Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland

Abstract

Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in Acanthamoeba castellanii from a composting soil sample in Jyväskylä, Central Finland. Its genome shares similarities with other marseilleviruses, including conserved Nucleocytoviricota genes, histone-like genes, and three unique ORFans. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus lifecycle, such as single virions attached to the cell membrane, likely triggering endocytosis, and virus-rich vesicle formation within the cytoplasm. We also reconstructed the Jyvaskylavirus particle to 6.3 Å resolution using cryo-EM. The ∼2,500 Å diameter virion displays structural similarities to other Marseilleviridae giant viruses. The capsid comprises of 9,240 copies of the major capsid protein ORF184, which possesses a double jellyroll fold arranged in trimers forming pseudo-hexameric capsomers. Below the capsid shell, the internal membrane vesicle encloses the genome. Through cross-structural and -sequence comparisons with other Marseilleviridae using AI-based software in model building and prediction, we elucidated ORF142 as the penton protein, which plugs the twelve vertices of the capsid. Five additional ORFs were identified, with models predicted and fitted into densities that either cap the capsomers externally or stabilize them internally.The isolation of Jyvaskylavirus, along with other virus-like particles, not only suggests that these viruses may be widespread in the boreal environment but also provide insights extendable to other marseilleviruses, addressing the previously lacking structural data on minor capsid proteins.