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. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus life cycle. We reconstructed the Jyvaskylavirus particle to 6.3 Å resolution using cryo-electron microscopy. The ~2500 Å diameter virion displays structural similarities to other Marseilleviridae giant viruses. The capsid comprises of 9240 copies of the major capsid protein, encoded by open reading frame (ORF) 184, 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 12 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 suggests that these viruses may be widespread in the boreal environment and provide structural insights extendable to other marseilleviruses. Viruses are everywhere. Some viruses can cause illness in humans, which has led to people often viewing them as threats. But most viruses are harmless to humans. Many viruses target microbes instead of humans. These viruses likely play essential roles in maintaining a healthy balance in ecosystems by preventing overpopulation of their target microbes. Yet, scientists know very little about most viruses and their role in ecosystems.Scientists have recently discovered a special group of giant viruses that target microscopic creatures called amoebas. The giant viruses that target them are much larger than most viruses and have some other unique features, such as having large genomes. A tough outer coating provides the structural reinforcement necessary to support their large size.Most of the giant viruses identified so far have been discovered in Europe and South America. A few have been found in North Africa, India, Japan and Siberia. But scientists still do not know how many giant viruses there are and where else they exist around the world. They are also still learning about the structures that allow these giant viruses to be so large. Almeida et al. describe the first giant virus ever discovered in Finland. In the experiments, the researchers mixed a type of amoeba called Acanthamoeba castellanii with environmental samples and monitored the amoebas for infection. The experiments revealed a giant amoeba-infecting virus in a compost sample. Almeida et al. named it Jyvaskylavirus after the city from which the compost sample came. The investigators then sequenced the virus’ DNA and used a cutting-edge imaging tool called cryogenic electron microscopy and artificial intelligence to determine details of the viral structure. This detailed structure of Jyvaskylavirus provided information about the structure of giant viruses and key structural proteins, which may also benefit scientists studying other kinds of viruses. The experiments confirm that giant viruses are a part of Finland’s boreal forest ecosystem, extending the known range of these unusual viruses. More studies are needed to identify the full range of giant viruses worldwide and to understand their role in ecosystems.