Genome Sequences of Two New Pandoravirus Strains Isolated from Brazil and France

Belhaouari, Djamal Brahim; Hannat, Sihem; Rodrigues, Rodrigo Araújo Lima; Aherfi, Sarah; Scola, Bernard La; Andréani, Julien

doi:10.1128/mra.00131-22

Cited by 4 publications

(1 citation statement)

References 23 publications

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“…Pandoravirus morphology is unique amongst giant viruses, being ovoid in shape and possessing an apical pore which facilitates the passing of particle contents into the Acanthamoeba host cytoplasm (Philippe et al ., 2013; Legendre et al ., 2018; Brahim Belhaouari et al ., 2019; Rolland et al ., 2019). As of June 2022 the Pandoraviridae family consists of 17 members: P. pampulha, P. quercus, P. celtis, P. inopinatum, P. salinus, P. dulcis, P. massiliensis, P. neocaledonia, P. braziliensis, P. macleodensis, P. hades, P. persephone, P. japonicus, P. tropicalis, P. kadiweu, P. aubagnensis, P. belohorizontensis (Brahim Belhaouari et al, 2022) . Pandoraviruses salinus, inopinatum, quercus, dulcis, macleodensis and neocaledonia have genome sizes ranging between ∼1.8 – 2.5Mb, encoding ∼926 – 1430 predicted Open Reading Frames (ORFs), approximately 70% of which encode uncharacterised proteins (Legendre et al ., 2018).…”

Section: Introductionmentioning

confidence: 99%

Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins

Horder,

Connor,

Duggan

et al. 2023

Preprint

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Giant viruses, including Pandoraviruses, contain large amounts of genomic ‘dark matter’ - genes encoding proteins of unknown function. New generation, deep learning-based protein structure modelling offers new opportunities to apply structure-based function inference to these sequences, often labelled as hypothetical proteins. However, the AlphaFold Protein Structure Database, a convenient resource covering the majority of UniProt, currently lacks models for most viral proteins. Here, we apply a panoply of predictive methods to protein structure predictions representative of large clusters of hypothetical proteins shared among four Pandoraviruses. In several cases, strong functional predictions can be made. Thus, we identify a likely nucleotidyltransferase putatively involved in viral tRNA maturation that has a BTB domain presumably involved in protein-protein interactions. We further identify a cluster of membrane channel sequences presenting three paralogous families which may, as seen in other giant viruses, induce host cell membrane depolarization. And we identify homologues of calcium-activated potassium channel beta subunits and pinpoint their likely Acanthamoeba cellular alpha subunit counterparts. Despite these successes, many other clusters remain cryptic, having folds that are either too functionally promiscuous or too novel to provide strong clues as to their role. These results suggest that significant structural and functional novelty remains to be uncovered in the giant virus proteomes.

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Section: Introductionmentioning

confidence: 99%

Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins

Horder,

Connor,

Duggan

et al. 2023

Preprint

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

de Freitas Almeida,

Leppänen,

de Azevedo

et al. 2024

Preprint

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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 inAcanthamoeba castellaniifrom 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 otherMarseilleviridaegiant 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 otherMarseilleviridaeusing 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.

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

de Freitas Almeida,

Leppänen,

de Azevedo

et al. 2024

Preprint

View full text Add to dashboard Cite

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.

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Genome Sequences of Two New Pandoravirus Strains Isolated from Brazil and France

Cited by 4 publications

References 23 publications

Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins

Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins

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

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

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