Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove

Many murine leukemia viruses (MLVs) are partially resistant to restriction by mouse APOBEC3 (mA3) and essentially fully resistant to induction of G-to-A mutations by mA3. In contrast, Vif-deficient HIV-1 (⌬Vif HIV-1) is profoundly restricted by mA3, and the restriction includes high levels of G-to-A mutation. Human APOBEC3G (hA3G), unlike mA3, is fully active against MLVs. We produced a glutathione S-transferase-mA3 fusion protein in insect cells and demonstrated that it possesses cytidine deaminase activity, as expected. This activity is localized within the N-terminal domain of this 2-domain protein; the C-terminal domain is enzymatically inactive but required for mA3 encapsidation into retrovirus particles. We found that a specific arginine residue and several aromatic residues, as well as the zinc-coordinating cysteines in the C-terminal domain, are necessary for mA3 packaging; a structural model of this domain suggests that these residues line a potential nucleic acid-binding interface. Mutation of a few potential phosphorylation sites in mA3 drastically reduces its antiviral activity by impairing either deaminase activity or its encapsidation. mA3 deaminates short single-stranded DNA oligonucleotides preferentially toward their 3= ends, whereas hA3G exhibits the opposite polarity. However, when packaged into infectious ⌬Vif HIV-1 virions, both mA3 and hA3G preferentially induce deaminations toward the 5= end of minus-strand viral DNA, presumably because of the sequence of events during reverse transcription in vivo. Despite the fact that mA3 in MLV particles does not induce detectable deaminations upon infection, its deaminase activity is easily detected in virus lysates. We still do not understand how MLV resists mA3-induced G-to-A mutation. IMPORTANCEOne way that mammalian cells defend themselves against infection by retroviruses is with APOBEC3 proteins. These proteins convert cytidine bases to uridine bases in retroviral DNA. However, mouse APOBEC3 protein blocks infection by murine leukemia viruses without catalyzing this base change, and the mechanism of inhibition is not understood in this case. We have produced recombinant mouse APOBEC3 protein for the first time and characterized it here in a number of ways. Our mutational studies shed light on the mechanism by which mouse APOBEC3 protein is incorporated into retrovirus particles. While mouse APOBEC3 does not catalyze base changes in murine leukemia virus DNA, it can be recovered from these virus particles in enzymatically active form; it is still not clear why it fails to induce base changes when these viruses infect new cells. M ammals possess several innate mechanisms for defense against retroviruses. One of these restriction factors is the APOBEC3 system. APOBEC3 proteins are cytidine deaminases (1). In many cases, they are encapsidated into assembling virions; when these virions infect a new cell and copy their RNA into DNA, the APOBEC3 protein from the virion binds to the singlestranded DNA (ssDNA; the initial DNA product) and deamin...

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

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Biochemical and Biological Studies of Mouse APOBEC3

Nair

Sánchez-Martínez

et al. 2014

“…The insertional polymorphism that produces variation in the ERV content of mouse strains and species could influence host processes governed by individual ERVs or by coordinately regulated ERV subtypes. ERV insertions are estimated to cause 10% of spontaneous mutations in mice (54), and ERV polymorphisms have been associated with changes in gene expression, especially in genes with differential expression across strains (37,55), suggesting that insertionally polymorphic ERVs like the XP-MLVs contribute to these strain-specific phenotypic differences.…”

Section: Discussionmentioning

confidence: 99%

Endogenous Gammaretrovirus Acquisition in Mus musculus Subspecies Carrying Functional Variants of the XPR1 Virus Receptor

Bamunusinghe

Liu

et al. 2013

Self Cite

The xenotropic and polytropic mouse leukemia viruses (X-MLVs and P-MLVs, respectively) have different host ranges but use the same functionally polymorphic receptor, XPR1, for entry. Endogenous retroviruses (ERVs) of these 2 gammaretrovirus subtypes are largely segregated in different house mouse subspecies, but both MLV types are found in the classical strains of laboratory mice, which are genetic mosaics of 3 wild mouse subspecies. To describe the subspecies origins of laboratory mouse XP-MLV ERVs and their coevolutionary trajectory with their XPR1 receptor, we screened the house mouse subspecies for known and novel Xpr1 variants and for the individual full-length XP-MLV ERVs found in the sequenced C57BL mouse genome. The 12 X-MLV ERVs predate the origins of laboratory mice; they were all traced to Japanese wild mice and are embedded in the 5% of the laboratory mouse genome derived from the Asian Mus musculus musculus and, in one case, in the <1% derived from M. m. castaneus. While all 31 P-MLV ERVs map to the 95% of the laboratory mouse genome derived from P-MLV-infected M. m. domesticus, no C57BL P-MLV ERVs were found in wild M. m. domesticus. All M. m. domesticus mice carry the fully permissive XPR1 receptor allele, but all of the various restrictive XPR1 receptors, including the X-MLV-restricting laboratory mouse Xpr1 n and a novel M. m. castaneus allele, originated in X-MLV-infected Asian mice. Thus, P-MLV ERVs show more insertional polymorphism than X-MLVs, and these differences in ERV acquisition and fixation are linked to subspecies-specific and functionally distinct XPR1 receptor variants. Gammaretroviruses of two distinctive host range groups that use the same XPR1 receptor have been isolated from laboratory mice. The xenotropic and polytropic mouse leukemia viruses (X-MLVs and P-MLVs, respectively) both are able to infect cells of nonrodent species, although P-MLVs but not X-MLVs can infect cells of their laboratory mouse strain hosts (1-3). These host range differences are due to polymorphisms in the viral envelope and in the XPR1 receptor (4).MLVs can be transmitted in mice as infectious virus (5, 6) or can be inherited as endogenous retroviruses (ERVs) inserted into the host germ line. X-MLV and P-MLV (collectively, XP-MLV) ERVs are present in the common strains of laboratory mice; these strains carry 1 to 20 copies of X-MLVs and 10 to 30 copies of P-MLV ERVs (7,8). The sequenced C57BL mouse genome has 3 distinct clades of X-MLV ERVs (Xmvs) (9), and P-MLV ERVs have been subgrouped as polytropic and modified polytropic murine viruses (Pmvs and Mpmvs, respectively) (10).The XP-MLV ERVs are recent acquisitions in the Mus genome and are essentially restricted to the 4 house mouse lineages that diverged from the other Mus species about 0.5 MYA and that live in close association with humans (11). The ERV subtypes are largely segregated in different house mouse subspecies. The western European Mus musculus domesticus carries only P-MLVs, whereas M. m. castaneus of southeast Asia, M. m. molossinus of Jap...

“…This segment of Xpr1 is hypervariable in rodent species (48), and we wanted to identify the presence of any novel polymorphisms due to substitutions that would be missed by the PCR screen for insertions or deletions. The 9 strains selected for sequencing included AKR and HRS, 2 strains that have been used in studies on viral leukemogenesis, and RIIIS, a strain that has acquired an XMV insertion in its Apobec3 gammaretrovirus resistance gene (36). We also sequenced exon 13 in strains expressing high levels of nonecotropic MLV envelope (Env) glycoprotein.…”

Section: Inbred Strain Distribution Of the Inducible Xmv Locus Bxv1mentioning

confidence: 99%

Common Inbred Strains of the Laboratory Mouse That Are Susceptible to Infection by Mouse Xenotropic Gammaretroviruses and the Human-Derived Retrovirus XMRV

Baliji

Liu

Kozak

2010

Self Cite

Laboratory mouse strains carry endogenous copies of the xenotropic mouse leukemia viruses (X-MLVs), named for their inability to infect cells of the laboratory mouse. This resistance to exogenous infection is due to a nonpermissive variant of the XPR1 gammaretrovirus receptor, a resistance that also limits in vivo expression of germ line X-MLV proviruses capable of producing infectious virus. Because laboratory mice vary widely in their proviral contents and in their virus expression patterns, we screened inbred strains for sequence and functional variants of the XPR1 receptor. We also typed inbred strains and wild mouse species for an endogenous provirus, Bxv1, that is capable of producing infectious X-MLV and that also contributes to the generation of pathogenic recombinant MLVs. We identified the active Bxv1 provirus in many common inbred strains and in some Japanese Mus molossinus mice but in none of the other wild mouse species that carry X-MLVs. Our screening for Xpr1 variants identified the permissive Xpr1 sxv allele in 7 strains of laboratory mice, including a Bxv1-positive strain, F/St, which is characterized by lifelong X-MLV viremia. Cells from three strains carrying Xpr1 sxv , namely, SWR, SJL, and SIM.R, were shown to be infectable by X-MLV and XMRV; these strains carry different alleles at Fv1 and vary in their sensitivities to specific X/P-MLV isolates and XMRV. Several strains with Xpr1 sxv lack the active Bxv1 provirus or other endogenous X-MLVs and may provide a useful model system to evaluate the in vivo spread of these gammaretroviruses and their disease potential in their natural host.