The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism

Harris, Reuben S.; Shaban, Nadine M.; Shi, Ke; Lauer, Kate V.; Carpenter, Michael A.; Richards, Christopher M.; Lopresti, Michael; Salamango, Daniel J.; Wang, Jiayi; Banerjee, Surajit; Brown, William L.; Aihara, Hideki

doi:10.1101/203000

Cited by 19 publications

(39 citation statements)

References 80 publications

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“…A third consideration could be negative interference by an as yet unidentified factor. For instance, both intra/inter-A3 oligomerization and RNA binding are known to inhibit the activity of multiple A3 family DNA deaminases including A3B and A3H (Cortez et al, 2019;Shaban et al, 2018). However, these considerations are tempered by the fact that our original human A3B 5 transgenic line was lost early in these studies likely due to its exerting negative selective pressure and catalyzing self-inactivation.…”

Section: Discussionmentioning

confidence: 99%

APOBEC3A Catalyzes Mutation and Drives CarcinogenesisIn Vivo

Law

Levin‐Klein

Jarvis

et al. 2019

Preprint

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The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other 5 APOBEC3 family members including APOBEC3B did not as strongly promote liver tumor formation. DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in 10 human tumor data sets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.

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Section: Discussionmentioning

confidence: 99%

APOBEC3A Catalyzes Mutation and Drives CarcinogenesisIn Vivo

Law

Levin‐Klein

Jarvis

et al. 2019

Preprint

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“…These findings suggest that A3H variants expressing the R105G and N15del mutations may share a common negative regulatory mechanism that affects the stability and localization of these mutants, and the N15del mutation leads to greater utilization of this mechanism. Several groups have recently described the mechanism by which stable A3H dimerizes through its interaction with duplex RNA, and this complex is maintained primarily through protein-RNA contacts [23,[25][26][27]. Interaction with duplex RNA is mediated by aromatic and positively-charged residues in Loop 1, Loop 7, and the C-terminal a6 helix [23,[25][26][27].…”

Section: Discussionmentioning

confidence: 99%

“…Recent structural studies of pig-tailed macaque [23], human [24,25], and chimpanzee [26] A3H have established a unique RNA interaction mechanism central to the antiviral function of A3H. Two A3H monomers interact with opposite sides of a short RNA duplex, and the A3H monomers in this complex interact primarily with the RNA duplex and not with one another.…”

Section: Introductionmentioning

confidence: 99%

“…Two A3H monomers interact with opposite sides of a short RNA duplex, and the A3H monomers in this complex interact primarily with the RNA duplex and not with one another. Importantly, mutagenesis of residues in the interaction interface between A3H and duplex RNA results in a decrease in A3H expression similar to the unstable human haplotypes [25][26][27]. Thus, formation of the A3H-RNA complex may be a critical regulator of A3H stability.…”

Section: Introductionmentioning

confidence: 99%

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Polymorphisms in human APOBEC3H differentially regulate ubiquitination and antiviral activity

Chesarino

Emerman

2020

Preprint

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The APOBEC3 family of cytidine deaminases are an important part of the host innate immune defense against endogenous retroelements and retroviruses like human immunodeficiency virus (HIV).APOBEC3H (A3H) is the most polymorphic of the human APOBEC3 genes, with four major haplotypes circulating in the population. Haplotype II is the only antivirally-active variant of A3H, while the majority of the population possess independently destabilizing polymorphisms present in haplotype I (R105G) and haplotypes III and IV (N15del). Here, we show that instability introduced by either polymorphism is positively correlated with degradative ubiquitination, while haplotype II is protected from this modification.Inhibiting ubiquitination by mutating all of the A3H lysines increased expression of haplotypes III and IV, but these stabilized forms of haplotype III and IV had a strict nuclear localization, and did not incorporate into virions, nor exhibit antiviral activity, thus separating stabilization from function. On the other hand, the instability and functional deficiencies of haplotype III could be rescued by fusion to haplotype II, supporting a model by which antiviral A3H is actively stabilized through a cytoplasmic retention mechanism. Thus, the evolutionary loss of A3H activity in many humans involves functional deficiencies independent of protein stability.

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“…Also, A3H is polymorphic in human populations like A3C, however, A3H haplotype II confers strong antiviral activity (25). Recent structural work has shown that A3H binds to RNA to make functional dimers (35–37). This suggests that perhaps A3H evolved an independent mechanism to form higher-order structures that is dependent on RNA, but that A3C is unable to do this unless the second cytidine deaminase domain is artificially engineered.…”

Section: Discussionmentioning

confidence: 99%

APOBEC3C tandem domain proteins create super restriction factors against HIV-1

McDonnell

Crawford

Dingens

et al. 2020

Preprint

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AbstractHumans encode proteins, called restriction factors, that inhibit replication of viruses like HIV-1. One family of antiviral proteins, apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3, shortened to A3) acts by deaminating cytidines to uridines during the reverse transcription reaction of HIV-1. The A3 locus encodes seven genes, named A3A-A3H. These genes either have one or two cytidine deaminase domains and several of these A3s potently restrict HIV-1. A3C, which has only a single cytidine deaminase domain, however, inhibits HIV-1 only very weakly. We tested novel double domain protein combinations by genetically linking two A3C genes to make a synthetic tandem domain protein. This protein created a “super restriction factor” that had more potent antiviral activity than the native A3C protein, which correlated with increased packaging into virions. Furthermore, disabling one of the active sites of the synthetic tandem domain protein results in an even greater increase in the antiviral activity—recapitulating a similar evolution seen in A3F and A3G (double domain A3s that only use a single catalytically active deaminase domain). These A3C tandem domain proteins do not have an increase in mutational activity, but instead inhibit formation of reverse transcription products which correlates with their ability to form large higher order complexes in cells. Finally, the A3C-A3C super restriction factor largely escaped antagonism by the HIV-1 viral protein, Vif.ImportanceAs a part of the innate immune system, humans encode proteins that inhibit viruses like HIV-1. These broadly acting antiviral proteins do not protect humans from viral infections because viruses encode proteins that antagonize the host antiviral proteins to evade the innate immune system. One such example of a host antiviral protein is APOBEC3C (A3C), which weakly inhibits HIV-1. Here, we show that we can improve the antiviral activity of A3C by duplicating the DNA sequence to create a synthetic tandem domain, and furthermore, are relatively resistant to the viral antagonist, Vif. Together, these data give insights about how nature has evolved a defense against viral pathogens like HIV.

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The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism

Abstract: SUMMARY

Cited by 19 publications

References 80 publications

APOBEC3A Catalyzes Mutation and Drives CarcinogenesisIn Vivo

APOBEC3A Catalyzes Mutation and Drives CarcinogenesisIn Vivo

Polymorphisms in human APOBEC3H differentially regulate ubiquitination and antiviral activity

APOBEC3C tandem domain proteins create super restriction factors against HIV-1

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