Evidence linking APOBEC3B genesis and evolution of innate immune antagonism by gamma-herpesvirus ribonucleotide reductases

Abstract

Viruses have evolved diverse mechanisms to antagonize host immunity such as direct inhibition and relocalization of cellular APOBEC3B (A3B) by the ribonucleotide reductase (RNR) of Epstein-Barr virus. Here, we investigate the mechanistic conservation and evolutionary origin of this innate immune counteraction strategy. First, we find that human gamma-herpesvirus RNRs engage A3B via largely distinct surfaces. Second, we show that RNR-mediated enzymatic inhibition and relocalization of A3B depend upon binding to different regions of the catalytic domain. Third, we show that the capability of viral RNRs to antagonize A3B is conserved among gamma-herpesviruses that infect humans and Old World monkeys that encode this enzyme but absent in homologous viruses that infect New World monkeys that naturally lack the A3B gene. Finally, we reconstruct the ancestral primate A3B protein and demonstrate that it is active and similarly engaged by the RNRs from viruses that infect humans and Old World monkeys but not by the RNRs from viruses that infect New World monkeys. These results combine to indicate that the birth of A3B at a critical branchpoint in primate evolution may have been a driving force in selecting for an ancestral gamma-herpesvirus with an expanded RNR functionality through counteraction of this antiviral enzyme.

Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism

“…Our studies here add HCMV to the list of herpesviruses that antagonize A3B, suggesting that this function is essential to the success of herpesvirus infection. Our studies are also consistent with the likelihood that this host-pathogen conflict is conserved evolutionarily (8, 11) with ancient origins and remains ongoing to present day. It is surprising, however, that the mechanisms differ on the molecular level in that HCMV (and perhaps other beta-herpesviruses) has evolved a distinct RNR-independent mechanism.…”

“…We previously reported the ability of gamma-and alpha-herpesviruses to bind to A3B and mediate its relocalization from the nuclear compartment into cytoplasmic aggregates (6)(7)(8). To investigate whether the beta-herpesvirus HCMV has similar functionality, immunofluorescence (IF) microscopy experiments were done using infected primary human foreskin fibroblast-1 (HFF-1) cells.…”

“…The only gamma-and alpha-herpesvirus protein required for A3B relocalization is the large subunit of the viral RNR (6)(7)(8). The large RNR subunit of EBV, BORF2, directly binds A3B, inhibits its catalytic activity, and relocalizes the protein from the nucleus to the cytoplasm.…”

“…Recently, a novel mechanism of A3 counteraction was discovered for the gamma-herpesviruses Epstain-Barr virus (EBV), which use the viral ribonucleotide reductase (RNR) large subunit, BORF2, to directly bind, inhibit, and relocalize APOBEC3B (A3B) from the nucleus to the cytoplasm, thus preserving viral genome integrity (6). This mechanism of A3 neutralization is likely to be conserved because at least two other herpesviruses, Kaposi's sarcoma-associated herpesvirus (KSHV), and herpes simplex virus 1 (HSV-1), whose RNRs (ORF61, and ICP6, respectively) physically interact with A3B, as well with APOBEC3A (A3A), and trigger their redistribution from the nucleus to the cytoplasmic compartment (7)(8)(9)(10). In further support of evolutionary conservation, a systematic analysis of a large panel of present-day gamma-herpesvirus RNRs and primate A3B proteins indicates that the evolution of this viral RNR-mediated A3B neutralization mechanism was likely selected by the birth of the A3B gene by unequal crossing-over in an ancestral Old World primate approximately 29-43 million years ago (8,11).…”

APOBECs: Our fickle friends?

“…(iv) Reduction of cytidine residues (and target motifs) from the viral RNA genome decreases susceptibility to APOBEC-induced mutations [ 25 ]. (v) Some gammaherpesvirus proteins trigger the export of APOBEC enzymes that function in the nucleus [ 35 , 36 ]. Although this list is not comprehensive, more than 1 mechanism likely provides susceptibility or resistance to APOBEC-mediated inhibition of individual viruses.…”