Rapid concentration and purification of polyoma virus and SV40 with polyethylene glycol

Extracellular Vesicles: A Novel Mode of Viral Propagation Exploited by Enveloped and Non-Enveloped Viruses

Extracellular vesicles (EVs) are small membrane-enclosed structures that have gained much attention from researchers across varying scientific fields in the past few decades. Cells secrete diverse types of EVs into the extracellular milieu which include exosomes, microvesicles, and apoptotic bodies. These EVs play a crucial role in facilitating intracellular communication via the transport of proteins, lipids, DNA, rRNA, and miRNAs. It is well known that a number of viruses hijack several cellular pathways involved in EV biogenesis to aid in their replication, assembly, and egress. On the other hand, EVs can also trigger host antiviral immune responses by carrying immunomodulatory molecules and viral antigens on their surface. Owing to this intricate relationship between EVs and viruses, intriguing studies have identified various EV-mediated viral infections and interrogated how EVs can alter overall viral spread and longevity. This review provides a comprehensive overview on the EV-virus relationship, and details various modes of EV-mediated viral spread in the context of clinically relevant enveloped and non-enveloped viruses.

Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast

Metabolic pathways are commonly organized by sequestration into discrete cellular compartments. Compartments prevent unfavorable interactions with other pathways and provide local environments conducive to the activity of encapsulated enzymes. Such compartments are also useful synthetic biology tools for examining enzyme/pathway behavior and for metabolic engineering. Here, we expand the intracellular compartmentalization toolbox for budding yeast (Saccharomyces cerevisiae) with Murine polyomavirus virus-like particles (MPyV VLPs). The MPyV system has two components: VP1 which self-assembles into the compartment shell and a short anchor, VP2C, which mediates cargo protein encapsulation via binding to the inner surface of the VP1 shell. Destabilized green fluorescent protein (GFP) fused to VP2C was specifically sorted into VLPs and thereby protected from host-mediated degradation. An engineered VP1 variant displayed improved cargo capture properties and differential subcellular localization compared to wild-type VP1. To demonstrate their ability to function as a metabolic compartment, MPyV VLPs were used to encapsulate myo-inositol oxygenase (MIOX), an unstable and rate-limiting enzyme in d-glucaric acid biosynthesis. Strains with encapsulated MIOX produced ∼20% more d-glucaric acid compared to controls expressing "free" MIOX─despite accumulating dramatically less expressed protein─and also grew to higher cell densities. This is the first demonstration in yeast of an artificial biocatalytic compartment that can participate in a metabolic pathway and establishes the MPyV platform as a promising synthetic biology tool for yeast engineering.

Modern Techniques for the Isolation of Extracellular Vesicles and Viruses

Extracellular signaling is pivotal to maintain organismal homeostasis. A quickly emerging field of interest within extracellular signaling is the study of extracellular vesicles (EV), which act as messaging vehicles for nucleic acids, proteins, metabolites, lipids, etc. from donor cells to recipient cells. This transfer of biologically active material within a vesicular body is similar to the infection of a cell through a virus particle, which transfers genetic material from one cell to another to preserve an infection state, and viruses are known to modulate EV. Although considerable heterogeneity exists within EV and viruses, this review focuses on those that are small (< 200 nm in diameter) and of relatively low density (< 1.3 g/mL). A multitude of isolation methods for EV and virus particles exist. In this review, we present an update on methods for their isolation, purification, and phenotypic characterization. We hope that the information we provide will be of use to basic science and clinical investigators, as well as biotechnologists in this emerging field. Graphical Abstract.

Assembly and Purification of Polyomavirus-Like Particles from Plants

Polyomaviruses are small DNA viruses that have a history of use in biotechnology. The capsids of a number of species have been developed into experimental prophylactic and therapeutic virus-like particle (VLP) vaccines. In order to explore plants as a host for the expression and purification of polyomavirus-like particles, we have transiently expressed the major capsid protein, VP1, in Nicotiana benthamiana leaves. Deletion of a polybasic motif from the N-terminal region of VP1 resulted in increased expression as well as reduced necrosis of leaf tissue, which was associated with differences in subcellular localisation and reduced DNA binding by the deletion variant (ΔVP1). Self-assembled VLPs were recovered from tissue expressing both wild-type VP1 and ΔVP1 by density gradient ultracentrifugation. VLPs composed of ΔVP1 were more homogenous than wtVPLs and, unlike the latter, did not encapsidate nucleic acid. Such homogenous, empty VLPs are of great interest in biotechnology and nanotechnology. In addition, we show that both MPyV VLP variants assembled in plants can be produced with encapsidated foreign protein. Thus, this study demonstrates the utility of plant-based expression of polyomavirus-like particles and the suitability of this host for further developments in polyomavirus-based technologies.

Polyethylene glycol precipitation for recovery of pathogenic viruses, including hepatitis A virus and human rotavirus, from oyster, water, and sediment samples

Polyethylene glycol 6000 precipitation was found to be an effective concentration method that enhanced the chances for detecting human virus pathogens in environmental samples. Percent recoveries from eluates of fresh and estuarine waters with 8% polyethylene glycol 6000 averaged 86 for hepatitis A virus, 77 for human rotavirus Wa, 87 for simian rotavirus SA11, and 68 for poliovirus. Percent recoveries of 97, 40, 97 and 105, respectively, for the same viruses were obtained from oyster eluates by the same procedure. Percent recoveries of 97 for hepatitis A virus and 78 for human rotavirus Wa were obtained from sediment eluates containing 2 M NaNO3 with a final concentration of 15% polyethylene glycol 6000. The polyethylene glycol method was shown to be more effective than the organic flocculation method for recovery of hepatitis A virus and rotaviruses Wa and SA11, but not of poliovirus 1 in laboratory studies. In field trials, hepatitis A virus or rotavirus or both were recovered from 12 of 18 eluates by polyethylene glycol, compared with recovery from 9 of 18 eluates by organic flocculation from fresh and estuarine waters subject to pollution.

Reconstruction of the three-dimensional structure of simian virus 40 and visualization of the chromatin core

The three-dimensional structure of the capsid and the nucleohistone core of simian virus 40 (SV40) has been reconstructed by image analysis of electron micrographs of frozen hydrated samples. The 72 prominent capsomere units that comprise the T = 7d icosahedral surface lattice of the capsid are clearly resolved. Both the pentavalent and hexavalent capsomeres appear with pentameric substructure, indicating that bonding specificity in the shell is not quasi-equivalent. There is a remarkable similarity between the structure of the SV40 virion capsid and the structure reported for the polyoma empty capsid. This result establishes that (i) the unexpected pentameric substructure of the hexavalent capsomeres is also present in virions and (ii) the arrangement of the 72 pentamers in the capsid lattice may be a characteristic feature of the entire papova family of viruses. The center of the SV40 reconstruction reveals electron density corresponding to the nucleohistone core. This density is smeared, suggesting that the minichromosome is not organized with icosahedral symmetry matching the capsid symmetry. The visualization of the virion chromatin provides a basis for invoking new models for the higher order structure of the encapsidated minichromosome.

Antipeptide antibodies directed against the carboxy-terminal region of SV40 structural proteins VP2 and VP3

Rabbits were immunized with a synthetic heptapeptide of the sequence Arg-Asn-Arg-Ser-Ser-Arg-Ser corresponding to the carboxy-terminal region of the SV40 viral proteins VP2 and VP3. The raised antibodies recognize the viral proteins in enzyme-linked immunosorbent (ELISA) and Western blot assay. Specificity of the antibodies were confirmed by competition experiments. The antibodies recognize VP2 and VP3 in infected cells by immunofluorescence and in subcellular fractions by ELISA. No interaction with virions was observed.

Tumor induction by simian virus 40 in mice is controlled by long-term persistence of the viral genome and the immune response of the host

Simian virus 40 (SV40), which transforms mouse cells in vitro, has not been previously observed to cause tumors when injected in immunocompetent mice. We have investigated both the fate of the injected virion in mice and several immunological parameters as potential factors controlling tumorigenicity. We find that although SV40 does not replicate in mouse cells, the viral DNA can persist for many months postinjection; the majority of the viral DNA is found in the cytoplasm, but a small amount of the viral DNA is integrated at multiple sites in the host nuclear DNA. The persistence of the viral genome is independent of the ability of the mouse to mount an SV40 TSTA specific cytotoxic T-cell response and may be attributed to the cytoplasmic location of the majority of the viral genome. However, in long-term studies of SV40-injected mice, genetically identical except for the major histocompatibility complex, we find that tumors were induced in some mice of the H-2d (low cytotoxic T-lymphocyte responder to SV40 TSTA) but not of the H-2k (high responder to SV40 TSTA) haplotype. Thus, a combination of inefficient disposal of the injected virion and inefficient immunological surveillance and elimination of cells containing nuclear SV40 DNA can eventually result in SV40-induced tumors at multiple sites in mice.

Pre-crisis mouse cells show strain-specific covariation in the amount of 54-kilodalton phosphoprotein and in susceptibility to transformation by simian virus 40

We have used several inbred mouse strains to examine the role of the 54-kilodalton (kDa) cellular phosphoprotein in transformation by the papovavirus simian virus 40. We have measured the endogenous 54-kDa phosphoprotein in cells obtained from these inbred mouse strains. To study the effect of passage, cell cultures were measured for amount of the 54-kDa phosphoprotein at the 2nd and 12th passages. In the absence of any transforming agent, the amount of endogenous 54-kDa phosphoprotein in early pre-crisis mouse cells varied in a strain-specific way. Transformation frequency varied coordinately with endogenous 54-kDa expression. Mouse strains whose cells produced a high level of endogenous 54-kDa phosphoprotein on passage did not further increase its expression after simian virus 40 transformation.

Concentration of human respiratory syncytial virus using ammonium sulfate, polyethylene glycol or hollow fiber ultrafiltration

Human respiratory syncytial virus was concentrated by polyethylene glycol or ammonium sulfate precipitation as well as by hollow ultrafiltration. Recoveries obtained were respectively 49.4%, 47.7%, and 75.2%; however, further analysis of these results by resuspension experiments showed that all the infectivity could be recovered from the different concentrates. The protein content of polyethylene glycol concentrates was much lower than those of ammonium sulfate or hollow fiber ultrafiltration. Electron microscopy revealed that the morphological integrity of virus particles was unaffected by the concentration methods used. Purified virus was obtained when polyethylene glycol concentrates were centrifuged through two successive density gradients.

Growth and purification of SV40 virus for biochemical studies

A detailed growth and purification scheme suitable for producing relatively large quantities of fully active, pure SV40 is presented together with data on recovery and purity at each step of the procedure. The scheme was designed to prevent the initial binding of virus to cell components as well as contamination of the extracted virus by cellular DNA.

Control of the Balb/c-3T3 cell cycle by nutrients and serum factors: analysis using platelet-derived growth factor and platelet-poor plasma

Much controversy regarding the relationship between nutrients and serum in regulation of cell growth can be reconciled by recognizing that serum contains multiple factors which regulate different events in the cell cycle. Serum was fractionated into a platelet-derived growth factor (PDGF), which induces cells to become competent to synthesize DNA, and plasma which allows competent cells to traverse G0/G1 and enter the S phase. Nutrients are not required for the cellular response to PDGF; however amino acids are required for plasma to promote the entry of PDGF-treated, competent cells into S phase. The nutrient independent, PDGF-modulated, growth regulatory event (competence) is located 12 hours prior to the G1/S phase boundary in quiescent, density-arrested Balb/c-3T3 cells. The nutrient dependent, plasma-modulated event is located six hours prior to the G1/S phase boundary and corresponds in concentration of amino acids required for DNA synthesis. Infection of density-arrested Balb/c3T3 cells with SV40 overrides both the nutrient independent and the nutrient dependent growth regulatory events.

Relationship of replication and transcription of Simian Virus 40 DNA

RNA produced by the Simian Virus 40 (SV40) mutant tsA30 during lytic infection of kidney cells of African green monkeys was examined by RNA-DNA competition-hybridization. This mutant is temperature-sensitive in a function (gene A) that regulates synthesis of viral DNA. No detectable difference between mutant RNA synthesized at the permissive temperature (33 degrees ) and wild-type viral RNA was found. During continuous infection with the mutant at the restrictive temperature (41 degrees ) only early viral RNA was produced. When mutant DNA and late RNA synthesis were initiated at the permissive temperature, a shift to the restrictive temperature rapidly terminated synthesis of viral DNA but not that of late viral RNA. The data indicate that the function of gene A is required before synthesis of late viral RNA and that after initiation, the production of late RNA continues without further expression of gene A or concomittant viral DNA synthesis.

Simian virus 40 deoxyribonucleic acid synthesis: analysis by gel electrophoresis

An agarose-gel electrophoresis technique has been developed to study simian virus 40 deoxyribonucleic acid (DNA) synthesis. Superhelical DNA I, relaxed DNA II, and replicative intermediate (RI) molecules were clearly resolved from one another for analytical purposes. Moreover, the RI molecules could be identified as early or late forms on the basis of their electrophoretic migration in relation to that of DNA II. The technique has been utilized to study the kinetics of simian virus 40 DNA synthesis in pulse and in pulse-chase experiments. The average time required to complete the replication of prelabeled RI molecules and to convert them into DNA I was approximately 10 min under the experimental conditions employed.

Characterization of an endonuclease associated with simian virus 40 virions

An endonucleolytic activity associated with purified simian virus 40 (SV40) virions has been found. The enzyme is present in virions prepared from a number of different host lines. The enzyme is present in all early and late temperature-sensitive mutants examined. Some aspects of the endonucleolytic activity have been examined with SV40 deoxyribonucleic acid as substrate.

Synthesis and assembly of simian virus 40. I. Differential synthesis of intact virions and empty shells

Intact virions and empty shells of simian virus 40 may be rapidly separated from each other and from cell contaminants by a procedure employing a CsCl cushion. This approach permits quantitation of their respective syntheses in infected cells labeled with radioactive amino acids. As much as 5 to 10% of the total acid-precipitable radioactive lysine in infected cell extracts was incorporated into viral particles in a two-hour pulse late in infection. Evidence for multiple origins of empty shells is presented. Some of the empty shells result from breakdown of intact virions. However, empty shells can also form independently of intact virions. First, labeling for periods of 15 min to 2 hr late in the course of infection results in preferential incorporation of (3)H-lysine into empty shells. Secondly, treatment with the deoxyribonucleic acid inhibitor cytosine-beta-d-arabinofuranoside late in infection results in a 50% inhibition in the rate of formation of intact virions with minimal reduction in the rate of appearance of empty shells.

Temperature-sensitive mutants of simian virus 40: infection of permissive cells

Ten temperature-sensitive mutants of simian virus 40 have been isolated and characterized in permissive cells. The mutants could be divided into three functional groups and two complementation groups. Seven mutants produced T antigen, infectious viral deoxyribonucleic acid (DNA), and structural viral antigen but predominantly the empty shell type of viral particles. Two mutants produced T antigen and infectious viral DNA, but, although viral structural protein(s) could be detected immunologically, no V antigen or viral particles were found. These two functional groups of mutants did not complement each other. A single mutant was defective in the synthesis of viral DNA, viral structural antigens, and viral particles. T antigen could be detected in infected cells by fluorescent antibody but was reduced by complement fixation assay. This mutant stimulated cell DNA synthesis at the restrictive temperature and complemented the other two functional groups of mutants.

In vitro reassembly of shell-like particles from disrupted polyoma virus

When purified polyoma virus is exposed to 0.01 M dithiothreitol in the presence of 0.2 M Na(2)CO(3)-NaHCO(3) (pH 10.6) at 0-4 degrees C, the capsids are rapidly disrupted to protein subunits of capsomere size, as judged by density gradient centrifugation, sedimentation equilibrium centrifugation, and electron microscopy. Hemagglutination activity and infectivity of disrupted virus are reduced to below detectable amounts. Removal of the disruption reagents by dialysis at 4 degrees C against 0.05 M Tris-0.14 M NaCl-1 mM EDTA and 0.1 mM 2-mercaptoethanol (pH 8.0) results in a time-dependent reappearance of up to 17% of the starting hemagglutination titer, under optimum conditions of ionic strength, pH, temperature, and virus protein concentration. The recovered hemagglutination activity is found in glycerol gradients associated with a 100S DNA-protein complex consisting mostly of linear aggregates of capsomeres. When the linear complex is treated with pancreatic DNase, the complex is converted into spherical particles, of approximately virus size, that sediment at 140 S (with aggregates at 180 S), as well as on the cushion of half-saturated CsCl at the bottom of the gradients. All reassembled particles are not infectious and have markedly reduced DNA to protein ratios.

Structural polypeptides of simian virus 40

To determine the number and molecular weights of the structural polypeptides of simian virus 40, we have analyzed purified virus by electrophoresis on 14% polyacrylamide gels containing sodium dodecyl sulfate. Full virus purified by several different methods showed six distinct bands with molecular weights of approximately 43,000 (VP1, containing 70% of virion protein), 32,000 (VP2, 9%), 23,000 (VP3, 10%), 14,000 (VP4, 6%), 12,500 (VP5, 4%), and 11,000 (VP6, 3%) both by analysis of radioactively labeled virions and by visualization of the polypeptide bands after staining. "Empty" virions contain decreased amounts of VP4, 5, and 6. The approximate molecular ratios of the polypeptides were 6.0, 1.0, 1.5, 1.5, 1.1, and 1.0. When virus degraded in an alkaline buffer was analyzed by velocity centrifugation in sucrose gradients, the two larger polypeptides (VP1 and VP2) remained at the top of the gradient, whereas the three smallest polypeptides (VP4, 5, and 6) sedimented as a complex with the viral deoxyribonucleic acid. VP3 was found in association with either VP1 and 2 or VP4, 5, and 6, depending on the conditions of degradation. Presumably, VP1 and VP2, comprising about 80% of the protein, form the capsid of the virus. VP4, 5, and 6 may form a nucleoprotein in the virion, and VP3 may serve as an intermediate structural component.