IFITMs restrict the replication of multiple pathogenic viruses

Abstract

The interferon-inducible transmembrane protein (IFITM) family inhibits a growing number of pathogenic viruses, among them influenza A virus, dengue virus, hepatitis C virus, and Ebola virus. This review covers recent developments in our understanding of the IFITM's molecular determinants, potential mechanisms of action, and impact on pathogenesis.

Keywords: AS; CCHFV; CD225 family; CIL; CMEM; Crimean Congo hemorrhagic fever virus; DENV; EBOV; Ebola virus; GP; HCV; HIV-1; IAV; IFITM; IFN; JSRV; Jaagsiekte sheep retrovirus; MARV; MLV; MS; Marburg virus; Moloney leukemia virus; N-terminal domain; NTD; OSBP; RVFV; Rift Valley fever virus; SARS CoV; SeV; Sendai virus; VAPA; alanine scanning; clathrin-mediated endocytosis motif; conserved intracellular loop; dengue virus; glycoprotein; hepatitis C virus; host virus interactions; human immunodeficiency virus type 1; influenza A virus; interferon; interferon effector genes; interferon-inducible transmembrane protein; mass spectrometry; oxysterol binding protein; restriction factor; severe acute respiratory syndrome coronavirus; vesicle-associated membrane protein-A.

Graphical abstract

Fig. 1

(a) Model of IFITM3-mediated restriction of viral replication. IAVs (blue with genomes in black) first interact with a cell surface receptor (green) and then enter the cell through endocytosis. IFITM1 (purple, with light and dark hues representing two distinct IFITM1 molecules), located in the cytosolic leaflet of the plasma membrane and endosomal membrane, prevents the fusion of viruses that enter in the early endosomes (i.e., HCV) as well as viruses fusing later in the endosomal pathway (i.e., IAV). IFITM3 (red, with dark and light hues representing two distinct IFITM3 molecules) resides in the late endosomal membranes and lysosomal membranes, and prevents viral fusion of viruses that enter from those compartments. Because of the block to fusion, there is no release of viral RNPs (vRNPs) and therefore no viral replication. As a result of IFITM-mediated restriction, the trapped viral particles are destroyed in the lysosomes and/or autolysosomes. IFITM3 is present at baseline; however, IFN up-regulates its levels and induces the expression of IFITM1 (broken lines). (b) IFITM3 prevents IAV cytosolic entry and nuclear entry. Confocal images of Mardin Darby canine kidney cells stably transduced with the empty retroviral vector, pQCXIP (Vector, Clontech), or one expressing IFITM3, that were infected with IAV [A/Puerto Rico/8/1934 (H1N1) (PR8, Charles River Labs)] for 90 min. The cells were then washed, fixed, permeabilized, and immunostained for IAV nucleoprotein (NP, green), IFITM3 (red), or nuclear DNA (blue) . In the vector cells, the IAV NP can be seen in the host cell nucleus (left panel). In contrast, in the IFITM3 cells, the virus is prevented from entering the cytosol and instead the NP is seen sequestered in the IFITM3-positive endosomal compartments. The scale bar represents 10 μm.

Fig. 2

(a) Alignment of the human IFITM1, IFITM2, IFITM3, IFITM5, and IFITM10 protein sequences (ClustalW2). The amino acids are color coded as follows: red, hydrophobic amino acids; green, polar amino acids; pink, basic amino acids; blue, acidic amino acids. The CD225 domain and the adjacent IM2s of the aligned proteins are outlined in red. Gaps introduced to maximize alignment are indicated by dashes. (b) Cartoon of IFITM3 in the endosomal membrane. The molecular determinants required for the IFITM3-mediated restriction, sites of posttranslational modifications, and nonsynonymous single-nucleotide polymorphisms (NS-SNP) are indicated in the key (bottom right). The NTD, intramembrane domain 1 (IM1), CIL, and intramembrane domain 2 (IM2) are indicated. IM1 and the CIL are in red font to convey that they comprise the canonical CD225 domain. The outer and inner leaflets of the endosomal membrane are noted. (c) Sequence logo for the CD225 domains and IM2s of the human IFITMs in (a). The respective amino acid properties color coded as above. Blue numbers indicate residues in IFITM3 found to be required for restriction, localization, or expression. These and similar figures were generated using Weblogo and the CLUSTALW freeware programs.

Fig. 3

(a) Alignment of the CD225 domains and IM2s of the human CD225 proteins (ClustalW2). The amino acids are color coded as above. (b) Sequence logo for the human CD225 proteins. Blue numbers indicate residues in IFITM3 found to be required for restriction, localization, or expression. This figure was generated using Weblogo.

Fig. 4

Model of IFITM antiviral action. We postulate that one or more of the following IFITM-mediated events “toughen” the host cell membrane and prevent viral fusion. (a) Inhibition of sequential host co-receptor interactions. After binding of the viral receptor-binding protein (blue, downward facing) to a host receptor (orange, upward facing, left panel), the pair then moves through the membrane surface until one or more required co-receptors (green) are encountered (middle panel), ultimately triggering fusion peptide insertion (not shown). In contrast, we postulate that adjacent IFITMs interact via their IM1s to decrease membrane fluidity and restrict the lateral movement of the partially assembled receptor complex. Black arrows, movement through the membrane; white arrows, diminished movement; red arrows, resistance within the membrane generated by IFITMs. (b) Inhibition of viral envelope protein clustering. Two HA receptors (blue) are shown with their fusion peptides (red) inserted into the host membrane (left panel). The engaged receptors then move through the membrane and coalesce (middle panel). This juxtapositioning permits the HA receptors to coordinately generate a fusion pore (c) . Similar to (a), the presence of intramembranous IFITMs decreases HA receptor movement and prevents their effective association. Arrows are as above. (c) HA-mediated fusion: Top row: As in (b), but in the absence of IFITMs, the HA receptors have now been able to coordinately generate a fusion pore (right panel). However, IFITMs residing in the membrane alter the properties of the host membrane due to intramolecular interactions and asymmetric membranous insertions. The association of IFITMs via their IM1s decreases membrane fluidity. Furthermore, the insertions of the IM domains of each IFITM into the outer leaflet of the membrane produces a curvature directed away from the HA receptors drawing force. We envision that this induced curvature would require that greater force be exerted by the viral fusion machinery, thus preventing the formation of a pore. Arrows are as above. (d) Superior view of IFITM–IFITM interactions occurring in the membrane. We speculate that IFITMs multiplex via their IM1s (assorted-color ovals binding to one another at a central IM1-generated hub, left panel). A pentamer is shown as one possible IFITM complex. Radiating from this common interaction point, the more distal IM2s form interactions with the transmembrane or intramembrane domains of additional proteins (blue), that is, the tetraspanins. When such IFITM units are symmetrically multiplied, they could possibly form an integrated matrix that alters the membrane's fluidity and bending modulus (right panel). This meshwork may also enhance the membrane-rigidifying properties of cholesterol (pink stars [119]) The CILs that connect IM1 and IM2 and lie in the cytosol are represented by dotted lines.