Positive Selection and Increased Antiviral Activity Associated with the PARP-Containing Isoform of Human Zinc-Finger Antiviral Protein

Abstract

Intrinsic immunity relies on specific recognition of viral epitopes to mount a cell-autonomous defense against viral infections. Viral recognition determinants in intrinsic immunity genes are expected to evolve rapidly as host genes adapt to changing viruses, resulting in a signature of adaptive evolution. Zinc-finger antiviral protein (ZAP) from rats was discovered to be an intrinsic immunity gene that can restrict murine leukemia virus, and certain alphaviruses and filoviruses. Here, we used an approach combining molecular evolution and cellular infectivity assays to address whether ZAP also acts as a restriction factor in primates, and to pinpoint which protein domains may directly interact with the virus. We find that ZAP has evolved under positive selection throughout primate evolution. Recurrent positive selection is only found in the poly(ADP-ribose) polymerase (PARP)–like domain present in a longer human ZAP isoform. This PARP-like domain was not present in the previously identified and tested rat ZAP gene. Using infectivity assays, we found that the longer isoform of ZAP that contains the PARP-like domain is a stronger suppressor of murine leukemia virus expression and Semliki forest virus infection. Our study thus finds that human ZAP encodes a potent antiviral activity against alphaviruses. The striking congruence between our evolutionary predictions and cellular infectivity assays strongly validates such a combined approach to study intrinsic immunity genes. Host–virus interactions are a classic example of genetic conflict in which both entities try to gain an evolutionary advantage over the other. This “back-and-forth” evolution is predicted to result in rapid changes of both host and viral proteins, which results in an evolutionary signature of positive selection, especially at the direct interaction interface. Recent studies have demonstrated that host proteins can target intracellular stages of the viral life cycle to potently inhibit viruses. Collectively, these host proteins are referred to as “intrinsic immunity” proteins. One such protein, zinc-finger antiviral protein (ZAP), was previously described from rats and shown to inhibit retroviruses and alphaviruses. We queried the primate orthologs of ZAP to ascertain both whether they have evolved under positive selection, and whether they have antiviral activity. We found that the signature of positive selection was restricted to a poly(ADP-ribose) polymerase–like domain in a longer isoform of primate ZAP. The longer human ZAP isoform has increased antiviral activity against both retroviruses and alphaviruses. Thus, positive selection correctly predicted the more potent antiviral isoform of this protein.