Large deletion mutations involving the first pyrimidine-rich tract of the 5' nontranslated RNA of human hepatitis A virus define two adjacent domains associated with distinct replication phenotypes

The 5' nontranslated RNA (5'NTR) of the HM175 strain of human hepatitis A virus contains several pyrimidine-rich regions, the largest and most 5' of which (pY1) is an almost pure polypyrimidine tract located between nucleotides (nt) 99 and 138, which includes five tandem repeats of the sequence motif (U)UUCC(C). Previous modeling of the RNA secondary structure suggested that this region was likely to be single-stranded, but repetitive RNase V1 cleavage sites within these (U)UUCC(C) motifs indicated that pY1 possesses an ordered structure. To assess the role of this domain in replication of the virus, a series of large deletion mutations were created which involved the pY1 domain of an infectious cDNA clone. Deletion of 44 nt between nt 96 and 139, including the entire pY1 domain, did not reduce the capacity of the virus to replicate in BS-C-1 or FRhK-4 cells, as assessed by the size of replication foci in radioimmunofocus assays or by virus yields under one-step growth conditions. In contrast, viable virus could not be recovered from transfected RNAs in which the deletion was extended in a 5' direction by an additional 3 nt (delta 93-134), most likely because of the destabilization of a predicted stem-loop structure upstream of pY1. Deletion mutations extending in a 3' fashion to nt 140, 141, or 144 resulted in moderately (delta 96-140 and delta 96-141) or strongly (delta 99-144, delta 116-144, and delta 131-144) temperature-sensitive replication phenotypes. Although deletion of the pY1 domain did not by itself affect the replication phenotype of virus, the additional deletion of sequence elements within the pY1 domain (nt 99 to 130) substantially enhanced the temperature-sensitive phenotype of delta 131-144 virus. These data suggest that the (U)UUCC(C) motifs within the pY1 domain are conserved among wild-type viruses in order to serve a function required during infection in vivo but not in cell culture. In contrast, the single-stranded region located immediately downstream of pY1 (nt 140 to 144) is essential for efficient replication in cultured cells at physiological temperature. Viruses with deletion mutations involving nt 140 to 144 and viruses with large pY1 deletions but normal replication phenotypes in cell culture may have attenuation properties which could be exploited for vaccine development.

Electron microscopic and molecular characterization of turnip vein-clearing virus

We recently isolated turnip vein-clearing virus (TVCV), a tobamovirus which causes vein clearing in Brassica rapa (turnip) and a mosaic in Nicotiana tabacum (tobacco). We present an electron microscopic and molecular characterization of TVCV. Viral particles from lower epidermis peel contained rod-shaped viral particles, typical of tobamoviruses. Viral RNA extracted from infected turnip leaves was used as template for cDNA synthesis prior to cloning in a plasmid vector. Inserts of selected cDNA clones were sequenced to obtain the nucleotide sequence of the 126 K replicase component. The nucleotide and predicted amino acid sequences were 56 to 59% identical to those of most other sequenced tobamoviruses. The least related sequence, that of cucumber green mottle mosaic virus, was more related to the TVCV lineage than it was to those of the other sequenced tobamoviruses. UV spectroscopy suggested a tryptophan content characteristic of the ribgrass mosaic virus (RMV) group. Fragmentation of the TVCV coat protein by cyanogen bromide treatment produced a profile of fragments indistinguishable from those generated from the coat protein of RMV. Thus, while symptoms of TVCV infection on Nicotiana tabacum cv. Samsun and Nicotiana clevelandii differ from those reported for RMV, TVCV appears to be closely related to RMV.

Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy. Effects of chromosome packaging on the kinetics of nucleotide exchanges

We describe the application of laser Raman spectroscopy to probe hydrogen isotope exchange dynamics of nucleic acid and protein constituents in a double-stranded DNA virus, the icosahedral bacteriophage P22. The Raman dynamic method employs a dialysis flow cell to control D2O efflux into an H2O solution of the virus sample while the rates of deuterium exchange of protons in the viral nucleic acid and protein molecules are measured spectrophotometrically in real time. The method provides structural and kinetic information about three different and distinct classes of exchangeable protons of the native virion: (1) labile imino (NH) and amino (NH2) protons of the bases which participate in Watson-Crick hydrogen bonding in the packaged genome; (2) pseudolabile purinic (8CH) protons that line the major groove of packaged P22 DNA; and (3) main-chain amide (NH) protons of viral subunits comprising the shell that encapsidates the DNA. The results obtained on P22 demonstrate that interchange of aqueous solvent with the virion interior is rapid and complete. We find that while labile protons of packaged DNA exchange rapidly, most amide protons in capsid subunits are resistant to solvent-catalyzed exchange. Further, stereospecific retardation of exchange is observed for major-groove protons of the packaged P22 genome. The quantitative measurements can be summarized and interpreted as follows. (1) Imino and amino protons of all bases in packaged P22 DNA exchange more rapidly (approximately 2-fold faster) than the corresponding protons in unpackaged P22 DNA. Remarkably, packaging actually accelerates labile imino and amino hydrogen exchanges of the viral DNA, an effect which can be attributed to selective stabilization in the packaged chromosome of a base-pair open state (breathing model). (2) Conversely, purine 8CH exchange rates in packaged P22 DNA are significantly retarded in comparison to those of unpackaged P22 DNA. The observed 8CH exchange retardation effects are similar for both adenine and guanine residues, indicating that they do not originate from purine-specific interactions but probably reflect steric shielding of the major groove of packaged DNA from free access to solvent. This effect is likely distributed throughout the 43,400 base-pair genome. (3) Only a small population (approximately 15 to 20%) of subunit amide protons exchanges within the time frame of complete exchange of all protons of packaged P22 DNA. Complete exchange of the capsid is not achieved even after several months of incubation at 40 degrees C.(ABSTRACT TRUNCATED AT 400 WORDS)

Mouse hepatitis virus gene 5b protein is a new virion envelope protein

Highly purified radiolabeled mouse hepatitis virus (MHV) A59 contained a previously overlooked protein which coelectrophoreses with the gene 5b product immunoprecipitated from infected cells. The gene 5b protein is post-translationally acylated. Rabbit antibody raised against a recombinant gene 5b protein expressed in Escherichia coli neutralized viral infectivity in the presence of complement, although not in the absence of complement. Immunofluorescent staining of MHV-infected cells with two anti-peptide antibodies revealed that the gene 5b product is membrane-associated and is transported to the cell surface, findings consistent with the prediction of a membrane-spanning segment in the gene 5b polypeptide. These results suggest strongly that the gene 5b polypeptide represents a new MHV virion envelope protein which is homologous to the TGEV ORF 4 and IBV 3c proteins.

The herpes simplex virus type 1 UL37 gene product is a component of virus particles

The herpes simplex virus type 1 UL37 gene encodes a protein with an M(r) of 120K that is produced at late times after infection. To study the properties of this protein we have linked a 10 amino acid epitope derived from a human cytomegalovirus protein to the UL37 polypeptide coding sequences by inserting an oligonucleotide at a SpeI site that is unique in the virus genome and lies close to the 3' end of the open reading frame. From studies on the resultant virus recombinant using a monoclonal antibody that recognizes the inserted epitope we find that, contrary to a previous report, the UL37 protein is a structural component of both virions and L particles and is present in the tegument of virus particles. Indirect immunofluorescence analysis revealed that the protein is distributed throughout infected cells but is more abundant in the cytoplasm than the nucleus.

In vitro expression of UL56 gene of herpes simplex virus type 1; detection of UL56 gene product in infected cells and in virions

In order to investigate the functional properties of the UL56 gene of herpes simplex virus type 1 (HSV-1), it was necessary to express the UL56 protein in vitro. The DNA sequences corresponding to the open reading frame of the UL56 gene of HSV-1 strain F were amplified from genomic viral DNA by PCR using primers corresponding to the translational start and termination regions of the UL56 ORF. The PCR product (705 bp) was inserted into the EcoRI/XbaI recognition sites of the bacterial expression vector pMal-c2. This procedure allowed the expression of the viral UL56 gene fused to the maltose-binding protein (MBP) of Escherichia coli, and subsequent cleavage of the fusion protein with the specific protease factor Xa. The induced fusion protein was purified by affinity chromatography using amylose columns. The apparent molecular weight of the fusion protein was about 70 kDa. Factor Xa cleaves the fusion protein into two subfragments of 42 kDa (MBP) and 30 kDa (UL56). Rabbit antisera induced against recombinant UL56 protein were used for detection of the UL56 gene product during the infection cycles of HSV-1. The presence of the UL56 protein was detected in infected cells and in HSV-1 virions by Western blot experiments and by immunofluorescence assays. A strong and increasing cytoplasmic fluorescence was observed in RC-37 cells infected with HSV-1 strain F between 6 and 16 h post-infection. In addition it was found that human HSV-1 IgM/IgG positive convalescent sera recognized the recombinant UL56 protein.

Characterization of the vaccinia virus L1R myristylprotein as a component of the intracellular virion envelope

In many cases, virus-encoded acylproteins appear to localize to specific cellular and viral membranes and to be directly involved with the processes of virus morphogenesis and/or egress from the infected cell. It was therefore of interest to determine whether the major vaccinia virus (VV) myristylprotein, L1R, is specifically associated with one or more of the membranes enveloping various infectious forms of VV virions. To this end, single-membraned intracellular virions (INV) and extracellular enveloped virions (EEV), which are surrounded by at least two distinct membranes, were purified from VV-infected cell lysates. The location of the VV L1R protein was determined by using a monospecific anti-L1R serum to detect the L1R protein by immunoblot in INV- and EEV-containing fractions, by examining the proteinase K sensitivity of the L1R protein in intact INV and EEV particles, and by immunoelectron microscopy. The data obtained clearly indicate that although the L1R protein is a constituent of both the INV and EEV particles, it is exclusively found in the inner INV-specific membrane. These results are discussed with regard to the potential role of the VV L1R protein in the primary intracellular envelopment of infectious VV particles.

Purification of viruses and macromolecular assemblies for structural investigations using a novel ion exchange method

We describe a novel ion exchange chromatographic technique suitable for large-scale preparation of viruses and other biomacromolecular assemblies in highly purified form. The method, which utilizes anion exchange on either of two commercially available cellulose cartridges, is applied to the Escherichia coli bacteriophage PRD1. Viral particles eluted from both QMA and DEAE cartridges retain infectivity and exhibit greater homogeneity of composition, as judged by gel electrophoresis and electron microscopy, than particles purified by rate zonal sucrose gradient centrifugation. The ion exchange protocols are rapid, requiring less than 15 min elution time, and permit retrieval of the purified viral particles at high concentration in aqueous media without centrifugal pelleting. The present method is particularly well suited to the preparation of milligram to decigram quantities of virus, sufficient for many biophysical structural analyses, including investigations by solution spectroscopic and crystal diffraction techniques. The feasibility and advantages of the ion exchange chromatographic procedure are demonstrated by application of laser Raman spectroscopy to ion exchange purified PRD1 virions and subviral assemblies.

Assignment of disulfide bridges in the fusion glycoprotein of Sendai virus

The mature fusion (F) glycoprotein of the paramyxovirus family consists of two disulfide-linked subunits, the N-terminal F2 and the C-terminal F1 subunits, and contains 10 cysteine residues which are highly conserved at specific positions. The high level of conservation strongly suggests that they are indeed disulfide linked and play important roles in the folding and functioning of the molecule. However, it has not even been clarified which cysteine residues link the F2 and F1 subunits. This report describes our assignment of the disulfide bridges in purified Sendai virus F glycoprotein by fragmentation of the polypeptide and isolation of cystine-containing peptides and determination of their N-terminal sequences. The data demonstrate that all of the 10 cysteine residues participate in disulfide bridges and that Cys-70, the only cysteine in F2, and Cys-199, the most upstream cysteine in F1, form the interchain bond. Of the remaining eight cysteine residues clustered near the transmembrane domain of F1, the specific bridges identified are Cys-338 to Cys-347 and Cys-362 to Cys-370. Although no exact pairings between the subsequent four residues were defined, it seems likely that the most downstream, Cys-424, is linked to Cys-394, Cys-399, or Cys-401. Thus, we conclude that the cysteine-rich domain indeed contributes to the formation of a bunched structure containing at least two tandem cystine loops.

The phospholipid composition of extracellular herpes simplex virions differs from that of host cell nuclei

Enveloped viruses of eukaryotes obtain their membrane by budding through a cellular membrane. Therefore, most frequently the lipid composition of the virion envelope reflects that of the membrane where budding took place. In the case of herpes simplex viruses, nucleocapsids assemble in the nucleus and bud through the inner nuclear membrane. The pathway from the perinuclear space to the extracellular medium is as yet poorly understood. Here we demonstrate that the phospholipid composition of extracellular herpes simplex virions differs from that of nuclei isolated from the infected cells. The viral membrane contains threefold higher concentrations of sphingomyelin and phosphatidylserine. These lipids are typically enriched in the Golgi apparatus and plasma membrane. The data are in agreement with a model in which herpes simplex virus, after budding through the inner nuclear membrane, loses its envelope by fusing with the outer nuclear membrane and obtains a new membrane by budding into a compartment late in the exocytotic pathway, very likely the Golgi apparatus or membranes derived from it. Alternatively, because the perinuclear space is continuous with the ER lumen, the virus after its first budding may be transported through the exocytotic pathway without ever leaving the lumen of the subsequent compartments. In that case, either the virions, while budding through the nuclear membrane select for sphingomyelin and phosphatidylserine, or the original lipids of the viral envelope are exchanged for lipids of an exocytotic membrane, most likely by a transient membrane continuity between the virion and the vesicle by which it is surrounded. Light particles, virus-like particles that lack capsid and DNA but contain tegument and envelope proteins, displayed the same lipid composition as complete herpes simplex virions, suggesting that they also acquired their envelope from a Golgi membrane.

The herpes simplex virus type 1 particle: structure and molecular functions. Review article

This review is a summary of our present knowledge with respect to the structure of the virion of herpes simplex virus type 1. The virion consists of a capsid into which the DNA is packaged, a tegument and an external envelope. The protein compositions of the structures outside the genome are described as well as the functions of individual proteins. Seven capsid proteins are identified, and two of them are mainly present in precursors of mature DNA-containing capsids. The protein components of the 150 hexamers and 12 pentamers in the icosahedral capsid are known. These capsomers all have a central channel and are connected by Y-shaped triplexes. In contrast to the capsid, the tegument has a less defined structure in which 11 proteins have been identified so far. Most of them are phosphorylated. Eleven virus-encoded glycoproteins are present in the envelope, and there may be a few more membrane proteins not yet identified. Functions of these glycoproteins include attachment to and penetration of the cellular membrane. The structural proteins, their functions, coding genes and localizations are listed in table form.

Temperature-sensitive mutations in the gene encoding the small subunit of the vaccinia virus early transcription factor impair promoter binding, transcription activation, and packaging of multiple virion components

The vaccinia virus D6R open reading frame encodes the small subunit of the heterodimeric vaccinia virus early transcription factor (VETF) that activates transcription of early genes in vitro. VETF binds early gene promoters and has a DNA-dependent ATPase activity that is essential for activation of transcription. To examine the relationship between the structure and function of VETF, we have localized the mutations in two temperature-sensitive viruses whose lesions previously were mapped to the D6R gene. For both mutants, a single G-to-A nucleotide change that would alter protein coding potential was identified. In mutant E93, the codon for alanine 25 was changed to that of threonine, and in mutant S4 the codon for valine 278 was replaced with that for methionine. The molecular phenotype of each mutant was assessed by expressing mutant transcription factors in HeLa cells by using a vaccinia virus-T7 system and characterizing the proteins' activities in vitro. The A25T mutant activated transcription to a lesser extent than wild-type VETF, and the V278M mutant had no demonstrable transcription factor activity. Both mutant proteins were shown to be defective for promoter binding, accounting for their impairment in transcription activation. The functional defects for both mutants were observed at permissive as well as nonpermissive temperatures. The mutant proteins retained ATPase activity but required higher DNA concentrations to activate the ATPase. These results indicate that the small subunit of VETF is essential for its promoter binding activity and likely contacts the promoter DNA. Immunoblotting experiments showed that the virion particles from the two mutant viruses contained about half the VETF of wild-type virus, suggesting that promoter binding may contribute to packaging of VETF into the virion particle. RNA polymerase, mRNA capping enzyme, and nucleoside triphosphate phosphohydrolase I were found at similarly reduced levels in the virion, indicating that packaging of some virion core enzymes may be interdependent.

A simple and reliable method to detect cell membrane proteins on infectious human immunodeficiency virus type 1 particles

Identification of cell-derived molecules on infectious human immunodeficiency virus type 1 (HIV-1) particles may be helpful in investigating mechanisms of HIV infection and in vaccine studies. Some of these molecules were detected on HIV-1 virions in previous studies, but rather elaborate methods were used. The method presented here allows an extensive characterization of the cell surface molecules associated with HIV-1 by capturing virus particles on monoclonal antibodies to cell membrane antigens bound to plastic wells. Binding of infectious virus was assessed by adding permissive target cells (C8166) and determining viral replication. With this procedure, beta 2-microglobulin, HLA-DR, intercellular adhesion molecule-1, and leukocyte function antigen-1 were found on HIV-1 particles from laboratory strains and primary clinical isolates. In contrast, CD19, CD4, and CD8 molecules were not detected.

Detection by immunogold labelling of P75 readthrough protein near an extremity of beet necrotic yellow vein virus particles

RNA 2 of beet necrotic yellow vein virus carries the cistron for the 21 kd coat protein at its 5'-extremity. During translation, the coat protein cistron termination codon is suppressed about 10% of the time so that translation continues into the adjacent open reading frame to produce a 75 kd species, known as P75, which contains the coat protein sequence at its N-terminus. Immunoblotting experiments with a P75-specific antiserum showed that P75 is present in only trace amounts in purified virus preparations. Electron microscopic visualization of immunogold-labelled virions in crude tissue extracts has provided evidence for an association between P75 and at least a fraction of the BNYVV particles, with P75 being predominantly located near one end of the rod-shaped virions. This finding is discussed in the context of the current model for the role of P75 in virus assembly and vector transmission.

The molecular biology of HIV. Insights into pathogenesis and targets for therapy

In the past 10 years, a large number of investigators have produced an enormous amount of information concerning the molecular biology of HIV. These studies at the most basic biological level have provided essential insights into the pathogenesis of the disease. They have supplied the information necessary for the creation of the antiviral therapies now available and have indicated the direction for the development of new therapies now in clinical trials and under investigation. Although the relatively ineffective therapies currently available serve as a constant source of disappointment for those practitioners who care for HIV-infected patients, there is some comfort to be gained from the rapid pace of investigation into the basic biology of the virus and the certainty that any more effective therapy must build upon the basic biological knowledge already obtained. A detailed study of some of the unique features observed during pediatric and perinatal HIV infection, particularly the relatively shortened time from infection to symptoms and the relative importance of CNS disease, may suggest new therapeutic approaches that will benefit both adult and pediatric patients. Finally, a comprehensive knowledge of HIV biology is an essential requirement for therapeutic maneuvers designed to interrupt the transmission of HIV from mother to child.

Characterization of filoviruses based on differences in structure and antigenicity of the virion glycoprotein

Eight different filovirus isolates, representing major episodes of filovirus hemorrhagic disease, were propagated for structural and antigenetic analyses of their glycoprotein (GP). Carbohydrate analysis revealed that N- and O-glycosylation are features of filovirus GPs. Oligosaccharide side chains differed in their sialylation pattern and seemed to be cell line-dependent. Marburg virus (MBG) isolates are clearly distinguished from Ebola (EBO) and Reston viruses by a lack of terminal sialic acids when propagated in E6 and MA-104 cells. It was also determined that GP-specific antisera failed to show any cross-reactivity between MBG isolates and other filoviruses. These data, together with prior findings, indicate that the genus Filovirus can be divided into a MBG group and EBO group.

Morphological and cytochemical analysis of human cytomegalovirus inoculum: correlation of free particles in inoculum with counterparts in infected cells

Electron microscopic examination of human cytomegalovirus (HCMV) inoculum, as used in the laboratory and generated by infection of human fibroblasts at low multiplicity, led to the distinction of 7 different structures. Complete virions constituted 38% of the inoculum. Non-infectious enveloped particles (NIEP) were also quite numerous (4.7%). Inoculum also contained other enveloped and non-enveloped particles. Dense bodies were the most numerous (50.2%). The Feulgen-like osmium ammine/SO2 reaction applied to ultrathin sections of inoculum suggests that NIEP, considered to be lacking DNA, may contain small and varying amounts of DNA. This DNA was lightly stained and appeared as a filamentous ring in the core structure, extending to the limits of the capsid. A correlation was established between particles identifiable in HCMV-infected cells and their free counterparts in the inoculum, which revealed that all intracytoplasmic particles are present in the inoculum. All of these elements could potentially contribute to virus-induced phenomena associated with HCMV infection of cells in vitro.

Novel tyrosine markers in Raman spectra of wild-type and mutant (Y21M and Y24M) Ff virions indicate unusual environments for coat protein phenoxyls

The tyrosine side chain generates a pair of distinctive Raman bands--a Fermi doublet near 850 and 830 cm-1--with relative intensities diagnostic of hydrogen bonding states of the phenolic acceptor and donor atoms [Siamwiza et al. (1975) Biochemistry 14, 4870-4876]. This structural correlation has been tested extensively and is used widely as an indicator of tyrosine interactions in globular proteins and their assemblies. However, in Ff filamentous viruses (fd, f1, M13) the apparent Fermi doublet intensity ratio (I853/I826 approximately 4.0) is much greater than the maximum predicted or observed in other proteins. To understand this anomaly, we have reevaluated the basis for the Fermi doublet assignment in Ff. We report Raman spectra of site-specific mutants of Ff in which either one (Y21M and Y24M) or both (Y21F/Y24S) tyrosines of the coat protein subunit (pVIII) have been mutated. These Raman data, together with those obtained from Ff virions carrying residue-specific tyrosyl (Y-d4) and phenylalanyl (F-d5) deuterations in pVIII, demonstrate conclusively that the 853 and 826 cm-1 bands of Ff do not constitute a typical tyrosine Fermi doublet: The observed 826 cm-1 Raman band of Ff is due not to tyrosine but to phenylalanine residues of pVIII. The 853 cm-1 Raman band thus constitutes the first known example of a "tyrosine singlet" in the Raman spectrum of a protein. The implications of this finding for Ff virion structure and its relevance to tyrosine markers in other proteins are discussed.

Expression of infectious pancreatic necrosis virus polyprotein and VP1 in insect cells and the detection of the polyprotein in purified virus

In order to study the molecular biology of infectious pancreatic necrosis virus (IPNV) replication, six different recombinant baculoviruses were constructed. The following four recombinants contained genome segment A-specific sequences; (i) AcPP contained the complete polyprotein coding region and Spodoptera frugiperda (Sf) cells infected by these recombinants synthesized the 106-kDa polyprotein (NH2-preVP2-NS protease-VP3-COOH), which was only partially processed by the protease to yield preVP2 and VP3 and unprocessed polyprotein; (ii) AcPP(S) and AcPP(Ss) represented 3' truncated sequences of the segment A cDNA where the VP3 coding region and that coding for 30 and 98 carboxy terminal amino acids of NS in the two constructs, respectively, were deleted. AcPP(S) demonstrated partial, and that of AcPP(Ss), complete loss of proteolytic activity, demonstrating that the carboxy one-third of the 29-kDa NS protease is necessary for the formation of the active enzyme; and (iii) AcPP(B/B) contained all but the first 180 nt of the pVP2 gene, the complete NS coding region, and the amino end of VP3. Analysis of cells coinfected with AcPP(Ss) and AcPP(B/B) showed either that the protease did not work in trans or that the alteration of the structure of the substrate prevented cleavage. Recombinant baculoviruses AcVP1VL and AcVP1ETL contained IPNV genome segment B cDNA encoding the 94-kDa VP1 which is the viral RNA-dependent RNA polymerase. AcVP1VL contained the whole segment B cDNA, whereas in AcVP1ETL, the 5' non-coding sequences were deleted resulting in the production of large amounts of VP1 when Sf cells were infected with this recombinant. The use of recombinants AcPP and AcVP1ETL as well as monoclonal antibodies and VP1-specific sera allowed the unambiguous identification of the high molecular weight minor polypeptides present in purified IPNV demonstrating the presence of both VP1 and the polyprotein in purified virus preparations.

Formation and rearrangement of disulfide bonds during maturation of the Sindbis virus E1 glycoprotein

The rigidly ordered icosahedral lattice of the Sindbis virus envelope is composed of a host-derived membrane bilayer in which the viral glycoproteins E1 and E2 reside. E1-E1 interactions stabilized by intramolecular disulfide bridges play a significant role in maintaining the envelope's structural integrity (R. P. Anthony and D. T. Brown, J. Virol. 65:1187-1194, 1991; R. P. Anthony, A. M. Paredes, and D. T. Brown, Virology 190:330-336, 1992). We have examined the acquisition of disulfide bridges within E1 during its maturation. Prior to exit from the endoplasmic reticulum, E1 folds via at least three intermediates, differing in the number and/or arrangement of their disulfides, into a single, compact form. This E1 species remains stable with respect to its disulfides until late in the secretory pathway, when E1 attains a metastable conformation. At this point, when appropriately triggered, intramolecular thiol-disulfide exchange reactions within E1 can occur, resulting in the generation of alternative E1 species. This metastable nature of mature E1 may have important implications for the mechanism of virus disassembly during the initial stages of the infection process (B. Abell and D. T. Brown, J. Virol. 67:5496-5501, 1993).

The refined three-dimensional structure of an insect virus at 2.8 A resolution

The structure of the black beetle nodavirus has been refined at 2.8 A resolution by alternate use of restrained least-squares atomic coordinate refinement and phase refinement by real space averaging with the 5-fold non-crystallographic symmetry in the crystal. The coordinates were also refined by simulated annealing. The final R-factor for all data with I/sigma(I) > 4 was 22.1%. A total of 7692 atoms were refined in one icosahedral asymmetric unit which included 273 oxygen atoms of ordered water molecules. Three identical gene products of 407 amino acids form one icosahedral asymmetric unit. Each is located in a structurally unique position, identified as A, B or C, consistent with a T = 3 quasi equivalent lattice. Icosahedral pentamers are formed by A subunits while B and C subunits alternate about icosahedral 3-fold axes to form quasi hexamers. Five calcium ions are located within the icosahedral asymmetric unit and stabilize the quasi 3-fold related intersubunit contacts between A, B and C. The final model consists of coordinates for residues 56 to 379 of all three subunits and residues 20 to 31 from the C subunit only. Atom positions for the sugar-phosphate backbone were modeled for ten nucleotides close to the icosahedral 2-fold axes. Symmetry equivalent polyribonucleotides form a helical duplex at each icosahedral 2-fold axis. The three subunits display an eight-stranded beta-barrel fold, very similar to the subunit structures observed in most other icosahedral RNA viruses analyzed. Quasi equivalence is regulated by the ordered RNA and residues 20 to 31 in the C subunit to form a "flat inter subunit contact" at icosahedral 2-fold joints. The RNA and polypeptide are disordered at the quasi 2-fold joints and this results in a "bent inter subunit contact". Although similar quaternary structures were seen in T = 3 plant viruses studied, RNA did not play a role as a molecular switch in those structures. The autocatalytic, post assembly, cleavage of the initial gene product at residue Asn363/Ala364 to form a stable and infectious particle is probably the result of an acid catalyzed main-chain hydrolysis in which Asp75 is the proton donor. The reaction is initiated by assembly which places Asp75 in a hydrophobic environment created by quaternary interactions which raises its pK to 5.6. The region in which the reaction occurs is formed by an internal helical bundle that has not been seen in other virus structures.

Analysis of messenger RNA within virions of IBV

The presence of subgenomic mRNAs (sgRNAs) in virions of infectious bronchitis virus was examined by probing Northern blots of RNA extracted from virions using as a probe a cDNA of the 3'-terminal nucleocapsid protein (N) gene. The sgRNAs were readily detected even after extensive purification of virions and after RNase A treatment of virions. The molar ratio of gRNA to each sgRNA was in the range 25 to 400 for IBV-M41 and 10 to 30 for IBV-Beaudette. After comparison with the molar ratios of genomic to intracellular viral sgRNAs it was estimated that the efficiency of incorporation of gRNA into virions was approximately 100 to 500-fold greater than for sgRNAs in the case of M41 and 20 to 100-fold for Beaudette, depending on the sgRNA species. It is concluded that sgRNAs can be present within IBV virions. Approximately 1 in 3 Beaudette virions and 1 in 20 M41 particles might contain a single copy of one sgRNA.

One retroviral RNA is sufficient for synthesis of viral DNA

We used previously characterized spleen necrosis virus-based retroviral vectors and helper cells to study the strand transfers that occur during the reverse-transcription phase of a single cycle of retroviral replication. The conditions used selected only for formation of an active provirus rather than for expression of multiple drug resistance markers. In nonrecombinant proviruses the minus- and plus-strand DNA primer transfers were almost completely intramolecular. However, as previously reported, recombinant proviruses contained approximately equal proportions of inter- and intramolecular minus-strand DNA primer transfers. Thus, we conclude that in the absence of recombination, one molecule of retroviral RNA is sufficient for viral DNA synthesis. Large deletions and deletions with insertions were detected primarily at a limited number of positions which appear to be hot spots for such events, the primer binding site and regions containing multiple inverted repeats. At these hot spots, the rate of deletions and deletions with insertions visible with PCR was about 10% per genome per replication cycle. Other deletions and deletions with insertions (detectable with PCR) occurred at a rate of about 0.5%/kb per replication cycle. Crossovers occurred at a rate of about 6%/kb per replication cycle under single-selection conditions. This rate is comparable to the rate that we reported previously under double-selection conditions, indicating that retroviral homologous recombination is not highly error prone. The combined rates of deletions and deletions with insertions at hot spots (10% per genome per replication cycle) and other sites (0.5%/kb per replication cycle) and the rate of crossovers (6%/kb per replication cycle) indicate that on average, full-size (10-kb) type C retroviruses undergo an additional or aberrant strand transfer about once per cycle of infection.

Equid herpesviruses 1 and 4 encode functional homologs of the herpes simplex virus type 1 virion transactivator protein, VP16

The herpes simplex virus type 1 (HSV-1) tegument protein VP16 is a potent transcriptional inducer of immediate-early gene expression, comprising an N-terminal domain involved in binding DNA linked to an acidic transactivating C-terminal domain. The gene encoding the counterpart of this protein in equid herpesvirus 4 (EHV-4) was sequenced. Comparisons with VP16 and the homologous proteins of equine herpesvirus 1 (EHV-1) and varicella-zoster virus (VZV) showed that a region in the N-terminal domain involved in formation of a complex with cellular proteins is partially conserved in all four proteins. In contrast, the C-terminal regions of the EHV proteins, like that of VZV, are not particularly acidic and are not significantly conserved with respect to the C-terminal region of VP16. Nevertheless, transient expression experiments indicated that the EHV-1 and EHV-4 proteins are able to transactivate HSV-1 and EHV-1 immediate-early promoters in a dose-dependent manner, which suggests that this activity is not dependent on an acidic C-terminal domain.

Isolation of a herpes simplex virus type 1 mutant with a deletion in the virion host shutoff gene and identification of multiple forms of the vhs (UL41) polypeptide

The virion host shutoff (vhs) gene (UL41) of herpes simplex virus type 1 (HSV-1) encodes a virion component that induces degradation of host mRNAs and the shutoff of most host protein synthesis. Subsequently, the vhs protein accelerates the turnover of all kinetic classes of viral mRNA. To identify the vhs (UL41) polypeptide within infected cells and virions, antisera raised against a UL41-lacZ fusion protein were used to characterize the polypeptides encoded by wild-type HSV-1 and two mutants: vhs1, a previously characterized mutant that lacks detectable virion host shutoff activity, and vhs-delta Sma, a newly constructed mutant containing a deletion of 196 codons from UL41. Two forms of the vhs (UL41) polypeptide were identified in cells infected with the wild-type virus or vhs1. Wild-type HSV-1 produced a major 58-kDa polypeptide, as well as a less abundant 59.5-kDa form of the protein, while vhs1 produced 57- and 59-kDa polypeptides that were approximately equally abundant. Although for either virus, both forms of the protein were phosphorylated, they differed in the extent of phosphorylation. While both vhs polypeptides were found in infected cells, only the faster migrating, less phosphorylated form was incorporated into virions. vhs-delta Sma encoded a smaller, 31-kDa polypeptide which, although present in infected cells, was not incorporated into virions. The results identify multiple forms of the vhs (UL41) polypeptide and suggest that posttranslational processing affects its packaging into virions, as well as its ability to induce mRNA degradation.

A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein

Two proteins, one of 31 kDa and one of 16 kDa, are encoded by a segment of the phage lambda tail gene region that contains two overlapping reading frames, neither of which is long enough to encode the larger protein. We show that the abundant 16-kDa protein (gpG) is encoded by the upstream open reading frame, gene G. The 31-kDa protein, gpG-T, is encoded jointly by gene G and the overlapping downstream T open reading frame. gpG-T is synthesized as the result of a translational frameshift that occurs when a ribosome translating the G gene slips back by one nucleotide at a position six codons from the C terminus of the gene and thereby bypasses the G termination codon to continue on in the T open reading frame. The resulting protein shares 135 residues of N-terminal amino acid sequence with gpG, followed by 144 amino acid residues of unique sequence. The frameshift event occurs with a frequency of approximately 4% at the sequence G GGA AAG, which encodes the dipeptide -Gly-Lys- in both the zero and -1 reading frames. The frameshift frequencies of point mutants in this "slippery sequence" argue that codon-anticodon interactions with both the glycyl and the lysyl-tRNA are important for frameshifting to occur. We find no clear evidence for a pausing mechanism to enhance frameshifting, as is seen in other well-characterized frameshifts. No simple secondary structure has been predicted for the region downstream from the slippery sequence, but this downstream sequence does contribute to the frameshifting rate. Our results together with those of Katsura and Kühl show that the frameshift product, gpG-T, has an essential role in lambda tail assembly, acting prior to tail shaft assembly. The role of gpG in tail assembly is not known. We find that both gpG and the gpG-T are absent from mature virions.

Dissecting the assembly of orbiviruses

Virus assembly within infected cells involves a precise sequence of macromolecular interactions. To unravel the individual steps involved in the assembly of a complete virion of bluetongue virus, we have engineered a series of recombinant baculoviruses to make multicomponent structures resembling virus structures. When combined with cryoelectron microscopy and image processing techniques the data reveal the organization and assembly of the various components of this virus.

fd coat protein structure in membrane environments

The membrane bound form of bacteriophage fd coat protein has a long hydrophobic membrane spanning helix and a shorter amphipathic helix in the plane of the bilayer. Residues near the N and C termini and in the turn connecting the two helices are mobile. The locations and orientations of the helical secondary structure elements and the protein backbone dynamics were characterized by combining results from multidimensional solution NMR experiments on protein samples in micelles and high resolution solid-state NMR experiments on protein samples in oriented and unoriented lipid bilayers. The coat protein is a monomer in micelles. The secondary structure of the membrane bound form of fd coat protein is very similar to that of the structural form found in the virus particles, since it is nearly all alpha helix. However, the membrane bound form of the protein differs from the structural form of the protein in virus particles in the arrangement of the secondary structure, since the membrane bound form of the protein has two distinct helical domains oriented perpendicular to each other and the structural form of the protein in the virus particles has a nearly continuous helix aligned approximately along the filament axis. In addition, there are substantial differences in the dynamics of residues in the bend between the two helices and near the C terminus, since they are mobile in the membrane bound form of the protein and not in the virus particles. Residues 1 to 5 at the N terminus are highly mobile and unstructured in both the membrane bound and structural forms of the coat protein.

Early steps in reovirus infection are associated with dramatic changes in supramolecular structure and protein conformation: analysis of virions and subviral particles by cryoelectron microscopy and image reconstruction

Three structural forms of type 1 Lang reovirus (virions, intermediate subviral particles [ISVPs], and cores) have been examined by cryoelectron microscopy (cryoEM) and image reconstruction at 27 to 32-A resolution. Analysis of the three-dimensional maps and known biochemical composition allows determination of capsid protein location, globular shape, stoichiometry, quaternary organization, and interactions with adjacent capsid proteins. Comparisons of the virion, ISVP and core structures and examination of difference maps reveal dramatic changes in supra-molecular structure and protein conformation that are related to the early steps of reovirus infection. The intact virion (approximately 850-A diam) is designed for environmental stability in which the dsRNA genome is protected not only by tight sigma 3-mu 1, lambda 2-sigma 3, and lambda 2-mu 1 interactions in the outer capsid but also by a densely packed core shell formed primarily by lambda 1 and sigma 2. The segmented genome appears to be packed in a liquid crystalline fashion at radii < 240 A. Depending on viral growth conditions, virions undergo cleavage by enteric or endosomal/lysosomal proteases, to generate the activated ISVP (approximately 800-A diam). This transition involves the release of an outer capsid layer spanning radii from 360 to 427 A that is formed by 60 tetrameric and 60 hexameric clusters of ellipsoidal subunits of sigma 3. The vertex-associated cell attachment protein, sigma 1, also undergoes a striking change from a poorly visualized, more compact form, to an extended, flexible fiber. This conformational change may maximize interactions of sigma 1 with cell surface receptors. Transcription of viral mRNAs is mediated by the core particle (approximately 600-A diam), generated from the ISVP after penetration and uncoating. The transition from ISVP to core involves release of the 12 sigma 1 fibers and the remaining outer capsid layer formed by 200 trimers of rod-shaped mu 1 subunits that span radii from 306 to 395 A. In the virion and ISVP, flower-shaped pentamers of the lambda 2 protein are centered at the vertices. In the ISVP-to-core transition, domains of the lambda 2 subunits rotate and swing upward and outward to form a turret-like structure extending from radii 305 to 400 A, with a diameter of 184 A, and a central channel 84 A wide. This novel conformational change allows the potential diffusion of substrates for transcription and exit of newly synthesized mRNA segments.(ABSTRACT TRUNCATED AT 400 WORDS)

Demonstration of sugar moiety on the surface of hepatitis C virions recovered from the circulation of infected humans

The amino acid sequence for the envelope protein(s) predicted from the nucleotide sequence of the E and E2/NS1 regions of the hepatitis C virus (HCV) genome is enriched with an N-linked glycosylation site motif, Asn-X-Thr/Ser, suggesting oligosaccharide moieties are present on the virion surface. We attempted to characterize the sugar moiety on the surface of HCV virions recovered from sera of infected humans to assess the natural properties of the virus. Six kinds of lectins were used to bind HCV virions in affinity column chromatographies: RCAI, WGA, Con A, AAL, LCA, and PNA. Lectin-bound virions were identified by detecting HCV RNA in eluted chromatography fractions with a polymerase chain reaction (PCR) method. Our results showed that HCV was similar to hepatitis B virus (HBV) in characteristics of binding to lectins: HCV showed a strong binding to RCAI and WGA, weak binding to Con A, and no detectable binding to AAL, LCA, or PNA. Treatment of the HCV virion preparation with an enzyme, glycopeptidase A, or a detergent, NP-40, resulted in a significant decrease in the ability to bind these lectins. Our results suggest that asparagine-linked sugar chains are present on the surface of native virions of HCV, very similar to those for HBV.

Host-specific hemagglutination of influenza A (H1N1) virus

H1N1 strains of influenza A virus isolated during the influenza season of 1991-92 were divided into two groups according to the property of host-specific hemagglutination. Group 1 viruses agglutinated human and chicken red blood cells. Group 2 viruses agglutinated human but not chicken red blood cells. The viruses of both groups, however, showed the same antigenic structure determined with ferret antisera. The virus clones which were plaque-purified twice from a group 2 virus retained the characteristic of host-specific hemagglutination after five successive passages in MDCK cells, indicating that this phenomenon is genetically determined. However, the amino acid sequences of the hemagglutinin (HA) polypeptides deduced from the nucleotide sequences of the HA gene of the two groups did not show any differences between them. This suggests a difference in amino acids in some other polypeptide(s), which affects the host-specific hemagglutination.

A mobile element on a virus particle surface identified by nuclear magnetic resonance spectroscopy

The presence of a mobile element in the coat protein of pepper ringspot tobravirus (PRV) has been established by 1H n.m.r. spectroscopy; two-dimensional correlation spectroscopy (COSY) measurements show that this element consists of alanine, asparagine, glycine, proline, serine and threonine only. By reference to the amino acid sequence of the coat protein, it is concluded that the mobile element is associated with the C-terminal region and consists of between 11 and 38 residues.

The HSV-1 UL45 18 kDa gene product is a true late protein and a component of the virion

Previously we constructed a null mutation in the HSV-1 UL45 gene, showed that the UL45 gene was not required for growth in Vero cells, and confirmed that it coded for an 18 kDa protein (R.J. Visalli and C.R. Brandt, Virology 185:419-423, 1991). In this study, we have continued our characterization of the UL45 gene and the 18 kDa protein. Analysis of UL45 RNA revealed that the gene was expressed late and was inhibited in the presence of phosphonoacetic acid (paa), indicating it is a gamma 2 class gene. Using a specific polyclonal antiserum, we found that the 18 kDa UL45 gene product was also expressed late and was inhibited in the presence of paa. The 18 kDa protein was present in purified virions and was substantially enriched in the envelope-tegument fraction of virions disrupted with NP-40 detergent. The 18 kDa protein is thus a structural protein of the virus and appears to be associated with the viral envelope. A 20 kDa protein that cross-reacted with a polyclonal HSV-1 UL45 antiserum was also detected in cells infected with HSV-2 strain 333.

Assembly, processing, and infectivity of human immunodeficiency virus type 1 gag mutants

We studied the effects of gag mutations on human immunodeficiency virus type 1 (HIV-1) assembly, processing, and infectivity by using a replication-defective HIV expression system. HIV mutants were screened for infectivity by transduction of a selectable marker and were examined for assembly by monitoring particle release from transfected cells. Gag protein processing and reverse transcriptase activities of mutant particles were also assayed. Surprisingly, most Gag protein mutants were assembled and processed. The two exceptions to this rule were a myristylation-minus mutant, and one gag matrix domain mutant which expressed proteins that were trapped intracellularly. Interestingly, a mutant with a 56-amino-acid deletion within the HIV gag capsid domain still could assemble and process virus particles, exhibited a wild-type retrovirus particle density, and had wild-type reverse transcriptase activity. Indeed, although most HIV-1 gag mutants were noninfectious or poorly infectious, they produced apparently normal particles which possessed significant reverse transcriptase activities. These results strongly support the notion that the HIV-1 Gag proteins are functionally involved in post-assembly, postprocessing stages of virus infectivity.

Ribonucleoprotein complexes of hepatitis delta virus

Human hepatitis delta virus (HDV) is a subviral satellite agent of hepatitis B virus (HBV). The envelope proteins of HDV are provided by the helper virus, HBV, but very little is known about the internal structure of HDV. The particles contain multiple copies of the delta antigen and an unusual RNA genome that is small, about 1,700 nucleotides in length, single stranded, and circular. By using UV cross-linking, equilibrium density centrifugation, and immunoprecipitation, we obtained evidence consistent with the interpretation that delta antigen and genomic RNA form a stable ribonucleoprotein (RNP) complex within the virion. Furthermore, electron-microscopic examination of the purified viral RNP revealed a roughly spherical core-like structure with a diameter of 18.7 +/- 2.5 nm. We also isolated HDV-specific RNP structures from the nuclei of cells undergoing HDV genome replication; both the genome and antigenome (a complement of the genome) of HDV were found to be in such complexes. From the equilibrium density analyses of the viral and nuclear RNPs, we were able to deduce the number of molecules of delta antigen per molecule of HDV RNA. For virions, this number was predominantly ca. 70, which was larger than for the nuclear RNPs, which were more heterogeneous, with an average value of ca. 30.

Isolation of a phospholipid-free protein shell of bacteriophage PRD1, an Escherichia coli virus with an internal membrane

PRD1 is a double-stranded DNA virus infecting Escherichia coli and Salmonella typhimurium. It has an icosahedral outer protein capsid which encloses the viral membrane, inside of which resides the phage genome. In this investigation we demonstrate the detergent resistance of the intact virus particles. The membrane of empty DNA-free particles, however, is very sensitive to detergent action. We assume that their sensitivity is due to the access of detergents through a portal structure to the virus interior. Using the anionic detergent sodium dodecyl sulfate, it is possible to obtain a shell structure composed of the major coat protein P3 alone. The treatment of empty particles with the milder nonionic detergents n-octyl beta-D-glucopyranoside and Triton X-100 yielded P3 particles which retained the membrane-associated proteins P7 and P11. Deoxycholic acid treatment yielded shells of intermediate composition between those obtained with the nonionic detergents and sodium dodecyl sulfate.

Identification and molecular characterization of two diagnostically relevant marker proteins of the Epstein-Barr virus capsid antigen complex

The molecular specificity of the IgG response against Epstein-Barr virus (EBV) was studied in 345 randomly collected sera of normal healthy individuals. The sera were tested on immunoblots containing antigens of the cell line HH514.c16 (a superinducible derivate of P3HR1), noninduced or induced for the expression of early antigens (EA) or viral capsid antigens (VCA), and from the EBV-negative cell line Ramos-Nut. This study reveals a remarkable similar antigen recognition pattern of IgG class antibodies in sera of healthy EBV carriers. The protein bands recognized predominantly have molecular weights of 18 kD, 36/38 kD, 40 kD, 72 kD, and 160 kD. The 72 kD and 36/38 kD bands were identified as EBNA1 and "Zebra," respectively, using reading frame-specific antisera. The bands at 160 kD (major capsid protein), 40 kD, and 18 kD were identified as VCA-class proteins. Of all EBV-seropositive sera tested, 98% reacted with either p18 or p40 or both. The synthesis of the antigens p18 and p40 was inhibited by phosphonoacetic acid, indicating that these were true late proteins. The detection of p18 and p40 in purified virion and capsid preparations confirms that these proteins are structural components of viral capsid antigen complex.

Characterization of the UL10 gene product of herpes simplex virus type 1 and investigation of its role in vivo

On the basis of predicted amino acid sequence characteristics, herpes simplex virus type 1 gene UL10 is thought likely to encode a membrane protein with eight potential transmembrane regions. Previously, a protein with an apparent M(r) 47,000 on SDS-PAGE was identified as a product of this gene. Here we have further characterized this protein, and show that it is modified by N-linked glycosylation, associates with membranes from infected cells, and is a component of the virus particle. It is not essential for virus growth in tissue culture. To investigate its role in vivo a deletion mutant lacking the majority of the UL10 open reading frame was constructed (UL10-del). The in vitro growth properties of this virus were consistent with previous studies; it grew to give slightly lower yields than wild-type and revertant viruses, and had no apparent temperature-sensitive or host range phenotype. In vivo, in a mouse model, UL10-del was capable of establishing a latent infection, although it was impaired for growth at the periphery, and for spread to and/or growth within the nervous system relative to wild-type or revertant viruses.

Sindbis virus attachment: isolation and characterization of mutants with impaired binding to vertebrate cells

Sindbis virus can infect a broad range of insect and vertebrate cell types. The ability to restrict tissue tropism and target virus infection to specific cell types would expand the usefulness of engineered alphaviruses as gene expression vectors. In this study, virus pools derived from libraries of full-length Sindbis virus cDNA clones containing random insertion mutations in the PE2 or E1 virion glycoprotein gene were screened for mutants defective for binding to vertebrate cells. Binding-competent mutants were depleted by serial adsorption to chicken embryo fibroblast (CEF) monolayers at 4 degrees C, and the remaining population was amplified by immune-enhanced infection of P388D1 cells. From the PE2 libraries, 12 candidate mutants showing reduced cytopathic effects on CEF monolayers were isolated and three representative mutants, NB1, NB2, and NB12, were characterized in detail. Insertion mutations for NB1 and NB12 were found near the PE2 cleavage site, whereas the insertion in NB2 occurred between residues 69 and 74 of E2. Although virion assembly and release occurred normally for all three mutants, PE2 cleavage was completely (NB1) or partially (NB12) blocked for the mutants with insertions near the PE2 cleavage site. Both NB1 and NB2 were defective for binding to CEF and BHK-21 cells. Mild trypsin digestion of isolated NB1 virions resulted in PE2 cleavage and partially restored binding to CEF. Besides defective binding, NB1 also exhibited slower CEF penetration kinetics. Consistent with previous work, these results implicate PE2 cleavage and domains in the N-terminal portion of E2 as important determinants of alphavirus binding and penetration. Binding-defective mutants such as NB2, which exhibit normal particle assembly, release, and penetration, may be useful for future efforts to target Sindbis virus infection.

Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution

The crystal structure of satellite tobacco mosaic virus (STMV) has been solved by a combination of multiple isomorphous replacement and molecular replacement methods and refined at 2.9 A resolution to a conventional R-factor of 0.215. STMV, a T = 1 icosahedral virus, is the smallest whose structure has been determined. The coat protein is an eight-stranded "Swiss roll" beta-barrel with an amino-terminal strand that extends away from the beta-barrel by more than 60 A. This strand is primarily responsible for quaternary interactions within the capsid. The most arresting feature of the virus structure is the intimate association of each capsid protein dimer with a Watson-Crick base-paired segment of RNA double helix on the interior of the virion. The icosahedral 2-fold axis of each dimer pair is coincident with that of the central base-pair of each helical RNA segment whose helical axis is along the edge of the icosahedron. The helical RNA segments are seven base-pairs in length with a stacked base at each 3' end so that a total of 16 nucleotides is clearly visible. The character of the RNA helix is somewhat different than any of the canonical forms. Assuming full occupancy, then approximately 45% of the total RNA genome is present in the electron density map. The close association of capsid with highly structured nucleic acid suggests that assembly of STMV is likely to be a highly co-operative process involving both protein and RNA. The nucleic acid is distributed within the virion with a high degree of order. The capsid protein is a true double helical RNA binding protein and a number of prominent interactions between protein and RNA can be clearly seen.

Basic amino acids flanking the zinc finger of Moloney murine leukemia virus nucleocapsid protein NCp10 are critical for virus infectivity

Nucleocapsid (NC) protein NCp10 of Moloney murine leukemia virus is encoded by the 3' domain of gag and contains a zinc finger surrounded by basic amino acids. During virion assembly, NC protein is necessary for core formation and the NC zinc finger is required for the packaging of the genomic RNA dimer. In vitro NCp10 has RNA-binding and -annealing activities critical for virus infectivity, since NCp10 promotes dimerization of viral RNA containing the Psi packaging element and annealing of replication primer tRNA(Pro) to the initiation site of reverse transcription (primer-binding site). To investigate the role of the basic amino acids flanking the NCp10 zinc finger, neutral residues were substituted for the basic amino acids and the effects of these mutations in vivo on virus assembly and infectivity and in vitro on the RNA-annealing activity of NCp10 were analyzed. Here we report that the substitution of 1 or 2 neutral amino acids for the basic residues did not impair the production of mature virions but that infectivity was either moderately or strongly attenuated. When more than 2 basic residues were replaced by neutral amino acids, viruses were poorly infectious because of a severe defect in genomic RNA dimer packaging and initiation of reverse transcription. In vitro NCp10-derived peptides with similar mutations were chemically synthesized and were found to be either fully or partially active or completely inactive. These data indicate that the basic residues flanking the zinc finger of NCp10 are required for the production of infectious Moloney murine leukemia virus virions.

Role of maturation cleavage in infectivity of picornaviruses: activation of an infectosome

Maturation of picornaviruses involves assembly of a "provirion," which undergoes an autocatalytic cleavage of VP0 to VP2 plus VP4. RNA transcripts from a cDNA clone of human rhinovirus 14 mutated at asparagine 68, one of the residues in the maturation cleavage site, generated normal yields of 150S particles which were noninfectious in the plaque assay because they were unable to initiate a second cycle of infection. These cleavage-defective provirions were otherwise indistinguishable from mature virions in sedimentation coefficient, binding affinity to monoclonal antibodies against neutralization sites IA, II, and III, attachment to HeLa cell receptors, and rate of cell-mediated conformational changes to form 125S A-particles and 80S empty capsids. These results suggest that maturation cleavage is required for the function of a previously undescribed intermediate which transfers packaged RNA across the membrane and into the cytosol. For this hypothetical intermediate, we propose the name infectosome. Since the native virus has a particle/PFU ratio of about 800, such an intermediate will be difficult to find. Mutations at serine 10 in VP2 reduced maturation cleavage to a rate sufficiently slow to show that the infectivity of virus particles increased with the degree of cleavage of VP0 to VP4 and VP2. This article describes the first characterization of a pure form of a picornaviral provirion, and hence the first direct evidence that provirions of picornaviruses lack infectivity.

Minus-strand DNA is present within murine type C ecotropic retroviruses prior to infection

Viral minus-strand DNA has been identified within ecotropic murine retroviruses prior to infection. The abundance of minus-strand DNA is inversely proportional to the distance from the primer binding site, suggesting that viral DNA is synthesized by reverse transcriptase with the genomic RNA as template. These findings demonstrate that replication of the retroviral genome is not initiated by infection and may begin after activation of reverse transcriptase by gag-pol cleavage during virus assembly.

Structural studies of the enveloped dsRNA bacteriophage phi 6 of Pseudomonas syringae by Raman spectroscopy. I. The virion and its membrane envelope

We report and interpret the first Raman spectrum of a double-stranded RNA virus containing a membrane envelope. Spectra of the native bacteriophage phi 6 and of its isolated host-attachment (spike) protein and phospholipid-free core assembly were collected from aqueous solutions over a wide range of temperature. Comparison of the vibrational spectra by digital difference methods permits the following structural conclusions regarding molecular constituents of the fully assembled virion. (1) The double-stranded RNA, phospholipid and protein components of the phage exhibit Raman amplitudes in accordance with their biochemically determined compositions in the native virion (10, 20 and 70%, respectively). (2) alpha-Helix and irregular conformations are the dominant secondary structures in proteins of both the viral membrane and nucleocapsid. This represents a departure from previously examined icosahedral phage and plant viruses, which are dominated by beta-sheet structures. (3) The phospholipids of the viral membrane are liquid crystalline throughout the determined range of virus thermostability (0 to 40 degrees C). (4) The P3 spike protein of phi 6, which is anchored to, but not sequestered within the viral membrane, is largely alpha-helical (approximately 35%) and highly thermolabile. Denaturation of P3 at temperatures above 30 degrees C leads to appreciable loss (approximately 20%) of alpha-helix in favor of beta-strand structure, and alters significantly the environments of many aromatic side-chains. (5) The secondary structures of integral membrane proteins of phi 6 are overwhelmingly alpha-helical (approximately 70 to 80%) and also thermolabile. In contrast to P3, which exhibits aspartate and glutamate carboxyls in the ionized form (CO2-), the integral membrane proteins exhibit only protonated carboxyl groups (COOH). Treatment of phi 6 with butylated hydroxytoluene (BHT), which has been shown to remove the P3 spike protein, does not significantly perturb phospholipids and associated integral proteins of the viral membrane or structural proteins and packaged double-stranded RNA of the nucleocapsid. However, P3 subunits, which are recovered after BHT treatment, exhibit radically altered secondary and tertiary structures, including the loss of most subunit alpha-helices. Among the P3 side-chains affected by BHT treatment, we note a general trend toward greater hydrophilicity and greater solvent exposure of the aromatic residues Trp and Tyr. On the other hand, the cysteine sulfhydryl groups of the BHT-isolated P3 monomer are not solvent exposed and function as strong hydrogen-bond donors in the protein core.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural studies of the enveloped dsRNA bacteriophage phi 6 of Pseudomonas syringae by Raman spectroscopy. II. Nucleocapsid structure and thermostability of the virion, nucleocapsid and polymerase complex

Structures and thermostabilities of the double-stranded (ds) RNA bacteriophage phi 6 and of its isolated nucleocapsid-polymerase complex (nucleocapsid core) and dsRNA components have been investigated by Raman spectroscopy. The spectra show that proteins of the phi 6 virion are collectively deficient in beta-sheet secondary structure. In particular, the major protein (P8) of the outer spherical shell of the phi 6 nucleocapsid exhibits a secondary structure dominated largely by alpha-helix and irregular conformations. The absence of appreciable beta-structure in the P8 subunit suggests a tertiary conformation lacking the beta-barrel motif common to subunits of most other spherical viral capsids. In addition, the Raman spectra show that subunits of the dodecahedral nucleocapsid core are also predominantly alpha-helical. The results thus indicate a largely alpha-helical secondary structure for the major subunit (P1) of the phi 6 nucleocapsid core, as well as for the P8 subunit of the outer spherical shell. Using Raman difference spectroscopy, we demonstrate that proteins of the nucleocapsid core (P1, P2, P4 and P7) interact extensively with the packaged phi 6 RNA genome, and further, that conformational stability of the packaged RNA is reduced upon removal from the core. Also, we find that proteins of the phi 6 nucleocapsid are significantly more thermostable than proteins of the viral membrane envelope, which are reported in the accompanying paper (Li et al., 1993). The present results suggest that both the architectural principles and modes of protein-RNA interaction in the phi 6 virion differ fundamentally from those of icosahedral single-stranded RNA viruses. Both Raman and circular dichroism spectra indicate that the dsRNA genome of phi 6 is an A-form structure. The Raman marker bands signify the presence only of C3'-endo/anti nucleoside conformers. The Raman signature of dsRNA, revealed in the spectrum of the phi 6 genome, is discussed here as a model for assessing base-pairing and base-stacking interactions in other ribonucleoprotein assemblies.

A mutant of herpes simplex virus type 1 in which the UL13 protein kinase gene is disrupted

Gene UL13 of herpes simplex virus type 1 (HSV-1) has previously been proposed to encode a protein kinase. An HSV-1 mutant with UL13 inactivated by insertion of the Escherichia coli lacZ gene was constructed. This UL13-lacZ mutant was found to grow to near wild-type (wt) titres in tissue culture. Comparison of silver-stained SDS-PAGE profiles of wt and UL13-lacZ virions demonstrated that the UL13 protein is a readily detectable component of wt virions, located in the tegument and probably equivalent to the previously described species VP18.8. Studies of in vitro phosphorylation with nuclear extracts of virus-infected cells and with detergent-treated virions showed that the UL13 protein is involved in phosphorylation of the tegument protein VP22. Extracts of cells engineered to express UL13, and infected with UL13-lacZ virus, were also capable of VP22 phosphorylation.

Herpes simplex virus type 1 UL46 and UL47 deletion mutants lack VP11 and VP12 or VP13 and VP14, respectively, and exhibit altered viral thymidine kinase expression

The gene products of herpes simplex virus type 1 UL46 and UL47 enhance the efficiency of alpha TIF (VP16)-mediated alpha gene expression through an unknown mechanism of action. To further characterize the function of the UL46- and UL47-encoded proteins during virus infection, a series of isogenic herpes simplex virus type 1 strain F-derived UL46 and UL47 single-deletion mutants and a UL46/47 double-deletion mutant were constructed and compared with the wild type. Analysis of purified virions obtained from the UL46 deletion mutant showed for the first time that UL46 encoded the viron tegument phosphoproteins VP11 and VP12 (VP11/12). Similar analyses of the UL47 deletion mutants confirmed an earlier report by McLean et al. that UL47 also encoded two virion tegument phosphoproteins, VP13 and VP14 (VP13/14) (G. McLean, F. Rixon, N. Langeland, L. Haarr, and H. Marsden, J. Gen. Virol. 71:2953-2960, 1990). Kinetic analysis demonstrated a delay of approximately 2 h in the appearance of thymidine kinase (TK) activity in all of the UL46 and UL47 single-deletion mutants. In the UL46/47 double-deletion mutant, the delay in TK activity increased twofold, suggesting that the proteins encoded by UL46 and UL47 may act at the same level. Since the delay in TK expression occurred within the first 4 h of infection, the actions of VP11/12 and VP13/14 resulted from their virion association and not from their de novo synthesis as late (beta gamma and gamma) genes. Densitometric analysis of purified virions showed that the levels of VP11/12 and VP13/14 in the virion tegument were near the molar ratios of alpha TIF. On the basis of these observations, we predict that the abilities of UL46 and UL47 to enhance alpha TIF-mediated transcription could result from a stoichiometric association of VP11/12 and VP13/14 with alpha TIF within the infecting virion.

Low-pH conformational changes of rabies virus glycoprotein and their role in membrane fusion

Fusion of rabies virus with membranes occurs at acidic pH and is mediated by the viral spike glycoprotein (G). In this paper, we provide the basis for a description of structural transitions associated with exposure to low pH and of their role in membrane fusion. First, we have extended previous studies of fusion kinetics and we have shown that low-pH inhibition of fusion is detectable at 0.5 pH units higher than fusion. Second, low-pH-induced conformational changes were analyzed by using electron microscopy and monoclonal antibody binding assays. The existence of a pH-dependent equilibrium between the native and a low-pH inactive conformation was demonstrated. Third, besides these two conformations, we, using the fluorescent probe ANS (8-anilino-1-naphthalenesulfonic acid), provide evidence for the existence of a transient third state which appears to be more hydrophobic than the native state. Our results suggest that this transient state is responsible for viral aggregation at low pH and could play a role in the first steps of the fusion mechanism.