Virus inactivation mechanisms: impact of disinfectants on virus function and structural integrity

Oxidative processes are often harnessed as tools for pathogen disinfection. Although the pathways responsible for bacterial inactivation with various biocides are fairly well understood, virus inactivation mechanisms are often contradictory or equivocal. In this study, we provide a quantitative analysis of the total damage incurred by a model virus (bacteriophage MS2) upon inactivation induced by five common virucidal agents (heat, UV, hypochlorous acid, singlet oxygen, and chlorine dioxide). Each treatment targets one or more virus functions to achieve inactivation: UV, singlet oxygen, and hypochlorous acid treatments generally render the genome nonreplicable, whereas chlorine dioxide and heat inhibit host-cell recognition/binding. Using a combination of quantitative analytical tools, we identified unique patterns of molecular level modifications in the virus proteins or genome that lead to the inhibition of these functions and eventually inactivation. UV and chlorine treatments, for example, cause site-specific capsid protein backbone cleavage that inhibits viral genome injection into the host cell. Combined, these results will aid in developing better methods for combating waterborne and foodborne viral pathogens and further our understanding of the adaptive changes viruses undergo in response to natural and anthropogenic stressors.

Bacteriophage inactivation by UV-A illuminated fullerenes: role of nanoparticle-virus association and biological targets

Inactivation rates of the MS2 bacteriophage and (1)O(2) generation rates by four different photosensitized aqueous fullerene suspensions were in the same order: aqu-nC(60) < C(60)(OH)(6) ≈ C(60)(OH)(24) < C(60)(NH(2))(6). Alterations to capsid protein secondary structures and protein oxidation were inferred by detecting changes in infrared vibrational frequencies and carbonyl groups respectively. MS2 inactivation appears to be the result of loss of capsid structural integrity (localized deformation) and the reduced ability to eject genomic RNA into its bacterial host. Evidence is also presented for possible capsid rupture in MS2 exposed to UV-A illuminated C(60)(NH(2))(6) through TEM imagery and detection of RNA infrared fingerprints in ATR-FTIR spectra. Fullerene-virus mixtures were also directly visualized in the aqueous phase using a novel enhanced darkfield transmission optical microscope fitted with a hyperspectral imaging (HSI) spectrometer. Perturbations in intermolecular extended chains, HSI, and electrostatic interactions suggest that inactivation is a function of the relative proximity between nanoparticles and viruses and (1)O(2) generation rate. MS2 log survival ratios were linearly related to CT (product of (1)O(2) concentration C and exposure time T) demonstrating the applicability of classical Chick-Watson kinetics for all fullerenes employed in this study. Results suggest that antiviral properties of fullerenes can be increased by adjusting the type of surface functionalization and extent of cage derivatization thereby increasing the (1)O(2) generation rate and facilitating closer association with biological targets.

Demonstration of the protective effects of fluorescent proteins in baculoviruses exposed to ultraviolet light inactivation

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) recombinants, namely AcRFP produced by fusion of the red fluorescent protein (RFP) gene with the polyhedrin gene, and a recombinant (pAcUW21-23GFP) carrying the green fluorescent protein (GFP) in its viral envelope, were evaluated for their resistance to inactivation by ultraviolet light. AcRFP recombinants produced incomplete polyhedra with low infectivity for Trichoplusia ni larvae, whereas AcuW21-23GFP produced normal polyhedra with high infectivity. Electron microscopy of AcRFP CL14 showed the incorporation of very few viral particles into polyhedrin matrix protein material. The LC50 for AcuW21-23GFP was 0.10 occlusion bodies/mm2, whereas the LC50 values for several AcRFP recombinants ranged from 20 to 329 occlusion bodies/mm2. When both the RFP and GFP recombinants were exposed to ultraviolet light (UV-B 280-320 nm), the results support the conclusion that these fluorescent proteins afford some protection against its damaging effects.

Stress-induced recrystallization of a protein crystal by electron irradiation

Ordering of a system of particles into its thermodynamically stable state usually proceeds by thermally activated mass transport of its constituents. Particularly at low temperature, the activation barrier often hinders equilibration--this is what prevents a glass from crystallizing and a pile of sand from flattening under gravity. But if the driving force for mass transport (that is, the excess energy of the system) is increased, the activation barrier can be overcome and structural changes are initiated. Here we report the reordering of radiation-damaged protein crystals under conditions where transport is initiated by stress rather than by thermal activation. After accumulating a certain density of radiation-induced defects during observation by transmission electron microscopy, the distorted crystal recrystallizes. The reordering is induced by stress caused by the defects at temperatures that are low enough to suppress diffusive mass transport. We propose that this defect-induced reordering might be a general phenomenon.

The use of oriC-dependent phage infection to characterize the ultra violet (UV)-induced inhibition of initiation of DNA replication in Escherichia coli

The oriC transducing phage lambda poriCc is a pseudovirulent phage capable of forming plaques on a lambda lysogen. This phenotype is dependent upon the presence of the oriC insert. The ability of lambda poriCc to form plaques on a lambda lysogen represents a potential phage assay system for studying aspects of oriC function. In the present study we establish that lambda poriCc infection of a lambda lysogen is a legitimate assay for oriC function. We use this assay to confirm the previously reported observation that initiation of DNA replication from oriC is transiently inhibited in a ultra violet (UV) irradiated cell at doses greater than 60 J/m2. We further demonstrate using this assay that the UV induced inhibition of initiation of DNA replication from oriC is not a SOS function nor a heat shock function. In the course of these studies, we found that lambda poriCc infection of a non-lysogenic cell is extremely sensitive to pre-irradiation of the Escherichia coli host. We postulate that the sensitivity of lambda poriCc replication to host cell pre-irradiation reflects in some way the transient inhibition of initiation of DNA replication from oriC following UV irradiation.

Herpes simplex virus proteins are damaged following photodynamic inactivation with phthalocyanines

The photodynamic inactivation of herpes simplex virus type 1 (HSV-1) by two phthalocyanines (Pcs), the cationic dye HOSi-PcOSi(CH3)2(CH2)3N+(CH3)3I-(Pc5) and the amphiphilic dye aluminum dibenzodisulfophthalocyanine hydroxide (AlN2SB2POH), has been compared with that by the anionic dye, Merocyanine 540 (Mc540). Both Pc derivatives demonstrate a remarkable virucidal activity upon light activation even 3 h after the onset of HSV-1 adsorption, while Mc540 is effective for only 30 min after adsorption. Since fusion and virus penetration are promoted by membrane glycoproteins, we have studied the damage to viral proteins following photodynamic treatment (PDT) of HSV-1 and its relation to inactivation. The effect of AlN2SB2POH PDT is assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Major changes are found in the protein profile of PDT-treated HSV-1. A reduced ability of specific antibodies to react with HSV-1 major envelope proteins is detected by employing the Western blot assay. In particular, we demonstrate the related changes of glycoprotein D (gD), a structural protein of the HSV envelope. Since the envelope proteins participate in viral entry into the host cell, these alterations to viral envelope proteins may impair their ability to participate in early events of viral entry, leading to reduced infectivity of HSV-1. In contrast, no significant changes in the proteins' electrophoretic mobility could be seen after PDT with Mc540 or with Pc5. When HSV-1 purified proteins are subjected to combined electrophoretic and electro osmotic forces on cellulose acetate, there is a shift in their cathode mobility, which may indicate changes in the protein mass and protein net charges following AlN2SB2POH photosensitization. There are only minor changes in the virus proteins, assayed as above, when HSV-1 is treated with Pc5.

Photoinactivation of virus infectivity by hypocrellin A

We investigated the photoinactivation of virus infectivity by hypocrellin A and its mechanism. The titers of vesicular stomatitis virus (VSV) and human immunodeficiency virus type 1 (HIV-1), both of which are enveloped viruses, were reduced upon illumination with hypocrellin A in a concentration-dependent manner, whereas canine parvovirus, a nonenveloped virus, was not killed. The removal of oxygen or addition of sodium azide or beta-carotene both inhibited VSV inactivation. Mannitol and superoxide dismutase had no effect on VSV inactivation. These results indicate that singlet oxygen was involved in the process of VSV inactivation. Of the three major VSV membrane proteins, peripheral membrane protein M was most damaged by the hypocrellin A phototreatment.

Analysis of viral DNA, protein and envelope damage after methylene blue, phthalocyanine derivative or merocyanine 540 photosensitization

Although numerous photosensitizers have been used experimentally to decontaminate viruses in cellular blood components, little is known about their mechanisms of photoinactivation. Using M13 bacteriophage and vesicular stomatitis virus (VSV) as model viruses, we have investigated alteration of the viral genome, protein and envelope after phototreatment. Methylene blue (MB) and aluminum phthalocyanine tetrasulfonate (AlPcS4) phototreatment inactivated bacteriophage M13 and decreased the fraction of single-stranded circular genomic DNA (sc-DNA) by converting it to linear form. This conversion was enhanced by treating the extracted DNA with piperidine at 55 degrees C. Piperidine-labile breaks were well correlated to phage survival (5.1% sc-DNA at 1.7% phage survival for MB) under conditions where only minor differences were seen in the relative abundance of M13 coat protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Neither aluminum phthalocyanine (AlPc) nor merocyanine 540 (MC540) inactivated M13 nor were there significant changes observed in DNA and coat protein. Methylene blue, AlPcS4 and AlPc inactivated VSV and inhibited fusion of the virus envelope to Vero cells at pH 5.7 (i.e. with plasma membrane). However, the degree of this inhibition was small compared to the extent of virus inactivation (43% inhibition vs. 4.7 log10 or 99.998% inactivation, for MB). In contrast, an antibody to VSV G-spike protein inhibited fusion at pH 5.7 by 52% with a concomitant decline in VSV infectivity of 0.15 log10 (30%). Few changes were observed in the relative abundance of G protein for MB and AlPcS4 phototreated samples and no additional protein bands were observed on SDS-PAGE.(ABSTRACT TRUNCATED AT 250 WORDS)

The tryptophan bridge is a critical feature of the papillomavirus E2 DNA binding domain

The papillomavirus E2 protein is a DNA binding protein that regulates viral transcription and replication. E2 binds DNA as a dimer. Recent crystallographic data for E2 complexed to DNA revealed that novel peptide structures in E2 mediated dimerization and DNA binding. To identify important features of these motifs we have used limited proteolysis and urea denaturation as biochemical probes for structure, applying these techniques to E2 alone, E2 bound to DNA, cross-linked products, and mutants that were targeted at Trp360, a contact point along the dimer interface. DNA binding stabilized E2 structure, shifting the point at which it denatures from 5 to 7.6 M urea. In contrast, Trp360 mutant proteins, while dimeric, were more sensitive to denaturation by urea when bound to DNA. The most striking results came from uv cross-linking studies in which Trp360 was targeted as the site of cross-linking. Ultraviolet cross-linking dramatically increased the resistance of E2 to proteolysis regardless of the protease tested and with no deleterious effect on the affinity of E2 for DNA. Cross-linking through Cys356 with bismaleimidohexane did not promote stabilization. The ability to stabilize or destabilize E2 by Trp360-targeted modifications demonstrates the importance of the Trp360-Trp360 interaction, which may represent a general feature of the beta-barrel motif.

The involvement of a spliceosome component in internal initiation of human rhinovirus RNA translation

Human rhinoviruses (HRVs) and encephalomyocarditis virus (EMCV) belong to different genera of the picornavirus family, but the translation of the RNAs of both viruses is by the same mechanism, that is, internal ribosome entry. In rabbit reticulocyte lysates this translation initiation is efficient for mRNAs bearing the EMCV 5' untranslated region (5' UTR), but very inefficient for mRNAs bearing the HRV 5' UTR, unless factors from HeLa cells are added. The copurification of the HeLa cell translation stimulatory activity with proteins which can be specifically cross-linked to the HRV 5' UTR by u.v. irradiation has been examined. Both the EMCV and HRV 5' UTRs can be cross-linked to a 58/60K protein doublet present in HeLa cell extracts in higher amounts than in reticulocyte lysates, which is shown to be very similar, if not identical to the polypyrimidine tract binding protein (PTB) previously identified as a component of a multi-subunit complex necessary for pre-mRNA splicing. However, the activity in HeLa cell extracts that specifically stimulates translation initiation on mRNAs with the HRV 5' UTR does not copurify with the majority of the 58/60K protein present in these extracts, but copurifies with a minor fraction of these proteins and with a 97K protein which can be cross-linked to the HRV 5' UTR but not to the EMCV 5' UTR, and which is absent from reticulocyte lysates. It is proposed that the specific translation initiation stimulatory activity found in HeLa cells is due to a high M(r) complex containing the 97K polypeptide and PTB.

Laser cross-linking of proteins to nucleic acids: photodegradation and alternative photoproducts of the bacteriophage T4 gene 32 protein

Pulsed laser cross-linking provides a means of introducing a covalent bond between proteins and the nucleic acids to which they are bound. This rapid cross-linking effectively traps the equilibrium that exists at the moment of irradiation and thus allows examination of the protein-nucleic acid interactions that existed. Laser irradiation may also induce photodestruction of protein and we have used the bacteriophage T4 gene 32 protein to investigate this phenomenon. Our results show that both nonspecific and specific photoproducts can occur, specifically at wavelengths where the peptide backbone of proteins is known to absorb. These results demonstrate that nonspecific photodegradation can be correlated with the formation of a specific photodegradation product. The formation of this product was monitored to show that product yield is nonlinearly dependent on laser power and wavelength. We have also investigated an unexpected photoproduct whose formation is dependent on the length of the polynucleotide to which the gene 32 protein binds and that further demonstrates the complexities of analyzing protein-nucleic acid interactions through the use of UV laser cross-linking. These data provide essential information for the establishment of appropriate conditions for future studies that use UV cross-linking of protein-nucleic acid complexes.

Functional role of the ultraviolet light responsive element (URE; TGACAACA) in the transcription and replication of polyoma DNA

We have previously identified a novel 8 bp sequence (UV-responsive element, URE: TGACAACA) present in the regulatory region of polyoma DNA that interacts with protein factors induced in rat fibroblast cells by exposure to UV light. In the present study, we demonstrate through competitive binding assays that this sequence is distinct from the partially homologous AP1 and CRE target sequences. The proteins that bind to the URE appear to have transcriptional activity in UV-exposed rat fibroblasts. In addition, the URE appears to play a role in promoting the replication of polyoma DNA as determined through two different experimental approaches. Together, these findings suggest that the URE is a novel DNA binding element that interacts with proteins involved in the transcription and replication of polyoma sequences.

[Determination of the effectiveness of RNA cross-linking with protein induced by UV-radiation in potato X-virus particles]

The UV-irradiation was found to induce formation of the RNA-protein cross-links and intraviral RNA chain breaks in the particles of flexuous potato virus X (PVX). Using the technique developed previously for the rod-like tobacco mosaic virus (TMV), the quantum yields of RNA-protein cross-links and intraviral RNA polynucleotide chain breaks formation in the PVX were determined and found to be more or less close to those found for the intraviral TMV RNA.

Effects of UV-irradiation upon Venezuelan equine encephalomyelitis virus

Venezuelan equine encephalomyelitis virus labelled with [14C]aminoacids or [3H]uridine was purified and UV-irradiated. The irradiation led to the formation of uracil photodimers and the covalent linking of the nucleocapsid protein C to virion RNA. The inactivation of infectivity correlated with the formation of uracil dimers, whereas the RNA-protein links were formed at much higher doses of UV irradiation. The analysis of covalent RNA-protein complexes suggests that a fairly large fraction (at least one third) of the whole content of C protein is able to participate in the formation of UV-induced links, suggesting extensive contacts of RNA with protein with the nucleocapsid.

Interaction of lambda Gam protein with the RecD subunit of RecBCD enzyme increases radioresistance of the wild-type Escherichia coli

By making use of the gam(+)-plasmid, the so-called gam-dependent radioresistance was studied. This resistance is the result of the interaction between Gam protein (encoded by the gam gene of lambda) and RecBCD enzyme of Escherichia coli. gam-dependent radioresistance is observed in recB+ recC+ recD+ but not in recB+ recC+ recD- cells. It is suggested that Gam protein interacts specifically with the RecD subunit of RecBCD enzyme; the RecBC complex probably retains its activity in the presence of this viral protein.

Effect of UV-irradiation on rotavirus

The effect of UV-irradiation on SAll rotavirus infectivity was followed. The time course of infectivity inactivation in general showed an one-hit pattern. Two basic effects of UV-irradiation on virus particles were investigated: the phenomenon of RNA-protein linkages and the formation of uracil dimers. To determine the number of uridine dimers, 3H-uridine labelled purified rotavirus was exposed to UV-irradiation, subsequently the RNA was extracted and analysed by ascending paper chromatography. Formation of photodimers was found to be an important mechanism of rotavirus inactivation at conventional UV-irradiation; the RNA-protein linkages were registered at high irradiation doses only.

[Covalent-bound aggregates of equine venezuelan encephalomyelitis virus induced by UV-irradiation]

Formation of Venecuelan equine encephalomyelitis virus (VEE) aggregates induced by UV-light has been studied. The high doses of UV-irradiation induced the protein-protein cross-links resulting in formation of fast sedimenting viral structures. The latter structures are supposed to be presented by the aggregates of several virions linked by the UV-light induced RNA-protein and protein-protein covalent bonds. The lesions in the fine structure of virion envelope was registered by the electron microscopy technique.

Alteration of vesicular stomatitis virus L and NS proteins by uv irradiation: implications for the mechanism of host cell shut-off

When purified, [35S]methionine-labeled vesicular stomatitis virus (VSV) was exposed to ultraviolet light, an irradiation-induced change in the viral proteins was detected by SDS-polyacrylamide gel electrophoresis and immunoblotting. With dose of uv irradiation in the same range as that required to inactivate VSV leader RNA, a loss occurred in the bands corresponding to the L and NS proteins concomitant with the appearance of several new bands of radioactivity throughout the gel. This alteration of viral proteins correlated with the loss of ability of the virus to inhibit host macromolecular synthesis. In light of these results, the role that has been ascribed to the VSV leader RNA in VSV-mediated host shut-off needs to be reevaluated.

A maximum of two tryptophan residues in gene-32 protein from phage T4 undergo stacking interactions with single-stranded polynucleotides

The effect of specific photochemical and radiochemical modification of tryptophyl and cysteinyl residues of the gene 32 protein (gp 32) of bacteriophage T4 on its affinity towards single-stranded polynucleotides has been investigated. Oxidation of Cys residues of gp 32 by the free-radical anion I-.2 induces a partial loss of the protein affinity, probably by affecting the metal-binding domain which includes three of the four cysteine residues of gp 32. Ultraviolet irradiation of gp 32 in the presence of trichloroethanol results in the modification of three of its five Trp residues and total loss of the protein binding. Analysis of the relative affinity of ultraviolet-irradiated gp 32 for single-stranded polynucleotides suggest that modification of a Trp of enhanced reactivity occurs first and has no effect on the protein binding. Radiochemical modification of three Trp residues of gp 32 by (SCN)-.2 results in total loss of activity. Complexation of gp 32 with denatured DNA prior to gamma-irradiation protects two Trp residues and prevents the protein inactivation. These results suggest that at most two Trp residues are involved in stacking interactions with nucleic acid bases. However, time-resolved spectroscopic methods which allow us to monitor selectively the stacked tryptophan residues have not yielded evidence of more than a single residue undergoing such interactions.

Effect of beta-decay of radionuclides incorporated into influenza virus RNA and proteins on the infectivity of the virus and antigenicity of its nucleoprotein

The effect of beta-decay of radionuclides incorporated into influenza virus on the properties of the two closely adjacent structures--RNA and nucleoprotein (NP)--was studied. The long-term storage of 3H-uridine labelled influenza virus was shown to lead to the loss of infectivity. This effect may be explained by lethal intra-molecular modifications of viral RNA, caused by beta-decay of 3H incorporated into the molecule. There was an accompanying decrease of monoclonal antibody (MAB) binding activity, this also being a plausible result of beta-decay. The different rates of inactivation of MAB binding activity of different epitopes of NP of the 3H-labelled virus shown in our studies suggest that there are different types of structural organization or different location of these epitopes in the NP. The effect of 3H-decay on the intracellular RNA of reproducing virus lead to a decrease in virus yield; this may be due to radiation- and transmutation-induced damage of messenger and progeny RNA populations synthesized during the infection. The storage of influenza virus labelled with 14C-aminoacids lead to a decrease in MAB binding activity of the NP that was unaccompanied by a decrease in infectivity. Furthermore, 14C-decay in proteins of reproducing virus had no adverse effect.

Mutagenic and lethal effects of near-ultraviolet radiation (290-400 nm) on bacteria and phage

Despite decades of study of the effect of near-ultraviolet radiation (NUV) on bacterial cells, insights into mechanisms of deleterious alterations and subsequent recovery are just now emerging. These insights are based on observations that 1) damage by NUV may be caused by a reactive oxygen molecule, since H2O2 may be a photoproduct of NUV; 2) some, but not all, of the effects of NUV and H2O2 are interchangeable; 3) there is an inducible regulon (oxyR) that responds to oxidative stress and is involved in protection against NUV; 4) a number of NUV-sensitive mutants are defective either in the capacity to detoxify reactive oxygen molecules or to repair DNA damage caused by NUV; and 5) recovery from NUV damage may not directly involve induction of the SOS response. Since several distinctly different photoreceptors and targets are involved, it is unknown whether NUV lethality and mutagenesis result from an accumulation of damages or whether there is a particularly critical photoeffect. To fully understand the mechanisms involved, it is important to identify the chromophore(s) of NUV, the mechanism of toxic oxygen species generation, the role of the oxidative defense regulon (oxyR), the specific lesions in the DNA, and the enzymatic events of subsequent repair.

[Physicochemical characteristics of an influenza virus population inactivated by gamma rays]

A study was made of the effect of 60Co-gamma-radiation on the integrity of particles of the influenza virus and on the structure of some of its proteins. The physicochemical changes in virions were shown to depend upon radiation conditions. A conclusion is made that it is possible to use gamma-rays in the production of a centrifuged virion influenza vaccine.

DNA injection proteins are targets of acridine-sensitized photoinactivation of bacteriophage P22

Viruses and other nucleoprotein complexes are inactivated on exposure to white light in the presence of acridine and related dyes. The mechanism is thought to involve generation of singlet oxygen or related species, but the actual molecular targets of the inactivating event have not been well defined. We have re-examined the mechanism of dye-sensitized photoinactivation taking advantage of the well characterized bacteriophage P22. Though the inactivated phage absorb to their host cells, the cells are not killed and genetic markers cannot be rescued from the inactivated phage. These observations indicate that the chromosome is not injected into the host cell. However, the DNA of the damaged particles shows no evidence of double-stranded breaks or crosslinking. The DNA injection process of P22 requires three particle-associated proteins, the products of genes 7, 16 and 20. Gp16, which can act in trans during injection, is inactivated in the killed particles. Sodium dodecyl sulfate/polyacrylamide gel analysis reveals that gp16, gp7 and gp20 are progressively covalently damaged during photoinactivation. However, this damage does not occur in particles lacking DNA, indicating that it is DNA-mediated. Similar findings were obtained with acridine orange, acridine yellow, proflavin and acriflavin. These results indicate that the actual targets for inactivation are the DNA injection proteins, and that the lethal events represent absorption of photons by acridine molecules stacked in a region of DNA closely associated with the injection proteins.

Analysis of the interaction between DNA and major core protein in adenovirus chromatin by circular dichroism and ultraviolet light induced cross-linking

Adenovirus chromatin is constituted with three kinds of core proteins, VII, V, and mu, that are coded by the virus genome. Since a hexamer of VII contributes to formation of the nucleosome-like structure of the virion chromatin, we analyzed the interaction between DNA and VII in vitro, by the use of ultraviolet light-induced cross-linking and circular dichroism (CD) spectroscopy. It was observed that DNA and VII in a plain mixture form a structure resembling viral chromatin. The DNA in the virion core or in the simply mixed complex appears to take a tight conformation by superfolding, based on the result that the ellipticity at 275 nm of DNA was reduced to approximately 3,000 degrees, and the wave-length of the positive peak was shifted from 275 to 285 nm. The change in CD spectrum caused by interaction of VII with DNA is similar to that of a protamine rather than that of a histone mixture. The interaction of VII with DNA is preferential, and VII is capable of associating more efficiently with double stranded DNA than with single stranded. The interaction is loosened by salt (0.3 M NaCl) and tightened by magnesium ion. However, the interaction of a precursor core protein pro-VII with DNA was not as tight as that of VII and was not influenced by magnesium ion, presumably because of the existence of a hydrophobic processing sequence in the molecule.

Gene order of translation of the flavivirus Kunjin: further evidence of internal initiation in vivo

The rates of inactivation of synthesis of individual virus-specified proteins by ultraviolet radiation provided an estimate of the target sizes of individual viral genes. In a control experiment with Semliki Forest virus, the genes for the structural proteins mapped in the known sequence 5' C-PE2-E1 3', and in accordance with initiation of translation from a single site on 26-S mRNA. Under the same conditions, the inactivation of synthesis of seven Kunjin virus-specified proteins also followed first-order kinetics, but the largest target size was equivalent to only about half the length of the genome. No gene sequence could be deduced using the premise that translation was initiated at a single site. However, genes for the major nonstructural proteins could be mapped in the order 5' P98-P71-P10 3' from a postulated ribosomal attachment site about midway along the RNA. The genes for the structural proteins C and E could then be mapped in a preceding sequence 5'...C-E-GP19-P21 3', with a vacant upstream region sufficient to code for at least one of two flavivirus genes not expressed in these experiments. The implications of the two postulated translational units are discussed in relation to previous data on translation strategy of flaviviruses.

Protein-RNA interaction in encephalomyocarditis virus as revealed by UV light-induced covalent linkages

UV irradiation of encephalomyocarditis virus led to an increase in the buoyant density of the virus in CsCl gradients from 1.34 to 1.46 g/cm3. Heat treatment of the irradiated virus (20 min at 54 degrees C) reduced the density to 1.40 g/cm3 and led to the loss of approximately 55% of the labeled RNA from the virions. The non-irradiated virions were converted by such heating into empty capsids. Irradiation also resulted in an increase in the accessibility of RNA inside the virions to the action of pancreatic RNase. An increase in the UV dose did not enlarge the fraction of RNA molecules covalently linked to protein; this was revealed by the lack of any secondary increase in the apparent RNase resistance of the labeled RNA in the irradiated virions. Destruction of the irradiated virus with sodium dodecyl sulfate and 2-mercaptoethanol allowed the isolation of a 40S structure containing viral RNA and RNA-linked proteins. The latter comprised no more than 2.5% of the whole protein content of the virion. Polyacrylamide gel electrophoretic analysis of the RNase-treated 40S structure revealed at least three viral structural proteins in the same ratio as was present in the intact virions.

[Synthesis of influenza virus protein in the inhibition of cellular DNA transcription]

After preliminary UV-irradiation of cells as well as in the presence of actinomycin D the doses of both agents inhibiting influenza virus production are slightly lower than those inhibiting formation of viral proteins and considerably lower than those producing complete blocking of viral genome expression. These data demonstrate the existence of a cellular DNA-dependent factor the blocking of which prevents the formation of virus progeny without preventing primary transcription and formation of virion proteins. It is assumed that, apart from relatively small genes of cellular DNA participating in primary transcription of viral genome, some larger genes of the cell take part in some process of influenza virus reproduction.

U.V.-enhanced reactivation of capsid protein synthesis and infectious centre formation in mouse cells infected with U.V.-irradiated Minute-Virus-of-Mice

The effect of U.V.-irradiation of mouse A9 cells on their ability to replicate unirradiated and U.V.-irradiated Minute-Virus-of-Mice was studied. The survival of two viral functions was measured in primary infected cells: the synthesis of viral structural proteins, as detected in situ using an immunoenzymatic assay, and the production of infectious centres, as detected by plaque formation onto appropriate indicator cells. Cell irradiation prior to infection enhanced virus survival over that in control cells (U.V.-enhanced reactivation phenomenon). The magnitude of this effect was similar for both viral functions, suggesting that the step(s) of the virus cycle sensitive to the reactivation process precede(s) the release of the primary burst and secondary infection.

[RNA-protein interactions in influenza virus A ribonucleoprotein detected by UV radiation]

RNA and protein interaction in the structure of influenza virus ribonucleoprotein (RNP) was studied by ultraviolet (UV) irradiation. After UV-irradiation of virion RNP for 1 hour only 6% of 3H-uridine-labeled RNA was found to go into the aqueous phase upon phenol-detergent extraction. Pretreatment of RNP with small doses of pancreatic RNase before RNA extraction slightly increased (up to 18%) the amount of RNA going into the aqueous phase. About 90% RNA was found after extraction in the aqueous phase in the nonirradiated material. As a result of UV-irradiation of RNP, RNA in RNP became more resistant to RNase: the residual acid-insoluble radioactivity was 21% whereas with nonirradiated RNP it was 3.2%. The results of the analysis of RNP labeled for protein in polyacrylamide gel and SDS-sucrose gradient after UV-irradiation and ribonuclease treatment indicate the formation of UV-induced linkages between RNA and NP protein.

Modification of the poliovirus capsid by ultraviolet light

Ultraviolet (UV) irradiation of type I poliovirus resulted in a modified (M) particle that had lost infectivity, lacked ability to adsorb to HeLa cells, lacked VP4, and reduced in S value. Additional irradiation resulted in the loss of VP2, further reduction in S value, and permeability of the capsid to RNAse, This particle (C) as well as M contain the genome. Acid pH (5.5-65) and sulfhydryl-reducing substances (dithiothreitol. reduced glutathione, and L-cysteine) inhibited UV-induced modification of the capsid. UV irradiation at alkaline pH (7.5-8.5) resulted in more extensive modification of the capsid than irradiation at neutral pH. Ionic compounds were found to inhibit the modifying reaction.

Identification of binding sites of turnip yellow mosaic virus protein and RNA by crosslinks induced in situ

Turnip yellow mosaic virus RNA and protein could be crosslinked in situ by ultraviolet irradiation at pH 4.8 but not at pH 7.3, and by bisulphite treatment at pH 7.3. Crosslinked peptides could be located in the primary structure of the viral coat protein. Three regions were bound covalently by ultraviolet irradiation, and two of these three regions were bound also by bisulphite treatment. The yield of the crosslinking reaction could be high, indicating that almost all protein subunits of each virion reacted with the viral RNA. The crosslinked peptides contain most of the acidic and basic amino acids of the protein, often associated into pairs of opposite charge. Implications for the folding of the RNA into the virion and for models of RNA--protein interactions are discussed.

Inactivation of phage T7 by near-ultraviolet radiation plus hydrogen peroxide: DNA-protein crosslinks prevent DNA injection

A nonlethal concentration of H2O2 (0.05%) greatly enhances near-ultraviolet (NUV) inactivation of phage T7. Simultaneous treatment with H2O2 and NUV reduces the amount of DNA injected into the bacterial host, but not the number of phage adsorbed. Not only were recombination and gene expression of late markers reduced upon treatment of phage T7 with NUV plus H2O2, but also a gradient of recombination resulted, with markers injected first reduced to a lesser extent than those injected last. Double-strand DNA breaks were not detected; however, DNA-protein crosslinks were observed upon NUV plus H2O2 treatment of double-labeled T7. Previous studies demonstrated that single-strand DNA breaks did not account for phage death by NUV plus H2O2. It is concluded that the DNA-protein crosslinks prevent normal injection of T7 phage DNA; such crosslinks may be important lesions in NUV cellular damage.

Quantitative determination of cross-linkage of bacteriophage DNA and protein by ionizing radiation

Coliphage T7 was dissolved in tryptone broth and exposted to 60C gamma-radiation. Cross-linkage of DNA and protein of the virion was assayed using phenol-water countercurrent distribution. The results are interpreted in terms of a statistical model of cross-linkage and double-strand breaks. It was found that protein--DNA cross-links accumulate linearly with dose at a rate of o.74 X 10(-11) cross-links per rad per nucleotide pair, which is of the order of 5 per cent of the formation rate of double-strand breaks.

High resolution bright field electron microscopy of biological specimens

Various parameters which affect the information content in bright field electron micrographs of biological specimens is discussed. Special attention is paid to the resolution of phase contrast imaging, specimen supports and radiation damage.

Induced formation of covalent bonds between nucleoprotein components. V. UV or bisulfite induced polynucleotide-protein crosslinkage in bacteriophage MS2

UV (lambda = 254 nm) irradiation of bacteriophage MS2 or its treatment with bisulfite induce covalent crosslinkage of the RNA to the coat protein. epilsonN-(2-oxopyrimidyl-4)-lysine was found in the phage hydrolysates after either type of treatment. An equimolar mixture of 0-methylhydroxylamine and bisulfite causes complete disappearance of the cross-links. This led to the conclusion that one of the factors responsible for the UV-induced polynucleotide-protein crosslinkage and the main factor in treatment with bisulfite is substitution of the exocyclic amino group of the activated cytosine nucleus by the lysine residue epilson-amino group of the protein.

Effect of ultraviolet light on mengovirus: formation of uracil dimers, instability and degradation of capsid, and covalent linkage of protein to viral RNA

UV irradiation of purified mengovirus resulted in a very rapid inactivation of the infectivity of the virions (D(37) [37% survival dose] = 700 ergs/mm(2)) which correlated in time with the formation of uracil dimers in the viral RNA. During the first 2 min of irradiation, an average of 1.7 uracil dimers were formed per PFU of virus inactivated. Hemagglutination activity of the virions began to decrease only after a lag period of about 5 min and at a much lower rate (D(37) = 84,000 ergs/mm(2)). This decrease coincided in time with the appearance of altered proteins in the capsid and a structural change in the capsid. Although 10- to 20-min irradiated virions appeared intact in the electron microscope and sedimented at 150S in sucrose density gradients, the RNA of the virions became accessible to RNase and extractable by low concentrations of sodium dodecyl sulfate, and the virions broke down upon equilibrium centrifugation in CsCl gradients. During longer periods of irradiation (30 to 60 min), a progressively greater proportion of the virions were converted to 14S protein particles and 80S ribonucleoprotein particles composed of intact viral RNA and about 30% of the capsid proteins, alpha, beta, and gamma. Empty capsids were not detectable at any time during 60 min of irradiation, by which time disruption of the virions was complete. Irradiation of complete virions also resulted in an increased sedimentation rate of the viral RNA and in the covalent linkage to the viral RNA of about 1% of the total capsid protein in the form of heterogeneous low-molecular-weight polypeptides. The two observations seem to be causally related, since irradiation of isolated viral RNA did not result in an increase in sedimentation rate of the RNA, even though uracil dimer formation in viral RNA occurred at about the same rate and to the same extent whether intact virions or viral RNA were irradiated.