The Avian XPR1 Gammaretrovirus Receptor Is under Positive Selection and Is Disabled in Bird Species in Contact with Virus-Infected Wild Mice

Abstract

Xenotropic mouse leukemia viruses (X-MLVs) are broadly infectious for mammals except most of the classical strains of laboratory mice. These gammaretroviruses rely on the XPR1 receptor for entry, and the unique resistance of laboratory mice is due to two mutations in different putative XPR1 extracellular loops. Cells from avian species differ in susceptibility to X-MLVs, and 2 replacement mutations in the virus-resistant chicken XPR1 (K496Q and Q579E) distinguish it from the more permissive duck and quail receptors. These substitutions align with the two mutations that disable the laboratory mouse XPR1. Mutagenesis of the chicken and duck genes confirms that residues at both sites are critical for virus entry. Among 32 avian species, the 2 disabling XPR1 mutations are found together only in the chicken, an omnivorous, ground-dwelling fowl that was domesticated in India and/or Southeast Asia, which is also where X-MLV-infected house mice evolved. The receptor-disabling mutations are also present separately in 5 additional fowl and raptor species, all of which are native to areas of Asia populated by the virus-infected subspecies Mus musculus castaneus. Phylogenetic analysis showed that the avian XPR1 gene is under positive selection at sites implicated in receptor function, suggesting a defensive role for XPR1 in the avian lineage. Contact between bird species and virus-infected mice may thus have favored selection of mouse virus-resistant receptor orthologs in the birds, and our data suggest that similar receptor-disabling mutations were fixed in mammalian and avian species exposed to similar virus challenges.T he transmission of retroviruses to new hosts can result in the emergence of new infectious diseases and can alter the host genomic architecture and gene-regulatory networks, but the factors that determine whether a pathogen can successfully infect a novel host are poorly understood (1). The xenotropic mouse leukemia viruses (X-MLVs) are gammaretroviruses originally isolated from laboratory mice that are unable to infect the cells of these mice (2). These viruses rely on the XPR1 cell surface receptor for entry (3-5), and receptor orthologs from other mammals, like humans and cats, as well as the various species of wild mice, all permit X-MLV entry (6, 7). The resistance of laboratory mouse cells to infection is due to mutations that alter two XPR1 residues, K500E in the putative third extracellular loop (ECL3) and T582⌬ in the fourth loop (ECL4) (8).There is substantial sequence variation in the receptor-determining regions of the mammalian XPR1 orthologs, and some of these receptor variants show altered ability to mediate entry of one or more of the 6 known host range variants in the XP-MLV family of xenotropic/polytropic viruses (6, 9). In addition to X-MLV, this family includes viruses first described as broadly polytropic (PMLVs) because of their ability to infect mouse cells, as well as cells of other species (10, 11). Other variants, like xenotropic murine leukemia virus-related virus (XMRV) (12) an...

Positive selection of primate genes that promote HIV-1 replication

“…Also, proteins like MAP4 that are involved in intracellular trafficking have also been shown to be a common target of viral hijacking (Radtke et al, 2006). We conclude that positive selection can shape the evolution of host factor genes, consistent with other recent studies on cell surface receptors (Demogines et al, 2013; Kaelber et al, 2012; Martin et al, 2013), components of the nuclear pore (Schaller et al, 2011), and DNA repair machinery (Demogines et al, 2010; Sawyer & Malik, 2006). …”

Broad-scale phylogenomics provides insights into retrovirus–host evolution

“…Host restriction factors have been shown to play a key role in host defense, as have mutations in the cell surface receptors required for retroviral infection (2). Of direct relevance here is a recent study that found that birds with a high risk of exposure to mice harboring an infective gammaretrovirus (ground-dwelling fowl and raptor species) have evolved receptordisabling mutations, suggestive of a defensive role (30). Examination of ERV distribution patterns among host taxa provides opportunities to frame further investigations into the evolution of host genetic factors against retroviruses.…”

Escape variants of the XPR1 gammaretrovirus receptor are rare due to reliance on a splice donor site and a short hypervariable loop

“…Most mammals are susceptible to XP-MLVs, and K500 is completely invariant in the mammals we examined previously with the single exception of the X-MLV-restrictive laboratory mouse which carries E500 (Figure 1A) (Yan et al, 2010). In the avian lineage, the homologous site, K496, is also critical for XPR1 receptor function, and avian XPR1 receptor function can be disabled by two naturally occurring mutations at this site, K496E and K496Q (Martin et al, 2013). The mouse mutation and both bird mutations all result from substitutions in the first position of this codon (CAA and GAA).…”