Are Viruses Inhibited by APOBEC3 Molecules from Their Host Species?

Organisms adapt to infectious agents by developing protective responses, and conversely, infectious agents develop adaptive countermeasures to these responses. Host defenses against infectious agents include adaptive and innate immune responses (e.g., natural killer cells, Toll-like receptors, and interferons). Recently, additional host defense systems against viruses have been identified. These include the TRIM [1], RIGI/MDA5 [2], Bst2/tetherin [3,4], and APOBEC3 (A3) [5] proteins. Many of these anti-viral defense mechanisms were identified through the discovery of viral gene products that counteract their action, and thus it has been proposed that only viruses resistant to host-encoded restriction factors persist. However, recent in vivo work in the murine system has indicated that endogenous A3 proteins play important roles in limiting pathogenicity by murine viruses even though they only partially restrict infection [6–8]. Here I argue that these recent studies emphasize the critical importance of studying natural pathogenic viruses and host restriction factors in vivo. A3 proteins belong to a family of genes that encode DNAand RNA-editing enzymes and confer innate immunity to HIV-1 and perhaps other viruses, such as hepatitis B virus (HBV) and human papilloma virus (HPV) [9,10]. The A3 genes arose through gene duplication of a single-copy primordial gene, are found in a tandem array, and have expanded or contracted in different species [11]; the human genome encodes seven A3 (hA3) genes, the feline four genes [12], the horse six genes [13], artiodactyls species two to three genes [14], and the mouse genome a single A3 (mA3) gene [15]. The A3 genes in general show a high degree of polymorphic variation, suggesting that they are under strong selective pressure [8,12,16– 19]. Additionally, alternatively spliced RNAs with the potential for generating different A3 proteins have been found in the mouse (Figure 1A; see below), felines [12], and artiodactyls [14]. hA3G, the first identified family member, was discovered because of its interaction with the HIV-1 virion infectivity factor (Vif) [5]. hA3G and subsequently hA3F were shown to inhibit HIV-1 lacking the vif gene. In vif-deficient HIV-1 producer cells, both hA3G and hA3F are packaged into progeny virions via interaction with the nucleocapsid (NC) protein and viral RNA. Once packaged, hA3 proteins inhibit infection in target cells by deaminating deoxycytidine residues on the DNA minus strand following reverse transcription, inducing G to A hypermutation in newly synthesized HIV-1 DNA. A3 proteins also inhibit replication by cytidine deaminase (CDA)-independent mechanisms [20]. In cells infected with vif+ HIV-1, Vif binds hA3G and hA3F and targets these proteins for ubiquitinylation and degradation in the proteosome, thereby overcoming the anti-viral activity [21– 24]. Simian immunodeficiency viruses (SIVs) also encode Vif proteins, while foamy viruses (FVs) encode a protein (Bet) that interacts with A3G and prevents its packaging via a mechanism that is apparently different from that of Vif [25– 27]. There are also a large number of studies demonstrating that A3 proteins inhibit transposition of human and mouse retroelements, such as LINE-1, Alu, MusD, human endogenous retroviruses (HERVs), and IAPs [28–34]. Although no study has directly examined the effect of A3 proteins on endogenous copies of these elements, both HERV and endogenous murine leukemia virus (MLV) sequences bear signatures of cytidine deamination [35–37]. Several studies have examined packaging of A3 proteins from different species into retroviruses endemic to the species using transfected tissue culture cells and have suggested that these viruses are resistant to the A3 proteins of their natural hosts. For example, it has been shown that human T cell leukemia virus I (HTLVI), Mason Pfizer monkey virus (MPMV), and MLV do not efficiently package human, monkey, or mouse A3 proteins, respectively, because of weak interactions between the NC proteins and the host A3 [38–46], although other studies have shown some packaging of host A3 proteins by HTLVI and MLV as well as viral restriction [47–50]. The MLV protease may also degrade mA3, thereby preventing its anti-viral function [45]. More recently, equine infectious anemia virus was shown to package several horse A3 proteins but these did not diminish infection as effectively as human A3 proteins [13]. In contrast to studies demonstrating that endogenous A3 proteins do not restrict retroviruses that infect the same species, there are many examples of crossspecies restriction in cultured cells. Human A3B and A3C restrict SIV [51] and hA3G restricts Rous sarcoma virus, feline FV, MLV, and mouse mammary tumor virus (MMTV) [6,25,42–44,48,52–54]. Indeed, several human A3 proteins including hA3G have been shown to restrict MLV via deamination [42,43,54,55], although to a lesser extent than HIV-1 [50]. There is also species-specific degradation of hA3G proteins by different Vifs. For example, Vifs encoded by SIVs that infect humans (chimpanzees and sooty mangabeys) can cause the degradation of hA3G, while Vifs from SIVs that don’t infect humans (African green monkeys) don’t interact with hA3G [56–59]. Additionally, mouse A3, which does not bind Vif, restricts HIV-1 infection [48], MPMV