Jonathan P. Stoye

TRIM family proteins: retroviral restriction and antiviral defence

Members of the tripartite motif (TRIM) protein family are involved in various cellular processes, including cell proliferation, differentiation, development, oncogenesis and apoptosis. Some TRIM proteins display antiviral properties, targeting retroviruses in particular. The potential activity of TRIM19, better known as promyelocytic leukaemia protein, against several viruses has been well documented and, recently, TRIM5α has been identified as the factor responsible for the previously described Lv1 and Ref1 antiretroviral activities. There is also evidence indicating that other TRIM proteins can influence viral replication. These findings are reviewed here, and the possibility that TRIMs represent a new and widespread class of antiviral proteins involved in innate immunity is also considered.

HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase

SAMHD1, an analogue of the murine interferon (IFN)-γ-induced gene Mg11 (ref. 1), has recently been identified as a human immunodeficiency virus-1 (HIV-1) restriction factor that blocks early-stage virus replication in dendritic and other myeloid cells and is the target of the lentiviral protein Vpx, which can relieve HIV-1 restriction. SAMHD1 is also associated with Aicardi–Goutières syndrome (AGS), an inflammatory encephalopathy characterized by chronic cerebrospinal fluid lymphocytosis and elevated levels of the antiviral cytokine IFN-α. The pathology associated with AGS resembles congenital viral infection, such as transplacentally acquired HIV. Here we show that human SAMHD1 is a potent dGTP-stimulated triphosphohydrolase that converts deoxynucleoside triphosphates to the constituent deoxynucleoside and inorganic triphosphate. The crystal structure of the catalytic core of SAMHD1 reveals that the protein is dimeric and indicates a molecular basis for dGTP stimulation of catalytic activity against dNTPs. We propose that SAMHD1, which is highly expressed in dendritic cells, restricts HIV-1 replication by hydrolysing the majority of cellular dNTPs, thus inhibiting reverse transcription and viral complementary DNA (cDNA) synthesis.

Two sets of human-tropic pig retrovirus

Advances in controlling immunological rejection have raised the possibility that pigs could be used as a source of organs and tissues for transplantation into humans,. However, the report that one pig kidney cell line, PK15, produces Ctype retroviruses capable of infecting human cells has reinforced fears over the potential risks of viral infections associated with xenotransplantation,. Further support for these fears comes from the discovery of two different classes of porcine endogenous proviruses (PERVs), capable of infecting human cells, in PK15 cells as well as in a variety of normal porcine tissues.

A Single Amino Acid Change in the SPRY Domain of Human Trim5α Leads to HIV-1 Restriction

Retroviral restriction factors are cellular proteins that interfere with retrovirus replication at a postpenetration, preintegration stage in the viral life cycle. The first restriction activity described was the mouse Fv1 gene. Three different alleles of Fv1, capable of restricting different murine leukaemia viruses (MLV), have been characterized at the molecular level. Two further activities, Ref1, which acts on MLV, and Lv1, which acts on lentiviruses, have been identified in other mammalian species. Recently, it has become clear that Ref1 and Lv1 are encoded by the same gene, Trim5alpha, which inhibits retrovirus replication in a species-specific manner. A series of chimeras between the human and rhesus monkey Trim5 genes were created to map and identify these specificity determinants. The Trim5alpha SPRY domain was found to be responsible for targeting HIV-1 restriction. By contrast, N-MLV restriction appears dependent on both the coiled-coil domain and the SPRY domain. A single amino acid substitution (R332P) in the human Trim5alpha can confer the ability to restrict HIV-1, suggesting that small changes during evolution may have profound effects on our susceptibility to cross-species infection.

Absence of xenotropic murine leukaemia virus-related virus in UK patients with chronic fatigue syndrome

BackgroundDetection of a retrovirus, xenotropic murine leukaemia virus-related virus (XMRV), has recently been reported in 67% of patients with chronic fatigue syndrome. We have studied a total of 170 samples from chronic fatigue syndrome patients from two UK cohorts and 395 controls for evidence of XMRV infection by looking either for the presence of viral nucleic acids using quantitative PCR (limit of detection <16 viral copies) or for the presence of serological responses using a virus neutralisation assay.ResultsWe have not identified XMRV DNA in any samples by PCR (0/299). Some serum samples showed XMRV neutralising activity (26/565) but only one of these positive sera came from a CFS patient. Most of the positive sera were also able to neutralise MLV particles pseudotyped with envelope proteins from other viruses, including vesicular stomatitis virus, indicating significant cross-reactivity in serological responses. Four positive samples were specific for XMRV.ConclusionsNo association between XMRV infection and CFS was observed in the samples tested, either by PCR or serological methodologies. The non-specific neutralisation observed in multiple serum samples suggests that it is unlikely that these responses were elicited by XMRV and highlights the danger of over-estimating XMRV frequency based on serological assays. In spite of this, we believe that the detection of neutralising activity that did not inhibit VSV-G pseudotyped MLV in at least four human serum samples indicates that XMRV infection may occur in the general population, although with currently uncertain outcomes.

Multiple Groups of Novel Retroviral Genomes in Pigs and Related Species

ABSTRACT In view of the concern over potential infection hazards in the use of porcine tissues and organs for xenotransplantation to humans, we investigated the diversity of porcine endogenous retrovirus (PERV) genomes in the DNA of domestic pigs and related species. In addition to the three known envelope subgroups of infectious gamma retroviruses (PERV-A, -B, and -C), classed together here as PERV group γ1, four novel groups of gamma retrovirus (γ2 to γ5) and four novel groups of beta retrovirus (β1 to β4) genomes were detected in pig DNA using generic and specific PCR primers. PCR quantification indicated that the retroviral genome copy number in the Landrace × Duroc F1 hybrid pig ranged from 2 (β2 and γ5) to approximately 50 (γ1). The γ1, γ2, and β4 genomes were transcribed into RNA in adult kidney tissue. Apart from γ1, the retroviral genomes are not known to be infectious, and sequencing of a small number of amplified genome fragments revealed stop codons in putative open reading frames in several cases. Analysis of DNA from wild boar and other species of Old World pigs (Suidae) and New World peccaries (Tayassuidae) showed that one retrovirus group, β2, was common to all species tested, while the others were present among all Old World species but absent from New World species. The PERV-C subgroup of γ1 genomes segregated among domestic pigs and were absent from two African species (red river hog and warthog). Thus domestic swine and their phylogenetic relatives harbor multiple groups of hitherto undescribed PERV genomes.

High-resolution structure of a retroviral capsid hexameric amino-terminal domain

Retroviruses are the aetiological agents of a range of human diseases including AIDS and T-cell leukaemias. They follow complex life cycles, which are still only partly understood at the molecular level. Maturation of newly formed retroviral particles is an essential step in production of infectious virions, and requires proteolytic cleavage of Gag polyproteins in the immature particle to form the matrix, capsid and nucleocapsid proteins present in the mature virion. Capsid proteins associate to form a dense viral core that may be spherical, cylindrical or conical depending on the genus of the virus. Nonetheless, these assemblies all appear to be composed of a lattice formed from hexagonal rings, each containing six capsid monomers. Here, we describe the X-ray structure of an individual hexagonal assembly from N-tropic murine leukaemia virus (N-MLV). The interface between capsid monomers is generally polar, consistent with weak interactions within the hexamer. Similar architectures are probably crucial for the regulation of capsid assembly and disassembly in all retroviruses. Together, these observations provide new insights into retroviral uncoating and how cellular restriction factors may interfere with viral replication.

Studies of endogenous retroviruses reveal a continuing evolutionary saga

Retroviral replication involves the formation of a DNA provirus integrated into the host genome. Through this process, retroviruses can colonize the germ line to form endogenous retroviruses (ERVs). ERV inheritance can have multiple adverse consequences for the host, some resembling those resulting from exogenous retrovirus infection but others arising by mechanisms unique to ERVs. Inherited retroviruses can also confer benefits on the host. To meet the different threats posed by endogenous and exogenous retroviruses, various host defences have arisen during evolution, acting at various stages on the retrovirus life cycle. In this Review, I describe our current understanding of the distribution and architecture of ERVs, the consequences of their acquisition for the host and the emerging details of the intimate evolutionary relationship between virus and vertebrate host.

Tripartite-motif proteins and innate immune regulation.

The tripartite motif containing (TRIM) proteins are a family of proteins that have been implicated in many biological processes including cell differentiation, apoptosis, transcriptional regulation and signaling pathways. Many TRIM proteins are upregulated by the immunologically important Type I and Type II interferons and several, including TRIM5α and TRIM19/PML, restrict viral replication. There is growing evidence that TRIMs also play an important role in the broader immune response through regulating signaling pathways such as the RIG-I pathway. In this review we discuss recent research elucidating TRIM regulation of a number of pathways important in immunity and review the latest findings relating to viral restriction by TRIMs.

All Three Variable Regions of the TRIM5α B30.2 Domain Can Contribute to the Specificity of Retrovirus Restriction

ABSTRACT Recent studies have revealed the contribution of TRIM5α to retrovirus restriction in cells from a variety of primate species. TRIM5α consists of a tripartite motif (the RBCC domain) followed by a B30.2 domain. The B30.2 domain is thought to be involved in determination of restriction specificity and contains three variable regions. To investigate the relationship between the phylogeny of primate TRIM5α and retrovirus restriction specificity, a series of chimeric TRIM5α consisting of the human RBCC domain followed by the B30.2 domain from various primates was constructed. These constructs showed restriction profiles largely consistent with the origin of the B30.2 domain. Restriction specificity was further investigated with a variety of TRIM5αs containing mixed or mutated B30.2 domains. This study revealed the importance of all three variable regions for determining restriction specificity. Based on the molecular structures of other PRYSPRY domains solved recently, a model for the molecular structure of the B30.2 domain of TRIM5α was developed. The model revealed that the variable regions of the B30.2 domain are present as loops located on one side of the B30.2 core structure. It is hypothesized that these three loops form a binding surface for virus and that evolutionary changes in any one of the loops can alter restriction specificity.