Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus

Abstract

The Fv1 virus resistance gene is a coopted endogenous retrovirus (ERV) sequence related to the gag gene of the MuERV-L ERV family. Three major Fv1 resistance alleles have been identified in laboratory mice, and they target virus capsid genes to produce characteristic patterns of resistance to mouse leukemia viruses (MLVs). We identified Fv1 in 3 of the 4 Mus subgenera; its absence from Coelomys and 1 of 3 species of Pyromys indicate Fv1 was acquired shortly after the origin of the Mus genus. We sequenced Fv1 genes from 21 mice representative of the major taxonomic groups of Mus. Two lines of evidence indicate that Fv1 has had antiviral function for 7 million years of evolution. First, 2 species of African pygmy mice (subgenus Nannomys) show an Fv1-like MLV resistance, and transduced cells expressing the Nannomys Fv1 gene reproduce this resistance pattern. Second, sequence comparisons suggest that Fv1 has been involved in genetic conflicts throughout Mus evolution. We found evidence for strong positive selection of Fv1 and identified 6 codons that show evidence of positive selection: 3 codons in the C-terminal region including 2 previously shown to contribute to Fv1 restriction in laboratory mice, and 3 codons in a 10-codon segment overlapping the major homology region of Fv1; this segment is known to be involved in capsid multimerization. This analysis suggests that Fv1 has had an antiviral role throughout Mus evolution predating exposure of mice to the MLVs restricted by laboratory mouse Fv1, and suggests a mechanism for Fv1 restriction.

Fig. 1.

Detection of Fv1 in DNAs of Mus species. (A) The structure of Fv1^b is shown with a gray box marking the MHR, open boxes representing B2 repeats and a dashed line representing the 1.3-kb segment deleted in Fv1ⁿ. The arrows represent the PCR primers Fb3003 and Rb4831, and the black box represents the segment used for blot hybridization. Fv1 is encoded by a single exon. (B) Southern blot analysis of BglI-digested Mus DNAs. All lanes taken from the same exposure of a single blot; deleted lanes are indicated by vertical lines. (C) PCR products of Mus DNAs.

Fig. 2.

Comparison of predicted amino acid sequence of the M. n. minutoides Fv1 gene and Fv1^b. The position of MHR is indicated by a solid bar and shading indicates the 3 amino acids identified as critical for restriction based on analysis of laboratory mouse Fv1 alleles (3, 5, 6).

Fig. 3.

Positive selection of Fv1 in the genus Mus. (A) Cladogram showing branch values of dN/dS calculated using the free-ratio model of PAML, with the number of replacement and synonymous changes in parentheses. When dS = 0, dN/dS is infinite (Inf). dN/dS > 1 suggests positive selection along that lineage. Bootstrap support for this tree topology was generally good, with most bootstrap percentages >90%. The thin lines represent branches with bootstrap values <70%. (B) Likelihood ratio tests were used to test for positive selection. Neutral models (M0, M1, M7) were compared with selection models (M2, M8) using 2 different models of codon frequency (F3 × 4 or F61). P values <0.0001 provide strong evidence of selection. Tree length is the average number of substitutions per codon along all branches. For codons under positive selection, the dN/dS ratio is given along with the % of codons with this ratio.

Fig. 4.

Fv1 sites that have been subject to positive selection. At the top are sequence alignments for 22 Mus genes in the regions containing the 6 positively selected codons; all changes relative to Fv1^b are shaded. MHR is boxed. At the bottom is a diagram of the Fv1 coding region showing the locations of the MHR (black box), the 6 positively selected codons and the 1 additional codon (358) implicated in restriction (3, 6).