Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae

Abstract

Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.

Virophage replication mode determines ecological and evolutionary changes in a host-virus-virophage system

“…For the host strain E4-10, which we used here, EMALE04 was reactivated by CroV infections but low copies were produced, and host died within several days after infection. However, they also showed that EMALE04 inhibition of the virus can amplify in subsequent rounds of infection reaching similar inhibition levels of the virus population as Mavirus (Koslová et al 2024). Whether and how EMALE04 reactivated and competed with Mavirus in our experiment is not known.…”

“…It is thus possible that other EMALEs have been reactivated affecting the ecological and/or evolutionary dynamics. Koslová et al (2024) characterized the reactivation of EMALES in a collection of globally distributed Cafeteria populations and they found that reactivation was stochastic, inefficient and EMALE-virus specific (e.g., only one out of eight EMALEs reactivate upon CroV infection). For the host strain E4-10, which we used here, EMALE04 was reactivated by CroV infections but low copies were produced, and host died within several days after infection.…”