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PubMed1993

Three-dimensional transformation of capsids associated with genome packaging in a bacterial virus.

Three-dimensional structures of the empty procapsid and the mature capsid of the Salmonella bacteriophage P22 have been determined to a resolution of 28 A using electron cryomicroscopy and computer image processing. The coat subunits in both the structures are arranged as pentamers and hexamers on a T = 7 icosahedral lattice. The two structures display significant differences in shape, size and intersubunit interactions. The empty procapsid is spherical in contrast to the distinctly larger and polyhedral mature capsid. The empty procapsid structure exhibits holes at all the quasi sixfold positions that are absent in the mature capsid. These holes may be the exit ports for scaffolding subunits. Detailed comparisons of the two structures indicate that extensive structural changes take place during maturation in all seven quasi-equivalent subunits. These changes cause flattening of the icosahedral facets, capsid expansion and closing of the holes. This process results in a stable and impenetrable capsid that protects the bacterial genome.

Bacteriophage P22↗
PubMed1998

Capsid expansion follows the initiation of DNA packaging in bacteriophage T4.

Most bacteriophages undergo a dramatic expansion of their capsids during morphogenesis. In phages lambda, T3, T7 and P22, it has been shown that expansion occurs during the packaging of DNA into the capsid. The terminase-DNA complex docks with the portal vertex of an unexpanded prohead and begins packaging. After some of the DNA has entered, the major head protein undergoes a conformational change that increases both the volume and stability of the capsid. In phage T4, the link between packaging and expansion has not been established. We explored the possibility of such a connection using a pulse-chase protocol and high resolution sucrose gradient analysis of capsid intermediates isolated from wild-type T4-infected cells. We show that the first particle appearing after the pulse is an unexpanded prohead, which can be isolated in vitro as the ESP (empty small particle). The next intermediate to appear is also unexpanded, but contains DNA. This new intermediate, the ISP (initiated small particle), can also be isolated on agarose gels, permitting confirmation of both its expansion state and DNA content ( approximately 10 kbp). It appears, therefore, that >/=8% of the T4 genome enters the head shell prior to expansion. Following packaging of an undetermined amount of DNA, the capsid expands, producing the ILP (initiated large particle), which is finally converted to a full head upon the completion of packaging. An expanded, empty prohead, the ELP (empty large particle), was also observed during 37 degrees C infections, but failed to mature to phage during the chase. Thus the ELP is unlikely to be an intermediate in normal head assembly. We conclude by suggesting that studies on assembly benefit from an emphasis on the processes involved, rather than on the structural intermediates which accumulate if these processes are interrupted.

Bacteriophage T4↗
PubMed1999

Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26.

Two crystal forms of recombinant p26 capsid protein (CA) from the equine infectious anemia virus (EIAV) have in common an antiparallel four-helix bundle dimer interface between N-terminal domains (NTDs). The dimer interface provides a lenient scaffold to accommodate the wide sequence variation in these helices within lentivirus CA. Pairs of dimers weakly associate to form exact or approximate D2 symmetry tetramers. In one of the two crystal forms, the tetramers are linked via dimerization of C-terminal domains (CTDs). We propose that the observed NTD and CTD homodimer interactions are involved in the assembly of the lentivirus capsid. The NTD homodimer shape readily suggests a model for the mature capsid core, based on hexagonal packing with dimensions and surface topology resembling described EIAV capsid cores. Combining available data for human immunodeficiency virus and EIAV CA, we also propose an assembly pathway for maturation of the lentivirus capsid core following proteolytic cleavage of the gag polyprotein precursor.

Amino Acid Sequence↗
PubMed1993

The roles of the red clover necrotic mosaic virus capsid and cell-to-cell movement proteins in systemic infection.

The red clover necrotic mosaic dianthovirus (RCNMV) genome is split between two single-stranded RNA species termed RNA-1 and RNA-2. RNA-2 is required for infection of whole plants but is dispensable for infection and virion formation in protoplasts. We have used full-length cDNA clones of RNA-1 and -2 from which infectious in vitro transcripts can be derived to construct a number of mutations in the RNA-1 encoded capsid protein and the RNA-2 encoded cell-to-cell movement protein genes. The capsid protein and the RNA sequence encoding the capsid protein were dispensable for infection of the inoculated leaves of Nicotiana benthamiana and N. clevelandii at both 15 and 25 degrees. In addition, capsid protein was not necessary for systemic infection of N. benthamiana at 15 degrees. As many as 39 amino acid residues could be deleted from the carboxyl-terminus of the RNA-2 encoded 35-kDa cell-to-cell movement protein without loss of or reduction in the rate of cell-to-cell movement or systemic infection. However, larger deletions within the cell-to-cell movement protein gene prevented cell-to-cell movement and systemic infection of N. benthamiana. These data suggest that the spread of RCNMV in a systemic host is a combination of two distinct events: cell-to-cell movement and long distance transport. We conclude that the RCNMV 35-kDa movement protein is required for cell-to-cell movement, whereas the capsid protein is not necessary for cell-to-cell movement and, depending on host genotype and environmental factors, may or may not be required for long distance transport.

Base Sequence↗
PubMed1994

Assembly of the major and the minor capsid protein of human papillomavirus type 33 into virus-like particles and tubular structures in insect cells.

Native virions of human papillomaviruses (HPV) can be isolated from genital lesions only in very limited amounts. Recent studies have shown that virus-like particles can be obtained by expression of the capsid proteins using vaccinia virus recombinants or the baculovirus system. We now present the first detailed characterization of virus-like particles of a human papillomavirus associated with malignant genital lesions, HPV-33, produced in high yield using the baculovirus expression system. Assembly of the major capsid protein L1 alone or together with the minor capsid protein L2 has been obtained. Both spherical virus-like particles of 50-60 nm diameter and tubular structures of either 25-30 nm or 50-60 nm diameter and variable length were extracted from nuclei of the infected insect cells. However, predominantly 50- to 60-nm spherical particles were found in the cell culture medium in long-term infections. The particles have icosahedral symmetry and a density of 1.29 g/cm3 in cesium chloride corresponding to empty papillomavirus capsids. Immunoelectron microscopy confirmed the presence of L1 and L2 in the virus-like particles. The L2 protein seemed to be modified and was shown to be tightly associated with L1 using density gradient and sedimentation analysis. Approximately 50% of the L1 molecules are cross-linked by intermolecular disulfide bonds. This is the first example for the production of HPV-like particles containing both the major and the minor capsid protein using the baculovirus expression system.

Animals↗
PubMed1996

Homologous and heterologous complementation of HBV and WHV capsid and polymerase functions in RNA encapsidation.

Successful encapsidation of hepadnaviral pregenomic RNA requires the orchestrated interaction of the viral capsid and polymerase proteins with each other and with the RNA packaging substrate. The early steps of this process involve binding of the polymerase to the encapsidation signal, epsilon, and are already understood in some detail. However, the underlying macromolecular interactions resulting in the subsequent encapsidation of this polymerase-epsilon complex by capsid proteins are less clearly defined. To approach this issue we have examined the ability of two different hepadnaviruses to encapsidate each other's pregenomic RNA. H. Okamoto et al. ((1990) J. Gen. Virol. 71, 959-963) have previously demonstrated that WHV polymerase could encapsidate an HBV pregenome, but the origin of the capsid proteins (i.e., HBV- or WHV-derived) required for this reaction was not clear; some evidence suggested that heterologous capsid and polymerase proteins might not be capable of interaction. To clarify this, we analyzed encapsidated RNA isolated from cytoplasmic cores produced following transient transfection of HepG2 cells with different combinations of plasmids encoding HBV or WHV core and polymerase genes. We found that (i) the essential encapsidation signal of WHV is comprised of a short region including epsilon, as in HBV; (ii) HBV and WHV polymerases are each competent to recognize both HBV and WHV packaging signals; therefore the encapsidation signals are functionally interchangeable; and (iii) HBV capsids encapsidate a WHV polymerase-epsilon complex, and vice versa, although the efficiency of heterologous packaging is slightly lower than that of homologous encapsidation. Our results underscore the close relationship of these two mammalian hepadnaviruses.

Animals↗
PubMed1999

Cyclophilin A incorporation is not required for human immunodeficiency virus type 1 particle maturation and does not destabilize the mature capsid.

The cellular protein cyclophilin A (CypA) is packaged into human immunodeficiency virus type 1 (HIV-1) virions through a specific interaction with the capsid (CA) domain of the Gag polyprotein. CypA is important for infectivity, but its role in viral replication is currently unknown. Previous reports suggested that CypA promotes uncoating or enhances maturation. We analyzed the morphology and capsid stability of HIV-1 variants defective in CypA binding and of virus grown in the presence of cyclosporin. Both cyclosporin treatment and alteration of Gly89 or Pro90 in the CypA-binding site of CA caused a 5- to 20-fold decrease in CypA incorporation. Virus produced from cyclosporin-treated cells and variants G89V and G89A were 10- to 100-fold less infectious but exhibited normal virion morphologies with regular cone-shaped capsids. Irregular capsid morphologies and lower infectivities were observed for some other variants in the CypA-binding region. Decreased CypA incorporation did not reduce the kinetics of intracellular polyprotein processing or of virus release. No increase in immature particles was observed. These results suggest that CypA does not promote virion maturation. Furthermore, detergent stripping of virus particles with various CypA contents revealed no difference in capsid stability. Based on these results and those reported in the accompanying paper, it appears likely that CypA also is not an uncoating factor. Alternative models for CypA function are discussed.

Capsid↗
PubMed2001

The structure of isometric capsids of bacteriophage T4.

The three-dimensional structure of DNA-filled, bacteriophage T4 isometric capsids has been determined by means of cryoelectron microscopy and image reconstruction techniques. The packing geometry of protein subunits on the capsid surface was confirmed to be that of the triangulation class T = 13. The reconstruction clearly shows pentamers, attributed to capsid protein gp24*, surrounded by hexamers of the major capsid protein, gp23*. Positions of the accessory proteins, Hoc and Soc, are also clearly delineated in the surface lattice. The Hoc protein is the most prominent surface feature and appears as an extended molecule with a rounded base from which a thin neck and a globular head protrude. One Hoc molecule associates with each hexamer. Nearly continuous "ridges" are formed at the periphery of the gp23* hexamers by an association of 12 Soc molecules; however, Soc is absent along the boundaries between the hexamers and the pentamers. The duplex DNA genome forms a highly condensed series of concentric layers, spaced about 2.36 nm apart, that follow the general contour of the inner wall of the protein capsid.

Bacteriophage T4↗
PubMed2002

The product of the UL12.5 gene of herpes simplex virus type 1 is not essential for lytic viral growth and is not specifically associated with capsids.

The herpes simplex virus type 1 UL12 gene encodes a pH-dependent deoxyribonuclease termed alkaline nuclease. An N-terminally truncated version of the UL12 gene, called UL12.5, was shown to be translated independently from a subgenic mRNA which shares its 3' terminus with the full-length UL12 mRNA. We showed previously that the UL12.5 gene product cannot compensate for the absence of the full-length UL12 gene product (R. Martinez, L. Shao, J. C. Bronstein, P. C. Weber, and S. K. Weller, 1996, Virology 215, 152-164); however, it was not known whether UL12.5 itself performs an essential function during lytic viral growth. In this article the initiation codon for the UL12.5 gene product was mapped and altered to create a gene no longer capable of producing UL12.5. This mutation was introduced into the viral genome to create a virus which was capable of producing full-length UL12 but not UL12.5. The growth properties of this virus indicate that UL12.5 is not essential for viral growth in culture. UL12.5 was previously reported to represent a capsid-associated form of alkaline nuclease (J. C. Bronstein, S. K. Weller, and P. C. Weber, 1997, J. Virol. 71, 3039-3047). Sucrose sedimentation analysis of capsids from cells infected with wild-type or mutant viruses indicates that both UL12 and UL12.5 are found in fractions from across the sucrose gradient which do not always correlate with the presence of viral capsids. Furthermore, UL12.5 is found in fractions across the gradient even in cells infected under conditions in which no capsids are formed. These results indicate that UL12.5 does not specifically associate with viral capsids. Taken together, these data indicate that UL12.5 is not likely to play an important role in lytic viral infection.

Animals↗
PubMed1987

Transfection of a DNA/protein complex into nuclei of mammalian cells using polyoma capsids and electroporation.

We used empty capsids of polyoma virus to transfer DNA fragments and DNA/protein complexes into human cells. We encapsulated labeled and unlabeled single stranded DNA fragments by viral capsids. A complex of DNA with a DNA binding protein, recA, will also be taken up by the capsids, whereas the free protein is not incorporated. We further compared this gentle biological method of DNA transfection with a well-established physical method, electroporation. Electroporation also allows the transfer of DNA as well as protein into cells, although there is no proof that a DNA/protein complex can survive the procedure functionally. Whereas the viability of capsid transfected cells is unaffected (100%), electroporation reduces the viability to 90-95%. On the other hand, the amount of DNA found in the nucleus of electroporated cells is higher than for cells treated with loaded viral capsids.

Capsid↗
PubMed1992

Comparison of the capsid protein cistron from serologically distinct strains of sweetpotato feathery mottle virus (SPFMV).

Complementary DNA clones corresponding to the 3' terminus of sweetpotato feathery mottle virus (SPFMV) strains RC and C were synthesized and sequenced. An open reading frame followed by a 3' terminal non-coding region of 222 nucleotides and a terminal polyadenylation track was present in clones from both strains. Putative N-terminal capsid protein cleavage sites were identified for both strains 945 nucleotides 5' of the first stop codon. Sequence comparisons of these strains show 98% nucleic acid identity in the last 351 nucleotides of the capsid protein cistron and 100% in the corresponding amino acids. This relatively short homologous sequence element near the C terminus is responsible for the wide spectrum hybridization among SPFMV strains using in vitro transcribed antiviral RNA probes (riboprobes). The sequence similarity in the remaining N terminal 645 nucleotides is only 62% and 65% for their predicted amino acids. A tendency of decreasing nucleotide mismatches in the alignment from 5' to 3' end of both capsid protein cistrons was detected. Although the alignment of the predicted amino acid sequence of the SPFMV-RC capsid protein with those of other potyviruses showed significant homology, hybridization with riboprobes from both the 5' and 3' regions of the capsid protein cistron of SPFMV was virus-specific.

Amino Acid Sequence↗
PubMed1983

Cell-free translation of Drosophila C virus RNA: identification of a virus protease activity involved in capsid protein synthesis and further studies on in vitro processing of cricket paralysis virus specified proteins.

Drosophila C virus RNA acted as mRNA in rabbit reticulocyte lysates and directed the synthesis of at least one capsid protein and a number of higher molecular weight proteins. Kinetic analysis by pulse-chase experiments showed that a number of high molecular weight products acted as precursors to the capsid protein(s). Various dilution experiments were performed which showed that the virus specified a protease activity essential for the correct processing of precursors to give the capsid protein(s). A similar result was obtained with Cricket paralysis virus, and mixing experiments showed that the protease activity specified by one virus could perform some of the cleavages resulting in the production of the capsid proteins of the other virus. Some of the cleavages involving the highest molecular weight precursors could not be performed by the protease activity of the other virus. We could find no evidence for intramolecular cleavage of the capsid precursors of either of the viruses.

Animals↗
PubMed2002

Folding of the rabbit hemorrhagic disease virus capsid protein and delineation of N-terminal domains dispensable for assembly.

Rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are caliciviruses that produce severe symptoms and are lethal to rabbits and hares. The folding of the capsid protein was studied by determination of the antigenic pattern of chimeric capsid proteins, composed of regions from RHDV and EBHSV capsid proteins. The anti-RHDV monoclonal antibody (MAb) E3, which is known to bind an external conformational epitope, recognized the RHDV C-terminal region. The anti-RHDV MAb A47, which binds a buried epitope, recognized the RHDV N-terminal region. Using a pGEX expression library, we more precisely mapped the MAb A47 epitope on a 31 residues length peptide, between residue 129 and 160 of the VP60, confirming its location in the N-terminal part of the protein. These results demonstrate that the C-terminal part of the protein is accessible to the exterior whereas the N-terminal domain of the protein constitutes the internal shell domain of the particle. With the aim of using virus-like particles (VLPs) of RHDV as epitope carriers or DNA transfer vectors, we produced in the baculovirus system three proteins, DeltaN1, DeltaN2 and DeltaN3, truncated at the N terminus. The DeltaN1 protein assembled into VLPs, demonstrating that the first 42 amino acid residues are not essential for capsid assembly. In contrast, DeltaN2, from which the first 75 residues were missing, was unable to form VLPs. The small particles obtained with the DeltaN3 protein lacking residues 31 to 93, located in the immunodominant region of the RHDV capsid protein, indicate that up to 62 amino acid residues can be eliminated without preventing assembly.

Amino Acid Sequence↗
PubMed1992

Molecular cloning, sequence analysis, in vitro expression, and immunoprecipitation of the major inner capsid protein of the IDIR strain of group B rotavirus (GBR).

The sixth genomic segment of the infectious diarrhea of infant rats (IDIR) strain of group B rotavirus (GBR) was cloned from double-stranded RNA purified from infected rat feces. Sequence comparison with group A rotaviruses (GAR) and the human ADRV strain of GBR indicated that IDIR gene 6 encoded the major inner capsid protein. The nucleic acid sequences of the two GBR genes were 72.9% conserved, and 83.4% of the amino acids were identical. Sequence substitutions between IDIR and ADRV were more numerous than reported for heterologous GAR strains, indicating that the two GBR strains may have diverged from one another over a longer period of time. Despite the sequence heterogeneity exhibited by the major inner capsid proteins of ADRV and IDIR, hydrophilicity plots of the two gene products were nearly indistinguishable. The GBR hydrophilicity plots displayed little similarity with those of rotavirus groups A or C, indicating substantial differences in the structures of those major inner capsid proteins. In vitro transcription and translation of IDIR gene 6 yielded a polypeptide product consistent in size with that predicted from the deduced amino acid sequence and the virion major inner capsid protein. The IDIR 6 polypeptide was immunoprecipitated by antisera directed against IDIR as well as antisera directed against ADRV and a heterologous bovine strain of GBR. No immunoprecipitation was observed with control sera or antisera directed against GAR. These results confirmed that group-specific epitopes were displayed by the major inner capsid protein encoded by IDIR gene 6. Reactivity with heterologous GBR antisera also indicated that the IDIR gene 6 product may prove useful as a standard reagent in immunoassays for the detection of GBR.

Amino Acid Sequence↗
PubMed1992

The Helminthosporium victoriae 190S mycovirus has two forms distinguishable by capsid protein composition and phosphorylation state.

Purified preparations of the Helminthosporium victoriae 190S (Hv190S) virus contain two sedimenting components that differ in capsid structure. The slower sedimenting component (190S-1) contained p88 and p83 as the major capsid proteins; the faster component (190S-2) contained p88 and p78. Previous peptide-mapping studies have shown the three capsid proteins to be closely related. Analysis by SDS-PAGE of in vivo-radiolabeled Hv190S virions indicated that 32P was predominantly incorporated in p88. Significantly less was detected in p83 and none in p78. Similar results were obtained in in vitro phosphorylation studies using [gamma-32P]ATP and purified 190S-1 and 190S-2. The in vitro results suggest that the Hv190S virions copurify with a protein kinase activity that catalyzes the transfer of gamma-phosphate from ATP to a target protein, presumably p78 in the 190S-2 virions and p83 in the 190S-1 component. Selective chemical cleavage at tryptophan residues of in vitro 32P-labeled capsid proteins revealed four labeled peptides among the cleavage products of both p83 and p88. Radioiodination studies with intact Hv190S virions indicated that p88 and p83, but not the nonphosphorylated p78, were accessible to iodination, suggesting that capsid protein phosphorylation entailed conformational changes.

Capsid↗
PubMed1992

Sequence and analysis of the capsid protein of Nudaurelia capensis omega virus, an insect virus with T = 4 icosahedral symmetry.

We have determined the nucleotide sequence of the RNA2 segment of the Nudaurelia capensis omega virus genome. It was found to consist of 2448 nucleotides and contained one long open reading frame (ORF) encoding the 644 residue capsid protein. The deduced amino acid sequence of this protein reveals a positively charged amino terminus, a characteristic exhibited by several other viral capsid proteins, that is thought to be important for interactions between the capsid and the genomic RNA. There are 366 and 150 bases of untranslated sequence on the 5' and 3' ends, respectively. The ORF encoding the capsid protein initiates at the second AUG from the 5' end. The 5' proximal AUG specifies a short ORF (30 codons) which terminates 1 base before the initiation codon for the coat protein. Our analysis also revealed the presence of a second, previously unidentified polypeptide associated with Nudaurelia capensis omega virus particles. The amino terminal sequence of this protein corresponds to a portion of the long ORF beginning at codon 571. The lack of an initiation codon near this sequence indicates that the small polypeptide is most likely produced as a carboxy terminal cleavage product from a 70-kDa capsid protein precursor, yielding the previously identified 62-kDa protein and the 8-kDa protein that we have observed. The putative cleavage site would be at an Asn/Phe pair, somewhat resembling known cleavage sites (Asn/Ala) in the T = 3 Nodaviridae. In addition, we have found that there is also a second polypeptide similar in size to that from Nudaurelia capensis omega virus associated with particles of Nudaurelia capensis beta virus, the type member of Tetraviridae.

Amino Acid Sequence↗
PubMed1986

Self-assembly of purified polyomavirus capsid protein VP1.

The polyomavirus major capsid protein VP1, purified after expression of the recombinant gene in E. coli, was isolated as oligomers resembling the dissociated capsomeres derived from viral capsids. Image analysis of low-dose electron micrographs demonstrates that these VP1 oligomers are exclusively pentamers. The purified VP1 pentamers associated to form capsid-like assemblies and polymorphic aggregates at high ionic strength. The capsid-like assemblies were stabilized at low ionic strength by the addition of calcium. Self-assembly of the unmodified, recombinant DNA-generated VP1 implies that the posttranslational charge modifications of VP1 and the minor virion protein components, VP2 and VP3, are not essential for capsid formation. The nonequivalently related subunits of the penta- and hexavalent capsomeres therefore must spontaneously switch their bonding specificity during assembly.

Capsid↗
PubMed1993

Antigenic analysis of feline calicivirus capsid precursor protein and its deleted polypeptides produced in a mammalian cDNA expression system.

An entire open reading frame in a cDNA encoding the capsid protein gene of feline calicivirus (FCV) was subcloned into a mammalian expression vector. After transfection of the constructed plasmid (pMCV-II) into COS-7 cells, the expressed protein was detected by indirect immunofluorescence assay (IFA) using a panel of monoclonal antibodies (MAbs) to the capsid protein of FCV. All of the MAbs reacted with the transfected COS-7 cells in IFA. The 76 kDa capsid precursor protein was demonstrated in an immunoblot analysis, indicating that the translated precursor protein was not processed into the matured capsid protein in this expression system. Two in-frame deleted and a frameshift mutated cDNAs were generated by using restriction sites within the capsid protein coding sequence in pMCV-II to analyze the antigenic sites of the protein. The results of IFA using the MAbs and COS-7 cells transfected with the deleted or mutated cDNAs suggested that three neutralizing epitopes had a conformational nature and that the other four linear epitopes were related to 74 amino acid residues between positions 381 and 454 in the protein, in which high variation was known to be present among three strains of FCV.

Antibodies, Monoclonal↗