Mutation in the VP-1 gene is responsible for the extended host range of a monkey B-lymphotropic papovavirus mutant capable of growing in T-lymphoblastoid cells

Structure based sequence analysis of viral and cellular protein assemblies

It is well accepted that, in general, protein structural similarity is strongly related to the amino acid sequence identity. To analyze in great detail the correlation, distribution and variation levels of conserved residues in the protein structure, we analyzed all available high-resolution structural data of 5245 cellular complex-forming proteins and 293 spherical virus capsid proteins (VCPs). We categorized and compare them in terms of protein structural regions. In all cases, the buried core residues are the most conserved, followed by the residues at the protein-protein interfaces. The solvent-exposed surface shows greater sequence variations. Our results provide evidence that cellular monomers and VCPs could be two extremes in the quaternary structural space, with cellular dimers and oligomers in between. Moreover, based on statistical analysis, we detected a distinct group of icosahedral virus families whose capsid proteins seem to evolve much slower than the rest of the protein complexes analyzed in this work.

Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity

Murine polyomavirus (MuPyV) causes tumors of various origins in newborn mice and hamsters. Infection is initiated by attachment of the virus to ganglioside receptors at the cell surface. Single amino acid exchanges in the receptor-binding pocket of the major capsid protein VP1 are known to drastically alter tumorigenicity and spread in closely related MuPyV strains. The virus represents a rare example of differential receptor recognition directly influencing viral pathogenicity, although the factors underlying these differences remain unclear. We performed structural and functional analyses of three MuPyV strains with strikingly different pathogenicities: the low-tumorigenicity strain RA, the high-pathogenicity strain PTA, and the rapidly growing, lethal laboratory isolate strain LID. Using ganglioside deficient mouse embryo fibroblasts, we show that addition of specific gangliosides restores infectability for all strains, and we uncover a complex relationship between virus attachment and infection. We identify a new infectious ganglioside receptor that carries an additional linear [α-2,8]-linked sialic acid. Crystal structures of all three strains complexed with representative oligosaccharides from the three main pathways of ganglioside biosynthesis provide the molecular basis of receptor recognition. All strains bind to a range of sialylated glycans featuring the central [α-2,3]-linked sialic acid present in the established receptors GD1a and GT1b, but the presence of additional sialic acids modulates binding. An extra [α-2,8]-linked sialic acid engages a protein pocket that is conserved among the three strains, while another, [α-2,6]-linked branching sialic acid lies near the strain-defining amino acids but can be accommodated by all strains. By comparing electron density of the oligosaccharides within the binding pockets at various concentrations, we show that the [α-2,8]-linked sialic acid increases the strength of binding. Moreover, the amino acid exchanges have subtle effects on their affinity for the validated receptor GD1a. Our results indicate that both receptor specificity and affinity influence MuPyV pathogenesis.

Viruses are obligate intracellular pathogens, and all of them share one crucial step in their life cycle—the attachment to their host cell via cellular receptors, which are usually proteins or carbohydrates. This step is decisive for the selection of target cells and virus entry. In this study, we investigated murine polyomavirus (MuPyV), which attaches to host gangliosides with its major capsid protein, VP1. We have solved the crystal structures of VP1 in complex with previously known interaction partners as well as with the ganglioside GT1a, which we have identified as a novel functional receptor for MuPyV. Earlier studies have shown that different strains with singular amino acid exchanges in the receptor binding pocket of VP1 display altered pathogenicity and viral spread. Our investigations show that, while these exchanges do not abolish binding or significantly alter interaction modes to our investigated carbohydrates, they have subtle effects on glycan affinity. The combination of receptor specificity, abundance, and affinity reveals a much more intricate regulation of pathogenicity than previously believed. Our results exemplify how delicate changes to the receptor binding pocket of MuPyV VP1 are able to drastically alter virus behavior. This system provides a unique example to study how the first step in the life cycle of a virus can dictate its biological properties.

Structures of B-lymphotropic polyomavirus VP1 in complex with oligosaccharide ligands

B-Lymphotropic Polyomavirus (LPyV) serves as a paradigm of virus receptor binding and tropism, and is the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). LPyV infection depends on sialic acid on host cells, but the molecular interactions underlying LPyV-receptor binding were unknown. We find by glycan array screening that LPyV specifically recognizes a linear carbohydrate motif that contains α2,3-linked sialic acid. High-resolution crystal structures of the LPyV capsid protein VP1 alone and in complex with the trisaccharide ligands 3′-sialyllactose and 3′-sialyl-N-acetyl-lactosamine (3SL and 3SLN, respectively) show essentially identical interactions. Most contacts are contributed by the sialic acid moiety, which is almost entirely buried in a narrow, preformed cleft at the outer surface of the capsid. The recessed nature of the binding site on VP1 and the nature of the observed glycan interactions differ from those of related polyomaviruses and most other sialic acid-binding viruses, which bind sialic acid in shallow, more exposed grooves. Despite their different modes for recognition, the sialic acid binding sites of LPyV and SV40 are half-conserved, hinting at an evolutionary strategy for diversification of binding sites. Our analysis provides a structural basis for the observed specificity of LPyV for linear glycan motifs terminating in α2,3-linked sialic acid, and links the different tropisms of known LPyV strains to the receptor binding site. It also serves as a useful template for understanding the ligand-binding properties and serological crossreactivity of HPyV9.

Viruses must engage specific receptors on host cells in order to initiate infection. The type of receptor and its concentration on cells determine viral spread and tropism, but for many viruses, the receptor and the mode of recognition by the virus are not known. We have characterized the structural requirements for receptor binding of B-lymphotropic polyomavirus (LPyV). This virus was originally isolated from African Green Monkey lymph node cultures and attracted interest because of its narrow tropism for a human tumor cell line. LPyV is also the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). We screened the LPyV coat protein VP1 on an carbohydrate microarray and found that it specifically recognizes a linear sugar motif that terminates in α2,3-linked sialic acid. We then determined the structures LPyV VP1 bound to these carbohydrates. The protein has a preformed, deeply recessed binding site for sialic acid. The binding site differs in both architecture and mode of recognition from the binding sites of other viruses. LPyV only binds linear carbohydrates that are able to penetrate into the binding slot.

Virus receptors and tropism

Polyomaviruses are small, tumorigenic, nonenveloped viruses that infect several different species. Interaction of these viruses with cell surface receptors represents the initial step during infection of host cells. This interaction can be a major determinant of viral host and tissue tropism. This chapter reviews what is currently known about the cellular receptors for each of five polyomavirus family members: Mouse polyomavirus (PyV), JC virus (JCV), BK virus (BKV), Lymphotropic papovavirus (LPV) and Simian virus 40 (SV40). These polyomaviruses serve to illustrate the enormous diversity of virus-cell surface interactions and allow us to closely evaluate the role of receptors in their life cycles. The contribution of other factors such as transcriptional regulators and signaling pathways are also summarized.

DNA sequences similar to those of simian virus 40 in ependymomas and choroid plexus tumors of childhood

BACKGROUND

Ependymomas and papillomas of the choroid plexus occur in early childhood. The ubiquitous human polyomaviruses, BK virus and JC virus, have been associated with the induction of these neoplasms in animal models. A related monkey polyomavirus, simian virus 40 (SV40), is highly tumorigenic in rodents and also induces choroid plexus papillomas.

METHODS

We tested the possibility that polyomaviruses were associated with these tumors in humans. Tumors from 31 children--20 with choroid plexus neoplasms and 11 with ependymomas--were evaluated for the presence of polyomavirus T-antigen gene sequences by means of amplification with the polymerase chain reaction.

RESULTS

Ten of the 20 choroid plexus tumors and 10 of the 11 ependymomas contained amplification products that preferentially hybridized to probes specific for SV40 viral DNA rather than BK or JC viral DNA. In two specimens, DNA sequencing demonstrated that the amplified sequence was identical to the sequence of that region of the SV40 gene. In three other specimens, amplification with SV40-specific primers revealed a 574-bp segment of the SV40 viral gene. In 7 of 11 tumors examined by immunohistochemical staining, viral T antigen was expressed in the nuclei of the neoplastic cells.

CONCLUSIONS

Half of the choroid plexus tumors and most of the ependymomas that we studied contained and expressed a segment of T-antigen gene related to SV40. These results suggest that SV40 or a closely related virus may have an etiologic role in the development of these neoplasms during childhood, as in animal models.

Polyomavirus tumor induction in mice: effects of polymorphisms of VP1 and large T antigen

By testing recombinants between "high tumor" (inducing a high incidence of tumors) and "low tumor" (inducing a low incidence of tumors) strains of polyomavirus, we have previously shown that the key determinant(s) for induction of a high tumor profile resides in coding regions of the high tumor strain (R. Freund, G. Mandel, G. G. Carmichael, J. P. Barncastle, C. J. Dawe, and T. L. Benjamin, J. Virol. 61:2232-2239, 1987). Three single-amino-acid differences between the PTA (high tumor) and RA (low tumor) virus strains have now been identified by DNA sequencing, one each in the large T antigen, in the region common to the middle and small T antigens, and in the major capsid protein VP1. Further tests of appropriate recombinants and oligonucleotide-induced mutants show that VP1 of PTA is the major determinant for induction of a high tumor profile, including all tumors of epithelial origin. The differential effect of the VP1s of PTA and RA on the tumor profile is discussed in terms of a likely contribution of the polymorphic region of VP1 to binding of receptors and infection of different cell types in the animal. The polymorphism in the large T antigen has a more restricted action, which is seen only when tested in virus carrying the VP1 type of PTA; the PTA large T antigen then promotes more rapid growth of tumors of salivary gland and thymus than the RA large T antigen.

Lymphotropic papovavirus early region is specifically regulated transgenic mice and efficiently induces neoplasia

Transgenic mice have been generated which carry the early region of lymphotropic papovavirus (LPV). Eight of eleven founder animals died before 3 months of age after developing one or both of two distinct proliferative disorders. Of the three surviving animals, two are known to have rearranged or partial copies of the LPV genes. The majority of the founder animals (six) developed debilitating choroid plexus tumors by 26 to 42 days. Although this is the same tumor type induced by the simian virus 40 T-antigen gene, those induced by LPV appeared at a much younger age. The LPV early region was expressed in the brain tumors of these mice, as well as in the thymus and spleen. Expression in the latter two tissues reflects the cell-type specificity of the LPV enhancer demonstrated in cultured cells (i.e., lymphoid cells). Two founder animals (LP41 and LP50) gave rise to lines of mice that routinely develop lymphoproliferative disorders. LP50 and its LPV-positive offspring developed aggressive lymphomas and choroid plexus tumors. The transgenic offspring of LP41 also developed lymphomas. High levels of LPV RNA were expressed in the lymphomas of these mice as well as in the spleens and thymuses. The origin of the lymphomas from B- and T-cell lineages suggests that the LPV early genes are expressed in and can transform both of these cell types in vivo.