane of infected cells leads to increased membrane permeability at low pH, our findings indicate that disassembly of alphavirus cores could be regulated by the proton concentration. We propose that the viral membrane proteins present in the endosomal membrane after fusion form a pore, which allows the flow of protons from the endosome into the cytoplasm. This process would generate a region of low pH in the cytoplasm at the correct time and place to allow the efficient disassembly of the incoming viral core by 60S subunits.

Identification of the pore forming element of Semliki Forest virus spikes

Pore formation at mildly acidic pH by SFV spike proteins was investigated using isolated and modified virions. Modification of the virions was performed by limited proteolysis in presence of octylglucoside and resulted in the formation of E1 particles and spikeless particles, respectively. Pore formation was detected by measuring the influx of propidium iodide into the viral particles. The results obtained clearly showed that the presence of E1 alone is sufficient to promote pore formation at mildly acidic pH. Thus E1 represents the pore forming element of the viral spike proteins.

The alphaviruses: gene expression, replication, and evolution

The alphaviruses are a genus of 26 enveloped viruses that cause disease in humans and domestic animals. Mosquitoes or other hematophagous arthropods serve as vectors for these viruses. The complete sequences of the +/- 11.7-kb plus-strand RNA genomes of eight alphaviruses have been determined, and partial sequences are known for several others; this has made possible evolutionary comparisons between different alphaviruses as well as comparisons of this group of viruses with other animal and plant viruses. Full-length cDNA clones from which infectious RNA can be recovered have been constructed for four alphaviruses; these clones have facilitated many molecular genetic studies as well as the development of these viruses as expression vectors. From these and studies involving biochemical approaches, many details of the replication cycle of the alphaviruses are known. The interactions of the viruses with host cells and host organisms have been exclusively studied, and the molecular basis of virulence and recovery from viral infection have been addressed in a large number of recent papers. The structure of the viruses has been determined to about 2.5 nm, making them the best-characterized enveloped virus to date. Because of the wealth of data that has appeared, these viruses represent a well-characterized system that tell us much about the evolution of RNA viruses, their replication, and their interactions with their hosts. This review summarizes our current knowledge of this group of viruses.

Entry and uncoating of enveloped viruses

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Semliki Forest virus core protein fragmentation: its possible role in nucleocapsid disassembly

Semliki Forest virus (SFV) envelope proteins function as proton pores under mildly acidic conditions and translocate protons across the viral membrane [Schlegel, A., Omar, A., Jentsch, P., Morell, A. and Kemp, F. C. (1991) Biosci. Rep. 11, 243-255]. As a consequence, during uptake of SFV by cells via receptor-mediated endocytosis the nucleocapsid is supposed to be exposed to protons. In this paper the effects of mildly acidic pH on SFV nucleocapsids were examined. A partial proteolytic fragmentation of core proteins was observed when nucleocapsids were exposed to mildly acidic pH. A similar proteolytic event was detected when intact SFV virions were exposed to identical conditions. Protease protection assays with exogenous bromelain provided evidence that the capsid protein degradation was due to an endogenous proteolytic activity and not to a proteolytic contamination. Detergent solubilization of virus particles containing degraded nucleocapsids followed by sucrose gradient centrifugation led to a separation of capsid protein fragments and remaining nucleocapsids. These data are discussed in terms of a putative biological significance, namely that the core protein fragmentation may play a role in nucleocapsid disassembly.

Semliki Forest virus envelope proteins function as proton channels

It has been shown that isolated nucleocapsids of Semliki Forest virus (SFV) contract upon low pH exposure (Soederlund et al., 1972). This contraction of the nucleocapsids has been used as an indicator to demonstrate that the spike proteins of SFV can translocate protons into the interior of the virus particle upon low pH (5.8) exposure. Spikeless virus particles obtained after bromelain digestion, which were used as a control, did not translocate protons. This implies that the ectodomain of the spike plays a crucial role for the proton translocation.

The T=4 envelope of Sindbis virus is organized by interactions with a complementary T=3 capsid

The three-dimensional structure of Sindbis virus, an enveloped animal virus, has been determined to a resolution of 35 A by using a common lines procedure to combine cryoelectron micrographs of vitrified particles. The spikes of the virus appear as columnar trimers arranged on a T=4 lattice. The lipid bilayer of the virus envelope is polyhedral and surrounds a smooth T=3 nucleocapsid. Hence, a complete Sindbis virion (molecular weight 46.4 X 10(6)) contains 240 copies of each of the spike proteins and 180 copies of the capsid protein. The arrangement of the spike proteins is complementary to that of the nucleocapsid. Two types of spike-capsid interactions are seen. Spike trimers near the fivefold axes interact tightly with triplets of capsid elements, whereas those on the threefold axes interact more loosely.

Semliki Forest virus: a probe for membrane traffic in the animal cell

The traffic among the cellular compartments is thought to be mediated by membrane vesicles, which bud from one compartment and fuse with the next. Despite the continuous exchange of membrane components among them, the organelles maintain their characteristic protein and lipid compositions such that the traffic remains selective, thus, avoiding intermixing of components. This membrane traffic recycles components from the cell surface to the interior of the cell and back to the cell surface again. The membrane traffic between the ER and the cell surface involves a major sorting problem. Little is known of how the animal cell has solved this problem in molecular terms. One experimental tool in this direction is provided by some enveloped animal viruses, which mature at the cell surface of infected cells. Such viruses include influenza virus, Semliki Forest virus (SFV), Sindbis virus, and vesicular stomatitis virus (VSV). They are extremely simple in makeup and hence are very well characterized. The purpose of this article is to illustrate the use of the enveloped viruses as tools in the study of membrane traffic in the animal cell. This is done in the context of the life cycle of the virus in the host cell. The article will be concerned mainly with Semliki Forest virus (SFV), which is the virus that has been worked upon in the chapter. SFV belongs to the alphaviruses, a genus of the togavirus family.

The capsid protein of Semliki Forest virus has clusters of basic amino acids and prolines in its amino-terminal region

The amino acid sequence of the capsid (C) protein was deduced from the nucleotide sequence of the C gene. This part of the viral 42S RNA genome was transcribed into double-stranded cDNA. The cDNA was cloned in the Escherichia coli chi 1776-pBR322 host-vector system and then the base sequence was determined with the technique described by Maxam and Gilbert. The amino acid sequence of the C protein shows a clustering of basic amino acids and prolines within the first 110 amino acids.

Analysis of Semliki-Forest-virus structural proteins to illustrate polyprotein processing of alpha viruses

The four structural proteins of Semliki Forest virus were purified in an amount of 30-50 nmol by preparative sodium dodecylsulfate/polyacrylamide gel electrophoresis. Each protein was subjected to N-terminal structural analysis by degradation in a liquid-phase sequencer. About 20 residues were determined for each of the two membrane glycoproteins E1 and E2. The amino acid sequence of E1 but not that of E2 showed extensive homology to the corresponding proteins of the closely related Sindbis virus. Both E1 and E2 seem to lack a signal sequence at the N terminus, since the proportion of polar amino acids in this region deviates from the proportion in the known hydrophobic signal sequences. The envelope glycoprotein E3 and the capsid protein did not yield any significant result on Edman degradation, suggesting that they have blocked N-terminal amino groups.

Core tetrasaccharide liberated by endo-beta-D-N-acetylglucosaminidase D from lactosamine-type oligosaccharides of Semliki Forest virus membrane proteins

[3H]Mannose- and [3H]glucosamine-labeled lactosamine-type glycopeptides of Semliki Forest virus membrane proteins were stripped of their fucose, sialic acid, galactose and distal N-acetylglucosamine residues and subsequently digested with endo-beta-D-N-acetylglucosaminidase D from Diplococcus pneumoniae. Two products were obtained, a neutral tetrasaccharide and a residual glycopeptide fraction. The tetrasaccharide appeared to consist of two alpha-mannose residues, one beta-mannose residue and one N-acetylglucosamine residue located at the reducing terminus of the molecule. Results of Smith degradation, beta-elimination and acetolysis were compatible with four structures; (1) Man alpha-1-3[Man alpha 1-6]Man beta 1-4GlcNAc; (2) Man alpha 1-3Man beta 1-4[Man alpha 1-6] GlcNAc; (3) Man alpha 1-3Man alpha 1-4[Man beta 1-6]GlcNAc, or (4) Man alpha 1-6Man alpha 1-3Man beta-1-4GlcNAc. The reactivity of the viral glycopeptides with endo-beta-D-N-acetylglucosaminidase D and the chromatographic properties of the liberated core tetrasaccharide suggest that its most likely structure was Man alpha 1-3[Man alpha-1-6]Man beta 1-4GlcNAc. The core tetrasaccharide of glycans of membrane protein E3, one of the viral membrane proteins obtained from infected cell, was similar to that of the virion glycans.

Separation of the integral membrane glycoproteins E1 and E2 of Semliki Forest virus by affinity chromatography on concanavalin A-Sepharose

The membrane glycoproteins E1 and E2 of Semliki Forest virus are of about equal size but can be separated from each other by affinity chromatography on a concanavalin A-Sepharose column in the presence of sodium dodecyl sulfate. The E1 protein eluted like glycopeptides containing two peripheral sugar branches composed of N-acetylglucosamine, mannose, galactose and sialic acid. The E2 eluted like glycopeptides containing only N-acetylglucosamine and mannose.

Reconstitution of Semliki forest virus membrane

The spike glycoproteins of the Semliki forest virus membrane have been incorporated into vesicular phospholipid bilayers by a detergent-dialysis method. The detergent used was beta-D-octylglucoside which is nonionic and has an exceptionally high critical micellar concentration which facilitates rapid removal by dialysis. The vesicles obtained were of varying sizes and had spikes on their surface. Two classes of vesicles were preferentially formed, small protein-rich and large lipid-rich (average lipid to protein weight ratios, 0.22 and 3.5, respectively). Both classes of vesicles retained the hemagglutinating activity of the virus. The proteins were attached to the lipid bilayer by hydrophobic peptide segments, as in the viral membrane. Most of the proteins were accessible to proteolytic digestion from the outside, suggesting an asymmetric orientation.

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.

Simultaneous translation of structural and nonstructural proteins from Semliki-forest-virus RNA in two eukaryotic systems in vitro

The Semliki Forest virus genome, 42-S RNA, and the virus-specific intracellular 26-S RNA were translated in two cell-free protein-synthesising systems, the wheat germ extract, and a partially purified system from mammalian tissues. The 26-S RNA directed the synthesis of structual proteins only, as revealed by tryptic peptide mapping. About 75--80% of the radioactivity in the products comigrated with capsid and about 4--8% with envelope protein peptides. All the capsid peptides and the full-sized capsid protein were found in the products in vitro, no complete envelope protein was formed and fewer than half of the envelope peptides were detected. This result is consistent with reports that there is only one initiation site for the translation of virus structural proteins, and that the capsid protein is N-terminal in the polyprotein followed by envelope proteins. The systems programmed with 42-S RNA yielded virtually the same structural peptides. However, the bulk of the radioactivity was in peptides which did not comigrate with the structural ones. These peptides were mostly associated with relatively small-sized products. This shows that Semliki Forest virus 42-S RNA has at least two initiation sites, one for the structural proteins and the other(s) for the nonstructural proteins.

Protein-bound oligosaccharides of Semliki Forest virus

Semliki Forest virus was grown in BHK cells and labeled in vivo with radioactive monosaccharides. Pronase digests of the virus chromatographed on Bio-Gel P6 revealed glycopeptides of A-type and B-type. (For the nomenclature see Johnson, J. and Clamp, J.R. (1971) Biochem. J. 123, 739-745.) The former was labeled with [3H]fucose, [3H]galactose, [3H]mannose and [14C]glucosamine, the latter only with [3H]mannose and [14C]glucosamine. The three envelope glycoproteins E1, E2 and E3 were isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subjected to pronase digestion. The glycoproteins E1 and E3 revealed glycopeptides of A-type. E2 revealed glycopeptides of B-type. E2 yielded additionally a glycopeptide (Mr3100) which was heavily labeled from [3H]galactose, but only marginally from [14C]glucosamine, [3H]fucose and [3H]mannose. Whether this glycopeptide belongs to the A-type or not remains uncertain. The apparent molecular weights of the A-type units measured by gel filtration were 3400 in E1 and 4000 in E3; the B-type unit of E2 had an apparent molecular weight of 2000. Combined with the findings of our earlier chemical analysis these data suggest that E1 and E3 contain on the average one A-type unit; E2 probably contains one 3100 dalton unit plus one or two B-type units.

Quantitation of Semlike Forest virus RNAs in infected cells using 32-P equilibrium labelling

In vitro cultured BHK and HeLa cells were labelled for several cell division cycles with 32-P-phosphate until they were equilibrated with radiophosphorus. After infection with Semliki forest virus (or mock-infection) these cells were analyzed for viral and ribosomal RNA by sucrose gradient centrifugation. From their radioactivities the mass of each RNA species was calculated. It was found that the BHK and HeLa cells contained on average 11.0 plus or minus 3.1 pg and 6.3 plus or minus 1.9 pg of ribosomal RNA (28 S + 18 S) respectively per cell. At the end of the viral growth cycle, i.e. at 8 h post infection the average mass of viral genome produced per cell was 1.0 -1.9 pg and 0.3 - 0.5 pg in BHK and HeLa cells respectively, of which only 1/10 to 1/20 was released as mature virus particles. The amount of the second major virus specific messenger, the 26 S RNA, was estimated from its ratio to the viral genome after labelling with 3-H-uridine in the presence of actinomycin D. These two viral RNAs were found to be present in roughly equimolar amounts.