Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions

Abstract

Several bat species act as asymptomatic reservoirs for many viruses that are instead highly pathogenic in other mammals. Here, we have characterized the functional diversification of the Protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats, in contrast to all studied mammals that possess a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. More importantly, we determined that duplicated PKRs of the Myotis species have undergone functional diversification allowing them to collectively escape from and enhance control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat specific immunity.

Systematic characterization of the local evolutionary space available to human PKR and vaccinia virus K3

“…Screening pairs of variant alleles first required the generation of single, nonsynonymous variants of both PKR and K3L . For PKR , we designed all variants accessible with a single nucleotide polymorphism (SNP) in four windows of interest (Figure 2A); these windows contain residues in the tertiary structure that interface with eIF2a and residues under positive selection (Figure 2B) (Elde et al, 2009; Jacquet et al, 2022; Rothenburg et al, 2009). These windows of interest are defined as Window 1: G255-F278, Window 2: K371-R385, Window 3: S448-M455, and Window 4: E480-I506.…”

“…This phenomenon is underpinned by the ‘Red Queen Hypothesis’, stating that constant adaptation between antagonistic interacting proteins is necessary to sustain their respective functions (Van Valen, 1973). Here we investigate an ongoing evolutionary arms race between a component of our immune system, Protein Kinase R (PKR), and a vaccinia virus (VACV) pseudo-substrate antagonist, K3, both of which are under positive selection (Elde et al, 2009; Jacquet et al, 2022; Rothenburg et al, 2009). Prior studies have characterized individual residue variants in both proteins that alter their interaction (Dar & Sicheri, 2002; Kawagishi-Kobayashi et al, 1997; Seo et al, 2008).…”

“…Previous work has found both PKR and K3 to be under positive selection, with specific residues highlighted throughout PKR that are rapidly evolving (Elde et al, 2009; Jacquet et al, 2022; Rothenburg et al, 2009). Others have identified single-residue variants of PKR and K3 that alter their interaction (Kawagishi-Kobayashi et al, 1997; Seo et al, 2008).…”

Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic

“…K3 competitively inhibits eIF2α from binding PKR through its sequence and structural similarity to eIF2α (17,(19)(20)(21). Vertebrate PKR homologs have many sites under positive selection, which suggests an evolutionary arms race between PKR and its inhibitors (22)(23)(24). Surprisingly, this includes PKR residues at its binding surface with eIF2α (Figure 1C) even though this interface is essential to PKR function (22,23), which could reflect evolutionary pressure from viral pseudosubstrate inhibitors.…”