Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs.

A structural rationale for SV40 Vp1 temperature-sensitive mutants and their complementation

Two groups of temperature-sensitive (ts) mutants, termed ts B and ts C, have mutations in the major capsid protein of SV40, Vp1. These mutants have virion assembly defects at the nonpermissive temperature, but can complement one another when two mutants, one from each group, coinfect a cell. A third group of mutants, termed ts BC, have related phenotypes, but do not complement other mutants. We found that the mutations fall into two structural and functional classes. All ts C and one ts BC mutations map to the region close to the Ca2+ binding sites, and are predicted to disrupt the insertion of the distal part of the C-terminal invading arm (C-arm) into the receiving clamp. They share a severe defect in assembly at the nonpermissive temperature, with few capsid proteins attached to the viral minichromosome. By contrast, all ts B and most ts BC mutations map to a contiguous region including acceptor sites for the proximal part of the C-arm and intrapentamer contacts. These mutants form assembly intermediates that carry substantial capsid proteins on the minichromosome. Thus, accurate virion assembly is prevented by mutations that disrupt interactions between the receiving pentamer and both the proximal and distal parts of the C-arms, with the latter having a greater effect. The distinct spatial localization and assembly defects of the two classes of mutants provide a rationale for their intracistronic complementation and suggest models of capsid assembly.

Temperature Sensitive Mutation in the 38 kDa Minor Structural Protein Gene of Phage MB78 Interferes with Phage Morphogenesis

Temperature sensitive mutation in the gene for the 38 kDa minor structural protein of the phage MB78, a virulent phage of Salmonella enterica serovar typhimurium, interferes with phage development at restrictive temperature. Electron microscopy of particles produced at non-permissive temperature indicated that the particles formed are tailless. Two types of particles are seen: (i) empty capsids, which are not perfect icosahedral (ii) icosahedral particles filled with DNA. The gene for the 38 kDa protein is located in the SalIG fragment of the phage genome. Nucleotide sequence of the SalIG fragment of MB78 as well as its temperature sensitive mutant has been determined and analysed. Such analysis indicated that in the mutant the codon GCA has been changed to GTA resulting in substitution of alanine at position 75 of the protein by valine (A75V). This makes the protein thermolabile. Our results suggest that normal functioning of this 38 kDa protein is necessary for attachment of tail fibre to the capsid. Or in other words, this 38 kDa protein is involved in phage morphogenesis.

The gene encoding the major viral structural protein stimulates recombination in polyomavirus DNA

RmI is a chimeric DNA molecule consisting of a polyoma genome in which a partly duplicated VP1-coding region brackets an insert of murine DNA (Ins); when transfected into mouse cells, RmI recombines intramolecularly to yield infectious, unit-length, polyoma DNA. We report here that RmI encodes a polypeptide of 337 amino acids (designated VmP1) which includes the N-terminal 328 amino acids of VP1 and 9 amino acids specified by Ins. Mutating the VmP1-coding sequence strongly reduces the ability of RmI to yield polyoma DNA. In contrast, mutating the portion of the VP1-coding sequence which is not part of the VmP1-coding sequence has little or no impact on the ability of RmI to yield polyoma DNA, even though it renders such DNA noninfectious. Thus, release of polyoma DNA from RmI involves a function of VP1 distinct from that ensuring virus assembly and propagation; since VP1 can arise only after recombination has occurred, VmP1, but not VP1, could carry such a function. We suggest that VmP1 acts in concert with VP2, which we have already reported to stimulate recombination in RmI.

Involvement of minor structural proteins in recombination of polyoma virus DNA

We have previously observed that a polyoma-mouse chimeric DNA molecule (RmI) in which the murine DNA insert is flanked by directly repeated viral sequences is effectively converted into unit-length polyoma DNA upon transfection of permissive mouse cells. This intramolecular recombination event appears to be dependent on VmP1, a protein encoded by RmI which includes the 328 N-terminal amino acids of polyoma VP1, and nine amino acids of murine origin carrying the C-terminus of the protein. We report here that introducing mutations into the VP2/VP3 coding sequence reduces the ability of RmI to generate polyoma DNA, even though the same mutations seem to exert little or no effect on the ability of polyoma DNA to either replicate or accumulate inside transfected cells. A mutation affecting VP2 alone being as effective as one that affects both VP2 and VP3, VP2 appears to be playing a critical role in recombination.

Maintenance of episomal SV40 genomes in GM637 human fibroblasts

Episomal SV40 (SV40: simian virus 40, Polyomavirus maccacae) has been reported in SV40-transformed human fibroblast cell lines the integrated SV40 sequences of which are unlikely to give rise to episomal copies by recombinational mechanisms. The levels of episomal viral DNA in these lines are high, being easily visualized by ethidium staining of agarose gels after electrophoresis. We find that the episomal mutant gmSV40 in GM637 cells represents a persistent lytic infection that can be cured by treatment with neutralizing antibody, leaving only the chromosomally integrated viral genomes. The finding that maintenance of the gmSV40 in GM637 cells is due to persistent infection raises a note of caution for SV40-transformed lines with episomal SV40 genomes because these lines often are used in studies of DNA replication and repair. An infective center assay that does not depend on plaque formation shows that gmSV40 is a host range mutant, with poor infectivity for CV-1 monkey kidney cells and greatly increased infectivity for human cells. Passage of gmSV40 through monkey kidney cells selects for variants with greatly increased infectivity for monkey cells and, independently, for cytopathic variants that produce plaques. Thus plaque assays can give very unreliable infective center values in studies of host range mutants.

Simian virus 40 large T antigen host range domain functions in virion assembly

The simian virus 40 (SV40) T antigen host range mutants dl1066 and dl1140 display a postreplicative block to plaque formation which suggests a novel role for T antigen late in the viral life cycle. The host range mutants dl1066 and dl1140 are able to grow in and plaque on BSC but not on CV1 monkey kidney cells, a normally permissive host. Previous work showed that in CV1 cells infected with dl1066 and dl1140, levels of viral DNA replication and of late capsid protein accumulation were only slightly reduced and the failure to accumulate agnoprotein was not likely to be the major factor responsible for the mutants' growth defect. Here we show that the host range mutants are defective in the assembly of viral particles. SV40 assembly proceeds as the progressive conversion of 75S viral chromatin complexes to 200S-240S assembled virions. When virus-infected cell extracts are separated on 5 to 40% sucrose gradients, wild-type extracts show the greatest accumulation of viral late protein in the 200S-240S fractions corresponding to the assembled virus peak and lesser amounts in the 75S-150S fractions corresponding to immature assembly intermediates. The host range mutants dl1066 and dl1140 grown in nonpermissive CV1 cells, however, failed to assemble any appreciable amounts of mature 200S-240S virions and accumulate 75S intermediates, whereas in permissive BSC cells, levels of assembly were more slightly reduced than those of the wild type. Analysis of the protein composition of gradient fractions suggests that SV40 assembly proceeds by a mechanism similar to that proposed for polyomavirus and suggests that the host range blockage may result from a failure of such mutants to add VP1 to 75S assembly intermediates.