TRIM5 Alpha and HIV-2 Infection
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KeywordsWorld Monkey Sooty Mangabey Capsid Sequence Host Restriction Factor Nascent Virion
This entry discusses the restriction of HIV-2 by the host restriction factor TRIM5α. Although most published studies focus on HIV-1, we looked at the parallels between the two viruses, paying particular attention to the differences between HIV-1 and HIV-2 and to studies that specifically focused on HIV-2, to put together a current synthesis of our understanding of HIV-2 restriction by TRIM5α.
HIV-2 is the second human retrovirus that can cause AIDS. While very similar to HIV-1 in terms of genomic sequence and protein function, HIV-2 infection usually leads to an attenuated disease course. About 80 % of HIV-2 infections do not lead to AIDS; they are instead characterized by a longer asymptomatic stage, lower plasma viral loads, slower decline in CD4 count, decreased mortality rate, and lower rates of vertical and sexual transmission (see “HIV-2 Transmission”). Nonetheless, a significant proportion of HIV-2-infected individuals eventually progress to AIDS, with high viral loads, low CD4 counts, and a clinical picture indistinguishable from HIV-1 disease progression (see “Natural History and Clinical Features of HIV-2 Infection”). The HIV-1 epidemic is characterized by extensive genetic variation, with four groups, several subtypes, and many circulating recombinant forms (CRF) (see “Origin and Distribution of HIV-1 Subtypes”), while the HIV-2 epidemic consists of only two groups (A and B) and six non-epidemic groups (C–H) (see “Phylogeographic Insights into the Origins and Epidemic History of HIV-2”). HIV-1 has spread throughout the world with high transmission rates, while HIV-2 is restricted mainly to West Africa, where prevalence has been declining (Tienen et al. 2010). The main difference between HIV-1 and HIV-2 is in their origin. HIV originated from SIV from chimpanzees (Pan troglodytes troglodytes), but HIV-2 arose from zoonotic transfer of SIV from the sooty mangabeys (Cercocebus atys) to humans (see “Phylogeographic Insights into the Origins and Epidemic History of HIV-2”): consequently HIV-2 and SIV from sooty mangabeys (SIVsm) and SIV-infected macaques (SIVmac) share about 75 % sequence homology compared to 40–50 % homology with HIV-1 (Hirsch et al. 1989). Several studies have revealed factors, immunological, virological, and molecular, that contribute to the attenuated course of HIV-2 infection. More recently, studies on host genetic factors, such as TRIM5α, have provided genetic contributions to understanding the reduced HIV-2 pathogenicity.
TRIM5α is a member of the tripartite motif family of proteins that has the three protein domains: RING, B-box, and coiled coil (see “TRIM Family and Viral Restriction”). TRIM5α has an additional domain, at its C-terminal, the PRYSPRY or B30.2 domain that interacts with the retroviral capsid and is responsible for species specificity (Stremlau et al. 2005). The retroviral restriction properties of TRIM5α were discovered because HIV-1 could not grow in certain Old World monkey cells. TRIM5α can mediate a postentry block of lentiviral replication either before or after reverse transcription, in a species-specific manner. Although the exact mechanism of retroviral restriction is not fully understood, several mechanisms, some of which are interdependent, have been proposed, with supporting experimental data. Oligomeric TRIM5α recognition of and binding to the incoming intact capsid destabilize the capsid core, leading to accelerated or premature uncoating, which perturbs reverse transcription. The E3 ligase activity of the RING domain can add ubiquitin molecules to itself and to other proteins, leading to proteasome-mediated protein degradation of the capsid-TRIM5α complex. TRIM5α forms occlusion bodies, where the virus is essentially trapped, and it also inhibits nuclear transport of the replicating virus (Veillette et al. 2013). TRIM5α is a pattern recognition receptor that recognizes and binds to the viral capsid, causing a cascade of innate immune signaling that leads to an antiviral state, restricting retroviral replication (Pertel et al. 2011).
TRIM5α and the Viral Capsid
HIV capsid was previously thought to be an inert packaging shell that protects the genomic material of the virus. However, it has emerged that it has several domains that allow interaction with host proteins, such as cyclophilin A, a peptidylprolyl isomerase. Cyclophilin A catalyzes the cis/trans isomerization of a surface-exposed proline (Pro-90) in a loop (residues 85–93) between helices 4 and 5 of the HIV-1 gag capsid (Gamble et al. 1996). Despite HIV-1 and HIV-2 capsids being very similar both in sequence and structure, HIV-1 has a high binding affinity for CypA, but HIV-2 does not. HIV-1 incorporates CypA into incoming and nascent virions, where they enhance viral infectivity. At the same time, this capsid-CypA interaction also increases HIV-1 sensitivity to restriction by Old World monkey TRIM5α. Unlike HIV-1, HIV-2, as well as SIVmac, and murine leukemia viruses (MLV) neither incorporate CypA into nascent virions nor require it for infectivity. HIV-2 binds very weakly to CypA, mainly because its proline (Pro-88) is not positioned correctly in the catalytic site of CypA, unlike Pro-90 of HIV-1 (Lahaye et al. 2013). Despite weak binding and independence of CypA for infectivity, mutational analysis has revealed that the determinants of HIV-2 TRIM5α sensitivity lie in the region of the HIV-2 capsid equivalent to the CypA binding loop of HIV-1, mapping specifically to the glycine-proline (Gly-Pro) motif at positions 87–88 on the HIV-2 capsid (Price et al. 2009). This Gly-Pro motif in HIV-1 has been linked to TRIM5α sensitivity, and the G87A (glycine to alanine) mutation in HIV-2 was associated with reduced HIV-2 titers in cell lines from different species (Ylinen et al. 2005). Available crystal structures of retroviral capsids from different species show an exposed loop structure, like HIV-1, in the region equivalent to the HIV-1 CypA binding loop. It was suggested that this structure can be recognized by TRIM5α from different species (Ylinen et al. 2005).
In at least two independent events, retrotransposition of the CypA gene into the C’-terminal into the TRIM5α gene has occurred, essentially replacing the PRYSPRY/B30.2 domain to form the TrimCyp gene. In New World monkeys of genus Aotus (owl monkey), the TrimCyp replaces exon 8, accounting for most of the PRYSPRY domain, and this protein is able potently to restrict CypA-binding retroviruses like HIV-1 and FIV. In Old World monkeys of genus Macaca (macaques), sequences from CypA in the rhesus macaque replace both exons 7 and 8, removing the entire PRYSPRY domain, to produce a protein that can potently inhibit HIV-2 and FIV, but not HIV-1 (Wilson et al. 2008). There are at least six species of macaques that express TrimCyp; some express this gene exclusively, while others express both TrimCyp and TRIM5α (Dietrich et al. 2011). It was shown that the ability of the rhesus macaque (Macaca mulatta) RhTrimCyps to restrict HIV-2 was due to the presence of two amino acid changes, D66N and R69H, in the CypA domain of the TrimCyp, allowing it to bind strongly to the HIV-2 capsid (Price et al. 2009). In the longtail macaque (Macaca fascicularis), HIV-2 specificity is mapped to amino acids 66 and 143 of the LtTrimCyp. The protein expressed by the 66 N-143E genotype binds to and potently restricts HIV-2 but not HIV-1, while that from the 66D-143 K genotype restricts HIV-1 and not HIV-2, while the 66D-143E protein restricts both viruses (Dietrich et al. 2011). Recent studies into host restriction factors have also shown that the capsid serves as a pathogen-associated molecular pattern (PAMP) for TRIM5α which can therefore be thought of as a pattern recognition receptor (PRR) (Pertel et al. 2011).
TRIM5α and HIV-2
Human TRIM5α potently restricts N-MLV and can moderately limit HIV-2 replication but has an insignificant effect on HIV-1. TRIM5α restriction has been shown to be mapped to the B30.2/PRYSPRY domain. Restriction of N-MLV is different from that of HIV-1, in that a larger area of the PRYSPRY domain is involved, as well as the coiled coil for restriction of the N-MLV mutant L117H (Yap et al. 2005). HIV-1 restriction by human TRIM5α maps to the V1 region of the PRYSPRY domain of TRIM5α, where a change from arginine (R) or any positively charged residue at position 332 to a proline (P) or any uncharged residue results in potent restriction of both HIV-1 and SIVmac (Yap et al. 2005; Li et al. 2006). This R332P change has been shown to lead to potent restriction of HIV-2 as well (Kono et al. 2008). In a study on HIV-2 restriction, another area of the V1 region, 337–339 (in human TRIM5α), has been shown to be important for both HIV-2 and HIV-1 restriction. The change from QTF in the V1 region of human TRIM5α to TRP found in some rhesus macaque (Rh) Trim5α (339–341) has been shown to result in potent restriction of both HIV-2 and HIV-1 even in the presence of arginine at position 332 (Kono et al. 2008).
In addition to the TRIM5α protein, the viral capsid also contains polymorphic determinants of TRIM5α restriction. In HIV-1, capsid mutations in the CypA binding region, such as V86M, result in resistance to RhTrim5α (Veillette et al. 2013). Human TRIM5α restriction of HIV-2 was mapped to a single amino acid at position 119 of HIV-2 ROD capsid that has no known link with CypA binding. HIV-2 viruses with a proline at this position were much more sensitive to human TRIM5α restriction than those without (glutamine or alanine) (Song et al. 2007). Further studies showed that the presence of hydrophobic amino acids or those with ring structures was associated with sensitivity to TRIM5α restriction and those with small side chains or amide groups were linked to TRIM5α resistance (Miyamoto et al. 2011). A study from our group showed that the presence of three prolines at positions 119, 159, and 178 in the HIV-2 capsid was significantly associated with low viral load or viral control (Onyango et al. 2010). This report further showed that the presence of these prolines was predicted to reduce the dimer binding energies of the “PPP” capsid, resulting in a weaker core and more unstable protein (Onyango et al. 2010). Three-dimensional modeling of the HIV-1 and HIV-2 capsids showed that the N-terminal domain consists of seven α-helices from which three loops protrude. Position 119 of the HIV-2 capsid is located in the loop between helices 6 and 7. When a proline is present at position 119, the loop between helices 6 and 7 (L6/7) is closer to the loop between helices 4 and 5 (L4/5), a region that directly interacts with Cyp A in HIV-1 (Miyamoto et al. 2011). The presence of hydrophobic or ring-structure residues at position 119 of the capsid maintains a certain conformation at L4/5 that is characteristic of TRIM5α sensitive viruses. Curiously, the equivalent position in N-MLV, at position 110, also determined N-MLV susceptibility to human TRIM5α. It was suggested that while HIV-1 and HIV-2 are restricted by different mechanisms, human TRIM5α utilizes a similar mechanism of recognition for N-MLV and HIV-2 (Miyamoto et al. 2011).
Studies utilizing the HIV-1 pNL43 backbone with the HIV-2 capsids from lab-adapted (HIV-2 ROD, HIV-2 GL) and primary isolates from different HIV-2 groups have shown that human TRIM5α can restrict all these capsids with similar efficiency (maximum of fourfold median difference) and restricts HIV-1pNL43 chimeras with an HIV-2 capsid (HIV-2 groups A, B, and AB) to a significantly higher extent than HIV-1pNL43 (mean range ~4.5–7-fold) (Takeuchi et al. 2013). However, chimeric viruses containing capsid sequences from non-epidemic HIV-2 groups C to H showed a wide range of susceptibilities to human TRIM5α, ranging from 1.3 to 7.5 (Takeuchi et al. 2013). In contrast, capsid sequences from patients infected with circulating recombinant forms from group A and B (HIV-2A/B) were found to be highly resistant to human TRIM5α (Miyamoto et al. 2012). Most HIV-2 infected individuals (~75 %) have asymptomatic disease, but interestingly, all three reported patients infected with HIV-2A/B presented at an advanced disease stage of AIDS (Miyamoto et al. 2012). Although the numbers were small, mainly due to very few reports of HIV-2A/HIV-2B, it may be that faster disease progression is a hallmark of HIV-2A/HIV-2B recombinant virus infection. The capsids of this recombinant virus were shown to be unique, possessing a glycine at position 119, instead of proline/glutamine/alanine, but most of the differences were observed in the C-terminal domain (CTD) (Miyamoto et al. 2012).
Studies on the association of human TRIM5α single nucleotide polymorphisms (SNPs) with HIV-1 and HIV-2 disease progression are limited, and most show few or no differences between genotypes. A study in Japan showed that an SNP in the L2 linker region, G249D, was more prevalent in Asians and Africans compared to Caucasians (Nakayama et al. 2013). Our unpublished data supports this information; we found a minor allele frequency (MAF) of 27.6 % for G249D, the second most frequent SNP in an HIV-2 cohort in Guinea-Bissau. The presence of this SNP was associated with reduced viral control for both HIV-1 and HIV-2 (Nakayama et al. 2013).
It has been postulated that the greater ability of human TRIM5α to restrict HIV-2 may be partially responsible for the slower disease progression observed in HIV-2-infected individuals; however, that does not fully account for the apparent dichotomy in outcome between progressors and non-progressors with HIV-2. Potentially, progression status may reflect particularly advantageous or disadvantageous combinations of TRIM5α sequence and the capsid sequence of the infecting virus. Although currently rare, the few HIV-2 group A/B recombinants that have been reported are all associated with rapid disease progression. The fact that the capsids from these recombinants are more resistant to human TRIM5α may indicate that viral evolution has occurred to provide escape from human TRIM5α restriction, further supporting the in vivo role of human TRIM5α in at least partial restriction of HIV-2. Further studies on the mechanism of restriction of HIV-2 may provide a better overall understanding of TRIM5α restriction in humans.
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