Paracrine rescue of MYR1-deficient <i>Toxoplasma gondii</i> mutants reveals limitations of pooled <i>in vivo</i> CRISPR screens.

Abstract

<i>Toxoplasma gondii</i> is an intracellular parasite that subverts host cell functions via secreted virulence factors. Up to 70% of parasite-controlled changes in the host transcriptome rely on the MYR1 protein, which is required for the translocation of secreted proteins into the host cell. Mice infected with MYR1 knock-out (KO) strains survive infection, supporting a paramount function of MYR1-dependent secreted proteins in <i>Toxoplasma</i> virulence and proliferation. However, we have previously shown that MYR1 mutants have no growth defect in pooled <i>in vivo</i> CRISPR-Cas9 screens in mice, suggesting that the presence of parasites that are wild-type at the <i>myr1</i> locus in pooled screens can rescue the phenotype. Here, we demonstrate that MYR1 is not required for the survival in IFN-γ-activated murine macrophages, and that parasites lacking MYR1 are able to expand during the onset of infection. While ΔMYR1 parasites have restricted growth in single-strain murine infections, we show that the phenotype is rescued by co-infection with wild-type (WT) parasites <i>in vivo</i>, independent of host functional adaptive immunity or key pro-inflammatory cytokines. These data show that the major function of MYR1-dependent secreted proteins is not to protect the parasite from clearance within infected cells. Instead, MYR-dependent proteins generate a permissive niche in a paracrine manner, which rescues ΔMYR1 parasites within a pool of CRISPR mutants in mice. Our results highlight an important limitation of otherwise powerful <i>in vivo</i> CRISPR screens and point towards key functions for MYR1-dependent <i>Toxoplasma</i>-host interactions beyond the infected cell.