Here we show that diverse Vpx proteins as well as some Vpr proteins have the ability to target their host species’ SAMHD1 for degradation. Both Vpx and Vpr antagonists display species-specific degradation of SAMHD1 which are in some cases quite specific to the virus's extant host. Such species specificity is a hallmark of an antagonistic ‘arms race’ between host and virus, in which both sides rapidly evolve to gain an advantage. Indeed, we show that SAMHD1 has been evolving under positive selection in primates. We demonstrate that the residues under positive selection in the SAM domain of SAMHD1 determine the specificity of degradation by Vpx, directly implicating Vpr/Vpx antagonism as the source of the remarkable signature of positive selection detected in SAMHD1, which is most pronounced in the Cercopithecina subfamily of Old World monkeys. By combining our functional results with phylogenetic analyses, we show that the ability to degrade SAMHD1 is a neofunctionalization of Vpr which preceded the birth of Vpx by recombination/duplication.
Based on our combined phylogenetic and functional analyses, the common ancestor of SIV viruses most likely encoded a single Vpr that was “inactive” against SAMHD1. The ability to recruit a protein degradation complex is important for Vpr-mediated cell cycle arrest (reviewed in (Dehart and Planelles, 2008
)) and thus may represent the ancestral function of Vpr/Vpx. Interestingly, although cell cycle arrest and SAMHD1 degradation functions are segregated into two separate proteins in those viruses that encode Vpr and a Vpx (Ayinde et al., 2010
), SIVagm Vpr is able to cause both cell cycle arrest (Planelles et al., 1996
; Stivahtis et al., 1997
) and SAMHD1 degradation (). This indicates that the two functions are not mutually exclusive. Furthermore, since cell cycle arrest by Vpr has species-specificity (Stivahtis et al., 1997
), it is likely that the substrate used by Vpr to cause cell cycle arrest will, like SAMHD1, have evolved under positive selection.
While the cellular protein targeted by Vpr to cause cycle cell arrest is not yet known, the adaptive evolution of SAMHD1 might provide a clue as to why some viruses evolved to encode a separate Vpx and Vpr gene. One scenario we propose is that the neofunctionalization of the ancestral Vpr/x to target SAMHD1 exerted a strong selective pressure on old world monkeys’ SAMHD1. As a result, variants of SAMHD1 that conferred protection from Vpr/x antagonism were selected for, leading to the signatures of rapid evolution in SAMHD1, especially localized within the SAM domain. This posed a unique challenge to the ancestral Vpr/x that had to recognize both the cell cycle arrest-factor and multiple rapidly evolving variants of SAMHD1. In order to maintain both functional capabilities, a recombination/duplication of Vpr might have given rise to Vpx. This subsequently allowed the subfunctionalization of Vpx to maximize its SAMHD1-targeting capability, while preserving the cell cycle arrest phenotype in Vpr. This model might explain the complicated evolutionary history of vpr
(Sharp et al., 1996
; Tristem et al., 1990
; Tristem et al., 1998
). Thus, we speculate that the “birth” of a new gene in some lineages leading to both vpr
in the same viral genome, was a more modern event compared to the neofunctionalization of Vpr, may have been directly driven by the rapid evolution of the SAMHD1 protein.
HIV-1 lacks the capability of degrading SAMHD1 since its Vpr protein is unable to degrade SAMHD1 and it does not encode Vpx. Since SIVcpz Vpr also lacks SAMHD1-degrading ability (), this function was missing in HIV-1 even prior to its cross-species transmission from chimpanzees into humans. Moreover, human SAMHD1 is not special in terms of its resistance to Vpr antagonism as it is readily degraded by HIV-2 Vpx. This situation is directly analogous to the two lentiviruses that infect mandrills. SIVmnd1 contains only a Vpr gene that has no activity against mandrill SAMHD1 (), whereas SIVmnd2 has both Vpr and Vpx, the latter of which is capable of degrading mandrill SAMHD1 (). Intriguingly, SIVmnd1 appears more pathogenic than SIVmnd2 similar to the higher pathogenicity of HIV-1 relative to HIV-2 (Souquière et al., 2009
). One possible explanation is that both HIV-1 and viruses like SIVmnd1 evolved unique antagonistic functions (or more effective countermeasures) that collectively allow HIV-1 to achieve sufficient replicative potential in target cells (including SAMHD1-expressing monocytes) even in the absence of SAMHD1-degrading abilities. On the other hand, Vpx-encoding viruses may have become more dependent on the ability to counteract SAMHD1 to achieve successful replication in target cells and have relaxed selection on alternate measures used by viruses like HIV-1.
Most of the signatures of positive selection in primate SAMHD1
appear to originate from the old world monkey lineages, specifically the subfamily Cercopithecinae
after its split from Colobinae
. This highly localized positive selection on the primate phylogeny is unusual. Most previously analyzed host immune genes, such as TRIM5alpha, Tetherin, PKR and APOBEC3G, display signatures of positive selection throughout many primate lineages including hominoids and new world monkeys (Elde et al., 2009
; Lim et al., 2010
; McNatt et al., 2009
; Meyerson and Sawyer, 2011
; Sawyer et al., 2004
; Sawyer et al., 2005
) while others have been restricted to hominoids and old world monkeys alone (TRIM22). Such a localized signature of positive selection might signal the advent of a highly specialized and unique antagonist. Orangutan SAMHD1 is the only primate species outside of the Cercopithecinae
subfamily that also has strong signals of positive selection. However, while there is no evidence of SIVs infecting orangutans to date, there have been reports of simian T-lymphotropic virus (STLV) and simian type D retrovirus (SRV) infecting orangutans (Verschoor et al., 2004
; Warren et al., 1998
Intriguingly, our phylogenetic framework () strongly argues that the Vpr/Vpx proteins’ ability to degrade SAMHD1 arose within the primate lentiviruses, and specifically among lentiviruses that infect Cercopithecinae and jumped into Hominidae, but not viruses that infect Colobinae. Together with our findings that residues in SAMHD1 under positive selection directly determine Vpx sensitivity, this suggests that the birth of the SAMHD1-degrading ability within primate lentiviruses initiated the evolutionary arms-race that led to such a highly localized signature of positive selection within Cercopithecinae. Thus, both the positive selection of SAMHD1 and consequently the birth of Vpx may have been driven by the neofunctionalization of Vpr to antagonize SAMHD1.