Natural mutations in IFITM 3 modulate post‐translational regulation and toggle antiviral specificity

Abstract

The interferon‐induced transmembrane ( IFITM ) proteins protect host cells from diverse virus infections. IFITM proteins also incorporate into HIV ‐1 virions and inhibit virus fusion and cell‐to‐cell spread, with IFITM 3 showing the greatest potency. Here, we report that amino‐terminal mutants of IFITM 3 preventing ubiquitination and endocytosis are more abundantly incorporated into virions and exhibit enhanced inhibition of HIV ‐1 fusion. An analysis of primate genomes revealed that IFITM 3 is the most ancient antiviral family member of the IFITM locus and has undergone a repeated duplication in independent host lineages. Some IFITM 3 genes in nonhuman primates, including those that arose following gene duplication, carry amino‐terminal mutations that modify protein localization and function. This suggests that “runaway” IFITM 3 variants could be selected for altered antiviral activity. Furthermore, we show that adaptations in IFITM 3 result in a trade‐off in antiviral specificity, as variants exhibiting enhanced activity against HIV ‐1 poorly restrict influenza A virus. Overall, we provide the first experimental evidence that diversification of IFITM 3 genes may boost the antiviral coverage of host cells and provide selective functional advantages. image By analyzing synthetic and naturally occurring mutations of interferon‐induced transmembrane 3 ( IFITM 3), this study provides novel insight into the antiviral mechanisms at play during HIV ‐1 infection. The authors further show that the diversification of IFITM 3 genes during evolution may boost the antiviral coverage of host cells and provides selective functional advantages. Amino‐terminal mutations of IFITM 3 result in an enhanced incorporation into HIV ‐1 virions and promote the inhibition of virus–cell fusion. Two adjacent regulatory motifs that control ubiquitination and endocytosis of IFITM 3 regulate its potency and antiviral specificity. IFITM 3 shows recurrent gene duplication and divergence during primate evolution.