Dynamic evolution of MLKL in primate and poxvirus genomes indicates necroptosis is a critical, not auxiliary, countermeasure during infection

Abstract

Pathogen infection triggers host innate defenses which can lead to the activation of regulated cell death (RCD) pathways such as apoptosis. Given a key role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptotic signaling. However, whether this emerging inflammatory RCD pathway functions primarily as a "back-up" or fundamental response remains inconclusive. We hypothesized that if necroptosis is an instrumental defense, then its effectors should display specific signatures associated with pathogen conflict that are rare in combination: rapid evolution, viral homolog hereafter virolog, and induction by cytokines (e.g. interferons). Our rapid evolution analysis across the necroptosis pathway revealed: 1) strong signatures of positive selection for RIPK3 and MLKL in primate genomes and to a lesser extent DAI/ZBP1, 2) elevated rates of amino acid substitution on multiple surfaces including the RIPK3/MLKL binding interface and 3) evidence supporting a means of activating RIPK3 independent of homotypic RHIM domain interactions. Interestingly, a poxvirus MLKL homolog has recently been identified that acts as a RIPK3 pseudosubstrate. Our findings indicate that poxvirus MLKLs are also subject to similar but distinct volatile patterns of evolution comparable to host necroptotic factors. Specifically, viral MLKLs have undergone numerous gains and losses in poxvirus evolution with some species harboring three distinct copies. Furthermore, we confirm that MLKL can be induced by cytokines like interferon gamma. In summary, MLKL displays all three hallmarks of pivotal immune factors of which only OAS1, but not other factors like cGAS, APOBEC3G, or PKR, exhibits. These data support the hypothesis that over evolutionary time, necroptosis has served as a key battleground during infection and is therefore, not an auxiliary response. SummaryRegulated cell death (RCD), such as apoptosis, is a common host defense against invading pathogens. Necroptosis, an inflammatory RCD pathway, is thought to have emerged as an auxiliary response when other cell death pathways are suppressed by pathogens during infection. In our analyses, we have identified genetic changes in host and viral factors associated with necroptosis that display signatures of adaptation and may have served as evolutionary countermeasures to shape infection outcomes. Consistent with repeated targeting by pathogen-encoded inhibitors, we found robust signatures of rapid evolution for the essential catalysts of necroptosis, RIPK3 and MLKL. Notably, an evolutionary signature specific to RIPK3 for a domain shared with other necroptotic factors suggests an undefined means to trigger this host defense pathway. In contrast, poxviruses appear to circumvent this pathway by constantly altering the number and nature of factors they deploy to suppress necroptosis including a mimic of MLKL, which was stolen from infected cells. Collectively, our findings provide new insights into host and viral genetics that may influence infection outcomes and the factors shaping the ability of pathogens to infect and spread to new species. Furthermore, these data support the notion that necroptosis is a fundamental, not auxiliary, host response during infection.