Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA

Abstract

MxA is an interferon-induced dynamin-like GTPase with wide-ranging antiviral activity, which hinges upon detection of unique viral structures that differ across virus families. Despite elucidation of its structure, the basis of MxA antiviral specificity remains enigmatic. We used an evolution-guided approach to identify the loop L4 of MxA as a hotspot for recurrent positive selection in primates. Further, we show that single amino acid changes in L4 are necessary and sufficient to explain dramatic differences in species-specific antiviral activity of primate MxA proteins against the orthomyxoviruses Thogoto virus and influenza A virus. Taken together, our findings identify a genetic determinant of MxA target recognition and suggest a model by which MxA achieves antiviral breadth without compromising viral specificity.

Figure 1. Evolution of primate MxA

A. The phylogeny was built using orthologous MxA sequences from 24 primate species (Figure S1 and Table S1), which is congruent with a previously published primate phylogeny (Perelman et al., 2011). B. The loop L4 (amino acids 533–572) protein sequence alignment is shown from representative primates (top). Specific codons found to be evolving under positive selection in primate MxA are indicated in a linear schematic (middle) or a model of the MxA crystal structure (bottom) (Gao et al., 2011), where sites with a posterior probability greater than 0.95 and 0.99 are highlighted in orange and red, respectively. In the linear structure “B” depicts the three parts of MxA that form the bundle-signaling element (BSE). C. Evolutionary analysis for positive selection in primate MxA. P values generated from maximum likelihood ratio tests that fit the data to models of neutral (M7) or adaptive (M8) evolution are given for the entire MxA coding sequence (including or excluding new world monkey (NWM) sequences) or specific domains of the protein as indicated. i. Percentage of codons evolving under positive selection (p1). ii. Associated average dN/dS (ω) of p1 sites. iii. Codons with a high posterior probability (PP > 0.90) that supports the likelihood of a site having a dN/dS > 1 are presented with the PP for each residue in parentheses. Amino acids refer to residues found at indicated positions in hsMxA. iv. Indels removed from alignment. v. StalkΔL4 refers to an analysis of the stalk with amino acids 533–572 removed.

Figure 2. Species-specific antiviral activity results from sequence divergence in loop L4 of primate MxA

A. THOV minireplicon activity (luciferase levels) was measured 24h post-transfection, and was reported relative to levels observed in the absence of MxA. hsMxA(T103A) is an antivirally inactive mutant of hsMxA. Error bars represent standard deviation across three biological replicates. HA-tagged MxA and βactin protein levels were detected in lysates by Western blot. The phylogenetic relationships of MxA derived from representative species within hominoid, old world monkey and new world monkey lineages are indicated by a cladogram. B. Differential antiviral activity of human and AGM MxA orthologs is dependent on loop L4. The loop L4 (amino acids 556–572) protein sequence alignment is shown with positively selected sites that differ between hsMxA and agmMxA in grey (top). Dose-responsiveness of the antiviral activity of wild-type MxA and L4 chimeras was determined by co-transfecting increasing amounts of MxA expression constructs with the THOV minireplicon into 293T cells. MxA antiviral activity is measured as described in Figure 2A (middle). The Western blot analysis depicts the expression levels of the wild-type and chimeric MxA proteins in the cell lysates (bottom). C. Restriction of THOV infectivity by human and AGM MxA is contingent on a single amino acid. Data are presented as percent THOV infected, Mx-positive cells as measured by immunofluorescence for THOV NP and MxA. Error bars represent standard deviation of three biological replicates. ***, p<0.0001 (t-test). See also Figure S2. D. Antiviral activity of hsMxA 561 variants. Data are presented as described in Figure 2A. **, p<0.001 (t-test) for values compared to hsMxA(T103A).

Figure 3. Loop L4 is a functional module of MxA antiviral activity

A. Human L4 rescues mouse Mx1 antiviral activity against the THOV minireplicon. mmMx1 expression constructs were co-transfected with the THOV minireplicon system into 293T cells; the experiment was otherwise carried out as in Figure 2B. mmMx1(hsL4) contains an exchange of mmL4 for the L4 of hsMxA. mmMx1(K49A) is a GTPase inactive mutant with no antiviral activity. B. Human L4 determines the antiviral activity of mmMx1 against THOV infection. Percent infectivity was measured as described in Figure 2C. Error bars represent standard deviation of three biological replicates. ***, p<0.0001. C. L4 mediates the interaction between MxA and THOV NP. Co-immunoprecipitation of viral NP with hsMxA and mmMx1 proteins was performed with lysates of THOV-infected (+) or uninfected (−) 293T cells transfected with the indicated Flag-tagged Mx expression constructs. Immunoprecipitation was performed using anti-Flag-affinity gel and the precipitated proteins were detected by Western blot with viral NP and MxA-specific antibodies. The lower panel shows the input of viral NP, MxA and β-tubulin in whole cell lysates. See also Figure S3.

Figure 4. The loop L4 mediates functional differences in primate MxA antiviral activity against influenza A virus

Restriction of A/Thailand/1/04 infection by hsMxA and agmMxA. Data are presented as percent of infected, Mx-positive cells as measured by immuno-fluorescence for viral NP and MxA. Error bars represent standard deviation of three biological replicates. ***, p<0.0001 (t-test).