Next Article in Journal
Epidemiological Investigation and Partial NS5 Sequence Analysis of Duck Tembusu Virus in Several Regions of China in 2024
Previous Article in Journal
Phage Stability Across Conditions: Ensuring Accurate Use of Viral Surrogates in Antiviral Testing
Previous Article in Special Issue
Mechanisms of APOBEC3 Packaging into HIV-1
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Viruses
Volume 18
Issue 4
10.3390/v18040399
viruses-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

A Viral Protein Antagonist for Both AID and APOBEC3

by
Jaquelin P. Dudley
Department of Molecular Biosciences and LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX 78712, USA
Viruses 2026, 18(4), 399; https://doi.org/10.3390/v18040399
Submission received: 4 January 2026 / Revised: 21 March 2026 / Accepted: 22 March 2026 / Published: 24 March 2026
(This article belongs to the Special Issue Host-Mediated Viral Mutations: APOBECs, ADARs, and Beyond)
Browse Figures
Versions Notes

Abstract

The APOBEC family of cytidine deaminases is part of the innate immune response to infections by multiple RNA- and DNA-containing viruses. Since the activity of these enzymes, typically APOBEC3, often involves mutations that inhibit or block viral replication, viruses have evolved antagonists that limit APOBEC function. The retrovirus mouse mammary tumor virus (MMTV) encodes an APOBEC antagonist, Rem. Surprisingly, Rem appears to inhibit APOBEC3 through proteasomal degradation of a different APOBEC enzyme, AID.

1. APOBEC Enzymes as Viral Antagonists

The innate immune response has many facets involving multiple cell types that are on the front lines of host defense against pathogens. Dendritic cells, macrophages, and natural killer (NK) cells are critical components of innate immunity as well as targets for viral infections [1]. Such cells can facilitate infections of B and T lymphocytes, which mediate adaptive immunity that provides both specificity and memory [2]. All these cell types are known to express molecules that block viral replication, including the apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) family of cytidine deaminases [3,4,5]. The human genome encodes 11 APOBEC enzymes: APOBEC1 (hA1), APOBEC2 (hA2), APOBEC3A (hA3A), APOBEC3B (hA3B), APOBEC3C (hA3C), APOBEC3D (hA3D), APOBEC3F (hA3F), APOBEC3G (hA3G), APOBEC3H (hA3H), APOBEC4 (hA4), and activation-induced cytidine deaminase (hAID) [3]. Each of these deaminases targets cytidines in preferred sequence contexts on single-stranded RNA and DNA [6,7,8] (reviewed in [3,5]). The mouse genome encodes APOBEC1, 2, 4 (mA1, mA2, mA4), and mAID, but only a single A3 enzyme (mA3) [3]. Recent evidence indicates that house mice have two mA3 alleles, which have different target specificities [9]. The A3 proteins are the primary viral antagonists and have been shown to block retroviral replication by inhibiting reverse transcription and/or deaminating cytidines during minus-strand DNA synthesis [10,11,12]. Cytidine deamination of the viral minus strand often leads to G-to-A substitution mutations on the plus strand, which inactivates required viral proteins [5]. Alternatively, host-encoded enzymes lead to degradation of damaged or incomplete reverse transcription products [13]. Therefore, the A3 deaminases represent a major block to viral replication in cell types likely to provide the first barrier to virus dissemination in the host.

2. Conceptual Overview

In this review, I present the idea that the retrovirus mouse mammary tumor virus (MMTV) has evolved to antagonize multiple APOBECs during replication in different cell types by targeting AID: the most ancient of this cytidine deaminase family. Genetic, virological, and biochemical data are consistent with a model in which the MMTV-encoded Rem protein degrades AID, which serves as an adapter and regulator of antiviral A3 enzymes.

3. MMTV-Encoded Rem as an APOBEC Inhibitor

Viruses, ever on the defensive to maintain their lifestyle, have evolved multiple methods to overcome APOBEC restrictions (reviewed in [3,5,14]). The first known viral APOBEC inhibitor was the Vif protein encoded by human immunodeficiency virus type 1 (HIV-1) [11]. HIV-1 strains lacking Vif expression were shown to accumulate G-to-A mutations in viral DNA, which restricted HIV-1 replication in certain T-cell lines, such as H9 and MT-2 [15]. This cell type-specific restriction later was attributed to hA3G expression levels, although hA3F also is a potent inhibitor of HIV-1 [16,17]. Interestingly, passage of Vif-minus HIV-1 in cells with hA3G expression does not lead to A3-resistant viruses [18]. Similarly, other retroviruses have been shown to encode inhibitors of A3 proteins [19,20,21], indicating that viral A3 inhibitors are essential for robust retroviral replication.
Unlike HIV-1, MMTV requires replication in both B and T cells for transmission from maternal milk in the gut to its ultimate target tissue, the mammary gland [22,23,24]. Relative to human viruses, advantages of studying MMTV and its interactions with APOBECs include the ability to infect the native host with an intact immune system. Our experiments to understand MMTV pathogenesis led to the discovery of the multifunctional protein, regulator of export and expression of MMTV mRNA (Rem) [25,26]. Rem is a 301-amino-acid protein produced in the same reading frame as the viral envelope (Env) protein from a doubly spliced mRNA [25] (Figure 1). After synthesis in association with the endoplasmic reticulum (ER), Rem goes through an extraordinary journey through different parts of the cell [27,28]. The 98-amino-acid signal peptide (SP) is cleaved by signal peptidase and extracted from the ER membrane by retrotranslocation (Figure 1A). SP, which is shared between Env and Rem, is imported into the nucleus using its nuclear localization sequence (NLS), where it binds to the Rem-responsive element (RmRE) on all viral mRNAs to allow export from the nucleus (Figure 1B) [29]. SP (translated primarily from the more abundant singly spliced env mRNA) is an adapter for CRM1-mediated export of MMTV transcripts from the nucleus [25]. Although Rem is required for nuclear export of unspliced genomic MMTV RNA, a reporter vector including the 3′ end of the MMTV provirus was dependent on the RmRE and presence of Rem, but did not measure nuclear export of vector RNA [29,30]. Thus, the N-terminal part of Rem is an HIV-1 Rev-like adapter that likely has a role in both export and translation [25,30].
The function of the C-terminal cleavage product of Rem (Rem-CT or CT in standard retroviral nomenclature) has been more enigmatic. The requirement for Rem-CT activity was explored using engineered infectious MMTV clones with a mutation in the second splice donor site (MMTV-SD) to eliminate generation of the doubly spliced rem mRNA [31]. This strategy allowed SP production from env mRNA, but prevented Rem and Rem-CT expression (Figure 1B) [27]. SP is required for replication [25]. Infections with Rem-minus MMTV in tissue culture allowed virus production [32], indicating that Rem and its cleavage product are accessory proteins.
Viruses 18 00399 g001
Figure 1. Diagram of Rem and MMTV proviral structure. (A) Rem structure. Rem is a 301-amino-acid protein that is synthesized at the ER membrane and then cleaved by signal peptidase as indicated by the arrow [27,29,33]. The 98-amino-acid signal peptide (SP; shown in black) has a nuclear localization signal (NLS) that also contains an arginine-rich motif (ARM). The ARM serves as an RNA-binding domain for the Rem-responsive element (RmRE) located at the 3′ end of all viral mRNAs [29]. The C-terminal cleavage product of Rem (Rem-CT; shown in green) is a deleted in-frame fusion product of the Env protein and retains two of the five glycosylation sites [27]. SP and uncleaved Rem are extracted from the ER membrane by retrotranslocation into the cytosol, after which both proteins can be imported into the nucleus through the NLS [27,33,34]. Rem-CT is localized primarily within the ER, but has an unusual trafficking pathway involving early and late endosomes without passing through the Golgi apparatus [28]. (B) Structure of the MMTV and TBLV proviruses and their mRNAs. The proviral long terminal repeats (LTRs) are shown in blue at the 5′ and 3′ ends of the provirus. Viral genes are in italics, and the two splice donor (SD1 and SD2) and splice acceptor (SA1 and SA2) sites are indicated. A variant of MMTV, TBLV, has a deletion within the LTRs that removes the C-terminal portion of the Sag-coding region (orange inverted triangles) and has a triplication that constitutes a T-cell-specific enhancer [35,36]. The genomic RNA (gRNA) is transcribed starting within the 5′ LTR and ends within the 3′ LTR. The gRNA also is the mRNA for the gag, dut, pro, and pol genes, which encode the non-glycosylated virion (Gag) proteins, the dUTPase, protease, integrase, and reverse transcriptase [37]. The V-shaped regions indicate introns within the spliced env, rem, and sag mRNAs. The superantigen (Sag) proteins are specified by two different singly spliced mRNAs, one originating in the 5′ LTR promoter and the other within the intragenic env promoter [38]. The X characters indicate the elimination of the SD2 site within the mutant MMTV and TBLV proviruses, which prevents the expression of Rem as well as Sag from the intragenic promoter [39].
Figure 1. Diagram of Rem and MMTV proviral structure. (A) Rem structure. Rem is a 301-amino-acid protein that is synthesized at the ER membrane and then cleaved by signal peptidase as indicated by the arrow [27,29,33]. The 98-amino-acid signal peptide (SP; shown in black) has a nuclear localization signal (NLS) that also contains an arginine-rich motif (ARM). The ARM serves as an RNA-binding domain for the Rem-responsive element (RmRE) located at the 3′ end of all viral mRNAs [29]. The C-terminal cleavage product of Rem (Rem-CT; shown in green) is a deleted in-frame fusion product of the Env protein and retains two of the five glycosylation sites [27]. SP and uncleaved Rem are extracted from the ER membrane by retrotranslocation into the cytosol, after which both proteins can be imported into the nucleus through the NLS [27,33,34]. Rem-CT is localized primarily within the ER, but has an unusual trafficking pathway involving early and late endosomes without passing through the Golgi apparatus [28]. (B) Structure of the MMTV and TBLV proviruses and their mRNAs. The proviral long terminal repeats (LTRs) are shown in blue at the 5′ and 3′ ends of the provirus. Viral genes are in italics, and the two splice donor (SD1 and SD2) and splice acceptor (SA1 and SA2) sites are indicated. A variant of MMTV, TBLV, has a deletion within the LTRs that removes the C-terminal portion of the Sag-coding region (orange inverted triangles) and has a triplication that constitutes a T-cell-specific enhancer [35,36]. The genomic RNA (gRNA) is transcribed starting within the 5′ LTR and ends within the 3′ LTR. The gRNA also is the mRNA for the gag, dut, pro, and pol genes, which encode the non-glycosylated virion (Gag) proteins, the dUTPase, protease, integrase, and reverse transcriptase [37]. The V-shaped regions indicate introns within the spliced env, rem, and sag mRNAs. The superantigen (Sag) proteins are specified by two different singly spliced mRNAs, one originating in the 5′ LTR promoter and the other within the intragenic env promoter [38]. The X characters indicate the elimination of the SD2 site within the mutant MMTV and TBLV proviruses, which prevents the expression of Rem as well as Sag from the intragenic promoter [39].
Viruses 18 00399 g001
Infection of BALB/c mice with wild-type MMTV or the Rem-minus mutant allowed mammary tumor production, but with a longer latency and lower incidence in mutant-injected animals [31]. Sequence analysis of tumor-derived proviruses revealed that proviruses lacking Rem expression had a statistically higher number of G-to-A mutations on the plus strand compared to wild-type MMTV proviruses. Furthermore, the increased mutations were primarily within the TYC motif typical of mA3 [31]. A number of proviruses lost the SD mutation due to recombination with endogenous MMTVs (Mtvs), which are often expressed in lymphocytes [40,41]. MMTV recombinants had significantly higher mutations in the WRC context attributed to mAID [31], suggesting that restoration of Rem expression was needed to reconstitute an infectious virus after APOBEC mutagenesis. These results also are consistent with mAID and mA3 expression in lymphocytes [42,43,44], which are required for MMTV replication and transmission [23,45]. Since SP is synthesized from env mRNA [25,27], these data suggested that Rem C-terminal sequences block the mutagenic effects of multiple APOBECs [31].

4. Type B Leukemogenic Virus and Rem Antagonism of APOBECs

MMTV is a complex retrovirus that encodes multiple genes at the 3′ end of the genome, including env, rem, and sag (Figure 1B) [25]. Because env and rem genes are in the same reading frame, rem mutations potentially will affect MMTV replication due to disruption of Env function. The site mutated in the 3′ MMTV splice donor site will not affect Env production, but is needed for Sag expression from the env intragenic promoter [38] as well as Rem or Rem-CT production [25] (Figure 1B). Sag is required for lymphocyte-mediated MMTV transmission to mammary glands in vivo [22,23,24]. Therefore, it is possible that loss of Sag, rather than Rem, contributes to the mutagenic phenotype observed in the MMTV splice donor mutant.
To distinguish the effects of Rem and Sag on proviral mutagenesis, an MMTV variant, type B leukemogenic virus (TBLV), was used to generate infectious proviral clones with the splice donor mutation. Unlike MMTV, TBLV does not encode functional Sag for replication or induction of tumors [35,39]. The TBLV sag gene is inactivated by an LTR deletion as well as triplication of flanking sequences to constitute a T-cell enhancer [39]. Moreover, TBLV does not require mature B-2 cells for tumor induction, as demonstrated by infection of mice lacking µ immunoglobulin heavy chain production [46], whereas MMTV does [45]. These experiments indicated that studies with Sag-independent TBLV could distinguish between the effects of Sag and Rem.
Wild-type TBLV and mutant TBLV lacking Rem expression were used for infection of BALB/c mice and induction of tumors. Unlike the results obtained with Sag-dependent MMTV, no difference was observed in the latency or incidence of T-cell lymphomas induced by wild-type or Rem-mutant TBLV. However, proviral loads were reduced in the absence of Rem expression [31]. High-throughput sequencing of tumor-derived viral DNA revealed a dramatic increase in G-to-A mutations on the viral DNA plus strand, particularly in proviruses that restored the splice site specific to Rem production by recombination with endogenous Mtvs [31]. Consistent with sequencing results from Rem-mutant MMTV proviruses, mutations occurred primarily in the TYC and WRC motifs preferred by mA3 and mAID, respectively. However, the numbers of mutations were higher in the TYC compared to the WRC motif in the absence of Rem. The appearance of revertants after infections with either Rem-mutant MMTV or TBLV revealed the importance of specific spliced mRNAs and their translation products for successful replication in vivo. The numbers of mutations were highly proportional to the numbers of recombinants isolated from tumors [31], suggesting that recombination of exogenous MMTVs with endogenous Mtvs was a mechanism to recover from the effects of APOBEC-mediated damage. Because TBLV does not make functional Sag protein [39], these experiments predicted that Rem, rather than Sag, limits APOBEC-mediated mutagenesis in vivo [31].

5. Genetic Evidence for Rem-Mediated AID Antagonism

Previous experiments have shown that mA3 is an inhibitor of MMTV replication in C57BL/6 (B6) mice [47,48]. However, current data suggest that MMTV infection of B6 mice does not result in proviral mutations regardless of Rem expression [46] (see below). Because MMTV replicates in both B and T cells for trafficking to the mammary gland [22], BALB/c mice with a knockout mutation in the Aicda (AID) gene were derived and infected with wild and Rem-defective MMTV independently. Mouse AID expressed in B-2 lymphocytes is known to be involved in immunoglobulin gene hypermutation and class switch recombination [43]. MMTV has a low replication profile in lymphocytes, does not cause viremia, and is very difficult to detect prior to replication in lactating mammary glands and tumors [37,49]. In contrast, cells from mammary tumors are uniformly infected [50,51]. Aicda−/− tumors induced by Rem-defective MMTV had longer latency and a lower incidence than tumors induced by wild-type MMTV. Unlike results obtained in wild-type BALB/c mice, there was no difference in proviral load in tumors from mAID-knockout animals after infection with wild-type or Rem-defective virus [31]. These results suggested that the absence of Rem compromised tumorigenesis in mAID-knockout mice without affecting proviral copy numbers. MMTV-induced tumors are known to be affected by mutations within the viral enhancer [35,52,53,54], which is required to activate specific oncogenes, such as Wnt1, Fgf3, and c-Myc [51,55,56]. One possibility is that Rem expression affects selection for viral enhancer mutations.
To determine the effect of mAID deficiency on Rem-associated mutations, tumor DNA was used for PCR of the envelope region at the 3′ end of MMTV proviruses. Products from MMTV-induced Aicda−/− tumors were cloned, sequenced, and compared to samples obtained from infected wild-type BALB/c mice. As anticipated, no differences were observed between proviral mutations within the WRC motifs in either wild-type or recombinant proviruses isolated from mAID-knockout tumors [31]. Unexpectedly, the absence of mAID expression also eliminated the increased proviral mutations in the TYC motif typical of mA3 in MMTV mutant (Rem-null) infections of wild-type BALB/c mice. These results were consistent with the idea that mAID is required for both WRC and TYC-motif mutations. In addition, mutations in the SYC motif were elevated in MMTV recombinants with endogenous Mtvs compared to either wild-type MMTV or MMTV-SD non-recombinant proviruses. Although SYC motifs have been considered low-level targets of mAID or hAID on the immunoglobulin locus [57,58], the discrepancy between these results and those obtained for the WRC motifs suggests that SYC is the target of another deaminase on the MMTV genome. Alternatively, mA3 target specificity may be changed by protein adapters and/or post-translational modifications.

6. Rem and Endogenous Mtvs

Endogenous Mtvs presumably were acquired by infections of germline cells with exogenous MMTVs [59]. Most Mtvs, distinguished by their independent insertion sites with separate numbers [60], have env gene mutations that would prevent infectious virion production and fusion functions [61]. Such Mtvs have lost Env function by deletion or point mutation [61,62], which potentially affects Rem activity due to rem being an in-frame deletion of env [25,26]. Some Mtv env deletions exactly coincide with one of the rem gene introns [61] (see Figure 1B), indicating incorporation into an exogenous MMTV by recombination between packaged viral genomic and rem mRNA prior to endogenization [61]. G-to-A mutations typical of APOBECs that result in stop codons are present in env, but not rem, in most Mtv proviruses [61]. These results suggest that endogenous Mtvs have been selected for their retention of Rem expression in mice. One idea is that APOBEC regulation by Rem has affected Mtv retention similar to the effects of Mtv Sag expression in shaping the T-cell repertoire of the mouse [23,63].

7. Mechanism of Rem-Mediated APOBEC Antagonism

HIV-1 Vif inhibits hA3G and hA3F activity by acting as an adapter to a ubiquitin E3 ligase complex [64,65]. Proteasomal degradation of the A3 proteins prevented their incorporation into viral particles. Without virion incorporation, the A3 enzymes could not inhibit reverse transcription or cause deamination of reverse transcripts. To determine if MMTV Rem used a similar mechanism, Rem expression constructs were transfected together with constructs for mA3 or mAID. Surprisingly, mAID was degraded in a dose-dependent manner, whereas mA3 was not. Proteasomal degradation of AID in the presence of Rem was confirmed by rescue of AID levels after incubation of transfected cells in the presence of the proteasomal inhibitor MG132 [31]. Furthermore, co-transfection of TBLV-WT proviruses expressing Rem in human Jurkat cells with tagged murine AID showed degradation of AID. Co-transfection of TBLV mutants lacking Rem expression with mAID revealed no evidence of reduced AID levels. Degradation was proportional to Rem expression [31], consistent with the idea that Rem reduces mAID, but not mA3 levels.
Multiple investigators have shown that mA3 is incorporated into wild-type MMTV [31,47,48] and MLV [66,67,68] virions, indicating that viral antagonists do not prevent mA3 packaging. In contrast, mAID is not packaged into Abelson MLV [69], and experiments to detect AID in MMTV virions have not been successful [31]. One idea is that mAID-mediated viral mutagenesis occurs outside of virions. Alternatively, AID may influence the activity of packaged mA3 or a cofactor that determines viral target specificity.

8. Mouse Strain-Specific Differences in APOBEC-Mediated Proviral Mutagenesis

Previous studies have reported that proviral mutations in the mA3 motif are not observed after MMTV infections of B6 mice [47]. Nevertheless, these experiments were performed with MMTV (RIII strain) that retained Rem expression, which would inhibit APOBEC-mediated mutations [31]. To avoid the potential effects of the mutation on both Rem and Sag expression that complicate results with MMTV, wild-type and Rem mutant TBLV were used for infection of wild-type B6 mice. Infections with Rem-mutant TBLV accelerated the appearance of T-cell lymphomas relative to TBLV-WT infections in both wild-type and AID-knockout mice. The incidences of tumors induced by the wild type and the Rem mutant were 20–30% and 80–90%, respectively, and the latency of lymphomas was delayed in tumors induced by wild-type TBLV [31,46]. Since TBLV does not make Sag [35,39], these results imply that loss of Rem expression provides an advantage for viral tumorigenesis in B6 mice.
One possibility is that Rem-mutant proviruses have increased mutations induced by APOBECs that cripple virus replication or increase the activity of LTR enhancers on nearby oncogenes. To test this, the 3′ end of proviruses from wild-type and Aicda−/− tumors induced by wild-type and Rem-mutant TBLV in B6 mice was subjected to PCR, cloning, and sequencing. In contrast to the results obtained for TBLV-infected BALB/c mice [31], analysis of the mutations/clone showed no differences between wild-type and Rem-mutant proviruses derived from wild-type or AID-knockout B6 mice for the WRC and TYC motifs associated with AID and mA3, respectively [46]. TYC mutations typical of mA3 were the most abundant sequence changes observed in any of the conditions tested (Table 1).
In a subsequent experiment, wild-type, Aicda−/−, and mA3/Aicda−/− (double-knockout) mice were used for infection by clonal TBLV proviruses with or without Rem expression. Tumor DNA was used for PCR to encompass the env/3′ LTR region and subjected to high-throughput sequencing. As previously observed, G-to-A changes on the viral plus strand were the most abundant [46]. Analysis of the results indicated that no statistical differences were observed between levels of G-to-A changes when comparing mutations in wild-type and Rem-minus proviruses in either wild-type B6 or AID-knockout mice. The G-to-A changes were significantly reduced in mA3/AID-double knockout tumors compared to those obtained from wild-type B6 or AID single-knockout animals. These experiments suggest that mA3 is a TBLV mutagen in B6 mice. However, significant numbers of G-to-A mutations were detected in the absence of both mAID and mA3 expression, consistent with additional deaminase activity on TBLV proviruses [31].

9. Apobec and Rem Expression in Mice

How can the differences in APOBEC mutagenesis of proviruses in BALB/c and B6 mice be explained? These mouse strains have multiple differences in their immune systems since BALB/c mice are known to have Th2-biased immunity, whereas B6 mice have Th1-biased cell-mediated responses [70,71]. These strains also have differences in mA3 and AID expression [46]. BALB/c mice express two isoforms of mA3 mRNA, one that is full-length and one that is missing exon5 (Δexon5). In contrast, B6 mice express only the Δexon5 isoform [67,72,73]. Furthermore, the B6 gene has a xenotropic mouse leukemia virus (MLV) LTR in the vicinity of the mA3 gene. This LTR is missing from the BALB/c mA3 gene, suggesting that the lower levels of mA3 transcripts in this strain are due to lack of the MLV LTR enhancer [74,75,76,77].
In addition to the higher mA3 mRNA levels in B6 mice, there are 15 amino acid differences specified by the mA3 gene of BALB/c mice. The majority of these amino acids (11 of 15) are under strong positive selection [9,73], consistent with their contribution to antiviral resistance. The mA3 protein has two deaminase domains: one in the N-terminus, which is catalytically active, and a second enzymatically inactive domain in the C-terminus [78]. The N-terminal mA3 domain mutations found in multiple mouse strains have been associated with substrate selection, rather than deaminase activity. This conclusion was based on comparisons to the domain structure and activities of the analogous hA3G amino acids [9]. The C-terminal mA3 mutations that differ between BALB/c and B6 also are under positive selection, but are not associated with the known function of this domain in virion incorporation [79,80]. The preferred target site for BALB/c mA3 is XTC, whereas the B6 enzyme preferentially mutates cytidines in the TYC motif [81]. Although experiments indicate that the high polymerization by MMTV reverse transcriptase interferes with mA3 activity [82], both endogenous Mtvs and exogenous MMTVs show evidence of proviral DNA hypermutation [9,31,46].
Published data indicate that mA3 is under positive selection [9,73], suggesting that this deaminase is responding to interactions with mouse pathogens. No information is available for AID. The levels of mAID protein are higher in BALB/c relative to B6 splenocytes and inducible within 48 h after induction by lipopolysaccharide (LPS) and IL-4 [46]. On the other hand, mA3 protein levels are ~5-fold higher than those in BALB/c in unstimulated splenocytes. B6 mA3 can be induced by LPS and IL-4 15-to−30-fold over BALB/c baseline expression, whereas BALB/c mA3 levels are elevated ~5-fold under the same conditions [46]. In summary, higher levels of AID relative to mA3 in lymphocytes correlate with responsiveness of TBLV proviral mutations to Rem expression (Table 1).

10. Model for Rem Antagonism of APOBECs

Since Rem affects mAID, but not mA3 levels, how does Rem affect MMTV proviral mutations that are typical of mA3? One possibility is that the AID-to-mA3 ratio contributes to the higher levels of mutations observed in TBLV proviruses after infections of BALB/c mice relative to those observed in B6 mice [46]. Moreover, Rem reduces AID levels by proteasomal degradation [31], leading to decreased AID/mA3 ratios in cells infected with wild-type MMTV or TBLV. Under this condition, few mutations are observed in BALB/c mice, which have higher basal levels of AID [46]. However, when Rem is absent (i.e., when the mAID/mA3 ratio is increased), infections of BALB/c mice with splice-donor mutant viruses show increased proviral G-to-A changes [31]. In B6 mice, which have lower baseline levels of mAID relative to mA3, little difference is observed in the presence and absence of Rem expression (Table 1) [46]. Our hypothesis is that the relative levels of AID are too low in some B6 cell types to affect mA3 function.
Genetic data also suggest that AID controls mA3 activity. MMTV infection of BALB/c AID-knockout mice with viruses with or without Rem-coding potential revealed that tumor-associated proviruses showed no significant mutational differences [31]. One interpretation of the loss of mA3-like proviral mutations in the absence of mAID expression is that there is an mA3/AID interaction. Published data indicate that hA3 enzymes are present in cytosolic bodies, such as stress granules and P-bodies [83,84], which are likely sites for interactions with hAID. Therefore, our untested hypothesis is that Rem-mediated degradation of AID will alter the localization and association between mA3 and mAID. This interaction (either direct or indirect through adapters) would then control the mutagenic activity of both enzymes.
What are the cytosolic bodies containing both deaminases? Previous reports have indicated that hA3G is associated with P-bodies and stress granules [84,85], which are dynamic structures enriched for RNAs, protein chaperones, RNA-binding proteins, and translation factors [86,87]. Rem, mA3, and mAID are all RNA-binding proteins [29,88]. Furthermore, hA3B has been shown to interact with polyA-binding protein C1 (PABPC1) and induce signaling through protein kinase RNA-activated (PKR) (also known as eukaryotic translation initiation factor 2-alpha kinase 2 or EIF2AK2) [83]. This signal occurs after various kinds of stress, including viral infection, ER stress, and the unfolded protein response [89,90,91], which leads to translational shutoff [83,92]. In addition, A3B shields viral mRNA from RNase L cleavage by assisting protein–RNA condensation using the stress granule assembly factor G3BP1 [83]. Cytoplasmic AID has been observed to interact with translation factors, such as eEF1A [93], and is tethered outside the nucleus by the chaperone protein Hsp90 [94,95]. Hsp90 has been associated with stress granule disassembly [96]. Furthermore, RNA sensors involved in innate immunity, such as melanoma differentiation associated gene-5 (MDA-5) and oligoadenylate synthetases (OASs), are localized to stress granules and other cytoplasmic ribonucleoprotein condensates [97,98]. Experimental results using multiple different viruses have shown the concentration of foreign nucleic acids in various RNA–DNA–antiviral protein condensates to modulate cell signaling and pathogen replication (reviewed in [99,100]). Therefore, this evidence is consistent with the A3 association with cytosolic bodies and innate immune responses.
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been reported to sustain multiple mutations induced by APOBECs [101,102,103,104]. Recent data indicate that SARS-CoV-2 nucleocapsid (N) protein acts as an adapter to both adenosine deaminase acting on RNA (ADAR) and APOBECs. These interactions localize the N packaging protein–deaminase complexes to stress granules to increase—not decrease—mutagenesis of viral RNA, presumably to provide viral diversity [105]. HTLV-1 nucleocapsid protein (NC) also appears to inhibit viral genome packaging of A3 proteins [106], yet has a low impact on HTLV-1 mutagenesis [107]. These observations suggest that APOBEC as well as ADAR enzymes colocalize with cytoplasmic complexes associated with stress, allowing them access to viral RNAs outside of virion particles. APOBEC interactions with viral proteins may lead to increased or decreased mutations. It remains unclear whether SARS-CoV-2 and HTLV-1 nucleocapsid interactions with APOBECs are mechanistically distinct.
Does the interaction of mA3 and mAID affect MMTV mutagenesis and inhibition of replication? If so, how? One model consistent with current data is that cellular stress, including viral infection, leads to sequestration of viral mRNAs and cellular deaminases in cytosolic stress granules or a related condensate (Figure 2). If A3 enzymes shield viral RNAs from RNase L degradation as proposed [83], the A3/AID deaminases would have an opportunity to associate with genomic RNA prior to packaging. Interactions of A3 and AID may influence the activity of other deaminases within cytoplasmic condensates and/or prolong viral RNA sequestration to prevent their translation. Moreover, mRNA translation of host immune genes may be affected since APOBECs have the ability to mutate both host and viral RNAs [101,108,109,110]. Multiple aspects of these ideas are untested. Regardless of the details, this model provides a framework for understanding the multiple mechanisms that cytidine deaminases use for viral inhibition, while promoting the emergence of variants [3,5,14]. Studies of viral antagonists, such as MMTV Rem, offer a window into these mechanisms.

Funding

This research was funded by the National Institute of Allergy and Infectious Disease, grant number R01AI131660.

Data Availability Statement

No new data were created or analyzed in this study.

Acknowledgments

The comments from members of the Dudley lab are appreciated. I thank Marianna Grenadier for her help with figure preparation.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
A3APOBEC3
ADARAdenosine deaminase acting on RNA
AicdaGene encoding AID
AIDActivation-induced cytidine deaminase
APOBECApolipoprotein B mRNA-editing catalytic polypeptide-like
CACapsid
CRM-1Chromosome maintenance 1, also known as Exportin 1 
eEF1AEukaryotic elongation factor 1A
EnvEnvelope
EREndoplasmic reticulum
HIV-1Human immunodeficiency virus type 1
HTLV-1Human T-cell leukemia virus type 1
IL-4Interleukin-4
LPSLipopolysaccharide
LTRLong terminal repeat
MLVMouse leukemia virus
MMTVMouse mammary tumor virus
MtvEndogenous mouse mammary tumor virus
NCNucleocapsid
NLSNuclear localization sequence
PABPC1PolyA-binding protein C1
PKRProtein kinase RNA-activated
RmRERem-responsive element
SARS-CoV-2Severe acute respiratory syndrome coronavirus 2
SDSplice donor 
SPMMTV-encoded signal peptide
TBLVType B leukemogenic virus

References

  1. Beirag, N.; Varghese, P.M.; Kishore, U. Innate Immune Response to Viral Infection. Adv. Exp. Med. Biol. 2025, 1476, 199–224. [Google Scholar] [CrossRef] [PubMed]
  2. Lam, N.; Lee, Y.; Farber, D.L. A Guide to Adaptive Immune Memory. Nat. Rev. Immunol. 2024, 24, 810–829. [Google Scholar] [CrossRef] [PubMed]
  3. Harris, R.S.; Dudley, J.P. APOBECs and Virus Restriction. Virology 2015, 479–480, 131–145. [Google Scholar] [CrossRef] [PubMed]
  4. Knisbacher, B.A.; Gerber, D.; Levanon, E.Y. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet. 2016, 32, 16–28. [Google Scholar] [CrossRef]
  5. Xu, W.K.; Byun, H.; Dudley, J.P. The Role of APOBECs in Viral Replication. Microorganisms 2020, 8, 1899. [Google Scholar] [CrossRef]
  6. Harari, A.; Ooms, M.; Mulder, L.C.F.; Simon, V. Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H. J. Virol. 2009, 83, 295–303. [Google Scholar] [CrossRef]
  7. Anant, S.; MacGinnitie, A.J.; Davidson, N.O. Apobec-1, the Catalytic Subunit of the Mammalian Apolipoprotein B mRNA Editing Enzyme, Is a Novel RNA-Binding Protein. J. Biol. Chem. 1995, 270, 14762–14767. [Google Scholar] [CrossRef]
  8. Jern, P.; Stoye, J.P.; Coffin, J.M. Role of APOBEC3 in Genetic Diversity among Endogenous Murine Leukemia Viruses. PLoS Genet. 2007, 3, 2014–2022. [Google Scholar] [CrossRef]
  9. Shaffer, E.; Boso, G.; Sadjadpour, R.; Yedavalli, V.V.S.R.K.; Lam, O.; Kozak, C.A. Apobec3 Shows Rapid Evolution in House Mouse Subspecies and Unusual Hypermutation Patterns of Endogenous Mouse Mammary Tumor Viruses. J. Virol. 2025, 99, e0125125. [Google Scholar] [CrossRef]
  10. Lecossier, D.; Bouchonnet, F.; Clavel, F.; Hance, A.J. Hypermutation of HIV-1 DNA in the Absence of the Vif Protein. Science 2003, 300, 1112. [Google Scholar] [CrossRef]
  11. Sheehy, A.M.; Gaddis, N.C.; Choi, J.D.; Malim, M.H. Isolation of a Human Gene That Inhibits HIV-1 Infection and Is Suppressed by the Viral Vif Protein. Nature 2002, 418, 646–650. [Google Scholar] [CrossRef] [PubMed]
  12. Guo, F.; Cen, S.; Niu, M.; Saadatmand, J.; Kleiman, L. Inhibition of tRNA3(Lys)-Primed Reverse Transcription by Human APOBEC3G during Human Immunodeficiency Virus Type 1 Replication. J. Virol. 2006, 80, 11710–11722. [Google Scholar] [CrossRef] [PubMed]
  13. Schröfelbauer, B.; Yu, Q.; Zeitlin, S.G.; Landau, N.R. Human Immunodeficiency Virus Type 1 Vpr Induces the Degradation of the UNG and SMUG Uracil-DNA Glycosylases. J. Virol. 2005, 79, 10978–10987. [Google Scholar] [CrossRef] [PubMed]
  14. Dudley, J.P. APOBECs: Our Fickle Friends? PLoS Pathog 2023, 19, e1011364. [Google Scholar] [CrossRef]
  15. Sova, P.; Volsky, D.J. Efficiency of Viral DNA Synthesis during Infection of Permissive and Nonpermissive Cells with Vif-Negative Human Immunodeficiency Virus Type 1. J. Virol. 1993, 67, 6322–6326. [Google Scholar] [CrossRef]
  16. Liddament, M.T.; Brown, W.L.; Schumacher, A.J.; Harris, R.S. APOBEC3F Properties and Hypermutation Preferences Indicate Activity against HIV-1 in Vivo. Curr. Biol. 2004, 14, 1385–1391. [Google Scholar] [CrossRef]
  17. Wiegand, H.L.; Doehle, B.P.; Bogerd, H.P.; Cullen, B.R. A Second Human Antiretroviral Factor, APOBEC3F, Is Suppressed by the HIV-1 and HIV-2 Vif Proteins. EMBO J. 2004, 23, 2451–2458. [Google Scholar] [CrossRef]
  18. Miyagi, E.; Kao, S.; Fumitaka, M.; Buckler-White, A.; Plishka, R.; Strebel, K. Long-Term Passage of Vif-Null HIV-1 in CD4+ T Cells Expressing Sub-Lethal Levels of APOBEC Proteins Fails to Develop APOBEC Resistance. Virology 2017, 504, 1–11. [Google Scholar] [CrossRef]
  19. Jaguva Vasudevan, A.A.; Perkovic, M.; Bulliard, Y.; Cichutek, K.; Trono, D.; Häussinger, D.; Münk, C. Prototype Foamy Virus Bet Impairs the Dimerization and Cytosolic Solubility of Human APOBEC3G. J. Virol. 2013, 87, 9030–9040. [Google Scholar] [CrossRef]
  20. Yoshikawa, R.; Takeuchi, J.S.; Yamada, E.; Nakano, Y.; Misawa, N.; Kimura, Y.; Ren, F.; Miyazawa, T.; Koyanagi, Y.; Sato, K. Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3. J. Virol. 2017, 91, e00250-17. [Google Scholar] [CrossRef]
  21. Stavrou, S.; Nitta, T.; Kotla, S.; Ha, D.; Nagashima, K.; Rein, A.R.; Fan, H.; Ross, S.R. Murine Leukemia Virus Glycosylated Gag Blocks Apolipoprotein B Editing Complex 3 and Cytosolic Sensor Access to the Reverse Transcription Complex. Proc. Natl. Acad. Sci. USA 2013, 110, 9078–9083. [Google Scholar] [CrossRef]
  22. Golovkina, T.V.; Dudley, J.P.; Ross, S.R. B and T Cells Are Required for Mouse Mammary Tumor Virus Spread within the Mammary Gland. J. Immunol. 1998, 161, 2375–2382. [Google Scholar] [CrossRef]
  23. Golovkina, T.V.; Chervonsky, A.; Dudley, J.P.; Ross, S.R. Transgenic Mouse Mammary Tumor Virus Superantigen Expression Prevents Viral Infection. Cell 1992, 69, 637–645. [Google Scholar] [CrossRef] [PubMed]
  24. Held, W.; Shakhov, A.N.; Izui, S.; Waanders, G.A.; Scarpellino, L.; MacDonald, H.R.; Acha-Orbea, H. Superantigen-Reactive CD4+ T Cells Are Required to Stimulate B Cells after Infection with Mouse Mammary Tumor Virus. J. Exp. Med. 1993, 177, 359–366. [Google Scholar] [CrossRef]
  25. Mertz, J.A.; Simper, M.S.; Lozano, M.M.; Payne, S.M.; Dudley, J.P. Mouse Mammary Tumor Virus Encodes a Self-Regulatory RNA Export Protein and Is a Complex Retrovirus. J. Virol. 2005, 79, 14737–14747. [Google Scholar] [CrossRef] [PubMed]
  26. Indik, S.; Günzburg, W.H.; Salmons, B.; Rouault, F. A Novel, Mouse Mammary Tumor Virus Encoded Protein with Rev-like Properties. Virology 2005, 337, 1–6. [Google Scholar] [CrossRef] [PubMed]
  27. Byun, H.; Halani, N.; Mertz, J.A.; Ali, A.F.; Lozano, M.M.; Dudley, J.P. Retroviral Rem Protein Requires Processing by Signal Peptidase and Retrotranslocation for Nuclear Function. Proc. Natl. Acad. Sci. USA 2010, 107, 12287–12292. [Google Scholar] [CrossRef]
  28. Xu, W.K.; Gou, Y.; Lozano, M.M.; Dudley, J.P. Unconventional P97/VCP-Mediated Endoplasmic Reticulum-to-Endosome Trafficking of a Retroviral Protein. J. Virol. 2021, 95, e0053121. [Google Scholar] [CrossRef]
  29. Mertz, J.A.; Chadee, A.B.; Byun, H.; Russell, R.; Dudley, J.P. Mapping of the Functional Boundaries and Secondary Structure of the Mouse Mammary Tumor Virus Rem-Responsive Element. J. Biol. Chem. 2009, 284, 25642–25652. [Google Scholar] [CrossRef]
  30. Mertz, J.A.; Lozano, M.M.; Dudley, J.P. Rev and Rex Proteins of Human Complex Retroviruses Function with the MMTV Rem-Responsive Element. Retrovirology 2009, 6, 10. [Google Scholar] [CrossRef]
  31. Singh, G.B.; Byun, H.; Ali, A.F.; Medina, F.; Wylie, D.; Shivram, H.; Nash, A.K.; Lozano, M.M.; Dudley, J.P. A Protein Antagonist of Activation-Induced Cytidine Deaminase Encoded by a Complex Mouse Retrovirus. mBio 2019, 10, 10–1128. [Google Scholar] [CrossRef] [PubMed]
  32. Mustafa, F.; Lozano, M.; Dudley, J.P. C3H Mouse Mammary Tumor Virus Superantigen Function Requires a Splice Donor Site in the Envelope Gene. J. Virol. 2000, 74, 9431–9440. [Google Scholar] [CrossRef] [PubMed][Green Version]
  33. Dultz, E.; Hildenbeutel, M.; Martoglio, B.; Hochman, J.; Dobberstein, B.; Kapp, K. The Signal Peptide of the Mouse Mammary Tumor Virus Rem Protein Is Released from the Endoplasmic Reticulum Membrane and Accumulates in Nucleoli. J. Biol. Chem. 2008, 283, 9966–9976. [Google Scholar] [CrossRef] [PubMed]
  34. Das, P.; Xu, W.K.; Gautam, A.K.S.; Lozano, M.M.; Dudley, J.P. A Retrotranslocation Assay That Predicts Defective VCP/P97-Mediated Trafficking of a Retroviral Signal Peptide. mBio 2022, 13, e0295321. [Google Scholar] [CrossRef]
  35. Ball, J.K.; Diggelmann, H.; Dekaban, G.A.; Grossi, G.F.; Semmler, R.; Waight, P.A.; Fletcher, R.F. Alterations in the U3 Region of the Long Terminal Repeat of an Infectious Thymotropic Type B Retrovirus. J. Virol. 1988, 62, 2985–2993. [Google Scholar] [CrossRef]
  36. Mertz, J.A.; Mustafa, F.; Meyers, S.; Dudley, J.P. Type B Leukemogenic Virus Has a T-Cell-Specific Enhancer That Binds AML-1. J. Virol. 2001, 75, 2174–2184. [Google Scholar] [CrossRef]
  37. Dudley, J.P.; Golovkina, T.V.; Ross, S.R. Lessons Learned from Mouse Mammary Tumor Virus in Animal Models. ILAR J. 2016, 57, 12–23. [Google Scholar] [CrossRef]
  38. Miller, C.L.; Garner, R.; Paetkau, V. An Activation-Dependent, T-Lymphocyte-Specific Transcriptional Activator in the Mouse Mammary Tumor Virus Env Gene. Mol. Cell. Biol. 1992, 12, 3262–3272. [Google Scholar]
  39. Mustafa, F.; Bhadra, S.; Johnston, D.; Lozano, M.; Dudley, J.P. The Type B Leukemogenic Virus Truncated Superantigen Is Dispensable for T-Cell Lymphomagenesis. J. Virol. 2003, 77, 3866–3870. [Google Scholar] [CrossRef][Green Version]
  40. Henrard, D.; Ross, S.R. Endogenous Mouse Mammary Tumor Virus Is Expressed in Several Organs in Addition to the Lactating Mammary Gland. J. Virol. 1988, 62, 3046–3049. [Google Scholar] [CrossRef]
  41. Barnett, A.; Mustafa, F.; Wrona, T.J.; Lozano, M.; Dudley, J.P. Expression of Mouse Mammary Tumor Virus Superantigen mRNA in the Thymus Correlates with Kinetics of Self-Reactive T-Cell Loss. J. Virol. 1999, 73, 6634–6645. [Google Scholar] [CrossRef] [PubMed]
  42. Ito, S.; Nagaoka, H.; Shinkura, R.; Begum, N.; Muramatsu, M.; Nakata, M.; Honjo, T. Activation-Induced Cytidine Deaminase Shuttles between Nucleus and Cytoplasm like Apolipoprotein B mRNA Editing Catalytic Polypeptide 1. Proc. Natl. Acad. Sci. USA 2004, 101, 1975–1980. [Google Scholar] [CrossRef]
  43. Muramatsu, M.; Kinoshita, K.; Fagarasan, S.; Yamada, S.; Shinkai, Y.; Honjo, T. Class Switch Recombination and Hypermutation Require Activation-Induced Cytidine Deaminase (AID), a Potential RNA Editing Enzyme. Cell 2000, 102, 553–563. [Google Scholar] [CrossRef]
  44. Tsukimoto, S.; Hakata, Y.; Tsuji-Kawahara, S.; Enya, T.; Tsukamoto, T.; Mizuno, S.; Takahashi, S.; Nakao, S.; Miyazawa, M. Distinctive High Expression of Antiretroviral APOBEC3 Protein in Mouse Germinal Center B Cells. Viruses 2022, 14, 832. [Google Scholar] [CrossRef] [PubMed]
  45. Beutner, U.; Kraus, E.; Kitamura, D.; Rajewsky, K.; Huber, B.T. B Cells Are Essential for Murine Mammary Tumor Virus Transmission, but Not for Presentation of Endogenous Superantigens. J. Exp. Med. 1994, 179, 1457–1466. [Google Scholar] [CrossRef] [PubMed]
  46. Byun, H.; Singh, G.B.; Xu, W.K.; Das, P.; Reyes, A.; Battenhouse, A.; Wylie, D.C.; Santiago, M.L.; Lozano, M.M.; Dudley, J.P. Apobec-Mediated Retroviral Hypermutation in Vivo Is Dependent on Mouse Strain. PLoS Pathog. 2024, 20, e1012505. [Google Scholar] [CrossRef] [PubMed]
  47. Okeoma, C.M.; Lovsin, N.; Peterlin, B.M.; Ross, S.R. APOBEC3 Inhibits Mouse Mammary Tumour Virus Replication in Vivo. Nature 2007, 445, 927–930. [Google Scholar] [CrossRef]
  48. Okeoma, C.M.; Huegel, A.L.; Lingappa, J.; Feldman, M.D.; Ross, S.R. APOBEC3 Proteins Expressed in Mammary Epithelial Cells Are Packaged into Retroviruses and Can Restrict Transmission of Milk-Borne Virions. Cell Host Microbe 2010, 8, 534–543. [Google Scholar] [CrossRef]
  49. Bhadra, S.; Lozano, M.M.; Payne, S.M.; Dudley, J.P. Endogenous MMTV Proviruses Induce Susceptibility to Both Viral and Bacterial Pathogens. PLoS Pathog. 2006, 2, e128. [Google Scholar] [CrossRef]
  50. Nusse, R.; van Ooyen, A.; Cox, D.; Fung, Y.K.; Varmus, H. Mode of Proviral Activation of a Putative Mammary Oncogene (Int-1) on Mouse Chromosome 15. Nature 1984, 307, 131–136. [Google Scholar] [CrossRef]
  51. Peters, G.; Brookes, S.; Smith, R.; Dickson, C. Tumorigenesis by Mouse Mammary Tumor Virus: Evidence for a Common Region for Provirus Integration in Mammary Tumors. Cell 1983, 33, 369–377. [Google Scholar] [CrossRef] [PubMed]
  52. Michalides, R.; Wagenaar, E.; Weijers, P. Rearrangements in the Long Terminal Repeat of Extra Mouse Mammary Tumor Proviruses in T-Cell Leukemias of Mouse Strain GR Result in a Novel Enhancer-like Structure. Mol. Cell. Biol. 1985, 5, 823–830. [Google Scholar] [PubMed]
  53. Hsu, C.L.; Fabritius, C.; Dudley, J. Mouse Mammary Tumor Virus Proviruses in T-Cell Lymphomas Lack a Negative Regulatory Element in the Long Terminal Repeat. J. Virol. 1988, 62, 4644–4652. [Google Scholar] [CrossRef] [PubMed]
  54. Bhadra, S.; Lozano, M.M.; Dudley, J.P. Conversion of Mouse Mammary Tumor Virus to a Lymphomagenic Virus. J. Virol. 2005, 79, 12592–12596. [Google Scholar] [CrossRef]
  55. Nusse, R.; Varmus, H.E. Many Tumors Induced by the Mouse Mammary Tumor Virus Contain a Provirus Integrated in the Same Region of the Host Genome. Cell 1982, 31, 99–109. [Google Scholar] [CrossRef]
  56. Rajan, L.; Broussard, D.; Lozano, M.; Lee, C.G.; Kozak, C.A.; Dudley, J.P. The C-Myc Locus Is a Common Integration Site in Type B Retrovirus-Induced T-Cell Lymphomas. J. Virol. 2000, 74, 2466–2471. [Google Scholar] [CrossRef]
  57. Wei, L.; Chahwan, R.; Wang, S.; Wang, X.; Pham, P.T.; Goodman, M.F.; Bergman, A.; Scharff, M.D.; MacCarthy, T. Overlapping Hotspots in CDRs Are Critical Sites for V Region Diversification. Proc. Natl. Acad. Sci. USA 2015, 112, E728–E737. [Google Scholar] [CrossRef]
  58. MacCarthy, T.; Kalis, S.L.; Roa, S.; Pham, P.; Goodman, M.F.; Scharff, M.D.; Bergman, A. V-Region Mutation in Vitro, in Vivo, and in Silico Reveal the Importance of the Enzymatic Properties of AID and the Sequence Environment. Proc. Natl. Acad. Sci. USA 2009, 106, 8629–8634. [Google Scholar] [CrossRef]
  59. Dopkins, N.; Nixon, D.F. Activation of Human Endogenous Retroviruses and Its Physiological Consequences. Nat. Rev. Mol. Cell Biol. 2024, 25, 212–222. [Google Scholar] [CrossRef]
  60. Kozak, C.; Peters, G.; Pauley, R.; Morris, V.; Michalides, R.; Dudley, J.; Green, M.; Davisson, M.; Prakash, O.; Vaidya, A. A Standardized Nomenclature for Endogenous Mouse Mammary Tumor Viruses. J. Virol. 1987, 61, 1651–1654. [Google Scholar] [CrossRef]
  61. Lam, O.; Shaffer, E.; Boso, G.; Kozak, C.A. Intact, Recombinant, and Spliced Forms of Endogenous Mouse Mammary Tumor Viruses in Inbred and Wild Mice. J. Virol. 2025, 99, e0007925. [Google Scholar] [CrossRef] [PubMed]
  62. Salmons, B.; Knedlitschek, G.; Kennedy, N.; Groner, B.; Ponta, H. The Endogenous Mouse Mammary Tumour Virus Locus Mtv-8 Contains a Defective Envelope Gene. Virus Res. 1986, 4, 377–389. [Google Scholar] [CrossRef] [PubMed]
  63. Held, W.; Waanders, G.A.; MacDonald, H.R.; Acha-Orbea, H. MHC Class II Hierarchy of Superantigen Presentation Predicts Efficiency of Infection with Mouse Mammary Tumor Virus. Int. Immunol. 1994, 6, 1403–1407. [Google Scholar] [CrossRef] [PubMed]
  64. Kobayashi, M.; Takaori-Kondo, A.; Miyauchi, Y.; Iwai, K.; Uchiyama, T. Ubiquitination of APOBEC3G by an HIV-1 Vif-Cullin5-Elongin B-Elongin C Complex Is Essential for Vif Function. J. Biol. Chem. 2005, 280, 18573–18578. [Google Scholar] [CrossRef]
  65. Liu, B.; Sarkis, P.T.N.; Luo, K.; Yu, Y.; Yu, X.-F. Regulation of Apobec3F and Human Immunodeficiency Virus Type 1 Vif by Vif-Cul5-ElonB/C E3 Ubiquitin Ligase. J. Virol. 2005, 79, 9579–9587. [Google Scholar] [CrossRef]
  66. Abudu, A.; Takaori-Kondo, A.; Izumi, T.; Shirakawa, K.; Kobayashi, M.; Sasada, A.; Fukunaga, K.; Uchiyama, T. Murine Retrovirus Escapes from Murine APOBEC3 via Two Distinct Novel Mechanisms. Curr. Biol. 2006, 16, 1565–1570. [Google Scholar] [CrossRef]
  67. Santiago, M.L.; Montano, M.; Benitez, R.; Messer, R.J.; Yonemoto, W.; Chesebro, B.; Hasenkrug, K.J.; Greene, W.C. Apobec3 Encodes Rfv3, a Gene Influencing Neutralizing Antibody Control of Retrovirus Infection. Science 2008, 321, 1343–1346. [Google Scholar] [CrossRef]
  68. Browne, E.P.; Littman, D.R. Species-Specific Restriction of Apobec3-Mediated Hypermutation. J. Virol. 2008, 82, 1305–1313. [Google Scholar] [CrossRef]
  69. Gourzi, P.; Leonova, T.; Papavasiliou, F.N. A Role for Activation-Induced Cytidine Deaminase in the Host Response against a Transforming Retrovirus. Immunity 2006, 24, 779–786. [Google Scholar] [CrossRef]
  70. Ferreira, B.L.; Ferreira, É.R.; de Brito, M.V.; Salu, B.R.; Oliva, M.L.V.; Mortara, R.A.; Orikaza, C.M. BALB/c and C57BL/6 Mice Cytokine Responses to Trypanosoma Cruzi Infection Are Independent of Parasite Strain Infectivity. Front. Microbiol. 2018, 9, 553. [Google Scholar] [CrossRef]
  71. Watanabe, H.; Numata, K.; Ito, T.; Takagi, K.; Matsukawa, A. INNATE IMMUNE RESPONSE IN TH1- AND TH2-DOMINANT MOUSE STRAINS. Shock 2004, 22, 460. [Google Scholar] [CrossRef] [PubMed]
  72. Takeda, E.; Tsuji-Kawahara, S.; Sakamoto, M.; Langlois, M.-A.; Neuberger, M.S.; Rada, C.; Miyazawa, M. Mouse APOBEC3 Restricts Friend Leukemia Virus Infection and Pathogenesis In Vivo. J. Virol. 2008, 82, 10998–11008. [Google Scholar] [CrossRef]
  73. Sanville, B.; Dolan, M.A.; Wollenberg, K.; Yan, Y.; Martin, C.; Yeung, M.L.; Strebel, K.; Buckler-White, A.; Kozak, C.A. Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove. PLoS Pathog. 2010, 6, e1000974. [Google Scholar] [CrossRef] [PubMed]
  74. Vogt, M.; Haggblom, C.; Swift, S.; Haas, M. Envelope Gene and Long Terminal Repeat Determine the Different Biological Properties of Rauscher, Friend, and Moloney Mink Cell Focus-Inducing Viruses. J. Virol. 1985, 55, 184–192. [Google Scholar] [CrossRef] [PubMed]
  75. Clark, S.P.; Kaufhold, R.; Chan, A.; Mak, T.W. Comparison of the Transcriptional Properties of the Friend and Moloney Retrovirus Long Terminal Repeats: Importance of Tandem Duplications and of the Core Enhancer Sequence. Virology 1985, 144, 481–494. [Google Scholar] [CrossRef]
  76. Rosen, C.A.; Haseltine, W.A.; Lenz, J.; Ruprecht, R.; Cloyd, M.W. Tissue Selectivity of Murine Leukemia Virus Infection Is Determined by Long Terminal Repeat Sequences. J. Virol. 1985, 55, 862–866. [Google Scholar] [CrossRef]
  77. Yoshimura, F.K.; Davison, B.; Chaffin, K. Murine Leukemia Virus Long Terminal Repeat Sequences Can Enhance Gene Activity in a Cell-Type-Specific Manner. Mol. Cell Biol. 1985, 5, 2832–2835. [Google Scholar] [CrossRef]
  78. Hakata, Y.; Landau, N.R. Reversed Functional Organization of Mouse and Human APOBEC3 Cytidine Deaminase Domains. J. Biol. Chem. 2006, 281, 36624–36631. [Google Scholar] [CrossRef]
  79. Boi, S.; Kolokithas, A.; Shepard, J.; Linwood, R.; Rosenke, K.; Van Dis, E.; Malik, F.; Evans, L.H. Incorporation of Mouse APOBEC3 into Murine Leukemia Virus Virions Decreases the Activity and Fidelity of Reverse Transcriptase. J. Virol. 2014, 88, 7659–7662. [Google Scholar] [CrossRef][Green Version]
  80. Rulli, S.J.; Mirro, J.; Hill, S.A.; Lloyd, P.; Gorelick, R.J.; Coffin, J.M.; Derse, D.; Rein, A. Interactions of Murine APOBEC3 and Human APOBEC3G with Murine Leukemia Viruses. J. Virol. 2008, 82, 6566–6575. [Google Scholar] [CrossRef]
  81. MacMillan, A.L.; Kohli, R.M.; Ross, S.R. APOBEC3 Inhibition of Mouse Mammary Tumor Virus Infection: The Role of Cytidine Deamination versus Inhibition of Reverse Transcription. J. Virol. 2013, 87, 4808–4817. [Google Scholar] [CrossRef] [PubMed]
  82. Hagen, B.; Kraase, M.; Indikova, I.; Indik, S. A High Rate of Polymerization during Synthesis of Mouse Mammary Tumor Virus DNA Alleviates Hypermutation by APOBEC3 Proteins. PLoS Pathog. 2019, 15, e1007533. [Google Scholar] [CrossRef] [PubMed]
  83. Manjunath, L.; Oh, S.; Ortega, P.; Bouin, A.; Bournique, E.; Sanchez, A.; Martensen, P.M.; Auerbach, A.A.; Becker, J.T.; Seldin, M.; et al. APOBEC3B Drives PKR-Mediated Translation Shutdown and Protects Stress Granules in Response to Viral Infection. Nat. Commun. 2023, 14, 820. [Google Scholar] [CrossRef] [PubMed]
  84. Gallois-Montbrun, S.; Kramer, B.; Swanson, C.M.; Byers, H.; Lynham, S.; Ward, M.; Malim, M.H. Antiviral Protein APOBEC3G Localizes to Ribonucleoprotein Complexes Found in P Bodies and Stress Granules. J. Virol. 2007, 81, 2165–2178. [Google Scholar] [CrossRef]
  85. Kozak, S.L.; Marin, M.; Rose, K.M.; Bystrom, C.; Kabat, D. The Anti-HIV-1 Editing Enzyme APOBEC3G Binds HIV-1 RNA and Messenger RNAs That Shuttle between Polysomes and Stress Granules. J. Biol. Chem. 2006, 281, 29105–29119. [Google Scholar] [CrossRef]
  86. Tauber, D.; Tauber, G.; Khong, A.; Van Treeck, B.; Pelletier, J.; Parker, R. Modulation of RNA Condensation by the DEAD-Box Protein eIF4A. Cell 2020, 180, 411–426.e16. [Google Scholar] [CrossRef]
  87. Cui, Q.; Liu, Z.; Bai, G. Friend or Foe: The Role of Stress Granule in Neurodegenerative Disease. Neuron 2024, 112, 2464–2485. [Google Scholar] [CrossRef]
  88. Pecori, R.; Di Giorgio, S.; Paulo Lorenzo, J.; Nina Papavasiliou, F. Functions and Consequences of AID/APOBEC-Mediated DNA and RNA Deamination. Nat. Rev. Genet. 2022, 23, 505–518. [Google Scholar] [CrossRef]
  89. Walter, P.; Ron, D. The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation. Science 2011, 334, 1081–1086. [Google Scholar] [CrossRef]
  90. Wang, M.; Kaufman, R.J. Protein Misfolding in the Endoplasmic Reticulum as a Conduit to Human Disease. Nature 2016, 529, 326–335. [Google Scholar] [CrossRef]
  91. Foo, J.; Bellot, G.; Pervaiz, S.; Alonso, S. Mitochondria-Mediated Oxidative Stress during Viral Infection. Trends Microbiol. 2022, 30, 679–692. [Google Scholar] [CrossRef] [PubMed]
  92. Gomes, M.T.R.; Guimarães, E.S.; Oliveira, S.C. ZBP1 Senses Brucella Abortus DNA Triggering Type I Interferon Signaling Pathway and Unfolded Protein Response Activation. Front. Immunol. 2024, 15, 1511949. [Google Scholar] [CrossRef]
  93. Häsler, J.; Rada, C.; Neuberger, M.S. Cytoplasmic Activation-Induced Cytidine Deaminase (AID) Exists in Stoichiometric Complex with Translation Elongation Factor 1α (eEF1A). Proc. Natl. Acad. Sci. USA 2011, 108, 18366–18371. [Google Scholar] [CrossRef]
  94. Methot, S.P.; Litzler, L.C.; Trajtenberg, F.; Zahn, A.; Robert, F.; Pelletier, J.; Buschiazzo, A.; Magor, B.G.; Di Noia, J.M. Consecutive Interactions with HSP90 and eEF1A Underlie a Functional Maturation and Storage Pathway of AID in the Cytoplasm. J. Exp. Med. 2015, 212, 581–596. [Google Scholar] [CrossRef] [PubMed]
  95. Orthwein, A.; Patenaude, A.-M.; Affar, E.B.; Lamarre, A.; Young, J.C.; Di Noia, J.M. Regulation of Activation-Induced Deaminase Stability and Antibody Gene Diversification by Hsp90. J. Exp. Med. 2010, 207, 2751–2765. [Google Scholar] [CrossRef]
  96. Mediani, L.; Antoniani, F.; Galli, V.; Vinet, J.; Carrà, A.D.; Bigi, I.; Tripathy, V.; Tiago, T.; Cimino, M.; Leo, G.; et al. Hsp90-Mediated Regulation of DYRK3 Couples Stress Granule Disassembly and Growth via mTORC1 Signaling. EMBO Rep. 2021, 22, e51740. [Google Scholar] [CrossRef]
  97. Briggs, S.; Blomqvist, E.K.; Cuellar, A.; Correa, D.; Burke, J.M. Condensation of Human OAS Proteins Initiates Diverse Antiviral Activities in Response to West Nile Virus. Genes. Dev. 2025, 39, 1162–1181. [Google Scholar] [CrossRef]
  98. Langereis, M.A.; Feng, Q.; van Kuppeveld, F.J. MDA5 Localizes to Stress Granules, but This Localization Is Not Required for the Induction of Type I Interferon. J. Virol. 2013, 87, 6314–6325. [Google Scholar] [CrossRef]
  99. Loucas, G.; Locker, N.; Parker, R. Nucleic Acid-Protein Condensates in Innate Immunity. Mol. Cell 2025, 85, 3823–3839. [Google Scholar] [CrossRef]
  100. Reineke, L.C.; Lloyd, R.E. Diversion of Stress Granules and P-Bodies during Viral Infection. Virology 2013, 436, 255–267. [Google Scholar] [CrossRef]
  101. Kim, K.; Calabrese, P.; Wang, S.; Qin, C.; Rao, Y.; Feng, P.; Chen, X.S. The Roles of APOBEC-Mediated RNA Editing in SARS-CoV-2 Mutations, Replication and Fitness. Sci. Rep. 2022, 12, 14972. [Google Scholar] [CrossRef] [PubMed]
  102. Di Giorgio, S.; Martignano, F.; Torcia, M.G.; Mattiuz, G.; Conticello, S.G. Evidence for Host-Dependent RNA Editing in the Transcriptome of SARS-CoV-2. Sci. Adv. 2020, 6, eabb5813. [Google Scholar] [CrossRef] [PubMed]
  103. De Maio, N.; Walker, C.R.; Turakhia, Y.; Lanfear, R.; Corbett-Detig, R.; Goldman, N. Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2. Genome Biol. Evol. 2021, 13, evab087. [Google Scholar] [CrossRef] [PubMed]
  104. Ratcliff, J.; Simmonds, P. Potential APOBEC-Mediated RNA Editing of the Genomes of SARS-CoV-2 and Other Coronaviruses and Its Impact on Their Longer Term Evolution. Virology 2021, 556, 62–72. [Google Scholar] [CrossRef]
  105. Li, Z.; Luo, L.; Ju, X.; Huang, S.; Lei, L.; Yu, Y.; Liu, J.; Zhang, P.; Chi, T.; Ma, P.; et al. Viral N Protein Hijacks Deaminase-Containing RNA Granules to Enhance SARS-CoV-2 Mutagenesis. EMBO J. 2024, 43, 6444–6468. [Google Scholar] [CrossRef]
  106. Derse, D.; Hill, S.A.; Princler, G.; Lloyd, P.; Heidecker, G. Resistance of Human T Cell Leukemia Virus Type 1 to APOBEC3G Restriction Is Mediated by Elements in Nucleocapsid. Proc. Natl. Acad. Sci. USA 2007, 104, 2915–2920. [Google Scholar] [CrossRef]
  107. Shichijo, T.; Yasunaga, J.I.; Sato, K.; Nosaka, K.; Toyoda, K.; Watanabe, M.; Zhang, W.; Koyanagi, Y.; Murphy, E.L.; Bruhn, R.L.; et al. Vulnerability to APOBEC3G Linked to the Pathogenicity of Deltaretroviruses. Proc. Natl. Acad. Sci. USA 2024, 121, e2309925121. [Google Scholar] [CrossRef]
  108. Van Norden, M.; Falls, Z.; Mandloi, S.; Segal, B.H.; Baysal, B.E.; Samudrala, R.; Elkin, P.L. The Implications of APOBEC3-Mediated C-to-U RNA Editing for Human Disease. Commun. Biol. 2024, 7, 529. [Google Scholar] [CrossRef]
  109. Bishop, K.N.; Holmes, R.K.; Sheehy, A.M.; Malim, M.H. APOBEC-Mediated Editing of Viral RNA. Science 2004, 305, 645. [Google Scholar] [CrossRef]
  110. Teng, B.; Burant, C.F.; Davidson, N.O. Molecular Cloning of an Apolipoprotein B Messenger RNA Editing Protein. Science 1993, 260, 1816–1819. [Google Scholar] [CrossRef]
Viruses 18 00399 g002
Figure 2. Model for Rem interactions with AID and mouse APOBEC3. Uncleaved Rem is synthesized at the ER membrane and extracted by retrotranslocation prior to cleavage into SP and Rem-CT [27]. The cleavage products SP and Rem-CT traffic to the nucleus and ER, respectively [25,27]. SP and Rem contain an NES that allows nuclear shuttling [25,26]. Rem serves as an adapter between the proteasome (gray double hexamer) and AID (orange) [31]. AID is polyubiquitylated by cellular enzymes, and the red X indicates AID degradation. Rem likely is associated with viral mRNAs exported from the nucleus through binding to the Rem-responsive element [29]. AID and mA3 (purple) are expected to interact with viral genomic RNA (gRNA) and mRNA as well as each other in association with cytosolic bodies, e.g., stress granules. It is unclear whether additional proteins (blue rectangle with question mark) mediate the interaction between AID and mA3 or act as cofactors for enzymatic activity. Retention of viral mRNA in cytosolic bodies by AID and mA3 may decrease virion packaging (gray hexagon) or mRNA association with ribosomes.
Figure 2. Model for Rem interactions with AID and mouse APOBEC3. Uncleaved Rem is synthesized at the ER membrane and extracted by retrotranslocation prior to cleavage into SP and Rem-CT [27]. The cleavage products SP and Rem-CT traffic to the nucleus and ER, respectively [25,27]. SP and Rem contain an NES that allows nuclear shuttling [25,26]. Rem serves as an adapter between the proteasome (gray double hexamer) and AID (orange) [31]. AID is polyubiquitylated by cellular enzymes, and the red X indicates AID degradation. Rem likely is associated with viral mRNAs exported from the nucleus through binding to the Rem-responsive element [29]. AID and mA3 (purple) are expected to interact with viral genomic RNA (gRNA) and mRNA as well as each other in association with cytosolic bodies, e.g., stress granules. It is unclear whether additional proteins (blue rectangle with question mark) mediate the interaction between AID and mA3 or act as cofactors for enzymatic activity. Retention of viral mRNA in cytosolic bodies by AID and mA3 may decrease virion packaging (gray hexagon) or mRNA association with ribosomes.
Viruses 18 00399 g002
Table 1. TBLV proviral mutations in response to Rem expression in BALB/c and B6 mice.
Table 1. TBLV proviral mutations in response to Rem expression in BALB/c and B6 mice.
Mouse StrainRelative AID
Splenocyte Levels		Relative mA3
Splenocyte Levels		Dominant TBLV APOBEC MutationsEffect of Rem Expression
on APOBEC Mutations
BALB/cHighLowTYCReduced 
B6LowHighTYCNo effect
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Dudley, J.P. A Viral Protein Antagonist for Both AID and APOBEC3. Viruses 2026, 18, 399. https://doi.org/10.3390/v18040399

AMA Style

Dudley JP. A Viral Protein Antagonist for Both AID and APOBEC3. Viruses. 2026; 18(4):399. https://doi.org/10.3390/v18040399

Chicago/Turabian Style

Dudley, Jaquelin P. 2026. "A Viral Protein Antagonist for Both AID and APOBEC3" Viruses 18, no. 4: 399. https://doi.org/10.3390/v18040399

APA Style

Dudley, J. P. (2026). A Viral Protein Antagonist for Both AID and APOBEC3. Viruses, 18(4), 399. https://doi.org/10.3390/v18040399

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop