Highly-potent, synthetic APOBEC3s restrict HIV-1 through deamination-independent mechanisms.

Mollie M Mcdonnell,Amit Gaba,Michael Emerman,Ben Flath,Suzanne C Karvonen,Linda Chelico,Welkin E Johnson

doi:10.1371/journal.ppat.1009523

Mollie M Mcdonnell, Amit Gaba + Show 5 more

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https://doi.org/10.1371/journal.ppat.1009523

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Abstract

The APOBEC3 (A3) genes encode cytidine deaminase proteins with potent antiviral and anti-retroelement activity. This locus is characterized by duplication, recombination, and deletion events that gave rise to the seven A3s found in primates. These include three single deaminase domain A3s (A3A, A3C, and A3H) and four double deaminase domain A3s (A3B, A3D, A3F, and A3G). The most potent of the A3 proteins against HIV-1 is A3G. However, it is not clear if double deaminase domain A3s have a generalized functional advantage to restrict HIV-1. In order to test whether superior restriction factors could be created by genetically linking single A3 domains into synthetic double domains, we linked A3C and A3H single domains in novel combinations. We found that A3C/A3H double domains acquired enhanced antiviral activity that is at least as potent, if not better than, A3G. Although these synthetic double domain A3s package into budding virions more efficiently than their respective single domains, this does not fully explain their gain of antiviral potency. The antiviral activity is conferred both by cytidine-deaminase dependent and independent mechanisms, with the latter correlating to an increase in RNA binding affinity. T cell lines expressing this A3C-A3H super restriction factor are able to control replicating HIV-1ΔVif infection to similar levels as A3G. Together, these data show that novel combinations of A3 domains are capable of gaining potent antiviral activity to levels similar to the most potent genome-encoded A3s, via a primarily non-catalytic mechanism.

Highlights

Positive selection in host antiviral genes is a result of the host-virus “arms-race” due to repeated cycles of host resistance and virus adaptation [1]
A previous study showed that a human A3C-A3H combination had antiviral activity [24], but here we used two variants of A3H: haplotype I, the less stable and less antiviral A3H protein, and haplotype II, the more stable and more antiviral A3H protein [17,18] (Fig 1A), as well as tested the orientation of the A3 domains in both directions, i.e. both A3C-A3H and A3H-A3C
We combined two single domain A3 proteins, A3C and A3H that encode A3Z2 and A3Z3 domains, respectively, into a single molecule to test the hypothesis that there is novel antiviral potential in the human A3 locus. We found that these A3C/A3H double domains can create super restriction factors with antiviral potency that is at least as potent as A3G both in single-cycle assays and in spreading infections of T cells

Summary

Introduction

Positive selection in host antiviral genes is a result of the host-virus “arms-race” due to repeated cycles of host resistance and virus adaptation [1]. These cycles of mutation-selection that increase the evolutionary rate of single amino acid substitutions are characteristic of many host genes that counteract HIV and related lentiviruses [1,2]. Human MxA has broad and potent activity against a diverse range of RNA and DNA viruses, while the antiviral scope of human MxB is more limited to lentiviruses and herpesviruses [3,4,5,6]. TRIM5, a potent restriction factor against lentiviruses, is present in only a single copy in most primates, whereas rodents have up to six [7]

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