Evolution of giant pandoravirus from small icosahedral viruses revealed by CRISPR/Cas9

Abstract

Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of Virus and the existence of a fourth domain of life1-3. While increasing knowledge of genome diversity has accumulated4, functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and its host Acanthamoeba castellanii using CRISPR/Cas9, allowing us to uncover the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the evolutionary intermediate mollivirus highlights a stepwise transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. Genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and demonstrate that viral gigantism can arise as an emerging trait.

Pithoviruses are invaded by repeats that contribute to their evolution and divergence from cedratviruses

“…It has been proposed that this accessory partition is a hotspot of frequent gene loss and gain through HGTs (Senkevich et al 2021), but the few HGT identified in Pithoviridae does not support this model. In Pandoraviridae, core and essential genes, and those whose proteins are identified in the viral particle, are mostly localized in the left part of the genome, while accessory genes are located on the right part (Legendre et al 2018;Bisio et al 2022). This likely reflects ongoing genome increase involving de novo gene creation (Legendre et al 2018) and accelerated gene duplications (Bisio et al 2022).…”

“…In Pandoraviridae, core and essential genes, and those whose proteins are identified in the viral particle, are mostly localized in the left part of the genome, while accessory genes are located on the right part (Legendre et al 2018;Bisio et al 2022). This likely reflects ongoing genome increase involving de novo gene creation (Legendre et al 2018) and accelerated gene duplications (Bisio et al 2022). In all cases, the dichotomous genome partitioning might also be linked to the epigenetic transcriptional regulation of core genes, through a peculiar 3D structure of this genomic region.…”